R3792T last accessed: 2022-11-04

metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Kyoto encyclopedia of genes and genomes (KEGG)
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

kegg
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

Other names: KEGG, Kyoto encyclopedia of genes and genomes (KEGG), kegg

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

Webpage:

https://www.kegg.jp

Licence:

Name: KEGG - specific
URL: https://www.nlm.nih.gov/databases/download/mesh.html

Publications: (10)

Publications
More detailed information about this field from each metasource.

KEGG: kyoto encyclopedia of genes and genomes
PMID: 10592173
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

KEGG for integration and interpretation of large-scale molecular data sets
PMID: 22080510
metasource: Fairsharing.org
version: FAIRsharing.org: KEGG; Kyoto Encyclopedia of Genes and Genomes; DOI: https://doi.org/10.25504/FAIRsharing.327nbg; Last edited: April 23, 2020, 1:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

KEGG: Kyoto Encyclopedia of Genes and Genomes
PMID: 9847135
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

Data, information, knowledge and principle: back to metabolism in KEGG
PMID: 24214961
metasource: Fairsharing.org
version: FAIRsharing.org: KEGG; Kyoto Encyclopedia of Genes and Genomes; DOI: https://doi.org/10.25504/FAIRsharing.327nbg; Last edited: April 23, 2020, 1:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

Toward understanding the origin and evolution of cellular organisms
PMID: 31441146
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

KEGG: integrating viruses and cellular organisms
PMID: 33125081
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

The KEGG database
PMID: 12539951
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

KEGG Atlas mapping for global analysis of metabolic pathways
PMID: 18477636
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

Medical subject headings
PMID: 13982385
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Using the KEGG database resource
PMID: 22700311
metasource: Fairsharing.org
version: FAIRsharing.org: KEGG; Kyoto Encyclopedia of Genes and Genomes; DOI: https://doi.org/10.25504/FAIRsharing.327nbg; Last edited: April 23, 2020, 1:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

KEGG: kyoto encyclopedia of genes and genomes PubMed citations: 9999.

9999 articles citing: KEGG: kyoto encyclopedia of genes and genomes

Prepubertal nutritional modulation in the bull and its impact on sperm DNA methylation. PMID:35779136
Whole-Genome Resequencing Deciphers New Insight Into Genetic Diversity and Signatures of Resistance in Cultivated Cotton Gossypium hirsutum. PMID:35778659
Identification of hub genes and regulatory networks in histologically unstable carotid atherosclerotic plaque by bioinformatics analysis. PMID:35773742
Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis. PMID:35773646
Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. PMID:35773462
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia. PMID:35773379
Differentially methylated and expressed genes in familial type 1 diabetes. PMID:35773317
N(6)-methyladenosine methylation-regulated polo-like kinase 1 cell cycle homeostasis as a potential target of radiotherapy in pancreatic adenocarcinoma. PMID:35773310
Survival-related indicators ALOX12B and SPRR1A are associated with DNA damage repair and tumor microenvironment status in HPV 16-negative head and neck squamous cell carcinoma patients. PMID:35768785
Transcriptome analysis of SerpinB2-deficient breast tumors provides insight into deciphering SerpinB2-mediated roles in breast cancer progression. PMID:35768767
Identification of stress-related genes by co-expression network analysis based on the improved turbot genome. PMID:35768602
Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production. PMID:35768515
GREM1 is required to maintain cellular heterogeneity in pancreatic cancer. PMID:35768509
Effects and associated transcriptomic landscape changes of methamphetamine on immune cells. PMID:35765053
Differential proteomics of placentas reveals metabolic disturbance and oxidative damage participate yak spontaneous miscarriage during late pregnancy. PMID:35761325
A comparative analysis of extracellular vesicles (EVs) from human and feline plasma. PMID:35761023
Inferring functional communities from partially observed biological networks exploiting geometric topology and side information. PMID:35760826
Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. PMID:35760817
Multi-omics reveals mechanisms of resistance to potato root infection by Spongospora subterranea. PMID:35752627
Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea. PMID:35751094
Adaptation insights from comparative transcriptome analysis of two Opisthopappus species in the Taihang mountains. PMID:35751010
Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection. PMID:35750797
CircRNAs in Xiang pig ovaries among diestrus and estrus stages. PMID:35739583
Comprehensive bioinformatic analysis reveals a cancer-associated fibroblast gene signature as a poor prognostic factor and potential therapeutic target in gastric cancer. PMID:35739492
Machine-learning algorithms based on personalized pathways for a novel predictive model for the diagnosis of hepatocellular carcinoma. PMID:35739471
Cancer cells depend on environmental lipids for proliferation when electron acceptors are limited. PMID:35739397
Predicting prognosis and clinical features of the tumor microenvironment based on ferroptosis score in patients with breast cancer. PMID:35739315
A cerumenolomic approach to bovine trypanosomosis diagnosis. PMID:35739279
Exploring the potential mechanism of emetine against coronavirus disease 2019 combined with lung adenocarcinoma: bioinformatics and molecular simulation analyses. PMID:35733175
Antennal transcriptome analysis of olfactory genes and tissue expression profiling of odorant binding proteins in Semanotus bifasciatus (cerambycidae: coleoptera). PMID:35733103
Transcriptome of the synganglion in the tick Ixodes ricinus and evolution of the cys-loop ligand-gated ion channel family in ticks. PMID:35733088
Biosynthetic potential of the global ocean microbiome. PMID:35732736
SILAC kinase screen identifies potential MASTL substrates. PMID:35732702
Anti-lipolysis-stimulated lipoprotein receptor monoclonal antibody as a novel therapeutic agent for endometrial cancer. PMID:35729527
Integrative transcriptome-wide analysis of atopic dermatitis for drug repositioning. PMID:35729261
Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function. PMID:35729225
Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings. PMID:35729190
Hyaluronic acid-GPRC5C signalling promotes dormancy in haematopoietic stem cells. PMID:35725769
Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis. PMID:35725367
Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat. PMID:35715737
Plant Host Traits Mediated by Foliar Fungal Symbionts and Secondary Metabolites. PMID:35713682
Integrated bioinformatics analysis reveals marker genes and immune infiltration for pulmonary arterial hypertension. PMID:35710932
Integrated analysis reveals the pivotal interactions between immune cells in the melanoma tumor microenvironment. PMID:35710862
Identification of HOX signatures contributing to oral cancer phenotype. PMID:35710803
CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. PMID:35710652
Identification of an inflammatory response signature associated with prognostic stratification and drug sensitivity in lung adenocarcinoma. PMID:35710585
miRNA-mRNA analysis of sheep adrenal glands reveals the network regulating reproduction. PMID:35710353
Genome-wide alternative splicing profile in the posterior kidney of brown trout (Salmo trutta) during proliferative kidney disease. PMID:35710345
Identification of ferroptosis-related genes for overall survival prediction in hepatocellular carcinoma. PMID:35705729
Combined transcriptome and metabolome analysis of Nerium indicum L. elaborates the key pathways that are activated in response to witches' broom disease. PMID:35701735
Anticancer effects of herbal medicines in pancreatic ductal adenocarcinoma through modulation of steroid hormone response proteins. PMID:35701649
Alterations in co-abundant bacteriome in colorectal cancer and its persistence after surgery: a pilot study. PMID:35701595
AGE/RAGE axis regulates reversible transition to quiescent states of ALK-rearranged NSCLC and pancreatic cancer cells in monolayer cultures. PMID:35701529
Transcriptomic and proteomic analyses of Cucurbita ficifolia Bouché (Cucurbitaceae) response to Fusarium oxysporum f.sp. cucumerium. PMID:35698057
Differing coronavirus genres alter shared host signaling pathways upon viral infection. PMID:35697915
Advances in understanding Norway spruce natural resistance to needle bladder rust infection: transcriptional and secondary metabolites profiling. PMID:35692040
Novel App knock-in mouse model shows key features of amyloid pathology and reveals profound metabolic dysregulation of microglia. PMID:35690868
Curcumin and metformin synergistically modulate peripheral and central immune mechanisms of pain. PMID:35690654
Linear programming based gene expression model (LPM-GEM) predicts the carbon source for Bacillus subtilis. PMID:35689204
Omics-based integrated analysis identified IKZF2 as a biomarker associated with lupus nephritis. PMID:35688845
Impact of AADAC gene expression on prognosis in patients with Borrmann type III advanced gastric cancer. PMID:35681154
The dynamic cellular and molecular features during the development of radiation proctitis revealed by transcriptomic profiling in mice. PMID:35681125
Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data. PMID:35680885
Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma. PMID:35676688
Integrative analysis of expression profile indicates the ECM receptor and LTP dysfunction in the glioma-related epilepsy. PMID:35676651
3-oxo-C12:2-HSL, quorum sensing molecule from human intestinal microbiota, inhibits pro-inflammatory pathways in immune cells via bitter taste receptors. PMID:35676403
Exploring the mechanism and experimental verification of puerarin in the treatment of endometrial carcinoma based on network pharmacology and bioinformatics analysis. PMID:35672846
Network pharmacology and in vivo experiments reveal the pharmacological effects and molecular mechanisms of Simiao Powder in prevention and treatment for gout. PMID:35672755
Synergistic anti-proliferative activity of JQ1 and GSK2801 in triple-negative breast cancer. PMID:35672711
Gene network analysis reveals candidate genes related with the hair follicle development in sheep. PMID:35672687
Potential prognosis index for m6A-related mRNA in cholangiocarcinoma. PMID:35672673
Comprehensive analysis of lncRNA-miRNA-mRNA networks during osteogenic differentiation of bone marrow mesenchymal stem cells. PMID:35672672
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Evaluating the tumor immune profile based on a three-gene prognostic risk model in HER2 positive breast cancer. PMID:35665772
Incubation of canine dermal fibroblasts with serum from dogs with atopic dermatitis activates extracellular matrix signalling and represses oxidative phosphorylation. PMID:35665445
A synaptomic analysis reveals dopamine hub synapses in the mouse striatum. PMID:35660742
Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR. PMID:35659305
Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus. PMID:35659263
The correlation of EZH2 expression with the progression and prognosis of hepatocellular carcinoma. PMID:35659256
UBE2S promotes the development of ovarian cancer by promoting PI3K/AKT/mTOR signaling pathway to regulate cell cycle and apoptosis. PMID:35658829
Pyroptosis is related to immune infiltration and predictive for survival of colon adenocarcinoma patients. PMID:35655081
The microbiome of cryospheric ecosystems. PMID:35655063
Analysis of immune related gene expression profiles and immune cell components in patients with Barrett esophagus. PMID:35654816
Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions. PMID:35650424
Identification of hub pathways and drug candidates in gastric cancer through systems biology. PMID:35650297
Comparative transcriptome analysis of heat-induced domesticated zebrafish during gonadal differentiation. PMID:35641933
A polyketide synthase from Verticillium dahliae modulates melanin biosynthesis and hyphal growth to promote virulence. PMID:35637443
Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations. PMID:35637371
MSNovelist: de novo structure generation from mass spectra. PMID:35637304
Comparative genomics highlight the importance of lineage-specific gene families in evolutionary divergence of the coral genus, Montipora. PMID:35624412
Polyploid giant cancer cells are dependent on cholesterol for progeny formation through amitotic division. PMID:35624221
Effect of berberine on global modulation of lncRNAs and mRNAs expression profiles in patients with stable coronary heart disease. PMID:35619068
Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3. PMID:35618829
Identifying drivers of breast cancer metastasis in progressively invasive subpopulations of zebrafish-xenografted MDA-MB-231. PMID:35614362
Lake microbiome and trophy fluctuations of the ancient hemp rettery. PMID:35614182
Mast cell marker gene signature in head and neck squamous cell carcinoma. PMID:35610596
Bioinformatics and Systems Biology of Circadian Rhythms: BIO_CYCLE and CircadiOmics. PMID:35610420
Expression of ferroptosis-related gene correlates with immune microenvironment and predicts prognosis in gastric cancer. PMID:35610340
Chromosome-scale genome assembly of an important medicinal plant honeysuckle. PMID:35610245
Disruption of β-catenin-mediated negative feedback reinforces cAMP-induced neuronal differentiation in glioma stem cells. PMID:35610201
Transcriptome analysis reveals fluid shear stress (FSS) and atherosclerosis pathway as a candidate molecular mechanism of short-term low salinity stress tolerance in abalone. PMID:35606721
Alanine-specific appetite in slow growing chickens is associated with impaired glucose transport and TCA cycle. PMID:35606689
Signal requirement for cortical potential of transplantable human neuroepithelial stem cells. PMID:35606347
Blood transcriptomics identifies immune signatures indicative of infectious complications in childhood cancer patients with febrile neutropenia. PMID:35602885
Integrative Analysis of lncRNA-miRNA-mRNA Regulatory Network Reveals the Key lncRNAs Implicated Potentially in the Differentiation of Adipocyte in Goats. PMID:35600305
RNA-seq analysis of extracellular vesicles from hyperphosphatemia-stimulated endothelial cells provides insight into the mechanism underlying vascular calcification. PMID:35597927
Combined use of specific length amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) for rapid identification of genes influencing fiber content of hemp (Cannabis sativa L.). PMID:35596150
Effects of the repression of GIGANTEA gene StGI.04 on the potato leaf transcriptome and the anthocyanin content of tuber skin. PMID:35596149
Relationship between gene expression networks and muscle contractile physiology differences in Anolis lizards. PMID:35596083
PI3K/AKT/mTOR Pathway-Associated Genes Reveal a Putative Prognostic Signature Correlated with Immune Infiltration in Hepatocellular Carcinoma. PMID:35592706
Identification of Alzheimer's Disease Molecular Subtypes Based on Parallel Large-Scale Sequencing. PMID:35592696
Identification and Verification of m7G Modification Patterns and Characterization of Tumor Microenvironment Infiltration via Multi-Omics Analysis in Clear Cell Renal Cell Carcinoma. PMID:35592316
Mitogen-activated protein kinase 4 is obligatory for late pollen and early fruit development in tomato. PMID:35591931
The potential effects and mechanisms of hispidulin in the treatment of diabetic retinopathy based on network pharmacology. PMID:35590353
KDM3A-mediated SP1 activates PFKFB4 transcription to promote aerobic glycolysis in osteosarcoma and augment tumor development. PMID:35590288
Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata. PMID:35590244
Exploring the underlying molecular mechanism of liver cancer cells under hypoxia based on RNA sequencing. PMID:35590240
Effects of interleukin 1β on long noncoding RNA and mRNA expression profiles of human synovial fluid derived mesenchymal stem cells. PMID:35589865
PCBP1 is associated with rheumatoid arthritis by affecting RNA products of genes involved in immune response in Th1 cells. PMID:35589811
Identification of AKIRIN2 as a potential biomarker and correlation with immunotherapy in gastric adenocarcinoma by integrated bioinformatics analysis. PMID:35589807
Exploration of the Potential Mechanism of the Common Differentially Expressed Genes in Psoriasis and Atopic Dermatitis. PMID:35586812
Drug-Drug Interactions Prediction Using Fingerprint Only. PMID:35586666
Horizontal gene transfer drives the evolution of dependencies in bacteria. PMID:35586069
Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660. PMID:35585492
Transcriptome and metabolome reveal the accumulation of secondary metabolites in different varieties of Cinnamomum longepaniculatum. PMID:35585490
Distinct gene clusters drive formation of ferrosome organelles in bacteria. PMID:35585231
Construction and comprehensive analysis of a lncRNA-mRNA interactive network to reveal a potential lncRNA for hepatic encephalopathy development. PMID:35583799
Radiogenomic analysis of primary breast cancer reveals [18F]-fluorodeoxglucose dynamic flux-constants are positively associated with immune pathways and outperform static uptake measures in associating with glucose metabolism. PMID:35581637
SYNJ2 is a novel and potential biomarker for the prediction and treatment of cancers: from lung squamous cell carcinoma to pan-cancer. PMID:35581615
An immune gene signature to predict prognosis and immunotherapeutic response in lung adenocarcinoma. PMID:35581376
Identification of miRNA biomarkers for stomach adenocarcinoma. PMID:35578189
Analysis of circRNAs and circRNA-associated competing endogenous RNA networks in β-thalassemia. PMID:35577924
Prediction of gestational age using urinary metabolites in term and preterm pregnancies. PMID:35577875
A Prognostic Gene Signature for Hepatocellular Carcinoma. PMID:35574316
Eutrema EsMYB90 Gene Improves Growth and Antioxidant Capacity of Transgenic Wheat Under Salinity Stress. PMID:35574106
Tetraploidy in Citrus wilsonii Enhances Drought Tolerance via Synergistic Regulation of Photosynthesis, Phosphorylation, and Hormonal Changes. PMID:35574073
Comparative Metabolomics and Lipidomics of Four Juvenoids Application to Scylla paramamosain Hepatopancreas: Implications of Lipid Metabolism During Ovarian Maturation. PMID:35574001
Microbiota-Associated Biofilm Regulation Leads to Vibrio cholerae Resistance Against Intestinal Environmental Stress. PMID:35573801
RNA-Seq Based Toxicity Analysis of Mesoporous Polydopamine Nanoparticles in Mice Following Different Exposure Routes. PMID:35573233
Identification of lncRNA Biomarkers and LINC01198 Promotes Progression of Chronic Rhinosinusitis with Nasal Polyps through Sponge miR-6776-5p. PMID:35572732
lncRNA-mRNA Expression Patterns in Invasive Pituitary Adenomas: A Microarray Analysis. PMID:35572729
Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas. PMID:35572705
Identification of significant genes with a poor prognosis in skin cutaneous malignant melanoma based on a bioinformatics analysis. PMID:35571409
Potential for reversing miR-634-mediated cytoprotective processes to improve efficacy of chemotherapy against oral squamous cell carcinoma. PMID:35571376
BioTAGME: A Comprehensive Platform for Biological Knowledge Network Analysis. PMID:35571058
Gene Expression Profiling of Glioblastoma to Recognize Potential Biomarker Candidates. PMID:35571016
Small RNA sequencing and identification of papaya (Carica papaya L.) miRNAs with potential cross-kingdom human gene targets. PMID:35570207
Integrative analysis identifies CXCL11 as an immune-related prognostic biomarker correlated with cell proliferation and immune infiltration in multiple myeloma microenvironment. PMID:35568859
A novel strategy for optimal component formula of anti-PRRSV from natural compounds using tandem mass tag labeled proteomic analyses. PMID:35568854
RNF38 suppress growth and metastasis via ubiquitination of ACTN4 in nasopharyngeal carcinoma. PMID:35568845
Dynamic changes in fecal bacterial microbiota of dairy cattle across the production line. PMID:35568809
Diabetes risk loci-associated pathways are shared across metabolic tissues. PMID:35568807
Modelling liver cancer microenvironment using a novel 3D culture system. PMID:35568708
Coordination Chemistry of Nucleotides and Antivirally Active Acyclic Nucleoside Phosphonates, including Mechanistic Considerations. PMID:35565975
Identification of Genes Related to Squab Muscle Growth and Lipid Metabolism from Transcriptome Profiles of Breast Muscle and Liver in Domestic Pigeon (Columba livia). PMID:35565488
Genome-Scale Metabolic Model Analysis of Metabolic Differences between Lauren Diffuse and Intestinal Subtypes in Gastric Cancer. PMID:35565469
A Data Science Approach for the Identification of Molecular Signatures of Aggressive Cancers. PMID:35565454
Space- and Time-Resolved Metabolomics of a High-Grade Serous Ovarian Cancer Mouse Model. PMID:35565391
Analytical Considerations of Large-Scale Aptamer-Based Datasets for Translational Applications. PMID:35565358
Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. PMID:35565274
Fast, Ungapped Reads Mapping Using Squid. PMID:35564837
Integrated Multiomics Analysis of Salivary Exosomes to Identify Biomarkers Associated with Changes in Mood States and Fatigue. PMID:35563647
Artificial Intelligence Predictor for Alzheimer's Disease Trained on Blood Transcriptome: The Role of Oxidative Stress. PMID:35563628
RNA-Seq, Bioinformatic Identification of Potential MicroRNA-like Small RNAs in the Edible Mushroom Agaricus bisporus and Experimental Approach for Their Validation. PMID:35563314
Transcriptome Analysis of the Cf-13-Mediated Hypersensitive Response of Tomato to Cladosporium fulvum Infection. PMID:35563232
Nitric Oxide Enhanced Salt Stress Tolerance in Tomato Seedlings, Involving Phytohormone Equilibrium and Photosynthesis. PMID:35562930
Identification and validation of TNFRSF4 as a high-profile biomarker for prognosis and immunomodulation in endometrial carcinoma. PMID:35562682
Diagnostic and prognostic values of pyroptosis-related genes for the hepatocellular carcinoma. PMID:35562678
Integrated computational analysis reveals HOX genes cluster as oncogenic drivers in head and neck squamous cell carcinoma. PMID:35562533
Differential expression analysis of genes and long non-coding RNAs associated with KRAS mutation in colorectal cancer cells. PMID:35562390
Boost-RS: boosted embeddings for recommender systems and its application to enzyme-substrate interaction prediction. PMID:35561204
Driver gene detection through Bayesian network integration of mutation and expression profiles. PMID:35561191
Identification of Potential Diagnoses Based on Immune Infiltration and Autophagy Characteristics in Major Depressive Disorder. PMID:35559009
Microbiomes and Planctomycete diversity in large-scale aquaria habitats. PMID:35551553
The Immunometabolic Atlas: A tool for design and interpretation of metabolomics studies in immunology. PMID:35550647
Chromosome-level genome assembly of Asian yellow pond turtle (Mauremys mutica) with temperature-dependent sex determination system. PMID:35550586
Role of CD68 in tumor immunity and prognosis prediction in pan-cancer. PMID:35550532
System-level investigation of anti-obesity effects and the potential pathways of Cordyceps militaris in ovariectomized rats. PMID:35550138
Deciphering the Underlying Mechanisms of Formula Le-Cao-Shi Against Liver Injuries by Integrating Network Pharmacology, Metabonomics, and Experimental Validation. PMID:35548342
A Comparative Study of Flavonoids and Carotenoids Revealed Metabolite Responses for Various Flower Colorations Between Nicotiana tabacum L. and Nicotiana rustica L. PMID:35548319
Genome-Wide Identification and Expression Profiling of KCS Gene Family in Passion Fruit (Passiflora edulis) Under Fusarium kyushuense and Drought Stress Conditions. PMID:35548275
Metabolomics Applied to Cord Serum in Preeclampsia Newborns: Implications for Neonatal Outcomes. PMID:35547553
Role of tRNA derived fragments in renal ischemia-reperfusion injury. PMID:35546262
Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN. PMID:35546170
The transcriptome-wide N6-methyladenosine (m6A) map profiling reveals the regulatory role of m6A in the yak ovary. PMID:35538402
Impact of salivary and pancreatic amylase gene copy numbers on diabetes, obesity, and functional profiles of microbiome in Northern Japanese population. PMID:35538098
Artificial intelligence in cancer target identification and drug discovery. PMID:35538061
Comparative transcriptome analysis of resistant and susceptible wheat in response to Rhizoctonia cerealis. PMID:35534832
Combined morpho-physiological, ionomic and transcriptomic analyses reveal adaptive responses of allohexaploid wheat (Triticum aestivum L.) to iron deficiency. PMID:35534803
Integrated transcriptome and endogenous hormone analysis provides new insights into callus proliferation in Osmanthus fragrans. PMID:35534621
Comprehensive computational analysis reveals H5N1 influenza virus-encoded miRNAs and host-specific targets associated with antiviral immune responses and protein binding. PMID:35533150
Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. PMID:35531351
Mining the prognostic significance and immune infiltration of STAT family members in human breast cancer by bioinformatics analysis. PMID:35531108
Computational Analysis of the Immune Infiltration Pattern and Candidate Diagnostic Biomarkers in Lumbar Disc Herniation. PMID:35531067
Biomarkers of PEGylated Liposomal Doxorubicin-Induced Hypersensitivity Reaction in Breast Cancer Patients Based on Metabolomics. PMID:35529437
Association Studies of Environmental Exposures, DNA Methylation and Children's Cognitive, Behavioral, and Mental Health Problems. PMID:35528545
Discovering Common Pathophysiological Processes between COVID-19 and Cystic Fibrosis by Differential Gene Expression Pattern Analysis. PMID:35528173
Identification and validation of an epigenetically regulated long noncoding RNA model for breast cancer metabolism and prognosis. PMID:35525949
Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus). PMID:35524260
The identification of miRNA and mRNA expression profiles associated with pediatric atypical teratoid/rhabdoid tumor. PMID:35524230
Microbial community functioning during plant litter decomposition. PMID:35523988
Rheumatoid arthritis T cell and muscle oxidative metabolism associate with exercise-induced changes in cardiorespiratory fitness. PMID:35523821
RhoA-ROCK competes with YAP to regulate amoeboid breast cancer cell migration in response to lymphatic-like flow. PMID:35520391
Elevated α-Ketoglutaric Acid Concentrations and a Lipid-Balanced Signature Are the Key Factors in Long-Term HIV Control. PMID:35514981
Bacterial community mapping of the intestinal tract in acute pancreatitis rats based on 16S rDNA gene sequence analysis. PMID:35514649
A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model. PMID:35513802
Changes in chemical composition, structural and functional microbiome during alfalfa (Medicago sativa) ensilage with Lactobacillus plantarum PS-8. PMID:35509811
Response of the Anaerobic Methanotrophic Archaeon Candidatus "Methanoperedens nitroreducens" to the Long-Term Ferrihydrite Amendment. PMID:35509320
Anthocyanin regulatory networks in Solanum tuberosum L. leaves elucidated via integrated metabolomics, transcriptomics, and StAN1 overexpression. PMID:35508980
Different effects of hydrogen-rich water intake and hydrogen gas inhalation on gut microbiome and plasma metabolites of rats in health status. PMID:35508571
Network pharmacology combined with molecular docking to explore the potential mechanisms for the antioxidant activity of Rheum tanguticum seeds. PMID:35505340
Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods. PMID:35505302
Associations of keratinocyte cancers with snp variants in the sonic hedgehog pathway. PMID:35505292
Rice (Oryza sativa L.) cytochrome P450 protein 716A subfamily CYP716A16 regulates disease resistance. PMID:35505282
Circulating microRNA sequencing revealed miRNome patterns in hematology and oncology patients aiding the prognosis of invasive aspergillosis. PMID:35504997
Integrated analysis of mRNA and long noncoding RNA profiles in peripheral blood mononuclear cells of patients with bronchial asthma. PMID:35501805
High MICAL-L2 expression and its role in the prognosis of colon adenocarcinoma. PMID:35501725
Gene expression profiling of RIP2-knockdown in HD11 macrophages - elucidation of potential pathways (gene network) when challenged with avian pathogenic E.coli (APEC). PMID:35501708
Bacterial communities associated with silage of different forage crops in Malaysian climate analysed using 16S amplicon metagenomics. PMID:35501317
Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis cerana and the Western honey bee Apis mellifera. PMID:35499050
Virtual screening and docking analysis of novel ligands for selective enhancement of tea (Camellia sinensis) flavonoids. PMID:35498963
Macroaggregates Serve as Micro-Hotspots Enriched With Functional and Networked Microbial Communities and Enhanced Under Organic/Inorganic Fertilization in a Paddy Topsoil From Southeastern China. PMID:35495701
Comparative Analysis of the Chalcone-Flavanone Isomerase Genes in Six Citrus Species and Their Expression Analysis in Sweet Orange (Citrus sinensis). PMID:35495138
Differential expression of circulating miRNAs after alemtuzumab induction therapy in lung transplantation. PMID:35490174
Identification of an autophagy-related gene signature for predicting prognosis and immune activity in pancreatic adenocarcinoma. PMID:35488119
Proteomics of lung tissue reveals differences in inflammation and alveolar-capillary barrier response between atelectasis and aerated regions. PMID:35487970
Prognostic biomarker SGSM1 and its correlation with immune infiltration in gliomas. PMID:35484511
Transcriptome and metabolome analyses reveal new insights into chlorophyll, photosynthesis, metal ion and phenylpropanoids related pathways during sugarcane ratoon chlorosis. PMID:35484490
Network pharmacology analysis and experimental validation to explore the mechanism of Bushao Tiaozhi capsule (BSTZC) on hyperlipidemia. PMID:35484204
Identification and validation of prognosis-associated DNA repair gene signatures in colorectal cancer. PMID:35484177
Chromosome-Level Genome Assembly of the Hemiparasitic Taxillus chinensis (DC.) Danser. PMID:35482027
Innovation and tinkering in the evolution of oxidases. PMID:35481655
m6A Regulator-Mediated RNA Methylation Modification Patterns are Involved in the Pathogenesis and Immune Microenvironment of Depression. PMID:35480327
Transcriptome Analysis and Identification of the Cholesterol Side Chain Cleavage Enzyme BbgCYP11A1 From Bufo bufo gargarizans. PMID:35480310
Metatranscriptomic Analysis of Corals Inoculated With Tolerant and Non-Tolerant Symbiont Exposed to High Temperature and Light Stress. PMID:35480050
A Cancer Associated Fibroblasts-Related Six-Gene Panel for Anti-PD-1 Therapy in Melanoma Driven by Weighted Correlation Network Analysis and Supervised Machine Learning. PMID:35479936
Characterization of differential gene expression of broiler chicken to thermal stress in discrete developmental stages. PMID:35479510
The identification of liver metastasis- and prognosis-associated genes in pancreatic ductal adenocarcinoma. PMID:35477379
Gene-SCOUT: identifying genes with similar continuous trait fingerprints from phenome-wide association analyses. PMID:35474393
Integrative analysis of TCGA data identifies miRNAs as drug-specific survival biomarkers. PMID:35474090
Effect of acute high-intensity exercise on myocardium metabolic profiles in rat and human study via metabolomics approach. PMID:35473956
Network- and enrichment-based inference of phenotypes and targets from large-scale disease maps. PMID:35473910
Antibacterial activities and action mode of anti-hyperlipidemic lomitapide against Staphylococcus aureus. PMID:35473561
Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng. PMID:35473500
Prediction of pregnancy-related hypertensive disorders using metabolomics: a systematic review. PMID:35470187
Transcriptomic analysis of OsRUS1 overexpression rice lines with rapid and dynamic leaf rolling morphology. PMID:35468979
Deletion and tandem duplications of biosynthetic genes drive the diversity of triterpenoids in Aralia elata. PMID:35468919
Machine learning assisted analysis of breast cancer gene expression profiles reveals novel potential prognostic biomarkers for triple-negative breast cancer. PMID:35465161
A Toolkit for Profiling the Immune Landscape of Pediatric Central Nervous System Malignancies. PMID:35464481
The Potential of Metabolism-Related Gene OGDHL as a Biomarker for Myocardial Remodeling in Dilated Cardiomyopathy. PMID:35463769
Integrated Bioinformatics-Based Analysis of Hub Genes and the Mechanism of Immune Infiltration Associated With Acute Myocardial Infarction. PMID:35463752
Postnatal Smad3 Inactivation in Murine Smooth Muscle Cells Elicits a Temporally and Regionally Distinct Transcriptional Response. PMID:35463747
Psoriasis Vulgaris of Blood Heat Syndrome in Plasma Based on Widely Targeted Techniques. PMID:35463691
Analysis of the Molecular Mechanism of Evodia rutaecarpa Fruit in the Treatment of Nasopharyngeal Carcinoma Using Network Pharmacology and Molecular Docking. PMID:35463684
A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson's Disease. PMID:35463646
Unraveling the expression of differentially expressed proteins and enzymatic activity in response to Phytophthora nicotianae across different flue-cured tobacco cultivars. PMID:35461247
Identification of the potential biological target molecules related to primary open-angle glaucoma. PMID:35461232
Transcriptome analysis of fasudil treatment in the APPswe/PSEN1dE9 transgenic (APP/PS1) mice model of Alzheimer's disease. PMID:35459923
ADAM12 is an independent predictor of poor prognosis in liver cancer. PMID:35459884
A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women. PMID:35459771
Ferroptosis-related lncRNA signature predicts the prognosis and immune microenvironment of hepatocellular carcinoma. PMID:35459272
GC/MS-based 13C metabolic flux analysis resolves the parallel and cyclic photomixotrophic metabolism of Synechocystis sp. PCC 6803 and selected deletion mutants including the Entner-Doudoroff and phosphoketolase pathways. PMID:35459213
The Potential Antipyretic Mechanism of Ellagic Acid with Brain Metabolomics Using Rats with Yeast-Induced Fever. PMID:35458665
The Genome of Bacillus velezensis SC60 Provides Evidence for Its Plant Probiotic Effects. PMID:35456817
Responses of Phyllosphere Microbiome to Ozone Stress: Abundance, Community Compositions and Functions. PMID:35456732
Additive and Interactive Genetically Contextual Effects of HbA1c on cg19693031 Methylation in Type 2 Diabetes. PMID:35456489
Identification of Potential Key Genes in Prostate Cancer with Gene Expression, Pivotal Pathways and Regulatory Networks Analysis Using Integrated Bioinformatics Methods. PMID:35456461
Transcriptomic and Proteomic Analysis of Marine Nematode Litoditis marina Acclimated to Different Salinities. PMID:35456458
Ovarian Transcriptomic Analysis of Ninghai Indigenous Chickens at Different Egg-Laying Periods. PMID:35456401
A Novel Transcription Factor VPA0041 Was Identified to Regulate the Swarming Motility in Vibrio parahaemolyticus. PMID:35456128
Treatment with Ad5-Porcine Interferon-α Attenuates Ebolavirus Disease in Pigs. PMID:35456124
Key Signaling in Alcohol-Associated Liver Disease: The Role of Bile Acids. PMID:35456053
Sphingolipid Metabolism as a New Predictive Target Correlated with Aging and AD: A Transcriptomic Analysis. PMID:35454332
Darling: A Web Application for Detecting Disease-Related Biomedical Entity Associations with Literature Mining. PMID:35454109
Semen Modulates Cell Proliferation and Differentiation-Related Transcripts in the Pig Peri-Ovulatory Endometrium. PMID:35453814
Prostanoid Signaling in Cancers: Expression and Regulation Patterns of Enzymes and Receptors. PMID:35453789
RNA-seq and Mitochondrial DNA Analysis of Adrenal Gland Metastatic Tissue in a Patient with Renal Cell Carcinoma. PMID:35453788
Plasma miRNA Profile of Crohn's Disease and Rheumatoid Arthritis Patients. PMID:35453708
Osteopontin-A Potential Biomarker for IgA Nephropathy: Machine Learning Application. PMID:35453484
Integrative Proteome and Ubiquitinome Analyses Reveal the Substrates of BTBD9 and Its Underlying Mechanism in Sleep Regulation. PMID:35449961
Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep. PMID:35449433
Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy. PMID:35449401
Single-cell transcriptomics identifies Mcl-1 as a target for senolytic therapy in cancer. PMID:35449130
Profiling the lncRNA-miRNA-mRNA interaction network in the submandibular gland of diabetic mice. PMID:35449001
Modular and mechanistic changes across stages of colorectal cancer. PMID:35448980
Transcriptome analysis of the growth-promoting effect of volatile organic compounds produced by Microbacterium aurantiacum GX14001 on tobacco (Nicotiana benthamiana). PMID:35448945
Comparative transcriptomic analyses of citrus cold-resistant vs. sensitive rootstocks might suggest a relevant role of ABA signaling in triggering cold scion adaption. PMID:35448939
Rewiring of the Liver Transcriptome across Multiple Time-Scales Is Associated with the Weight Loss-Independent Resolution of NAFLD Following RYGB. PMID:35448506
Network Reconstruction and Modelling Made Reproducible with moped. PMID:35448462
An Extracytoplasmic Function Sigma Factor Required for Full Virulence in Xanthomonas citri pv. citri. PMID:35446118
In-Silico Functional Annotation of Plasmodium falciparum Hypothetical Proteins to Identify Novel Drug Targets. PMID:35444689
Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. PMID:35444687
The Effects of Sesquiterpene Lactones on the Differentiation of Human or Animal Cells Cultured In-Vitro: A Critical Systematic Review. PMID:35444549
Identification of Immune-Related Key Genes as Potential Diagnostic Biomarkers of Sepsis in Children. PMID:35444449
Chemotaxis shapes the microscale organization of the ocean's microbiome. PMID:35444277
Inflammatory response mediates cross-talk with immune function and reveals clinical features in acute myeloid leukemia. PMID:35441668
Long-term artificial selection of Hanwoo (Korean) cattle left genetic signatures for the breeding traits and has altered the genomic structure. PMID:35440706
Identification of ubiquitin-specific protease 32 as an oncogene in glioblastoma and the underlying mechanisms. PMID:35440702
Tanshinone I attenuates fibrosis in fibrotic kidneys through down-regulation of inhibin beta-A. PMID:35439976
De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet. PMID:35439941
Small HSPs play an important role in crosstalk between HSF-HSP and ROS pathways in heat stress response through transcriptomic analysis in lilies (Lilium longiflorum). PMID:35439940
Gene expression profiles provide insights into the survival strategies in deep-sea mussel (Bathymodiolus platifrons) of different developmental stages. PMID:35439939
Improving ovarian cancer treatment decision using a novel risk predictive tool. PMID:35439731
Transcriptomics Coupled to Proteomics Reveals Novel Targets for the Protective Role of Spermine in Diabetic Cardiomyopathy. PMID:35437457
Construction of a circRNA-Mediated ceRNA Network Reveals Novel Biomarkers for Aortic Dissection. PMID:35437351
Integrative analysis of key microRNA-mRNA complexes and pathways in aortic aneurysm. PMID:35433971
Integrated Bioinformatics Algorithms and Experimental Validation to Explore Robust Biomarkers and Landscape of Immune Cell Infiltration in Dilated Cardiomyopathy. PMID:35433865
Integrative Analyses of Circulating mRNA and lncRNA Expression Profile in Plasma of Lung Cancer Patients. PMID:35433477
lncRNA CDKN2B-AS1 Could Be an Indicator to Identify Prognosis and Status of Immune Microenvironment in Thyroid Cancer. PMID:35432631
Chromosome-Level Genome Assembly of Bupleurum chinense DC Provides Insights Into the Saikosaponin Biosynthesis. PMID:35432473
Combined Hypothesis Testing on Graphs with Applications to Gene Set Enrichment Analysis. PMID:35431372
MCTR3 reprograms arthritic monocytes to upregulate Arginase-1 and exert pro-resolving and tissue-protective functions in experimental arthritis. PMID:35430453
Oogenesis and lipid metabolism in the deep-sea sponge Phakellia ventilabrum (Linnaeus, 1767). PMID:35428825
Transcriptome analysis reveals anthocyanin regulation in Chinese cabbage (Brassica rapa L.) at low temperatures. PMID:35428824
Transcriptome profiling of flower buds of male-sterile lines provides new insights into male sterility mechanism in alfalfa. PMID:35428186
Discovery of moiety preference by Shapley value in protein kinase family using random forest models. PMID:35428180
Network pharmacology-based analysis for unraveling potential cancer-related molecular targets of Egyptian propolis phytoconstituents accompanied with molecular docking and in vitro studies. PMID:35423607
Potential therapeutic targets and molecular details of anthocyan-treated inflammatory bowel disease: a systematic bioinformatics analysis of network pharmacology. PMID:35423341
Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment. PMID:35422890
Bioinformatics Analysis Identified the Hub Genes, mRNA-miRNA-lncRNA Axis, and Signaling Pathways Involved in Rheumatoid Arthritis Pathogenesis. PMID:35422654
Interactive single-cell data analysis using Cellar. PMID:35422041
Proteomics analysis: inhibiting the expression of P62 protein by chloroquine combined with dacarbazine can reduce the malignant progression of uveal melanoma. PMID:35421957
SNCA correlates with immune infiltration and serves as a prognostic biomarker in lung adenocarcinoma. PMID:35421944
Structural and Evolutionary Adaptations of Nei-Like DNA Glycosylases Proteins Involved in Base Excision Repair of Oxidative DNA Damage in Vertebrates. PMID:35419164
Computed Tomography Imaging-Based Radiogenomics Analysis Reveals Hypoxia Patterns and Immunological Characteristics in Ovarian Cancer. PMID:35418998
A draft genome of Drung cattle reveals clues to its chromosomal fusion and environmental adaptation. PMID:35418663
MicroRNA profiles in aqueous humor between pseudoexfoliation glaucoma and normal tension glaucoma patients in a Korean population. PMID:35418653
Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. PMID:35418617
Integration of Aspergillus niger transcriptomic profile with metabolic model identifies potential targets to optimise citric acid production from lignocellulosic hydrolysate. PMID:35418297
Molecular signatures of tumor progression in pancreatic adenocarcinoma identified by energy metabolism characteristics. PMID:35418066
An Integrated Approach to Recognize Potential Protective Effects of Culinary Herbs Against Chronic Diseases. PMID:35415428
Bovine host genome acts on rumen microbiome function linked to methane emissions. PMID:35414107
Aggresome assembly at the centrosome is driven by CP110-CEP97-CEP290 and centriolar satellites. PMID:35411088
Unchecked oxidative stress in skeletal muscle prevents outgrowth of disseminated tumour cells. PMID:35411081
Multiomics implicate gut microbiota in altered lipid and energy metabolism in Parkinson's disease. PMID:35411052
Clone and Function Verification of the OPR gene in Brassica napus Related to Linoleic Acid Synthesis. PMID:35410118
Candidate Genes and Pathways in Rice Co-Responding to Drought and Salt Identified by gcHap Network. PMID:35409377
Bioinformatics Screening of Potential Biomarkers from mRNA Expression Profiles to Discover Drug Targets and Agents for Cervical Cancer. PMID:35409328
TNF-α Induced Myotube Atrophy in C2C12 Cell Line Uncovers Putative Inflammatory-Related lncRNAs Mediating Muscle Wasting. PMID:35409236
Identification and New Indication of Melanin-Concentrating Hormone Receptor 1 (MCHR1) Antagonist Derived from Machine Learning and Transcriptome-Based Drug Repositioning Approaches. PMID:35409167
Transcriptome Analysis of Populus euphratica under Salt Treatment and PeERF1 Gene Enhances Salt Tolerance in Transgenic Populus alba × Populus glandulosa. PMID:35409087
Circulating Vitreous microRNA as Possible Biomarker in High Myopic Eyes with Macular Hole. PMID:35409006
In Silico Characterisation of the Late Embryogenesis Abundant (LEA) Protein Families and Their Role in Desiccation Tolerance in Ramonda serbica Panc. PMID:35408906
miRNAs Contained in Extracellular Vesicles Cargo Contribute to the Progression of Idiopathic Pulmonary Fibrosis: An In Vitro Aproach. PMID:35406675
Robust Validation and Comprehensive Analysis of a Novel Signature Derived from Crucial Metabolic Pathways of Pancreatic Ductal Adenocarcinoma. PMID:35406597
TIA1 Loss Exacerbates Fatty Liver Disease but Exerts a Dual Role in Hepatocarcinogenesis. PMID:35406476
Transcriptional CDK Inhibitors as Potential Treatment Option for Testicular Germ Cell Tumors. PMID:35406461
Investigation of the Effect of Curcumin on Protein Targets in NAFLD Using Bioinformatic Analysis. PMID:35405942
Integrative Analyses of Antler Cartilage Transcriptome and Proteome of Gansu Red Deer (Cervus elaphus kansuensis) at Different Growth Stages. PMID:35405922
Cardiovascular signatures of COVID-19 predict mortality and identify barrier stabilizing therapies. PMID:35405523
Evaluation of Host Depletion and Extraction Methods for Shotgun Metagenomic Analysis of Bovine Vaginal Samples. PMID:35404108
Similarity-Based Method with Multiple-Feature Sampling for Predicting Drug Side Effects. PMID:35401786
Integrative Analysis of Elicitor-Induced Camptothecin Biosynthesis in Camptotheca acuminata Plantlets Through a Combined Omics Approach. PMID:35401649
Preclinical Studies on Convalescent Human Immune Plasma-Derived Exosome: Omics and Antiviral Properties to SARS-CoV-2. PMID:35401544
A new finding in the key prognosis-related proto-oncogene FYN in hepatocellular carcinoma based on the WGCNA hub-gene screening trategy. PMID:35397600
Integrative proteomic characterization of trace FFPE samples in early-stage gastrointestinal cancer. PMID:35397555
Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis. PMID:35397550
A new nomogram model for prognosis of hepatocellular carcinoma based on novel gene signature that regulates cross-talk between immune and tumor cells. PMID:35397536
Pan-cancer analysis on the role of PIK3R1 and PIK3R2 in human tumors. PMID:35395865
Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria. PMID:35395818
TGF-β induced reprogramming and drug resistance in triple-negative breast cells. PMID:35395809
Zinc supplementation modifies brain tissue transcriptome of Apis mellifera honeybees. PMID:35395723
Oxylipin profile in saliva from patients with cystic fibrosis reveals a balance between pro-resolving and pro-inflammatory molecules. PMID:35393448
Large-scale analysis of MicroRNA expression in motor neuron-like cells derived from human umbilical cord blood mesenchymal stem cells. PMID:35393444
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
CircUBE2Q2 promotes differentiation of cattle muscle stem cells and is a potential regulatory molecule of skeletal muscle development. PMID:35387588
Use of a Minimal Microbial Consortium to Determine the Origin of Kombucha Flavor. PMID:35387069
Expansion of Schizophrenia Gene Network Knowledge Using Machine Learning Selected Signals From Dorsolateral Prefrontal Cortex and Amygdala RNA-seq Data. PMID:35386517
Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa. PMID:35384379
A high-quality assembly reveals genomic characteristics, phylogenetic status, and causal genes for leucism plumage of Indian peafowl. PMID:35383847
Feedlot diets containing different starch levels and additives change the cecal proteome involved in cattle's energy metabolism and inflammatory response. PMID:35383279
Plasma proteomics reveals crosstalk between lipid metabolism and immunity in dairy cows receiving essential fatty acids and conjugated linoleic acid. PMID:35383209
Multiomic profiling of the acute stress response in the mouse hippocampus. PMID:35383160
Genome-scale transcriptomic insights into the gene co-expression network of seed abortion in triploid Siraitia grosvenorii. PMID:35382733
TMT-based proteomic analysis reveals integrins involved in the synergistic infection of reticuloendotheliosis virus and avian leukosis virus subgroup J. PMID:35379256
Downregulation of KRAB zinc finger proteins in 5-fluorouracil resistant colorectal cancer cells. PMID:35379199
Weighted gene co-expression network indicates that the DYNLL2 is an important regulator of chicken breast muscle development and is regulated by miR-148a-3p. PMID:35379193
Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage. PMID:35379173
Text Mining-Based Drug Discovery for Connective Tissue Disease-Associated Pulmonary Arterial Hypertension. PMID:35370713
Key Disease Mechanisms Linked to Amyotrophic Lateral Sclerosis in Spinal Cord Motor Neurons. PMID:35370543
Physiological and multi-omics responses of Neoporphyra haitanensis to dehydration-rehydration cycles. PMID:35369869
Correlation between intestinal flora disruption and protein-energy wasting in patients with end-stage renal disease. PMID:35369865
Physiological adjustment of pomegranate pericarp responding to sunburn and its underlying molecular mechanisms. PMID:35369864
Physiological Roles of Short-Chain and Long-Chain Menaquinones (Vitamin K2) in Lactococcus cremoris. PMID:35369466
Identification of Potential Diagnostic Biomarkers From Circulating Cells During the Course of Sleep Deprivation-Related Myocardial Infarction Based on Bioinformatics Analyses. PMID:35369343
A Novel Deep Learning Method to Predict Lung Cancer Long-Term Survival With Biological Knowledge Incorporated Gene Expression Images and Clinical Data. PMID:35368657
Characterization of polyhydroxyalkanoate production capacity, composition and weight synthesized by Burkholderia cepacia JC-1 from various carbon sources. PMID:35368536
Identification of potential pathways and microRNA-mRNA networks associated with benzene metabolite hydroquinone-induced hematotoxicity in human leukemia K562 cells. PMID:35366954
Based on multiple machine learning to identify the ENO2 as diagnosis biomarkers of glaucoma. PMID:35366826
Predict the role of lncRNA in kidney aging based on RNA sequencing. PMID:35366793
A high-quality assembled genome and its comparative analysis decode the adaptive molecular mechanism of the number one Chinese cotton variety CRI-12. PMID:35365835
Microbial metabolites in the marine carbon cycle. PMID:35365785
A multi-omics approach to elucidate the mechanisms of action of a dietary muramidase administered to broiler chickens. PMID:35365750
Metabolomics approach to assess the effect of siphonal autotomy on metabolic characteristics of razor clam Solen grandis. PMID:35365742
Molecular mechanisms of Huanglian jiedu decoction on ulcerative colitis based on network pharmacology and molecular docking. PMID:35365737
Metabonomics analysis of flavonoids in seeds and sprouts of two Chinese soybean cultivars. PMID:35365712
Compositions of gut microbiota before and shortly after hepatitis C viral eradication by direct antiviral agents. PMID:35361930
Black pepper and tarragon essential oils suppress the lipolytic potential and the type II secretion system of P. psychrophila KM02. PMID:35361821
Widely targeted analysis of metabolomic changes of Cucumis sativus induced by cucurbit chlorotic yellows virus. PMID:35361125
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
Identification of Pathologic and Prognostic Genes in Prostate Cancer Based on Database Mining. PMID:35360870
Protective Mechanism of Leucine and Isoleucine against H2O2-Induced Oxidative Damage in Bovine Mammary Epithelial Cells. PMID:35360198
Distinct N and C Cross-Feeding Networks in a Synthetic Mouse Gut Consortium. PMID:35357218
Functional and Biochemical Characterization of the MazEF6 Toxin-Antitoxin System of Mycobacterium tuberculosis. PMID:35357163
Mass Spectrometric Behavior and Molecular Mechanisms of Fermented Deoxyanthocyanidins to Alleviate Ulcerative Colitis Based on Network Pharmacology. PMID:35356765
Comparative transcriptome analysis reveals significant differences in gene expression between pathogens of apple Glomerella leaf spot and apple bitter rot. PMID:35354401
Microbial communities of Auka hydrothermal sediments shed light on vent biogeography and the evolutionary history of thermophily. PMID:35352015
Network Crosstalk as a Basis for Drug Repurposing. PMID:35350247
DAMPs/PAMPs induce monocytic TLR activation and tolerance in COVID-19 patients; nucleic acid binding scavengers can counteract such TLR agonists. PMID:35349874
Evaluation of Early Biomarkers of Atherosclerosis Associated with Polychlorinated Biphenyl Exposure: An in Vitro and in Vivo Study. PMID:35349355
COVID-19: impact on Public Health and hypothesis-driven investigations on genetic susceptibility and severity. PMID:35348847
Hallmarks of aging-based dual-purpose disease and age-associated targets predicted using PandaOmics AI-powered discovery engine. PMID:35347083
Prognostic significance of SNCA and its methylation in bladder cancer. PMID:35346107
Bioinformatics analysis of potential therapeutic targets for COVID-19 infection in patients with carotid atherosclerosis. PMID:35344771
Bioinformatics Analysis of Differential Gene and MicroRNA Expression in Lung Adenocarcinoma: Genetic Effects on Patient Prognosis, as Indicated by the TCGA Database. PMID:35342284
Transcriptomic analysis of methyl jasmonate treatment reveals gene networks involved in drought tolerance in pearl millet. PMID:35338214
MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode. PMID:35338210
Effects of varicocele and microsurgical varicocelectomy on the metabolites in semen. PMID:35338186
Temporal dynamics from phosphoproteomics using endoscopic biopsy specimens provides new therapeutic targets in stage IV gastric cancer. PMID:35338158
Metabolomic strategies and biochemical analysis of the effect of processed Rehmanniae radix extract on a blood-deficient rat model. PMID:35337319
Pharmacometabolomics Applied to Personalized Medicine in Urological Cancers. PMID:35337093
Transcriptome and Small RNA Profiling of Potato Virus Y Infected Potato Cultivars, Including Systemically Infected Russet Burbank. PMID:35336930
GXP: Analyze and Plot Plant Omics Data in Web Browsers. PMID:35336631
The Macronutrient Composition of Infant Formula Produces Differences in Gut Microbiota Maturation That Associate with Weight Gain Velocity and Weight Status. PMID:35334900
Down-regulation of the bacterial protein biosynthesis machinery in response to weeks, years, and decades of soil warming. PMID:35333567
Transcriptome profiling of cashew apples (Anacardium occidentale) genotypes reveals specific genes linked to firmness and color during pseudofruit development. PMID:35332428
Stripenn detects architectural stripes from chromatin conformation data using computer vision. PMID:35332165
Adrenal tropism of SARS-CoV-2 and adrenal findings in a post-mortem case series of patients with severe fatal COVID-19. PMID:35332140
Comprehensive analysis of tumor immune microenvironment and prognosis of m6A-related lncRNAs in gastric cancer. PMID:35331183
Microbe-Immune Crosstalk: Evidence That T Cells Influence the Development of the Brain Metabolome. PMID:35328680
Using Transcriptome Analysis to Explore Gray Mold Resistance-Related Genes in Onion (Alliumcepa L.). PMID:35328095
Identification of Key Modules and Genes Associated with Major Depressive Disorder in Adolescents. PMID:35328018
Characterization of a Read-through Fusion Transcript, BCL2L2-PABPN1, Involved in Porcine Adipogenesis. PMID:35327999
Potential Anti-Inflammatory Effects of a New Lyophilized Formulation of the Conditioned Medium Derived from Periodontal Ligament Stem Cells. PMID:35327485
Distinct and Common Features of Numerical and Structural Chromosomal Instability across Different Cancer Types. PMID:35326573
Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. PMID:35323968
Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data. PMID:35323700
Microbial Interactions in Kombucha through the Lens of Metabolomics. PMID:35323678
Screening of Carbofuran-Degrading Bacteria Chryseobacterium sp. BSC2-3 and Unveiling the Change in Metabolome during Carbofuran Degradation. PMID:35323662
Microwave radiation induces neuronal autophagy through miR-30a-5p/AMPKα2 signal pathway. PMID:35322852
The comparisons of expression pattern reveal molecular regulation of fruit metabolites in S. nigrum and S. lycopersicum. PMID:35322121
Identification of potentially functional circular RNAs hsa_circ_0070934 and hsa_circ_0004315 as prognostic factors of hepatocellular carcinoma by integrated bioinformatics analysis. PMID:35322101
Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx. PMID:35322036
Comparative transcriptome analysis of heat stress responses of Clematis lanuginosa and Clematis crassifolia. PMID:35321648
Identifying large-scale interaction atlases using probabilistic graphs and external knowledge. PMID:35321220
Prognostic and biological role of the N-Myc downstream-regulated gene family in hepatocellular carcinoma. PMID:35321174
Analysis of Gene Expression Profiles in the Liver of Rats With Intrauterine Growth Retardation. PMID:35321016
Identification and Characterization of the Roles of circCASP9 in Gastric Cancer Based on a circRNA-miRNA-mRNA Regulatory Network. PMID:35320976
COMMIT: Consideration of metabolite leakage and community composition improves microbial community reconstructions. PMID:35320266
Integrative interactomics applied to bovine fescue toxicosis. PMID:35318361
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation. PMID:35315433
The proteomic characterization of the peritumor microenvironment in human hepatocellular carcinoma. PMID:35314790
Identification of co-expression hub genes for ferroptosis in kidney renal clear cell carcinoma based on weighted gene co-expression network analysis and The Cancer Genome Atlas clinical data. PMID:35314744
Transposon insertional mutagenesis of diverse yeast strains suggests coordinated gene essentiality polymorphisms. PMID:35314699
scINSIGHT for interpreting single-cell gene expression from biologically heterogeneous data. PMID:35313930
Comparison of tumor and two types of paratumoral tissues highlighted epigenetic regulation of transcription during field cancerization in non-small cell lung cancer. PMID:35313869
Systematic analysis of the expression and prognostic value of ITPR1 and correlation with tumor infiltrating immune cells in breast cancer. PMID:35313846
Surgical Treatment for Colorectal Cancer Partially Restores Gut Microbiome and Metabolome Traits. PMID:35311577
Target-Dependent Coordinated Biogenesis of Secondary MicroRNAs by miR-146a Balances Macrophage Activation Processes. PMID:35311564
Temporally Selective Modification of the Tomato Rhizosphere and Root Microbiome by Volcanic Ash Fertilizer Containing Micronutrients. PMID:35311513
Increasing the diversity of dietary fibers in a daily-consumed bread modifies gut microbiota and metabolic profile in subjects at cardiometabolic risk. PMID:35311446
CAF-Associated Paracrine Signaling Worsens Outcome and Potentially Contributes to Chemoresistance in Epithelial Ovarian Cancer. PMID:35311102
Integrated Metabolome and Transcriptome Analyses Reveal Dissimilarities in the Anthocyanin Synthesis Pathway Between Different Developmental Leaf Color Transitions in Hopea hainanensis (Dipterocarpaceae). PMID:35310646
Identification of key microorganisms in facultative stabilization ponds from dairy industries, using metagenomics. PMID:35310160
Identification of Potential Ferroptosis-Related Biomarkers and Immune Infiltration in Human Coronary Artery Atherosclerosis. PMID:35308568
Perfluoroalkyl substances influence DNA methylation in school-age children highly exposed through drinking water contaminated from firefighting foam: a cohort study in Ronneby, Sweden. PMID:35308102
Beta-blocker/ACE inhibitor therapy differentially impacts the steady state signaling landscape of failing and non-failing hearts. PMID:35306519
Ferroptosis-related gene SLC1A5 is a novel prognostic biomarker and correlates with immune infiltrates in stomach adenocarcinoma. PMID:35305616
Heat Shock Procedure Affects Cell Division-Associated Genes in Gynogenetic Manipulation. PMID:35305189
Identification of hub genes and transcription factors in patients with rheumatoid arthritis complicated with atherosclerosis. PMID:35304503
Bioinformatical analysis of the key differentially expressed genes and associations with immune cell infiltration in development of endometriosis. PMID:35303800
Antifungals influence the immune-related transcriptomic landscape of human monocytes after Aspergillus fumigatus infection. PMID:35301416
Integrative analysis identifies key genes related to metastasis and a robust gene-based prognostic signature in uveal melanoma. PMID:35300699
Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients. PMID:35300688
Metatranscriptomic Analyses Unravel Dynamic Changes in the Microbial and Metabolic Transcriptional Profiles in Artisanal Austrian Hard-Cheeses During Ripening. PMID:35300479
An Oxidative Stress-Related Genes Signature for Predicting Survival in Bladder Cancer: Based on TCGA Database and Bioinformatics. PMID:35300137
Identification of Down-Regulated ADH1C is Associated With Poor Prognosis in Colorectal Cancer Using Bioinformatics Analysis. PMID:35300114
Healthcare-associated infections caused by chlorhexidine-tolerant Serratia marcescens carrying a promiscuous IncHI2 multi-drug resistance plasmid in a veterinary hospital. PMID:35298517
Integrative analysis reveals the functional implications and clinical relevance of pyroptosis in low-grade glioma. PMID:35296768
Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia. PMID:35295737
Identification of hub genes and pathways in bladder cancer using bioinformatics analysis. PMID:35291419
Prediction of response and adverse drug reaction of pemetrexed plus platinum-based chemotherapy in lung adenocarcinoma by serum metabolomic profiling. PMID:35290920
Gut microbiome correlates of response and toxicity following anti-CD19 CAR T cell therapy. PMID:35288695
Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum. PMID:35287589
Cold stress tolerance of the intertidal red alga Neoporphyra haitanensis. PMID:35287582
Comparative transcriptome analysis reveals immunoregulation mechanism of lncRNA-mRNA in gill and skin of large yellow croaker (Larimichthys crocea) in response to Cryptocaryon irritans infection. PMID:35287569
Distinct metabolic profiling is correlated with bisexual flowers formation resulting from exogenous ethephon induction in melon (Cucumis melo L.). PMID:35287348
Transcriptomic Analysis Revealed Reactive Oxygen Species Scavenging Mechanisms Associated With Ferrous Iron Toxicity in Aromatic Keteki Joha Rice. PMID:35283928
Genome Analysis of the Broad Host Range Necrotroph Nalanthamala psidii Highlights Genes Associated With Virulence. PMID:35283890
Microbial Community and Metabolite Dynamics During Soy Sauce Koji Making. PMID:35283863
Salicylic Acid-Mediated Disturbance Increases Bacterial Diversity in the Phyllosphere but Is Overcome by a Dominant Core Community. PMID:35283825
Soil Properties Interacting With Microbial Metagenome in Decreasing CH4 Emission From Seasonally Flooded Marshland Following Different Stages of Afforestation. PMID:35283824
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
Cold Exposure Induces Depot-Specific Alterations in Fatty Acid Composition and Transcriptional Profile in Adipose Tissues of Pigs. PMID:35282453
Identifying Environmental Endocrine Disruptors Associated With the Age at Menarche by Integrating a Transcriptome-Wide Association Study With Chemical-Gene-Interaction Analysis. PMID:35282430
CerealESTDb: A Comprehensive Resource for Abiotic Stress-Responsive Annotated ESTs With Predicted Genes, Gene Ontology, and Metabolic Pathways in Major Cereal Crops. PMID:35281847
Network Analysis Reveals Different Cellulose Degradation Strategies Across Trichoderma harzianum Strains Associated With XYR1 and CRE1. PMID:35281818
Solasonine Induces Apoptosis and Inhibits Proliferation of Bladder Cancer Cells by Suppressing NRP1 Expression. PMID:35281516
Insights Into the Impact of Small RNA SprC on the Metabolism and Virulence of Staphylococcus aureus. PMID:35281456
Gut microbial composition in developmental stages of gall inducing thrips Gynaikothrips uzeli and associated plant pathogenesis. PMID:35280592
HCK is a Potential Prognostic Biomarker that Correlates with Immune Cell Infiltration in Acute Myeloid Leukemia. PMID:35280440
Identification of differentially expressed and methylated genes and construction of a co-expression network in age-related macular degeneration. PMID:35280389
Structure and activity of the DHNA Coenzyme-A Thioesterase from Staphylococcus aureus providing insights for innovative drug development. PMID:35279696
The expanded inhibitor of apoptosis gene family in oysters possesses novel domain architectures and may play diverse roles in apoptosis following immune challenge. PMID:35279090
Nicotinamide (niacin) supplement increases lipid metabolism and ROS-induced energy disruption in triple-negative breast cancer: potential for drug repositioning as an anti-tumor agent. PMID:35278276
Chromosome-level genome assembly, annotation, and phylogenomics of the gooseneck barnacle Pollicipes pollicipes. PMID:35277961
Novel alleles gained during the Beringian isolation period. PMID:35277570
Computational identification of host genomic biomarkers highlighting their functions, pathways and regulators that influence SARS-CoV-2 infections and drug repurposing. PMID:35277538
The vaccine-site microenvironment: impacts of antigen, adjuvant, and same-site vaccination on antigen presentation and immune signaling. PMID:35277457
Maize plant architecture trait QTL mapping and candidate gene identification based on multiple environments and double populations. PMID:35277127
Hydrolyzed Proteins and Vegetable Peptides: Anti-Inflammatory Mechanisms in Obesity and Potential Therapeutic Targets. PMID:35277049
Embryonic Exposure to Tryptophan Yields Bullying Victimization via Reprogramming the Microbiota-Gut-Brain Axis in a Chicken Model. PMID:35277020
Different Alterations in Gut Microbiota between Bifidobacterium longum and Fecal Microbiota Transplantation Treatments in Propionic Acid Rat Model of Autism. PMID:35276971
A genome-scale gain-of-function CRISPR screen in CD8 T cells identifies proline metabolism as a means to enhance CAR-T therapy. PMID:35276062
Integrated analysis of differentially expressed genes and a ceRNA network to identify hub lncRNAs and potential drugs for multiple sclerosis. PMID:35273684
Integrative Analyses of Genes Associated With Otologic Disorders in Turner Syndrome. PMID:35273637
Metabolomic Impact of Lidocaine on a Triple Negative Breast Cancer Cell Line. PMID:35273500
Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus. PMID:35272716
Uncovering the Gene Regulatory Network of Maize Hybrid ZD309 under Heat Stress by Transcriptomic and Metabolomic Analysis. PMID:35270147
Transcriptome Profiling and Functional Validation of RING-Type E3 Ligases in Halophyte Sesuvium verrucosum under Salinity Stress. PMID:35269961
Coenzyme A Restriction as a Factor Underlying Pre-Eclampsia with Polycystic Ovary Syndrome as a Risk Factor. PMID:35269927
Better Agreement of Human Transcriptomic and Proteomic Cancer Expression Data at the Molecular Pathway Activation Level. PMID:35269755
Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions: The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control. PMID:35269716
Imbalances in TCA, Short Fatty Acids and One-Carbon Metabolisms as Important Features of Homeostatic Disruption Evidenced by a Multi-Omics Integrative Approach of LPS-Induced Chronic Inflammation in Male Wistar Rats. PMID:35269702
Transcriptomics of Parental Care in the Hypothalamic-Septal Region of Female Zebra Finch Brain. PMID:35269661
Integrated Metabolomics and Lipidomics Reveal High Accumulation of Glycerophospholipids in Human Astrocytes under the Lipotoxic Effect of Palmitic Acid and Tibolone Protection. PMID:35269616
Comprehensive Analysis of the Effect of 20(R)-Ginsenoside Rg3 on Stroke Recovery in Rats via the Integrative miRNA-mRNA Regulatory Network. PMID:35268674
Widely-Targeted Metabolic Profiling in Lyciumbarbarum Fruits under Salt-Alkaline Stress Uncovers Mechanism of Salinity Tolerance. PMID:35268665
Is Genetic Engineering a Route to Enhance Microalgae-Mediated Bioremediation of Heavy Metal-Containing Effluents? PMID:35268582
A Computational Text Mining-Guided Meta-Analysis Approach to Identify Potential Xerostomia Drug Targets. PMID:35268532
Comparative analysis of the daily brain transcriptomes of Asian particolored bat. PMID:35264653
Quantitative proteomic analysis of the lysine acetylome reveals diverse SIRT2 substrates. PMID:35264593
Comparative whole transcriptome analysis of Parkinson's disease focusing on the efficacy of zonisamide. PMID:35264450
Transcriptomic profiling of the telomerase transformed Mesenchymal stromal cells derived adipocytes in response to rosiglitazone. PMID:35264099
Whole genome sequence of pan drug-resistant clinical isolate of Acinetobacter baumannii ST1890. PMID:35263355
Urgent need for consistent standards in functional enrichment analysis. PMID:35263338
RNA-seq and integrated network analysis reveals the hub genes and key pathway of paclitaxel inhibition on Adriamycin resistant diffuse large B cell lymphoma cells. PMID:35263200
Gut microbiota and the prevalence and incidence of renal stones. PMID:35260689
MicroRNome analysis generates a blood-based signature for endometriosis. PMID:35260677
Investigation of bacterial diversity using 16S rRNA sequencing and prediction of its functionalities in Moroccan phosphate mine ecosystem. PMID:35260670
Computing microRNA-gene interaction networks in pan-cancer using miRDriver. PMID:35260634
Metagenomics reveals differences in microbial composition and metabolic functions in the rumen of dairy cows with different residual feed intake. PMID:35260198
Comprehensive characterization of m6A methylation and its impact on prognosis, genome instability, and tumor microenvironment in hepatocellular carcinoma. PMID:35260168
Integrative Genome-Scale Metabolic Modeling Reveals Versatile Metabolic Strategies for Methane Utilization in Methylomicrobium album BG8. PMID:35258342
Changes in the liver transcriptome and physiological parameters of Japanese Black steers during the fattening period. PMID:35256743
Patients with low muscle mass have characteristic microbiome with low potential for amino acid synthesis in chronic liver disease. PMID:35256716
Shared genetic loci for body fat storage and adipocyte lipolysis in humans. PMID:35256633
The fiber diameter traits of Tibetan cashmere goats are governed by the inherent differences in stress, hypoxic, and metabolic adaptations: an integrative study of proteome and transcriptome. PMID:35255833
Determining extracellular vesicles properties and miRNA cargo variability in bovine milk from healthy cows and cows undergoing subclinical mastitis. PMID:35255807
Whole-genome sequencing reveals host factors underlying critical COVID-19. PMID:35255492
A network-based computational and experimental framework for repurposing compounds toward the treatment of non-alcoholic fatty liver disease. PMID:35252807
Identification and Comprehensive Analysis of FREM2 Mutation as a Potential Prognostic Biomarker in Colorectal Cancer. PMID:35252356
Changes of Intestinal Microflora in Colorectal Cancer Patients after Surgical Resection and Chemotherapy. PMID:35251295
Early Brain microRNA/mRNA Expression is Region-Specific After Neonatal Hypoxic-Ischemic Injury in a Mouse Model. PMID:35251138
A High-Quality, Chromosome-Level Genome Provides Insights Into Determinate Flowering Time and Color of Cotton Rose (Hibiscus mutabilis). PMID:35251086
Reconstruction and analysis of a large-scale binary Ras-effector signaling network. PMID:35246154
Predicting biochemical-recurrence-free survival using a three-metabolic-gene risk score model in prostate cancer patients. PMID:35246070
Co‑expressed microRNAs, target genes and pathways related to metabolism, inflammation and endocrine function in individuals at risk for type 2 diabetes. PMID:35244194
Ligand-mediated PAI-1 inhibition in a mouse model of peritoneal carcinomatosis. PMID:35243423
Tertiary lymphoid structure and decreased CD8+ T cell infiltration in minimally invasive adenocarcinoma. PMID:35243243
The Role of Intestinal Microbiota in Regulating the Metabolism of Bile Acids Is Conserved Across Vertebrates. PMID:35242120
Altered Expression of Specific MicroRNAs in Plasma of Aneurysmal Subarachnoid Hemorrhage Patients. PMID:35242102
Network pharmacology-based predictions of active components and pharmacological mechanisms of Artemisia annua L. for the treatment of the novel Corona virus disease 2019 (COVID-19). PMID:35241045
Prognostic value and immune relevancy of a combined autophagy-, apoptosis- and necrosis-related gene signature in glioblastoma. PMID:35241019
Identification of DDX31 as a Potential Oncogene of Invasive Metastasis and Proliferation in PDAC. PMID:35237592
Identifying Potential Mitochondrial Proteome Signatures Associated with the Pathogenesis of Pulmonary Arterial Hypertension in the Rat Model. PMID:35237384
Prognostication of Pancreatic Cancer Using The Cancer Genome Atlas Based Ferroptosis-Related Long Non-Coding RNAs. PMID:35237306
Microbiome and metabolome profiles of high screen time in a cohort of healthy college students. PMID:35236903
Combination of ferroptosis and pyroptosis to construct a prognostic classifier and predict immune landscape, chemotherapeutic efficacy and immunosuppressive molecules in hepatocellular carcinoma. PMID:35236323
Comprehensive analysis of the autophagy-dependent ferroptosis-related gene FANCD2 in lung adenocarcinoma. PMID:35236309
Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction. PMID:35236286
Transcriptome sequencing and lncRNA-miRNA-mRNA network construction in cardiac fibrosis and heart failure. PMID:35235759
Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming. PMID:35235716
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. PMID:35234924
Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus). PMID:35233245
Sow vaccination against virulent Glaesserella parasuis shapes the nasal microbiota of their offspring. PMID:35233006
Preterm birth buccal cell epigenetic biomarkers to facilitate preventative medicine. PMID:35232984
Comprehensive analysis of ferroptosis-related genes and prognosis of cutaneous melanoma. PMID:35232428
Network Approaches for Precision Oncology. PMID:35230690
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Microbial Consortiums of Putative Degraders of Low-Density Polyethylene-Associated Compounds in the Ocean. PMID:35229650
Global profiling of phosphorylation-dependent changes in cysteine reactivity. PMID:35228727
Neuronal-glial communication perturbations in murine SOD1G93A spinal cord. PMID:35228715
GAIT-GM integrative cross-omics analyses reveal cholinergic defects in a C. elegans model of Parkinson's disease. PMID:35228596
Full-length transcriptome analysis of multiple organs and identification of adaptive genes and pathways in Mikania micrantha. PMID:35228580
Comparative systeomics to elucidate physiological differences between CHO and SP2/0 cell lines. PMID:35228567
Short-term physiologic response of the green microalga Picochlorum sp. (BPE23) to supra-optimal temperature. PMID:35228560
Screening the components of Saussurea involucrata for novel targets for the treatment of NSCLC using network pharmacology. PMID:35227278
DLRAPom: a hybrid pipeline of Optimized XGBoost-guided integrative multiomics analysis for identifying targetable disease-related lncRNA-miRNA-mRNA regulatory axes. PMID:35224615
Comparative transcriptomes of three different skin sites for the Asiatic toad (Bufo gargarizans). PMID:35223212
Construction and Verification of a Combined Hypoxia and Immune Index for Clear Cell Renal Cell Carcinoma. PMID:35222525
Weighted Co-Expression Network Analysis Identifies RNF181 as a Causal Gene of Coronary Artery Disease. PMID:35222523
Metabolomic Profiling Reveals That 5-Hydroxylysine and 1-Methylnicotinamide Are Metabolic Indicators of Keloid Severity. PMID:35222522
Physio-Morphological, Biochemical and Transcriptomic Analyses Provide Insights Into Drought Stress Responses in Mesona chinensis Benth. PMID:35222473
Exploration of Diverse Secondary Metabolites From Streptomyces sp. YINM00001, Using Genome Mining and One Strain Many Compounds Approach. PMID:35222341
Multi-Omics Profiling Specifies Involvement of Alternative Ribosomal Proteins in Response to Zinc Limitation in Mycobacterium smegmatis. PMID:35222334
Metagenomic Analysis Reveals a Changing Microbiome Associated With the Depth of Invasion of Oral Squamous Cell Carcinoma. PMID:35222330
Comparative Metabolic Pathways Analysis and Subtractive Genomics Profiling to Prioritize Potential Drug Targets Against Streptococcus pneumoniae. PMID:35222301
Duchenne muscular dystrophy gene expression is an independent prognostic marker for IDH mutant low-grade glioma. PMID:35217778
The transcriptomic responses of blunt snout bream (Megalobrama amblycephala) to acute hypoxia stress alone, and in combination with bortezomib. PMID:35216548
Unlike Chloroquine, Mefloquine Inhibits SARS-CoV-2 Infection in Physiologically Relevant Cells. PMID:35215969
The Anticancer Ruthenium Compound BOLD-100 Targets Glycolysis and Generates a Metabolic Vulnerability towards Glucose Deprivation. PMID:35213972
Identification of a new RNA-binding proteins-based signature for prognostic prediction in gastric cancer. PMID:35212295
HOXB4 Mis-Regulation Induced by Microcystin-LR and Correlated With Immune Infiltration Is Unfavorable to Colorectal Cancer Prognosis. PMID:35211403
Virulence Biomarkers of Bursaphelenchus xylophilus: A Proteomic Approach. PMID:35211137
Fermentation Profiles, Bacterial Community Compositions, and Their Predicted Functional Characteristics of Grass Silage in Response to Epiphytic Microbiota on Legume Forages. PMID:35211107
MicroRNA editing patterns in Huntington's disease. PMID:35210471
Complete genome sequence of biocontrol strain Paenibacillus peoriae HJ-2 and further analysis of its biocontrol mechanism. PMID:35209846
Assessment of Hydrocarbon Degradation Potential in Microbial Communities in Arctic Sea Ice. PMID:35208784
Application of Whole Exome Sequencing and Functional Annotations to Identify Genetic Variants Associated with Marfan Syndrome. PMID:35207686
SmileGNN: Drug-Drug Interaction Prediction Based on the SMILES and Graph Neural Network. PMID:35207606
Transcriptomics-Based Identification of Genes Related to Tapetum Degradation and Microspore Development in Lily. PMID:35205410
Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm. PMID:35205393
Genomic Analyses of the Fungus Paraconiothyrium sp. Isolated from the Chinese White Wax Scale Insect Reveals Its Symbiotic Character. PMID:35205383
Whole Genome DNA Methylation Profiling of D2 Medium Spiny Neurons in Mouse Nucleus Accumbens Using Two Independent Library Preparation Methods. PMID:35205351
A Genome-Scale Metabolic Model for the Human Pathogen Candida Parapsilosis and Early Identification of Putative Novel Antifungal Drug Targets. PMID:35205348
miRNome Profiling Detects miR-101-3p and miR-142-5p as Putative Blood Biomarkers of Frailty Syndrome. PMID:35205276
Single-Cell Sequencing Reveals an Intrinsic Heterogeneity of the Preovulatory Follicular Microenvironment. PMID:35204732
Benzaldehyde Attenuates the Fifth Stage Larval Excretory-Secretory Product of Angiostrongylus cantonensis-Induced Injury in Mouse Astrocytes via Regulation of Endoplasmic Reticulum Stress and Oxidative Stress. PMID:35204678
Multi-Omics Analysis of Multiple Glucose-Sensing Receptor Systems in Yeast. PMID:35204676
Integrative Identification of Genetic Loci Jointly Influencing Diabetes-Related Traits and Sleep Traits of Insomnia, Sleep Duration, and Chronotypes. PMID:35203577
Impact of Maternal Obesity on Liver Disease in the Offspring: A Comprehensive Transcriptomic Analysis and Confirmation of Results in a Murine Model. PMID:35203502
Genes Involved in Immune Reinduction May Constitute Biomarkers of Response for Metastatic Melanoma Patients Treated with Targeted Therapy. PMID:35203494
Overexpression of MET4 Leads to the Upregulation of Stress-Related Genes and Enhanced Sulfite Tolerance in Saccharomyces uvarum. PMID:35203287
CobraMod: A pathway-centric curation tool for constraint-based metabolic models. PMID:35201291
Amniotic Fluid microRNA in Severe Twin-Twin Transfusion Syndrome Cardiomyopathy-Identification of Differences and Predicting Demise. PMID:35200691
Effect of Different Initial Fermentation pH on Exopolysaccharides Produced by Pseudoalteromonas agarivorans Hao 2018 and Identification of Key Genes Involved in Exopolysaccharide Synthesis via Transcriptome Analysis. PMID:35200619
Identification of Potential Immune Checkpoint Inhibitor Targets in Gliomas via Bioinformatic Analyses. PMID:35198632
Biomarker Value of miR-221 and miR-222 as Potential Substrates in the Differential Diagnosis of Papillary Thyroid Cancer Based on Data Synthesis and Bioinformatics Approach. PMID:35197926
Identification of immune-infiltrated hub genes as potential biomarkers of Moyamoya disease by bioinformatics analysis. PMID:35197088
tensorGSEA: Detecting Differential Pathways in Type 2 Diabetes via Tensor-Based Data Reconstruction. PMID:35195883
A systematic review of gut microbiota composition in observational studies of major depressive disorder, bipolar disorder and schizophrenia. PMID:35194166
Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. PMID:35194091
Functional buffering via cell-specific gene expression promotes tissue homeostasis and cancer robustness. PMID:35194081
Clinical implications and molecular mechanisms of Cyclin-dependent kinases 4 for patients with hepatocellular carcinoma. PMID:35193513
Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy. PMID:35192691
Using AnnoTree to Get More Assignments, Faster, in DIAMOND+MEGAN Microbiome Analysis. PMID:35191776
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
WDR72 regulates vesicle trafficking in ameloblasts. PMID:35181734
Identification of candidate genes that specifically regulate subcutaneous and intramuscular fat deposition using transcriptomic and proteomic profiles in Dingyuan pigs. PMID:35181733
Regulated cell death joins in atherosclerotic plaque silent progression. PMID:35181730
Comprehensive analysis of the expression and significance of CXCLs in human diffuse large B-cell lymphoma. PMID:35181719
Integrated analysis of the prognostic and oncogenic roles of OPN3 in human cancers. PMID:35180853
Rebalance of the Polyamine Metabolism Suppresses Oxidative Stress and Delays Senescence in Nucleus Pulposus Cells. PMID:35178160
Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes. PMID:35178025
Whole-transcriptome analysis and construction of an anther development-related ceRNA network in Chinese cabbage (Brassica campestris L. ssp. pekinensis). PMID:35177672
Whole-genome analysis of human embryonic stem cells enables rational line selection based on genetic variation. PMID:35176222
Transcriptome-wide association study of coronary artery disease identifies novel susceptibility genes. PMID:35175464
RNA-Sequencing Analysis of the Spleen and Gill of Takifugu rubripes in Response to Vibrio harveyi Infection. PMID:35174239
Metabolic Variation Dictates Cardiac Pathogenesis in Patients With Tetralogy of Fallot. PMID:35174118
Effects of Antibiotic Use on Saliva Antibody Content and Oral Microbiota in Sprague Dawley Rats. PMID:35174102
Integrating single-cell sequencing data with GWAS summary statistics reveals CD16+monocytes and memory CD8+T cells involved in severe COVID-19. PMID:35172892
METABOLIC: high-throughput profiling of microbial genomes for functional traits, metabolism, biogeochemistry, and community-scale functional networks. PMID:35172890
Exosomes derived from human placental mesenchymal stem cells ameliorate myocardial infarction via anti-inflammation and restoring gut dysbiosis. PMID:35172728
Time-course RNA-seq analysis reveals stage-specific and melatonin-triggered gene expression patterns during the hair follicle growth cycle in Capra hircus. PMID:35172715
Mechanism of action of Tripterygium wilfordii for treatment of idiopathic membranous nephropathy based on network pharmacology. PMID:35172688
HIV-1 Tat and cocaine coexposure impacts piRNAs to affect astrocyte energy metabolism. PMID:35170353
Transcriptome analysis of genes associated with autolysis of Coprinus comatus. PMID:35169137
LINE-1 expression in cancer correlates with p53 mutation, copy number alteration, and S phase checkpoint. PMID:35169076
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. PMID:35168652
Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans. PMID:35168569
Global pleiotropic effects in adaptively evolved Escherichia coli lacking CRP reveal molecular mechanisms that define the growth physiology. PMID:35167766
IL-17 Receptor C Signaling Controls CD4+ TH17 Immune Responses and Tissue Injury in Immune-Mediated Kidney Diseases. PMID:35167487
Hyaluronidase-1-mediated glycocalyx impairment underlies endothelial abnormalities in polypoidal choroidal vasculopathy. PMID:35164755
AQP4 Attenuated TRAF6/NFκB Activation in Acrylamide-Induced Neurotoxicity. PMID:35164330
Single-Cell Analysis Uncovers Osteoblast Factor Growth Differentiation Factor 10 as Mediator of Vascular Smooth Muscle Cell Phenotypic Modulation Associated with Plaque Rupture in Human Carotid Artery Disease. PMID:35163719
De Novo Assembly and Annotation of the Vaginal Metatranscriptome Associated with Bacterial Vaginosis. PMID:35163545
Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior. PMID:35163386
Treatment of Pheochromocytoma Cells with Recurrent Cycles of Hypoxia: A New Pseudohypoxic In Vitro Model. PMID:35159368
Single-Cell RNA-Seq Reveals a Crosstalk between Hyaluronan Receptor LYVE-1-Expressing Macrophages and Vascular Smooth Muscle Cells. PMID:35159221
Syntenin Regulated by miR-216b Promotes Cancer Progression in Pancreatic Cancer. PMID:35155233
Organ-Specific Gene Expression Reveals the Role of the Cymbidium ensifolium-miR396/Growth-Regulating Factors Module in Flower Development of the Orchid Plant Cymbidium ensifolium. PMID:35154190
Identification and Tracking of Alloreactive T Cell Clones in Rhesus Macaques Through the RM-scTCR-Seq Platform. PMID:35154078
Genomic Insights Into Cadmium Resistance of a Newly Isolated, Plasmid-Free Cellulomonas sp. Strain Y8. PMID:35154027
A novel 4 immune-related genes as diagnostic markers and correlated with immune infiltrates in major depressive disorder. PMID:35152883
Gene-Interaction-Sensitive enrichment analysis in congenital heart disease. PMID:35151364
A computational system for Bayesian benchmark dose estimation of genomic data in BBMD. PMID:35151117
A microRNA-based liquid biopsy signature for the early detection of esophageal squamous cell carcinoma: a retrospective, prospective and multicenter study. PMID:35148754
Forgetting generates a novel state that is reactivatable. PMID:35148188
Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure. PMID:35147192
Chromosome-level genome assembly of Aristolochia contorta provides insights into the biosynthesis of benzylisoquinoline alkaloids and aristolochic acids. PMID:35147168
Developmental alterations in DNA methylation during gametogenesis from primordial germ cells to sperm. PMID:35146397
Immune Infiltration of CD8+ T Cells in Patients With Diabetic Pancreatic Cancer Reduces the Malignancy of Cancer Tissues: An In Silico Study. PMID:35145483
ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells. PMID:35145187
Serine, N-acetylaspartate differentiate adolescents with juvenile idiopathic arthritis compared with healthy controls: a metabolomics cross-sectional study. PMID:35144633
Micronutrient supplementation affects DNA methylation in male gonads with potential intergenerational epigenetic inheritance involving the embryonic development through glutamate receptor-associated genes. PMID:35144563
Fitness benefits play a vital role in the retention of the Pi-ta susceptible alleles. PMID:35143673
Second Heart Field-Derived Cells Contribute to Angiotensin II-Mediated Ascending Aortopathies. PMID:35143327
Changes in Gut Microbiota of Patients with Atopic Dermatitis During Balneotherapy. PMID:35140493
The induction of peripheral trained immunity in the pancreas incites anti-tumor activity to control pancreatic cancer progression. PMID:35140221
Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida. PMID:35135479
Temporal analyses of postnatal liver development and maturation by single-cell transcriptomics. PMID:35134346
Transcriptome Analysis of Detoxification-Related Genes in Spodoptera frugiperda (Lepidoptera: Noctuidae). PMID:35134188
Deciphering the etiology and role in oncogenic transformation of the CpG island methylator phenotype: a pan-cancer analysis. PMID:35134107
A High-Density Genetic Map Enables Genome Synteny and QTL Mapping of Vegetative Growth and Leaf Traits in Gardenia. PMID:35132310
Role of mitochondrial genetic interactions in determining adaptation to high altitude human population. PMID:35132109
NamZ1 and NamZ2 from the Oral Pathogen Tannerella forsythia Are Peptidoglycan Processing Exo-β-N-Acetylmuramidases with Distinct Substrate Specificities. PMID:35129368
β-catenin perturbations control differentiation programs in mouse embryonic stem cells. PMID:35128356
Identification of Key Genes and Pathways Involved in Circulating Tumor Cells in Colorectal Cancer. PMID:35127345
Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. PMID:35127303
Non-Invasive microRNA Profiling in Saliva can Serve as a Biomarker of Alcohol Exposure and Its Effects in Humans. PMID:35126468
Identification of the Association Between Toll-Like Receptors and T-Cell Activation in Takayasu's Arteritis. PMID:35126357
PBK/TOPK Inhibitor Suppresses the Progression of Prolactinomas. PMID:35126305
Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water. PMID:35124766
Exploring the total flavones of Abelmoschus manihot against IAV-induced lung inflammation by network pharmacology. PMID:35123452
Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma. PMID:35123404
Identification and validation of an autophagy-related gene signature for predicting prognosis in patients with esophageal squamous cell carcinoma. PMID:35121801
Ionic mitigation of CD4+ T cell metabolic fitness, Th1 central nervous system autoimmunity and Th2 asthmatic airway inflammation by therapeutic zinc. PMID:35121767
Mechanisms of the host immune response and helminth-induced pathology during Trichobilharzia regenti (Schistosomatidae) neuroinvasion in mice. PMID:35120185
Field cancerization profile-based prognosis signatures lead to more robust risk evaluation in hepatocellular carcinoma. PMID:35118360
Identification of key biomarkers and potential signaling pathway associated with poor progression of gastric cancer. PMID:35117911
Candidate genes for predicting the survival of patients with gastric cancer: a study based on The Cancer Genome Atlas (TCGA) database. PMID:35117619
Comprehensive analysis reveals a four-gene signature in colorectal cancer. PMID:35117487
Screening of potential genes and transcription factors involved in post-radiation cognitive dysfunction in mice via bioinformatics. PMID:35117246
Integrated bioinformatics analysis to identify key genes related to the prognosis of esophageal squamous cell carcinoma. PMID:35116493
Transcriptome analysis of the effect of a novel human serine protease inhibitor SPINK13 on gene expression in MHCC97-H cells. PMID:35116303
ZERO-INFLATED QUANTILE RANK-SCORE BASED TEST (ZIQRANK) WITH APPLICATION TO SCRNA-SEQ DIFFERENTIAL GENE EXPRESSION ANALYSIS. PMID:35116085
RNA-Seq Transcriptome Analysis Provides Candidate Genes for Resistance to Tomato Leaf Curl New Delhi Virus in Melon. PMID:35116050
Identification of Inflammation-Related Biomarker Pro-ADM for Male Patients With Gout by Comprehensive Analysis. PMID:35116032
Integrated physiological, proteomic, and metabolomic analyses of pecan cultivar 'Pawnee' adaptation to salt stress. PMID:35115595
Single cell RNA sequencing reveals differentiation related genes with drawing implications in predicting prognosis and immunotherapy response in gliomas. PMID:35115572
Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis. PMID:35115503
Probabilistic Graphical Models Applied to Biological Networks. PMID:35113399
Screening of Important Markers in Peripheral Blood Mononuclear Cells to Predict Female Osteoporosis Risk Using LASSO Regression Algorithm and SVM Method. PMID:35110962
Metagenomic analysis of microbial community structure and function in a improved biofilter with odorous gases. PMID:35110663
m6A-related lncRNAs predict prognosis and indicate immune microenvironment in acute myeloid leukemia. PMID:35110624
Morphological and molecular features of early regeneration in the marine annelid Ophryotrocha xiamen. PMID:35110576
RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures. PMID:35109825
DDX10 promotes the proliferation and metastasis of colorectal cancer cells via splicing RPL35. PMID:35109823
Simultaneous Single-Cell Genome and Transcriptome Sequencing of Termite Hindgut Protists Reveals Metabolic and Evolutionary Traits of Their Endosymbionts. PMID:35107338
Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. PMID:35105312
Intergenerational effects of preconception opioids on glucose homeostasis and hepatic transcription in adult male rats. PMID:35102183
Five hypoxia and immunity related genes as potential biomarkers for the prognosis of osteosarcoma. PMID:35102149
De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots. PMID:35100996
Expression profiles and functions of ferroptosis-related genes in the placental tissue samples of early- and late-onset preeclampsia patients. PMID:35100981
Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. PMID:35099752
Effects of Chronic Arginase Inhibition with Norvaline on Tau Pathology and Brain Glucose Metabolism in Alzheimer's Disease Mice. PMID:35098420
Circular Network of Coregulated Sphingolipids Dictates Chronic Hypoxia Damage in Patients With Tetralogy of Fallot. PMID:35097000
Identification of Diagnostic Markers for Breast Cancer Based on Differential Gene Expression and Pathway Network. PMID:35096840
UCP1 Knockin Induces Lipid Dynamics and Transcriptional Programs in the Skeletal Muscles of Pigs. PMID:35096834
Mycobacterium leprae Transcriptome During In Vivo Growth and Ex Vivo Stationary Phases. PMID:35096659
The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. PMID:35096646
Single-Cell Ribonucleic Acid Sequencing Clarifies Cold Tolerance Mechanisms in the Pacific White Shrimp (Litopenaeus Vannamei). PMID:35096009
Gene Expression in Embryos From Norwegian Red Bulls With High or Low Non Return Rate: An RNA-Seq Study of in vivo-Produced Single Embryos. PMID:35096004
Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity. PMID:35094093
Single-cell transcriptomic analysis reveals a novel cell state and switching genes during hepatic stellate cell activation in vitro. PMID:35093101
Metabolome analysis of key genes for synthesis and accumulation of triterpenoids in Wolfiporia cocos. PMID:35091582
Co-expression of cancer stem cell markers, SALL4/ALDH1A1, is associated with tumor aggressiveness and poor survival in patients with serous ovarian carcinoma. PMID:35090523
Multi-omic landscaping of human midbrains identifies disease-relevant molecular targets and pathways in advanced-stage Parkinson's disease. PMID:35090094
Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum. PMID:35087909
GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring. PMID:35087491
Impact of high platelet turnover on the platelet transcriptome: Results from platelet RNA-sequencing in patients with sepsis. PMID:35085240
A novel pyroptosis-related signature predicts prognosis and response to treatment in breast carcinoma. PMID:35085103
Wounding response in Porifera (sponges) activates ancestral signaling cascades involved in animal healing, regeneration, and cancer. PMID:35079031
Bioinformatics screening the novel and promising targets of curcumin in hepatocellular carcinoma chemotherapy and prognosis. PMID:35078445
The role of SPI1-TYROBP-FCER1G network in oncogenesis and prognosis of osteosarcoma, and its association with immune infiltration. PMID:35078433
Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle. PMID:35077540
Genome-wide analysis of mRNAs, lncRNAs, and circRNAs during intramuscular adipogenesis in Chinese Guizhou Congjiang pigs. PMID:35077458
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Genome-Scale Modeling Specifies the Metabolic Capabilities of Rhizophagus irregularis. PMID:35076269
Bioinformatic Analysis Identifies Biomarkers and Treatment Targets in Primary Sjögren's Syndrome Patients with Fatigue. PMID:35075430
Construction and validation of a novel gene signature for predicting the prognosis of osteosarcoma. PMID:35075228
Identification of key regulators in Sarcoidosis through multidimensional systems biological approach. PMID:35075176
Identification of Molecular Biomarkers and Key Pathways for Esophageal Carcinoma (EsC): A Bioinformatics Approach. PMID:35071597
A comprehensive characterization of the transcriptome in enzalutamide resistance prostate cancer. PMID:35071476
Modular characteristics and the mechanism of Chinese medicine's treatment of gastric cancer: a data mining and pharmacology-based identification. PMID:35071471
Immune-related gene expression in skin, inflamed and keloid tissue from patients with keloids. PMID:35069881
Potential biomarkers of acute myocardial infarction based on co-expression network analysis. PMID:35069843
Comparison between Heat-Clearing Medicine and Antirheumatic Medicine in Treatment of Gastric Cancer Based on Network Pharmacology, Molecular Docking, and Tumor Immune Infiltration Analysis. PMID:35069767
Evaluation of the Prognostic Value of Long Noncoding RNAs in Lung Squamous Cell Carcinoma. PMID:35069738
Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin (Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication. PMID:35069640
Insight Into the Anti-staphylococcal Activity of JBC 1847 at Sub-Inhibitory Concentration. PMID:35069485
CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. PMID:35069469
Genetic context of oncogenic drivers dictates vascular sarcoma development in aP2-Cre mice. PMID:35066877
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. PMID:35064122
HERV-W Envelope Triggers Abnormal Dopaminergic Neuron Process through DRD2/PP2A/AKT1/GSK3 for Schizophrenia Risk. PMID:35062349
Tumor microenvironment-related multigene prognostic prediction model for breast cancer. PMID:35060926
Isolation, Classification, and Growth-Promoting Effects of Pantoea sp. YSD J2 from the Aboveground Leaves of Cyperus Esculentus L. var. sativus. PMID:35059843
Pcyt2 deficiency causes age-dependant development of nonalcoholic steatohepatitis and insulin resistance that could be attenuated with phosphoethanolamine. PMID:35058529
Gene expression profiles in Malpighian tubules of the vector leafhopper Psammotettix striatus (L.) revealed regional functional diversity and heterogeneity. PMID:35057738
Structural Identification of Metalloproteomes in Marine Diatoms, an Efficient Algae Model in Toxic Metals Bioremediation. PMID:35056698
Genetic and Comparative Genome Analysis of Exiguobacterium aurantiacum SW-20, a Petroleum-Degrading Bacteria with Salt Tolerance and Heavy Metal-Tolerance Isolated from Produced Water of Changqing Oilfield, China. PMID:35056515
Metabolomic Profiles of the Creeping Wood Sorrel Oxalis corniculata in Radioactively Contaminated Fields in Fukushima: Dose-Dependent Changes in Key Metabolites. PMID:35054508
The Interplay between Pathophysiological Pathways in Early-Onset Severe Preeclampsia Unveiled by Metabolomics. PMID:35054479
Proteomic Response of Deinococcus radiodurans to Short-Term Real Microgravity during Parabolic Flight Reveals Altered Abundance of Proteins Involved in Stress Response and Cell Envelope Functions. PMID:35054415
Deciphering Biomarkers for Leptomeningeal Metastasis in Malignant Hemopathies (Lymphoma/Leukemia) Patients by Comprehensive Multipronged Proteomics Characterization of Cerebrospinal Fluid. PMID:35053611
Genomic Landscape of Vinflunine Response in Metastatic Urothelial Cancer. PMID:35053540
Construction of Light-Responsive Gene Regulatory Network for Growth, Development and Secondary Metabolite Production in Cordyceps militaris. PMID:35053069
Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection. PMID:35052429
Cytological, Biochemical, and Transcriptomic Analyses of a Novel Yellow Leaf Variation in a Paphiopedilum (Orchidaceae) SCBG COP15. PMID:35052412
Stingray Venom Proteins: Mechanisms of Action Revealed Using a Novel Network Pharmacology Approach. PMID:35049882
Genome-wide identification of bacterial colonization and fitness determinants on the floating macrophyte, duckweed. PMID:35046504
A potential target gene CD63 for different degrees of intervertebral disc degeneration. PMID:35046480
Analysis of soil bacterial communities and physicochemical properties associated with Fusarium wilt disease of banana in Malaysia. PMID:35046475
Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis. PMID:35045818
Identification of hub genes associated with COVID-19 and idiopathic pulmonary fibrosis by integrated bioinformatics analysis. PMID:35045126
Comparative analysis of protein-protein interaction networks in metastatic breast cancer. PMID:35045088
Bioengineered models of Parkinson's disease using patient-derived dopaminergic neurons exhibit distinct biological profiles in a 3D microenvironment. PMID:35044538
Valine feeding reduces ammonia production through rearrangement of metabolic fluxes in central carbon metabolism of CHO cells. PMID:35044498
HER3 activation contributes toward the emergence of ALK inhibitor-tolerant cells in ALK-rearranged lung cancer with mesenchymal features. PMID:35042943
Maternal-fetal immune responses in pregnant women infected with SARS-CoV-2. PMID:35042863
N6-Methyladenosine-Related lncRNAs as potential biomarkers for predicting prognoses and immune responses in patients with cervical cancer. PMID:35042477
Functional analysis of ADARs in planarians supports a bilaterian ancestral role in suppressing double-stranded RNA-response. PMID:35041722
Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils. PMID:35040702
Molecular docking-based computational platform for high-throughput virtual screening. PMID:35039800
Two novel prognostic models for ovarian cancer respectively based on ferroptosis and necroptosis. PMID:35039008
Intestinal Claudin-7 deficiency impacts the intestinal microbiota in mice with colitis. PMID:35039003
An integrative analysis of DNA methylation and transcriptome showed the dysfunction of MAPK pathway was involved in the damage of human chondrocyte induced by T-2 toxin. PMID:35038982
Inflammatory activation and immune cell infiltration are main biological characteristics of SARS-CoV-2 infected myocardium. PMID:35037831
Screening and Identification of Key Biomarkers in Lower Grade Glioma via Bioinformatical Analysis. PMID:35035531
Autoimmune gastritis induces aberrant DNA methylation reflecting its carcinogenic potential. PMID:35034200
Bi-allelic SMO variants in hypothalamic hamartoma: a recessive cause of Pallister-Hall syndrome. PMID:35034092
Impact of Helicobacter pylori infection on fluid duodenal microbial community structure and microbial metabolic pathways. PMID:35033024
Identification of a ferroptosis-related gene pair biomarker with immune infiltration landscapes in ischemic stroke: a bioinformatics-based comprehensive study. PMID:35033021
Aristotle: stratified causal discovery for omics data. PMID:35033007
Enrichment of phosphate-accumulating organisms (PAOs) in a microfluidic model biofilm system by mimicking a typical aerobic granular sludge feast/famine regime. PMID:35032186
Pathogen resistance in Sphagneticola trilobata (Singapore daisy): molecular associations and differentially expressed genes in response to disease from a widespread fungus. PMID:35031940
Human plasma pregnancy-associated miRNAs and their temporal variation within the first trimester of pregnancy. PMID:35031065
BATF promotes group 2 innate lymphoid cell-mediated lung tissue protection during acute respiratory virus infection. PMID:35030033
Plasma metabolomics of autism spectrum disorder and influence of shared components in proband families. PMID:35028569
Promising novel biomarkers and candidate small-molecule drugs for lung adenocarcinoma: Evidence from bioinformatics analysis of high-throughput data. PMID:35028418
Single-cell transcriptomics of human iPSC differentiation dynamics reveal a core molecular network of Parkinson's disease. PMID:35027645
Respiratory tract infections and gut microbiome modifications: A systematic review. PMID:35025938
Danger signal extracellular calcium initiates differentiation of monocytes into SPP1/osteopontin-producing macrophages. PMID:35022393
Tubastatin A maintains adult skeletal muscle stem cells in a quiescent state ex vivo and improves their engraftment ability in vivo. PMID:35021050
Endothelial and systemic upregulation of miR-34a-5p fine-tunes senescence in progeria. PMID:35020601
Metagenomic and Metatranscriptomic Responses of Chemical Dispersant Application during a Marine Dilbit Spill. PMID:35020455
Identification of the Key Immune-Related Genes in Chronic Obstructive Pulmonary Disease Based on Immune Infiltration Analysis. PMID:35018096
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
Chromosome-level genome assembly of Zizania latifolia provides insights into its seed shattering and phytocassane biosynthesis. PMID:35017643
Identification of the pivotal role of SPP1 in kidney stone disease based on multiple bioinformatics analysis. PMID:35016690
Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes. PMID:35014868
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
Transplantation of umbilical cord-derived mesenchymal stem cells promotes the recovery of thin endometrium in rats. PMID:35013490
Linkage mapping and QTL analysis of growth traits in Rhopilema esculentum. PMID:35013486
The impact of methodology on the reproducibility and rigor of DNA methylation data. PMID:35013473
RNAseq reveals extensive metabolic disruptions in the sensitive SF-295 cell line treated with schweinfurthins. PMID:35013404
Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry. PMID:35013269
A pilot exploration of multi-omics research of gut microbiome in major depressive disorders. PMID:35013099
The genome of oil-Camellia and population genomics analysis provide insights into seed oil domestication. PMID:35012630
Comprehensive analysis of expression profile and prognostic significance of interferon regulatory factors in pancreatic cancer. PMID:35012444
UHPLC-HRMS-Based Untargeted Lipidomics Reveal Mechanism of Antifungal Activity of Carvacrol against Aspergillus flavus. PMID:35010219
Preventive Effect of Anemarrhenae rhizome and Phellodendri cortex on Danazol-Induced in Precocious Puberty in Female Rats and Network Pharmacological Analysis of Active Compounds. PMID:35009026
Metabolic Processes Are Differentially Regulated During Wild-Type and Attenuated Dengue Virus Infection in Aedes aegypti. PMID:35008057
Comprehensive Analysis Revealed that CDKN2A is a Biomarker for Immune Infiltrates in Multiple Cancers. PMID:35004697
Comprehensive Analysis of the Prognostic Values of the TRIM Family in Hepatocellular Carcinoma. PMID:35004288
Searching beyond the streetlight: Neonicotinoid exposure alters the neurogenomic state of worker honey bees. PMID:35003705
CYP1B1-AS1 Is a Novel Biomarker in Glioblastoma by Comprehensive Analysis. PMID:35003394
Identification of Keratinocyte Differentiation-Involved Genes for Metastatic Melanoma by Gene Expression Profiles. PMID:35003328
Bacteriome of Moist Smokeless Tobacco Products Consumed in India With Emphasis on the Predictive Functional Potential. PMID:35003015
ADAMTS8 Expression is a Potential Prognostic Biomarker for Postoperative Metastasis in Lymph Node-Negative Early-Stage Invasive Breast Carcinoma Patients. PMID:35002288
CD73 induces GM-CSF/MDSC-mediated suppression of T cells to accelerate pancreatic cancer pathogenesis. PMID:35001076
A Chromosome-Level Genome Assembly of the Pygmy Mole Cricket Xya riparia. PMID:34999819
MIMOSA2: A metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. PMID:34999748
Membrane tension sensing molecule-FNBP1 is a prognostic biomarker related to immune infiltration in BRCA, LUAD and STAD. PMID:34998385
Chicken blastoderms and primordial germ cells possess a higher expression of DNA repair genes and lower expression of apoptosis genes to preserve their genome stability. PMID:34997179
Epithelial-mesenchymal transition related genes in unruptured aneurysms identified through weighted gene coexpression network analysis. PMID:34997174
Stage specific comparative transcriptomic analysis to reveal gene networks regulating iron and zinc content in pearl millet [Pennisetum glaucum (L.) R. Br.]. PMID:34997160
Objective to identify and verify the regulatory mechanism of DTNBP1 as a prognostic marker for hepatocellular carcinoma. PMID:34997064
Regulation of gene expression by the APP family in the adult cerebral cortex. PMID:34997052
Identification of vaccine and drug targets in Shigella dysenteriae sd197 using reverse vaccinology approach. PMID:34997046
Identification of an at-risk subpopulation with high immune infiltration based on the peroxisome pathway and TIM3 in colorectal cancer. PMID:34996408
Digital gene expression analysis of NSCLC-patients reveals strong immune pressure, resulting in an immune escape under immunotherapy. PMID:34996407
Maize/peanut intercropping improves nutrient uptake of side-row maize and system microbial community diversity. PMID:34996375
Long-read transcriptome sequencing provides insight into lignan biosynthesis during fruit development in Schisandra chinensis. PMID:34996357
Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. PMID:34996356
Deep learning-based brain transcriptomic signatures associated with the neuropathological and clinical severity of Alzheimer's disease. PMID:34993477
mmu-miR-145a-5p Accelerates Diabetic Wound Healing by Promoting Macrophage Polarization Toward the M2 Phenotype. PMID:34993211
Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches. PMID:34992619
Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing. PMID:34991478
Predicting the targets of IRF8 and NFATc1 during osteoclast differentiation using the machine learning method framework cTAP. PMID:34991467
Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711. PMID:34991451
Marine pollutant exposures and human milk extracellular vesicle-microRNAs in a mother-infant cohort from the Faroe Islands. PMID:34991248
In search of autophagy biomarkers in breast cancer: Receptor status and drug agnostic transcriptional changes during autophagy flux in cell lines. PMID:34990474
Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation. PMID:34989990
Evaluation of CRISPR gene-editing tools in zebrafish. PMID:34986794
Exploration the potential mechanism of the SIRT1 and its target gene FOXO1/PPARGC1A in uteropelvic junction obstruction. PMID:34984185
Trifolium pratense ethanolic extract alters the gut microbiota composition and regulates serum lipid profile in the ovariectomized rats. PMID:34983484
Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam. PMID:34983398
Inferring the genetic responses to acute drought stress across an ecological gradient. PMID:34983380
Transcriptome analysis to identify the downstream genes of androgen receptor in dermal papilla cells. PMID:34983378
Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. PMID:34983376
Genome-wide analysis of genetic predisposition to common polygenic cancers. PMID:34981446
Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19. PMID:34981034
Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail. PMID:34980289
Screening and analysis of RNAs associated with activated memory CD4 and CD8 T cells in liver cancer. PMID:34980144
Canine transmissible venereal tumour established in immunodeficient mice reprograms the gene expression profiles associated with a favourable tumour microenvironment to enable cancer malignancy. PMID:34980125
Genome-wide association studies for growth traits in broilers. PMID:34979907
Comprehensive analysis of the long noncoding RNA-associated competitive endogenous RNA network in the osteogenic differentiation of periodontal ligament stem cells. PMID:34979896
Analysis of Microarray Data from Medulloblastoma Tissue Samples. PMID:34978688
Capturing the transcription factor interactome in response to sub-lethal insecticide exposure. PMID:34977825
Antigen presentation and interferon signatures in B cells driven by localized ablative cancer immunotherapy correlate with extended survival. PMID:34976205
A Novel Model of Tumor-Infiltrating B Lymphocyte Specific RNA-Binding Protein-Related Genes With Potential Prognostic Value and Therapeutic Targets in Multiple Myeloma. PMID:34976013
Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet. PMID:34972826
Multiplex-Heterogeneous Network-Based Capturing Potential SNP "Switches" of Pathways Associating With Diverse Disease Characteristics of Asthma. PMID:34970542
Inositol 1,4,5-trisphosphate receptor type 3 is involved in resistance to apoptosis and maintenance of human hepatocellular carcinoma. PMID:34966448
Energy at Origins: Favorable Thermodynamics of Biosynthetic Reactions in the Last Universal Common Ancestor (LUCA). PMID:34966373
Spatiotemporal localization of proteins in mycobacteria. PMID:34965429
Network pharmacology-based strategy to investigate the active ingredients and molecular mechanisms of Scutellaria Barbata D. Don against radiation pneumonitis. PMID:34964782
Bioinformatics analysis of candidate genes and potential therapeutic drugs targeting adipose tissue in obesity. PMID:34964707
Absorbance or organization into ankylosis: a microarray analysis of haemarthrosis in a sheep model of temporomandibular joint trauma. PMID:34961493
Plasma metabolomic profiling of hypertrophic cardiomyopathy patients before and after surgical myectomy suggests postoperative improvement in metabolic function. PMID:34961475
Investigating the biochemical effects of heat stress and sample quenching approach on the metabolic profiling of abalone (Haliotis iris). PMID:34958425
Integral Analyses of Competing Endogenous RNA Mechanisms and DNA Methylation Reveal Regulatory Mechanisms in Osteosarcoma. PMID:34957096
Combined Metabolome and Transcriptome Analyses of Young, Mature, and Old Rhizome Tissues of Zingiber officinale Roscoe. PMID:34956334
Vitamin D Treatment Sequence Is Critical for Transcriptome Modulation of Immune Challenged Primary Human Cells. PMID:34956186
Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems. PMID:34956130
Plasma Exosomal Mir-423-5p Is Involved in the Occurrence and Development of Bicuspid Aortopathy via TGF-β/SMAD2 Pathway. PMID:34955881
9-ING-41, a Small Molecule Inhibitor of GSK-3β, Potentiates the Effects of Chemotherapy on Colorectal Cancer Cells. PMID:34955846
A high-resolution mass spectrometry based proteomic dataset of human regulatory T cells. PMID:34950757
Captivity Influences the Gut Microbiome of Rhinopithecus roxellana. PMID:34950117
In Silico Prediction and Bioactivity Evaluation of Chemical Ingredients Against Influenza A Virus From Isatis tinctoria L. PMID:34950027
Limited allele-specific gene expression in highly polyploid sugarcane. PMID:34949669
NMR Hydrophilic Metabolomic Analysis of Bacterial Resistance Pathways Using Multivalent Antimicrobials with Challenged and Unchallenged Wild Type and Mutated Gram-Positive Bacteria. PMID:34948402
Drought and Subsequent Soil Flooding Affect the Growth and Metabolism of Savoy Cabbage. PMID:34948111
Combined Transcriptome and Metabolome Analysis of Alfalfa Response to Thrips Infection. PMID:34946916
Analysis of Serum Biochemical Indexes, Egg Quality, and Liver Transcriptome in Laying Hens Fed Diets Supplemented with Gynostemma pentaphyllum Powder. PMID:34946891
Microbial Community Dynamics during Biodegradation of Crude Oil and Its Response to Biostimulation in Svalbard Seawater at Low Temperature. PMID:34946026
Predictive Biomarkers of Age-Related Macular Degeneration Response to Anti-VEGF Treatment. PMID:34945801
Clinicopathological and Molecular Prognostic Classifier for Intermediate/High-Risk Clear Cell Renal Cell Carcinoma. PMID:34944958
8-Hydroxydaidzein Downregulates JAK/STAT, MMP, Oxidative Phosphorylation, and PI3K/AKT Pathways in K562 Cells. PMID:34944720
Sedimentary Cobalt Protoporphyrin as a Potential Precursor of Prosthetic Heme Group for Bacteria Inhabiting Fossil Organic Matter-Rich Shale Rock. PMID:34944556
A System-Level Mechanism of Anmyungambi Decoction for Obesity: A Network Pharmacological Approach. PMID:34944525
Deepening into Intracellular Signaling Landscape through Integrative Spatial Proteomics and Transcriptomics in a Lymphoma Model. PMID:34944421
Ascorbic Acid/Retinol and/or Inflammatory Stimuli's Effect on Proliferation/Differentiation Properties and Transcriptomics of Gingival Stem/Progenitor Cells. PMID:34943818
CCN2 Aggravates the Immediate Oxidative Stress-DNA Damage Response following Renal Ischemia-Reperfusion Injury. PMID:34943123
Genome-Wide RNAi Screening Identifies Novel Pathways/Genes Involved in Oxidative Stress and Repurposable Drugs to Preserve Cystic Fibrosis Airway Epithelial Cell Integrity. PMID:34943039
Amycolatopsis aidingensis sp. nov., a Halotolerant Actinobacterium, Produces New Secondary Metabolites. PMID:34938275
Untargeted metabolomics study on the effects of rearing ducks in cages on bone quality. PMID:34936950
Transcriptomic analysis of synchrony and productivity in self-cycling fermentation of engineered yeast producing shikimic acid. PMID:34934640
Identification of potential key genes and functional role of CENPF in osteosarcoma using bioinformatics and experimental analysis. PMID:34934449
Whole Genome Sequencing of First Janibacter indicus Isolate in China Revealed Three Unique Genomic Islands Compared with Saprophytic Strains. PMID:34934330
Comprehensive analysis of the ceRNA network in coronary artery disease. PMID:34930980
MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains. PMID:34930932
Circadian key component CLOCK/BMAL1 interferes with segmentation clock in mouse embryonic organoids. PMID:34930826
Comparative transcriptome and DNA methylation analysis in temperature-sensitive genic male sterile wheat BS366. PMID:34930131
GIP: an open-source computational pipeline for mapping genomic instability from protists to cancer cells. PMID:34928370
Biochar Addition Altered Bacterial Community and Improved Photosynthetic Rate of Seagrass: A Mesocosm Study of Seagrass Thalassia hemprichii. PMID:34925287
Altered microRNAs in C3H10T1/2 cells induced by p.E95K mutant IHH signaling. PMID:34922634
Profiles of immune cell infiltration and immune-related genes in the tumor microenvironment of osteosarcoma cancer. PMID:34922489
Recurring exposure to low humidity induces transcriptional and protein level changes in the vocal folds of rabbits. PMID:34921171
Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar. PMID:34919575
Worldwide distribution and environmental origin of the Adelaide imipenemase (AIM-1), a potent carbapenemase in Pseudomonas aeruginosa. PMID:34919514
Identification of a Lipid Metabolism-Associated Gene Signature Predicting Survival in Breast Cancer. PMID:34916832
Oxidative stress and expression of inflammatory factors in lung tissue of acute mountain sickness rats. PMID:34913080
Identification of Key Deregulated RNA-Binding Proteins in Pancreatic Cancer by Meta-Analysis and Prediction of Their Role as Modulators of Oncogenesis. PMID:34912796
Exploring Pathway-Based Group Lasso for Cancer Survival Analysis: A Special Case of Multi-Task Learning. PMID:34912376
Integrated Metabolic Profiling and Transcriptional Analysis Reveals Therapeutic Modalities for Targeting Rapidly Proliferating Breast Cancers. PMID:34911787
Understanding the Gut Microbiota in Pediatric Patients with Alopecia Areata and their Siblings: A Pilot Study. PMID:34909748
Complete Genome Sequence of the Type Strain Tepidimonas taiwanensis LMG 22826T, a Thermophilic Alkaline Protease and Polyhydroxyalkanoate Producer. PMID:34908127
Competitive endogenous RNA network and pathway-based analysis of LncRNA single-nucleotide polymorphism in myasthenia gravis. PMID:34907261
Genetic stability of Aedes aegypti populations following invasion by wMel Wolbachia. PMID:34906084
Mammalian gut metabolomes mirror microbiome composition and host phylogeny. PMID:34903850
Longitudinal DNA methylation dynamics as a practical indicator in clinical epigenetics. PMID:34903243
Effects of various artificial agarwood-induction techniques on the metabolome of Aquilaria sinensis. PMID:34903180
The effect of lipocalin-2 (LCN2) on apoptosis: a proteomics analysis study in an LCN2 deficient mouse model. PMID:34903175
Analogous Metabolic Decoupling in Pseudomonas putida and Comamonas testosteroni Implies Energetic Bypass to Facilitate Gluconeogenic Growth. PMID:34903058
Development of an Oxidative Phosphorylation-Related and Immune Microenvironment Prognostic Signature in Uterine Corpus Endometrial Carcinoma. PMID:34901000
Whole-transcriptome analysis of aluminum-exposed rat hippocampus and identification of ceRNA networks to investigate neurotoxicity of Al. PMID:34900398
Wheat Apoplast-Localized Lipid Transfer Protein TaLTP3 Enhances Defense Responses Against Puccinia triticina. PMID:34899796
The prognostic value of plasma complement factor B (CFB) in thyroid carcinoma. PMID:34898340
Transcriptional Profiling of Early and Late Phases of Bovine Tuberculosis. PMID:34898250
Soluble amyloid-beta isoforms predict downstream Alzheimer's disease pathology. PMID:34895338
Transcriptome sequencing reveals a lncRNA-mRNA interaction network in extramammary Paget's disease. PMID:34895219
Genome-wide association of single nucleotide polymorphism loci and candidate genes for frogeye leaf spot (Cercospora sojina) resistance in soybean. PMID:34895144
Exploiting Aerobic Carboxydotrophic Bacteria for Industrial Biotechnology. PMID:34894287
Genetic insights into the regulatory pathways for continuous flowering in a unique orchid Arundina graminifolia. PMID:34893019
PIK3R1, SPNB2, and CRYAB as Potential Biomarkers for Patients with Diabetes and Developing Acute Myocardial Infarction. PMID:34887920
Chromosome-Level Genome Assembly of the Burbot (Lota lota) Using Nanopore and Hi-C Technologies. PMID:34887901
Transcriptomic Characterization of the Effects of Selenium on Maize Seedling Growth. PMID:34887883
S100A2 Is a Prognostic Biomarker Involved in Immune Infiltration and Predict Immunotherapy Response in Pancreatic Cancer. PMID:34887861
Evolution of a histone variant involved in compartmental regulation of NAD metabolism. PMID:34887560
Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations. PMID:34887548
iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean. PMID:34887505
Identifying the essential nutritional requirements of the probiotic bacteria Bifidobacterium animalis and Bifidobacterium longum through genome-scale modeling. PMID:34887435
Meta-analyses identify DNA methylation associated with kidney function and damage. PMID:34887417
Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. PMID:34887389
Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis). PMID:34886808
Deep Proteomic Analysis on Biobanked Paraffine-Archived Melanoma with Prognostic/Predictive Biomarker Read-Out. PMID:34885218
A Computational Analysis in a Cohort of Parkinson's Disease Patients and Clock-Modified Colorectal Cancer Cells Reveals Common Expression Alterations in Clock-Regulated Genes. PMID:34885088
The MAPK Signaling Pathway Presents Novel Molecular Targets for Therapeutic Intervention after Traumatic Spinal Cord Injury: A Comparative Cross-Species Transcriptional Analysis. PMID:34884738
Alterations in Metabolome and Microbiome Associated with an Early Stress Stage in Male Wistar Rats: A Multi-Omics Approach. PMID:34884735
The salivary metatranscriptome as an accurate diagnostic indicator of oral cancer. PMID:34880265
Integrated analysis of the functions and prognostic values of RNA-binding proteins in neuroblastoma. PMID:34879089
Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis. PMID:34877936
Functional organization of the maternal and paternal human 4D Nucleome. PMID:34877507
A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks. PMID:34876593
Attenuated expression of SNF5 facilitates progression of bladder cancer via STAT3 activation. PMID:34876150
Comparative transcriptome analysis reveals compatible and recalcitrant genotypic response of barley microspore-derived embryogenic callus toward Agrobacterium infection. PMID:34876002
The effect and mechanism of Jiao-tai-wan in the treatment of diabetes mellitus with depression based on network pharmacology and experimental analysis. PMID:34875999
Adapting Macroecology to Microbiology: Using Occupancy Modeling To Assess Functional Profiles across Metagenomes. PMID:34874772
Understanding host-microbiota interactions in the commercial piglet around weaning. PMID:34873196
reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization. PMID:34873191
iTRAQ-based quantitative proteome analysis insights into cold stress of Winter Rapeseed (Brassica rapa L.) grown in the field. PMID:34873178
Single cell sequencing analysis identifies genetics-modulated ORMDL3+ cholangiocytes having higher metabolic effects on primary biliary cholangitis. PMID:34872583
Transcriptomic Characterization of Tuberculous Sputum Reveals a Host Warburg Effect and Microbial Cholesterol Catabolism. PMID:34872348
Identification of Galectin-3 as Potential Biomarkers for Renal Fibrosis by RNA-Sequencing and Clinicopathologic Findings of Kidney Biopsy. PMID:34869439
Single-Cell RNA Sequencing Defines the Regulation of Spermatogenesis by Sertoli-Cell Androgen Signaling. PMID:34869354
Starvation to Glucose Reprograms Development of Neurovascular Unit in Embryonic Retinal Cells. PMID:34869314
Transcriptome Profiling of the Salt Stress Response in the Leaves and Roots of Halophytic Eutrema salsugineum. PMID:34868259
Artificial Intelligence in Functional Food Ingredient Discovery and Characterisation: A Focus on Bioactive Plant and Food Peptides. PMID:34868255
Chromosome-Scale Reference Genome of Amphicarpaea edgeworthii: A New Resource for Amphicarpic Plants Research and Complex Flowering Pattern. PMID:34868169
Identification of Potential Genes in Pathogenesis and Diagnostic Value Analysis of Partial Androgen Insensitivity Syndrome Using Bioinformatics Analysis. PMID:34867780
Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function. PMID:34867441
Computational Network Pharmacology-Based Strategy to Capture Key Functional Components and Decode the Mechanism of Chai-Hu-Shu-Gan-San in Treating Depression. PMID:34867413
The Pharmacological Mechanism of Guchangzhixie Capsule Against Experimental Colitis. PMID:34867387
Sparse Regression in Cancer Genomics: Comparing Variable Selection and Predictions in Real World Data. PMID:34866896
Network analytics for drug repurposing in COVID-19. PMID:34864885
Association of low-frequency and rare coding variants with information processing speed. PMID:34864818
Comparative transcriptomic analysis of gonadal development and renewal in the ovoviviparous black rockfish (Sebastes schlegelii). PMID:34863110
Integrated metabolic and microbial analysis reveals host-microbial interactions in IgE-mediated childhood asthma. PMID:34862469
Identification of the ferroptosis-related long non-coding RNAs signature to improve the prognosis prediction and immunotherapy response in patients with NSCLC. PMID:34861872
Potential Mechanism of Dingji Fumai Decoction Against Atrial Fibrillation Based on Network Pharmacology, Molecular Docking, and Experimental Verification Integration Strategy. PMID:34859062
The Transcriptional Differences of Avian CD4+CD8+ Double-Positive T Cells and CD8+ T Cells From Peripheral Blood of ALV-J Infected Chickens Revealed by Smart-Seq2. PMID:34858872
Topical Application of Temperature-Sensitive Gel Containing Caerin 1.1 and 1.9 Peptides on TC-1 Tumour-Bearing Mice Induced High-Level Immune Response in the Tumour Microenvironment. PMID:34858827
Key Markers Involved in the Anticolon Cancer Response of CD8+ T Cells through the Regulation of Cholesterol Metabolism. PMID:34858500
Comparative Transcriptome Sequencing of Taro Corm Development With a Focus on the Starch and Sucrose Metabolism Pathway. PMID:34858484
Inferring Differential Networks by Integrating Gene Expression Data With Additional Knowledge. PMID:34858477
Bacterial challenge-associated metabolic phenotypes in Hermetia illucens defining nutritional and functional benefits. PMID:34857836
Multiomics analysis of soybean meal induced marine fish enteritis in juvenile pearl gentian grouper, Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂. PMID:34857775
Functional enrichment of alternative splicing events with NEASE reveals insights into tissue identity and diseases. PMID:34857024
Exploring cell-specific miRNA regulation with single-cell miRNA-mRNA co-sequencing data. PMID:34856921
Identification of the Active Constituents and Significant Pathways of Shen-qi-Yi-zhu Decoction on Antigastric Cancer: A Network Pharmacology Research and Experimental Validation. PMID:34853601
Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis. PMID:34852788
PRODORIC: state-of-the-art database of prokaryotic gene regulation. PMID:34850133
Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues. PMID:34849383
Oral microbiome associated with lymph node metastasis in oral squamous cell carcinoma. PMID:34848792
Genome-wide unbalanced expression bias and expression level dominance toward Brassica oleracea in artificially synthesized intergeneric hybrids of Raphanobrassica. PMID:34848691
Identification and Potential Mechanisms of a 7-MicroRNA Signature That Predicts Prognosis in Patients with Lower-Grade Glioma. PMID:34845420
The impact of bacterial diversity on resistance to biocides in oilfields. PMID:34845279
Tracing TET1 expression in prostate cancer: discovery of malignant cells with a distinct oncogenic signature. PMID:34844636
Transcriptome analysis of lncRNA expression patterns in human congenital lung malformations. PMID:34844556
Knowledge-guided artificial intelligence technologies for decoding complex multiomics interactions in cells. PMID:34844399
Epididymal mRNA and miRNA transcriptome analyses reveal important genes and miRNAs related to sperm motility in roosters. PMID:34844112
Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica. PMID:34843573
Brain transcriptomes of zebrafish and mouse Alzheimer's disease knock-in models imply early disrupted energy metabolism. PMID:34842276
Living with a giant, flowering parasite: metabolic differences between Tetrastigma loheri Gagnep. (Vitaceae) shoots uninfected and infected with Rafflesia (Rafflesiaceae) and potential applications for propagation. PMID:34841446
The mRNA-LNP platform's lipid nanoparticle component used in preclinical vaccine studies is highly inflammatory. PMID:34841223
Identification of Hub Gene GRIN1 Correlated with Histological Grade and Prognosis of Glioma by Weighted Gene Coexpression Network Analysis. PMID:34840971
Network Pharmacology-Based Study on the Active Component and Mechanism of the Anti-Gastric-Cancer Effect of Herba Sarcandrae. PMID:34840695
Bacteroidota and Lachnospiraceae integration into the gut microbiome at key time points in early life are linked to infant neurodevelopment. PMID:34839801
A rice gene encoding glycosyl hydrolase plays contrasting roles in immunity depending on the type of pathogens. PMID:34839574
Cluster analysis and profiling of airway fluid metabolites in pediatric acute hypoxemic respiratory failure. PMID:34836982
Identification of transcriptomics biomarkers for the early prediction of the prognosis of septic shock from pneumopathies. PMID:34836493
Vaccine Hyporesponse Induced by Individual Antibiotic Treatment in Mice and Non-Human Primates Is Diminished upon Recovery of the Gut Microbiome. PMID:34835271
Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata. PMID:34834626
Identification of Differentially Expressed Genes in Different Glioblastoma Regions and Their Association with Cancer Stem Cell Development and Temozolomide Response. PMID:34834399
Automated Exploration of Prebiotic Chemical Reaction Space: Progress and Perspectives. PMID:34833016
PI3K/AKT/mTOR Signaling Pathway Is Required for JCPyV Infection in Primary Astrocytes. PMID:34831441
Identification of Impacted Pathways and Transcriptomic Markers as Potential Mediators of Pulmonary Fibrosis in Transgenic Mice Expressing Human IGFBP5. PMID:34830489
Global Analysis of Transcriptome and Translatome Revealed That Coordinated WNT and FGF Regulate the Carapacial Ridge Development of Chinese Soft-Shell Turtle. PMID:34830331
Excess Heritability Contribution of Alcohol Consumption Variants in the "Missing Heritability" of Type 2 Diabetes Mellitus. PMID:34830198
Identification of Disease-Related Genes That Are Common between Alzheimer's and Cardiovascular Disease Using Blood Genome-Wide Transcriptome Analysis. PMID:34829754
MicroRNA Sequencing Analysis in Obstructive Sleep Apnea and Depression: Anti-Oxidant and MAOA-Inhibiting Effects of miR-15b-5p and miR-92b-3p through Targeting PTGS1-NF-κB-SP1 Signaling. PMID:34829725
The Role of CDK4 in the Pathogenesis of Pancreatic Cancer. PMID:34828525
Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle. PMID:34827757
Proteasome Inhibition Is an Effective Treatment Strategy for Microsporidia Infection in Honey Bees. PMID:34827599
Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes. PMID:34827437
Fine-mapping and identification of a candidate gene controlling seed coat color in melon (Cucumis melo L. var. chinensis Pangalo). PMID:34825925
Mechanism of quercetin therapeutic targets for Alzheimer disease and type 2 diabetes mellitus. PMID:34824300
The telomere length landscape of prostate cancer. PMID:34824250
Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression with cell volume. PMID:34824198
Identification of miRNA-mRNA network and immune-related gene signatures in IgA nephropathy by integrated bioinformatics analysis. PMID:34823491
MetaFetcheR: An R Package for Complete Mapping of Small-Compound Data. PMID:34822401
The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. PMID:34822371
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
Development of a bioinformatics platform for analysis of quantitative transcriptomics and proteomics data: the OMnalysis. PMID:34820180
An evolutionary functional genomics approach identifies novel candidate regions involved in isoniazid resistance in Mycobacterium tuberculosis. PMID:34819627
Development of a chemogenomics library for phenotypic screening. PMID:34819133
Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy. PMID:34819020
A 3D primary human cell-based in vitro model of non-alcoholic steatohepatitis for efficacy testing of clinical drug candidates. PMID:34815444
Secondary electrospray ionization-high resolution mass spectrometry (SESI-HRMS) fingerprinting enabled treatment monitoring of pulmonary carcinoma cells in real time. PMID:34815037
Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata. PMID:34814836
Microbiota links to neural dynamics supporting threat processing. PMID:34811847
Effect of Insulin Receptor-Knockdown on the Expression Levels of Blood-Brain Barrier Functional Proteins in Human Brain Microvascular Endothelial Cells. PMID:34811625
Nutritional evaluation and transcriptome analyses of short-time germinated seeds in soybean (Glycine max L. Merri.). PMID:34811436
Integrative transcriptomic and metabolomic analysis of D-leaf of seven pineapple varieties differing in N-P-K% contents. PMID:34809576
Bacteroides spp. promotes branched-chain amino acid catabolism in brown fat and inhibits obesity. PMID:34805797
Mechanistic Target of Rapamycin Complex 2 Regulation of the Primary Human Trophoblast Cell Transcriptome. PMID:34805133
A Single Human-Relevant Fast Food Meal Rapidly Reorganizes Metabolomic and Transcriptomic Signatures in a Gut Microbiota-Dependent Manner. PMID:34804604
Comprehensive Metabolome and Volatilome Analyses in Eggplant and Tomato Reveal Their Differential Responses to Tuta absoluta Infestation. PMID:34804095
Genome-Wide Analyses of Proteome and Acetylome in Zymomonas mobilis Under N2-Fixing Condition. PMID:34803957
Selecting Hub Genes and Predicting Target Genes of microRNAs in Tuberculosis via the Bioinformatics Analysis. PMID:34803519
Analyzing differentially expressed genes and pathways of Bex2-deficient mouse lung via RNA-Seq. PMID:34803456
Molecular pathways involved in COVID-19 and potential pathway-based therapeutic targets. PMID:34801852
Seasonal diets supersede host species in shaping the distal gut microbiota of Yaks and Tibetan sheep. PMID:34799677
Insulin resistance rewires the metabolic gene program and glucose utilization in human white adipocytes. PMID:34799672
CD4+ effector T cells accelerate Alzheimer's disease in mice. PMID:34798897
Comparison of carbohydrate ABC importers from Mycobacterium tuberculosis. PMID:34798821
USH2A Mutation is Associated With Tumor Mutation Burden and Antitumor Immunity in Patients With Colon Adenocarcinoma. PMID:34795697
A pan-cancer analysis revealing the role of TIGIT in tumor microenvironment. PMID:34795387
De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.). PMID:34795371
Role of FRG1 in predicting the overall survivability in cancers using multivariate based optimal model. PMID:34795329
Construction of a single nucleotide variant score-related gene-based prognostic model in hepatocellular carcinoma: analysis of multi-independent databases and validation in vitro. PMID:34794449
Small RNA sequencing reveals various microRNAs involved in piperine biosynthesis in black pepper (Piper nigrum L.). PMID:34794378
Dichotomous effects of cellular expression of STAT3 on tumor growth of HNSCC. PMID:34793974
Assessment of metabolic perturbations associated with exposure to phthalates among pregnant African American women. PMID:34793805
Transcriptomic survey reveals multiple adaptation mechanisms in response to nitrogen deprivation in marine Porphyridium cruentum. PMID:34793503
Technical note: overcoming host contamination in bovine vaginal metagenomic samples with nanopore adaptive sequencing. PMID:34791313
Genetic architecture of orbital telorism. PMID:34791242
The length scale of multivalent interactions is evolutionarily conserved in fungal and vertebrate phase-separating proteins. PMID:34791214
Identification of biomarkers and ceRNA network in glioblastoma through bioinformatic analysis and evaluation of potential prognostic values. PMID:34790767
Hypothalamic Transcriptome Analysis Reveals the Crucial MicroRNAs and mRNAs Affecting Litter Size in Goats. PMID:34790713
Identification of Cross-Pathway Connections via Protein-Protein Interactions Linked to Altered States of Metabolic Enzymes in Cervical Cancer. PMID:34790674
Topological Analysis of the Carbon-Concentrating CETCH Cycle and a Photorespiratory Bypass Reveals Boosted CO2-Sequestration by Plants. PMID:34790651
Six mutator-derived lncRNA signature of genome instability for predicting the clinical outcome of colon cancer. PMID:34790382
Transcriptome provides potential insights into how calcium affects the formation of stone cell in Pyrus. PMID:34789145
Identification of Key Pathways and Genes in SARS-CoV-2 Infecting Human Intestines by Bioinformatics Analysis. PMID:34787756
Identification and Validation of Autophagy-Related Genes as Potential Biomarkers and Therapeutic Targets in Atrial Fibrillation. PMID:34785936
Comparative transcriptomic profiling of susceptible and resistant cultivars of pigeonpea demonstrates early molecular responses during Fusarium udum infection. PMID:34785701
Apoptosis-associated speck-like protein containing a CARD regulates the growth of pancreatic ductal adenocarcinoma. PMID:34785680
Heme auxotrophy in abundant aquatic microbial lineages. PMID:34785591
Compendium of 530 metagenome-assembled bacterial and archaeal genomes from the polar Arctic Ocean. PMID:34782724
Neuroprotective effects of long noncoding RNAs involved in ischemic postconditioning after ischemic stroke. PMID:34782575
Hub microRNAs and genes in the development of atrial fibrillation identified by weighted gene co-expression network analysis. PMID:34781940
Transcriptomic responses to drought stress in Polygonatum kingianum tuber. PMID:34781887
Comprehensive analysis of expression, prognosis and immune infiltration for TIMPs in glioblastoma. PMID:34781885
Linking Diabetes Mellitus with Alzheimer's Disease: Bioinformatics Analysis for the Potential Pathways and Characteristic Genes. PMID:34779951
Chromosome-scale assembly reveals asymmetric paleo-subgenome evolution and targets for the acceleration of fungal resistance breeding in the nut crop, pecan. PMID:34778752
Trends in biological data integration for the selection of enzymes and transcription factors related to cellulose and hemicellulose degradation in fungi. PMID:34777932
Construction of the circRNA-miRNA-mRNA Regulatory Network of an Abdominal Aortic Aneurysm to Explore Its Potential Pathogenesis. PMID:34777635
Novel Enzymes From the Red Sea Brine Pools: Current State and Potential. PMID:34777282
Analysis of transcriptomic data sets supports the role of IL-6 in NETosis and immunothrombosis in severe COVID-19. PMID:34775962
Whole-transcriptome sequencing reveals a vernalization-related ceRNA regulatory network in chinese cabbage (Brassica campestris L. ssp. pekinensis). PMID:34773977
Systems pharmacology to reveal multi-scale mechanisms of traditional Chinese medicine for gastric cancer. PMID:34773055
Identification of key genes and pathways associated with resting mast cells in meningioma. PMID:34772393
Revealing the Molecular Mechanisms of Alzheimer's Disease Based on Network Analysis. PMID:34768988
Association of microRNA-34a rs2666433 (A/G) Variant with Systemic Lupus Erythematosus in Female Patients: A Case-Control Study. PMID:34768615
Single-cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS iPSC-derived motor neurons. PMID:34767750
RBS and Promoter Strengths Determine the Cell-Growth-Dependent Protein Mass Fractions and Their Optimal Synthesis Rates. PMID:34767708
The Proteomic Signature of Recombinant Growth Hormone in Recreational Athletes. PMID:34765854
Computational Studies of the Intestinal Host-Microbiota Interactome. PMID:34765258
Factors that influence the quality of metabolomics data in in vitro cell toxicity studies: a systematic survey. PMID:34764412
Spontaneous pulmonary emphysema in mice lacking all three nitric oxide synthase isoforms. PMID:34764368
Chronic pathophysiological changes in the normal brain parenchyma caused by radiotherapy accelerate glioma progression. PMID:34764346
Integrative Bioinformatics approaches to therapeutic gene target selection in various cancers for Nitroglycerin. PMID:34764329
Myeloid Cell-Derived Oxidized Lipids and Regulation of the Tumor Microenvironment. PMID:34764204
Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada. PMID:34763673
Integrated analyses of miRNA-mRNA expression profiles of ovaries reveal the crucial interaction networks that regulate the prolificacy of goats in the follicular phase. PMID:34763659
An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome. PMID:34763597
DNA methylation-based classifier and gene expression signatures detect BRCAness in osteosarcoma. PMID:34762643
Inhibition of the renin-angiotensin system causes concentric hypertrophy of renal arterioles in mice and humans. PMID:34762601
Tlr2/4 Double Knockout Attenuates the Degeneration of Primary Auditory Neurons: Potential Mechanisms From Transcriptomic Perspectives. PMID:34760891
Prioritisation of Candidate Genes Underpinning COVID-19 Host Genetic Traits Based on High-Resolution 3D Chromosomal Topology. PMID:34759959
Pyrophosphate and Irreversibility in Evolution, or why PPi Is Not an Energy Currency and why Nature Chose Triphosphates. PMID:34759911
Resolving the Microalgal Gene Landscape at the Strain Level: a Novel Hybrid Transcriptome of Emiliania huxleyi CCMP3266. PMID:34757817
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling. PMID:34755844
Identification of genes and gene expression associated with dispersal capacity in the mountain pine beetle, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). PMID:34754626
The effects of exosomes derived from trabecular meshwork cells on Schlemm's canal endothelial cells. PMID:34754027
A dry immersion model of microgravity modulates platelet phenotype, miRNA signature, and circulating plasma protein biomarker profile. PMID:34753989
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
Pyroptosis-related gene mediated modification patterns and immune cell infiltration landscapes in cutaneous melanoma to aid immunotherapy. PMID:34753832
Impact of spaceflight and artificial gravity on sulfur metabolism in mouse liver: sulfur metabolomic and transcriptomic analysis. PMID:34750416
Restorative potential of (-)-epicatechin in a rat model of Gulf War illness muscle atrophy and fatigue. PMID:34750405
Trait correlated expression combined with eQTL and ASE analyses identified novel candidate genes affecting intramuscular fat. PMID:34749647
A genetic screen in macrophages identifies new regulators of IFNγ-inducible MHCII that contribute to T cell activation. PMID:34747695
The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis. PMID:34747331
Study on the Mechanism of Liuwei Dihuang Pills in Treating Parkinson's Disease Based on Network Pharmacology. PMID:34746302
Genome Instability and Long Noncoding RNA Reveal Biomarkers for Immunotherapy and Prognosis and Novel Competing Endogenous RNA Mechanism in Colon Adenocarcinoma. PMID:34746134
Identification of Gene-Set Signature in Early-Stage Hepatocellular Carcinoma and Relevant Immune Characteristics. PMID:34745960
A Novel Three-LncRNA Signature Predicting Tumor Recurrence in Nonfunctioning Pituitary Adenomas. PMID:34745223
The Correlation between Gut Microbiota and Serum Metabolomic in Elderly Patients with Chronic Heart Failure. PMID:34744513
Identification of the antibacterial mechanism of cryptotanshinone on methicillin-resistant Staphylococcus aureus using bioinformatics analysis. PMID:34741111
The rumen microbiome inhibits methane formation through dietary choline supplementation. PMID:34741032
MCLR-elicited hepatic fibrosis and carcinogenic gene expression changes persist in rats with diet-induced nonalcoholic steatohepatitis through a 4-week recovery period. PMID:34740672
Integrated Single-Cell Bioinformatics Analysis Reveals Intrinsic and Extrinsic Biological Characteristics of Hematopoietic Stem Cell Aging. PMID:34737765
High-quality reference genome sequences of two coconut cultivars provide insights into evolution of monocot chromosomes and differentiation of fiber content and plant height. PMID:34736486
Genomic and epigenomic adaptation in SP-R210 (Myo18A) isoform-deficient macrophages. PMID:34735924
A novel strategy for combination of clofarabine and pictilisib is synergistic in gastric cancer. PMID:34735897
A novel immune-related ceRNA network that predicts prognosis and immunotherapy response in lung adenocarcinoma. PMID:34734036
An integrated analysis of DNA promoter methylation, microRNA regulation, and gene expression in gastric adenocarcinoma. PMID:34733966
Comparison of critical biomarkers in 2 erectile dysfunction models based on GEO and NOS-cGMP-PDE5 pathway. PMID:34731136
The Overexpression of Phasin and Regulator Genes Promoting the Synthesis of Polyhydroxybutyrate in Cupriavidus necator H16 under Nonstress Conditions. PMID:34731058
Precise pathological classification of non-small cell lung adenocarcinoma and squamous carcinoma based on an integrated platform of targeted metabolome and lipidome. PMID:34729658
Proteogenomic discovery of sORF-encoded peptides associated with bacterial virulence in Yersinia pestis. PMID:34728737
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation. PMID:34728675
Genome-Wide Identification of Tomato Xylem Sap Fitness Factors for Three Plant-Pathogenic Ralstonia Species. PMID:34726495
Interactions of the Intracellular Bacterium Cardinium with Its Host, the House Dust Mite Dermatophagoides farinae, Based on Gene Expression Data. PMID:34726490
Transcriptome and Exome Analyses of Hepatocellular Carcinoma Reveal Patterns to Predict Cancer Recurrence in Liver Transplant Patients. PMID:34725972
Venatorbacter cucullus gen. nov sp. nov a novel bacterial predator. PMID:34725408
Nitecap: An Exploratory Circadian Analysis Web Application. PMID:34724846
A gap-filling algorithm for prediction of metabolic interactions in microbial communities. PMID:34723959
DCcov: Repositioning of drugs and drug combinations for SARS-CoV-2 infected lung through constraint-based modeling. PMID:34723158
Local delivery of FTY720 induces neutrophil activation through chemokine signaling in an oronasal fistula model. PMID:34722855
Distinct Mitochondrial Remodeling During Mesoderm Differentiation in a Human-Based Stem Cell Model. PMID:34722525
Serum Anti-14-3-3 Zeta Autoantibody as a Biomarker for Predicting Hepatocarcinogenesis. PMID:34722278
Migration effects on the intestinal microbiota of Tibetans. PMID:34721954
Metagenomic Analysis Reveals Neisseria bacilliformis Variation in the Early Childhood Caries Plaque Microbiome. PMID:34721624
Viral Strain-Specific Activation of Pathogen-Associated Molecular Pattern-Triggered Immunity Enhances Symptom Severity in Broad Bean Wilt Virus 2 Infection. PMID:34721473
Transcriptomic and Network Meta-Analysis of Frontotemporal Dementias. PMID:34720873
A Beginner's Guide to the COBRA Toolbox. PMID:34719002
Curating COBRA Models of Microbial Metabolism. PMID:34719001
EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study. PMID:34718752
Maternal methionine supplementation during gestation alters alternative splicing and DNA methylation in bovine skeletal muscle. PMID:34717556
PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes. PMID:34716373
Determining oncogenic patterns and cancer predisposition through the transcriptomic profile in Mitchell-Riley syndrome with heterotopic gastric mucosa and duodenal atresia: a case report. PMID:34715892
GFICLEE: ultrafast tree-based phylogenetic profile method inferring gene function at the genomic-wide level. PMID:34715785
Exploration of the anti-insomnia mechanism of Ganoderma by central-peripheral multi-level interaction network analysis. PMID:34715778
The Eco-Exposome Concept: Supporting an Integrated Assessment of Mixtures of Environmental Chemicals. PMID:34714945
The landscape of DNA methylation in asthma: a data mining and validation. PMID:34714718
Responses of Escherichia coli and Listeria monocytogenes to ozone treatment on non-host tomato: Efficacy of intervention and evidence of induced acclimation. PMID:34710139
Characterizing the breast cancer lipidome and its interaction with the tissue microbiota. PMID:34707244
Nutritional restriction during the peri-conceptional period alters the myometrial transcriptome during the peri-implantation period. PMID:34707153
Potential value and chemical characterization of gut microbiota derived nitrogen containing metabolites in feces from Periplaneta americana (L.) at different growth stages. PMID:34707100
RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation. PMID:34706646
ANAT 3.0: a framework for elucidating functional protein subnetworks using graph-theoretic and machine learning approaches. PMID:34706638
Natural products for infectious microbes and diseases: an overview of sources, compounds, and chemical diversities. PMID:34705221
Fecal Microbiota Transplantation Increases Colonic IL-25 and Dampens Tissue Inflammation in Patients with Recurrent Clostridioides difficile. PMID:34704776
Protocol for using NoBadWordsCombiner to merge and minimize "bad words" from BLAST hits against multiple eukaryotic gene annotation databases. PMID:34704076
Exploring biological basis of Syndrome differentiation in coronary heart disease patients with two distinct Syndromes by integrated multi-omics and network pharmacology strategy. PMID:34702323
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. PMID:34702190
Comparative genomics reveals molecular mechanisms underlying health and reproduction in cryptorchid mammals. PMID:34702182
Circadian miR-449c-5p regulates uterine Ca2+ transport during eggshell calcification in chickens. PMID:34702171
Influence of formic acid treatment on the proteome of the ectoparasite Varroa destructor. PMID:34699527
Discrimination of Bacterial Community Structures among Healthy, Gingivitis, and Periodontitis Statuses through Integrated Metatranscriptomic and Network Analyses. PMID:34698525
Elucidate multidimensionality of type 1 diabetes mellitus heterogeneity by multifaceted information. PMID:34697343
Physiologic biomechanics enhance reproducible contractile development in a stem cell derived cardiac muscle platform. PMID:34697315
Prioritization of Diagnostic and Prognostic Biomarkers for Lupus Nephritis Based on Integrated Bioinformatics Analyses. PMID:34692653
Convergent adaptation of the genomes of woody plants at the land-sea interface. PMID:34692119
Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows. PMID:34692022
Optical Coherence Tomography Angiography Characteristics Serve as Retinal Vein Occlusion Therapeutic Biomarkers for Dexamethasone Intravitreal Implant. PMID:34691285
Transcriptome and Metabolome Comparison of Smooth and Rough Citrus limon L. Peels Grown on Same Trees and Harvested in Different Seasons. PMID:34691126
New Arsenite Oxidase Gene (aioA) PCR Primers for Assessing Arsenite-Oxidizer Diversity in the Environment Using High-Throughput Sequencing. PMID:34690945
TPSC: a module detection method based on topology potential and spectral clustering in weighted networks and its application in gene co-expression module discovery. PMID:34689740
Identification of four novel QTL linked to the metabolic syndrome in the Berlin Fat Mouse. PMID:34689180
Identification of C3 and FN1 as potential biomarkers associated with progression and prognosis for clear cell renal cell carcinoma. PMID:34688260
Altered gene expression in slc4a11-/- mouse cornea highlights SLC4A11 roles. PMID:34686736
Multi-omics analysis of m6A modification-related patterns based on m6A regulators and tumor microenvironment infiltration in lung adenocarcinoma. PMID:34686691
A human multi-lineage hepatic organoid model for liver fibrosis. PMID:34686668
Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer. PMID:34686186
Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill. PMID:34686131
The Semi-Supervised Strategy of Machine Learning on the Gene Family Diversity to Unravel Resveratrol Synthesis. PMID:34685867
Lineage-Selective Disturbance of Early Human Hematopoietic Progenitor Cell Differentiation by the Commonly Used Plasticizer Di-2-ethylhexyl Phthalate via Reactive Oxygen Species: Fatty Acid Oxidation Makes the Difference. PMID:34685682
Ambient Air Pollution Shapes Bacterial and Fungal Ivy Leaf Communities. PMID:34683409
Precise Characterization of Genetic Interactions in Cancer via Molecular Network Refining Processes. PMID:34681774
Stage Specificity, the Dynamic Regulators and the Unique Orchid Arundina graminifolia. PMID:34681593
Identification of Five Hub Genes as Key Prognostic Biomarkers in Liver Cancer via Integrated Bioinformatics Analysis. PMID:34681056
Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage. PMID:34681032
Methanogenesis and Salt Tolerance Genes of a Novel Halophilic Methanosarcinaceae Metagenome-Assembled Genome from a Former Solar Saltern. PMID:34681003
Modulation of Global Gene Expression by Aneuploidy and CNV of Dosage Sensitive Regulatory Genes. PMID:34681000
Silver: Forging almost Gold Standard Datasets. PMID:34680918
Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol. PMID:34680891
Trends in the Application of "Omics" to Ecotoxicology and Stress Ecology. PMID:34680873
Expression of Cytokine-Coding Genes BMP8B, LEFTY1 and INSL5 Could Distinguish between Ulcerative Colitis and Crohn's Disease. PMID:34680872
De Novo Genome Assembly of Chinese Plateau Honeybee Unravels Intraspecies Genetic Diversity in the Eastern Honeybee, Apis cerana. PMID:34680661
A Systems Approach to Interrogate Gene Expression Patterns in African American Men Presenting with Clinically Localized Prostate Cancer. PMID:34680291
PaIRKAT: A pathway integrated regression-based kernel association test with applications to metabolomics and COPD phenotypes. PMID:34679079
Pathways and microbiome modifications related to surgery and enterocolitis in Hirschsprung disease. PMID:34677676
Metabolomics Reveals That Bisphenol Pollutants Impair Protein Synthesis-Related Pathways in Daphnia magna. PMID:34677381
Metabolomics and Inflammatory Mediator Profiling for the Differentiation of Life-Threatening and Non-Severe Appendicitis in the Pediatric Population. PMID:34677379
Yeast metabolic innovations emerged via expanded metabolic network and gene positive selection. PMID:34676984
Genome-wide distribution of 5hmC in the dental pulp of mouse molars and incisors. PMID:34676418
Cell Wall Proteomics Reveal Phenotypic Adaption of Drug-Resistant Mycobacterium smegmatis to Subinhibitory Rifampicin Exposure. PMID:34676224
The nomogram based on the 6-lncRNA model can promote the prognosis prediction of patients with breast invasive carcinoma. PMID:34675301
Enhancement of Campylobacter hepaticus culturing to facilitate downstream applications. PMID:34675257
An Emiliania huxleyi pan-transcriptome reveals basal strain specificity in gene expression patterns. PMID:34675226
Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens. PMID:34675224
Association between genetic variants of the cholinergic system and postoperative delirium and cognitive dysfunction in elderly patients. PMID:34674705
Starch branching enzymes as putative determinants of postharvest quality in horticultural crops. PMID:34674662
Identification of Key Differentially Methylated/Expressed Genes and Pathways for Ovarian Endometriosis by Bioinformatics Analysis. PMID:34671938
An Atypical Autoinflammatory Disease Due to an LRR Domain NLRP3 Mutation Enhancing Binding to NEK7. PMID:34671876
Pan-cancer analysis of pathway-based gene expression pattern at the individual level reveals biomarkers of clinical prognosis. PMID:34671755
Genomic Changes and Genetic Divergence of Vibrio alginolyticus Under Phage Infection Stress Revealed by Whole-Genome Sequencing and Resequencing. PMID:34671325
Reduced expression of OXPHOS and DNA damage genes is linked to protection from microvascular complications in long-term type 1 diabetes: the PROLONG study. PMID:34671071
Investigation of the transcriptomic response in Atlantic salmon (Salmo salar) gill exposed to Paramoeba perurans during early onset of disease. PMID:34667245
Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds. PMID:34667187
Deep learning allows genome-scale prediction of Michaelis constants from structural features. PMID:34665809
Construction of a 5 immune-related lncRNA-based prognostic model of NSCLC via bioinformatics. PMID:34664861
Microarray analysis of hub genes and pathways in damaged cartilage tissues of knee. PMID:34664844
Investigation on the mechanisms of guiqi huoxue capsule for treating cervical spondylosis based on network pharmacology and molecular docking. PMID:34664825
The structure of behavioral variation within a genotype. PMID:34664550
Extracellular calcium alters calcium-sensing receptor network integrating intracellular calcium-signaling and related key pathway. PMID:34663830
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. PMID:34663219
Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus. PMID:34663092
Modular Evolution of the Drosophila Metabolome. PMID:34662414
Qualitative lysine crotonylome analysis in the ovarian tissue of Harmonia axyridis (Pallas). PMID:34662345
Identification of a prognostic chemoresistance-related gene signature associated with immune microenvironment in breast cancer. PMID:34661511
DNA Repair and Immune Response Pathways Are Deregulated in Melanocyte-Keratinocyte Co-cultures Derived From the Healthy Skin of Familial Melanoma Patients. PMID:34660619
Identification of Novel Biomarkers Related to Lung Squamous Cell Carcinoma Using Integrated Bioinformatics Analysis. PMID:34659450
Transcriptome Profiling Reveals Important Transcription Factors and Biological Processes in Skin Regeneration Mediated by Mechanical Stretch. PMID:34659370
Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae. PMID:34659355
Genome-Based Taxonomic Rearrangement of the Order Geobacterales Including the Description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. PMID:34659166
Sex-Specific Cross Tissue Meta-Analysis Identifies Immune Dysregulation in Women With Alzheimer's Disease. PMID:34658838
Non-coding RNA in raw and commercially processed milk and putative targets related to growth and immune-response. PMID:34657595
Deep post-GWAS analysis identifies potential risk genes and risk variants for Alzheimer's disease, providing new insights into its disease mechanisms. PMID:34654853
Chromosome-scale assembly and high-density genetic map of the yellow drum, Nibea albiflora. PMID:34654820
Effect of the spatial-temporal specific theca cell Cyp17 overexpression on the reproductive phenotype of the novel TC17 mouse. PMID:34654452
A comparative analysis of differentially expressed mRNAs, miRNAs and circRNAs provides insights into the key genes involved in the high-altitude adaptation of yaks. PMID:34654374
Performance of Multiple Metagenomics Pipelines in Understanding Microbial Diversity of a Low-Biomass Spacecraft Assembly Facility. PMID:34650522
Large-scale k-mer-based analysis of the informational properties of genomes, comparative genomics and taxonomy. PMID:34648558
Tryptophan metabolism is inversely regulated in the tumor and blood of patients with glioblastoma. PMID:34646367
The cyclin dependent kinase inhibitor Roscovitine prevents diet-induced metabolic disruption in obese mice. PMID:34645915
Untargeted metabolomics reveals sex-specific differences in lipid metabolism of adult rats exposed to dexamethasone in utero. PMID:34645877
Physiological responses and transcriptomic changes reveal the mechanisms underlying adaptation of Stylosanthes guianensis to phosphorus deficiency. PMID:34645406
Clarifying the molecular mechanism of tomentosin‑induced antiproliferative and proapoptotic effects in human multiple myeloma via gene expression profile and genetic interaction network analysis. PMID:34643251
A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations. PMID:34641974
Neutrophil Pathways of Inflammation Characterize the Blood Transcriptomic Signature of Patients with Psoriasis and Cardiovascular Disease. PMID:34639156
Impact of the Pd2Spm (Spermine) Complex on the Metabolism of Triple-Negative Breast Cancer Tumors of a Xenograft Mouse Model. PMID:34639114
A Secreted Chorismate Mutase from Xanthomonas arboricola pv. juglandis Attenuates Virulence and Walnut Blight Symptoms. PMID:34638715
Risk Prediction of Cardiovascular Events by Exploration of Molecular Data with Explainable Artificial Intelligence. PMID:34638627
Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters. PMID:34637433
Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome. PMID:34636676
Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. PMID:34636668
Identification of loci associated with pathological outcomes in Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis using whole-genome sequence data. PMID:34635747
Anthrahydroquinone-2-6-disulfonate is a novel, powerful antidote for paraquat poisoning. PMID:34635711
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
Integrated analysis of mRNA-seq and miRNA-seq reveals the advantage of polyploid Solidago canadensis in sexual reproduction. PMID:34635057
Metabolic gene regulation by Drosophila GATA transcription factor Grain. PMID:34634038
Reconstructing Boolean network ensembles from single-cell data for unraveling dynamics in the aging of human hematopoietic stem cells. PMID:34630946
The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis. PMID:34630371
Serum Metabolic Profiles of Chinese Women With Perimenopausal Obesity Explored by the Untargeted Metabolomics Approach. PMID:34630316
p53-dependent induction of P2X7 on hematopoietic stem and progenitor cells regulates hematopoietic response to genotoxic stress. PMID:34625535
Development of a Toll-Like Receptor-Based Gene Signature That Can Predict Prognosis, Tumor Microenvironment, and Chemotherapy Response for Hepatocellular Carcinoma. PMID:34621787
Identification of biomarkers of brown adipose tissue aging highlights the role of dysfunctional energy and nucleotide metabolism pathways. PMID:34620947
Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production. PMID:34620937
Western and non-western gut microbiomes reveal new roles of Prevotella in carbohydrate metabolism and mouth-gut axis. PMID:34620880
A protocol for dynamic model calibration. PMID:34619769
Tumor-propagating side population cells are a dynamic subpopulation in undifferentiated pleomorphic sarcoma. PMID:34618689
Metabolic network-based identification of plasma markers for non-small cell lung cancer. PMID:34617154
Novel ACE2 protein interactions relevant to COVID-19 predicted by evolutionary rate correlations. PMID:34616619
Scoparone inhibits pancreatic cancer through PI3K/Akt signaling pathway. PMID:34616521
Lipidomic approaches to dissect dysregulated lipid metabolism in kidney disease. PMID:34616096
Inhibition of Vascular Growth by Modulation of the Anandamide/Fatty Acid Amide Hydrolase Axis. PMID:34615374
CyanoOmicsDB: an integrated omics database for functional genomic analysis of cyanobacteria. PMID:34614159
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC. PMID:34613979
Overexpression of EWSR1 (Ewing sarcoma breakpoint region 1/EWS RNA binding protein 1) predicts poor survival in patients with hepatocellular carcinoma. PMID:34612781
Targeting the miRNA-155/TNFSF10 network restrains inflammatory response in the retina in a mouse model of Alzheimer's disease. PMID:34611142
Novel Drivers of Virulence in Clostridioides difficile Identified via Context-Specific Metabolic Network Analysis. PMID:34609164
Proteomics changes after negative pressure wound therapy in diabetic foot ulcers. PMID:34608502
A Chinese host genetic study discovered IFNs and causality of laboratory traits on COVID-19 severity. PMID:34608450
Potential roles of 1,5-anhydro-D-fructose in modulating gut microbiome in mice. PMID:34608200
A Computational Framework to Identify Transcriptional and Network Differences between Hepatocellular Carcinoma and Normal Liver Tissue and Their Applications in Repositioning Drugs. PMID:34604388
Transcriptomic Analysis Reveals a Sex-Dimorphic Influence of GAT-2 on Murine Liver Function. PMID:34604287
Effects of Helicobacter pylori Infection on the Oral Microbiota of Reflux Esophagitis Patients. PMID:34604113
Identification of LINC00173 in Myasthenia Gravis by Integration Analysis of Aberrantly Methylated- Differentially Expressed Genes and ceRNA Networks. PMID:34603387
Interferon-inducible protein, IFIX, has tumor-suppressive effects in oral squamous cell carcinoma. PMID:34599264
Toward understanding of the methoxylated flavonoid biosynthesis pathway in Dracocephalum kotschyi Boiss. PMID:34599246
Dietary, Cultural, and Pathogens-Related Selective Pressures Shaped Differential Adaptive Evolution among Native Mexican Populations. PMID:34597392
Using a Two-Sample Mendelian Randomization Method in Assessing the Causal Relationships Between Human Blood Metabolites and Heart Failure. PMID:34595216
X-Ray Causes mRNA Transcripts Change to Enhance Orai2-Mediated Ca2+ Influx in Rat Brain Microvascular Endothelial Cells. PMID:34595206
Heme Oxygenase-1 at the Nexus of Endothelial Cell Fate Decision Under Oxidative Stress. PMID:34595164
Comparative Immunogenomics of Canine Natural Killer Cells as Immunotherapy Target. PMID:34594320
Repurposing haloperidol for the treatment of rheumatoid arthritis: an integrative approach using data mining techniques. PMID:34589142
Insights into the gut bacterial communities of spider from wild with no evidence of phylosymbiosis. PMID:34588907
Tanshinone IIA affects the malignant growth of Cholangiocarcinoma cells by inhibiting the PI3K-Akt-mTOR pathway. PMID:34588580
Global identification of long non-coding RNAs involved in the induction of spinach flowering. PMID:34587906
Ecological Dichotomies Arise in Microbial Communities Due to Mixing of Deep Hydrothermal Waters and Atmospheric Gas in a Circumneutral Hot Spring. PMID:34586901
Whole-genome assembly of Ganoderma leucocontextum (Ganodermataceae, Fungi) discovered from the Tibetan Plateau of China. PMID:34586388
RNA-RNA interactions between SARS-CoV-2 and host benefit viral development and evolution during COVID-19 infection. PMID:34585235
Identifying metabolic alterations in newly diagnosed small cell lung cancer patients. PMID:34585134
The genome of the naturally evolved obesity-prone Ossabaw miniature pig. PMID:34585119
Phagocytosis by stroma confounds coculture studies. PMID:34585113
Oxysterol binding protein-like 3 (OSBPL3) is a novel driver gene that promotes tumor growth in part through R-Ras/Akt signaling in gastric cancer. PMID:34584127
Exploration of the lactation function of protein phosphorylation sites in goat mammary tissues by phosphoproteome analysis. PMID:34583635
Molecular regulation of anthocyanin discoloration under water stress and high solar irradiance in pluckable shoots of purple tea cultivar. PMID:34581909
Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis. PMID:34580642
Short-term transcriptomic response to plasma membrane injury. PMID:34580330
A New Murine Liver Fibrosis Model Induced by Polyhexamethylene Guanidine-Phosphate. PMID:34580237
Wnt pathway-related three-mRNA clinical outcome signature in bladder urothelial carcinoma: computational biology and experimental analyses. PMID:34579753
Predicting metabolic pathway membership with deep neural networks by integrating sequential and ontology information. PMID:34579673
Morphological, physiological, and transcriptional responses to low nitrogen stress in Populus deltoides Marsh. clones with contrasting nitrogen use efficiency. PMID:34579659
Recombinant Antigen of Type 2 Porcine Reproductive and Respiratory Syndrome Virus (PRRSV-2) Promotes M1 Repolarization of Porcine Alveolar Macrophages and Th1 Type Response. PMID:34579246
Association Study among Comethylation Modules, Genetic Polymorphisms and Clinical Features in Mexican Teenagers with Eating Disorders: Preliminary Results. PMID:34579086
Plasma Metabolome Profiling by High-Performance Chemical Isotope-Labelling LC-MS after Acute and Medium-Term Intervention with Golden Berry Fruit (Physalis peruviana L.), Confirming Its Impact on Insulin-Associated Signaling Pathways. PMID:34579001
The MAPK/ERK Pathway and the Role of DUSP1 in JCPyV Infection of Primary Astrocytes. PMID:34578413
NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data. PMID:34576734
Genome-Resolved Meta-Analysis of the Microbiome in Oil Reservoirs Worldwide. PMID:34576708
Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. PMID:34576133
WGCNA Identifies Translational and Proteasome-Ubiquitin Dysfunction in Rett Syndrome. PMID:34576118
Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning. PMID:34575658
Study of Triticum aestivum Resistome in Response to Wheat dwarf India Virus Infection. PMID:34575104
Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets. PMID:34573438
Years of Schooling Could Reduce Epigenetic Aging: A Study of a Mexican Cohort. PMID:34573390
Identification of Long Non-Coding RNAs Involved in Porcine Fat Deposition Using Two High-Throughput Sequencing Methods. PMID:34573356
HMGB1 Protein Interactions in Prostate and Ovary Cancer Models Reveal Links to RNA Processing and Ribosome Biogenesis through NuRD, THOC and Septin Complexes. PMID:34572914
Identifying GPSM Family Members as Potential Biomarkers in Breast Cancer: A Comprehensive Bioinformatics Analysis. PMID:34572330
Single-cell RNA Sequencing Reveals Sexually Dimorphic Transcriptome and Type 2 Diabetes Genes in Mouse Islet β Cells. PMID:34571259
A biallelic SNIP1 Amish founder variant causes a recognizable neurodevelopmental disorder. PMID:34570759
A highly multiplexed quantitative phosphosite assay for biology and preclinical studies. PMID:34569154
Changes in the Gut Microbiome Contribute to the Development of Behcet's Disease via Adjuvant Effects. PMID:34568329
Mammary Tumorigenesis and Metabolome in Male Adipose Specific Monocyte Chemotactic Protein-1 Deficient MMTV-PyMT Mice Fed a High-Fat Diet. PMID:34568008
Identification of a miRNA-mRNA Regulatory Networks in Placental Tissue Associated With Tibetan High Altitude Adaptation. PMID:34567059
CD49a Identifies Polyfunctional Memory CD8 T Cell Subsets that Persist in the Lungs After Influenza Infection. PMID:34566986
Systems-Level Proteomics Evaluation of Microglia Response to Tumor-Supportive Anti-Inflammatory Cytokines. PMID:34566949
VicPred: A Vibrio cholerae Genotype Prediction Tool. PMID:34566903
Gene clusters based on OLIG2 and CD276 could distinguish molecular profiling in glioblastoma. PMID:34565408
Glycolysis related gene expression signature in predicting prognosis of laryngeal squamous cell carcinoma. PMID:34565301
Phylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species. PMID:34564766
An Extensive Metabolomics Workflow to Discover Cardiotoxin-Induced Molecular Perturbations in Microtissues. PMID:34564460
Profiles of microRNA in aqueous humor of normal tension glaucoma patients using RNA sequencing. PMID:34561506
Differentially expressed genes reflect disease-induced rather than disease-causing changes in the transcriptome. PMID:34561431
Discovery of ancestral L-ornithine and L-lysine decarboxylases reveals parallel, pseudoconvergent evolution of polyamine biosynthesis. PMID:34560100
Identification of a Novel Ferroptosis-Related Gene Prognostic Signature in Bladder Cancer. PMID:34557413
Malignant Tumor Purity Reveals the Driven and Prognostic Role of CD3E in Low-Grade Glioma Microenvironment. PMID:34557404
Identification of Key Candidate Genes and Chemical Perturbagens in Diabetic Kidney Disease Using Integrated Bioinformatics Analysis. PMID:34557161
Network neighbors of viral targets and differentially expressed genes in COVID-19 are drug target candidates. PMID:34556735
Proteomics reveals the effects of drought stress on the kernel development and starch formation of waxy maize. PMID:34556041
Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae). PMID:34555059
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. PMID:34554246
MEK-inhibitor-mediated rescue of skeletal myopathy caused by activating Hras mutation in a Costello syndrome mouse model. PMID:34553752
A High-Throughput Method to Analyze the Interaction Proteins With p22 Protein of African Swine Fever Virus In Vitro. PMID:34552974
Mass spectrometry-based metabolomics in microbiome investigations. PMID:34552265
Primate-specific stress-induced transcription factor POU2F1Z protects human neuronal cells from stress. PMID:34552146
Proliferative diabetic retinopathy transcriptomes reveal angiogenesis, anti-angiogenic therapy escape mechanisms, fibrosis and lymphatic involvement. PMID:34552123
Deep GONet: self-explainable deep neural network based on Gene Ontology for phenotype prediction from gene expression data. PMID:34551707
Microbiota composition and intestinal integrity remain unaltered after the inclusion of hydrolysed Nannochloropsis gaditana in Sparus aurata diet. PMID:34548549
Caveolin-1 and Sox-2 are predictive biomarkers of cetuximab response in head and neck cancer. PMID:34546978
Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. PMID:34546072
Screening and Bioinformatics Analysis of Competitive Endogenous RNA Regulatory Network --Related to Circular RNA in Breast Cancer. PMID:34545330
Non-invasive diagnostic tool for Parkinson's disease by sebum RNA profile with machine learning. PMID:34545158
The molecular interplay of the establishment of an infection - gene expression of Diaphorina citri gut and Candidatus Liberibacter asiaticus. PMID:34544390
A Rickettsiella Endosymbiont Is a Potential Source of Essential B-Vitamins for the Poultry Red Mite, Dermanyssus gallinae. PMID:34539600
DELEAT: gene essentiality prediction and deletion design for bacterial genome reduction. PMID:34537011
GenNet framework: interpretable deep learning for predicting phenotypes from genetic data. PMID:34535759
PlantGSAD: a comprehensive gene set annotation database for plant species. PMID:34534340
Characterization of fecal metabolome changes in patients with obstructive sleep apnea. PMID:34534066
Whole genome sequencing of Enterobacter mori, an emerging pathogen of kiwifruit and the potential genetic adaptation to pathogenic lifestyle. PMID:34533621
Identification of Novel Choroidal Neovascularization-Related Genes Using Laplacian Heat Diffusion Algorithm. PMID:34532497
Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation. PMID:34532163
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. PMID:34531741
Protective mechanism of Erigeron breviscapus injection on blood-brain barrier injury induced by cerebral ischemia in rats. PMID:34531475
TFTenricher: a python toolbox for annotation enrichment analysis of transcription factor target genes. PMID:34530727
Identification of key genes and immune infiltration modulated by CPAP in obstructive sleep apnea by integrated bioinformatics analysis. PMID:34529670
Transcriptome analysis of two Pogostemon cablin chemotypes reveals genes related to patchouli alcohol biosynthesis. PMID:34527441
Integrative Analysis of the Roles of lncRNAs and mRNAs in Itaconate-Mediated Protection Against Liver Ischemia-Reperfusion Injury in Mice. PMID:34526799
Empagliflozin maintains capillarization and improves cardiac function in a murine model of left ventricular pressure overload. PMID:34526601
Disease-induced changes in plant microbiome assembly and functional adaptation. PMID:34526096
ARHGAP4-SEPT2-SEPT9 complex enables both up- and down-modulation of integrin-mediated focal adhesions, cell migration, and invasion. PMID:34524873
Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism in Nostoc sp. PCC 7120. PMID:34523988
Aspects of the Neurospora crassa Sulfur Starvation Response Are Revealed by Transcriptional Profiling and DNA Affinity Purification Sequencing. PMID:34523983
Bioinformatics analysis identified shared differentially expressed genes as potential biomarkers for Hashimoto's thyroiditis-related papillary thyroid cancer. PMID:34522174
Characterization of m6A-Related Genes Landscape in Skin Cutaneous Melanoma to Aid Immunotherapy and Assess Prognosis. PMID:34522131
Metabolic effect of drought stress on the leaves of young oil palm (Elaeis guineensis) plants using UHPLC-MS and multivariate analysis. PMID:34521943
Analysis of weighted gene co-expression network of triterpenoid-related transcriptome characteristics from different strains of Wolfiporia cocos. PMID:34521885
Immunoregulatory mechanism studies of ginseng leaves on lung cancer based on network pharmacology and molecular docking. PMID:34521875
E2F transcription factor 1 (E2F1) promotes the transforming growth factor TGF-β1 induced human cardiac fibroblasts differentiation through promoting the transcription of CCNE2 gene. PMID:34521301
Screening Strategies for Biosurfactant Discovery. PMID:34518910
Prokaryotic viruses impact functional microorganisms in nutrient removal and carbon cycle in wastewater treatment plants. PMID:34518545
FLT3L Release by Natural Killer Cells Enhances Response to Radioimmunotherapy in Preclinical Models of HNSCC. PMID:34518311
Arsenic exposure and human blood DNA methylation and hydroxymethylation profiles in two diverse populations from Bangladesh and Spain. PMID:34516978
Podocyte-specific KLF4 is required to maintain parietal epithelial cell quiescence in the kidney. PMID:34516901
Identification of hsa_circ_0002024 as a prognostic competing endogenous RNA (ceRNA) through the hsa_miR_129-5p/Anti-Silencing Function 1B Histone Chaperone (ASF1B) axis in renal cell carcinoma. PMID:34516341
Oral Phenotype and Salivary Microbiome of Individuals With Papillon-Lefèvre Syndrome. PMID:34513733
Prediction of the mechanism of miRNAs in laryngeal squamous cell carcinoma based on the miRNA-mRNA regulatory network. PMID:34513340
Full-length transcriptome analysis of Spodoptera frugiperda larval brain reveals detoxification genes. PMID:34513339
Identification of Potential Biomarkers for Psoriasis by DNA Methylation and Gene Expression Datasets. PMID:34512732
Proteomic profiling identifies CLEC4C expression as a novel biomarker of primary graft dysfunction after heart transplantation. PMID:34511330
Complete genome sequence and identification of polyunsaturated fatty acid biosynthesis genes of the myxobacterium Minicystis rosea DSM 24000T. PMID:34511070
The chromosome-scale genome of Magnolia officinalis provides insight into the evolutionary position of magnoliids. PMID:34505009
De novo transcriptome assembly, polymorphic SSR markers development and population genetics analyses for southern corn rust (Puccinia polysora). PMID:34504267
Global analysis of lysine acetylation in soybean leaves. PMID:34504199
The tumor suppressor miR-642a-5p targets Wilms Tumor 1 gene and cell-cycle progression in prostate cancer. PMID:34504167
Dietary calcium supplementation promotes the accumulation of intramuscular fat. PMID:34503581
De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma. PMID:34503445
Common Genetic Aberrations Associated with Metabolic Interferences in Human Type-2 Diabetes and Acute Myeloid Leukemia: A Bioinformatics Approach. PMID:34502231
Mutation landscape of multiple myeloma measurable residual disease: identification of targets for precision medicine. PMID:34500459
Construction and analysis of a novel ferroptosis-related gene signature predicting prognosis in lung adenocarcinoma. PMID:34499810
Recipient APOL1 risk alleles associate with death-censored renal allograft survival and rejection episodes. PMID:34499625
Herbaspirillum seropedicae expresses non-phosphorylative pathways for D-xylose catabolism. PMID:34499201
Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility. PMID:34499026
Identification of Immune-Related Risk Signatures for the Prognostic Prediction in Oral Squamous Cell Carcinoma. PMID:34497859
Early phase of effective treatment induces distinct transcriptional changes in Mycobacterium tuberculosis expelled by pulmonary tuberculosis patients. PMID:34497280
Cabazitaxel suppresses colorectal cancer cell growth via enhancing the p53 antitumor pathway. PMID:34496154
Mitochondrial dysfunction-induced H3K27 hyperacetylation perturbs enhancers in Parkinson's disease. PMID:34494552
Weakly activated core inflammation pathways were identified as a central signaling mechanism contributing to the chronic neurodegeneration in Alzheimer's disease. PMID:34494019
Integrative Analyses of Genes Associated with Hashimoto's Thyroiditis. PMID:34493981
RNA-seq profiling reveals PBMC RNA as a potential biomarker for hepatocellular carcinoma. PMID:34493740
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PMID:34492007
Identification of Potential Biomarkers Associated with Acute Myocardial Infarction by Weighted Gene Coexpression Network Analysis. PMID:34490057
Comparative Proteomic Analysis of the Defense Response to Gibberella Stalk Rot in Maize and Reveals That ZmWRKY83 Is Involved in Plant Disease Resistance. PMID:34489999
Gelatin methacrylate hydrogels culture model for glioblastoma cells enriches for mesenchymal-like state and models interactions with immune cells. PMID:34489494
Dectin-2 mediates phagocytosis of Lactobacillus paracasei KW3110 and IL-10 production by macrophages. PMID:34489491
The genome sequence provides insights into salt tolerance of Achnatherum splendens (Gramineae), a constructive species of alkaline grassland. PMID:34487631
Gene expression and prognosis of x-ray repair cross-complementing family members in non-small cell lung cancer. PMID:34486486
Identifying Breast Cancer-Related Genes Based on a Novel Computational Framework Involving KEGG Pathways and PPI Network Modularity. PMID:34484285
Metagenomic Investigation Uncovers Presence of Probiotic-Type Microbiome in Kalparasa® (Fresh Unfermented Coconut Inflorescence Sap). PMID:34484136
Antibacterial Activity and Membrane-Targeting Mechanism of Aloe-Emodin Against Staphylococcus epidermidis. PMID:34484130
Centromere protein E as a novel biomarker and potential therapeutic target for retinoblastoma. PMID:34482803
Proteomic traits vary across taxa in a coastal Antarctic phytoplankton bloom. PMID:34482372
Proteome analysis identified proteins associated with mitochondrial function and inflammation activation crucially regulating the pathogenesis of fatty liver disease. PMID:34481473
Ischemic stroke induces cardiac dysfunction and alters transcriptome profile in mice. PMID:34481466
Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. PMID:34480029
SOD2- and NRF2-associated Gene Signature to Predict Radioresistance in Head and Neck Cancer. PMID:34479919
Arms race in a cell: genomic, transcriptomic, and proteomic insights into intracellular phage-bacteria interplay in deep-sea snail holobionts. PMID:34479645
Sulfarotene, a synthetic retinoid, overcomes stemness and sorafenib resistance of hepatocellular carcinoma via suppressing SOS2-RAS pathway. PMID:34479623
Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages. PMID:34479505
DTI-HeNE: a novel method for drug-target interaction prediction based on heterogeneous network embedding. PMID:34479477
Bioinformatics-based study to identify immune infiltration and inflammatory-related hub genes as biomarkers for the treatment of rheumatoid arthritis. PMID:34477936
INHBA is a novel mediator regulating cellular senescence and immune evasion in colorectal cancer. PMID:34476008
Duo: A Signature Based Method to Batch-Analyze Functional Similarities of Proteins. PMID:34475860
A ferroptosis-associated gene signature for the prediction of prognosis and therapeutic response in luminal-type breast carcinoma. PMID:34475496
Transcriptional expression of ZICs as an independent indicator of survival in gliomas. PMID:34475426
Proteomic response and molecular regulatory mechanisms of Bacillus cereus spores under ultrasound treatment. PMID:34474268
Metabolomics reveal alterations in arachidonic acid metabolism in Schistosoma mekongi after exposure to praziquantel. PMID:34473691
Assembling stable syntrophic Escherichia coli communities by comprehensively identifying beneficiaries of secreted goods. PMID:34469744
Therapeutic targeting of both dihydroorotate dehydrogenase and nucleoside transport in MYCN-amplified neuroblastoma. PMID:34462431
Increased expression of fragmented tRNA promoted neuronal necrosis. PMID:34462418
Host metabolic shift during systemic Salmonella infection revealed by comparative proteomics. PMID:34461813
Multitrait GWAS to connect disease variants and biological mechanisms. PMID:34460823
Small Intestinal Levels of the Branched Short-Chain Fatty Acid Isovalerate Are Elevated during Infection with Heligmosomoides polygyrus and Can Promote Helminth Fecundity. PMID:34460289
Comparative transcriptomic analysis of the brain in Takifugu rubripes shows its tolerance to acute hypoxia. PMID:34460041
Transcriptomic Analyses of the Adenoma-Carcinoma Sequence Identify Hallmarks Associated With the Onset of Colorectal Cancer. PMID:34458146
Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19. PMID:34457122
In silico identification of MicroRNAs targeting the key nucleator of stress granules, G3BP: Promising therapeutics for SARS-CoV-2 infection. PMID:34456603
Microbial composition differs between production systems and is associated with growth performance and carcass quality in pigs. PMID:34454609
Bayesian metamodeling of complex biological systems across varying representations. PMID:34453000
A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity. PMID:34451735
Subtractive Genomics Approach for Identification of Novel Therapeutic Drug Targets in Mycoplasma genitalium. PMID:34451385
Microvesicles transfer mitochondria and increase mitochondrial function in brain endothelial cells. PMID:34450196
The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort. PMID:34449791
Safety Assessment of Microbicide 2P23 on the Rectal and Vaginal Microbiota and Its Antiviral Activity on HIV Infection. PMID:34447373
Icariin, an Up-and-Coming Bioactive Compound Against Neurological Diseases: Network Pharmacology-Based Study and Literature Review. PMID:34447243
Identification of key proteins in the signaling crossroads between wound healing and cancer hallmark phenotypes. PMID:34446793
Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance. PMID:34446725
Drug Discovery of Spinal Muscular Atrophy (SMA) from the Computational Perspective: A Comprehensive Review. PMID:34445667
Gene-Metabolite Network Analysis Revealed Tissue-Specific Accumulation of Therapeutic Metabolites in Mallotus japonicus. PMID:34445541
Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. PMID:34445339
Differential Retinal Protein Expression in Primary and Secondary Retinal Ganglion Cell Degeneration Identified by Integrated SWATH and Target-Based Proteomics. PMID:34445296
High Concentration of an ISS-N1-Targeting Antisense Oligonucleotide Causes Massive Perturbation of the Transcriptome. PMID:34445083
Genomic Insights into Drug Resistance Determinants in Cedecea neteri, A Rare Opportunistic Pathogen. PMID:34442820
Cross-Shore and Depth Zonations in Bacterial Diversity Are Linked to Age and Source of Dissolved Organic Matter across the Intertidal Area of a Sandy Beach. PMID:34442799
JDSNMF: Joint Deep Semi-Non-Negative Matrix Factorization for Learning Integrative Representation of Molecular Signals in Alzheimer's Disease. PMID:34442330
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. PMID:34442314
Transcriptional Profiles of Diploid Mutant Apis mellifera Embryos after Knockout of csd by CRISPR/Cas9. PMID:34442270
Overexpression and Activation of αvβ3 Integrin Differentially Affects TGFβ2 Signaling in Human Trabecular Meshwork Cells. PMID:34440692
Identification of Targeted Proteins by Jamu Formulas for Different Efficacies Using Machine Learning Approach. PMID:34440610
Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death. PMID:34440357
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
Quantitative Proteomic Analysis of Plasma after Remote Ischemic Conditioning in a Rhesus Monkey Ischemic Stroke Model. PMID:34439830
Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription. PMID:34439819
Subanesthetic ketamine rapidly alters medial prefrontal miRNAs involved in ubiquitin-mediated proteolysis. PMID:34437591
Gut Microbiome and Metabolome Profiles Associated with High-Fat Diet in Mice. PMID:34436423
Isolation, Phylogenetic and Gephyromycin Metabolites Characterization of New Exopolysaccharides-Bearing Antarctic Actinobacterium from Feces of Emperor Penguin. PMID:34436297
Utilizing a Biology-Driven Approach to Map the Exposome in Health and Disease: An Essential Investment to Drive the Next Generation of Environmental Discovery. PMID:34435882
A Comparative Taxonomic Profile of Microbial Polyethylene and Hydrocarbon-Degrading Communities in Diverse Environments. PMID:34435063
Ferroptosis-Related Genes in Lung Adenocarcinoma: Prognostic Signature and Immune, Drug Resistance, Mutation Analysis. PMID:34434214
Genetic response to nitrogen starvation in the aggressive Eucalyptus foliar pathogen Teratosphaeria destructans. PMID:34432124
Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide. PMID:34430812
Intratumoral injection of caerin 1.1 and 1.9 peptides increases the efficacy of vaccinated TC-1 tumor-bearing mice with PD-1 blockade by modulating macrophage heterogeneity and the activation of CD8+ T cells in the tumor microenvironment. PMID:34429969
Identification of new target proteins of a Urotensin-II receptor antagonist using transcriptome-based drug repositioning approach. PMID:34429474
Transcriptomic analysis of a wild and a cultivated varieties of Capsicum annuum over fruit development and ripening. PMID:34428253
Metagenome-wide association study revealed disease-specific landscape of the gut microbiome of systemic lupus erythematosus in Japanese. PMID:34426398
Circulating MicroRNAs predict glycemic improvement and response to a behavioral intervention. PMID:34425916
Identification of fibronectin 1 (FN1) and complement component 3 (C3) as immune infiltration-related biomarkers for diabetic nephropathy using integrated bioinformatic analysis. PMID:34424825
C-X-C motif chemokine ligand 12: a potential therapeutic target in Duchenne muscular dystrophy. PMID:34424816
KEGG mapping tools for uncovering hidden features in biological data. PMID:34423492
TCF3 Regulates the Proliferation and Apoptosis of Human Spermatogonial Stem Cells by Targeting PODXL. PMID:34422820
Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes. PMID:34422660
CD86 Molecule Might Be a Novel Immune-Related Prognostic Biomarker for Patients With Bladder Cancer by Bioinformatics and Experimental Assays. PMID:34422632
Long Non-coding RNA RP11-395G23.3 Acts as a Competing Endogenous RNA of miR-124-3p to Regulate ROR1 in Anaplastic Thyroid Carcinoma. PMID:34421987
Metabolomic Analysis Provides New Insight Into Tolerance of Huanglongbing in Citrus. PMID:34421957
Dual Transcriptomic Analyses Unveil Host-Pathogen Interactions Between Salmonella enterica Serovar Enteritidis and Laying Ducks (Anas platyrhynchos). PMID:34421865
Identifying causal models between genetically regulated methylation patterns and gene expression in healthy colon tissue. PMID:34419169
Comparison of 16S and whole genome dog microbiomes using machine learning. PMID:34419136
A novel survival model based on a Ferroptosis-related gene signature for predicting overall survival in bladder cancer. PMID:34418989
Pathogen and drought stress affect cell wall and phytohormone signaling to shape host responses in a sorghum COMT bmr12 mutant. PMID:34418969
HIV-1 Tat and cocaine impact astrocytic energy reservoir influence on miRNA epigenetic regulation. PMID:34418497
Metabolic Alterations in Preneoplastic Development Revealed by Untargeted Metabolomic Analysis. PMID:34414180
Resource-diversity relationships in bacterial communities reflect the network structure of microbial metabolism. PMID:34413507
SARS-CoV-2 infection initiates interleukin-17-enriched transcriptional response in different cells from multiple organs. PMID:34413339
The metabolic footprint of Clostridia and Erysipelotrichia reveals their role in depleting sugar alcohols in the cecum. PMID:34412707
Searchlight: automated bulk RNA-seq exploration and visualisation using dynamically generated R scripts. PMID:34412594
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Complete Genome Sequence of Gelria sp. Strain Kuro-4, a Thermophilic Anaerobe Isolated from a Thermophilic Anaerobic Digestion Reactor Treating Poly(L-Lactic Acid). PMID:34410156
Gene expression profile analysis of gallic acid-induced cell death process. PMID:34408198
RNA sequencing reveals niche gene expression effects of beta-hydroxybutyrate in primary myotubes. PMID:34407998
A metabolic daylength measurement system mediates winter photoperiodism in plants. PMID:34407427
Molecular remission at T cell level in patients with rheumatoid arthritis. PMID:34404865
Phylogenomics of a new fungal phylum reveals multiple waves of reductive evolution across Holomycota. PMID:34404788
Identification of PLA2G7 as a novel biomarker of diffuse large B cell lymphoma. PMID:34404374
Bioinformatics analysis of the transcriptional expression of minichromosome maintenance proteins as potential indicators of survival in patients with cervical cancer. PMID:34404366
Pterin-based pigmentation in animals. PMID:34403644
Metabolic profiling of maternal serum of women at high-risk of spontaneous preterm birth using NMR and MGWAS approach. PMID:34402867
XOmiVAE: an interpretable deep learning model for cancer classification using high-dimensional omics data. PMID:34402865
KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism. PMID:34402428
Key sunitinib-related biomarkers for renal cell carcinoma. PMID:34402193
Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis. PMID:34401567
Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics. PMID:34401530
Association study of taste preference: Analysis in the Lithuanian population. PMID:34401081
Bacterial composition and function during fermentation of Mongolia koumiss. PMID:34401066
MiR-508-3p promotes proliferation and inhibits apoptosis of middle ear cholesteatoma cells by targeting PTEN/PI3K/AKT pathway. PMID:34400892
Microarray Analysis of Differential Gene Expression Between Traumatic Temporomandibular Joint Fibrous and Bony Ankylosis in a Sheep Model. PMID:34400603
Identification of novel biomarkers in Hunner's interstitial cystitis using the CIBERSORT, an algorithm based on machine learning. PMID:34399738
The PilB-PilZ-FimX regulatory complex of the Type IV pilus from Xanthomonas citri. PMID:34398935
Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age. PMID:34398307
A systematic comparison of data- and knowledge-driven approaches to disease subtype discovery. PMID:34396389
Bioinformatics Analysis of Potential Biomarkers and Pathway Identification for Major Depressive Disorder. PMID:34394704
m5C-Related Signatures for Predicting Prognosis in Cutaneous Melanoma with Machine Learning. PMID:34394351
Potential genes and pathways associated with heterotopic ossification derived from analyses of gene expression profiles. PMID:34389038
RNA-Seq analysis reveals potential regulators of programmed cell death and leaf remodelling in lace plant (Aponogeton madagascariensis). PMID:34388962
Comprior: facilitating the implementation and automated benchmarking of prior knowledge-based feature selection approaches on gene expression data sets. PMID:34384353
Identification of candidate biomarkers correlated with poor prognosis of breast cancer based on bioinformatics analysis. PMID:34384030
Integration of chronological omics data reveals mitochondrial regulatory mechanisms during the development of hepatocellular carcinoma. PMID:34383828
Amphiregulin promotes hair regeneration of skin-derived precursors via the PI3K and MAPK pathways. PMID:34382262
Arabidopsis Coexpression Tool: a tool for gene coexpression analysis in Arabidopsis thaliana. PMID:34381973
Exploring tissue architecture using spatial transcriptomics. PMID:34381231
Molecular and functional characterization of detrusor PDGFRα positive cells in spinal cord injury-induced detrusor overactivity. PMID:34381120
Differential and shared effects of eicosapentaenoic acid and docosahexaenoic acid on serum metabolome in subjects with chronic inflammation. PMID:34381108
Lactobacillus fermentum PS150 promotes non-rapid eye movement sleep in the first night effect of mice. PMID:34381098
Unique Gut Microbiome in HIV Patients on Antiretroviral Therapy (ART) Suggests Association with Chronic Inflammation. PMID:34378948
Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma. PMID:34376710
The molecular basis, genetic control and pleiotropic effects of local gene co-expression. PMID:34376650
Elucidation of dynamic microRNA regulations in cancer progression using integrative machine learning. PMID:34373890
Comparative transcriptome analysis of the gills and hepatopancreas from Macrobrachium rosenbergii exposed to the heavy metal Cadmium (Cd2+). PMID:34373575
A genome-scale metabolic model of Saccharomyces cerevisiae that integrates expression constraints and reaction thermodynamics. PMID:34373465
FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity. PMID:34373452
Integrative oncogene-dependency mapping identifies RIT1 vulnerabilities and synergies in lung cancer. PMID:34373451
Inhibiting Type VI Secretion System Activity with a Biomimetic Peptide Designed To Target the Baseplate Wedge Complex. PMID:34372705
Defense-Related Gene Expression Following an Orthotospovirus Infection Is Influenced by Host Resistance in Arachis hypogaea. PMID:34372510
Transcriptome and Small RNA Combined Sequencing Analysis of Cold Tolerance in Non-heading Chinese Cabbage. PMID:34367230
A Tissue-Specific Landscape of Alternative Polyadenylation, lncRNAs, TFs, and Gene Co-expression Networks in Liriodendron chinense. PMID:34367224
Cellular costs underpin micronutrient limitation in phytoplankton. PMID:34362734
Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms. PMID:34361929
CYPstrate: A Set of Machine Learning Models for the Accurate Classification of Cytochrome P450 Enzyme Substrates and Non-Substrates. PMID:34361831
Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens. PMID:34361691
Long-Term Fluoxetine Administration Causes Substantial Lipidome Alteration of the Juvenile Macaque Brain. PMID:34360852
SARS-CoV-2 Infected Pediatric Cerebral Cortical Neurons: Transcriptomic Analysis and Potential Role of Toll-like Receptors in Pathogenesis. PMID:34360824
Altered Root Growth, Auxin Metabolism and Distribution in Arabidopsis thaliana Exposed to Salt and Osmotic Stress. PMID:34360759
Transcriptomic and Metabolic Network Analysis of Metabolic Reprogramming and IGF-1 Modulation in SCA3 Transgenic Mice. PMID:34360740
Comparative Proteomic and Metabolomic Analysis of Human Osteoblasts, Differentiated from Dental Pulp Stem Cells, Hinted Crucial Signaling Pathways Promoting Osteogenesis. PMID:34360674
Two-Pore Channels Regulate Expression of Various Receptors and Their Pathway-Related Proteins in Multiple Ways. PMID:34359976
WIP1 Inhibition by GSK2830371 Potentiates HDM201 through Enhanced p53 Phosphorylation and Activation in Liver Adenocarcinoma Cells. PMID:34359777
Functional Analysis of Non-Genetic Resistance to Platinum in Epithelial Ovarian Cancer Reveals a Role for the MBD3-NuRD Complex in Resistance Development. PMID:34359703
Characterization of an Ex Vivo Equine Endometrial Tissue Culture Model Using Next-Generation RNA-Sequencing Technology. PMID:34359123
Efficacy of signal peptide predictors in identifying signal peptides in the experimental secretome of Picrophilous torridus, a thermoacidophilic archaeon. PMID:34358261
The USDA-ARS Ag100Pest Initiative: High-Quality Genome Assemblies for Agricultural Pest Arthropod Research. PMID:34357286
Sorghum's Whole-Plant Transcriptome and Proteome Responses to Drought Stress: A Review. PMID:34357076
mRNA Inventory of Extracellular Vesicles from Ustilago maydis. PMID:34356940
Identification of Potential Kinase Inhibitors within the PI3K/AKT Pathway of Leishmania Species. PMID:34356660
FLAME: A Web Tool for Functional and Literature Enrichment Analysis of Multiple Gene Lists. PMID:34356520
Reelin Alleviates Mesenchymal Stem Cell Senescence and Reduces Pathological α-Synuclein Expression in an In Vitro Model of Parkinson's Disease. PMID:34356083
Expanding the MECP2 network using comparative genomics reveals potential therapeutic targets for Rett syndrome. PMID:34355696
Feeding Systems and Host Breeds Influence Ruminal Fermentation, Methane Production, Microbial Diversity and Metagenomic Gene Abundance. PMID:34354694
Efficacy of Plant Growth-Promoting Bacteria Bacillus cereus YN917 for Biocontrol of Rice Blast. PMID:34354684
Understanding the impact of SNPs associated with autism spectrum disorder on biological pathways in the human fetal and adult cortex. PMID:34354167
An extended reconstruction of human gut microbiota metabolism of dietary compounds. PMID:34354065
Can We Estimate Functionality of Soil Microbial Communities from Structure-Derived Predictions? A Reality Test in Agricultural Soils. PMID:34346741
Comprehensive analysis of the expression and prognosis for TNFAIPs in head and neck cancer. PMID:34344926
Effects of low lead exposure on sperm quality and sperm DNA methylation in adult men. PMID:34344450
Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer. PMID:34344319
Diet-derived transmission of MicroRNAs from host plant into honey bee Midgut. PMID:34344297
Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation. PMID:34342539
Plasma expression of microRNA-425-5p and microRNA-451a as biomarkers of cardiovascular disease in rheumatoid arthritis patients. PMID:34341435
Longitudinal stability of urinary extracellular vesicle protein patterns within and between individuals. PMID:34341426
Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata. PMID:34341423
Genomic insights into the antibiotic resistance pattern of the tetracycline-degrading bacterium, Arthrobacter nicotianae OTC-16. PMID:34341372
The Meloidogyne javanica effector Mj2G02 interferes with jasmonic acid signalling to suppress cell death and promote parasitism in Arabidopsis. PMID:34339585
A Metabolomic Signature of Glucagon Action in Healthy Individuals With Overweight/Obesity. PMID:34337278
Uncovering Potential lncRNAs and mRNAs in the Progression From Acute Myocardial Infarction to Myocardial Fibrosis to Heart Failure. PMID:34336943
Impact of Weaning and Maternal Immune Activation on the Metabolism of Pigs. PMID:34336923
Prognostic Value of a Novel Signature With Nine Hepatitis C Virus-Induced Genes in Hepatic Cancer by Mining GEO and TCGA Databases. PMID:34336819
A Personalized Therapeutics Approach Using an In Silico Drosophila Patient Model Reveals Optimal Chemo- and Targeted Therapy Combinations for Colorectal Cancer. PMID:34336681
The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach. PMID:34335678
Host habitat is the major determinant of the gut microbiome of fish. PMID:34332628
Computational identification of repurposed drugs against viruses causing epidemics and pandemics via drug-target network analysis. PMID:34332351
Physiological and interactomic analysis reveals versatile functions of Arabidopsis 14-3-3 quadruple mutants in response to Fe deficiency. PMID:34330973
A chromosome-level genome assembly of Cairina moschata and comparative genomic analyses. PMID:34330207
Clinical Genetic Risk Variants Inform a Functional Protein Interaction Network for Tetralogy of Fallot. PMID:34328347
Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis. PMID:34327145
Neurotranscriptomic changes associated with chick-directed parental care in adult non-reproductive Japanese quail. PMID:34326416
Morpho-metabotyping the oxidative stress response. PMID:34326354
Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon. PMID:34325657
Transcriptional Profiling During Neural Conversion. PMID:34324187
Anti-Microbiota Vaccines Modulate the Tick Microbiome in a Taxon-Specific Manner. PMID:34322135
Cardiac-specific deletion of voltage dependent anion channel 2 leads to dilated cardiomyopathy by altering calcium homeostasis. PMID:34321484
RCA2: a scalable supervised clustering algorithm that reduces batch effects in scRNA-seq data. PMID:34320202
LncRNA AC007255.1, an immune-related prognostic enhancer RNA in esophageal cancer. PMID:34316393
Identification of ferroptosis genes in immune infiltration and prognosis in thyroid papillary carcinoma using network analysis. PMID:34315405
VarSAn: associating pathways with a set of genomic variants using network analysis. PMID:34313777
Integrative analysis reveals the prognostic value and functions of splicing factors implicated in hepatocellular carcinoma. PMID:34312475
Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. PMID:34312399
Network Pharmacology-Based Mechanistic Investigation of Jinshui Huanxian Formula Acting on Idiopathic Pulmonary Fibrosis. PMID:34306156
The Role of INAPERTURATE POLLEN1 as a Pollen Aperture Factor Is Conserved in the Basal Eudicot Eschscholzia californica (Papaveraceae). PMID:34305989
Genome skimming-based simple sequence repeat (SSR) marker discovery and characterization in Grevillea robusta. PMID:34305342
Local intestinal microbiota response and systemic effects of feeding black soldier fly larvae to replace soybean meal in growing pigs. PMID:34302029
Dynamic regulation of small RNAs in anthocyanin accumulation during blueberry fruit maturation. PMID:34301985
A graph neural network model to estimate cell-wise metabolic flux using single-cell RNA-seq data. PMID:34301623
Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. PMID:34301595
Compatibility of Distinct Label-Free Proteomic Workflows in Absolute Quantification of Proteins Linked to the Oocyte Quality in Human Follicular Fluid. PMID:34299044
An Integrative Study of Aortic mRNA/miRNA Longitudinal Changes in Long-Term LVAD Support. PMID:34299034
Analysis of Immune Associated Co-Expression Networks Reveals Immune-Related Long Non-Coding RNAs during MI in the Presence and Absence of HDC. PMID:34299019
Pectobacterium parmentieri SCC 3193 Mutants with Altered Synthesis of Cell Surface Polysaccharides Are Resistant to N4-Like Lytic Bacteriophage ϕA38 (vB_Ppp_A38) but Express Decreased Virulence in Potato (Solanum tuberosum L.) Plants. PMID:34298965
Effect of the Electromagnetic Field (EMF) Radiation on Transcriptomic Profile of Pig Myometrium during the Peri-Implantation Period-An In Vitro Study. PMID:34298942
SPTAN1 Expression Predicts Treatment and Survival Outcomes in Colorectal Cancer. PMID:34298848
Study on the mechanism of the Modified Ginseng-Schisandra Decoction (MGSD) in the treatment of recurrent respiratory tract infection (RRTI) based on network pharmacology. PMID:34295785
Transcriptome-level assessment of the impact of deformed wing virus on honey bee larvae. PMID:34294840
Transcriptome analysis of flowering regulation by sowing date in Japonica Rice (Oryza sativa L.). PMID:34294838
Dissecting the chromosome-level genome of the Asian Clam (Corbicula fluminea). PMID:34294825
Genomic analysis of field pennycress (Thlaspi arvense) provides insights into mechanisms of adaptation to high elevation. PMID:34294107
Systemic characterization of alternative splicing related to prognosis and immune infiltration in malignant mesothelioma. PMID:34294080
Mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress. PMID:34290351
Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration. PMID:34290335
Identification of Key Genes and Underlying Mechanisms in Acute Kawasaki Disease Based on Bioinformatics Analysis. PMID:34290221
Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far. PMID:34288947
Genome-scale metabolic modeling reveals key features of a minimal gene set. PMID:34288418
D- and l-amino acid concentrations in culture broth of Lactobacillus are highly dependent on the phylogenetic group of Lactobacillus. PMID:34286112
Comparative transcriptomic analysis of two Saccharopolyspora spinosa strains reveals the relationships between primary metabolism and spinosad production. PMID:34285307
Characterization of two closely related citrus cultivars using UPLC-ESI-MS/MS-based widely targeted metabolomics. PMID:34283861
Transcriptome and proteome of the corm, leaf and flower of Hypoxis hemerocallidea (African potato). PMID:34283859
Ear wound healing in MRL/MpJ mice is associated with gut microbiome composition and is transferable to non-healer mice via microbiome transplantation. PMID:34283837
Differential Regulation of Lacto-/Neolacto- Glycosphingolipid Biosynthesis Pathway Reveals Transcription Factors as Potential Candidates in Triple-Negative Breast Cancer. PMID:34283051
Untargeted metabolomics and transcriptomics identified glutathione metabolism disturbance and PCS and TMAO as potential biomarkers for ER stress in lung. PMID:34282162
Functional annotation of noncoding mutations in cancer. PMID:34282050
RNA sequencing indicates age-dependent shifts in the cardiac fibroblast transcriptome between fetal, neonatal, and adult developmental ages. PMID:34281425
Map of dimorphic switching‑related signaling pathways in Sporothrix schenckii based on its transcriptome. PMID:34278493
Transcriptomics and Metabolomics Reveal Purine and Phenylpropanoid Metabolism Response to Drought Stress in Dendrobium sinense, an Endemic Orchid Species in Hainan Island. PMID:34276795
Experimental and Genomic Evaluation of the Oestrogen Degrading Bacterium Rhodococcus equi ATCC13557. PMID:34276604
Prognostic significance and oncogene function of cathepsin A in hepatocellular carcinoma. PMID:34272452
Proteomics and metabonomics analyses of Covid-19 complications in patients with pulmonary fibrosis. PMID:34272434
Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein-protein interaction network. PMID:34272422
KLRD1, FOSL2 and LILRB3 as potential biomarkers for plaques progression in acute myocardial infarction and stable coronary artery disease. PMID:34271875
A novel immune-related gene pair prognostic signature for predicting overall survival in bladder cancer. PMID:34266411
Global analysis of protein lysine 2-hydroxyisobutyrylation (Khib) profiles in Chinese herb rhubarb (Dahuang). PMID:34266380
Data integration uncovers the metabolic bases of phenotypic variation in yeast. PMID:34264947
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data. PMID:34264744
Profiling Basal Forebrain Cholinergic Neurons Reveals a Molecular Basis for Vulnerability Within the Ts65Dn Model of Down Syndrome and Alzheimer's Disease. PMID:34263425
Global Screening of LUBAC and OTULIN Interacting Proteins by Human Proteome Microarray. PMID:34262903
Physiological and transcriptome analyses for assessing the effects of exogenous uniconazole on drought tolerance in hemp (Cannabis sativa L.). PMID:34262091
A system biology approach based on metabolic biomarkers and protein-protein interactions for identifying pathways underlying schizophrenia and bipolar disorder. PMID:34262063
Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia. PMID:34262034
Let-7b-5p in vesicles secreted by human airway cells reduces biofilm formation and increases antibiotic sensitivity of P. aeruginosa. PMID:34260396
Mechanisms of Antiviral Cytotoxic CD4 T Cell Differentiation. PMID:34260270
Computational strategies for the discovery of biological functions of health foods, nutraceuticals and cosmeceuticals: a review. PMID:34258685
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids. PMID:34256691
Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma. PMID:34255396
A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. PMID:34253796
Integrative biology defines novel biomarkers of resistance to strongylid infection in horses. PMID:34253752
The role of CCR2 in prognosis of patients with endometrial cancer and tumor microenvironment remodeling. PMID:34251980
Using Cell Type-Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions. PMID:34249906
Systems Biomedicine of Primary and Metastatic Colorectal Cancer Reveals Potential Therapeutic Targets. PMID:34249670
Comparative analysis of fatty acid metabolism based on transcriptome sequencing of wild and cultivated Ophiocordyceps sinensis. PMID:34249512
Analysis of ceRNA network of differentially expressed genes in FaDu cell line and a cisplatin-resistant line derived from it. PMID:34249502
Overlapping Structures Detection in Protein-Protein Interaction Networks Using Community Detection Algorithm Based on Neighbor Clustering Coefficient. PMID:34249104
A Chromosome-Level Genome Assembly of the Mandarin Fish (Siniperca chuatsi). PMID:34249093
Identification of an EMT-Related Gene Signature for Predicting Overall Survival in Gastric Cancer. PMID:34249086
E183K Mutation in Chalcone Synthase C2 Causes Protein Aggregation and Maize Colorless. PMID:34249050
In vivo Inhibition of the 3-Dehydroquinate Synthase by 7-Deoxysedoheptulose Depends on Promiscuous Uptake by Sugar Transporters in Cyanobacteria. PMID:34248919
Endophytic Bacillus altitudinis Strain Uses Different Novelty Molecular Pathways to Enhance Plant Growth. PMID:34248918
Low Global Diversity of Candidatus Microthrix, a Troublesome Filamentous Organism in Full-Scale WWTPs. PMID:34248915
Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt. PMID:34248891
Surfaceome and Exoproteome Dynamics in Dual-Species Pseudomonas aeruginosa and Staphylococcus aureus Biofilms. PMID:34248881
Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy. PMID:34248876
Interplay of Various Evolutionary Modes in Genome Diversification and Adaptive Evolution of the Family Sulfolobaceae. PMID:34248865
Unravelling the Importance of Diazotrophy in Corals - Combined Assessment of Nitrogen Assimilation, Diazotrophic Community and Natural Stable Isotope Signatures. PMID:34248863
Microbiota Modulates Cardiac Transcriptional Responses to Intermittent Hypoxia and Hypercapnia. PMID:34248668
DNA methylation analysis reveals epimutation hotspots in patients with dilated cardiomyopathy-associated laminopathies. PMID:34246298
Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea. PMID:34246248
MicroRNA-378a-3p is overexpressed in psoriasis and modulates cell cycle arrest in keratinocytes via targeting BMP2 gene. PMID:34244572
Trehalose in pine wood nematode participates in DJ3 formation and confers resistance to low-temperature stress. PMID:34243706
Key Technologies for Progressing Discovery of Microbiome-Based Medicines. PMID:34239510
Integrative analysis of key candidate genes and signaling pathways in acute coronary syndrome related to obstructive sleep apnea by bioinformatics. PMID:34239024
Exosomal hsa_circRNA_104484 and hsa_circRNA_104670 may serve as potential novel biomarkers and therapeutic targets for sepsis. PMID:34238972
Identification of anticancer drug target genes using an outside competitive dynamics model on cancer signaling networks. PMID:34238960
TBX5-AS1, an enhancer RNA, is a potential novel prognostic biomarker for lung adenocarcinoma. PMID:34238250
Identification of viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
Application of Machine Learning for Drug-Target Interaction Prediction. PMID:34234813
Selection of functional EPHB2 genotypes from ENU mutated grass carp treated with GCRV. PMID:34233620
Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis. PMID:34233597
Gut microbiota signature of pathogen-dependent dysbiosis in viral gastroenteritis. PMID:34230563
A circular RNAs dataset landscape reveals potential signatures for the detection and prognosis of early-stage lung adenocarcinoma. PMID:34229638
Transcriptome analysis of five ovarian stages reveals gonad maturation in female Macrobrachium nipponense. PMID:34229608
Transcriptome analysis of chloride intracellular channel knockdown in Drosophila identifies oxidation-reduction function as possible mechanism of altered sensitivity to ethanol sedation. PMID:34228751
Genome-wide association study of stimulant dependence. PMID:34226506
Protocol for HSDFinder: Identifying, annotating, categorizing, and visualizing duplicated genes in eukaryotic genomes. PMID:34223195
Integrated Metagenomic and Transcriptomic Analyses Reveal the Dietary Dependent Recovery of Host Metabolism From Antibiotic Exposure. PMID:34222250
Intestinal Microbiota Mediates High-Fructose and High-Fat Diets to Induce Chronic Intestinal Inflammation. PMID:34222037
Pooled Sequencing Analysis of Geese (Anser cygnoides) Reveals Genomic Variations Associated With Feather Color. PMID:34220935
9-Gene Signature Correlated With CD8+ T Cell Infiltration Activated by IFN-γ: A Biomarker of Immune Checkpoint Therapy Response in Melanoma. PMID:34220795
Bacterial Protein Interaction Networks: Connectivity is Ruled by Gene Conservation, Essentiality and Function. PMID:34220298
Integrated analysis of long non-coding RNAs and mRNAs associated with malignant transformation of gastrointestinal stromal tumors. PMID:34218261
Aberrantly methylated-differentially genes and pathways among Iranian patients with colorectal cancer. PMID:34217303
Genetic determinants of multiple myeloma risk within the Wnt/beta-catenin signaling pathway. PMID:34216957
eVIP2: Expression-based variant impact phenotyping to predict the function of gene variants. PMID:34214079
Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1. PMID:34214075
Introducing the novel Cytoscape app TimeNexus to analyze time-series data using temporal MultiLayer Networks (tMLNs). PMID:34211067
Machine learning compensates fold-change method and highlights oxidative phosphorylation in the brain transcriptome of Alzheimer's disease. PMID:34211065
A pan-cancer transcriptomic study showing tumor specific alterations in central metabolism. PMID:34211032
Ganoderma lucidum promotes sleep through a gut microbiota-dependent and serotonin-involved pathway in mice. PMID:34211003
High expression of DNA damage-inducible transcript 4 (DDIT4) is associated with advanced pathological features in the patients with colorectal cancer. PMID:34211002
Clinical characteristics and genetic spectrum of 26 individuals of Chinese origin with primary ciliary dyskinesia. PMID:34210339
Comparative Transcriptome Analysis Reveals Regulatory Networks during the Maize Ear Shank Elongation Process. PMID:34209973
Proteomic Profiling of Tissue Exosomes Indicates Continuous Release of Malignant Exosomes in Urinary Bladder Cancer Patients, Even with Pathologically Undetectable Tumour. PMID:34209558
Comparison of Transcriptomic Profiles of MiaPaCa-2 Pancreatic Cancer Cells Treated with Different Statins. PMID:34207840
Genome-Wide Transcriptomic Analysis of Non-Tumorigenic Tissues Reveals Aging-Related Prognostic Markers and Drug Targets in Renal Cell Carcinoma. PMID:34207247
Expression Status and Prognostic Value of m6A RNA Methylation Regulators in Lung Adenocarcinoma. PMID:34206803
MicroRNA Expression Changes in Kidney Transplant: Diagnostic Efficacy of miR-150-5p as Potential Rejection Biomarker, Pilot Study. PMID:34206682
Transcriptomic and Metabolic Profiling of High-Temperature Treated Storage Roots Reveals the Mechanism of Saccharification in Sweetpotato (Ipomoea batatas (L.) Lam.). PMID:34206151
Right Ventricle Remodeling Metabolic Signature in Experimental Pulmonary Hypertension Models of Chronic Hypoxia and Monocrotaline Exposure. PMID:34205639
Molecular Human Targets of Bioactive Alkaloid-Type Compounds from Tabernaemontana cymose Jacq. PMID:34205626
Comparative Transcriptome Profiling of Kappaphycus alvarezii (Rhodophyta, Solieriaceae) in Response to Light of Different Wavelengths and Carbon Dioxide Enrichment. PMID:34204578
Impact of Nosema Disease and American Foulbrood on Gut Bacterial Communities of Honeybees Apis mellifera. PMID:34204079
Gene Expression and Isoform Identification of PacBio Full-Length cDNA Sequences for Berberine Biosynthesis in Berberis koreana. PMID:34203474
Analysis of Host Jejunum Transcriptome and Associated Microbial Community Structure Variation in Young Calves with Feed-Induced Acidosis. PMID:34201826
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. PMID:34201152
Extensive Metabolite Profiling in the Unexploited Organs of Black Tiger for Their Potential Valorization in the Pharmaceutical Industry. PMID:34200589
HGF/c-Met Inhibition as Adjuvant Therapy Improves Outcomes in an Orthotopic Mouse Model of Pancreatic Cancer. PMID:34199452
A prognostic nomogram based on competing endogenous RNA network for clear-cell renal cell carcinoma. PMID:34196116
Subtractive proteomics approach to Unravel the druggable proteins of the emerging pathogen Waddlia chondrophila and drug repositioning on its MurB protein. PMID:34195427
Comparative transcriptome analysis of the hyperaccumulator plant Phytolacca americana in response to cadmium stress. PMID:34194911
Draft genome sequence and potential identification of a biosurfactant from Brevibacterium casei strain LS14 an isolate from fresh water Loktak Lake. PMID:34194910
Transcriptome analysis insight into ethylene metabolism and pectinase activity of apricot (Prunus armeniaca L.) development and ripening. PMID:34193901
Identification of potential microRNAs and KEGG pathways in denervation muscle atrophy based on meta-analysis. PMID:34193880
Gene-rich UV sex chromosomes harbor conserved regulators of sexual development. PMID:34193417
Down-regulation of BCL2L13 renders poor prognosis in clear cell and papillary renal cell carcinoma. PMID:34193180
Upregulated CD58 is associated with clinicopathological characteristics and poor prognosis of patients with pancreatic ductal adenocarcinoma. PMID:34193136
The subtype-specific molecular function of SPDEF in breast cancer and insights into prognostic significance. PMID:34191390
In-Frame and Frameshift Mutations in Zebrafish Presenilin 2 Affect Different Cellular Functions in Young Adult Brains. PMID:34189411
16S rRNA gene sequencing data of the human skin microbiome before and after swimming in the ocean. PMID:34189199
The maintenance of microbial community in human fecal samples by a cost effective preservation buffer. PMID:34188136
Comprehensive high-throughput meta-analysis of differentially expressed microRNAs in transcriptomic datasets reveals significant disruption of MAPK/JNK signal transduction pathway in Adult T-cell leukemia/lymphoma. PMID:34187521
Reconstruction of the full-length transcriptome of cigar tobacco without a reference genome and characterization of anion channel/transporter transcripts. PMID:34187357
StrongestPath: a Cytoscape application for protein-protein interaction analysis. PMID:34187355
A diagnostic miRNA signature for pulmonary arterial hypertension using a consensus machine learning approach. PMID:34186489
Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide-rich springs. PMID:34185679
Drug-Drug Interaction Predictions via Knowledge Graph and Text Embedding: Instrument Validation Study. PMID:34185011
Insights into the phylogeny and transcriptional response of serine proteases in a halotolerant cyanobacterium Halothece sp. PCC7418. PMID:34184613
The glycosyltransferase ST3GAL2 is regulated by miR-615-3p in the intestinal tract of Campylobacter jejuni infected mice. PMID:34183045
Gene expression analysis in EBV-infected ataxia-telangiectasia cell lines by RNA-sequencing reveals protein synthesis defect and immune abnormalities. PMID:34183044
Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae). PMID:34182921
Ethnicity-specific alterations of plasma and hepatic lipidomic profiles are related to high NAFLD rate and severity in Hispanic Americans, a pilot study. PMID:34182070
Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola. PMID:34181797
Analysis of Nuclear Encoded Mitochondrial Gene Networks in Cervical Cancer. PMID:34181336
Potential therapeutic target genes for systemic lupus erythematosus: a bioinformatics analysis. PMID:34180358
Identification of Suitable Meloidogyne spp. Housekeeping Genes. PMID:34179799
Competing Endogenous RNA in Colorectal Cancer: An Analysis for Colon, Rectum, and Rectosigmoid Junction. PMID:34178670
Cellular Metabolomics Profiles Associated With Drug Chemosensitivity in AML. PMID:34178663
Assembling Disease Networks From Causal Interaction Resources. PMID:34178043
A Combined Morphological and Molecular Evolutionary Analysis of Karst-Environment Adaptation for the Genus Urophysa (Ranunculaceae). PMID:34177982
Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving. PMID:34177613
Bioinformatics analysis of differentially expressed genes and pathways in the development of cervical cancer. PMID:34174849
MCT4 is induced by metastasis-enhancing pathogenic mitochondrial NADH dehydrogenase gene mutations and can be a therapeutic target. PMID:34172808
Lung adenocarcinoma and lung squamous cell carcinoma cancer classification, biomarker identification, and gene expression analysis using overlapping feature selection methods. PMID:34172784
Genome-wide association analyses identify genotype-by-environment interactions of growth traits in Simmental cattle. PMID:34172761
Attenuation of clinical and immunological outcomes during SARS-CoV-2 infection by ivermectin. PMID:34170074
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity. PMID:34169837
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome. PMID:34168315
A mouse model of prenatal exposure to Interleukin-6 to study the developmental origin of health and disease. PMID:34168254
Low-density lipoprotein receptor-related protein 1 (LRP1) is a novel receptor for apolipoprotein A4 (APOA4) in adipose tissue. PMID:34168225
Transmitting silks of maize have a complex and dynamic microbiome. PMID:34168223
Sodium lignosulfonate improves shoot growth of Oryza sativa via enhancement of photosynthetic activity and reduced accumulation of reactive oxygen species. PMID:34168171
A comprehensive database for integrated analysis of omics data in autoimmune diseases. PMID:34167460
Identification of hub genes in thyroid carcinoma to predict prognosis by integrated bioinformatics analysis. PMID:34167437
The mechanisms of celastrol in treating papillary thyroid carcinoma based on network pharmacology and experiment verification. PMID:34164500
Identification and Validation of a Novel Prognosis Prediction Model in Adrenocortical Carcinoma by Integrative Bioinformatics Analysis, Statistics, and Machine Learning. PMID:34164395
Anticancer gold(iii)-bisphosphine complex alters the mitochondrial electron transport chain to induce in vivo tumor inhibition. PMID:34163837
Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease. PMID:34162989
Long-chain saturated fatty acids in breast milk are associated with the pathogenesis of atopic dermatitis via induction of inflammatory ILC3s. PMID:34162906
Differences in molecular phenotype in mouse and human hypertrophic cardiomyopathy. PMID:34162896
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Genome-wide association study of signature genetic alterations among pseudomonas aeruginosa cystic fibrosis isolates. PMID:34161396
Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment. PMID:34161254
Sea-Ice Bacteria Halomonas sp. Strain 363 and Paracoccus sp. Strain 392 Produce Multiple Types of Poly-3-Hydroxyalkaonoic Acid (PHA) Storage Polymers at Low Temperature. PMID:34160268
Long-term disease control and survival observed after stereotactic ablative body radiotherapy for oligometastatic breast cancer. PMID:34159748
Evolving scenario of big data and Artificial Intelligence (AI) in drug discovery. PMID:34159484
Genome-wide expression and network analyses of mutants in key brassinosteroid signaling genes. PMID:34157989
Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis. PMID:34155325
Disentangling transcriptional responses in plant defense against arthropod herbivores. PMID:34155286
The risk of pancreatic adenocarcinoma following SARS-CoV family infection. PMID:34155232
Niche adaptation promoted the evolutionary diversification of tiny ocean predators. PMID:34155140
Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches. PMID:34154659
Network-based systems pharmacology reveals heterogeneity in LCK and BCL2 signaling and therapeutic sensitivity of T-cell acute lymphoblastic leukemia. PMID:34151288
An integrative analysis of genome-wide 5-hydroxymethylcytosines in circulating cell-free DNA detects noninvasive diagnostic markers for gliomas. PMID:34151267
Analysis of differentially expressed genes responsible for the suppressive effect of anisomycin on cell proliferation of DLD-1 cells. PMID:34151031
Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli. PMID:34150501
An SNP Mutation of Gene RsPP Converts Petal Color From Purple to White in Radish (Raphanus sativus L.). PMID:34149748
Analysis of Two SusE-Like Enzymes From Bacteroides thetaiotaomicron Reveals a Potential Degradative Capacity for This Protein Family. PMID:34149636
A Chromosome-Level Genome Assembly of the Spotted Scat (Scatophagus argus). PMID:34146395
Comprehensive transcriptome and metabolome profiling reveal metabolic mechanisms of Nitraria sibirica Pall. to salt stress. PMID:34145354
A chromosome-level genome assembly of rugged rose (Rosa rugosa) provides insights into its evolution, ecology, and floral characteristics. PMID:34145222
A Novel Metric to Quantify the Effect of Pathway Enrichment Evaluation With Respect to Biomedical Text-Mined Terms: Development and Feasibility Study. PMID:34142969
Low CLOCK and CRY2 in 2nd trimester human maternal blood and risk of preterm birth: a nested case-control study†. PMID:34142702
Molecular docking-aided identification of small molecule inhibitors targeting β-catenin-TCF4 interaction. PMID:34142050
Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities. PMID:34142036
Prickle morphogenesis in rose is coupled with secondary metabolite accumulation and governed by canonical MBW transcriptional complex. PMID:34142001
Photoperiodically driven transcriptome-wide changes in the hypothalamus reveal transcriptional differences between physiologically contrasting seasonal life-history states in migratory songbirds. PMID:34140553
MolDiscovery: learning mass spectrometry fragmentation of small molecules. PMID:34140479
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Identification of Genes Related to Immune Infiltration in the Tumor Microenvironment of Cutaneous Melanoma. PMID:34136377
Herbaspirillum seropedicae strain HRC54 expression profile in response to sugarcane apoplastic fluid. PMID:34136329
Combination of network and molecule structure accurately predicts competitive inhibitory interactions. PMID:34136091
Comparative Analysis of MicroRNA Expression Profiles Between Skeletal Muscle- and Adipose-Derived Exosomes in Pig. PMID:34135937
Host-Parasite Interaction of Atlantic salmon (Salmo salar) and the Ectoparasite Neoparamoeba perurans in Amoebic Gill Disease. PMID:34135900
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. PMID:34135895
The nearly complete genome of Ginkgo biloba illuminates gymnosperm evolution. PMID:34135482
Triple RNA-Seq characterizes aphid gene expression in response to infection with unequally virulent strains of the endosymbiont Hamiltonella defensa. PMID:34134631
Transcriptomics of type 2 diabetic and healthy human neutrophils. PMID:34134627
SARS-CoV-2 mutations altering regulatory properties: Deciphering host's and virus's perspectives. PMID:34131596
Potential prognostic markers and significant lncRNA-mRNA co-expression pairs in laryngeal squamous cell carcinoma. PMID:34131588
Deficiency of myostatin protects skeletal muscle cells from ischemia reperfusion injury. PMID:34131275
Lipidomic profiling of the developing kernel clarifies the lipid metabolism of Paeonia ostii. PMID:34131230
Inferring transcriptomic cell states and transitions only from time series transcriptome data. PMID:34131182
Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner. PMID:34130712
Cytokinins initiate secondary growth in the Arabidopsis root through a set of LBD genes. PMID:34129827
Doxycycline host-directed therapy in human pulmonary tuberculosis. PMID:34128838
Unique phage-bacterium interplay in sponge holobionts from the southern Okinawa Trough hydrothermal vent. PMID:34128329
Interaction Between the Intestinal Microbial Community and Transcriptome Profile in Common Carp (Cyprinus carpio L.). PMID:34127924
Genome-wide CRISPR screen identifies protein pathways modulating tau protein levels in neurons. PMID:34127790
Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML. PMID:34127725
Population-scale peach genome analyses unravel selection patterns and biochemical basis underlying fruit flavor. PMID:34127667
Utilizing single-cell RNA sequencing for analyzing the characteristics of PBMC in patients with Kawasaki disease. PMID:34126969
Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany. PMID:34125309
Gene Instability-Related lncRNA Prognostic Model of Melanoma Patients via Machine Learning Strategy. PMID:34122546
Based on Plasma Metabonomics and Network Pharmacology Exploring the Therapeutic Mechanism of Gynura procumbens on Type 2 Diabetes. PMID:34122100
Network Pharmacology-Based Validation of the Efficacy of Huiyangjiuji Decoction in the Treatment of Experimental Colitis. PMID:34122086
De novo genome assembly of a foxtail millet cultivar Huagu11 uncovered the genetic difference to the cultivar Yugu1, and the genetic mechanism of imazethapyr tolerance. PMID:34118890
β-elemene alleviates airway stenosis via the ILK/Akt pathway modulated by MIR143HG sponging miR-1275. PMID:34118875
Circulating microRNA profile in humans and mice with congenital GH deficiency. PMID:34118183
Revealing the Modular Similarities and Differences Among Alzheimer's Disease, Vascular Dementia, and Parkinson's Disease in Genomic Networks. PMID:34117614
Melatonin influences the early growth stage in Zoysia japonica Steud. by regulating plant oxidation and genes of hormones. PMID:34117332
Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses. PMID:34117322
Multiple functions of reversine on the biological characteristics of sheep fibroblasts. PMID:34117304
Drug target gene-based analyses of drug repositionability in rare and intractable diseases. PMID:34117295
Investigation of monogenic causes of familial breast cancer: data from the BEACCON case-control study. PMID:34117267
Genomic adaptations enabling Acidithiobacillus distribution across wide-ranging hot spring temperatures and pHs. PMID:34116726
Age related gene DST represents an independent prognostic factor for MYCN non-amplified neuroblastoma. PMID:34116676
CCDC114, DNAI2 and TOP2A involves in the effects of tibolone treatment on postmenopausal endometrium. PMID:34116668
Genome analysis to decipher syntrophy in the bacterial consortium 'SCP' for azo dye degradation. PMID:34116639
Transcriptome analysis of Cinnamomum migao seed germination in medicinal plants of Southwest China. PMID:34116632
netgsa: Fast computation and interactive visualization for topology-based pathway enrichment analysis. PMID:34115744
Measuring pathway database coverage of the phosphoproteome. PMID:34113485
Transcriptome Profile Analysis of Arabidopsis Reveals the Drought Stress-Induced Long Non-coding RNAs Associated With Photosynthesis, Chlorophyll Synthesis, Fatty Acid Synthesis and Degradation. PMID:34113361
Host specific endophytic microbiome diversity and associated functions in three varieties of scented black rice are dependent on growth stage. PMID:34112830
Integrated proteomic and transcriptomic profiling identifies aberrant gene and protein expression in the sarcomere, mitochondrial complex I, and the extracellular matrix in Warmblood horses with myofibrillar myopathy. PMID:34112090
A meta-analysis of transcriptomic profiles of Huntington's disease patients. PMID:34111223
A novel role of ADGRF1 (GPR110) in promoting cellular quiescence and chemoresistance in human epidermal growth factor receptor 2-positive breast cancer. PMID:34110646
Functional prediction of environmental variables using metabolic networks. PMID:34108539
Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema. PMID:34108536
Central nervous system (CNS) transcriptomic correlates of human immunodeficiency virus (HIV) brain RNA load in HIV-infected individuals. PMID:34108514
Overexpression of DDIT4 and TPTEP1 are associated with metastasis and advanced stages in colorectal cancer patients: a study utilizing bioinformatics prediction and experimental validation. PMID:34107956
SARS-CoV-2 infection activates a subset of intrinsic pathways to inhibit type I interferons in vitro and in vivo. PMID:34104087
A defective interleukin-17 receptor A1 causes weight loss and intestinal metabolism-related gene downregulation in Japanese medaka, Oryzias latipes. PMID:34103614
Tumor metabolism and associated serum metabolites define prognostic subtypes of Asian hepatocellular carcinoma. PMID:34103600
Integrating longitudinal clinical laboratory tests with targeted proteomic and transcriptomic analyses reveal the landscape of host responses in COVID-19. PMID:34103487
Effects of FUdR on gene expression in the C. elegans bacterial diet OP50. PMID:34103088
Molecular omics resources should require sex annotation: a call for action. PMID:34099934
Identifying molecular pathways and candidate genes associated with knob traits by transcriptome analysis in the goose (Anser cygnoides). PMID:34099774
Predicting anticancer hyperfoods with graph convolutional networks. PMID:34099048
Characterization of terminal-ileal and colonic Crohn's disease in treatment-naïve paediatric patients based on transcriptomic profile using logistic regression. PMID:34098982
Integrated proteomics and metabolomics analysis of transgenic and gene-stacked maize line seeds. PMID:34097556
Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes. PMID:34095109
Cancer cell-selective modulation of mitochondrial respiration and metabolism by potent organogold(iii) dithiocarbamates. PMID:34094305
PredTAD: A machine learning framework that models 3D chromatin organization alterations leading to oncogene dysregulation in breast cancer cell lines. PMID:34093998
Galectin-9 and PSMB8 overexpression predict unfavorable prognosis in patients with AML. PMID:34093826
Comprehensive evaluation of microRNA-10b in digestive system cancers reveals prognostic implication and signaling pathways associated with tumor progression. PMID:34093806
Comparing Statistical Tests for Differential Network Analysis of Gene Modules. PMID:34093641
Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People. PMID:34093637
Azohydromonas caseinilytica sp. nov., a Nitrogen-Fixing Bacterium Isolated From Forest Soil by Using Optimized Culture Method. PMID:34093463
Cold-shock gene cspC in the genome of Massilia polaris sp. nov. revealed cold-adaptation. PMID:34091798
Construction of a prognostic model with histone modification-related genes and identification of potential drugs in pancreatic cancer. PMID:34090418
Exposure to hypoxia causes stress erythropoiesis and downregulates immune response genes in spleen of mice. PMID:34090336
TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes. PMID:34090334
First dynamics of bacterial community during development of Acropora humilis larvae in aquaculture. PMID:34083731
High-resolution metabolomic biomarkers for lung cancer diagnosis and prognosis. PMID:34083687
Superior production of heavy pamamycin derivatives using a bkdR deletion mutant of Streptomyces albus J1074/R2. PMID:34082758
Post-diapause transcriptomic restarts: insight from a high-latitude copepod. PMID:34082716
Construction of a novel mRNA-miRNA-lncRNA network and identification of potential regulatory axis associated with prognosis in colorectal cancer liver metastases. PMID:34081622
Eleven genomic loci affect plasma levels of chronic inflammation marker soluble urokinase-type plasminogen activator receptor. PMID:34079037
Rootstock effects on scion gene expression in maritime pine. PMID:34078936
Complete genome sequence of Arthrobacter sp. PAMC25564 and its comparative genome analysis for elucidating the role of CAZymes in cold adaptation. PMID:34078272
Integrative Analysis of Colonic Biopsies from Inflammatory Bowel Disease Patients Identifies an Interaction Between Microbial Bile Acid-inducible Gene Abundance and Human Angiopoietin-like 4 Gene Expression. PMID:34077506
Identification of biomarkers, pathways and potential therapeutic target for docetaxel resistant prostate cancer. PMID:34077304
noisyR: enhancing biological signal in sequencing datasets by characterizing random technical noise. PMID:34076236
Chromosome-level genome assembly of the Chinese longsnout catfish Leiocassis longirostris. PMID:34075735
Comparative analysis of tuberous root metabolites between cultivated and wild varieties of Rehmannia glutinosa by widely targeted metabolomics. PMID:34075137
Comparative analyses of transcriptional responses of Dectes texanus LeConte (Coleoptera: Cerambycidae) larvae fed on three different host plants and artificial diet. PMID:34075134
Comparative transcriptome analysis reveals key genes associated with pigmentation in radish (Raphanus sativus L.) skin and flesh. PMID:34075070
A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma. PMID:34075060
The C0-C1f Region of Cardiac Myosin Binding Protein-C Induces Pro-Inflammatory Responses in Fibroblasts via TLR4 Signaling. PMID:34073556
Genetic Predisposition to the Mortality in Septic Shock Patients: From GWAS to the Identification of a Regulatory Variant Modulating the Activity of a CISH Enhancer. PMID:34072601
Electroretinography and Gene Expression Measures Implicate Phototransduction and Metabolic Shifts in Chick Myopia and Hyperopia Models. PMID:34072440
Global Transcriptional Response of Aspergillus niger to Blocked Active Citrate Export through Deletion of the Exporter Gene. PMID:34071072
Propionate Fermentative Genes of the Gut Microbiome Decrease in Inflammatory Bowel Disease. PMID:34070019
Taxonomic and Gene Category Analyses of Subgingival Plaques from a Group of Japanese Individuals with and without Periodontitis. PMID:34069916
Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle. PMID:34068162
Lupeol Accumulation Correlates with Auxin in the Epidermis of Castor. PMID:34067825
Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. PMID:34067383
Identification of Critical Genes and Signaling Pathways in Human Monocytes Following High-Intensity Exercise. PMID:34067297
Integrating Transcriptome and Coexpression Network Analyses to Characterize Salicylic Acid- and Jasmonic Acid-Related Genes in Tolerant Poplars Infected with Rust. PMID:34066822
Western Diet Induced Remodelling of the Tongue Proteome. PMID:34066295
Epigenetic Alterations of Maternal Tobacco Smoking during Pregnancy: A Narrative Review. PMID:34064931
Small-RNA Sequencing Reveals Altered Skeletal Muscle microRNAs and snoRNAs Signatures in Weanling Male Offspring from Mouse Dams Fed a Low Protein Diet during Lactation. PMID:34064819
Prophage Genomics and Ecology in the Family Rhodobacteraceae. PMID:34064105
Nucleoporin TPR Affects C2C12 Myogenic Differentiation via Regulation of Myh4 Expression. PMID:34063931
Genome-Wide Analysis of Sex Disparities in the Genetic Architecture of Lung and Colorectal Cancers. PMID:34062886
Expanded transcriptomic view of strawberry fruit ripening through meta-analysis. PMID:34061906
Molecular characteristics and tumorigenicity of ascites-derived tumor cells: mitochondrial oxidative phosphorylation as a novel therapy target in ovarian cancer. PMID:34060699
Proteomics analysis reveals the effect of 1α,25(OH)2VD3-glycosides on development of early testes in piglets. PMID:34059707
The chromosome-level Stevia genome provides insights into steviol glycoside biosynthesis. PMID:34059662
Gaining Insights Into Metabolic Networks Using Chemometrics and Bioinformatics: Chronic Kidney Disease as a Clinical Model. PMID:34055893
Lipidomic and Transcriptomic Analysis of the Longissimus Muscle of Luchuan and Duroc Pigs. PMID:34055857
MicroRNA panel in serum reveals novel diagnostic biomarkers for prostate cancer. PMID:34055487
Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy. PMID:34054852
Identifying Subgroups of Patients With Autism by Gene Expression Profiles Using Machine Learning Algorithms. PMID:34054599
Multi-Dimensional Transcriptome Analysis Reveals Modulation of Cholesterol Metabolism as Highly Integrated Response to Brain Injury. PMID:34054419
A 3D Fiber-Hydrogel Based Non-Viral Gene Delivery Platform Reveals that microRNAs Promote Axon Regeneration and Enhance Functional Recovery Following Spinal Cord Injury. PMID:34050637
Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma. PMID:34050187
CRISPR/Cas9 mediated deletion of the adenosine A2A receptor enhances CAR T cell efficacy. PMID:34050151
In Situ Localization of Plant Lipid Metabolites by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI-MSI). PMID:34047991
Exome sequencing of early-onset patients supports genetic heterogeneity in colorectal cancer. PMID:34045552
Glycoproteomic analysis of the changes in protein N-glycosylation during neuronal differentiation in human-induced pluripotent stem cells and derived neuronal cells. PMID:34045517
Transcriptomic insights into the effects of CytCo, a novel nematotoxic protein, on the pine wood nematode Bursaphelenchus xylophilus. PMID:34044778
Using Interpretable Deep Learning to Model Cancer Dependencies. PMID:34042953
Transcriptional signatures of human peripheral blood mononuclear cells can identify the risk of tuberculosis progression from latent infection among individuals with silicosis. PMID:34042560
An Immunometabolic Shift Modulates Cytotoxic Lymphocyte Activation During Melanoma Progression in TRPA1 Channel Null Mice. PMID:34041030
Loss of 15-lipoxygenase disrupts Treg differentiation altering their pro-resolving functions. PMID:34040168
Comprehensive profiling analysis of the N6-methyladenosine-modified circular RNA transcriptome in cultured cells infected with Marek's disease virus. PMID:34040106
In Arabidopsis thaliana Cd differentially impacts on hormone genetic pathways in the methylation defective ddc mutant compared to wild type. PMID:34040101
The carbon source-dependent pattern of antimicrobial activity and gene expression in Pseudomonas donghuensis P482. PMID:34040089
Common pathways and functional profiles reveal underlying patterns in Breast, Kidney and Lung cancers. PMID:34039407
Identification of significant genes as prognostic markers and potential tumor suppressors in lung adenocarcinoma via bioinformatical analysis. PMID:34039311
Evaluation of clinical value and potential mechanism of MTFR2 in lung adenocarcinoma via bioinformatics. PMID:34039308
A spatial vascular transcriptomic, proteomic, and phosphoproteomic atlas unveils an angiocrine Tie-Wnt signaling axis in the liver. PMID:34038707
Aviator: a web service for monitoring the availability of web services. PMID:34038559
Transcriptome analysis unveils survival strategies of Streptococcus parauberis against fish serum. PMID:34038483
CPA: a web-based platform for consensus pathway analysis and interactive visualization. PMID:34037798
Broad Concordance in the Spatial Distribution of Adaptive and Neutral Genetic Variation across an Elevational Gradient in Deer Mice. PMID:34037784
The Potential Genes Mediate the Pathogenicity of Allogeneic CD4+T Cell in aGVHD Mouse Model. PMID:34036106
Differential gene expression profile by RNA sequencing study of elderly osteoporotic hip fracture patients with sarcopenia. PMID:34036042
Integrated RNA and miRNA sequencing analysis reveals a complex regulatory network of Magnolia sieboldii seed germination. PMID:34035372
PhenCards: a data resource linking human phenotype information to biomedical knowledge. PMID:34034817
Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice. PMID:34034704
Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius. PMID:34031502
Health monitoring in birds using bio-loggers and whole blood transcriptomics. PMID:34031452
Transcriptomic and metabolomic characterization of post-hatch metabolic reprogramming during hepatic development in the chicken. PMID:34030631
driveR: a novel method for prioritizing cancer driver genes using somatic genomics data. PMID:34030627
Identification of a Hypoxia-Related Signature for Predicting Prognosis and the Immune Microenvironment in Bladder Cancer. PMID:34026819
Analysis of decomposition in 23 seafood products by liquid chromatography with high-resolution mass spectrometry with sensory-driven modeling. PMID:34026079
Genome sequence and transcriptome profiles of pathogenic fungus Paecilomyces penicillatus reveal its interactions with edible fungus Morchella importuna. PMID:34025947
IDO1 Expression in Ovarian Cancer Induces PD-1 in T Cells via Aryl Hydrocarbon Receptor Activation. PMID:34025677
Meanders as a scaling motif for understanding of floodplain soil microbiome and biogeochemical potential at the watershed scale. PMID:34022966
Up-regulated RFC2 predicts unfavorable progression in hepatocellular carcinoma. PMID:34022962
A comparative analysis of the intrauterine transcriptome in fertile and subfertile mares using cytobrush sampling. PMID:34022808
Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori. PMID:34022797
Deep ocean metagenomes provide insight into the metabolic architecture of bathypelagic microbial communities. PMID:34021239
Common DNA methylation dynamics in endometriod adenocarcinoma and glioblastoma suggest universal epigenomic alterations in tumorigenesis. PMID:34021236
Multiscale-omic assessment of EWSR1-NFATc2 fusion positive sarcomas identifies the mTOR pathway as a potential therapeutic target. PMID:34021224
Meta-omics Reveal Gallionellaceae and Rhodanobacter Species as Interdependent Key Players for Fe(II) Oxidation and Nitrate Reduction in the Autotrophic Enrichment Culture KS. PMID:34020935
The gutSMASH web server: automated identification of primary metabolic gene clusters from the gut microbiota. PMID:34019648
Rcl1 depletion impairs 18S pre-rRNA processing at the A1-site and up-regulates a cohort of ribosome biogenesis genes in zebrafish. PMID:34019640
Ultra-high Magnification Endocytoscopy and Molecular Markers for Defining Endoscopic and Histologic Remission in Ulcerative Colitis-An Exploratory Study to Define Deep Remission. PMID:34019073
Upregulated functional gene expression programmes in tumour pericytes mark progression in patients with low-grade glioma. PMID:34018679
Identification of potential diagnostic and prognostic biomarkers for LUAD based on TCGA and GEO databases. PMID:34017995
Evaluation of Quantitative Structure Property Relationship Algorithms for Predicting Plasma Protein Binding in Humans. PMID:34017929
The Zinc Nutritional Immunity of Epinephelus coioides Contributes to the Importance of znuC During Pseudomonas plecoglossicida Infection. PMID:34017347
Genome-Wide Transcriptional Responses of Marine Nematode Litoditis marina to Hyposaline and Hypersaline Stresses. PMID:34017268
Whole transcriptome RNA-seq reveals key regulatory factors involved in type 2 diabetes pathology in peripheral fat of Asian Indians. PMID:34017037
Examination of gender differences in patients with takotsubo syndrome according to left ventricular biopsy: two case reports. PMID:34016184
Platelets orchestrate the resolution of pulmonary inflammation in mice by T reg cell repositioning and macrophage education. PMID:34014253
Targeted 16S rRNA gene and ITS2 amplicon sequencing of leaf and spike tissues of Piper longum identifies new candidates for bioprospecting of bioactive compounds. PMID:34013420
The protective effect and mechanism of epidermal growth factor on necrotizing enterocolitis in a neonatal rat model. PMID:34012839
Genome variation in colorectal cancer patient with liver metastasis measured by whole-exome sequencing. PMID:34012644
Midgut bacterial diversity of a leaf-mining beetle, Dactylispa xanthospila (Gestro) (Coleoptera: Chrysomelidae: Cassidinae). PMID:34012315
PIF4 negatively modulates cold tolerance in tomato anthers via temperature-dependent regulation of tapetal cell death. PMID:34009394
DNA Methylation in Babies Born to Nonsmoking Mothers Exposed to Secondhand Smoke during Pregnancy: An Epigenome-Wide Association Study. PMID:34009014
Sex-specific nicotine sensitization and imprinting of self-administration in rats inform GWAS findings on human addiction phenotypes. PMID:34007041
A general non-self response as part of plant immunity. PMID:34007033
Next-generation sequencing revealed recurrent ZFPM1 mutations in encapsulated papillary carcinoma of the breast. PMID:34007008
Revealing the developmental dynamics in male strobilus transcriptome of Gnetum luofuense using nanopore sequencing technology. PMID:34006996
De novo transcriptome assembly and comparative transcriptomic analysis provide molecular insights into low temperature stress response of Canarium album. PMID:34006894
De novo genome assembly and analysis unveil biosynthetic and metabolic potentials of Pseudomonas fragi A13BB. PMID:34006216
Analyzing host-viral interactome of SARS-CoV-2 for identifying vulnerable host proteins during COVID-19 pathogenesis. PMID:34004362
An overview of graph databases and their applications in the biomedical domain. PMID:34003247
Alternative splicing acts as an independent prognosticator in ovarian carcinoma. PMID:34001978
Identification of targets of JS-K against HBV-positive human hepatocellular carcinoma HepG2.2.15 cells with iTRAQ proteomics. PMID:34001947
RcTGA1 and glucosinolate biosynthesis pathway involvement in the defence of rose against the necrotrophic fungus Botrytis cinerea. PMID:34001006
Impairment of the ER/mitochondria compartment in human cardiomyocytes with PLN p.Arg14del mutation. PMID:33998164
Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data. PMID:33996828
Transcriptome Analyses Reveal IL6/Stat3 Signaling Involvement in Radial Glia Proliferation After Stab Wound Injury in the Adult Zebrafish Optic Tectum. PMID:33996824
Genomic and Transcriptomic Investigation of the Physiological Response of the Methylotroph Bacillus methanolicus to 5-Aminovalerate. PMID:33995329
Metagenomic Insights Into Functional and Taxonomic Compositions of an Activated Sludge Microbial Community Treating Leachate of a Completed Landfill: A Pathway-Based Analysis. PMID:33995301
Network Pharmacology-Based Strategy for Elucidating the Molecular Basis Forthe Pharmacologic Effects of Licorice (Glycyrrhiza spp.). PMID:33995004
β-Arrestin2 Inhibits the Apoptosis and Facilitates the Proliferation of Fibroblast-like Synoviocytes in Diffuse-type Tenosynovial Giant Cell Tumor. PMID:33994368
Structure-based drug repurposing against COVID-19 and emerging infectious diseases: methods, resources and discoveries. PMID:33993214
Long non-coding RNAs and their targets as potential biomarkers in breast cancer. PMID:33991433
Transcriptome analysis of ovary tissues from low- and high-yielding Changshun green-shell laying hens. PMID:33990173
Transcriptomic Analysis of Skin Color in Anole Lizards. PMID:33988681
An Ensemble Learning-Based Method for Inferring Drug-Target Interactions Combining Protein Sequences and Drug Fingerprints. PMID:33987446
Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PMID:33987018
Transcriptome profiling of Capsicum annuum using Illumina- and PacBio SMRT-based RNA-Seq for in-depth understanding of genes involved in trichome formation. PMID:33986344
Thymic transcriptome analysis after Newcastle disease virus inoculation in chickens and the influence of host small RNAs on NDV replication. PMID:33986327
Metabolic classification of bladder cancer based on multi-omics integrated analysis to predict patient prognosis and treatment response. PMID:33985530
Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing. PMID:33985436
Deconvolution of sarcoma methylomes reveals varying degrees of immune cell infiltrates with association to genomic aberrations. PMID:33980253
A comprehensive RNA-Seq-based gene expression atlas of the summer squash (Cucurbita pepo) provides insights into fruit morphology and ripening mechanisms. PMID:33980145
Prediction and analysis of novel key genes ITGAX, LAPTM5, SERPINE1 in clear cell renal cell carcinoma through bioinformatics analysis. PMID:33976979
Overcoming false-positive gene-category enrichment in the analysis of spatially resolved transcriptomic brain atlas data. PMID:33976144
Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities. PMID:33975974
Rapid Response of Nitrogen Cycling Gene Transcription to Labile Carbon Amendments in a Soil Microbial Community. PMID:33975966
Human and preclinical studies of the host-gut microbiome co-metabolite hippurate as a marker and mediator of metabolic health. PMID:33975870
The genome of Nautilus pompilius illuminates eye evolution and biomineralization. PMID:33972735
Pests, diseases, and aridity have shaped the genome of Corymbia citriodora. PMID:33972666
Development of genic SSR marker resources from RNA-seq data in Camellia japonica and their application in the genus Camellia. PMID:33972624
The transcriptional landscape analysis of basal cell carcinomas reveals novel signalling pathways and actionable targets. PMID:33972406
Discovery and validation of novel protein markers in mucosa of portal hypertensive gastropathy. PMID:33971821
Transcriptomic analysis reveals pronounced changes in gene expression due to sub-lethal pyrethroid exposure and ageing in insecticide resistance Anopheles coluzzii. PMID:33971808
Integrative-omics for discovery of network-level disease biomarkers: a case study in Alzheimer's disease. PMID:33971669
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
A model of dopamine and serotonin-kynurenine metabolism in cortisolemia: Implications for depression. PMID:33970902
Genome-Wide Changes of Regulatory Non-Coding RNAs Reveal Pollen Development Initiated at Ecodormancy in Peach. PMID:33968979
Predict Colon Cancer by Pairing Plasma miRNAs: Establishment of a Normalizer-Free, Cross-Platform Model. PMID:33968711
Circular RNA expression profiles in the plasma of patients with infantile hemangioma determined using microarray analysis. PMID:33968165
CBP-JMF: An Improved Joint Matrix Tri-Factorization Method for Characterizing Complex Biological Processes of Diseases. PMID:33968140
A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population. PMID:33968136
Medicago sativa and Medicago truncatula Show Contrasting Root Metabolic Responses to Drought. PMID:33968107
Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast. PMID:33967978
Evidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome. PMID:33963386
Integration of peripheral transcriptomics, genomics, and interactomics following trauma identifies causal genes for symptoms of post-traumatic stress and major depression. PMID:33963278
Genome-wide association studies of grain quality traits in maize. PMID:33963265
Cold-induction of afadin in brown fat supports its thermogenic capacity. PMID:33963248
A candidate gene identified in converting platycoside E to platycodin D from Platycodon grandiflorus by transcriptome and main metabolites analysis. PMID:33963244
Ubiquitin-mediated DNA damage response is synthetic lethal with G-quadruplex stabilizer CX-5461. PMID:33963218
Elevated dimethylarginine, ATP, cytokines, metabolic remodeling involving tryptophan metabolism and potential microglial inflammation characterize primary open angle glaucoma. PMID:33963197
CXCL1 Clone Evolution Induced by the HDAC Inhibitor Belinostat Might Be a Favorable Prognostic Indicator in Triple-Negative Breast Cancer. PMID:33959656
Neuronal ApoE upregulates MHC-I expression to drive selective neurodegeneration in Alzheimer's disease. PMID:33958804
An integrative network analysis framework for identifying molecular functions in complex disorders examining major depressive disorder as a test case. PMID:33958659
Metabolomic and phenotypic implications of the application of fertilization products containing microcontaminants in lettuce (Lactuca sativa). PMID:33958645
Histological and transcriptomic analysis of adipose and muscle of dairy calves supplemented with 5-hydroxytryptophan. PMID:33958639
Computational study of zebrafish immune-targeted microarray data for prediction of preventive drug candidates. PMID:33953878
Ecologically coherent population structure of uncultivated bacterioplankton. PMID:33953362
Association of urinary ketamine and APOA1 levels with bladder dysfunction in ketamine abusers revealed via proteomics and targeted metabolite analyses. PMID:33953300
Network pharmacology approach to decipher signaling pathways associated with target proteins of NSAIDs against COVID-19. PMID:33953223
A data-independent acquisition-based global phosphoproteomics system enables deep profiling. PMID:33953186
Potential role of indolelactate and butyrate in multiple sclerosis revealed by integrated microbiome-metabolome analysis. PMID:33948576
Particulate Metabolites and Transcripts Reflect Diel Oscillations of Microbial Activity in the Surface Ocean. PMID:33947808
Predicted Metabolic Function of the Gut Microbiota of Drosophila melanogaster. PMID:33947801
Metabolic Profiling of VOCs Emitted by Bacteria Isolated from Pressure Ulcers and Treated with Different Concentrations of Bio-AgNPs. PMID:33946710
Integrative Systems Biology Approaches to Identify Potential Biomarkers and Pathways of Cervical Cancer. PMID:33946372
Untargeted metabolomics for uncovering plasma biological markers of wet age-related macular degeneration. PMID:33946050
3D heterospecies spheroids of pancreatic stroma and cancer cells demonstrate key phenotypes of pancreatic ductal adenocarcinoma. PMID:33946033
Longitudinal virological changes and underlying pathogenesis in hospitalized COVID-19 patients in Guangzhou, China. PMID:33945070
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Microbial iron and carbon metabolism as revealed by taxonomy-specific functional diversity in the Southern Ocean. PMID:33941887
Comparative transcriptome analysis of cells from different areas reveals ROS responsive mechanism at sclerotial initiation stage in Morchella importuna. PMID:33941791
Prognostic relevance of the hexosamine biosynthesis pathway activation in leiomyosarcoma. PMID:33941787
COVID-19-related anosmia is associated with viral persistence and inflammation in human olfactory epithelium and brain infection in hamsters. PMID:33941622
Anna Karenina and the subgingival microbiome associated with periodontitis. PMID:33941275
Genomic analysis of novel Yarrowia-like yeast symbionts associated with the carrion-feeding burying beetle Nicrophorus vespilloides. PMID:33941076
RIP1 Perturbation Induces Chondrocyte Necroptosis and Promotes Osteoarthritis Pathogenesis via Targeting BMP7. PMID:33937236
Transcriptome Based Estrogen Related Genes Biomarkers for Diagnosis and Prognosis in Non-small Cell Lung Cancer. PMID:33936178
Comparative Small RNA Profiling and Functional Exploration on Wheat With High- and Low-Cadmium Accumulation. PMID:33936166
Genome-Wide Gene Expression Analysis of Mtb-Infected DC Highlights the Rapamycin-Driven Modulation of Regulatory Cytokines via the mTOR/GSK-3β Axis. PMID:33936070
Comprehensive RNA-Seq Analysis of Potential Therapeutic Targets of Gan-Dou-Fu-Mu Decoction for Treatment of Wilson Disease Using a Toxic Milk Mouse Model. PMID:33935715
Phase 1 trial of nelfinavir added to standard cisplatin chemotherapy with concurrent pelvic radiation for locally advanced cervical cancer. PMID:33932031
Proteomic and phosphoproteomic profiling of shammah induced signaling in oral keratinocytes. PMID:33931671
Identification of key pseudogenes in nasopharyngeal carcinoma based on RNA-Seq analysis. PMID:33931030
CladeOScope: functional interactions through the prism of clade-wise co-evolution. PMID:33928243
Machine Learning Neuroprotective Strategy Reveals a Unique Set of Parkinson Therapeutic Nicotine Analogs. PMID:33927788
Deep Learning Enables Fast and Accurate Imputation of Gene Expression. PMID:33927746
An Overview of Biological and Computational Methods for Designing Mechanism-Informed Anti-biofilm Agents. PMID:33927701
Dinoflagellate symbionts escape vomocytosis by host cell immune suppression. PMID:33927382
Best practices on the differential expression analysis of multi-species RNA-seq. PMID:33926528
Genome-wide analyses of the relict gull (Larus relictus): insights and evolutionary implications. PMID:33926388
Influence of Extraction Solvent on Nontargeted Metabolomics Analysis of Enrichment Reactor Cultures Performing Enhanced Biological Phosphorus Removal (EBPR). PMID:33925970
Categorization of Orthologous Gene Clusters in 92 Ascomycota Genomes Reveals Functions Important for Phytopathogenicity. PMID:33925458
Proteomic Charting of Imipenem Adaptive Responses in a Highly Carbapenem Resistant Clinical Enterobacter roggenkampii Isolate. PMID:33924830
RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation. PMID:33922274
From Proteomic Mapping to Invasion-Metastasis-Cascade Systemic Biomarkering and Targeted Drugging of Mutant BRAF-Dependent Human Cutaneous Melanomagenesis. PMID:33922182
Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling. PMID:33922083
Analysis of LAGEs Family Gene Signature and Prognostic Relevance in Breast Cancer. PMID:33921749
Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast. PMID:33920164
Key Disease Mechanisms Linked to Alzheimer's Disease in the Entorhinal Cortex. PMID:33920138
Transcriptome Profiling of Cucumber (Cucumis sativus L.) Early Response to Pseudomonas syringae pv. lachrymans. PMID:33919557
An Introduction to Next Generation Sequencing Bioinformatic Analysis in Gut Microbiome Studies. PMID:33918473
Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. PMID:33917562
The Protein Interactome of Glycolysis in Escherichia coli. PMID:33917325
Changes in Bacterial Endophyte Community Following Aspergillus flavus Infection in Resistant and Susceptible Maize Kernels. PMID:33916873
Phylogenomic Insights into Distribution and Adaptation of Bdellovibrionota in Marine Waters. PMID:33916768
Sphingosine Promotes Embryo Biomass in Upland Cotton: A Biochemical and Transcriptomic Analysis. PMID:33915924
Multi-Omics Approaches to Define Calcific Aortic Valve Disease Pathogenesis. PMID:33914608
Identification of Expression Patterns and Potential Prognostic Significance of m5C-Related Regulators in Head and Neck Squamous Cell Carcinoma. PMID:33912441
Identification of Molecular Signatures in Mild Intrinsic Atopic Dermatitis by Bioinformatics Analysis. PMID:33911724
Regulatory role of non-coding RNA in ginseng rusty root symptom tissue. PMID:33911151
Adulthood blood levels of hsa-miR-29b-3p associate with preterm birth and adult metabolic and cognitive health. PMID:33911114
Cyanophage Diversity and Community Structure in Dead Zone Sediments. PMID:33910994
Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs. PMID:33910518
Erosion of human X chromosome inactivation causes major remodeling of the iPSC proteome. PMID:33910018
Gene network and biological pathways associated with susceptibility to differentiated thyroid carcinoma. PMID:33903625
SCD5 expression correlates with prognosis and response to neoadjuvant chemotherapy in breast cancer. PMID:33903614
Genome-wide toxicogenomic study of the lanthanides sheds light on the selective toxicity mechanisms associated with critical materials. PMID:33903247
Drug target ranking for glioblastoma multiforme. PMID:33902757
Unravelling the effects of tropical land use conversion on the soil microbiome. PMID:33902736
Tax4Fun2: prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences. PMID:33902725
Multi-omics integration strategies for animal epigenetic studies - A review. PMID:33902167
Adrenal Hormone Interactions and Metabolism: A Single Sample Multi-Omics Approach. PMID:33902135
Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing. PMID:33901201
Identification of Metastasis-Associated MicroRNAs in Metastatic Melanoma by miRNA Expression Profile and Experimental Validation. PMID:33897771
Evolution of the Subgroup 6 R2R3-MYB Genes and Their Contribution to Floral Color in the Perianth-Bearing Piperales. PMID:33897722
The Regulation of Adaptation to Cold and Drought Stresses in Poa crymophila Keng Revealed by Integrative Transcriptomics and Metabolomics Analysis. PMID:33897721
Thiocyanate and Organic Carbon Inputs Drive Convergent Selection for Specific Autotrophic Afipia and Thiobacillus Strains Within Complex Microbiomes. PMID:33897653
Assessment of Biological Contribution to Natural Recovery of Anthropized Freshwater Sediments From Argentina: Autochthonous Microbiome Structure and Functional Prediction. PMID:33897628
Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities. PMID:33896739
Transgenic mice overexpressing the LH receptor in the female reproductive system spontaneously develop endometrial tumour masses. PMID:33893331
G-Protein-coupled Estrogen Receptor 1 Agonist G-1 Perturbs Sunitinib Resistance-related Phosphoproteomic Signatures in Renal Cell Carcinoma. PMID:33893075
Reprogramming epiblast stem cells into pre-implantation blastocyst cell-like cells. PMID:33891866
Exploring the dermotoxicity of the mycotoxin deoxynivalenol: combined morphologic and proteomic profiling of human epidermal cells reveals alteration of lipid biosynthesis machinery and membrane structural integrity relevant for skin barrier function. PMID:33890134
Reverse vaccinology and subtractive genomics approaches for identifying common therapeutics against Mycobacterium leprae and Mycobacterium lepromatosis. PMID:33889182
System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. PMID:33889174
Investigating the effects of chronic perinatal alcohol and combined nicotine and alcohol exposure on dopaminergic and non-dopaminergic neurons in the VTA. PMID:33888815
The plasminogen protein is associated with high myopia as revealed by the iTRAQ-based proteomic analysis of the aqueous humor. PMID:33888814
The Chinese mitten crab genome provides insights into adaptive plasticity and developmental regulation. PMID:33888695
Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. PMID:33888068
Transcriptome analysis of early stages of sorghum grain mold disease reveals defense regulators and metabolic pathways associated with resistance. PMID:33888060
scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropy. PMID:33888056
Expression Profiles Reveal Involvement of VEGF, IGF1, BIRC5, and MMP1 in Vulvar Carcinogenesis. PMID:33888009
Transcriptome profiling of immune response to Yersinia ruckeri in spleen of rainbow trout (Oncorhynchus mykiss). PMID:33882827
Transcriptomic alterations in malignant pleural mesothelioma cells in response to long‑term treatment with bullfrog sialic acid‑binding lectin. PMID:33880588
KEGG2Net: Deducing gene interaction networks and acyclic graphs from KEGG pathways. PMID:33880340
Identification of key genes and pathways in discoid lupus skin via bioinformatics analysis. PMID:33879674
Use of RNA Sequencing to Perform Comprehensive Analysis of Long Noncoding RNA Expression Profiles in Macrophages Infected with Trichosporon asahii. PMID:33877524
Altered metabolic pathways in a transgenic mouse model suggest mechanistic role of amyloid precursor protein overexpression in Alzheimer's disease. PMID:33876332
Transcriptomic analysis to infer key molecular players involved during host response to NDV challenge in Gallus gallus (Leghorn & Fayoumi). PMID:33875770
Identification and functional analyses of host factors interacting with the 17-kDa protein of Barley yellow dwarf virus-GAV. PMID:33875710
Three PilZ Domain Proteins, PlpA, PixA, and PixB, Have Distinct Functions in Regulation of Motility and Development in Myxococcus xanthus. PMID:33875546
Dynamic Pneumococcal Genetic Adaptations Support Bacterial Growth and Inflammation during Coinfection with Influenza. PMID:33875471
Identification of the specific long-noncoding RNAs involved in night-break mediated flowering retardation in Chenopodium quinoa. PMID:33874907
Reverse Plasticity Underlies Rapid Evolution by Clonal Selection within Populations of Fibroblasts Propagated on a Novel Soft Substrate. PMID:33871606
Urinary Metabolomic and Proteomic Analyses in a Mouse Model of Prostatic Inflammation. PMID:33870183
A structural analysis of the hypoxia response network. PMID:33868803
Microglial Nox2 Plays a Key Role in the Pathogenesis of Experimental Autoimmune Encephalomyelitis. PMID:33868265
Non-Genomic AhR-Signaling Modulates the Immune Response in Endotoxin-Activated Macrophages After Activation by the Environmental Stressor BaP. PMID:33868237
Halobellus ruber sp. nov., a deep red-pigmented extremely halophilic archaeon isolated from a Korean solar saltern. PMID:33864546
Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation. PMID:33863325
Bioinformatics and survival analysis of glia maturation factor-γ in pan-cancers. PMID:33863293
Bioinformatic Analysis of Key Genes and Pathways Related to Keloids. PMID:33860039
Utilizing network pharmacology and molecular docking to explore the underlying mechanism of Guizhi Fuling Wan in treating endometriosis. PMID:33859874
Disruption of Circadian Transcriptome in Lung by Acute Sleep Deprivation. PMID:33859677
Transcriptome analysis reveals the encystment-related lncRNA expression profile and coexpressed mRNAs in Pseudourostyla cristata. PMID:33859278
Novel, non-invasive markers for detecting therapy induced neuroendocrine differentiation in castration-resistant prostate cancer patients. PMID:33859239
Eudiplozoon nipponicum (Monogenea, Diplozoidae) and its adaptation to haematophagy as revealed by transcriptome and secretome profiling. PMID:33858339
Comparative physiological and full-length transcriptome analyses reveal the molecular mechanism of melatonin-mediated salt tolerance in okra (Abelmoschus esculentus L.). PMID:33858330
Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs. PMID:33856433
Drug-Target Interaction Prediction via Dual Laplacian Graph Regularized Logistic Matrix Factorization. PMID:33855072
Unraveling Heterogeneity of Tumor Cells and Microenvironment and Its Clinical Implications for Triple Negative Breast Cancer. PMID:33854958
Expression analysis of genes related to cold tolerance in Dendroctonus valens. PMID:33854828
Genomic insights into population history and biological adaptation in Oceania. PMID:33854233
Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14. PMID:33854112
Transcriptome-wide study revealed m6A regulation of embryonic muscle development in Dingan goose (Anser cygnoides orientalis). PMID:33853538
A long non-coding RNAs expression signature to improve prognostic prediction of Wilms tumor in children. PMID:33850811
Metabolic pathways inferred from a bacterial marker gene illuminate ecological changes across South Pacific frontal boundaries. PMID:33850115
Identification of genes and pathways involved in malignant pleural mesothelioma using bioinformatics methods. PMID:33849532
Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. PMID:33849070
Genome-wide characterization of human minisatellite VNTRs: population-specific alleles and gene expression differences. PMID:33849068
Protein acylation by saturated very long chain fatty acids and endocytosis are involved in necroptosis. PMID:33848465
Identification of differentially expressed miRNAs in human cells infected with different Zika virus strains. PMID:33847814
Identification and analysis of key genes associated with acute myocardial infarction by integrated bioinformatics methods. PMID:33847684
Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures. PMID:33846556
Discovering key transcriptomic regulators in pancreatic ductal adenocarcinoma using Dirichlet process Gaussian mixture model. PMID:33846515
Transcriptomic analysis of human brain microvascular endothelial cells exposed to laminin binding protein (adhesion lipoprotein) and Streptococcus pneumoniae. PMID:33846455
Interferon-γ Response of Mycobacterium avium subsp. paratuberculosis Infected Goats to Recombinant and Synthetic Mycobacterial Antigens. PMID:33842578
Overexpression of GINS4 Is Associated With Tumor Progression and Poor Survival in Hepatocellular Carcinoma. PMID:33842367
Potential targets identified in adenoid cystic carcinoma point out new directions for further research. PMID:33841642
Integrated Multi-Omic Analyses of the Genomic Modifications by Gut Microbiome-Derived Metabolites of Epicatechin, 5-(4'-Hydroxyphenyl)-γ-Valerolactone, in TNFalpha-Stimulated Primary Human Brain Microvascular Endothelial Cells. PMID:33841078
MiR-33a plays an crucial role in the proliferation of bovine preadipocytes. PMID:33840361
Elucidating molecular mechanisms of acquired resistance to BRAF inhibitors in melanoma using a microfluidic device and deep sequencing. PMID:33840166
Oncogenic KRAS Recruits an Expansive Transcriptional Network through Mutant p53 to Drive Pancreatic Cancer Metastasis. PMID:33839689
Aging features of the migratory locust at physiological and transcriptional levels. PMID:33838645
Bayesian estimation of cell type-specific gene expression with prior derived from single-cell data. PMID:33837133
Identification of co-expression network correlated with different periods of adipogenic and osteogenic differentiation of BMSCs by weighted gene co-expression network analysis (WGCNA). PMID:33836657
Tumor Microenvironment Proteomics: Lessons From Multiple Myeloma. PMID:33833982
Molecular mechanisms detected in yak lung tissue via transcriptome-wide analysis provide insights into adaptation to high altitudes. PMID:33833362
Prediction of Streptococcus uberis clinical mastitis treatment success in dairy herds by means of mass spectrometry and machine-learning. PMID:33833319
lncRNA C2dat2 facilitates autophagy and apoptosis via the miR-30d-5p/DDIT4/mTOR axis in cerebral ischemia-reperfusion injury. PMID:33833132
A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses. PMID:33831050
Prognostic Implication of the Expression Level of PECAM-1 in Non-small Cell Lung Cancer. PMID:33828969
Comparative Metagenomics Reveals Microbial Signatures of Sugarcane Phyllosphere in Organic Management. PMID:33828538
Gaussian graphical modeling of the serum exposome and metabolome reveals interactions between environmental chemicals and endogenous metabolites. PMID:33828161
An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests. PMID:33828122
Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay. PMID:33827913
The draft genome of the specialist flea beetle Altica viridicyanea (Coleoptera: Chrysomelidae). PMID:33827435
Prediction of biological age and evaluation of genome-wide dynamic methylomic changes throughout human aging. PMID:33826720
Plasma microrna expression profile for reduced ejection fraction in dilated cardiomyopathy. PMID:33824379
Children with Autism and Their Typically Developing Siblings Differ in Amplicon Sequence Variants and Predicted Functions of Stool-Associated Microbes. PMID:33824194
Establishing a consensus for the hallmarks of cancer based on gene ontology and pathway annotations. PMID:33823788
miRSM: an R package to infer and analyse miRNA sponge modules in heterogeneous data. PMID:33822666
Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses. PMID:33821873
Integrative microbiomics in bronchiectasis exacerbations. PMID:33820995
The Selenophosphate Synthetase Gene, selD, Is Important for Clostridioides difficile Physiology. PMID:33820795
The construction and analysis of a ferroptosis-related gene prognostic signature for pancreatic cancer. PMID:33819918
A bioinformatic analysis of the inhibin-betaglycan-endoglin/CD105 network reveals prognostic value in multiple solid tumors. PMID:33819300
Glutathionylation chemistry promotes interleukin-1 beta-mediated glycolytic reprogramming and pro-inflammatory signaling in lung epithelial cells. PMID:33817836
Screening of Hub Genes Associated with Pulmonary Arterial Hypertension by Integrated Bioinformatic Analysis. PMID:33816621
COVID-19 co-infection mathematical model as guided through signaling structural framework. PMID:33815692
Effects of Simulated Microgravity on the Proteome and Secretome of the Polyextremotolerant Black Fungus Knufia chersonesos. PMID:33815472
A Comparison of Differential Gene Expression in Response to the Onset of Water Stress Between Three Hybrid Brachiaria Genotypes. PMID:33815444
Comparative Analysis of Adelphocoris suturalis Jakovlev (Hemiptera: Miridae) Immune Responses to Fungal and Bacterial Pathogens. PMID:33815150
Profiling of microRNAs in actinic keratosis and cutaneous squamous cell carcinoma patients. PMID:33813600
Identification of the molecular regulation of differences in lipid deposition in dedifferentiated preadipocytes from different chicken tissues. PMID:33812382
Traditional Chinese Medicine (TCM) in the treatment of COVID-19 and other viral infections: Efficacies and mechanisms. PMID:33811957
A bioactive molecule made by unusual salvage of radical SAM enzyme byproduct 5-deoxyadenosine blurs the boundary of primary and secondary metabolism. PMID:33811856
Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide. PMID:33809699
Strategies to Modulate Specialized Metabolism in Mediterranean Crops: From Molecular Aspects to Field. PMID:33809189
Metabolome and Transcriptome Analyses Reveal the Regulatory Mechanisms of Photosynthesis in Developing Ginkgo biloba Leaves. PMID:33807564
Sirtuins-Mediated System-Level Regulation of Mammalian Tissues at the Interface between Metabolism and Cell Cycle: A Systematic Review. PMID:33806509
Highly Species-Specific Foliar Metabolomes of Diverse Woody Species and Relationships with the Leaf Economics Spectrum. PMID:33805842
Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum. PMID:33805816
Withholding of M-CSF Supplement Reprograms Macrophages to M2-Like via Endogenous CSF-1 Activation. PMID:33805444
The Potential Equivalents of TET2 Mutations. PMID:33805247
Molecular Pathways and Pigments Underlying the Colors of the Pearl Oyster Pinctada margaritifera var. cumingii (Linnaeus 1758). PMID:33804186
Candidate Markers of Olaparib Response from Genomic Data Analyses of Human Cancer Cell Lines. PMID:33803939
Innate Resistance and Phosphite Treatment Affect Both the Pathogen's and Host's Transcriptomes in the Tanoak-Phytophthora ramorum Pathosystem. PMID:33803362
Indole-3-Acetic Acid Is Synthesized by the Endophyte Cyanodermella asteris via a Tryptophan-Dependent and -Independent Way and Mediates the Interaction with a Non-Host Plant. PMID:33800748
A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders. PMID:33800722
Retinal Genomic Fabric Remodeling after Optic Nerve Injury. PMID:33799827
Complete genome sequence of the Pseudomonas oleovorans strain ODT-83 isolated from oyster. PMID:33797591
Biosyntheses characterization of alkaloids and flavonoids in Sophora flavescens by combining metabolome and transcriptome. PMID:33795823
Network pharmacology and molecular docking study on the active ingredients of qidengmingmu capsule for the treatment of diabetic retinopathy. PMID:33795817
Transcriptional circuitry atlas of genetic diverse unstimulated murine and human macrophages define disparity in population-wide innate immunity. PMID:33795737
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). PMID:33793824
Mass Spectrometry-Based Shotgun Lipidomics for Cancer Research. PMID:33791973
Weighted Gene Coexpression Network Analysis Uncovers Critical Genes and Pathways for Multiple Brain Regions in Parkinson's Disease. PMID:33791366
Computational Tumor Infiltration Phenotypes Enable the Spatial and Genomic Analysis of Immune Infiltration in Colorectal Cancer. PMID:33791196
Construction of a Prognostic Gene Signature Associated with Immune Infiltration in Glioma: A Comprehensive Analysis Based on the CGGA. PMID:33790966
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. PMID:33790324
Somatic mutations in lymphocytes in patients with immune-mediated aplastic anemia. PMID:33785863
Proteomics study on the effect of silybin on cardiomyopathy in obese mice. PMID:33785854
Delineating proinflammatory microenvironmental signals by ex vivo modeling of the immature intestinal stroma. PMID:33785826
Representative Diatom and Coccolithophore Species Exhibit Divergent Responses throughout Simulated Upwelling Cycles. PMID:33785571
Global Transcriptional Regulators Fine-Tune the Translational and Metabolic Efficiency for Optimal Growth of Escherichia coli. PMID:33785570
Deciphering the transcriptomic regulation of heat stress responses in Nothofagus pumilio. PMID:33784314
Metabolomic Biomarkers of Healthy Dietary Patterns and Cardiovascular Outcomes. PMID:33782776
Screening of osteoarthritis diagnostic markers based on immune-related genes and immune infiltration. PMID:33782454
Insights into Acinetobacter baumannii fatty acid synthesis 3-oxoacyl-ACP reductases. PMID:33782435
Integrating Systems and Synthetic Biology to Understand and Engineer Microbiomes. PMID:33781078
Generic injuries are sufficient to induce ectopic Wnt organizers in Hydra. PMID:33779545
Expansion and persistence of antibiotic-specific resistance genes following antibiotic treatment. PMID:33779498
The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia. PMID:33778322
SOCS2 is a potential prognostic marker that suppresses the viability of hepatocellular carcinoma cells. PMID:33777222
Gene Expression Analysis Suggests Immunological Changes of Peripheral Blood Monocytes in the Progression of Patients With Coronary Artery Disease. PMID:33777109
Analysis of human total antibody repertoires in TIF1γ autoantibody positive dermatomyositis. PMID:33772100
The Burkholderia pseudomallei intracellular 'TRANSITome'. PMID:33772012
RNA sequencing and bioinformatics analysis of human lens epithelial cells in age-related cataract. PMID:33771123
Prioritization of candidate genes for a South African family with Parkinson's disease using in-silico tools. PMID:33770142
Pathway-level analysis of genome-wide circadian dynamics in diverse tissues in rat and mouse. PMID:33768484
Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function in mice. PMID:33767339
Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis. PMID:33767308
Hepatic steatosis and steatohepatitis: a functional meta-analysis of sex-based differences in transcriptomic studies. PMID:33766130
Comparative proteomics reveals mechanisms that underlie insecticide resistance in Culex pipiens pallens Coquillett. PMID:33764997
Identification of a Metabolism-Related Signature for the Prediction of Survival in Endometrial Cancer Patients. PMID:33763366
Fasciola hepatica hijacks host macrophage miRNA machinery to modulate early innate immune responses. PMID:33762636
Genome-wide impact of hydrogen peroxide on maintenance DNA methylation in replicating cells. PMID:33761969
A 2 miRNAs-based signature for the diagnosis of atherosclerosis. PMID:33761890
Deep learning assisted multi-omics integration for survival and drug-response prediction in breast cancer. PMID:33761889
Mitochondrial genotype alters the impact of rapamycin on the transcriptional response to nutrients in Drosophila. PMID:33761878
Transcriptome analyses of 7-day-old zebrafish larvae possessing a familial Alzheimer's disease-like mutation in psen1 indicate effects on oxidative phosphorylation, ECM and MCM functions, and iron homeostasis. PMID:33761877
Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. PMID:33758323
Herb-target virtual screening and network pharmacology for prediction of molecular mechanism of Danggui Beimu Kushen Wan for prostate cancer. PMID:33758314
Transcriptomic insight into the translational value of two murine models in human atopic dermatitis. PMID:33758305
Genome insight and description of antibiotic producing Massilia antibiotica sp. nov., isolated from oil-contaminated soil. PMID:33758279
Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. PMID:33758196
Overexpression of CCNE1 confers a poorer prognosis in triple-negative breast cancer identified by bioinformatic analysis. PMID:33757543
Scarcity of scale-free topology is universal across biochemical networks. PMID:33753807
Genome-wide identification of MIKC-type genes related to stamen and gynoecium development in Liriodendron. PMID:33753780
A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study. PMID:33753735
The number of catalytic cycles in an enzyme's lifetime and why it matters to metabolic engineering. PMID:33753504
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau. PMID:33753478
DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus. PMID:33753477
Human Corneal Epithelial Cells Internalize Aspergillus flavus Spores by Actin-Mediated Endocytosis. PMID:33753415
Critical role of the BAF chromatin remodeling complex during murine neural crest development. PMID:33750945
The identification of circular RNAs from peripheral blood mononuclear cells in systemic lupus erythematosus. PMID:33750387
Non-coding RNA Identification in Osteonecrosis of the Femoral Head Using Competitive Endogenous RNA Network Analysis. PMID:33749138
DNA repair pathway activation features in follicular and papillary thyroid tumors, interrogated using 95 experimental RNA sequencing profiles. PMID:33748479
Stochastic Simulation of Cellular Metabolism. PMID:33747671
Widely targeted metabolic analysis revealed the changed pigmentation and bioactive compounds in the ripening Berchemia floribunda (Wall.) Brongn. fruit. PMID:33747452
Transcriptomic Analysis of Inflammatory Cardiomyopathy Identifies Molecular Signatures of Disease and Informs in silico Prediction of a Network-Based Rationale for Therapy. PMID:33746983
A network pharmacology based approach for predicting active ingredients and potential mechanism of Lianhuaqingwen capsule in treating COVID-19. PMID:33746604
Identification of key genes and pathways in scleral extracellular matrix remodeling in glaucoma: Potential therapeutic agents discovered using bioinformatics analysis. PMID:33746571
Comparative transcriptomic analysis of the different developmental stages of ovary in red swamp crayfish Procambarus clarkii. PMID:33745451
RNA-seq analysis and gene expression dynamics in the salivary glands of the argasid tick Ornithodoros erraticus along the trophogonic cycle. PMID:33743776
Identification of molecular biomarkers and pathways of NSCLC: insights from a systems biomedicine perspective. PMID:33742334
Identification of oxytocin-related lncRNAs and assessment of their expression in breast cancer. PMID:33742056
A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives. PMID:33741955
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. PMID:33741058
Identification of regulatory factors promoting embryogenic callus formation in barley through transcriptome analysis. PMID:33740900
Differential microRNAs expression profiles in liver from three different lifestyle modification mice models. PMID:33740891
NEK1 deficiency affects mitochondrial functions and the transcriptome of key DNA repair pathways. PMID:33740813
High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer. PMID:33739392
Applications of Machine Learning in Human Microbiome Studies: A Review on Feature Selection, Biomarker Identification, Disease Prediction and Treatment. PMID:33737920
Specialization of the Reiterated Copies of the Heterodimeric Integration Host Factor Genes in Geobacter sulfurreducens. PMID:33737919
A ceRNA-associated risk model predicts the poor prognosis for head and neck squamous cell carcinoma patients. PMID:33737696
Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr. PMID:33737673
Global network analysis in Schizosaccharomyces pombe reveals three distinct consequences of the common 1-kb deletion causing juvenile CLN3 disease. PMID:33737578
Genes for degradation and utilization of uronic acid-containing polysaccharides of a marine bacterium Catenovulum sp. CCB-QB4. PMID:33732545
Latent Anti-nutrients and Unintentional Breeding Consequences in Australian Sorghum bicolor Varieties. PMID:33732274
Application of text mining to develop AOP-based mucus hypersecretion genesets and confirmation with in vitro and clinical samples. PMID:33731770
Potential benefits of L. acidophilus in dyslipidemic rats. PMID:33731756
Differential gene expression profile between progressive and de novo muscle invasive bladder cancer and its prognostic implication. PMID:33731721
Ultrafast functional profiling of RNA-seq data for nonmodel organisms. PMID:33731361
Effects of sevoflurane anesthesia and abdominal surgery on the systemic metabolome: a prospective observational study. PMID:33731015
Chronic villitis of unknown etiology: Investigations into viral pathogenesis. PMID:33730616
In-silico structural analysis of Pseudomonas syringae effector HopZ3 reveals ligand binding activity and virulence function. PMID:33730245
Detection of horizontal gene transfer in the genome of the choanoflagellate Salpingoeca rosetta. PMID:33727612
Integration of summary data from GWAS and eQTL studies identified novel risk genes for coronary artery disease. PMID:33725943
Carotenoids produced by the deep-sea bacterium Erythrobacter citreus LAMA 915: detection and proposal of their biosynthetic pathway. PMID:33723710
Specific microbiome profile in Takayasu's arteritis and giant cell arteritis. PMID:33723291
COVID-19 patient transcriptomic and genomic profiling reveals comorbidity interactions with psychiatric disorders. PMID:33723208
Gut microbiota-mediated lysophosphatidylcholine generation promotes colitis in intestinal epithelium-specific Fut2 deficiency. PMID:33722220
Genome-scale model reconstruction of the methylotrophic yeast Ogataea polymorpha. PMID:33722219
The characteristics of circRNA as competing endogenous RNA in pathogenesis of acute myeloid leukemia. PMID:33722210
A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness. PMID:33720976
Modeling dynamic correlation in zero-inflated bivariate count data with applications to single-cell RNA sequencing data. PMID:33720414
Transcriptome Analysis Reveals Photoperiod-Associated Genes Expressed in Rice Anthers. PMID:33719293
iTRAQ-based comparative proteome analyses of different growth stages revealing the regulatory role of reactive oxygen species in the fruiting body development of Ophiocordyceps sinensis. PMID:33717691
Microbial Functional Responses in Marine Biofilms Exposed to Deepwater Horizon Spill Contaminants. PMID:33717029
The Counteracting Effects of Demography on Functional Genomic Variation: The Roma Paradigm. PMID:33713133
Evolutionary Contribution of Duplicated Genes to Genome Evolution in the Ginseng Species Complex. PMID:33713106
Nutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates. PMID:33712682
Human milk extracellular vesicle miRNA expression and associations with maternal characteristics in a population-based cohort from the Faroe Islands. PMID:33712635
Coronary artery disease: differential expression of ceRNAs and interaction analyses. PMID:33708856
Dysbiosis of Oral Microbiota During Oral Squamous Cell Carcinoma Development. PMID:33708627
Novel and Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice Created by Physiological Coupling-Uncoupling and Network Rewiring Effects. PMID:33708229
Transcriptome Analysis of the Inhibitory Effect of Sennoside A on the Metastasis of Hepatocellular Carcinoma Cells. PMID:33708105
Transcriptomic responses to aluminum stress in tea plant leaves. PMID:33707704
Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells. PMID:33707642
The gut microbiota composition of Trichoplusia ni is altered by diet and may influence its polyphagous behavior. PMID:33707556
Pan-cancer analysis of RNA expression of ANGIOTENSIN-I-CONVERTING ENZYME 2 reveals high variability and possible impact on COVID-19 clinical outcomes. PMID:33707526
Exovesicular-Shh confers Imatinib resistance by upregulating Bcl2 expression in chronic myeloid leukemia with variant chromosomes. PMID:33707419
Consumption of High-Fructose Corn Syrup Compared with Sucrose Promotes Adiposity and Increased Triglyceridemia but Comparable NAFLD Severity in Juvenile Iberian Pigs. PMID:33693900
Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development. PMID:33693822
Reconstruction of the Origin of a Neo-Y Sex Chromosome and Its Evolution in the Spotted Knifejaw, Oplegnathus punctatus. PMID:33693787
Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress. PMID:33693623
Calcium-binding and coiled-coil domain 2 promotes the proliferation and suppresses apoptosis of prostate cancer cells. PMID:33692836
Changes in protein expression due to metformin treatment and hyperinsulinemia in a human endometrial cancer cell line. PMID:33690729
A functional chromogen gene C from wild rice is involved in a different anthocyanin biosynthesis pathway in indica and japonica. PMID:33688983
The mRNA-LNP platform's lipid nanoparticle component used in preclinical vaccine studies is highly inflammatory. PMID:33688649
Long non-coding RNAs ENST00000429730.1 and MSTRG.93125.4 are associated with metabolic activity in tuberculosis lesions of sputum-negative tuberculosis patients. PMID:33686954
An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community. PMID:33683131
Analysis of MicroRNAs Associated With Carotid Atherosclerotic Plaque Rupture With Thrombosis. PMID:33679879
The Comparative Methylome and Transcriptome After Change of Direction Compared to Straight Line Running Exercise in Human Skeletal Muscle. PMID:33679435
Physiological and transcriptional response to drought stress among bioenergy grass Miscanthus species. PMID:33676571
Major ceRNA regulation and key metabolic signature analysis of intervertebral disc degeneration. PMID:33676464
Key metabolism pathways and regulatory mechanisms of high polysaccharide yielding in Hericium erinaceus. PMID:33676419
Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing. PMID:33676414
Association of maternal gut microbiota and plasma metabolism with congenital heart disease in offspring: a multi-omic analysis. PMID:33674681
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells. PMID:33674641
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma. PMID:33674593
Germline and Somatic Whole-Exome Sequencing Identifies New Candidate Genes Involved in Familial Predisposition to Serrated Polyposis Syndrome. PMID:33672345
The Autotrophic Core: An Ancient Network of 404 Reactions Converts H2, CO2, and NH3 into Amino Acids, Bases, and Cofactors. PMID:33672143
Accumulation of the Auxin Precursor Indole-3-Acetamide Curtails Growth through the Repression of Ribosome-Biogenesis and Development-Related Transcriptional Networks. PMID:33670805
Comparison of SYK Signaling Networks Reveals the Potential Molecular Determinants of Its Tumor-Promoting and Suppressing Functions. PMID:33670716
A Pilot Study for Metabolic Profiling of Obesity-Associated Microbial Gut Dysbiosis in Male Wistar Rats. PMID:33670496
Ranking Metabolite Sets by Their Activity Levels. PMID:33670102
Gut Microbiome-Based Analysis of Lipid A Biosynthesis in Individuals with Autism Spectrum Disorder: An In Silico Evaluation. PMID:33669978
Transporters at the Interface between Cytosolic and Mitochondrial Amino Acid Metabolism. PMID:33669382
Knowledge-Guided "Community Network" Analysis Reveals the Functional Modules and Candidate Targets in Non-Small-Cell Lung Cancer. PMID:33669233
Comparative Transcriptome Profiling of Human and Pig Intestinal Epithelial Cells after Porcine Deltacoronavirus Infection. PMID:33668405
Identify potential miRNA-mRNA regulatory networks contributing to high-risk neuroblastoma. PMID:33666785
Acute Kidney Injury Results in Long-Term Diastolic Dysfunction That Is Prevented by Histone Deacetylase Inhibition. PMID:33665513
Deletion of hippocampal Glucocorticoid receptors unveils sex-biased microRNA expression and neuronal morphology alterations in mice. PMID:33665240
Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae. PMID:33664713
Wnt-β-catenin activation epigenetically reprograms Treg cells in inflammatory bowel disease and dysplastic progression. PMID:33664518
Pharmacological inhibition of tumor anabolism and host catabolism as a cancer therapy. PMID:33664364
Alterations in skin microbiome mediated by radiotherapy and their potential roles in the prognosis of radiotherapy-induced dermatitis: a pilot study. PMID:33664352
Bayesian network-driven clustering analysis with feature selection for high-dimensional multi-modal molecular data. PMID:33664338
Comparative analysis of drought-responsive and -adaptive genes in Chinese wingnut (Pterocarya stenoptera C. DC). PMID:33663380
The Changes of Leukocytes in Brain and Blood After Intracerebral Hemorrhage. PMID:33659003
Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments. PMID:33658614
B2M overexpression correlates with malignancy and immune signatures in human gliomas. PMID:33658560
Identification of candidate genes and pathways in retinopathy of prematurity by whole exome sequencing of preterm infants enriched in phenotypic extremes. PMID:33654115
Human Chorionic Gonadotropin Modulates the Transcriptome of the Myometrium and Cervix in Late Gestation. PMID:33650091
Complete genome sequencing of Bacillus sp. TK-2, analysis of its cold evolution adaptability. PMID:33649356
Novel gene signatures for stage classification of the squamous cell carcinoma of the lung. PMID:33649335
Differential regulation of β-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells. PMID:33649334
Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer. PMID:33649218
Effects of non-vascularized adipose tissue transplantation on its genetic profile. PMID:33648423
Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PMID:33647016
Gene Size Matters: An Analysis of Gene Length in the Human Genome. PMID:33643374
Potential Molecular Mechanism of TNF Superfamily-Related Genes in Glioblastoma Multiforme Based on Transcriptome and Epigenome. PMID:33643183
Robust Physiological Metrics From Sparsely Sampled Networks. PMID:33643068
Combination of Ginsenosides Rb2 and Rg3 Promotes Angiogenic Phenotype of Human Endothelial Cells via PI3K/Akt and MAPK/ERK Pathways. PMID:33643049
The Corylus mandshurica genome provides insights into the evolution of Betulaceae genomes and hazelnut breeding. PMID:33642584
PIWI-interacting RNA sequencing profiles in maternal plasma-derived exosomes reveal novel non-invasive prenatal biomarkers for the early diagnosis of nonsyndromic cleft lip and palate. PMID:33639402
Response of the ileum transcriptome to probiotic and fructo-oligosaccharides in Taiping chicken. PMID:33638812
The role of gut microbiota and amino metabolism in the effects of improvement of islet β-cell function after modified jejunoileal bypass. PMID:33637880
Retroviral integrations contribute to elevated host cancer rates during germline invasion. PMID:33637755
Dynamic Allocation of Carbon Storage and Nutrient-Dependent Exudation in a Revised Genome-Scale Model of Prochlorococcus. PMID:33633777
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. PMID:33633572
Enhanced Understanding of Molecular Interactions and Function Underlying Pain Processes Through Networks of Transcript Isoforms, Genes, and Gene Families. PMID:33633454
The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation. PMID:33633374
Genetic architectures of proximal and distal colorectal cancer are partly distinct. PMID:33632709
Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri. PMID:33632122
Identification of UBE2C as hub gene in driving prostate cancer by integrated bioinformatics analysis. PMID:33630978
Uncovering the Anti-Lung-Cancer Mechanisms of the Herbal Drug FDY2004 by Network Pharmacology. PMID:33628308
A Network Pharmacology Study on the Molecular Mechanisms of FDY003 for Breast Cancer Treatment. PMID:33628298
An Expanded Gene Catalog of Mouse Gut Metagenomes. PMID:33627510
Distinct, dosage-sensitive requirements for the autism-associated factor CHD8 during cortical development. PMID:33627187
Comprehensive Analysis of Gene Expression Changes and Validation in Hepatocellular Carcinoma. PMID:33623390
Automating parameter selection to avoid implausible biological pathway models. PMID:33623016
Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberculosis Beijing strain. PMID:33619301
mRNA Transcriptome Analysis of Bone in a Mouse Model of Implant-Associated Staphylococcus aureus Osteomyelitis. PMID:33619031
Mitonuclear Coevolution, but not Nuclear Compensation, Drives Evolution of OXPHOS Complexes in Bivalves. PMID:33616640
Identifying Thyroid Carcinoma-Related Genes by Integrating GWAS and eQTL Data. PMID:33614667
Osmotic stress in banana is relieved by exogenous nitric oxide. PMID:33614294
Transcriptomic analysis of nonylphenol effect on Saccharomyces cerevisiae. PMID:33614281
Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. PMID:33613634
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. PMID:33611340
Modulating the unfolded protein response with ONC201 to impact on radiation response in prostate cancer cells. PMID:33608585
Laboratory Evolution and Reverse Engineering of Clostridium thermocellum for Growth on Glucose and Fructose. PMID:33608285
Naked mole rat TRF1 safeguards glycolytic capacity and telomere replication under low oxygen. PMID:33608273
Novel signaling pathways regulate SARS-CoV and SARS-CoV-2 infectious disease. PMID:33607766
Transcriptomic Signatures and Functional Network Analysis of Chronic Rhinosinusitis With Nasal Polyps. PMID:33603773
Cerebrospinal fluid proteome shows disrupted neuronal development in multiple sclerosis. PMID:33602999
Enrichment analyses of diseases and pathways associated with precocious puberty using PrecocityDB. PMID:33602974
Identification of biomarkers and pathogenesis in severe asthma by coexpression network analysis. PMID:33602227
Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation. PMID:33602141
Quantitative proteomic analysis of pear (Pyrus pyrifolia cv. "Hosui") flesh provides novel insights about development and quality characteristics of fruit. PMID:33599839
Gut Microbial and Metabolic Profiling Reveal the Lingering Effects of Infantile Iron Deficiency Unless Treated with Iron. PMID:33599094
Celastrol inhibits intestinal lipid absorption by reprofiling the gut microbiota to attenuate high-fat diet-induced obesity. PMID:33598642
Investigation of allele specific expression in various tissues of broiler chickens using the detection tool VADT. PMID:33597613
Mitochondrial Inhibitor Atovaquone Increases Tumor Oxygenation and Inhibits Hypoxic Gene Expression in Patients with Non-Small Cell Lung Cancer. PMID:33597271
PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data. PMID:33597026
Ferroptosis-related gene signature as a prognostic marker for lower-grade gliomas. PMID:33594759
Hepatic connective tissue growth factor expression and regulation differ between non-steatotic and non-alcoholic steatotic livers from brain-dead donor. PMID:33594198
Digital gene expression analysis of the response to Ralstonia solanacearum between resistant and susceptible tobacco varieties. PMID:33594109
Genetic characteristics of Bursaphelenchus xylophilus third-stage dispersal juveniles. PMID:33594100
Genome-scale meta-analysis of breast cancer datasets identifies promising targets for drug development. PMID:33593445
Creation of a gene expression portrait of depression and its application for identifying potential treatments. PMID:33589676
Profiling plasma-extracellular vesicle proteins and microRNAs in diabetes onset in middle-aged male participants in the ELSA-Brasil study. PMID:33587339
GWAS of three molecular traits highlights core genes and pathways alongside a highly polygenic background. PMID:33587031
SARS-CoV-2 Proteins Exploit Host's Genetic and Epigenetic Mediators for the Annexation of Key Host Signaling Pathways. PMID:33585554
Hierarchical Microbial Functions Prediction by Graph Aggregated Embedding. PMID:33584804
Gene Annotation in High Schools: Successful Student Pipeline and Teacher Professional Development in Bioscience Using GENI-ACT. PMID:33584559
Catalpol Protects Against Pulmonary Fibrosis Through Inhibiting TGF-β1/Smad3 and Wnt/β-Catenin Signaling Pathways. PMID:33584272
Identification of Potential Biomarkers Associated with Prognosis in Gastric Cancer via Bioinformatics Analysis. PMID:33582701
In Esophageal Squamous Cells From Eosinophilic Esophagitis Patients, Th2 Cytokines Increase Eotaxin-3 Secretion Through Effects on Intracellular Calcium and a Non-Gastric Proton Pump. PMID:33581123
Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem. PMID:33580159
The potential pathways underlying the association of propyl-paraben exposure with aeroallergen sensitization and EASI score using metabolomics analysis. PMID:33580129
Comparative transcriptome analysis of Rheum australe, an endangered medicinal herb, growing in its natural habitat and those grown in controlled growth chambers. PMID:33580100
MSN, MWCNT and ZnO nanoparticle-induced CHO-K1 cell polarisation is linked to cytoskeleton ablation. PMID:33579304
Clinically significant genomic alterations in the Chinese and Western patients with intrahepatic cholangiocarcinoma. PMID:33579226
Apple Peel and Flesh Contain Pro-neurogenic Compounds. PMID:33577796
Intermedilysin cytolytic activity depends on heparan sulfates and membrane composition. PMID:33577603
Effects of glyphosate residues and different concentrate feed proportions in dairy cow rations on hepatic gene expression, liver histology and biochemical blood parameters. PMID:33577576
MicroRNA‑592 promotes cell proliferation, migration and invasion in colorectal cancer by directly targeting SPARC. PMID:33576452
CAMAMED: a pipeline for composition-aware mapping-based analysis of metagenomic data. PMID:33575649
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms. PMID:33575609
Omics Playground: a comprehensive self-service platform for visualization, analytics and exploration of Big Omics Data. PMID:33575569
UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network. PMID:33575553
A Multi-Platform Metabolomics Approach Identifies Urinary Metabolite Signatures That Differentiate Ketotic From Healthy Dairy Cows. PMID:33575283
Comparative analysis of the transcriptomes of two rice subspecies during domestication. PMID:33574456
Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat. PMID:33574419
The effect of acute moderate-intensity exercise on the serum and fecal metabolomes and the gut microbiota of cross-country endurance athletes. PMID:33574413
Transcriptome analysis of genes involved in starch biosynthesis in developing Chinese chestnut (Castanea mollissima Blume) seed kernels. PMID:33574357
A mixture model to detect edges in sparse co-expression graphs with an application for comparing breast cancer subtypes. PMID:33571253
Correlation between cortical gene expression and resting-state functional network centrality in healthy young adults. PMID:33570215
Elucidating the involvement of apoptosis in postmortem proteolysis in porcine muscles from two production cycles using metabolomics approach. PMID:33568769
Role of PDK1 in skeletal muscle hypertrophy induced by mechanical load. PMID:33568757
Functionally selective activation of the dopamine receptor D2 is mirrored by the protein expression profiles. PMID:33568753
Comparative transcriptomic analysis revealed novel potential therapeutic targets of traditional Chinese medicine (Pinggan-Qianyang decoction) on vascular remodeling in spontaneously hypertensive rats. PMID:33568194
Comparative transcriptome analysis reveals novel insights into transcriptional responses to phosphorus starvation in oil palm (Elaeis guineensis) root. PMID:33568046
Application of computational approaches to analyze metagenomic data. PMID:33565054
System Pharmacology-Based Strategy to Decode the Synergistic Mechanism of GanDouLing for Wilson's Disease. PMID:33564316
Classification of node-positive melanomas into prognostic subgroups using keratin, immune, and melanogenesis expression patterns. PMID:33564068
RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. PMID:33563338
Guild-based analysis for understanding gut microbiome in human health and diseases. PMID:33563315
Paroxetine-Overview of the Molecular Mechanisms of Action. PMID:33562229
A functional genomics screen identifying blood cell development genes in Drosophila by undergraduates participating in a course-based research experience. PMID:33561251
Differential immune signatures in the tumor microenvironment are associated with colon cancer racial disparities. PMID:33560598
Contribution of horizontal gene transfer to the functionality of microbial biofilm on a macroalgae. PMID:33558686
Antibiotic-resistant bacteria and gut microbiome communities associated with wild-caught shrimp from the United States versus imported farm-raised retail shrimp. PMID:33558614
In silico identification of natural products from Traditional Chinese Medicine for cancer immunotherapy. PMID:33558586
Integrated analysis identifies oxidative stress genes associated with progression and prognosis in gastric cancer. PMID:33558567
Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes. PMID:33558540
RNA Sequencing Reveals Distinct Immune Responses in the Chorioamniotic Membranes of Women with Preterm Labor and Microbial or Sterile Intra-amniotic Inflammation. PMID:33558326
The screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus. PMID:33553571
Prior Biological Knowledge Improves Genomic Prediction of Growth-Related Traits in Arabidopsis thaliana. PMID:33552126
Impact of Processed Food (Canteen and Oil Wastes) on the Development of Black Soldier Fly (Hermetia illucens) Larvae and Their Gut Microbiome Functions. PMID:33552039
Integrative Analyses of Genes Associated With Osteoporosis in CD16+ Monocyte. PMID:33551990
Genetic and functional interaction network analysis reveals global enrichment of regulatory T cell genes influencing basal cell carcinoma susceptibility. PMID:33549134
Identification of S1PR3 gene signature involved in survival of sepsis patients. PMID:33549110
Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network. PMID:33549042
Transcriptome comparisons of in vitro intestinal epithelia grown under static and microfluidic gut-on-chip conditions with in vivo human epithelia. PMID:33547413
Meta-omics characteristics of intestinal microbiota associated to HBeAg seroconversion induced by oral antiviral therapy. PMID:33547384
N-linked glycosylation enzymes in the diatom Thalassiosira oceanica exhibit a diel cycle in transcript abundance and favor for NXT-type sites. PMID:33547363
Involvement of the miR156/SPL module in flooding response in Medicago sativa. PMID:33547346
Detecting survival-associated biomarkers from heterogeneous populations. PMID:33547332
Integrative molecular characterization of sarcomatoid and rhabdoid renal cell carcinoma. PMID:33547292
Sialotranscriptomics of the argasid tick Ornithodoros moubata along the trophogonic cycle. PMID:33544727
Modeling drug response using network-based personalized treatment prediction (NetPTP) with applications to inflammatory bowel disease. PMID:33544718
Multi-layered network-based pathway activity inference using directed random walks: application to predicting clinical outcomes in urologic cancer. PMID:33543748
Identification of Genes Universally Differentially Expressed in Gastric Cancer. PMID:33542925
Identifications of immune-responsive genes for adaptative traits by comparative transcriptome analysis of spleen tissue from Kazakh and Suffolk sheep. PMID:33542475
Complement and coagulation cascades activation is the main pathophysiological pathway in early-onset severe preeclampsia revealed by maternal proteomics. PMID:33542402
The Genetics of Sudden Infant Death Syndrome-Towards a Gene Reference Resource. PMID:33540853
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
Genome annotation of disease-causing microorganisms. PMID:33537706
Comprehensively Analyzed Macrophage-Regulated Genes Indicate That PSMA2 Promotes Colorectal Cancer Progression. PMID:33537240
4-Hydroxyphenylpyruvate Dioxygenase-Like Protein Promotes Pancreatic Cancer Cell Progression and Is Associated With Glutamine-Mediated Redox Balance. PMID:33537239
The acidified drinking water-induced changes in the behavior and gut microbiota of wild-type mice depend on the acidification mode. PMID:33536529
Parvimonas micra, Peptostreptococcus stomatis, Fusobacterium nucleatum and Akkermansia muciniphila as a four-bacteria biomarker panel of colorectal cancer. PMID:33536501
Immature symbiotic system between horizontally transmitted green algae and brown hydra. PMID:33536483
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
Histone modification dynamics at H3K27 are associated with altered transcription of in planta induced genes in Magnaporthe oryzae. PMID:33534835
The Genomes of Two Billfishes Provide Insights into the Evolution of Endothermy in Teleosts. PMID:33533895
Applications of stable isotopes in MALDI imaging: current approaches and an eye on the future. PMID:33532914
Metabolic dysfunction in pregnancy: Fingerprinting the maternal metabolome using proton nuclear magnetic resonance spectroscopy. PMID:33532625
Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy. PMID:33531650
A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa. PMID:33531406
Genomic and functional analyses of fungal and bacterial consortia that enable lignocellulose breakdown in goat gut microbiomes. PMID:33526884
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
Known Drugs Identified by Structure-Based Virtual Screening Are Able to Bind Sigma-1 Receptor and Increase Growth of Huntington Disease Patient-Derived Cells. PMID:33525510
Long-Term Waterlogging as Factor Contributing to Hypoxia Stress Tolerance Enhancement in Cucumber: Comparative Transcriptome Analysis of Waterlogging Sensitive and Tolerant Accessions. PMID:33525400
Gene expression signatures of target tissues in type 1 diabetes, lupus erythematosus, multiple sclerosis, and rheumatoid arthritis. PMID:33523973
Transcriptomic and Functional Analyses of Mitochondrial Dysfunction in Pressure Overload-Induced Right Ventricular Failure. PMID:33522250
Pathway-Based Drug-Repurposing Schemes in Cancer: The Role of Translational Bioinformatics. PMID:33520715
American lobster postlarvae alter gene regulation in response to ocean warming and acidification. PMID:33520168
Integrative Analyses of mRNA Expression Profile Reveal SOCS2 and CISH Play Important Roles in GHR Mutation-Induced Excessive Abdominal Fat Deposition in the Sex-Linked Dwarf Chicken. PMID:33519913
Identification of Key MicroRNAs and Mechanisms in Prostate Cancer Evolution Based on Biomarker Prioritization Model and Carcinogenic Survey. PMID:33519899
A Qualitative Transcriptional Signature for the Risk Assessment of Precancerous Colorectal Lesions. PMID:33519891
Quantitative Proteomic Profiling of Marine Diatom Skeletonema dohrnii in Response to Temperature and Silicate Induced Environmental Stress. PMID:33519723
High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. PMID:33519501
Insights into triterpene synthesis and unsaturated fatty-acid accumulation provided by chromosomal-level genome analysis of Akebia trifoliata subsp. australis. PMID:33518712
A novel microbiome metabolic modulator improves the growth performance of broiler chickens in multiple trials and modulates targeted energy and amino acid metabolic pathways in the cecal metagenome. PMID:33518302
Combined genomic, transcriptomic, and metabolomic analyses provide insights into chayote (Sechium edule) evolution and fruit development. PMID:33517348
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
Signalling pathways and mechanistic cues highlighted by transcriptomic analysis of primordial, primary, and secondary ovarian follicles in domestic cat. PMID:33514822
Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume. PMID:33514804
Transcriptome analysis reveals the long intergenic noncoding RNAs contributed to skeletal muscle differences between Yorkshire and Tibetan pig. PMID:33514792
Verifying explainability of a deep learning tissue classifier trained on RNA-seq data. PMID:33514769
Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. PMID:33513807
CTD: An information-theoretic algorithm to interpret sets of metabolomic and transcriptomic perturbations in the context of graphical models. PMID:33513132
Herbicide stress-induced DNA methylation changes in two Zea mays inbred lines differing in Roundup® resistance. PMID:33512663
Identifying virulence determinants of multidrug-resistant Klebsiella pneumoniae in Galleria mellonella. PMID:33512418
High-throughput screening in postimplantation haploid epiblast stem cells reveals Hs3st3b1 as a modulator for reprogramming. PMID:33511777
A control theoretic three timescale model for analyzing energy management in mammalian cancer cells. PMID:33510857
Gene signature of children with severe respiratory syncytial virus infection. PMID:33510411
Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep. PMID:33510350
Systematic profiling of the effective ingredients and mechanism of Scabiosa comosa and S. tschilliensis against hepatic fibrosis combined with network pharmacology. PMID:33510287
Inhibition of mitochondrial function by metformin increases glucose uptake, glycolysis and GDF-15 release from intestinal cells. PMID:33510216
Development and characterization of patient-derived xenografts from non-small cell lung cancer brain metastases. PMID:33510214
[Pregnancy-preserving and maternal-fetal management in a patient with rare large cell neuroendocrine carcinoma of the uterine cervix]. PMID:33509747
The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy. PMID:33509017
ICN: Extracting interconnected communities in gene Co-expression networks. PMID:33508087
Vertical sleeve gastrectomy induces distinctive transcriptomic responses in liver, fat and muscle. PMID:33504853
Integrative analysis of transcriptomic data for identification of T-cell activation-related mRNA signatures indicative of preterm birth. PMID:33504832
Identifying RNA Biomarkers and Molecular Pathways Involved in Multiple Subtypes of Uveitis. PMID:33503442
Transcriptomic markers in pediatric septic shock prognosis: an integrative analysis of gene expression profiles. PMID:33503200
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia. PMID:33500463
Seasonal dynamics and starvation impact on the gut microbiome of urochordate ascidian Halocynthia roretzi. PMID:33499981
Development of the equine hindgut microbiome in semi-feral and domestic conventionally-managed foals. PMID:33499959
In Silico Inference of Synthetic Cytotoxic Interactions from Paclitaxel Responses. PMID:33499282
Genome-resolved metagenomics reveals site-specific diversity of episymbiotic CPR bacteria and DPANN archaea in groundwater ecosystems. PMID:33495623
Clinical Responsiveness to All-trans Retinoic Acid Is Potentiated by LSD1 Inhibition and Associated with a Quiescent Transcriptome in Myeloid Malignancies. PMID:33495312
A network pharmacology perspective for deciphering potential mechanisms of action of Solanum nigrum L. in bladder cancer. PMID:33494738
Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. PMID:33494351
Nanoemulsions of Satureja montana Essential Oil: Antimicrobial and Antibiofilm Activity against Avian Escherichia coli Strains. PMID:33494240
Cross-platform genomic identification and clinical validation of breast cancer diagnostic biomarkers. PMID:33493140
Short hairpin RNA attenuates liver fibrosis by regulating the PPAR‑γ and NF‑κB pathways in HBV‑induced liver fibrosis in mice. PMID:33491741
Propionic acid production from apple pomace in bioreactor using Propionibacterium freudenreichii: an economic analysis of the process. PMID:33489679
iMPTCE-Hnetwork: A Multilabel Classifier for Identifying Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network. PMID:33488764
Transcriptomic and Network Analysis of Minor Salivary Glands of Patients With Primary Sjögren's Syndrome. PMID:33488608
Gene co-expression network analysis of Trypanosoma brucei in tsetse fly vector. PMID:33482903
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. PMID:33479378
Network analysis of Down syndrome and SARS-CoV-2 identifies risk and protective factors for COVID-19. PMID:33479353
Multi-omic analysis unveils biological pathways in peripheral immune system associated to minimal hepatic encephalopathy appearance in cirrhotic patients. PMID:33479266
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Discovery and function exploration of microRNA-155 as a molecular biomarker for early detection of breast cancer. PMID:33475963
MiR-144-3p is associated with pathological inflammation in patients infected with Mycobacteroides abscessus. PMID:33473145
Global metabolomics profiling of colorectal cancer in Malaysian patients. PMID:33469506
Review on Databases and Bioinformatic Approaches on Pharmacogenomics of Adverse Drug Reactions. PMID:33469342
A genomic view of the microbiome of coral reef demosponges. PMID:33469166
Weighted gene co-expression network analysis identifies molecular pathways and hub genes involved in broiler White Striping and Wooden Breast myopathies. PMID:33469097
Blood-based protein profiling identifies serum protein c-KIT as a novel biomarker for hypertrophic cardiomyopathy. PMID:33469076
Chronic exposure of humans to high level natural background radiation leads to robust expression of protective stress response proteins. PMID:33469066
The relationships between microbiota and the amino acids and organic acids in commercial vegetable pickle fermented in rice-bran beds. PMID:33469050
Global tissue transcriptomic analysis to improve genome annotation and unravel skin pigmentation in goldfish. PMID:33469041
BAFF Inhibition Effectively Suppresses the Development of Anti-HLA.A2 Antibody in the Highly Sensitized Mouse Model. PMID:33467096
Development of prognostic signature based on immune-related genes in muscle-invasive bladder cancer: bioinformatics analysis of TCGA database. PMID:33465047
A multifaceted cellular damage repair and prevention pathway promotes high-level tolerance to β-lactam antibiotics. PMID:33463026
RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic. PMID:33462736
Genome analysis of a halophilic bacterium Halomonas malpeensis YU-PRIM-29T reveals its exopolysaccharide and pigment producing capabilities. PMID:33462335
Association of variably methylated tumour DNA regions with overall survival for invasive lobular breast cancer. PMID:33461604
Prediction and mechanistic analysis of drug-induced liver injury (DILI) based on chemical structure. PMID:33461600
Pathway crosstalk effects: Shrinkage and disentanglement using a Bayesian hierarchical model. PMID:33456621
Newly discovered Asgard archaea Hermodarchaeota potentially degrade alkanes and aromatics via alkyl/benzyl-succinate synthase and benzoyl-CoA pathway. PMID:33452484
Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets. PMID:33452398
lncRNA expression profiles and associated ceRNA network analyses in epicardial adipose tissue of patients with coronary artery disease. PMID:33452392
Targeted metabolomics analysis of postoperative delirium. PMID:33452279
Comprehensive Analysis of Cardiac Xeno-Graft Unveils Rejection Mechanisms. PMID:33451076
Differentially expressed lncRNAs in liver tissues of TX mice with hepatolenticular degeneration. PMID:33446761
Combined transcriptomic and lipidomic analysis reveals aberrant lipid metabolism in central nervous system hemangioblastomas. PMID:33446752
Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece. PMID:33446715
Omega 3 fatty acids stimulate thermogenesis during torpor in the Arctic Ground Squirrel. PMID:33446684
Multiscale Regulation of the Intervertebral Disc: Achievements in Experimental, In Silico, and Regenerative Research. PMID:33445782
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Multiple microarray analyses identify key genes associated with the development of Non-Small Cell Lung Cancer from Chronic Obstructive Pulmonary Disease. PMID:33442399
Transcriptional analysis reveals key insights into seasonal induced anthocyanin degradation and leaf color transition in purple tea (Camellia sinensis (L.) O. Kuntze). PMID:33441891
Molecular mechanism of the anti-inflammatory effects of Sophorae Flavescentis Aiton identified by network pharmacology. PMID:33441867
Immune modulation resulting from MR-guided high intensity focused ultrasound in a model of murine breast cancer. PMID:33441763
MicroRNA expression profiling after recurrent febrile seizures in rat and emerging role of miR-148a-3p/SYNJ1 axis. PMID:33441699
Structural and functional analysis of the Francisella lysine decarboxylase as a key actor in oxidative stress resistance. PMID:33441661
TNF-α Regulates Human Plasmacytoid Dendritic Cells by Suppressing IFN-α Production and Enhancing T Cell Activation. PMID:33441439
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease. PMID:33441415
Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients. PMID:33441124
Application of graphical lasso in estimating network structure in gene set. PMID:33437755
Prognosis Prediction for Colorectal Cancer Patients: A Risk Score Based on The Metabolic-Related Genes. PMID:33437216
Individual fate and gut microbiome composition in the European wild rabbit (Oryctolagus cuniculus). PMID:33436896
Alterations observed in the interferon α and β signaling pathway in MDD patients are marginally influenced by cis-acting alleles. PMID:33436853
Gene expression in blood reflects smoking exposure among cancer-free women in the Norwegian Women and Cancer (NOWAC) postgenome cohort. PMID:33436844
Transcriptomics analysis for the identification of potential age-related genes and cells associated with three major urogenital cancers. PMID:33436826
Integrated mRNA and miRNA expression profile analysis of female and male gonads in Hyriopsis cumingii. PMID:33436779
Genome wide methylation profiling of selected matched soft tissue sarcomas identifies methylation changes in metastatic and recurrent disease. PMID:33436720
Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2. PMID:33436670
A logical network-based drug-screening platform for Alzheimer's disease representing pathological features of human brain organoids. PMID:33436582
R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis. PMID:33434505
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
Distribution of sigma factors delineates segregation of virulent and avirulent Mycobacterium. PMID:33432378
Novel circRNA discovery in sheep shows evidence of high backsplice junction conservation. PMID:33432020
Metagenomic analysis of formalin-fixed paraffin-embedded tumor and normal mucosa reveals differences in the microbiome of colorectal cancer patients. PMID:33432015
The application of a biostimulant based on tannins affects root architecture and improves tolerance to salinity in tomato plants. PMID:33432010
Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism. PMID:33431991
A systems pharmacology approach to identify the autophagy-inducing effects of Traditional Persian medicinal plants. PMID:33431946
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Multi-responses of O-methyltransferase genes to salt stress and fiber development of Gossypium species. PMID:33430775
Maternal folic acid impacts DNA methylation profile in male rat offspring implicated in neurodevelopment and learning/memory abilities. PMID:33430764
MALDI TOF Mass Spectrometry Imaging of Blood Smear: Method Development and Evaluation. PMID:33430160
Structure-Activity Relationship Modeling and Experimental Validation of the Imidazolium and Pyridinium Based Ionic Liquids as Potential Antibacterials of MDR Acinetobacter Baumannii and Staphylococcus Aureus. PMID:33429999
TMEM158 May Serve as a Diagnostic Biomarker for Anaplastic Thyroid Carcinoma: An Integrated Bioinformatic Analysis. PMID:33428142
Metabolites Associated with Early Cognitive Changes Implicated in Alzheimer's Disease. PMID:33427733
Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. PMID:33426377
Discriminating Microbial Community Structure Between Peri-Implantitis and Periodontitis With Integrated Metagenomic, Metatranscriptomic, and Network Analysis. PMID:33425781
MicroRNAs Regulate Metabolic Phenotypes During Multicellular Tumor Spheroids Progression. PMID:33425736
Secrete or perish: The role of secretion systems in Xanthomonas biology. PMID:33425257
Dietary Lipid:Protein Ratio and n-3 Long-Chain Polyunsaturated Fatty Acids Alters the Gut Microbiome of Atlantic Salmon Under Hypoxic and Normoxic Conditions. PMID:33424792
Saccharibacteria as Organic Carbon Sinks in Hydrocarbon-Fueled Communities. PMID:33424787
Oyster Calcifying Fluid Harbors Persistent and Dynamic Autochthonous Bacterial Populations That May Aid in Shell Formation. PMID:33424068
Identification of key modules and hub genes in glioblastoma multiforme based on co-expression network analysis. PMID:33423377
Re-purposing software for functional characterization of the microbiome. PMID:33422152
Combined whole cell wall analysis and streamlined in silico carbohydrate-active enzyme discovery to improve biocatalytic conversion of agricultural crop residues. PMID:33422151
Use of Untargeted Metabolomics to Explore the Air Pollution-Related Disease Continuum. PMID:33420964
Optimization of metabolite extraction and analytical methods from shrimp intestine for metabolomics profile analysis using LC-HRMS/MS. PMID:33420663
Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis. PMID:33420624
Gut microbiota impact on the peripheral immune response in non-alcoholic fatty liver disease related hepatocellular carcinoma. PMID:33420074
Longitudinal evaluation of fecal microbiota transplantation for ameliorating calf diarrhea and improving growth performance. PMID:33420064
Mammalian cell proliferation requires noncatalytic functions of O-GlcNAc transferase. PMID:33419956
Gastric Adenocarcinomas and Signet-Ring Cell Carcinoma: Unraveling Gastric Cancer Complexity through Microbiome Analysis-Deepening Heterogeneity for a Personalized Therapy. PMID:33419357
Transcriptome of nasopharyngeal samples from COVID-19 patients and a comparative analysis with other SARS-CoV-2 infection models reveal disparate host responses against SARS-CoV-2. PMID:33413422
Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons. PMID:33413102
Genomic imbalances in the placenta are associated with poor fetal growth. PMID:33413077
Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PMID:33411815
Integration of gene expression data identifies key genes and pathways in colorectal cancer. PMID:33411100
Machine Learning Models to Predict Primary Sites of Metastatic Cervical Carcinoma From Unknown Primary. PMID:33408743
Transcriptome Analysis of the Cerebellum of Mice Fed a Manganese-Deficient Diet. PMID:33408735
Type 2 diabetes mellitus-associated transcriptome alterations in cortical neurones and associated neurovascular unit cells in the ageing brain. PMID:33407907
The complete genome sequence of Hafnia alvei A23BA; a potential antibiotic-producing rhizobacterium. PMID:33407900
Analysis of sex differences in dietary copper-fructose interaction-induced alterations of gut microbial activity in relation to hepatic steatosis. PMID:33407877
Genome-scale metabolic modeling underscores the potential of Cutaneotrichosporon oleaginosus ATCC 20509 as a cell factory for biofuel production. PMID:33407779
Bioinformatics analysis of common key genes and pathways of intracranial, abdominal, and thoracic aneurysms. PMID:33407182
ATAC-Seq identifies regions of open chromatin in the bronchial lymph nodes of dairy calves experimentally challenged with bovine respiratory syncytial virus. PMID:33407093
Shared Blood Transcriptomic Signatures between Alzheimer's Disease and Diabetes Mellitus. PMID:33406707
Sequencing, de novo assembly and annotation of Digitalis ferruginea subsp. schischkinii transcriptome. PMID:33403559
Identification of Seven Cell Cycle-Related Genes with Unfavorable Prognosis and Construction of their TF-miRNA-mRNA regulatory network in Breast Cancer. PMID:33403032
Temperature modulates immune gene expression in mosquitoes during arbovirus infection. PMID:33401993
Genome survey sequencing and genetic diversity of cultivated Akebia trifoliata assessed via phenotypes and SSR markers. PMID:33400074
Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways. PMID:33398248
Transcriptomic Analysis of a Diabetic Skin-Humanized Mouse Model Dissects Molecular Pathways Underlying the Delayed Wound Healing Response. PMID:33396192
Effect of Senecio scandens ethanol extract on gut microbiota composition in mice. PMID:33394080
DYRK1A regulates B cell acute lymphoblastic leukemia through phosphorylation of FOXO1 and STAT3. PMID:33393494
Epigenome-wide association study (EWAS) for potential transgenerational disease epigenetic biomarkers in sperm following ancestral exposure to the pesticide methoxychlor. PMID:33391823
Specific MiRNAs in naïve T cells associated with Hepatitis C Virus-induced Hepatocellular Carcinoma. PMID:33391397
The Large Scale Structure of Human Metabolism Reveals Resilience via Extensive Signaling Crosstalk. PMID:33391012
Discovery of acquired molecular signature on immune checkpoint inhibitors in paired tumor tissues. PMID:33389015
Zone of Interaction Between the Parasite and the Host: Protein Profile of the Body Cavity Fluid of Gasterosteus aculeatus L. Infected with the Cestode Schistocephalus solidus (Muller, 1776). PMID:33387269
SkinBug: an artificial intelligence approach to predict human skin microbiome-mediated metabolism of biotics and xenobiotics. PMID:33385118
Functional Gene Expression Differentiation of the Notch Signaling Pathway in Female Reproductive Tract Tissues-A Comprehensive Review With Analysis. PMID:33384996
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
Integrated Analysis of Key Pathways and Drug Targets Associated With Vogt-Koyanagi-Harada Disease. PMID:33384687
Metabolomic Analysis of Response to Nitrogen-Limiting Conditions in Yarrowia spp. PMID:33383744
Feasible-metabolic-pathway-exploration technique using chemical latent space. PMID:33381845
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
Changes in Cecal Microbiota and Short-chain Fatty Acid During Lifespan of the Rat. PMID:33380558
Transcriptomic Analysis of Naïve Human Embryonic Stem Cells Cultured in Three-Dimensional PEG Scaffolds. PMID:33379237
Comparing Circadian Rhythmicity in the Human Gut Microbiome. PMID:33377042
Isobaric tags for relative and absolute quantitation-based proteomics analysis of the effect of ginger oil on bisphenol A-induced breast cancer cell proliferation. PMID:33376534
Effect of let-7c on the PI3K/Akt/FoxO signaling pathway in hepatocellular carcinoma. PMID:33376529
A thermodynamic atlas of carbon redox chemical space. PMID:33376214
The Developmental Transcriptome of Bagworm, Metisa plana (Lepidoptera: Psychidae) and Insights into Chitin Biosynthesis Genes. PMID:33374651
Proteomic Signatures of Lifestyle Risk Factors for Cardiovascular Disease: A Cross-Sectional Analysis of the Plasma Proteome in the Framingham Heart Study. PMID:33372532
Multipath: An R Package to Generate Integrated Reproducible Pathway Models. PMID:33371258
Novel therapeutic compounds for prostate adenocarcinoma treatment: An analysis using bioinformatic approaches and the CMap database. PMID:33371142
ProkSeq for complete analysis of RNA-Seq data from prokaryotes. PMID:33367516
Whole Transcriptome Analysis Provides Insights Into the Molecular Mechanisms of Chlamydospore-Like Cell Formation in Phanerochaete chrysosporium. PMID:33365015
Metabolic Engineering Strategies of Industrial Hemp (Cannabis sativa L.): A Brief Review of the Advances and Challenges. PMID:33363552
iTRAQ-Based Phosphoproteomic Analysis of Toxoplasma gondii Tachyzoites Provides Insight Into the Role of Phosphorylation for its Invasion and Egress. PMID:33363051
A Metagenome-Wide Association Study of Gut Microbiome in Patients With Multiple Sclerosis Revealed Novel Disease Pathology. PMID:33363050
Comparative Transcriptome, Metabolome, and Ionome Analysis of Two Contrasting Common Bean Genotypes in Saline Conditions. PMID:33362832
A Clinical Extensively-Drug Resistant (XDR) Escherichia coli and Role of Its β-Lactamase Genes. PMID:33362736
Traditional Human Populations and Nonhuman Primates Show Parallel Gut Microbiome Adaptations to Analogous Ecological Conditions. PMID:33361321
Effect of dietary oil from Camelina sativa on the growth performance, fillet fatty acid profile and gut microbiome of gilthead Sea bream (Sparus aurata). PMID:33354421
Identification of key genes and pathways in endometriosis by integrated expression profiles analysis. PMID:33354413
CHOmics: A web-based tool for multi-omics data analysis and interactive visualization in CHO cell lines. PMID:33351794
Essential interpretations of bioinformatics in COVID-19 pandemic. PMID:33349792
CheckV assesses the quality and completeness of metagenome-assembled viral genomes. PMID:33349699
ARPIR: automatic RNA-Seq pipelines with interactive report. PMID:33349239
An Integrated Analysis of miRNA and Gene Expression Changes in Response to an Obesogenic Diet to Explore the Impact of Transgenerational Supplementation with Omega 3 Fatty Acids. PMID:33348802
Recognition of plausible therapeutic agents to combat COVID-19: An omics data based combined approach. PMID:33346100
Bioinformatics analysis identifies COL1A1, THBS2 and SPP1 as potential predictors of patient prognosis and immunotherapy response in gastric cancer. PMID:33345281
Identification of Tamoxifen-Resistant Breast Cancer Cell Lines and Drug Response Signature. PMID:33344500
An Investigation of the Molecular Mechanisms Underlying the Analgesic Effect of Jakyak-Gamcho Decoction: A Network Pharmacology Study. PMID:33343676
Highly accurate diagnosis of papillary thyroid carcinomas based on personalized pathways coupled with machine learning. PMID:33341874
An international classification of inherited metabolic disorders (ICIMD). PMID:33340416
Comparison of thrombus, gut, and oral microbiomes in Korean patients with ST-elevation myocardial infarction: a case-control study. PMID:33339953
Leaf proteome modulation and cytological features of seagrass Cymodocea nodosa in response to long-term high CO2 exposure in volcanic vents. PMID:33339849
Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair. PMID:33339161
Identification of a Candidate Starch Utilizing Strain of Prevotella albensis from Bovine Rumen. PMID:33339094
A structurally unique Fusobacterium nucleatum tannase provides detoxicant activity against gallotannins and pathogen resistance. PMID:33336898
Aspartame, acesulfame K and sucralose- influence on the metabolism of Escherichia coli. PMID:33336183
Screening and Identification of Prognostic Tumor-Infiltrating Immune Cells and Genes of Endometrioid Endometrial Adenocarcinoma: Based on The Cancer Genome Atlas Database and Bioinformatics. PMID:33335850
MicroRNA-451a prevents cutaneous squamous cell carcinoma progression via the 3-phosphoinositide-dependent protein kinase-1-mediated PI3K/AKT signaling pathway. PMID:33335579
From Glucose to Lactate and Transiting Intermediates Through Mitochondria, Bypassing Pyruvate Kinase: Considerations for Cells Exhibiting Dimeric PKM2 or Otherwise Inhibited Kinase Activity. PMID:33335484
Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions. PMID:33335165
A biomimetic engineered bone platform for advanced testing of prosthetic implants. PMID:33335113
Impact of Staphylococcus aureus Small Colony Variants on Human Lung Epithelial Cells with Subsequent Influenza Virus Infection. PMID:33333815
Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease. PMID:33333559
A Chromosome-Level Genome Assembly of the Anglerfish Lophius litulon. PMID:33329719
QTL mapping and candidate gene analysis of seed vigor-related traits during artificial aging in wheat (Triticum aestivum). PMID:33328518
Genome sequencing and phylogenetic analysis of allotetraploid Salix matsudana Koidz. PMID:33328474
A chromosome-scale reference genome of Lobularia maritima, an ornamental plant with high stress tolerance. PMID:33328471
The genome and transcriptome analysis of snake gourd provide insights into its evolution and fruit development and ripening. PMID:33328440
The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy. PMID:33328438
Identification of Hub Genes of Mesio Temporal Lobe Epilepsy and Prognostic Biomarkers of Brain Low-grade Gliomas Based on Bioinformatics Analysis. PMID:33327771
Long non-coding RNAs expression profile and functional analysis of acute ischemic stroke. PMID:33327229
Epigenome-wide association study for atrazine induced transgenerational DNA methylation and histone retention sperm epigenetic biomarkers for disease. PMID:33326428
mTORC1 Transcriptional Regulation of Ribosome Subunits, Protein Synthesis, and Molecular Transport in Primary Human Trophoblast Cells. PMID:33324640
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
NF-κB Signaling Is Regulated by Fucosylation in Metastatic Breast Cancer Cells. PMID:33322811
Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression. PMID:33322692
Genome sequencing of deep-sea hydrothermal vent snails reveals adaptions to extreme environments. PMID:33319911
Different expression of lipid metabolism-related genes in Shandong black cattle and Luxi cattle based on transcriptome analysis. PMID:33318614
Comparative proteomic analysis reveals novel insights into the interaction between rice and Xanthomonas oryzae pv. oryzae. PMID:33317452
Statistical Optimisation of Phenol Degradation and Pathway Identification through Whole Genome Sequencing of the Cold-Adapted Antarctic Bacterium, Rhodococcus sp. Strain AQ5-07. PMID:33316871
Micronutrient supplementation affects transcriptional and epigenetic regulation of lipid metabolism in a dose-dependent manner. PMID:33315488
Chromosome-level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi-C technology. PMID:33314728
Effect of EZH2 on pulmonary artery smooth muscle cell migration in pulmonary hypertension. PMID:33313943
Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants. PMID:33313545
Long-term exposure of human endothelial cells to metformin modulates miRNAs and isomiRs. PMID:33311640
A multivariable miRNA signature delineates the systemic hemodynamic impact of arteriovenous shunt placement in a pilot study. PMID:33311598
Segregation distortion: high genetic load suggested by a Chinese shrimp family under high-intensity selection. PMID:33311524
A meta-learning approach for genomic survival analysis. PMID:33311484
Tissue-specific Gene Expression Changes Are Associated with Aging in Mice. PMID:33309863
Improved risk stratification in younger IDH wild-type glioblastoma patients by combining a 4-miRNA signature with MGMT promoter methylation status. PMID:33305269
Comparative transcriptome profiling of pomegranate genotypes having resistance and susceptible reaction to Xanthomonas axonopodis pv. punicae. PMID:33304163
Multi-omic approach provides insights into osmoregulation and osmoconformation of the crab Scylla paramamosain. PMID:33303836
Probiotic Lactobacillus fermentum strain JDFM216 improves cognitive behavior and modulates immune response with gut microbiota. PMID:33303803
Understanding Mechanisms Underlying Non-Alcoholic Fatty Liver Disease (NAFLD) in Mental Illness: Risperidone and Olanzapine Alter the Hepatic Proteomic Signature in Mice. PMID:33302598
A Comparison of Gene Expression Changes in the Blood of Individuals Consuming Diets Supplemented with Olives, Nuts or Long-Chain Omega-3 Fatty Acids. PMID:33302351
Precision targeting of bacterial pathogen via bi-functional nanozyme activated by biofilm microenvironment. PMID:33302119
DrivAER: Identification of driving transcriptional programs in single-cell RNA sequencing data. PMID:33301553
Chromosome-level draft genome of a diploid plum (Prunus salicina). PMID:33300949
BMP2 induces hMSC osteogenesis and matrix remodeling. PMID:33300084
Next-generation sequencing analysis of circulating micro-RNA expression in response to parabolic flight as a spaceflight analogue. PMID:33298968
Integrated Physiological and Transcriptomic Analyses Reveal a Regulatory Network of Anthocyanin Metabolism Contributing to the Ornamental Value in a Novel Hybrid Cultivar of Camellia Japonica. PMID:33297392
An Integrated Bioinformatic Analysis of the S100 Gene Family for the Prognosis of Colorectal Cancer. PMID:33294444
Are losartan and imatinib effective against SARS-CoV2 pathogenesis? A pathophysiologic-based in silico study. PMID:33294307
Reconstruction of a directed acyclic graph with intervention. PMID:33294093
Network Pharmacology-Based Study on the Mechanism of Gegen Qinlian Decoction against Colorectal Cancer. PMID:33294000
An animal model study on the gene expression profile of meniscal degeneration. PMID:33293598
Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus. PMID:33293569
Donkey genomes provide new insights into domestication and selection for coat color. PMID:33293529
Comprehensive Bioenergetic Evaluation of Microbial Pathway Variants in Syntrophic Propionate Oxidation. PMID:33293404
LKB1 Differently Regulates Adipogenesis in Intramuscular and Subcutaneous Adipocytes through Metabolic and Cytokine-Related Signaling Pathways. PMID:33291665
Maternal lipodome across pregnancy is associated with the neonatal DNA methylome. PMID:33290095
Bioinformatic analysis of key pathways and genes involved in pediatric atopic dermatitis. PMID:33289509
Hidden in plain sight: The effects of BCG vaccination in the COVID-19 pandemic. PMID:33289122
Nitrogen recycling buffers against ammonia toxicity from skeletal muscle breakdown in hibernating arctic ground squirrels. PMID:33288952
Matrix stiffness epigenetically regulates the oncogenic activation of the Yes-associated protein in gastric cancer. PMID:33288878
TMEA: A Thermodynamically Motivated Framework for Functional Characterization of Biological Responses to System Acclimation. PMID:33286800
Thermodynamic Limits and Optimality of Microbial Growth. PMID:33286054
Chronic circadian shift leads to adipose tissue inflammation and fibrosis. PMID:33285245
Interaction of preimplantation factor with the global bovine endometrial transcriptome. PMID:33284816
Metabolic Landscape of the Mouse Liver by Quantitative 31 P Nuclear Magnetic Resonance Analysis of the Phosphorome. PMID:33284502
Assembly of the non-heading pak choi genome and comparison with the genomes of heading Chinese cabbage and the oilseed yellow sarson. PMID:33283404
Overexpression of exogenous biuret hydrolase in rice plants confers tolerance to biuret toxicity. PMID:33283141
TTK, CDC25A, and ESPL1 as Prognostic Biomarkers for Endometrial Cancer. PMID:33282948
A comparative UPLC-Q-Orbitrap-MS untargeted metabolomics investigation of different parts of Clausena lansium (Lour.) Skeels. PMID:33282233
Identification of miRNA Biomarkers for Diverse Cancer Types Using Statistical Learning Methods at the Whole-Genome Scale. PMID:33281862
High-Quality Genome-Scale Models From Error-Prone, Long-Read Assemblies. PMID:33281796
Krüppel-Like Factors 9 and 13 Block Axon Growth by Transcriptional Repression of Key Components of the cAMP Signaling Pathway. PMID:33281552
Replaying the evolutionary tape to investigate subgenome dominance in allopolyploid Brassica napus. PMID:33280122
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity. PMID:33278344
Transcriptome comparison between pluripotent and non-pluripotent calli derived from mature rice seeds. PMID:33277567
Transcriptome analysis reveals that exogenous ethylene activates immune and defense responses in a high late blight resistant potato genotype. PMID:33277549
Complex subsurface hydrothermal fluid mixing at a submarine arc volcano supports distinct and highly diverse microbial communities. PMID:33277434
The critical role of MetR/MetB/MetC/MetX in cysteine and methionine metabolism, fungal development and virulence of Alternaria alternata. PMID:33277273
In-depth secretome analysis of Puccinia striiformis f. sp. tritici in infected wheat uncovers effector functions. PMID:33275764
Screening of T Cell-Related Long Noncoding RNA-MicroRNA-mRNA Regulatory Networks in Non-Small-Cell Lung Cancer. PMID:33274216
Physiological and transcriptomic analyses reveal the roles of secondary metabolism in the adaptive responses of Stylosanthes to manganese toxicity. PMID:33272205
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. PMID:33270889
Tgfb3 and Mmp13 regulated the initiation of liver fibrosis progression as dynamic network biomarkers. PMID:33269546
SITC cancer immunotherapy resource document: a compass in the land of biomarker discovery. PMID:33268350
Candida Species (Volatile) Metabotyping through Advanced Comprehensive Two-Dimensional Gas Chromatography. PMID:33266330
Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives. PMID:33266128
Ensemble Estimation of Information Divergence †. PMID:33265649
YAP/TAZ deficiency reprograms macrophage phenotype and improves infarct healing and cardiac function after myocardial infarction. PMID:33264286
Gene Transfer Agents in Symbiotic Microbes. PMID:33263868
Predicting the relationships between gut microbiota and mental disorders with knowledge graphs. PMID:33262885
Functionally impaired plasmacytoid dendritic cells and non-haematopoietic sources of type I interferon characterize human autoimmunity. PMID:33262343
A Paradox in Bacterial Pathogenesis: Activation of the Local Macrophage Inflammasome Is Required for Virulence of Streptococcus uberis. PMID:33260788
Chromosomal assembly of the Antarctic toothfish ( Dissostichus mawsoni) genome using third-generation DNA sequencing and Hi-C technology. PMID:33258338
Diversification of methanogens into hyperalkaline serpentinizing environments through adaptations to minimize oxidant limitation. PMID:33257813
Elucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing. PMID:33257523
MiR-215-5p Reduces Liver Metastasis in an Experimental Model of Colorectal Cancer through Regulation of ECM-Receptor Interactions and Focal Adhesion. PMID:33255928
Application of Differential Network Enrichment Analysis for Deciphering Metabolic Alterations. PMID:33255384
Identifying longevity associated genes by integrating gene expression and curated annotations. PMID:33253142
Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host. PMID:33252330
Genome-Scale Metabolic Modeling for Unraveling Molecular Mechanisms of High Threat Pathogens. PMID:33251208
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
Selective Bacterial Colonization of the Murine Larynx in a Gnotobiotic Model. PMID:33250883
Manganese Depletion Leads to Multisystem Changes in the Transcriptome of the Opportunistic Pathogen Streptococcus sanguinis. PMID:33250881
iTRAQ-based proteomics reveals serum protein changes in hypertensive rats induced by a high-salt diet. PMID:33250683
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
Transcriptional response of human articular chondrocytes treated with fibronectin fragments: an in vitro model of the osteoarthritis phenotype. PMID:33248223
Effects of dietary n-3-PUFA supplementation, post-insemination plane of nutrition and pregnancy status on the endometrial transcriptome of beef heifers. PMID:33247230
Environmental flexibility does not explain metabolic robustness. PMID:33247119
Comparative transcriptome analysis of scaled and scaleless skins in Gymnocypris eckloni provides insights into the molecular mechanism of scale degeneration. PMID:33246415
Does the proteasome inhibitor bortezomib sensitize to DNA-damaging therapy in gastroenteropancreatic neuroendocrine neoplasms? - A preclinical assessment in vitro and in vivo. PMID:33246310
Single-cell RNA sequencing and lipidomics reveal cell and lipid dynamics of fat infiltration in skeletal muscle. PMID:33244879
Depthwise microbiome and isotopic profiling of a moderately saline microbial mat in a solar saltern. PMID:33244085
Salt-responsive transcriptome analysis of triticale reveals candidate genes involved in the key metabolic pathway in response to salt stress. PMID:33244037
scREAD: A Single-Cell RNA-Seq Database for Alzheimer's Disease. PMID:33241205
Differential expression between drought-tolerant and drought-sensitive sugarcane under mild and moderate water stress as revealed by a comparative analysis of leaf transcriptome. PMID:33240580
Polyphyllin VII suppresses cell proliferation, the cell cycle and cell migration in colorectal cancer. PMID:33240431
Identification of Novel BRCA1 and RAD50 Mutations Associated With Breast Cancer Predisposition in Tunisian Patients. PMID:33240314
Assessing the Risk of Transfer of Microorganisms at the International Space Station Due to Cargo Delivery by Commercial Resupply Vehicles. PMID:33240227
Functional characterisation of the transcriptome from leaf tissue of the fluoroacetate-producing plant, Dichapetalum cymosum, in response to mechanical wounding. PMID:33239700
Single cell profiling of capillary blood enables out of clinic human immunity studies. PMID:33239690
Integrative genomic meta-analysis reveals novel molecular insights into cystic fibrosis and ΔF508-CFTR rescue. PMID:33239626
MicroRNAs and Mammarenaviruses: Modulating Cellular Metabolism. PMID:33238430
Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity. PMID:33235355
Uncovering the pharmacological mechanism of the effects of the Banxia-Xiakucao Chinese Herb Pair on sleep disorder by a systems pharmacology approach. PMID:33235305
Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L. PMID:33235240
Anti-Tick Microbiota Vaccine Impacts Ixodes ricinus Performance during Feeding. PMID:33233316
Androgen Signaling Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. PMID:33232663
Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients. PMID:33232475
Investigation of drugs affecting hypertension in bevacizumab-treated patients and examination of the impact on the therapeutic effect. PMID:33231381
Limits to the cellular control of sequestered cryptophyte prey in the marine ciliate Mesodinium rubrum. PMID:33230263
Inhibition of 3-phosphoinositide-dependent protein kinase 1 (PDK1) can revert cellular senescence in human dermal fibroblasts. PMID:33229519
ClpX Is Essential and Activated by Single-Strand DNA Binding Protein in Mycobacteria. PMID:33229461
Gene Mapping, Genome-Wide Transcriptome Analysis, and WGCNA Reveals the Molecular Mechanism for Triggering Programmed Cell Death in Rice Mutant pir1. PMID:33228024
In silico identification of effector proteins from generalist herbivore Spodoptera litura. PMID:33225897
The expression of the acarbose biosynthesis gene cluster in Actinoplanes sp. SE50/110 is dependent on the growth phase. PMID:33225887
Investigation of the Potential Mechanism Governing the Effect of the Shen Zhu San on COVID-19 by Network Pharmacology. PMID:33224256
Systems toxicogenomics of prenatal low-dose BPA exposure on liver metabolic pathways, gut microbiota, and metabolic health in mice. PMID:33221593
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. PMID:33219670
Unique maternal immune and functional microbial profiles during prenatal stress. PMID:33219314
Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis. PMID:33219248
Circulating miRNA-181b-5p, miRNA-223-3p, miRNA-210-3p, let 7i-5p, miRNA-21-5p and miRNA-29a-3p in patients with localized scleroderma as potential biomarkers. PMID:33214624
LOXL2 promotes aggrecan and gender-specific anabolic differences to TMJ cartilage. PMID:33214607
Variable Selection in Untargeted Metabolomics and the Danger of Sparsity. PMID:33213095
Proteogenomic Landscape of Breast Cancer Tumorigenesis and Targeted Therapy. PMID:33212010
BAP1 mutant uveal melanoma is stratified by metabolic phenotypes with distinct vulnerability to metabolic inhibitors. PMID:33208912
Elevated CO2 and nitrate levels increase wheat root-associated bacterial abundance and impact rhizosphere microbial community composition and function. PMID:33208893
Machine learning approaches reveal genomic regions associated with sugarcane brown rust resistance. PMID:33208862
RNA sequencing as an alternative tool for detecting measurable residual disease in core-binding factor acute myeloid leukemia. PMID:33208771
The effect of hypoxia on the proteomic signature of pig adipose-derived stromal/stem cells (pASCs). PMID:33208768
Comprehensive ESI-Q TRAP-MS/MS based characterization of metabolome of two mango (Mangifera indica L) cultivars from China. PMID:33208758
8-Hydroxydaidzein, an Isoflavone from Fermented Soybean, Induces Autophagy, Apoptosis, Differentiation, and Degradation of Oncoprotein BCR-ABL in K562 Cells. PMID:33207739
BCG Vaccination Induces Long-Term Functional Reprogramming of Human Neutrophils. PMID:33207187
Evolution of Oxidative Phosphorylation (OXPHOS) Genes Reflecting the Evolutionary and Life Histories of Fig Wasps (Hymenoptera, Chalcidoidea). PMID:33203150
Microarray expression profile analysis of circular RNAs and their potential regulatory role in bladder carcinoma. PMID:33200221
Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters. PMID:33199808
Awakening a latent carbon fixation cycle in Escherichia coli. PMID:33199707
Transcriptional response of Bacillus megaterium FDU301 to PEG200-mediated arid stress. PMID:33198631
Towards a More Reliable Identification of Isomeric Metabolites Using Pattern Guided Retention Validation. PMID:33198249
Transcriptome Analysis Identifies SenZfp536, a Sense LncRNA that Suppresses Self-renewal of Cortical Neural Progenitors. PMID:33196962
A comparison of mRNA and circRNA expression between squamous cell carcinoma and adenocarcinoma of the lungs. PMID:33196759
CXC Chemokine/Receptor Axis Profile and Metastasis in Prostate Cancer. PMID:33195424
A Middle-Out Modeling Strategy to Extend a Colon Cancer Logical Model Improves Drug Synergy Predictions in Epithelial-Derived Cancer Cell Lines. PMID:33195403
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PMID:33194391
Differentially expressed serum proteins in children with or without asthma as determined using isobaric tags for relative and absolute quantitation proteomics. PMID:33194371
Contributions of Adaptive Plant Architecture to Transgressive Salinity Tolerance in Recombinant Inbred Lines of Rice: Molecular Mechanisms Based on Transcriptional Networks. PMID:33193743
Transcriptome Analyses of β-Thalassemia -28(A>G) Mutation Using Isogenic Cell Models Generated by CRISPR/Cas9 and Asymmetric Single-Stranded Oligodeoxynucleotides (assODNs). PMID:33193694
Plant miRNAs Reduce Cancer Cell Proliferation by Targeting MALAT1 and NEAT1: A Beneficial Cross-Kingdom Interaction. PMID:33193626
Identification of Potential Core Genes Associated With the Progression of Stomach Adenocarcinoma Using Bioinformatic Analysis. PMID:33193601
Insights Into the Albinism Mechanism for Two Distinct Color Morphs of Northern Snakehead, Channa argus Through Histological and Transcriptome Analyses. PMID:33193565
The Eruca sativa Genome and Transcriptome: A Targeted Analysis of Sulfur Metabolism and Glucosinolate Biosynthesis Pre and Postharvest. PMID:33193472
Interpretations of Environmental Microbial Community Studies Are Biased by the Selected 16S rRNA (Gene) Amplicon Sequencing Pipeline. PMID:33193131
GWAS SNPs Impact Shared Regulatory Pathways Amongst Multimorbid Psychiatric Disorders and Cognitive Functioning. PMID:33192679
Transcriptome Analysis and Knockdown of the Juvenile Hormone Esterase Gene Reveal Abnormal Feeding Behavior in the Sugarcane Giant Borer. PMID:33192604
Virtual screening and network pharmacology-based synergistic mechanism identification of multiple components contained in Guanxin V against coronary artery disease. PMID:33187508
Analysis of miR-9-5p, miR-124-3p, miR-21-5p, miR-138-5p, and miR-1-3p in Glioblastoma Cell Lines and Extracellular Vesicles. PMID:33187334
Mechanisms of EGFR Resistance in Glioblastoma. PMID:33187135
Whole-Genome Transcriptome Analyses of Native Symbionts Reveal Host Coral Genomic Novelties for Establishing Coral-Algae Symbioses. PMID:33185681
LncRNA and mRNA expression profile of peripheral blood mononuclear cells in primary Sjögren's syndrome patients. PMID:33184486
The effect of Rbfox2 modulation on retinal transcriptome and visual function. PMID:33184471
Transcriptome profiling and weighted gene co-expression network analysis of early floral development in Aquilegia coerulea. PMID:33184405
Insights into malaria pathogenesis gained from host metabolomics. PMID:33180883
TISCH: a comprehensive web resource enabling interactive single-cell transcriptome visualization of tumor microenvironment. PMID:33179754
Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Melanoma. PMID:33178610
Cryptosporidium parvum Infection Depletes Butyrate Producer Bacteria in Goat Kid Microbiome. PMID:33178145
Transcriptome Profiling and Cytological Assessments for Identifying Regulatory Pathways Associated With Diorcinol N-Induced Autophagy in A3 Cells. PMID:33178020
A network-based approach to deciphering a dynamic microbiome's response to a subtle perturbation. PMID:33177547
Changes in transcriptomic and metabolomic profiles of morphotypes of Ophiocordyceps sinensis within the hemocoel of its host larvae, Thitarodes xiaojinensis. PMID:33176684
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. PMID:33174596
Co‑expression network analysis identified specific miRNAs and genes in association with slow‑transit constipation. PMID:33174045
Narasin inhibits tumor metastasis and growth of ERα‑positive breast cancer cells by inactivation of the TGF‑β/SMAD3 and IL‑6/STAT3 signaling pathways. PMID:33174044
Upregulated lnc‑HRK‑2:1 prompts nucleus pulposus cell senescence in intervertebral disc degeneration. PMID:33174041
Identification of inflammation‑associated circulating long non‑coding RNAs and genes in intracranial aneurysm rupture‑induced subarachnoid hemorrhage. PMID:33174039
Using mRNA deep sequencing to analyze differentially expressed genes during Panax notoginseng saponin treatment of ischemic stroke. PMID:33173991
Cytokines CCL2 and CXCL1 may be potential novel predictors of early bone loss. PMID:33173955
Integrated microarray analysis of key genes and a miRNA‑mRNA regulatory network of early‑onset preeclampsia. PMID:33173953
Developmental differences in the intestinal microbiota of Chinese 1-year-old infants and 4-year-old children. PMID:33173227
Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy. PMID:33173052
Cancer Alters the Metabolic Fingerprint of Extracellular Vesicles. PMID:33172086
Response of Horticultural Soil Microbiota to Different Fertilization Practices. PMID:33171888
Differential Expression Profiling Reveals Stress-Induced Cell Fate Divergence in Soybean Microspores. PMID:33171842
A Novel Aminoacyl-tRNA Synthetase Appended Domain Can Supply the Core Synthetase with Its Amino Acid Substrate. PMID:33171705
Biological network analysis with deep learning. PMID:33169146
Deciphering cell-cell interactions and communication from gene expression. PMID:33168968
Pathway information extracted from 25 years of pathway figures. PMID:33168034
Identifying genetic variants associated with ritodrine-induced pulmonary edema. PMID:33166306
Ethnobotany and the Role of Plant Natural Products in Antibiotic Drug Discovery. PMID:33164487
Comparative Transcriptome Analysis of the Regenerating Zebrafish Telencephalon Unravels a Resource With Key Pathways During Two Early Stages and Activation of Wnt/β-Catenin Signaling at the Early Wound Healing Stage. PMID:33163496
Metabolic Perturbations Caused by the Over-Expression of mcr-1 in Escherichia coli. PMID:33162965
Microbial Key Players Involved in P Turnover Differ in Artificial Soil Mixtures Depending on Clay Mineral Composition. PMID:33161521
Bioinformatics-based identification of miRNA-, lncRNA-, and mRNA-associated ceRNA networks and potential biomarkers for preeclampsia. PMID:33157942
Drug sensitivity prediction with normal inverse Gaussian shrinkage informed by external data. PMID:33155717
Omics approaches for conservation biology research on the bivalve Chamelea gallina. PMID:33154500
RNA Sequencing Reveals Diverse Functions of Amniotic Fluid Neutrophils and Monocytes/Macrophages in Intra-Amniotic Infection. PMID:33152737
Isolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum. PMID:33150080
Potential Molecular Mechanisms of Plantain in the Treatment of Gout and Hyperuricemia Based on Network Pharmacology. PMID:33149752
Desmoglein 3 and Keratin 14 for Distinguishing Between Lung Adenocarcinoma and Lung Squamous Cell Carcinoma. PMID:33149622
Characterization of somatic mutation-associated microenvironment signatures in acute myeloid leukemia patients based on TCGA analysis. PMID:33149230
Airway Microbiota-Host Interactions Regulate Secretory Leukocyte Protease Inhibitor Levels and Influence Allergic Airway Inflammation. PMID:33147448
Metagenomic Analysis Exploring Taxonomic and Functional Diversity of Soil Microbial Communities in Sugarcane Fields Applied with Organic Fertilizer. PMID:33145361
Exploration in the Mechanism of Kaempferol for the Treatment of Gastric Cancer Based on Network Pharmacology. PMID:33145355
Comparative physiological and transcriptomic analysis of pear leaves under distinct training systems. PMID:33144674
Transcriptomic profiling of feline teeth highlights the role of matrix metalloproteinase 9 (MMP9) in tooth resorption. PMID:33144645
Analysis of a radiation-induced dwarf mutant of a warm-season turf grass reveals potential mechanisms involved in the dwarfing mutant. PMID:33144613
Broad genic repression domains signify enhanced silencing of oncogenes. PMID:33144558
Microbiota-Derived Short-Chain Fatty Acids Promote LAMTOR2-Mediated Immune Responses in Macrophages. PMID:33144310
Seasonal Patterns of Dominant Microbes Involved in Central Nutrient Cycles in the Subsurface. PMID:33143231
Revealing Alteration in the Hepatic Glucose Metabolism of Genetically Improved Carp, Jayanti Rohu Labeo rohita Fed a High Carbohydrate Diet Using Transcriptome Sequencing. PMID:33142948
Integrated analysis of phosphoproteome and ubiquitylome in epididymal sperm of buffalo (Bubalus bubalis). PMID:33140506
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus. PMID:33139884
Extraction and Integration of Genetic Networks from Short-Profile Omic Data Sets. PMID:33137869
High Expression of UBB, RAC1, and ITGB1 Predicts Worse Prognosis among Nonsmoking Patients with Lung Adenocarcinoma through Bioinformatics Analysis. PMID:33134373
Functional and Clinical Characterization of Tumor-Infiltrating T Cell Subpopulations in Hepatocellular Carcinoma. PMID:33133170
Epigenetic Programming Through Breast Milk and Its Impact on Milk-Siblings Mating. PMID:33133155
From sequence to information. PMID:33131436
An in-silico method leads to recognition of hub genes and crucial pathways in survival of patients with breast cancer. PMID:33128008
Whole transcriptome analysis of adrenal glands from prenatal glucocorticoid programmed hypertensive rodents. PMID:33127986
LAMP: disease classification derived from layered assessment on modules and pathways in the human gene network. PMID:33126852
Long non‑coding RNA expression profiles identify lncRNA‑XLOC_I2_006631 as a potential novel blood biomarker for Hashimoto's thyroiditis. PMID:33125100
Depletion of eukaryotic initiation factor 5B (eIF5B) reprograms the cellular transcriptome and leads to activation of endoplasmic reticulum (ER) stress and c-Jun N-terminal kinase (JNK). PMID:33123915
The Oncometabolite 5'-Deoxy-5'-Methylthioadenosine Blocks Multiple Signaling Pathways of NK Cell Activation. PMID:33123121
PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom. PMID:33123113
Local Conditions Influence the Prokaryotic Communities Associated With the Mesophotic Black Coral Antipathella subpinnata. PMID:33123099
An Integrative Serum Pharmacology-Based Approach to Study the Anti-Tumor Activity of B. paniculatum Aqueous Bulb Extract on the Human Hepatocellular Carcinoma Cell Line BEL-7404. PMID:33123002
Functional in vivo and in vitro effects of 20q11.21 genetic aberrations on hPSC differentiation. PMID:33122739
Feature selection algorithm based on dual correlation filters for cancer-associated somatic variants. PMID:33121438
The Status of Soil Microbiome as Affected by the Application of Phosphorus Biofertilizer: Fertilizer Enriched with Beneficial Bacterial Strains. PMID:33121206
Impact of Zika Virus Infection on Human Neural Stem Cell MicroRNA Signatures. PMID:33121145
Screening and identification of key genes and pathways in metastatic uveal melanoma based on gene expression using bioinformatic analysis. PMID:33120861
Identification of key genes and pathways for melanoma in the TRIM family. PMID:33118318
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. PMID:33118035
RNA Profiling Reveals a Common Mechanism of Histone Gene Downregulation and Complementary Effects for Radioprotectants in Response to Ionizing Radiation. PMID:33117095
Identification of Novel Therapeutic Molecular Targets in Inflammatory Bowel Disease by Using Genetic Databases. PMID:33116744
Analysis of Differential Expression Proteins of Paclitaxel-Treated Lung Adenocarcinoma Cell A549 Using Tandem Mass Tag-Based Quantitative Proteomics. PMID:33116610
RUNX3 methylation drives hypoxia-induced cell proliferation and antiapoptosis in early tumorigenesis. PMID:33116296
Dynamic transcriptional response of Saccharomyces cerevisiae cells to copper. PMID:33116258
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. PMID:33116115
Multiplexed Quantitative Assessment of the Fate of Taurine and Sulfoquinovose in the Intestinal Microbiome. PMID:33114761
Correlation between the Antimicrobial Activity and Metabolic Profiles of Cell Free Supernatants and Membrane Vesicles Produced by Lactobacillus reuteri DSM 17938. PMID:33114410
Differential Gene Expression in Brain and Liver Tissue of Wistar Rats after Rapid Eye Movement Sleep Deprivation. PMID:33114225
Parallel Social Information Processing Circuits Are Differentially Impacted in Autism. PMID:33113347
Genome-wide DNA methylation analysis of Hashimoto's thyroiditis during pregnancy. PMID:33113271
Cp1/cathepsin L is required for autolysosomal clearance in Drosophila. PMID:33112206
Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress. PMID:33110158
Transcriptome analysis of chicken intraepithelial lymphocyte natural killer cells infected with very virulent infectious bursal disease virus. PMID:33110122
Deciphering the Microbial Taxonomy and Functionality of Two Diverse Mangrove Ecosystems and Their Potential Abilities To Produce Bioactive Compounds. PMID:33109752
Analysing the meta-interaction between pathways by gene set topological impact analysis. PMID:33109101
Single-cell patterning and axis characterization in the murine and human definitive endoderm. PMID:33106598
Data on chemical-gene interactions and biological categories enriched with genes sensitive to chemical exposures. PMID:33102660
Cross-Sectional Transcriptional Analysis of the Aging Murine Heart. PMID:33102519
Forkhead box P3 promotes breast cancer cell apoptosis by regulating programmed cell death 4 expression. PMID:33101486
Plasmatic Membrane Expression of Adhesion Molecules in Human Cardiac Progenitor/Stem Cells Might Explain Their Superior Cell Engraftment after Cell Transplantation. PMID:33101423
Systematic Identification of Hub Genes in Placenta Accreta Spectrum Based on Integrated Transcriptomic and Proteomic Analysis. PMID:33101378
Genome-wide analysis of therapeutic response uncovers molecular pathways governing tamoxifen resistance in ER+ breast cancer. PMID:33099086
Dietary Phytase- and Lactic Acid-Treated Cereals Caused Greater Taxonomic Adaptations than Functional Adaptations in the Cecal Metagenome of Growing Pigs. PMID:33097516
Amino Sugars Reshape Interactions between Streptococcus mutans and Streptococcus gordonii. PMID:33097515
Similarities and Differences of Photosynthesis Establishment Related mRNAs and Novel lncRNAs in Early Seedlings (Coleoptile/Cotyledon vs. True Leaf) of Rice and Arabidopsis. PMID:33093843
Systems analysis of avascular necrosis of femoral head using integrative data analysis and literature mining delineates pathways associated with disease. PMID:33093559
Chronic stress and antidepressant treatment alter purine metabolism and beta oxidation within mouse brain and serum. PMID:33093530
In vivo vaccination with cell line-derived whole tumor lysates: neoantigen quality, not quantity matters. PMID:33087163
A method for estimating coherence of molecular mechanisms in major human disease and traits. PMID:33087046
Interferon-Mediated Long Non-Coding RNA Response in Macrophages in the Context of HIV. PMID:33086748
Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake. PMID:33086464
Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma. PMID:33086064
Integrative Analyses of Genes Associated with Fulminant Type 1 Diabetes. PMID:33083497
Identification of Key Genes Involved in Acute Myocardial Infarction by Comparative Transcriptome Analysis. PMID:33083450
Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma. PMID:33083449
Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages. PMID:33083113
The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species. PMID:33082971
Low expression of Talin1 is associated with advanced pathological features in colorectal cancer patients. PMID:33082414
Insights into the Gryllus bimaculatus Immune-Related Transcriptomic Profiling to Combat Naturally Invading Pathogens. PMID:33080980
Organophosphorus flame retardants are developmental neurotoxicants in a rat primary brainsphere in vitro model. PMID:33078273
Finding disease modules for cancer and COVID-19 in gene co-expression networks with the Core&Peel method. PMID:33077837
Epigenetic regulation of gene expression improves Fusarium head blight resistance in durum wheat. PMID:33077800
Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea. PMID:33077635
Brain transcriptome analysis reveals subtle effects on mitochondrial function and iron homeostasis of mutations in the SORL1 gene implicated in early onset familial Alzheimer's disease. PMID:33076949
Expression of mitochondrial protein genes encoded by nuclear and mitochondrial genomes correlate with energy metabolism in dairy cattle. PMID:33076826
Shewanella oneidensis NADH dehydrogenase mutants exhibit an amino acid synthesis defect. PMID:33072733
Cell Development Deficiency and Gene Expression Dysregulation of Trisomy 21 Retina Revealed by Single-Nucleus RNA Sequencing. PMID:33072724
Gut Microbiota-Metabolome Changes in Children With Diarrhea by Diarrheagenic E. coli. PMID:33072619
Alternative Splicing Enhances the Transcriptome Complexity of Liriodendron chinense. PMID:33072153
Role of BgaA as a Pneumococcal Virulence Factor Elucidated by Molecular Evolutionary Analysis. PMID:33072054
Transcriptomic Profiling of Various Developmental Stages of Aphis Aurantii to Provide a Genetic Resource for Gene Expression and SSR Analysis. PMID:33071832
Unpaired data empowers association tests. PMID:33070196
Distinct expression profiles of peptides in placentae from preeclampsia and normal pregnancies. PMID:33067549
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell. PMID:33067542
Integrated genomics analysis highlights important SNPs and genes implicated in moderate-to-severe asthma based on GWAS and eQTL datasets. PMID:33066754
Combined Transcriptome and Proteome Analysis of Masson Pine (Pinus massoniana Lamb.) Seedling Root in Response to Nitrate and Ammonium Supplementations. PMID:33066140
Seeding Biochemistry on Other Worlds: Enceladus as a Case Study. PMID:33064954
A practical guide to mechanistic systems modeling in biology using a logic-based approach. PMID:33064138
Identification of G2 and S Phase-Expressed-1 as a Potential Biomarker in Patients with Prostate Cancer. PMID:33061616
Exploration of the Potential Biomarkers of Papillary Thyroid Cancer (PTC) Based on RT2 Profiler PCR Arrays and Bioinformatics Analysis. PMID:33061614
Identification of epigenetic variation associated with synchronous pod maturity in mungbean (Vigna radiata L.). PMID:33060755
De novo transcriptome analysis of Chlorella sorokiniana: effect of glucose assimilation, and moderate light intensity. PMID:33060668
Health and disease markers correlate with gut microbiome composition across thousands of people. PMID:33060586
What happens after a blood meal? A transcriptome analysis of the main tissues involved in egg production in Rhodnius prolixus, an insect vector of Chagas disease. PMID:33057354
In vivo estrogenicity of p-phenoxyphenol and p-pentyloxyphenol. PMID:33057140
Petal abscission in fragrant roses is associated with large scale differential regulation of the abscission zone transcriptome. PMID:33057097
smORFunction: a tool for predicting functions of small open reading frames and microproteins. PMID:33054771
Temporal Proteomic Profiling of SH-SY5Y Differentiation with Retinoic Acid Using FAIMS and Real-Time Searching. PMID:33054241
Effect of Citric Acid Cycle Genetic Variants and Their Interactions with Obesity, Physical Activity and Energy Intake on the Risk of Colorectal Cancer: Results from a Nested Case-Control Study in the UK Biobank. PMID:33053772
Present and Future of Anti-Glioblastoma Therapies: A Deep Look into Molecular Dependencies/Features. PMID:33053763
Human oral microbiome dysbiosis as a novel non-invasive biomarker in detection of colorectal cancer. PMID:33052235
Identification of potential key genes and miRNAs involved in Hepatoblastoma pathogenesis and prognosis. PMID:33051830
Learning graph representations of biochemical networks and its application to enzymatic link prediction. PMID:33051674
Proteome Analysis of Walnut Bacterial Blight Disease. PMID:33050347
Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle. PMID:33050182
A Comparative Transcriptome Analysis, Conserved Regulatory Elements and Associated Transcription Factors Related to Accumulation of Fusariotoxins in Grain of Rye (Secale cereale L.) Hybrids. PMID:33049995
Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. PMID:33048460
Inhibition of O-GlcNAc transferase activates tumor-suppressor gene expression in tamoxifen-resistant breast cancer cells. PMID:33046784
Role of a genetic variation in the microRNA-4421 binding site of ERP29 regarding risk of oropharynx cancer and prognosis. PMID:33046743
Micro RNA Targets in HIV Latency: Insights into Novel Layers of Latency Control. PMID:33045840
Perfluorooctanesulfonic Acid-Induced Toxicity on Zebrafish Embryos in the Presence or Absence of the Chorion. PMID:33044770
SYTL4 downregulates microtubule stability and confers paclitaxel resistance in triple-negative breast cancer. PMID:33042263
Transcriptome Analysis of Different Tissues Reveals Key Genes Associated With Galanthamine Biosynthesis in Lycoris longituba. PMID:33042169
VapC21 Toxin Contributes to Drug-Tolerance and Interacts With Non-cognate VapB32 Antitoxin in Mycobacterium tuberculosis. PMID:33042034
Genomic, proteomic, and systems biology approaches in biomarker discovery for multiple sclerosis. PMID:33039896
Metformin elicits antitumour effect by modulation of the gut microbiota and rescues Fusobacterium nucleatum-induced colorectal tumourigenesis. PMID:33039709
Analysis of microRNA-34a expression profile and rs2666433 variant in colorectal cancer: a pilot study. PMID:33037254
Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing. PMID:33037003
DockCoV2: a drug database against SARS-CoV-2. PMID:33035337
Gene-set Enrichment with Mathematical Biology (GEMB). PMID:33034635
A review of protein-protein interaction network alignment: From pathway comparison to global alignment. PMID:33033584
Identification of Potential Biomarkers for CAD Using Integrated Expression and Methylation Data. PMID:33033488
Suppression of inflammatory arthritis in human serum paraoxonase 1 transgenic mice. PMID:33033318
The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. PMID:33032658
Application of compound material alleviates saline and alkaline stress in cotton leaves through regulation of the transcriptome. PMID:33032521
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. PMID:33031577
BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms. PMID:33028629
Identification of a new pseudogenes/lncRNAs-hsa-miR-26b-5p-COL12A1 competing endogenous RNA network associated with prognosis of pancreatic cancer using bioinformatics analysis. PMID:33027767
Immunometabolism in the Single-Cell Era. PMID:33027638
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. PMID:33024988
EAT-UpTF: Enrichment Analysis Tool for Upstream Transcription Factors of a Group of Plant Genes. PMID:33024441
A glance at the gut microbiota of five experimental animal species through fecal samples. PMID:33024229
HMGR overexpression and interference affect the expression of steroidogenic genes and cholesterol content in bovine intramuscular adipocytes. PMID:33024216
Atribacteria Reproducing over Millions of Years in the Atlantic Abyssal Subseafloor. PMID:33024037
Identification of Parkinson's disease-related pathways and potential risk factors. PMID:33021140
A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci. PMID:33020633
Identification of Key Genes in Gastric Cancer by Bioinformatics Analysis. PMID:33015179
Putative genome features of relic green alga-derived nuclei in dinoflagellates and future perspectives as model organisms. PMID:33014260
Cyberlindnera jadinii Yeast as a Protein Source for Weaned Piglets-Impact on Immune Response and Gut Microbiota. PMID:33013844
Neural Network Deconvolution Method for Resolving Pathway-Level Progression of Tumor Clonal Expression Programs With Application to Breast Cancer Brain Metastases. PMID:33013452
Mouse Genetic Reference Populations: Cellular Platforms for Integrative Systems Genetics. PMID:33010949
Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing. PMID:33009591
Database: web application for visualization of the cumulated RNAseq data against the salicylic acid (SA) and methyl jasmonate (MeJA) treatment of Arabidopsis thaliana. PMID:33008298
Differential network analysis of bovine muscle reveals changes in gene coexpression patterns in response to changes in maternal nutrition. PMID:33008289
Oxidative pentose phosphate pathway and glucose anaplerosis support maintenance of mitochondrial NADPH pool under mitochondrial oxidative stress. PMID:33005744
Molecular study of drought response in the Mediterranean conifer Pinus pinaster Ait.: Differential transcriptomic profiling reveals constitutive water deficit-independent drought tolerance mechanisms. PMID:33005345
Integrated transcriptomic and metabolomic data reveal the flavonoid biosynthesis metabolic pathway in Perilla frutescens (L.) leaves. PMID:33004940
Exploring celiac disease candidate pathways by global gene expression profiling and gene network cluster analysis. PMID:33004927
Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm. PMID:33004875
Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis). PMID:33002025
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Uncovering potential differentially expressed miRNAs and targeted mRNAs in myocardial infarction based on integrating analysis. PMID:33000230
Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L. PMID:32999341
Antimicrobial Peptide Exposure Selects for Resistant and Fit Stenotrophomonas maltophilia Mutants That Show Cross-Resistance to Antibiotics. PMID:32999081
Efficient Propagation of Circulating Tumor Cells: A First Step for Probing Tumor Metastasis. PMID:32998338
Identification of the significant pathways of Banxia Houpu decoction in the treatment of depression based on network pharmacology. PMID:32997725
IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis. PMID:32997660
Broad range shuttle vector construction and promoter evaluation for the use of Lactobacillus plantarum WCFS1 as a microbial engineering platform. PMID:32995537
Tailor-made exopolysaccharides-CRISPR-Cas9 mediated genome editing in Paenibacillus polymyxa. PMID:32995508
Regeneration of unconventional natural gas by methanogens co-existing with sulfate-reducing prokaryotes in deep shale wells in China. PMID:32994524
Safety and functional enrichment of gut microbiome in healthy subjects consuming a multi-strain fermented milk product: a randomised controlled trial. PMID:32994487
Adaptation of Arginine Synthesis among Uropathogenic Branches of the Escherichia coli Phylogeny Reveals Adjustment to the Urinary Tract Habitat. PMID:32994329
In vitro resynthesis of lichenization reveals the genetic background of symbiosis-specific fungal-algal interaction in Usnea hakonensis. PMID:32993496
Co-Administration of Propionate or Protocatechuic Acid Does Not Affect DHA-Specific Transcriptional Effects on Lipid Metabolism in Cultured Hepatic Cells. PMID:32993128
YB-1 Interferes with TNFα-TNFR Binding and Modulates Progranulin-Mediated Inhibition of TNFα Signaling. PMID:32992926
Ionotropic Receptors as a Driving Force behind Human Synapse Establishment. PMID:32986821
Distinctiveness of genes contributing to growth of Pseudomonas syringae in diverse host plant species. PMID:32986776
Genomic and experimental data provide new insights into luciferin biosynthesis and bioluminescence evolution in fireflies. PMID:32985577
Understanding salt tolerance mechanism using transcriptome profiling and de novo assembly of wild tomato Solanum chilense. PMID:32985535
Mapping the bacterial metabolic niche space. PMID:32985497
High quality genome of Erigeron breviscapus provides a reference for herbal plants in Asteraceae. PMID:32985109
Cancer-associated fibroblasts of the prostate promote a compliant and more invasive phenotype in benign prostate epithelial cells. PMID:32984808
Complement C7 (C7), a Potential Tumor Suppressor, Is an Immune-Related Prognostic Biomarker in Prostate Cancer (PC). PMID:32984006
Genome-Wide Identification of Dickeya solani Transcriptional Units Up-Regulated in Response to Plant Tissues From a Crop-Host Solanum tuberosum and a Weed-Host Solanum dulcamara. PMID:32983224
Accelerated Biodegradation of the Agrochemical Ametoctradin by Soil-Derived Microbial Consortia. PMID:32982997
Network pharmacology based virtual screening of active constituents of Prunella vulgaris L. and the molecular mechanism against breast cancer. PMID:32978480
Extracellular vesicles shuttle protective messages against heat stress in bovine granulosa cells. PMID:32978452
Global identification and characterization of miRNA family members responsive to potassium deprivation in wheat (Triticum aestivum L.). PMID:32978439
A Structurally Novel Lipoyl Synthase in the Hyperthermophilic Archaeon Thermococcus kodakarensis. PMID:32978128
Longitudinal Metatranscriptomic Analysis of a Meat Spoilage Microbiome Detects Abundant Continued Fermentation and Environmental Stress Responses during Shelf Life and Beyond. PMID:32978125
Systems pharmacological study illustrates the immune regulation, anti-infection, anti-inflammation, and multi-organ protection mechanism of Qing-Fei-Pai-Du decoction in the treatment of COVID-19. PMID:32978039
Genetic background dependent modifiers of craniosynostosis severity. PMID:32976998
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain Design. PMID:32974289
The photo-inhibition of camphor leaves (Cinnamomum camphora L.) by NaCl stress based on physiological, chloroplast structure and comparative proteomic analysis. PMID:32974090
Systemic Expression Analysis Reveals Prognostic Significance of WIPI3 in Hepatocellular Carcinoma. PMID:32973867
H2S Regulation of Metabolism in Cucumber in Response to Salt-Stress Through Transcriptome and Proteome Analysis. PMID:32973842
Likelihood ratio tests for a large directed acyclic graph. PMID:32973370
Correlation between Expression Profiles of Key Signaling Genes in Colorectal Cancer Samples from Type 2 Diabetic and Non-Diabetic Patients. PMID:32971867
Identification of potential specific biomarkers and key signaling pathways between osteogenic and adipogenic differentiation of hBMSCs for osteoporosis therapy. PMID:32967719
Pathway-Based Integrative Analysis of Metabolome and Microbiome Data from Hepatocellular Carcinoma and Liver Cirrhosis Patients. PMID:32967314
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
SARS-CoV-2 and the possible connection to ERs, ACE2, and RAGE: Focus on susceptibility factors. PMID:32965736
Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. PMID:32964109
Systematic Elucidation of the Mechanism of Quercetin against Gastric Cancer via Network Pharmacology Approach. PMID:32964029
Identification of hub genes associated with esophageal cancer progression using bioinformatics analysis. PMID:32963620
Long non-coding RNA LPP-AS2 promotes glioma tumorigenesis via miR-7-5p/EGFR/PI3K/AKT/c-MYC feedback loop. PMID:32962742
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Identification of modules and novel prognostic biomarkers in liver cancer through integrated bioinformatics analysis. PMID:32961635
Influenza A virus co-opts ERI1 exonuclease bound to histone mRNA to promote viral transcription. PMID:32960265
Preanalytical Sample Handling Conditions and Their Effects on the Human Serum Metabolome in Epidemiologic Studies. PMID:32959873
Reconstructing organisms in silico: genome-scale models and their emerging applications. PMID:32958892
DNA methylation across the genome in aged human skeletal muscle tissue and muscle-derived cells: the role of HOX genes and physical activity. PMID:32958812
Transcription factor expression as a predictor of colon cancer prognosis: a machine learning practice. PMID:32957968
In silico transcriptional analysis of mRNA and miRNA reveals unique biosignatures that characterizes different types of diabetes. PMID:32956382
Nutriome-metabolome relationships provide insights into dietary intake and metabolism. PMID:32954362
Identification of hub genes in diabetic kidney disease via multiple-microarray analysis. PMID:32953797
Serum proteins differentially expressed in early- and late-onset preeclampsia assessed using iTRAQ proteomics and bioinformatics analyses. PMID:32953262
Knockdown of SAR1B suppresses proliferation and induces apoptosis of RKO colorectal cancer cells. PMID:32952655
Gut microbiota steroid sexual dimorphism and its impact on gonadal steroids: influences of obesity and menopausal status. PMID:32951609
Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge. PMID:32948522
Bioinformatics Data Mining Repurposes the JAK2 (Janus Kinase 2) Inhibitor Fedratinib for Treating Pancreatic Ductal Adenocarcinoma by Reversing the KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog)-Driven Gene Signature. PMID:32947833
Revealing antimicrobial resistance in stormwater with MinION. PMID:32947654
Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development. PMID:32946788
Small RNA deep sequencing reveals novel miRNAs in peripheral blood mononuclear cells from patients with IgA nephropathy. PMID:32945407
Comparison of l-tyrosine containing dipeptides reveals maximum ATP availability for l-prolyl-l-tyrosine in CHO cells. PMID:32944013
The phosphoproteomic responses of duck (Cairna moschata) to classical/novel duck reovirus infections in the spleen tissue. PMID:32943705
Analyzing Differentially Expressed Genes and Pathways Associated with Pistil Abortion in Japanese Apricot via RNA-Seq. PMID:32942711
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma). PMID:32938378
Infection with Bacteroides Phage BV01 Alters the Host Transcriptome and Bile Acid Metabolism in a Common Human Gut Microbe. PMID:32937127
Chitinase 3-Like 1 Contributes to Food Allergy via M2 Macrophage Polarization. PMID:32935492
Immunotyping of tumor-infiltrating lymphocytes in triple-negative breast cancer and genetic characterization. PMID:32934708
Identification of Potential Drug Targets in Helicobacter pylori Using In Silico Subtractive Proteomics Approaches and Their Possible Inhibition through Drug Repurposing. PMID:32932580
Unraveling the Genetic Basis for the Rapid Diversification of Male Genitalia between Drosophila Species. PMID:32931587
The gut microbiota may be a novel pathogenic mechanism in loosening of orthopedic implants in rats. PMID:32931052
Investigating the influence of perinatal nicotine and alcohol exposure on the genetic profiles of dopaminergic neurons in the VTA using miRNA-mRNA analysis. PMID:32929144
Teleological role of L-2-hydroxyglutarate dehydrogenase in the kidney. PMID:32928875
Investigating potential molecular mechanisms of serum exosomal miRNAs in colorectal cancer based on bioinformatics analysis. PMID:32925795
Identification of genes and pathways associated with subchondral bone in osteoarthritis via bioinformatic analysis. PMID:32925767
Chlamydial contribution to anaerobic metabolism during eukaryotic evolution. PMID:32923644
Nitrogen as the major factor influencing gene expression in Yarrowia lipolytica. PMID:32923379
The Phoebe genome sheds light on the evolution of magnoliids. PMID:32922818
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals. PMID:32917913
The Heterotrophic Bacterium Cupriavidus pinatubonensis JMP134 Oxidizes Sulfide to Sulfate with Thiosulfate as a Key Intermediate. PMID:32917752
Multi-omics analysis reveals the influence of genetic and environmental risk factors on developing gut microbiota in infants at risk of celiac disease. PMID:32917289
Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing. PMID:32915778
A mutation in the intron splice acceptor site of a GA3ox gene confers dwarf architecture in watermelon (Citrullus lanatus L.). PMID:32913219
The overexpression of OsACBP5 protects transgenic rice against necrotrophic, hemibiotrophic and biotrophic pathogens. PMID:32913218
Transcriptional analysis of cleft palate in TGFβ3 mutant mice. PMID:32913205
Draft Genome Sequence of Lactobacillus helveticus Lh 23, Isolated from Natural Whey Starter. PMID:32912904
Dissecting the immunosuppressive tumor microenvironments in Glioblastoma-on-a-Chip for optimized PD-1 immunotherapy. PMID:32909947
Comprehensive Characterization of Prognostic Long Noncoding RNAs in Osteosarcoma. PMID:32908905
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
Bioinformatics Analysis of Key Genes and circRNA-miRNA-mRNA Regulatory Network in Gastric Cancer. PMID:32908877
Network Pharmacology to Uncover the Biological Basis of Spleen Qi Deficiency Syndrome and Herbal Treatment. PMID:32908629
Nanoparticle treatment of maize analyzed through the metatranscriptome: compromised nitrogen cycling, possible phytopathogen selection, and plant hormesis. PMID:32907632
Modeling Novel Putative Drugs and Vaccine Candidates against Tick-Borne Pathogens: A Subtractive Proteomics Approach. PMID:32906620
Finding semantic patterns in omics data using concept rule learning with an ontology-based refinement operator. PMID:32905086
RNA-Seq-Based Whole Transcriptome Analysis of IPEC-J2 Cells During Swine Acute Diarrhea Syndrome Coronavirus Infection. PMID:32903570
iTRAQ‑based proteomic analysis reveals potential regulatory networks in dust mite‑related asthma treated with subcutaneous allergen immunotherapy. PMID:32901873
Chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing. PMID:32901005
Gut Microbiome Associated with the Psychoneurological Symptom Cluster in Patients with Head and Neck Cancers. PMID:32899975
Association between Metabolites and the Risk of Lung Cancer: A Systematic Literature Review and Meta-Analysis of Observational Studies. PMID:32899527
Comprehensive Transcriptomic Analysis for Developing Seeds of a Synthetic Brassica Hexaploid. PMID:32899324
Spliced genes in muscle from Nelore Cattle and their association with carcass and meat quality. PMID:32895448
Transcriptomic analysis links diverse hypothalamic cell types to fibroblast growth factor 1-induced sustained diabetes remission. PMID:32895383
Bioinformatics analysis reveals novel hub gene pathways associated with IgA nephropathy. PMID:32894197
A systematic study of critical miRNAs on cells proliferation and apoptosis by the shortest path. PMID:32894041
Single-Cell NGS-Based Analysis of Copy Number Alterations Reveals New Insights in Circulating Tumor Cells Persistence in Early-Stage Breast Cancer. PMID:32887501
Decomposing the molecular complexity of brewing. PMID:32885047
Chemotype classification and biomarker screening of male Eucommia ulmoides Oliv. flower core collections using UPLC-QTOF/MS-based non-targeted metabolomics. PMID:32884862
Transcriptomic analysis of a Clostridium thermocellum strain engineered to utilize xylose: responses to xylose versus cellobiose feeding. PMID:32884054
Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection. PMID:32880630
Molecular Changes in Tissue Proteome during Prostate Cancer Development: Proof-of-Principle Investigation. PMID:32878211
Genome-Wide DNA Methylation Signatures of Sea Cucumber Apostichopus japonicus during Environmental Induced Aestivation. PMID:32877994
Carriership of the rs113883650/rs2287120 haplotype of the SLC7A5 (LAT1) gene increases the risk of obesity in infants with phenylketonuria. PMID:32874918
Myocardial proteomic profile in pulmonary arterial hypertension. PMID:32873862
The ClpX and ClpP2 Orthologs of Chlamydia trachomatis Perform Discrete and Essential Functions in Organism Growth and Development. PMID:32873765
Sterile Spikelets Contribute to Yield in Sorghum and Related Grasses. PMID:32873633
High expression of MKK3 is associated with worse clinical outcomes in African American breast cancer patients. PMID:32873298
Combined Genome and Transcriptome Analyses of the Ciliate Schmidingerella arcuata (Spirotrichea) Reveal Patterns of DNA Elimination, Scrambling, and Inversion. PMID:32870974
Genomic landscape of the immune microenvironments of brain metastases in breast cancer. PMID:32867782
Keep Calm and Survive: Adaptation Strategies to Energy Crisis in Fruit Trees under Root Hypoxia. PMID:32867316
Pregnancy-specific transcriptional changes upon endotoxin exposure in mice. PMID:32866128
Simple Targeted Assays for Metabolic Pathways and Signaling: A Powerful Tool for Targeted Proteomics. PMID:32865986
Multi-omics analysis to examine microbiota, host gene expression and metabolites in the intestine of black tiger shrimp (Penaeus monodon) with different growth performance. PMID:32864208
Systemic vitamin intake impacting tissue proteomes. PMID:32863845
RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva. PMID:32859978
Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics. PMID:32859911
Endosymbionts of Metazoans Dwelling in the PACManus Hydrothermal Vent: Diversity and Potential Adaptive Features Revealed by Genome Analysis. PMID:32859597
Assessment of tumor suppressor promoter methylation in healthy individuals. PMID:32859265
Machine learning based refined differential gene expression analysis of pediatric sepsis. PMID:32859206
Tracking down carbon inputs underground from an arid zone Australian calcrete. PMID:32857799
Systemic Mesenchymal Stem Cell Treatment Mitigates Structural and Functional Retinal Ganglion Cell Degeneration in a Mouse Model of Multiple Sclerosis. PMID:32855863
Association of microRNA 17 host gene variant (rs4284505) with susceptibility and severity of systemic lupus erythematosus. PMID:32852903
Identifying the Potential Mechanism of Action of SNPs Associated With Breast Cancer Susceptibility With GVITamIN. PMID:32850701
A Novel Immune-Related Competing Endogenous RNA Network Predicts Prognosis of Acute Myeloid Leukemia. PMID:32850463
Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis: An Approach to Elucidate Pathogenicity at the Metabolic Level. PMID:32849823
Integrated Bioinformatics Analysis Reveals Key Candidate Genes and Pathways Associated With Clinical Outcome in Hepatocellular Carcinoma. PMID:32849813
Systems Biology Approaches to Understanding the Human Immune System. PMID:32849587
Alterations in the Gut Microbiome and Cecal Metabolome During Klebsiella pneumoniae-Induced Pneumosepsis. PMID:32849494
Commonalities and Differences in the Transcriptional Response of the Model Fungus Saccharomyces cerevisiae to Different Commercial Graphene Oxide Materials. PMID:32849484
Ustilago maydis Serves as a Novel Production Host for the Synthesis of Plant and Fungal Sesquiterpenoids. PMID:32849341
Longitudinal Stroke Recovery Associated With Dysregulation of Complement System-A Proteomics Pathway Analysis. PMID:32849183
Systems Analysis of Biliary Atresia Through Integration of High-Throughput Biological Data. PMID:32848883
Strategies to Enhance Logic Modeling-Based Cell Line-Specific Drug Synergy Prediction. PMID:32848834
Characterization and analysis of full-length transcriptomes from two grasshoppers, Gomphocerus licenti and Mongolotettix japonicus. PMID:32848169
Metabolite Patterns in Human Myeloid Hematopoiesis Result from Lineage-Dependent Active Metabolic Pathways. PMID:32847028
IL-13 as Target to Reduce Cholestasis and Dysbiosis in Abcb4 Knockout Mice. PMID:32846954
MicroRNAs Modulate the Pathogenesis of Alzheimer's Disease: An In Silico Analysis in the Human Brain. PMID:32846925
Single-Cell Transcriptome Analysis of Colon Cancer Cell Response to 5-Fluorouracil-Induced DNA Damage. PMID:32846134
The small compound, TD-198946, protects against intervertebral degeneration by enhancing glycosaminoglycan synthesis in nucleus pulposus cells. PMID:32843678
A Pipeline for Integrated Theory and Data-Driven Modeling of Biomedical Data. PMID:32841121
Systematic determination of the mitochondrial proportion in human and mice tissues for single-cell RNA-sequencing data quality control. PMID:32840568
Identification of differentially expressed genes between mucinous adenocarcinoma and other adenocarcinoma of colorectal cancer using bioinformatics analysis. PMID:32840168
Transcriptional and functional insights into the host immune response against the emerging fungal pathogen Candida auris. PMID:32839538
Integrated proteomics and metabolomics reveals the comprehensive characterization of antitumor mechanism underlying Shikonin on colon cancer patient-derived xenograft model. PMID:32839531
DNA repair gene expression is increased in HPV positive head and neck squamous cell carcinomas. PMID:32838940
Mass Spectrometry-Based Non-targeted Metabolic Profiling for Disease Detection: Recent Developments. PMID:32831436
Underground isoleucine biosynthesis pathways in E. coli. PMID:32831171
Identification of methylated-differentially expressed genes and pathways in esophageal squamous cell carcinoma. PMID:32825936
Genetic deletion of microRNA-22 blunts the inflammatory transcriptional response to status epilepticus and exacerbates epilepsy in mice. PMID:32825833
Genes Modulating the Increase in Sexuality in the Facultative Diplosporous Grass Eragrostis curvula under Water Stress Conditions. PMID:32825586
Gluconobacter dominates the gut microbiome of the Asian palm civet Paradoxurus hermaphroditus that produces kopi luwak. PMID:32821539
Peripheral serum metabolomic profiles inform central cognitive impairment. PMID:32820198
MYCN drives chemoresistance in small cell lung cancer while USP7 inhibition can restore chemosensitivity. PMID:32820040
MARTX Toxin-Stimulated Interplay between Human Cells and Vibrio vulnificus. PMID:32817457
Experimental and Biological Insights from Proteomic Analyses of Extracellular Vesicle Cargos in Normalcy and Disease. PMID:32815324
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics. PMID:32813693
Transcriptome analysis reveals the genetic basis underlying the development of skin appendages and immunity in hedgehog (Atelerix albiventris). PMID:32811876
Development of a species-specific transformation system using the novel endogenous promoter calreticulin from oleaginous microalgae Ettlia sp. PMID:32811857
Molecular insights into biochar-mediated plant growth promotion and systemic resistance in tomato against Fusarium crown and root rot disease. PMID:32811849
The current landscape of coronavirus-host protein-protein interactions. PMID:32811513
Extreme Phenotype Approach Suggests Taste Transduction Pathway for Carotid Plaque in a Multi-Ethnic Cohort. PMID:32811377
Mercury oxidation coupled to autotrophic denitrifying branched sulfur oxidation and sulfur disproportionation for simultaneous removal of Hg0 and NO. PMID:32808049
Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing. PMID:32807825
Actinobacteria from Antarctica as a source for anticancer discovery. PMID:32807803
Deciphering serous ovarian carcinoma histopathology and platinum response by convolutional neural networks. PMID:32807164
Radioprotectors.org: an open database of known and predicted radioprotectors. PMID:32805729
Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection. PMID:32802507
Identification of UBE2T as an independent prognostic biomarker for gallbladder cancer. PMID:32802166
The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds. PMID:32797216
Genomic Characteristics and Potential Metabolic Adaptations of Hadal Trench Roseobacter and Alteromonas Bacteria Based on Single-Cell Genomics Analyses. PMID:32793171
Metatranscriptomic Analysis Reveals Active Bacterial Communities in Diabetic Foot Infections. PMID:32793159
Targeted Cell Sorting Combined With Single Cell Genomics Captures Low Abundant Microbial Dark Matter With Higher Sensitivity Than Metagenomics. PMID:32793124
Upregulation of circ_0000199 in circulating exosomes is associated with survival outcome in OSCC. PMID:32792549
An autophagy-related model of 4 key genes for predicting prognosis of patients with laryngeal cancer. PMID:32791689
Novel variants in women with premature ovarian function decline identified via whole-exome sequencing. PMID:32789750
Gut microbiome of endangered Tor putitora (Ham.) as a reservoir of antibiotic resistance genes and pathogens associated with fish health. PMID:32787773
Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PMID:32785287
Comparative Metabolomic Analysis of Dendrobium officinale under Different Cultivation Substrates. PMID:32785071
Hydroxytyrosol as a Promising Ally in the Treatment of Fibromyalgia. PMID:32784915
Compositional and Functional Characteristics of Swine Slurry Microbes through 16S rRNA Metagenomic Sequencing Approach. PMID:32784779
Genomic Analysis of Localized High-Risk Prostate Cancer Circulating Tumor Cells at the Single-Cell Level. PMID:32784507
Complete genome of a unicellular parasite (Antonospora locustae) and transcriptional interactions with its host locust. PMID:32783805
Identification of transcriptomic markers for developing idiopathic pulmonary fibrosis: an integrative analysis of gene expression profiles. PMID:32782692
Downregulation of the let-7 family of microRNAs may promote insulin receptor/insulin-like growth factor signalling pathways in pancreatic ductal adenocarcinoma. PMID:32782579
Structure identification, antitumor activity and mechanisms of a novel polysaccharide from Ramaria flaccida (Fr.) Quél. PMID:32782534
Identification of Hidradenitis Suppurativa-Related mRNA Expression Patterns Through Analysis of Gene Expression Omnibus. PMID:32782449
Dissecting diagnostic heterogeneity in depression by integrating neuroimaging and genetics. PMID:32781460
A framework for pathway knowledge driven prioritization in genome-wide association studies. PMID:32779262
De novo transcriptome assembly, functional annotation, and expression profiling of rye (Secale cereale L.) hybrids inoculated with ergot (Claviceps purpurea). PMID:32778722
A field-based quantitative analysis of sublethal effects of air pollution on pollinators. PMID:32778582
Characterization of the Exopolysaccharide Biosynthesis Pathway in Myxococcus xanthus. PMID:32778557
The chromosome-level wintersweet (Chimonanthus praecox) genome provides insights into floral scent biosynthesis and flowering in winter. PMID:32778152
A common approach for absolute quantification of short chain CoA thioesters in prokaryotic and eukaryotic microbes. PMID:32778124
The characterization of extracellular vesicles-derived microRNAs in Thai malaria patients. PMID:32778117
ImmunoGlobe: enabling systems immunology with a manually curated intercellular immune interaction network. PMID:32778050
THOC1 deficiency leads to late-onset nonsyndromic hearing loss through p53-mediated hair cell apoptosis. PMID:32776944
Data on the de novo transcriptome assembly for the migratory bird, the Common quail (Coturnix coturnix). PMID:32775561
Analysis and identification of novel biomarkers involved in neuroblastoma via integrated bioinformatics. PMID:32772341
Bioinformatics analysis of differentially expressed genes in subchondral bone in early experimental osteoarthritis using microarray data. PMID:32771051
Genomic and enzymatic evidence of acetogenesis by anaerobic methanotrophic archaea. PMID:32770005
Circular RNA profiling in plasma exosomes from patients with gastric cancer. PMID:32765789
Epigenetic Regulator miRNA Pattern Differences Among SARS-CoV, SARS-CoV-2, and SARS-CoV-2 World-Wide Isolates Delineated the Mystery Behind the Epic Pathogenicity and Distinct Clinical Characteristics of Pandemic COVID-19. PMID:32765592
Temperature-dependent life history and transcriptomic responses in heat-tolerant versus heat-sensitive Brachionus rotifers. PMID:32764662
Induction of a Timed Metabolic Collapse to Overcome Cancer Chemoresistance. PMID:32763164
Comprehensive Network Analysis Reveals Alternative Splicing-Related lncRNAs in Hepatocellular Carcinoma. PMID:32760422
Abnormal expression and prognostic significance of EPB41L1 in kidney renal clear cell carcinoma based on data mining. PMID:32760223
SWATH-MS-based quantitative proteomics reveals a uniquely intricate defense response in Cnaphalocrocis medinalis-resistant rice. PMID:32759951
MDM2-Dependent Rewiring of Metabolomic and Lipidomic Profiles in Dedifferentiated Liposarcoma Models. PMID:32759684
Comparative gene expression profiling between optic nerve and spinal cord injury in Xenopus laevis reveals a core set of genes inherent in successful regeneration of vertebrate central nervous system axons. PMID:32758133
Fungal-host interactions: insights into microRNA in response to Paracoccidioides species. PMID:32756740
Bioinformatics analysis of microRNA profiles and identification of microRNA-mRNA network and biological markers in intracranial aneurysm. PMID:32756097
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of the CsrA Family in the Genus Pseudomonas. PMID:32754614
The Dysregulation and Prognostic Analysis of STRIPAK Complex Across Cancers. PMID:32754603
In vivo High-Content Screening in Zebrafish for Developmental Nephrotoxicity of Approved Drugs. PMID:32754590
Hepatopancreas immune response during molt cycle in the mud crab, Scylla paramamosain. PMID:32753724
An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. PMID:32753478
An Integrated Metabolomics Study of Glucosinolate Metabolism in Different Brassicaceae Genera. PMID:32751925
RNAAgeCalc: A multi-tissue transcriptional age calculator. PMID:32750074
The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients. PMID:32747678
A chromosome-scale reference genome and genome-wide genetic variations elucidate adaptation in yak. PMID:32745324
Comparative gut transcriptome analysis of Diatraea saccharalis in response to the dietary source. PMID:32745084
Large-scale Multi-omic Analysis of COVID-19 Severity. PMID:32743614
NetCore: a network propagation approach using node coreness. PMID:32735660
GADL1 is a multifunctional decarboxylase with tissue-specific roles in β-alanine and carnosine production. PMID:32733999
Clinical Multi-Omics Study on the Gut Microbiota in Critically Ill Patients After Cardiovascular Surgery Combined With Cardiopulmonary Bypass With or Without Sepsis (MUL-GM-CSCPB Study): A Prospective Study Protocol. PMID:32733902
Systematic Elucidation of the Mechanism of Oroxylum indicum via Network Pharmacology. PMID:32733583
Shensong Yangxin Protects Against Metabolic Syndrome-Induced Ventricular Arrhythmias by Inhibiting Electrical Remodeling. PMID:32733242
Cellular response of Brevibacterium casei #NIOSBA88 to arsenic and chromium-a proteomic approach. PMID:32729030
Index and biological spectrum of human DNase I hypersensitive sites. PMID:32728217
The soluble glycoprotein NMB (GPNMB) produced by macrophages induces cancer stemness and metastasis via CD44 and IL-33. PMID:32728200
The relationship between blood metabolites of the tryptophan pathway and kidney function: a bidirectional Mendelian randomization analysis. PMID:32728058
Microarray profiling and functional analysis of differentially expressed plasma exosomal circular RNAs in Graves' disease. PMID:32727578
The Expression of Cold-Inducible RNA-Binding Protein mRNA in Sow Genital Tract Is Modulated by Natural Mating, But Not by Seminal Plasma. PMID:32727091
In Vivo Chimeric Alzheimer's Disease Modeling of Apolipoprotein E4 Toxicity in Human Neurons. PMID:32726626
Transcriptome analysis of contrasting resistance to herbivory by Empoasca fabae in two shrub willow species and their hybrid progeny. PMID:32726362
Circulating miRNA-3552 as a Potential Biomarker for Ischemic Stroke in Rats. PMID:32724801
Identification of glioblastoma-specific prognostic biomarkers via an integrative analysis of DNA methylation and gene expression. PMID:32724403
Identifying key genes and drug screening for preeclampsia based on gene expression profiles. PMID:32724400
GGCT promotes colorectal cancer migration and invasion via epithelial-mesenchymal transition. PMID:32724344
Comparative Genomic Analysis of Rapidly Evolving SARS-CoV-2 Reveals Mosaic Pattern of Phylogeographical Distribution. PMID:32723797
Microbiome and Metagenome Analyses of a Closed Habitat during Human Occupation. PMID:32723791
Parental Selenium Nutrition Affects the One-Carbon Metabolism and the Hepatic DNA Methylation Pattern of Rainbow Trout (Oncorhynchus mykiss) in the Progeny. PMID:32722369
Transcriptomic and Metabolic Responses to a Live-Attenuated Francisella tularensis Vaccine. PMID:32722194
Regulator combinations identify systemic sclerosis patients with more severe disease. PMID:32721949
Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis. PMID:32714363
Neospora caninum infection induces an isolate virulence-dependent pro-inflammatory gene expression profile in bovine monocyte-derived macrophages. PMID:32711550
Genes associated with survival of female bovine blastocysts produced in vivo. PMID:32710275
A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota. PMID:32709972
Endogenous toxic metabolites and implications in cancer therapy. PMID:32709924
Transcriptional Profiling of Primate Central Nucleus of the Amygdala Neurons to Understand the Molecular Underpinnings of Early-Life Anxious Temperament. PMID:32709417
Consumption of identically formulated foods extruded under low and high shear force reveals that microbiome redox ratios accompany canine immunoglobulin A production. PMID:32705743
Risk gene identification and support vector machine learning to construct an early diagnosis model of myocardial infarction. PMID:32705275
Effects of Egr1 on pancreatic acinar intracellular trypsinogen activation and the associated ceRNA network. PMID:32705196
IL-21 Stimulates the expression and activation of cell cycle regulators and promotes cell proliferation in EBV-positive diffuse large B cell lymphoma. PMID:32704112
Inherited variations in human pigmentation-related genes modulate cutaneous melanoma risk and clinicopathological features in Brazilian population. PMID:32699307
A G-quadruplex-binding compound shows potent activity in human gemcitabine-resistant pancreatic cancer cells. PMID:32699225
Multi-faceted epigenetic dysregulation of gene expression promotes esophageal squamous cell carcinoma. PMID:32699215
Blood DNA methylation sites predict death risk in a longitudinal study of 12, 300 individuals. PMID:32697766
Identification of potential molecular mechanisms and small molecule drugs in myocardial ischemia/reperfusion injury. PMID:32696819
The Potential of Anti-Diabetic Rākau Rongoā (Māori Herbal Medicine) to Treat Type 2 Diabetes Mellitus (T2DM) Mate Huka: A Review. PMID:32694996
Selenium detoxification is required for cancer-cell survival. PMID:32694795
Integrative structural, functional, and transcriptomic analyses of sex-biased brain organization in humans. PMID:32690678
Transcriptomic analysis on the effects of melatonin in gastrointestinal carcinomas. PMID:32689938
MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse. PMID:32686713
Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses. PMID:32686190
Footprint-based functional analysis of multiomic data. PMID:32685770
Comparative Transcriptome Analysis Reveals the Potential Cardiovascular Protective Targets of the Thyroid Hormone Metabolite 3-Iodothyronamine (3-T1AM). PMID:32685439
Integrative analyses of biomarkers and pathways for adipose tissue after bariatric surgery. PMID:32684073
AXL confers cell migration and invasion by hijacking a PEAK1-regulated focal adhesion protein network. PMID:32681075
Gene expression profiling identifies the role of Zac1 in cervical cancer metastasis. PMID:32678267
Degradome, small RNAs and transcriptome sequencing of a high-nicotine cultivated tobacco uncovers miRNA's function in nicotine biosynthesis. PMID:32678207
First Reports of Effects of Insulin, Human-like Insulin Receptors and Adapter Proteins in Acanthamoeba castellanii. PMID:32678116
Synthetic repurposing of drugs against hypertension: a datamining method based on association rules and a novel discrete algorithm. PMID:32677879
Co-Expression Networks for Causal Gene Identification Based on RNA-Seq Data of Corynebacterium pseudotuberculosis. PMID:32674507
The identification of differentially expressed genes in male and female gametophytes of simple thalloid liverwort Pellia endiviifolia sp. B using an RNA-seq approach. PMID:32671488
Deep learning decodes the principles of differential gene expression. PMID:32671330
From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes. PMID:32670511
Immune and Metabolic Signatures of COVID-19 Revealed by Transcriptomics Data Reuse. PMID:32670298
Microbial Communities Associated With Long-Term Tillage and Fertility Treatments in a Corn-Soybean Cropping System. PMID:32670235
Peroxisome proliferator-activated receptor alpha is involved in the temperature-induced sex differentiation of a vertebrate. PMID:32669596
Impact of Sacbrood Virus on Larval Microbiome of Apis mellifera and Apis cerana. PMID:32668740
Glyceroglycolipid Metabolism Regulations under Phosphate Starvation Revealed by Transcriptome Analysis in Synechococcus elongatus PCC 7942. PMID:32668657
Selection for Reducing Energy Cost of Protein Production Drives the GC Content and Amino Acid Composition Bias in Gene Transfer Agents. PMID:32665274
Impact of Facultative Bacteria on the Metabolic Function of an Obligate Insect-Bacterial Symbiosis. PMID:32665268
A scan for genes associated with cancer mortality and longevity in pedigree dog breeds. PMID:32661568
Transcriptomic analysis of Dubas bug (Ommatissus lybicus Bergevin) infestation to Date Palm. PMID:32661358
Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis. PMID:32661339
Tauopathy in the young autistic brain: novel biomarker and therapeutic target. PMID:32661233
Radiation Response of Murine Embryonic Stem Cells. PMID:32660081
Robust and accurate deconvolution of tumor populations uncovers evolutionary mechanisms of breast cancer metastasis. PMID:32657393
Integrated multiomics analysis of hepatoblastoma unravels its heterogeneity and provides novel druggable targets. PMID:32656360
Transcriptomic Analysis of Extracellular RNA Governed by the Endocytic Adaptor Protein Cin1 of Cryptococcus deneoformans. PMID:32656093
Investigation of microbial community interactions between Lake Washington methanotrophs using -------genome-scale metabolic modeling. PMID:32655999
Integrative analysis of competitive endogenous RNA network reveals the regulatory role of non-coding RNAs in high-glucose-induced human retinal endothelial cells. PMID:32655995
Comparison of Transcriptome Profiles of the Fungus Botrytis cinerea and Insect Pest Bradysia odoriphaga in Response to Benzothiazole. PMID:32655508
Understanding the Mechanism of Cell Death in Gemcitabine Resistant Pancreatic Ductal Adenocarcinoma: A Systems Biology Approach. PMID:32655287
A bioinformatics investigation into molecular mechanism of Yinzhihuang granules for treating hepatitis B by network pharmacology and molecular docking verification. PMID:32651427
Transcriptomic analysis of regulatory pathways involved in female reproductive physiology of Rhodnius prolixus under different nutritional states. PMID:32651410
Pharmacologic induction of innate immune signaling directly drives homologous recombination deficiency. PMID:32651270
Escher-Trace: a web application for pathway-based visualization of stable isotope tracing data. PMID:32650717
A Genomic Perspective on the Potential of Wild-Type Rumen Bacterium Enterobacter sp. LU1 as an Industrial Platform for Bio-Based Succinate Production. PMID:32650546
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma. PMID:32649874
Glioma-derived exosomes drive the differentiation of neural stem cells to astrocytes. PMID:32649728
LDHA-mediated ROS generation in chondrocytes is a potential therapeutic target for osteoarthritis. PMID:32647171
Circulating miRNAs as molecular markers of occupational grain dust exposure. PMID:32647120
The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells. PMID:32645014
The duodenal microbiome is altered in small intestinal bacterial overgrowth. PMID:32645011
NMR-based metabolomics characterizes metabolic changes in different brain regions of streptozotocin-induced diabetic mice with cognitive decline. PMID:32643092
Insight in the transcriptome data of hairy root disease-causing bacterium-Agrobacterium rhizogenes. PMID:32642520
The genome insights of Streptomyces lannensis T1317-0309 reveals actinomycin D production. PMID:32641781
A systematic strategy for the investigation of vaccines and drugs targeting bacteria. PMID:32637049
Single-cell ATAC sequencing analysis: From data preprocessing to hypothesis generation. PMID:32637041
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Comparison of methods and characterization of small RNAs from plasma extracellular vesicles of HIV/HCV coinfected patients. PMID:32636456
Mechanism of Astragalus membranaceus in the treatment of laryngeal cancer based on gene co-expression network and molecular docking. PMID:32636440
Toxicology of tramadol following chronic exposure based on metabolomics of the cerebrum in mice. PMID:32636435
MTFMT deficiency correlates with reduced mitochondrial integrity and enhanced host susceptibility to intracellular infection. PMID:32636430
A Comprehensive Coexpression Network Analysis in Vibrio cholerae. PMID:32636337
Depletion of the DarG antitoxin in Mycobacterium tuberculosis triggers the DNA-damage response and leads to cell death. PMID:32634279
Bioinformatics analysis of high-throughput data to validate potential novel biomarkers and small molecule drugs for glioblastoma multiforme. PMID:32634050
Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment. PMID:32630754
Metabolic Characterisation of the Midgut of Bombyx mori Varieties after BmNPV Infection Using GC-MS-Based Metabolite Profiling. PMID:32630275
Calcium Signaling Alterations Caused by Epigenetic Mechanisms in Pancreatic Cancer: From Early Markers to Prognostic Impact. PMID:32629766
Developmental origins of transgenerational sperm histone retention following ancestral exposures. PMID:32628935
Upregulated proteoglycan-related signaling pathways in fluid flow shear stress-treated podocytes. PMID:32628542
Key miRNAs associated with memory and learning disorder upon exposure to sevoflurane determined by RNA sequencing. PMID:32626949
CYP1B1 gene: Implications in glaucoma and cancer. PMID:32626511
Flavescence Dorée-Derived Leaf Yellowing in Grapevine (Vitis vinifera L.) Is Associated to a General Repression of Isoprenoid Biosynthetic Pathways. PMID:32625230
Gene Regulatory Network Guided Investigations and Engineering of Storage Root Development in Root Crops. PMID:32625220
Impact of Different Trace Elements on the Growth and Proteome of Two Strains of Granulicella, Class "Acidobacteriia". PMID:32625179
Global proteome response of Escherichia coli BL21 to production of human basic fibroblast growth factor in complex and defined medium. PMID:32624836
Construction and Comprehensive Analysis of Dysregulated Long Noncoding RNA-Associated Competing Endogenous RNA Network in Moyamoya Disease. PMID:32617116
Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. PMID:32616809
Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations. PMID:32616808
Complete Genome Sequence of Methylosinus sp. Strain C49, a Methane-Oxidizing Bacterium Harboring phaABC Genes for Polyhydroxyalkanoate Synthesis. PMID:32616630
Fluctuating expression of miR-584 in primary and high-grade gastric cancer. PMID:32615958
Shedding light on cashmere goat hair follicle biology: from morphology analyses to transcriptomic landascape. PMID:32615938
Protein profile of well-differentiated versus un-differentiated human bronchial/tracheal epithelial cells. PMID:32613119
Seq-ing answers: Current data integration approaches to uncover mechanisms of transcriptional regulation. PMID:32612756
Directed evolution approach to enhance efficiency and speed of outgrowth during single cell subcloning of Chinese Hamster Ovary cells. PMID:32612755
Flexible experimental designs for valid single-cell RNA-sequencing experiments allowing batch effects correction. PMID:32612268
Novel candidate drugs in anti-tumor necrosis factor refractory Crohn's diseases: in silico study for drug repositioning. PMID:32612148
The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle. PMID:32612135
Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma-Do They Exist? PMID:32610693
Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis). PMID:32607180
Influence of genetic diversity of seventeen Beauveria bassiana isolates from different hosts on virulence by comparative genomics. PMID:32605539
Identification of Novel microRNA Profiles Dysregulated in Plasma and Tissue of Abdominal Aortic Aneurysm Patients. PMID:32605321
A guide to human microbiome research: study design, sample collection, and bioinformatics analysis. PMID:32604176
Long noncoding RNA H19X is a key mediator of TGF-β-driven fibrosis. PMID:32603313
Alteration in Lysophospholipids and Converting Enzymes in Glaucomatous Optic Nerves. PMID:32602905
Comparative transcriptome analysis of a taxol-producing endophytic fungus, Aspergillus aculeatinus Tax-6, and its mutant strain. PMID:32601443
Integration of genomics, metagenomics, and metabolomics to identify interplay between susceptibility alleles and microbiota in adenoma initiation. PMID:32600361
Comparative analysis of full-length transcriptomes based on hybrid population reveals regulatory mechanisms of anthocyanin biosynthesis in sweet potato (Ipomoea batatas (L.) Lam). PMID:32600332
Comparative Pathway Integrator: A Framework of Meta-Analytic Integration of Multiple Transcriptomic Studies for Consensual and Differential Pathway Analysis. PMID:32599927
The chromatin landscape at the HIV-1 provirus integration site determines viral expression. PMID:32597987
Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells. PMID:32596448
RNA Sequencing for Gene Expression Profiles in Peripheral Blood Mononuclear Cells with Ankylosing Spondylitis RNA. PMID:32596323
Identification of miRNA-mRNA-TFs Regulatory Network and Crucial Pathways Involved in Tetralogy of Fallot. PMID:32595699
Global transcriptomic changes occur in aged mouse podocytes. PMID:32592814
Regulating appetite in broilers for improving body and muscle development - A review. PMID:32592266
The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia. PMID:32591557
Expansions of chemosensory gene orthologs among selected tsetse fly species and their expressions in Glossina morsitans morsitans tsetse fly. PMID:32589659
Redox States of Protein Cysteines in Pathways of Protein Turnover and Cytoskeleton Dynamics Are Changed with Aging and Reversed by Slc7a11 Restoration in Mouse Lung Fibroblasts. PMID:32587657
Impact of a natural disaster on access to care and biopsychosocial outcomes among Hispanic/Latino cancer survivors. PMID:32587352
LEF1 Induces DHRS2 Gene Expression in Human Acute Leukemia Jurkat T-Cells. PMID:32586085
Minichromosome maintenance 6 complex component identified by bioinformatics analysis and experimental validation in esophageal squamous cell carcinoma. PMID:32583000
Comprehensive Analysis of Key Genes and Regulatory Elements in Osteosarcoma Affected by Bone Matrix Mineral With Prognostic Values. PMID:32582282
Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer. PMID:32582275
Xenobiotic Effects of Chlorine Dioxide to Escherichia coli O157:H7 on Non-host Tomato Environment Revealed by Transcriptional Network Modeling: Implications to Adaptation and Selection. PMID:32582084
Identification and Characterization of Genes Involved in Ecdysteroid Esterification Pathway Contributing to the High 20-Hydroxyecdysone Resistance of Helicoverpa armigera. PMID:32581827
Helicobacter pylori Reactivates Human Immunodeficiency Virus-1 in Latently Infected Monocytes with Increased Expression of IL-1β and CXCL8. PMID:32581644
Identification of Target Genes and Transcription Factors in Mice with LMNA-Related Dilated Cardiomyopathy by Integrated Bioinformatic Analyses. PMID:32581210
Revealing the microbial assemblage structure in the human gut microbiome using latent Dirichlet allocation. PMID:32576288
Wheat growth, applied water use efficiency and flag leaf metabolome under continuous and pulsed deficit irrigation. PMID:32572060
Immune-related genes in tumor-specific CD4+ and CD8+ T cells in colon cancer. PMID:32571262
Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress. PMID:32570789
Dealing with aflatoxin B1 dihydrodiol acute effects: Impact of aflatoxin B1-aldehyde reductase enzyme activity in poultry species tolerant to AFB1 toxic effects. PMID:32569334
Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase. PMID:32569318
Transcriptome analysis of a social caterpillar, Drepana arcuata: De novo assembly, functional annotation and developmental analysis. PMID:32569288
Are synthetic biology standards applicable in everyday research practice? PMID:32567248
Metabolomic Description of Ivacaftor Elevating Polymyxin B Mediated Antibacterial Activity in Cystic Fibrosis Pseudomonas aeruginosa. PMID:32566909
A novel prognostic signature of immune-related genes for patients with colorectal cancer. PMID:32564470
An improvement in skeletal muscle mitochondrial capacity with short-term aerobic training is associated with changes in Tribbles 1 expression. PMID:32562350
The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways. PMID:32561656
Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis. PMID:32560580
Identification of lncRNAs Involved in PCV2 Infection of PK-15 Cells. PMID:32560439
TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma. PMID:32560331
Whole-blood dysregulation of actin-cytoskeleton pathway in adult spinal muscular atrophy patients. PMID:32558393
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
Sequencing of RNA in single cells reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency. PMID:32556286
Identification of functionally connected multi-omic biomarkers for Alzheimer's disease using modularity-constrained Lasso. PMID:32555747
CRISPR/Cas9 knockout of human arylamine N-acetyltransferase 1 in MDA-MB-231 breast cancer cells suggests a role in cellular metabolism. PMID:32555504
Genetic variants associated with alcohol dependence co-ordinate regulation of ADH genes in gastrointestinal and adipose tissues. PMID:32555468
The bovine cumulus proteome is influenced by maturation condition and maturational competence of the oocyte. PMID:32555221
Complete Genome Sequence of Stenotrophomonas maltophilia Strain CPBW01, Isolated from the Wings of the Colorado Potato Beetle in Xinjiang, China. PMID:32554788
Phylogenomics of expanding uncultured environmental Tenericutes provides insights into their pathogenicity and evolutionary relationship with Bacilli. PMID:32552739
Transcriptome analysis reveals a molecular understanding of nicotinamide and butyrate sodium on meat quality of broilers under high stocking density. PMID:32552672
Draft genome of the famous ornamental plant Paeonia suffruticosa. PMID:32551041
Comparative RNA-Seq profiling of a resistant and susceptible peanut (Arachis hypogaea) genotypes in response to leaf rust infection caused by Puccinia arachidis. PMID:32550103
Identification of Potential Key Genes for Pathogenesis and Prognosis in Prostate Cancer by Integrated Analysis of Gene Expression Profiles and the Cancer Genome Atlas. PMID:32547947
Mass Spectrometry-Based Discovery of in vitro Kinome Substrates. PMID:32547896
iTRAQ-Based Proteomic Profile Analysis of the Hepatopancreas of Caribbean Spiny Lobsters Infected With Panulirus argus Virus 1: Metabolic and Physiological Implications. PMID:32547519
Changes of the Gastric Mucosal Microbiome Associated With Histological Stages of Gastric Carcinogenesis. PMID:32547510
Increased Connexin36 Phosphorylation in AII Amacrine Cell Coupling of the Mouse Myopic Retina. PMID:32547367
Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis. PMID:32547141
Plasmid-Encoded blaNDM-5 Gene That Confers High-Level Carbapenem Resistance in Salmonella Typhimurium of Pork Origin. PMID:32547117
Bacterial Secondary Metabolite Biosynthetic Potential in Soil Varies with Phylum, Depth, and Vegetation Type. PMID:32546614
Cotargeting of XPO1 Enhances the Antileukemic Activity of Midostaurin and Gilteritinib in Acute Myeloid Leukemia. PMID:32545904
Immune profiling reveals prognostic genes in high-grade serous ovarian cancer. PMID:32544083
Simulating the evolutionary trajectories of metabolic pathways for insect symbionts in the genus Sodalis. PMID:32543366
Serum Metabolomic Profiles Associated With Untreated Metabolic Syndrome Patients in the Chinese Population. PMID:32543029
Semantic text mining in early drug discovery for type 2 diabetes. PMID:32542027
Motifs enable communication efficiency and fault-tolerance in transcriptional networks. PMID:32541819
Genomic insights into a plant growth-promoting Pseudomonas koreensis strain with cyclic lipopeptide-mediated antifungal activity. PMID:32537904
Enhanced Triacylglycerol Metabolism Contributes to Efficient Oil Utilization and High-Level Production of Salinomycin in Streptomyces albus ZD11. PMID:32532869
Bioinformatics Analyses of the Transcriptome Reveal Ube3a-Dependent Effects on Mitochondrial-Related Pathways. PMID:32532103
Transcriptome Profiling of Haloxylon persicum (Bunge ex Boiss and Buhse) an Endangered Plant Species under PEG-Induced Drought Stress. PMID:32531994
Insights into the mechanism of cyanobacteria removal by the algicidal fungi Bjerkandera adusta and Trametes versicolor. PMID:32529805
Dissecting the genome of star fruit (Averrhoa carambola L.). PMID:32528706
Screening and functional identification of lncRNAs in antler mesenchymal and cartilage tissues using high-throughput sequencing. PMID:32528134
Bacterial symbionts support larval sap feeding and adult folivory in (semi-)aquatic reed beetles. PMID:32528063
Genome wide meta-analysis of cDNA datasets reveals new target gene signatures of colorectal cancer based on systems biology approach. PMID:32523911
Weighted Gene Coexpression Network Analysis Reveals the Dynamic Transcriptome Regulation and Prognostic Biomarkers of Hepatocellular Carcinoma. PMID:32523331
Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A. PMID:32522834
VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. PMID:32522236
Effects of Genetic Variation on Urinary Small Molecule Signatures of Mice after Exposure to Ionizing Radiation: A Study of p53 Deficiency. PMID:32521675
Rrp6 Moonlights in an RNA Exosome-Independent Manner to Promote Cell Survival and Gene Expression during Stress. PMID:32521279
Selection of reference genes for quantitative PCR: identifying reference genes for airway epithelial cells exposed to Pseudomonas aeruginosa. PMID:32521165
Adverse effects of electronic cigarettes on the disease-naive oral microbiome. PMID:32518820
Spatial Compartmentalization of the Microbiome between the Lumen and Crypts Is Lost in the Murine Cecum following the Process of Surgery, Including Overnight Fasting and Exposure to Antibiotics. PMID:32518197
Interaction of Varroa destructor and Sublethal Clothianidin Doses during the Larval Stage on Subsequent Adult Honey Bee (Apis mellifera L.) Health, Cellular Immunity, Deformed Wing Virus Levels and Differential Gene Expression. PMID:32517245
Gut-Brain Axis and Neurodegeneration: State-of-the-Art of Meta-Omics Sciences for Microbiota Characterization. PMID:32516966
Identification of enzymatic genes with the potential to reduce biomass recalcitrance through lignin manipulation in Arabidopsis. PMID:32514309
Integrative phenotyping of glycemic responders upon clinical weight loss using multi-omics. PMID:32514005
Agonist binding directs dynamic competition among nuclear receptors for heterodimerization with retinoid X receptor. PMID:32513869
Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations. PMID:32513234
Androgen Regulates SARS-CoV-2 Receptor Levels and Is Associated with Severe COVID-19 Symptoms in Men. PMID:32511360
Integration of Transcriptome and Metabolome Provides Unique Insights to Pathways Associated With Obese Breast Cancer Patients. PMID:32509585
Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage. PMID:32508885
Compound Heterozygous Variants in Pediatric Cancers: A Systematic Review. PMID:32508881
Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships. PMID:32504002
Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity? PMID:32503292
NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. PMID:32503277
Could the Heat Shock Proteins 70 Family Members Exacerbate the Immune Response in Multiple Sclerosis? An in Silico Study. PMID:32503176
Entinostat augments NK cell functions via epigenetic upregulation of IFIT1-STING-STAT4 pathway. PMID:32499867
De novo RNA sequencing analysis of Aeluropus littoralis halophyte plant under salinity stress. PMID:32499577
Soil Bacterial Diversity and Potential Functions Are Regulated by Long-Term Conservation Tillage and Straw Mulching. PMID:32498450
Genetic Factors Involved in Cardiomyopathies and in Cancer. PMID:32498335
Urethral luminal epithelia are castration-insensitive cells of the proximal prostate. PMID:32497356
Developmental alterations in the transcriptome of three distinct rodent models of schizophrenia. PMID:32497066
Differential miRNAs expression pattern of irradiated breast cancer cell lines is correlated with radiation sensitivity. PMID:32493932
Inferring Active Metabolic Pathways from Proteomics and Essentiality Data. PMID:32492430
Functional and Genomic Variation between Human-Derived Isolates of Lachnospiraceae Reveals Inter- and Intra-Species Diversity. PMID:32492369
A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. PMID:32490206
Guizhi Fuling Decoction inhibiting the PI3K and MAPK pathways in breast cancer cells revealed by HTS2 technology and systems pharmacology. PMID:32489526
Genome sequence and comparative analysis of reindeer (Rangifer tarandus) in northern Eurasia. PMID:32488117
Core functional nodes and sex-specific pathways in human ischaemic and dilated cardiomyopathy. PMID:32487995
An investigation into the beneficial effects and molecular mechanisms of humic acid on foxtail millet under drought conditions. PMID:32484836
Cadmium, Smoking, and Human Blood DNA Methylation Profiles in Adults from the Strong Heart Study. PMID:32484362
Integrative omics analysis of the termite gut system adaptation to Miscanthus diet identifies lignocellulose degradation enzymes. PMID:32483294
Proteome and transcriptome reveal the involvement of heat shock proteins and antioxidant system in thermotolerance of Clematis florida. PMID:32483281
Implications of Skeletal Muscle Extracellular Matrix Remodeling in Metabolic Disorders: Diabetes Perspective. PMID:32481704
Differential Effects of Post-Weaning Diet and Maternal Obesity on Mouse Liver and Brain Metabolomes. PMID:32481497
Differential gene expression in response to water deficit in leaf and root tissues of soybean genotypes with contrasting tolerance profiles. PMID:32478791
Possible key microRNAs and corresponding molecular mechanisms for atrial fibrillation. PMID:32478689
A potential prognostic model based on miRNA expression profile in The Cancer Genome Atlas for bladder cancer patients. PMID:32477968
Repurposed Analog of GLP-1 Ameliorates Hyperglycemia in Type 1 Diabetic Mice Through Pancreatic Cell Reprogramming. PMID:32477262
Comparative transcriptome analysis digs out genes related to antifreeze between fresh and frozen-thawed rooster sperm. PMID:32475417
Dietary inflammatory potential in relation to the gut microbiome: results from a cross-sectional study. PMID:32475373
MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression. PMID:32471342
Ubiquitome analysis reveals the involvement of lysine ubiquitination in the spermatogenesis process of adult buffalo (Bubalus bubalis) testis. PMID:32469046
Bioinformatics analysis of the network of histone H3 lysine 9 trimethylation in acute myeloid leukaemia. PMID:32468066
Dental Calculus as a Tool to Study the Evolution of the Mammalian Oral Microbiome. PMID:32467975
Overcoming Genetically Based Resistance Mechanisms to PD-1 Blockade. PMID:32467343
The Possible Influence of Mediterranean Diet on Extracellular Vesicle miRNA Expression in Breast Cancer Survivors. PMID:32466456
Transcriptomic changes across the life cycle of Trypanosoma cruzi II. PMID:32461822
Transcript expression-aware annotation improves rare variant interpretation. PMID:32461655
Extracting chemical reactions from text using Snorkel. PMID:32460703
Specific adaptations are selected in opposite sun exposed Antarctic cryptoendolithic communities as revealed by untargeted metabolomics. PMID:32460306
iTRAQ-Based Comparative Proteomic Analysis of Larval Midgut From the Beet Armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae) Challenged With the Entomopathogenic Bacteria Serratia marcescens. PMID:32457652
Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer. PMID:32457603
Differential Expression of Plasma Exo-miRNA in Neurodegenerative Diseases by Next-Generation Sequencing. PMID:32457573
Inferring Virus-Host relationship between HPV and its host Homo sapiens using protein interaction network. PMID:32457456
The Msi1-mTOR pathway drives the pathogenesis of mammary and extramammary Paget's disease. PMID:32457396
An Integrated Genomic Strategy to Identify CHRNB4 as a Diagnostic/Prognostic Biomarker for Targeted Therapy in Head and Neck Cancer. PMID:32455963
Insight into the Lifestyle of Amoeba Willaertia magna during Bioreactor Growth Using Transcriptomics and Proteomics. PMID:32455615
Alterations in Tissue Metabolite Profiles with Amifostine-Prophylaxed Mice Exposed to Gamma Radiation. PMID:32455594
Draft Genome of the Liver Fluke Fasciola gigantica. PMID:32455229
Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PMID:32453742
Follicular extracellular vesicles enhance meiotic resumption of domestic cat vitrified oocytes. PMID:32451384
Lifestyle and the presence of helminths is associated with gut microbiome composition in Cameroonians. PMID:32450885
ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses. PMID:32449934
Transcriptome analysis of lateral buds from Phyllostachys edulis rhizome during germination and early shoot stages. PMID:32448144
Expression of genes of the Pho regulon is altered in Streptomyces coelicolor. PMID:32444655
The intestinal virome in children with cystic fibrosis differs from healthy controls. PMID:32442222
Metagenome Assembly and Metagenome-Assembled Genome Sequences from a Historical Oil Field Located in Wietze, Germany. PMID:32439669
The microbiome as a biosensor: functional profiles elucidate hidden stress in hosts. PMID:32438915
Proteomic and Metabolomic Correlates of Healthy Dietary Patterns: The Framingham Heart Study. PMID:32438708
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. PMID:32438566
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. PMID:32437556
Changes in the gut microbiota during Asian particolored bat (Vespertilio sinensis) development. PMID:32435532
β-Glucan Induces Protective Trained Immunity against Mycobacterium tuberculosis Infection: A Key Role for IL-1. PMID:32433977
In vitro passage alters virulence, immune activation and proteomic profiles of Burkholderia pseudomallei. PMID:32433516
A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimer's disease. PMID:32433480
Prognostic Value of a Stemness Index-Associated Signature in Primary Lower-Grade Glioma. PMID:32431729
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
In Vitro Effects of Streptococcus oralis Biofilm on Peri-Implant Soft Tissue Cells. PMID:32429151
Summary-Based Methylome-Wide Association Analyses Suggest Potential Genetically Driven Epigenetic Heterogeneity of Alzheimer's Disease. PMID:32429084
The Biotechnological Potential of the Marine Diatom Skeletonema dohrnii to the Elevated Temperature and pCO2 Concentration. PMID:32429035
Multiomics-based characterization of specialized metabolites biosynthesis in Cornus Officinalis. PMID:32426807
Transcriptomic evidence that insulin signalling pathway regulates the ageing of subterranean termite castes. PMID:32424344
Tools for successful proliferation: diverse strategies of nutrient acquisition by a benthic cyanobacterium. PMID:32424245
The genome of Mekong tiger perch (Datnioides undecimradiatus) provides insights into the phylogenetic position of Lobotiformes and biological conservation. PMID:32424221
Detecting qualitative changes in biological systems. PMID:32424123
Immunorthodontics: in vivo gene expression of orthodontic tooth movement. PMID:32424121
Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power. PMID:32421310
Epigenome-Wide Tobacco-Related Methylation Signature Identification and Their Multilevel Regulatory Network Inference for Lung Adenocarcinoma. PMID:32420331
Dietary zinc source impacts intestinal morphology and oxidative stress in young broilers. PMID:32416829
Whole genome bisulfite sequencing methylome analysis of mulberry (Morus alba) reveals epigenome modifications in response to drought stress. PMID:32415195
Metabolomics analyses to characterize metabolic alterations in Korean native calves by oral vitamin A supplementation. PMID:32415141
Differential blood miRNA expression in brain amyloid imaging-defined Alzheimer's disease and controls. PMID:32414413
Revisiting the Metabolic Capabilities of Bifidobacterium longum susbp. longum and Bifidobacterium longum subsp. infantis from a Glycoside Hydrolase Perspective. PMID:32413974
Prognostic implication and functional exploration for microRNA-20a as a molecular biomarker of gastrointestinal cancer. PMID:32410584
Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients. PMID:32407669
Identification of transforming growth factor beta induced (TGFBI) as an immune-related prognostic factor in clear cell renal cell carcinoma (ccRCC). PMID:32406866
Community-level signatures of ecological succession in natural bacterial communities. PMID:32404904
Integrated small RNA and mRNA expression profiles reveal miRNAs and their target genes in response to Aspergillus flavus growth in peanut seeds. PMID:32404101
Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells. PMID:32403229
Integrating biological knowledge and gene expression data using pathway-guided random forests: a benchmarking study. PMID:32399562
Multi-omics reveals that the rumen microbiome and its metabolome together with the host metabolome contribute to individualized dairy cow performance. PMID:32398126
Zonation of Ribosomal DNA Transcription Defines a Stem Cell Hierarchy in Colorectal Cancer. PMID:32396863
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
Feeding Faba Beans (Vicia faba L.) Reduces Myocyte Metabolic Activity in Grass Carp (Ctenopharyngodon idellus). PMID:32395106
MicroRNA regulatory pattern in spinal cord ischemia-reperfusion injury. PMID:32394971
A practical guide to amplicon and metagenomic analysis of microbiome data. PMID:32394199
Evaluation of plant sources for antiinfective lead compound discovery by correlating phylogenetic, spatial, and bioactivity data. PMID:32393619
Dynamic Transcriptome Analysis Reveals Uncharacterized Complex Regulatory Pathway Underlying Genotype-Recalcitrant Somatic Embryogenesis Transdifferentiation in Cotton. PMID:32392816
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization. PMID:32392297
Intrinsic Genetic and Transcriptomic Patterns Reflect Tumor Immune Subtypes Facilitating Exploring Possible Combinatory Therapy. PMID:32391377
CK14 Expression Identifies a Basal/Squamous-Like Type of Papillary Non-Muscle-Invasive Upper Tract Urothelial Carcinoma. PMID:32391279
Microbial community dynamics in mesophilic and thermophilic batch reactors under methanogenic, phenyl acid-forming conditions. PMID:32391081
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
The loss of photosynthesis pathway and genomic locations of the lost plastid genes in a holoparasitic plant Aeginetia indica. PMID:32384868
Comprehensive analysis of mutations of renal cell carcinoma in an autosomal dominant polycystic kidney disease patient. PMID:32384474
Differential Metabolic Pathways and Metabolites in a C57BL/6J Mouse Model of Alcoholic Liver Disease. PMID:32384076
CRY1-CBS binding regulates circadian clock function and metabolism. PMID:32383312
A putative competing endogenous RNA network in cisplatin-resistant lung adenocarcinoma cells identifying potentially rewarding research targets. PMID:32382346
Comprehensive analysis of the long non-coding RNA-associated competitive endogenous RNA network reveals novel prognostic biomarkers in Wilms' tumor. PMID:32382326
Effect of Huangqin Tang on Urine Metabolic Profile in Rats with Ulcerative Colitis Based on UPLC-Q-Exactive Orbitrap MS. PMID:32382278
Perturbations of the Gut Microbiome and Metabolome in Children with Calcium Oxalate Kidney Stone Disease. PMID:32381601
PIRs mediate innate myeloid cell memory to nonself MHC molecules. PMID:32381589
Epigenome-wide association study of DNA methylation and adult asthma in the Agricultural Lung Health Study. PMID:32381493
A Penicillium rubens platform strain for secondary metabolite production. PMID:32376967
Different effects of methylphenidate and atomoxetine on the behavior and brain transcriptome of zebrafish. PMID:32375837
Comprehensive dissection of dispensable genomic regions in Streptomyces based on comparative analysis approach. PMID:32375781
Pathway-Activity Likelihood Analysis and Metabolite Annotation for Untargeted Metabolomics Using Probabilistic Modeling. PMID:32375258
Transcriptome Analysis Reveals Clues into leaf-like flower mutant in Chinese orchid Cymbidium ensifolium. PMID:32373767
Transcriptome profiling reveals insertional mutagenesis suppressed the expression of candidate pathogenicity genes in honeybee fungal pathogen, Ascosphaera apis. PMID:32372055
Transcriptional profiling of murine macrophages stimulated with cartilage fragments revealed a strategy for treatment of progressive osteoarthritis. PMID:32371954
A Genome-scale CRISPR Screen Identifies the ERBB and mTOR Signaling Networks as Key Determinants of Response to PI3K Inhibition in Pancreatic Cancer. PMID:32371585
Identification of key genes, pathways and potential therapeutic agents for IgA nephropathy using an integrated bioinformatics analysis. PMID:32370650
Phenylpyrazalopyrimidines as Tyrosine Kinase Inhibitors: Synthesis, Antiproliferative Activity, and Molecular Simulations. PMID:32370213
Integrative Analysis of Fecal Metagenomics and Metabolomics in Colorectal Cancer. PMID:32370168
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Transcriptome-wide analysis reveals different categories of response to a standardised immune challenge in a wild rodent. PMID:32366957
In Vitro Evaluation of the Effects of Commercial Prebiotic GOS and FOS Products on Human Colonic Caco-2 Cells. PMID:32366023
Biochemical Characteristics and a Genome-Scale Metabolic Model of an Indian Euryhaline Cyanobacterium with High Polyglucan Content. PMID:32365713
Decoding the language of microbiomes using word-embedding techniques, and applications in inflammatory bowel disease. PMID:32365061
PaACL silencing accelerates flower senescence and changes the proteome to maintain metabolic homeostasis in Petunia hybrida. PMID:32364241
Proteomic profiling of Serratia marcescens by high-resolution mass spectrometry. PMID:32363156
Constructing gene network for type 1 narcolepsy based on genome-wide association study and differential gene expression analysis (STROBE). PMID:32358372
Human adipose-derived mesenchymal stem cell-conditioned medium ameliorates polyneuropathy and foot ulceration in diabetic BKS db/db mice. PMID:32357914
Negative binomial additive model for RNA-Seq data analysis. PMID:32357831
Promising diagnostic and prognostic value of six genes in human hepatocellular carcinoma. PMID:32355538
Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile. PMID:32354351
Are Pathogenic Germline Variants in Metastatic Melanoma Associated with Resistance to Combined Immunotherapy? PMID:32354124
Role of GPRC6A in Regulating Hepatic Energy Metabolism in Mice. PMID:32350388
Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans. PMID:32350386
Anti-inflammatory effects of α-MSH through p-CREB expression in sarcoidosis like granuloma model. PMID:32350353
High-throughput, Label-Free Quantitative Proteomic Studies of the Anticancer Effects of Electrical Pulses with Turmeric Silver Nanoparticles: an in vitro Model Study. PMID:32350346
Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae. PMID:32350099
Honey-bee-associated prokaryotic viral communities reveal wide viral diversity and a profound metabolic coding potential. PMID:32341166
Histidine Utilization Is a Critical Determinant of Acinetobacter Pathogenesis. PMID:32341119
Time Course of Changes in Sorafenib-Treated Hepatocellular Carcinoma Cells Suggests Involvement of Phospho-Regulated Signaling in Ferroptosis Induction. PMID:32336023
A Cross-linking Mass Spectrometry Approach Defines Protein Interactions in Yeast Mitochondria. PMID:32332106
Resistance of Tick Gut Microbiome to Anti-Tick Vaccines, Pathogen Infection and Antimicrobial Peptides. PMID:32331444
A STAT3 of Addiction: Adipose Tissue, Adipocytokine Signalling and STAT3 as Mediators of Metabolic Remodelling in the Tumour Microenvironment. PMID:32331320
A multiple genomic data fused SF2 prediction model, signature identification, and gene regulatory network inference for personalized radiotherapy. PMID:32329416
Temporal transcriptome change of Oncomelania hupensis revealed by Schistosoma japonicum invasion. PMID:32328235
Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. PMID:32327732
Amyloid Precursor Protein (APP) Controls the Expression of the Transcriptional Activator Neuronal PAS Domain Protein 4 (NPAS4) and Synaptic GABA Release. PMID:32327470
Charcot-Marie-Tooth Type 2B: A New Phenotype Associated with a Novel RAB7A Mutation and Inhibited EGFR Degradation. PMID:32326241
Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana. PMID:32325728
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. PMID:32323921
Application of weighted gene co‑expression network analysis to explore the potential diagnostic biomarkers for colorectal cancer. PMID:32323816
METTL14 promotes the migration and invasion of breast cancer cells by modulating N6‑methyladenosine and hsa‑miR‑146a‑5p expression. PMID:32323801
Metagenomics Reveals a Core Macrolide Resistome Related to Microbiota in Chronic Respiratory Disease. PMID:32320621
Molecular Events Controlling Cessation of Trunk Neural Crest Migration and Onset of Differentiation. PMID:32318567
Identification of tipifarnib sensitivity biomarkers in T-cell acute lymphoblastic leukemia and T-cell lymphoma. PMID:32317694
Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew. PMID:32317662
Chromosome-level reference genome of the jellyfish Rhopilema esculentum. PMID:32315029
SPEED2: inferring upstream pathway activity from differential gene expression. PMID:32313938
Hemocyte phagosomal proteome is dynamically shaped by cytoskeleton remodeling and interorganellar communication with endoplasmic reticulum during phagocytosis in a marine invertebrate, Crassostrea gigas. PMID:32313134
A fungal pathogen induces systemic susceptibility and systemic shifts in wheat metabolome and microbiome composition. PMID:32313046
Mesenchymal-endothelial transition-derived cells as a potential new regulatory target for cardiac hypertrophy. PMID:32313043
Comprehensive insights on pivotal prognostic signature involved in clear cell renal cell carcinoma microenvironment using the ESTIMATE algorithm. PMID:32311223
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Transcriptome Analysis Reveals the Negative Effect of 16 T High Static Magnetic Field on Osteoclastogenesis of RAW264.7 Cells. PMID:32309435
Screening TCGA database for prognostic genes in lower grade glioma microenvironment. PMID:32309356
Identification of key candidate genes and pathways revealing the protective effect of liraglutide on diabetic cardiac muscle by integrated bioinformatics analysis. PMID:32309328
Impaired Metabolic Pathways Related to Colorectal Cancer Progression and Therapeutic Implications. PMID:32309224
ZGRF1 Is Associated with Poor Prognosis in Triple-Negative Breast Cancer and Promotes Cancer Stemness Based on Bioinformatics. PMID:32308418
Analysis of deep sequencing exosome-microRNA expression profile derived from CP-II reveals potential role of gga-miRNA-451 in inflammation. PMID:32307881
Genome of extreme halophyte Puccinellia tenuiflora. PMID:32306894
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
Pleiotropy-Based Decomposition of Genetic Risk Scores: Association and Interaction Analysis for Type 2 Diabetes and CAD. PMID:32302534
Analysis of neurotransmitters in rat placenta exposed to flame retardants using IR-MALDESI mass spectrometry imaging. PMID:32300844
Identification of Pan-Cancer Prognostic Biomarkers Through Integration of Multi-Omics Data. PMID:32300588
Draft Genome Assembly for the Tibetan Black Bear (Ursus thibetanus thibetanus). PMID:32300354
Microarray data analysis on gene and miRNA expression to identify biomarkers in non-small cell lung cancer. PMID:32299382
The novel microRNAs hsa-miR-nov7 and hsa-miR-nov3 are over-expressed in locally advanced breast cancer. PMID:32298266
Requirement for cleavage factor IIm in the control of alternative polyadenylation in breast cancer cells. PMID:32295865
Functional Interactomes of Genes Showing Association with Type-2 Diabetes and Its Intermediate Phenotypic Traits Point towards Adipo-Centric Mechanisms in Its Pathophysiology. PMID:32294959
Insulin-Like Growth Factors Are Key Regulators of T Helper 17 Regulatory T Cell Balance in Autoimmunity. PMID:32294406
Genomic characterization of an emerging Enterobacteriaceae species: the first case of co-infection with a typical pathogen in a human patient. PMID:32293254
A Chromosome-Scale Assembly of the Asian Honeybee Apis cerana Genome. PMID:32292419
Transcriptomic Changes in the Rumen Epithelium of Cattle after the Induction of Acidosis. PMID:32292009
Transcriptomic Prediction of Pig Liver-Enriched Gene 1 Functions in a Liver Cell Line. PMID:32290278
Comprehensive immunogenomic landscape analysis of prognosis-related genes in head and neck cancer. PMID:32286381
Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress. PMID:32286374
Single-cell transcriptomics identifies an effectorness gradient shaping the response of CD4+ T cells to cytokines. PMID:32286271
Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida. PMID:32280587
Weighted gene correlation network analysis reveals novel biomarkers associated with mesenchymal stromal cell differentiation in early phase. PMID:32280568
iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model. PMID:32277147
Developmentally Driven Changes in Adipogenesis in Different Fat Depots Are Related to Obesity. PMID:32273869
Network Systems Pharmacology-Based Mechanism Study on the Beneficial Effects of Vitamin D against Psychosis in Alzheimer's Disease. PMID:32273551
Draft genome of multiple resistance donor plant Sinapis alba: An insight into SSRs, annotations and phylogenetics. PMID:32271806
Molecular mechanisms and prognostic markers in head and neck squamous cell carcinoma: a bioinformatic analysis. PMID:32269674
Integrative Analysis for the Roles of lncRNAs in the Immune Responses of Mouse PBMC Exposed to Low-Dose Ionizing Radiation. PMID:32269503
The Scaly-foot Snail genome and implications for the origins of biomineralised armour. PMID:32269225
Integrative genomics analysis of eQTL and GWAS summary data identifies PPP1CB as a novel bone mineral density risk genes. PMID:32266926
Investigation of miRNA and mRNA Co-expression Network in Ependymoma. PMID:32266223
Impact of ex vivo Sample Handling on DNA Methylation Profiles in Human Cord Blood and Neonatal Dried Blood Spots. PMID:32265984
Erosion of Gene Co-expression Networks Reveal Deregulation of Immune System Processes in Late-Onset Alzheimer's Disease. PMID:32265636
De novo transcriptome assembly and data for the blue-winged teal (Spatula discors). PMID:32258268
Transcriptome Analysis Reveals Key Pathways and Hormone Activities Involved in Early Microtuber Formation of Dioscorea opposita. PMID:32258146
Essential Metabolic Routes as a Way to ESKAPE From Antibiotic Resistance. PMID:32257985
Network Pharmacology-Based Strategy for Predicting Therapy Targets of Traditional Chinese Medicine Xihuang Pill on Liver Cancer. PMID:32256653
Influenza-Induced Interferon Lambda Response Is Associated With Longer Time to Delivery Among Pregnant Kenyan Women. PMID:32256497
Searching for Drug Synergy Against Cancer Through Polyamine Metabolism Impairment: Insight Into the Metabolic Effect of Indomethacin on Lung Cancer Cells. PMID:32256343
Insights into the metabolic responses of two contrasting Tibetan hulless barley genotypes under low nitrogen stress. PMID:32256004
Combined transcriptomic and metabolomic analyses uncover rearranged gene expression and metabolite metabolism in tobacco during cold acclimation. PMID:32251321
Urinary Exosomes from Bladder Cancer Patients Show a Residual Cancer Phenotype despite Complete Pathological Downstaging. PMID:32249794
Anticancer Effect of Radix Astragali on Cholangiocarcinoma In Vitro and Its Mechanism via Network Pharmacology. PMID:32246704
The First Genome Survey of the Antarctic Krill (Euphausia superba) Provides a Valuable Genetic Resource for Polar Biomedical Research. PMID:32244466
Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. PMID:32243546
Novel insights into host-pathogen interactions of large yellow croakers ( Larimichthys crocea) and pathogenic bacterium Pseudomonas plecoglossicida using time-resolved dual RNA-seq of infected spleens. PMID:32242645
Single-cell analysis of a mutant library generated using CRISPR-guided deaminase in human melanoma cells. PMID:32242071
Cell cycle-dependent localization of the proteasome to chromatin. PMID:32242037
SCNrank: spectral clustering for network-based ranking to reveal potential drug targets and its application in pancreatic ductal adenocarcinoma. PMID:32241274
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection. PMID:32241270
EpiMOLAS: an intuitive web-based framework for genome-wide DNA methylation analysis. PMID:32241255
Metabolic disturbance in hippocampus and liver of mice: A primary response to imidacloprid exposure. PMID:32235887
Molecular Profiling for Predictors of Radiosensitivity in Patients with Breast or Head-and-Neck Cancer. PMID:32235817
Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer. PMID:32235589
Therapeutically actionable PAK4 is amplified, overexpressed, and involved in bladder cancer progression. PMID:32231273
Comparative Genomics of Lactobacillus crispatus from the Gut and Vagina Reveals Genetic Diversity and Lifestyle Adaptation. PMID:32230824
Identification of novel biomarkers in ischemic stroke: a genome-wide integrated analysis. PMID:32228489
Characterising the mechanisms underlying genetic resistance to amoebic gill disease in Atlantic salmon using RNA sequencing. PMID:32228433
Gut Microbiomes of Endangered Przewalski's Horse Populations in Short- and Long-Term Captivity: Implication for Species Reintroduction Based on the Soft-Release Strategy. PMID:32226419
Integrative differential expression and gene set enrichment analysis using summary statistics for scRNA-seq studies. PMID:32221292
Identification of hub genes associated with outcome of clear cell renal cell carcinoma. PMID:32218839
Comparative Transcriptome Analysis Provides Insights Into Yellow Rind Formation and Preliminary Mapping of the Clyr (Yellow Rind) Gene in Watermelon. PMID:32218790
Biological potential alterations of migratory chondrogenic progenitor cells during knee osteoarthritic progression. PMID:32216831
Metabolic changes during respiratory syncytial virus infection of epithelial cells. PMID:32214395
Proteomic mapping of Drosophila transgenic elav.L-GAL4/+ brain as a tool to illuminate neuropathology mechanisms. PMID:32214222
In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis - A Kinetic Modeling Approach. PMID:32211028
Bioinformatic Analysis Identifies Potential Key Genes in the Pathogenesis of Turner Syndrome. PMID:32210915
Modular Characteristics and Mechanism of Action of Herbs for Endometriosis Treatment in Chinese Medicine: A Data Mining and Network Pharmacology-Based Identification. PMID:32210799
Formate Utilization by the Crenarchaeon Desulfurococcus amylolyticus. PMID:32210133
An atlas of human metabolism. PMID:32209698
Variation in the microbiota across different developmental stages of Aedes albopictus is affected by ampicillin exposure. PMID:32207564
Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PMID:32203501
Autotrophic carbon fixation pathways along the redox gradient in oxygen-depleted oceanic waters. PMID:32202395
Comprehensive bioinformatic analysis of Wnt1 and Wnt1-associated diseases. PMID:32201670
MetaBridge: An Integrative Multi-Omics Tool for Metabolite-Enzyme Mapping. PMID:32199034
Detection of Early Disease Risk Factors Associated with Metabolic Syndrome: A New Era with the NMR Metabolomics Assessment. PMID:32197513
Pharmacological Mechanisms Underlying the Neuroprotective Effects of Alpinia oxyphylla Miq. on Alzheimer's Disease. PMID:32197305
The landscape of coadaptation in Vibrio parahaemolyticus. PMID:32195663
The genome of jojoba (Simmondsia chinensis): A taxonomically isolated species that directs wax ester accumulation in its seeds. PMID:32195345
ADH7, miR-3065 and LINC01133 are associated with cervical cancer progression in different age groups. PMID:32194732
Prognostic value of key genes of the JAK-STAT signaling pathway in patients with cutaneous melanoma. PMID:32194688
Overexpression of miR-206 in osteosarcoma and its associated molecular mechanisms as assessed through TCGA and GEO databases. PMID:32194668
MicroRNA Alterations for Diagnosis, Prognosis, and Treatment of Osteoporosis: A Comprehensive Review and Computational Functional Survey. PMID:32194637
A Metabolic Insight Into the Neuroprotective Effect of Jin-Mai-Tong (JMT) Decoction on Diabetic Rats With Peripheral Neuropathy Using Untargeted Metabolomics Strategy. PMID:32194428
Repositioning of Hypoglycemic Drug Linagliptin for Cancer Treatment. PMID:32194417
The role of semen and seminal plasma in inducing large-scale genomic changes in the female porcine peri-ovulatory tract. PMID:32193402
Identification of Key Components in Colon Adenocarcinoma Using Transcriptome to Interactome Multilayer Framework. PMID:32193399
Coxsackievirus B3 Infection of Human Neural Progenitor Cells Results in Distinct Expression Patterns of Innate Immune Genes. PMID:32192194
Microbiota Alters Urinary Bladder Weight and Gene Expression. PMID:32192034
Chromosome-level genome assembly of Aldrichina grahami, a forensically important blowfly. PMID:32191812
GSTM1 and GSTT1 genetic polymorphisms and their association with antituberculosis drug-induced liver injury. PMID:32190303
Translating traditional herbal formulas into modern drugs: a network-based analysis of Xiaoyao decoction. PMID:32190105
Description of Virulent Factors and Horizontal Gene Transfers of Keratitis-Associated Amoeba Acanthamoeba Triangularis by Genome Analysis. PMID:32188120
Identification of Deregulated Pathways, Key Regulators, and Novel miRNA-mRNA Interactions in HPV-Mediated Transformation. PMID:32188026
Epigenetic engineering of yeast reveals dynamic molecular adaptation to methylation stress and genetic modulators of specific DNMT3 family members. PMID:32187373
Muscle metabolomics analysis reveals potential biomarkers of exercise‑dependent improvement of the diaphragm function in chronic obstructive pulmonary disease. PMID:32186768
PDGFD induces ibrutinib resistance of diffuse large B‑cell lymphoma through activation of EGFR. PMID:32186759
New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. PMID:32184419
Extensive splicing changes in an ALS/FTD transgenic mouse model overexpressing cytoplasmic fused in sarcoma. PMID:32184412
In Vivo Thermodynamic Analysis of Glycolysis in Clostridium thermocellum and Thermoanaerobacterium saccharolyticum Using 13C and 2H Tracers. PMID:32184362
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324
Cyclosporine a directly affects human and mouse b cell migration in vitro by disrupting a hIF-1 αdependent, o2 sensing, molecular switch. PMID:32183695
Reveals of New Candidate Active Components in Hemerocallis Radix and Its Anti-Depression Action of Mechanism Based on Network Pharmacology Approach. PMID:32182911
Hepamine - A Liver Disease Microarray Database, Visualization Platform and Data-Mining Resource. PMID:32179762
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis. PMID:32178397
Adjustment of photosynthetic activity to drought and fluctuating light in wheat. PMID:32176335
Identification of hub genes and potential molecular mechanisms of chickpea isoflavones on MCF-7 breast cancer cells by integrated bioinformatics analysis. PMID:32175379
Identifying Significant Metabolic Pathways Using Multi-Block Partial Least-Squares Analysis. PMID:32174118
Metagenomic analysis of bacterial species in tongue microbiome of current and never smokers. PMID:32170059
Functional cooperation of the glycine synthase-reductase and Wood-Ljungdahl pathways for autotrophic growth of Clostridium drakei. PMID:32170009
Systems Metabolic Alteration in a Semi-Dwarf Rice Mutant Induced by OsCYP96B4 Gene Mutation. PMID:32168953
Reconstruction and Analysis of Cattle Metabolic Networks in Normal and Acidosis Rumen Tissue. PMID:32168900
Analyses of energy metabolism and stress defence provide insights into Campylobacter concisus growth and pathogenicity. PMID:32165925
Genes associated with inflammation may serve as biomarkers for the diagnosis of coronary artery disease and ischaemic stroke. PMID:32164735
Network hub-node prioritization of gene regulation with intra-network association. PMID:32164570
Temporal specificity and heterogeneity of Drosophila immune cells. PMID:32162708
Thyroid Hormone Metabolite 3-Iodothyronamine (T1AM) Alleviates Hypoxia/Reoxygenation-Induced Cardiac Myocyte Apoptosis via Akt/FoxO1 Pathway. PMID:32162616
CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming. PMID:32161720
Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis. PMID:32161689
Engrailed 2 (EN2) acts as a glioma suppressor by inhibiting tumor proliferation/invasion and enhancing sensitivity to temozolomide. PMID:32158355
Feedback analysis identifies a combination target for overcoming adaptive resistance to targeted cancer therapy. PMID:32157217
Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil. PMID:32156798
Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer. PMID:32156795
Transcriptome Analyses of Diaphorina citri Midgut Responses to Candidatus Liberibacter Asiaticus Infection. PMID:32156093
Long noncoding RNA and messenger RNA abnormalities in pediatric sepsis: a preliminary study. PMID:32151258
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
The influence of rare variants in circulating metabolic biomarkers. PMID:32150548
Transcriptome analysis of Panax ginseng response to high light stress. PMID:32148414
Application of NanoString technologies in angioimmunoblastic T cell lymphoma. PMID:32146712
Tuning up microbiome analysis to monitor WWTPs' biological reactors functioning. PMID:32139809
Functionally Enigmatic Genes in Cancer: Using TCGA Data to Map the Limitations of Annotations. PMID:32139709
Changes in Intestinal Microbiota and Predicted Metabolic Pathways During Colonic Fermentation of Mango (Mangifera indica L.)-Based Bar Indigestible Fraction. PMID:32138281
Identification of PTPRR and JAG1 as key genes in castration-resistant prostate cancer by integrated bioinformatics methods. PMID:32133801
Identification of Milk and Cheese Intake Biomarkers in Healthy Adults Reveals High Interindividual Variability of Lewis System-Related Oligosaccharides. PMID:32133503
Identification of the Molecular Mechanisms of Peimine in the Treatment of Cough Using Computational Target Fishing. PMID:32131410
Bacteria Boost Mammalian Host NAD Metabolism by Engaging the Deamidated Biosynthesis Pathway. PMID:32130883
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Bioinformatics analysis and identification of potential genes related to pathogenesis of cervical intraepithelial neoplasia. PMID:32127942
Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry. PMID:32126136
PHARMIP: An insilico method to predict genetics that underpin adverse drug reactions. PMID:32123669
Recent advances in functional research in Giardia intestinalis. PMID:32122532
Identification of a robust functional subpathway signature for pancreatic ductal adenocarcinoma by comprehensive and integrated analyses. PMID:32122386
Investigating the multi-target pharmacological mechanism of danhong injection acting on unstable angina by combined network pharmacology and molecular docking. PMID:32122353
Comparative Analysis of miRNA Expression Profiles Between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing. PMID:32121287
Protein Aggregation is Associated with Acinetobacter baumannii Desiccation Tolerance. PMID:32121206
Effect of Caloric Restriction on BMI, Gut Microbiota, and Blood Amino Acid Levels in Non-Obese Adults. PMID:32120990
Derivation of a metabolic signature associated with bacterial meningitis in infants. PMID:32120377
Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids. PMID:32117908
Hydrolyzed Fat Formula Increases Brain White Matter in Small for Gestational Age and Appropriate for Gestational Age Neonatal Piglets. PMID:32117837
Targeting Metabolic Deregulation Landscapes in Breast Cancer Subtypes. PMID:32117749
Identification and Validation of an Individualized Prognostic Signature of Bladder Cancer Based on Seven Immune Related Genes. PMID:32117435
Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification. PMID:32117426
Enterococcus faecalis Adapts to Antimicrobial Conjugated Oligoelectrolytes by Lipid Rearrangement and Differential Expression of Membrane Stress Response Genes. PMID:32117172
Copper and Melanin Play a Role in Myxococcus xanthus Predation on Sinorhizobium meliloti. PMID:32117124
Chronic Sublethal Aluminum Exposure and Avena fatua Caryopsis Colonization Influence Gene Expression of Fusarium avenaceum F.a.1. PMID:32117103
Proteomic Investigation Uncovers Potential Targets and Target Sites of Pneumococcal Serine-Threonine Kinase StkP and Phosphatase PhpP. PMID:32117081
Co-expression network analysis reveals the pivotal role of mitochondrial dysfunction and interferon signature in juvenile dermatomyositis. PMID:32110496
DISNET: a framework for extracting phenotypic disease information from public sources. PMID:32110491
Postprandial transfer of colostral extracellular vesicles and their protein and miRNA cargo in neonatal calves. PMID:32109241
Network Pharmacology-Based Investigation of the System-Level Molecular Mechanisms of the Hematopoietic Activity of Samul-Tang, a Traditional Korean Herbal Formula. PMID:32104198
Metabolic alterations in the erythrocyte during blood-stage development of the malaria parasite. PMID:32103749
Prediction of Alzheimer's disease using blood gene expression data. PMID:32103140
Novel pathways of HIV latency reactivation revealed by integrated analysis of transcriptome and target profile of bryostatin. PMID:32103135
Leishmania donovani infection induce differential miRNA expression in CD4+ T cells. PMID:32103111
Association between MIR499A rs3746444 polymorphism and breast cancer susceptibility: a meta-analysis. PMID:32103099
Transcriptome analysis of life stages of the house cricket, Acheta domesticus, to improve insect crop production. PMID:32103047
Single-cell Transcriptome Mapping Identifies Common and Cell-type Specific Genes Affected by Acute Delta9-tetrahydrocannabinol in Humans. PMID:32103029
Learning Pathway Dynamics from Single-Cell Proteomic Data: A Comparative Study. PMID:32100455
A Metabolomic Investigation of the Effect of Eosin B on Game-tocyte of Plasmodium falciparum Using 1HNMR Spectroscopy. PMID:32099562
Horizontal Gene Transfer to a Defensive Symbiont with a Reduced Genome in a Multipartite Beetle Microbiome. PMID:32098813
Comparative Genomics and Evolutionary Analysis of RNA-Binding Proteins of Burkholderia cenocepacia J2315 and Other Members of the B. cepacia Complex. PMID:32098200
Functional traits of the gut microbiome correlated with host lipid content in a natural population of Drosophila melanogaster. PMID:32097599
Systems biology analysis of publicly available transcriptomic data reveals a critical link between AKR1B10 gene expression, smoking and occurrence of lung cancer. PMID:32097409
SOCS1 blocks G1-S transition in hepatocellular carcinoma by reducing the stability of the CyclinD1/CDK4 complex in the nucleus. PMID:32096766
Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells. PMID:32095352
Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets. PMID:32094381
The sequence and de novo assembly of the wild yak genome. PMID:32094352
Chlamydia trachomatis Oligopeptide Transporter Performs Dual Functions of Oligopeptide Transport and Peptidoglycan Recycling. PMID:32094256
Transcriptome Analysis and Identification of Genes Associated with Starch Metabolism in Castanea henryi Seed (Fagaceae). PMID:32093295
Bioinformatics Approaches to the Understanding of Molecular Mechanisms in Antimicrobial Resistance. PMID:32085478
A Guide to Conquer the Biological Network Era Using Graph Theory. PMID:32083072
Comparative in-silico proteomic analysis discerns potential granuloma proteins of Yersinia pseudotuberculosis. PMID:32080254
Pan-cancer analysis reveals cooperativity of both strands of microRNA that regulate tumorigenesis and patient survival. PMID:32080184
Rhizosphere Bacterial Community Structure and Predicted Functional Analysis in the Water-Level Fluctuation Zone of the Danjiangkou Reservoir in China During the Dry Period. PMID:32079120
Integrative Transcriptomic and Metabolic Analyses Provide Insights into the Role of Trichomes in Tea Plant (Camellia Sinensis). PMID:32079100
Interaction of field realistic doses of clothianidin and Varroa destructor parasitism on adult honey bee (Apis mellifera L.) health and neural gene expression, and antagonistic effects on differentially expressed genes. PMID:32078633
Multiple Pathways Involved in Palmitic Acid-Induced Toxicity: A System Biology Approach. PMID:32076395
Examination of Genomic and Transcriptomic Alterations in a Morphologically Stable Line, MU1, Generated by Intergeneric Pollination. PMID:32075264
Changes in the proteome of sea urchin Paracentrotus lividus coelomocytes in response to LPS injection into the body cavity. PMID:32074628
Transcriptome Analysis Reveals Biosynthesis of Important Bioactive Constituents and Mechanism of Stem Formation of Dendrobium huoshanense. PMID:32071345
IPCO: Inference of Pathways from Co-variance analysis. PMID:32070271
Genome-Wide Profiling and Phylogenetic Analysis of the SWEET Sugar Transporter Gene Family in Walnut and Their Lack of Responsiveness to Xanthomonas arboricola pv. juglandis Infection. PMID:32070009
Impact of Hydrogen on the Transcriptome of Sinorhizobium meliloti 1021 Using RNA-sequencing Technology. PMID:32067442
Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families. PMID:32066727
Network Pharmacology-Based Strategy to Investigate the Pharmacologic Mechanisms of Atractylodes macrocephala Koidz. for the Treatment of Chronic Gastritis. PMID:32063848
A systems approach to infectious disease. PMID:32060427
Seasonal Variability and Shared Molecular Signatures of Inactivated Influenza Vaccination in Young and Older Adults. PMID:32060136
RNA sequencing profiles and diagnostic signatures linked with response to ramucirumab in gastric cancer. PMID:32060041
Responses of Acidobacteria Granulicella sp. WH15 to High Carbon Revealed by Integrated Omics Analyses. PMID:32059463
Identification of Hub Genes and Pathways in Gastric Adenocarcinoma Based on Bioinformatics Analysis. PMID:32058995
An update on the Symbiotic Genomes Database (SymGenDB): a collection of metadata, genomic, genetic and protein sequences, orthologs and metabolic networks of symbiotic organisms. PMID:32055857
Exploration of databases and methods supporting drug repurposing: a comprehensive survey. PMID:32055842
Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response. PMID:32052037
Pan-tissue transcriptome analysis of long noncoding RNAs in the American beaver Castor canadensis. PMID:32050897
The Progress of Multi-Omics Technologies: Determining Function in Lactic Acid Bacteria Using a Systems Level Approach. PMID:32047482
Trait-Based Comparison of Coral and Sponge Microbiomes. PMID:32047192
Common and Unique microRNAs in Multiple Carcinomas Regulate Similar Network of Pathways to Mediate Cancer Progression. PMID:32047181
Designing minimal genomes using whole-cell models. PMID:32047145
Adaptive selection in the evolution of programmed cell death-1 and its ligands in vertebrates. PMID:32045365
DeepKinZero: zero-shot learning for predicting kinase-phosphosite associations involving understudied kinases. PMID:32044914
Transcriptomic changes in the nasal epithelium associated with diesel engine exhaust exposure. PMID:32044442
Mammalian gene expression variability is explained by underlying cell state. PMID:32043799
The hornwort genome and early land plant evolution. PMID:32042158
Modification of the head proteome of nurse honeybees (Apis mellifera) exposed to field-relevant doses of pesticides. PMID:32042077
Genome-wide association study (GWAS) reveals genetic loci of lead (Pb) tolerance during seedling establishment in rapeseed (Brassica napus L.). PMID:32041524
Cytokinins Are Abundant and Widespread Among Insect Species. PMID:32041320
Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids. PMID:32041193
Screening the Cancer Genome Atlas Database for Genes of Prognostic Value in Acute Myeloid Leukemia. PMID:32039005
Text-mining in cancer research may help identify effective treatments. PMID:32038938
IGFBP6 Is Downregulated in Unstable Carotid Atherosclerotic Plaques According to an Integrated Bioinformatics Analysis and Experimental Verification. PMID:32037372
Chitin degradation potential and whole-genome sequence of Streptomyces diastaticus strain CS1801. PMID:32036475
Identification and characterization of a bacterial core methionine synthase. PMID:32034217
IGF1-mediated human embryonic stem cell self-renewal recapitulates the embryonic niche. PMID:32034154
Gastric bypass surgery in a rat model alters the community structure and functional composition of the intestinal microbiota independently of weight loss. PMID:32033593
Nitrogen Source Affects the Composition of Metabolites in Pepper (Capsicum annuum L.) and Regulates the Synthesis of Capsaicinoids through the GOGAT-GS Pathway. PMID:32033346
MicroRNA exporter HuR clears the internalized pathogens by promoting pro-inflammatory response in infected macrophages. PMID:32031337
Multiple genome pattern analysis and signature gene identification for the Caucasian lung adenocarcinoma patients with different tobacco exposure patterns. PMID:32030321
Protein expression profile changes of lung tissue in patients with pulmonary hypertension. PMID:32030316
Identification of key genes and pathways in calcific aortic valve disease by bioinformatics analysis. PMID:32030260
Genome analysis of a wild rumen bacterium Enterobacter aerogenes LU2 - a novel bio-based succinic acid producer. PMID:32029880
Red versus green leaves: transcriptomic comparison of foliar senescence between two Prunus cerasifera genotypes. PMID:32029804
Screening of Prognostic Factors in Early-Onset Breast Cancer. PMID:32028860
The Genome Assembly and Annotation of the Southern Elephant Seal Mirounga leonina. PMID:32028680
TGF-Beta-Activated Cancer-Associated Fibroblasts Limit Cetuximab Efficacy in Preclinical Models of Head and Neck Cancer. PMID:32028632
Pathway and network analysis of more than 2500 whole cancer genomes. PMID:32024854
Cytosolic GLUTAMINE SYNTHETASE1;1 Modulates Metabolism and Chloroplast Development in Roots. PMID:32024696
Poor clinical outcome in metastatic melanoma is associated with a microRNA-modulated immunosuppressive tumor microenvironment. PMID:32024530
Soil Inoculation Alters Leaf Metabolic Profiles in Genetically Identical Plants. PMID:32020484
Selective deletion of MyD88 signaling in α-SMA positive cells ameliorates experimental intestinal fibrosis via post-transcriptional regulation. PMID:32020030
Structural and functional differentiation of bacterial communities in post-coal mining reclamation soils of South Africa: bioindicators of soil ecosystem restoration. PMID:32019965
Host identity and symbiotic association affects the taxonomic and functional diversity of the clownfish-hosting sea anemone microbiome. PMID:32019466
Construction of a prognosis‑associated long noncoding RNA‑mRNA network for multiple myeloma based on microarray and bioinformatics analysis. PMID:32016443
Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy. PMID:32016442
MicroRNA gga-miR-200a-3p modulates immune response via MAPK signaling pathway in chicken afflicted with necrotic enteritis. PMID:32014061
Identification of 34 genes conferring genetic and pharmacological risk for the comorbidity of schizophrenia and smoking behaviors. PMID:32012119
Draft Genome of the Asian Buffalo Leech Hirudinaria manillensis. PMID:32010187
Functional Signatures of the Epiphytic Prokaryotic Microbiome of Agaves and Cacti. PMID:32010100
Metagenomic analysis exploring taxonomic diversity of rumen microbial communities in Vechur and crossbred cattle of Kerala state, India. PMID:32006353
Adult Human Glioblastomas Harbor Radial Glia-like Cells. PMID:32004492
Dysregulated FXR-FGF19 signaling and choline metabolism are associated with gut dysbiosis and hyperplasia in a novel pig model of pediatric NASH. PMID:32003601
Tools for Analysis of the Microbiome. PMID:32002757
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. PMID:32001720
Genomic analyses reveal selection footprints in rice landraces grown under on-farm conservation conditions during a short-term period of domestication. PMID:31993077
Activation of Myd88-Dependent TLRs Mediates Local and Systemic Inflammation in a Mouse Model of Primary Sjögren's Syndrome. PMID:31993047
Advanced identification of global bioactivity hotspots via screening of the metabolic fingerprint of entire ecosystems. PMID:31992728
Horizontally Acquired Quorum-Sensing Regulators Recruited by the PhoP Regulatory Network Expand the Host Adaptation Repertoire in the Phytopathogen Pectobacterium brasiliense. PMID:31992632
Effects of Antibiotic Pretreatment of an Ulcerative Colitis-Derived Fecal Microbial Community on the Integration of Therapeutic Bacteria In Vitro. PMID:31992630
Key genes with prognostic values in suppression of osteosarcoma metastasis using comprehensive analysis. PMID:31992246
Coexpression and Transcriptome analyses identify active Apomixis-related genes in Paspalum notatum leaves. PMID:31992196
Diverse biological processes coordinate the transcriptional response to nutritional changes in a Drosophila melanogaster multiparent population. PMID:31992183
A comparison of curated gene sets versus transcriptomics-derived gene signatures for detecting pathway activation in immune cells. PMID:31992182
Comparative transcriptome analysis revealed genes involved in the fruiting body development of Ophiocordyceps sinensis. PMID:31988806
Genetic architecture study of rheumatoid arthritis and juvenile idiopathic arthritis. PMID:31988799
Structural and Biomolecular Analyses of Borrelia burgdorferi BmpD Reveal a Substrate-Binding Protein of an ABC-Type Nucleoside Transporter Family. PMID:31988175
NAPAbench 2: A network synthesis algorithm for generating realistic protein-protein interaction (PPI) network families. PMID:31986158
Patient similarity by joint matrix trifactorization to identify subgroups in acute myeloid leukemia. PMID:31984320
Mutation Enrichment and Transcriptomic Activation Signatures of 419 Molecular Pathways in Cancer. PMID:31979117
Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses. PMID:31978162
Reconstruction of a regulated two-cell metabolic model to study biohydrogen production in a diazotrophic cyanobacterium Anabaena variabilis ATCC 29413. PMID:31978122
Comparative proteomic and genomic analyses of Brucella abortus biofilm and planktonic cells. PMID:31974592
Imputation of Gene Expression Data in Blood Cancer and Its Significance in Inferring Biological Pathways. PMID:31970084
Microarray Expression Profiling and Raman Spectroscopy Reveal Anti-Fatty Liver Action of Berberine in a Diet-Induced Larval Zebrafish Model. PMID:31969822
Circulating miR-330-3p in Late Pregnancy is Associated with Pregnancy Outcomes Among Lean Women with GDM. PMID:31969632
Environmental arginine controls multinuclear giant cell metabolism and formation. PMID:31969567
A novel risk score model for stomach adenocarcinoma based on the expression levels of 10 genes. PMID:31966067
MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors. PMID:31965022
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. PMID:31964916
Study of the Royal Jelly Free Fatty Acids by Liquid Chromatography-High Resolution Mass Spectrometry (LC-HRMS). PMID:31963373
Establishment and Characterization of Paired Primary Cultures of Human Pancreatic Cancer Cells and Stellate Cells Derived from the Same Tumor. PMID:31963309
A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy. PMID:31961962
Identification of Cartilage Microbial DNA Signatures and Associations With Knee and Hip Osteoarthritis. PMID:31961065
Genetic studies of urinary metabolites illuminate mechanisms of detoxification and excretion in humans. PMID:31959995
Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. PMID:31959971
The dynamic response of the Arabidopsis root metabolome to auxin and ethylene is not predicted by changes in the transcriptome. PMID:31959762
Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its "Jekyll and Hyde" Mode of Infection Pattern. PMID:31958110
Re-initiation of Oral Food Intake Following Enteral Nutrition Alters Oral and Gut Microbiota Communities. PMID:31956606
Niche differentiation is spatially and temporally regulated in the rhizosphere. PMID:31953507
Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. PMID:31953253
Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering. PMID:31952478
Accumulation of genetic variants associated with immunity in the selective breeding of broilers. PMID:31952471
Cell Adhesion-Related Molecules Play a Key Role in Renal Cancer Progression by Multinetwork Analysis. PMID:31950034
Lag penalized weighted correlation for time series clustering. PMID:31948388
A high-quality chromosomal genome assembly of Diospyros oleiferaCheng. PMID:31944244
Heavy Metals as a Factor Increasing the Functional Genetic Potential of Bacterial Community for Polycyclic Aromatic Hydrocarbon Biodegradation. PMID:31941126
Proteomic Analysis of Irradiation with Millimeter Waves on Soybean Growth under Flooding Conditions. PMID:31940953
A Biostimulant Obtained from the Seaweed Ascophyllum nodosum Protects Arabidopsis thaliana from Severe Oxidative Stress. PMID:31940839
Whole Genome Analysis of the Red-Crowned Crane Provides Insight into Avian Longevity. PMID:31940721
DNA methylation profiling in recurrent miscarriage. PMID:31938574
Metabolomic networks and pathways associated with feed efficiency and related-traits in Duroc and Landrace pigs. PMID:31937890
Human Colon Mucosal Biofilms and Murine Host Communicate via Altered mRNA and microRNA Expression during Cancer. PMID:31937674
Identification of key genes involved in the pathogenesis of cutaneous melanoma using bioinformatics analysis. PMID:31937175
Skeletal Muscle Myofibrillar Protein Abundance Is Higher in Resistance-Trained Men, and Aging in the Absence of Training May Have an Opposite Effect. PMID:31936810
Uncovering the Pharmacological Mechanism of Stemazole in the Treatment of Neurodegenerative Diseases Based on a Network Pharmacology Approach. PMID:31936558
Duodenum Intestine-Chip for preclinical drug assessment in a human relevant model. PMID:31933478
miRNAs as radio-response biomarkers for breast cancer stem cells. PMID:31930680
Computational Tools for Discovering and Engineering Natural Product Biosynthetic Pathways. PMID:31926431
Unraveling Asian Soybean Rust metabolomics using mass spectrometry and Molecular Networking approach. PMID:31924833
Improving the organization and interactivity of metabolic pathfinding with precomputed pathways. PMID:31924164
Gambogenic acid exerts anticancer effects in cisplatin‑resistant non‑small cell lung cancer cells. PMID:31922223
Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data. PMID:31921888
Persistent Exposure to Fusobacterium nucleatum Triggers Chemokine/Cytokine Release and Inhibits the Proliferation and Osteogenic Differentiation Capabilities of Human Gingiva-Derived Mesenchymal Stem Cells. PMID:31921705
Di (2-ethylhexyl) Phthalate Exposure Impairs the microRNAs Expression Profile During Primordial Follicle Assembly. PMID:31920986
Temporal Changes of Spinal Transcriptomic Profiles in Mice With Spinal Nerve Ligation. PMID:31920516
Integrative analysis of time course metabolic data and biomarker discovery. PMID:31918658
Evidence in support of chromosomal sex influencing plasma based metabolome vs APOE genotype influencing brain metabolome profile in humanized APOE male and female mice. PMID:31917799
Transcriptome analyses identify hub genes and potential mechanisms in adenoid cystic carcinoma. PMID:31914060
Genome- and Community-Level Interaction Insights into Carbon Utilization and Element Cycling Functions of Hydrothermarchaeota in Hydrothermal Sediment. PMID:31911466
Systems biology approaches toward autosomal dominant polycystic kidney disease (ADPKD). PMID:31907669
Horizontal Gene Transfer of Short-Chain Dehydrogenase Coding Genes Contribute to the Biofilm Formation and Pathogenicity on Mycobacterium grossiae sp. nov. PB739T (=DSM 104744T). PMID:31907602
Temporal analysis of mRNA expression profiles in Orientia infected C3HeB/FeJ mouse. PMID:31906849
Network Pharmacology Approach Reveals the Potential Immune Function Activation and Tumor Cell Apoptosis Promotion of Xia Qi Decoction in Lung Cancer. PMID:31905767
High-Throughput Identification of Putative Antimicrobial Peptides from Multi-Omics Data of the Lined Seahorse (Hippocampus erectus). PMID:31905755
Brain Imaging Genomics: Integrated Analysis and Machine Learning. PMID:31902950
YAP1 mediates survival of ALK-rearranged lung cancer cells treated with alectinib via pro-apoptotic protein regulation. PMID:31900393
Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels. PMID:31900328
Transcriptomic analyses of Pinus koraiensis under different cold stresses. PMID:31900194
Identification of key candidate tumor biomarkers in non-small-cell lung cancer by in silico analysis. PMID:31897214
Expression profile of miRNA in NSCLC tissues in middle-altitude area. PMID:31897195
Draft Genome Sequence of Plant Growth-Promoting Streptomyces sp. Strain SA51, Isolated from Olive Trees. PMID:31896622
Identification of potential key genes for HER-2 positive breast cancer based on bioinformatics analysis. PMID:31895772
Genome and population sequencing of a chromosome-level genome assembly of the Chinese tapertail anchovy (Coilia nasus) provides novel insights into migratory adaptation. PMID:31895412
Phellinus gilvus‑derived protocatechualdehyde induces G0/G1 phase arrest and apoptosis in murine B16‑F10 cells. PMID:31894337
Weighted gene co‑expression network analysis to identify key modules and hub genes associated with atrial fibrillation. PMID:31894294
Developing preliminary blood metabolomics-based biomarkers of insufficient sleep in humans. PMID:31894238
Omics Integration for Mitochondria Systems Biology. PMID:31891667
Integrated analysis of gene modulation profile identifies pathogenic factors and pathways in the liver of diabetic mice. PMID:31890673
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. PMID:31888466
A Pathway-Based Genomic Approach to Identify Medications: Application to Alcohol Use Disorder. PMID:31888299
Human Plasma-like Medium Improves T Lymphocyte Activation. PMID:31887663
Study on the Multitarget Mechanism and Key Active Ingredients of Herba Siegesbeckiae and Volatile Oil against Rheumatoid Arthritis Based on Network Pharmacology. PMID:31885670
MicroRNAs and their targeted genes associated with phase changes of stem explants during tissue culture of tea plant. PMID:31882926
Acute pancreatitis promotes the generation of two different exosome populations. PMID:31882721
Identification of diagnostic biomarkers in patients with gestational diabetes mellitus based on transcriptome gene expression and methylation correlation analysis. PMID:31881887
Investigating host-bacterial interactions among enteric pathogens. PMID:31881845
Effect of growth rate on transcriptomic responses to immune stimulation in wild-type, domesticated, and GH-transgenic coho salmon. PMID:31881844
Identifying miRNA synergism using multiple-intervention causal inference. PMID:31881825
Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis. PMID:31878883
Draft Genomes of Two Artocarpus Plants, Jackfruit (A. heterophyllus) and Breadfruit (A. altilis). PMID:31878322
Advancing the Role of Gamma-Tocotrienol as Proteasomes Inhibitor: A Quantitative Proteomic Analysis of MDA-MB-231 Human Breast Cancer Cells. PMID:31877708
Refining modules to determine functionally significant clusters in molecular networks. PMID:31874644
Causal network perturbations for instance-specific analysis of single cell and disease samples. PMID:31873725
Identification of circulating microRNA signatures as potential biomarkers in the serum of elk infected with chronic wasting disease. PMID:31873177
Discovery of metabolic alterations in the serum of patients infected with Plasmodium spp. by high-resolution metabolomics. PMID:31872321
The persimmon (Diospyros oleifera Cheng) genome provides new insights into the inheritance of astringency and ancestral evolution. PMID:31871686
Identification of Pparγ-modulated miRNA hubs that target the fibrotic tumor microenvironment. PMID:31871210
Joint learning improves protein abundance prediction in cancers. PMID:31870366
Metabolic disassembler for understanding and predicting the biosynthetic units of natural products. PMID:31870296
Broad-Spectrum Profiling of Drug Safety via Learning Complex Network. PMID:31868917
Metabolic Modeling Elucidates the Transactions in the Rumen Microbiome and the Shifts Upon Virome Interactions. PMID:31866953
Focused screening reveals functional effects of microRNAs differentially expressed in colorectal cancer. PMID:31864341
Transcriptome-wide analysis associates ID2 expression with combined pre- and post-capillary pulmonary hypertension. PMID:31862991
Time-critical influences of gestational diet in a seahorse model of male pregnancy. PMID:31862853
Investigating skewness to understand gene expression heterogeneity in large patient cohorts. PMID:31861976
In vitro metabolomic footprint of the Echinococcus multilocularis metacestode. PMID:31857639
Expression alteration of microRNAs in Nucleus Accumbens is associated with chronic stress and antidepressant treatment in rats. PMID:31856805
A novel graph theoretical approach for modeling microbiomes and inferring microbial ecological relationships. PMID:31856723
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries. PMID:31856718
Identification of prognostic genes in adrenocortical carcinoma microenvironment based on bioinformatic methods. PMID:31856409
In Vivo RNAi-Mediated eIF3m Knockdown Affects Ribosome Biogenesis and Transcription but Has Limited Impact on mRNA-Specific Translation. PMID:31855834
A network pharmacology approach to reveal the protective mechanism of Salvia miltiorrhiza-Dalbergia odorifera coupled-herbs on coronary heart disease. PMID:31852981
Growth hormone-mediated reprogramming of macrophage transcriptome and effector functions. PMID:31852980
Evaluation of knowledge graph embedding approaches for drug-drug interaction prediction in realistic settings. PMID:31852427
The MathIOmica Toolbox: General Analysis Utilities for Dynamic Omics Datasets. PMID:31851777
Survival-Associated Alternative Splicing Events in Pan-Renal Cell Carcinoma. PMID:31850211
Assessing Chemical-Induced Liver Injury In Vivo From In Vitro Gene Expression Data in the Rat: The Case of Thioacetamide Toxicity. PMID:31850077
Master Regulators of Signaling Pathways: An Application to the Analysis of Gene Regulation in Breast Cancer. PMID:31850059
Small RNA ArcZ Regulates Oxidative Stress Response Genes and Regulons in Erwinia amylovora. PMID:31849909
Species Interaction and Selective Carbon Addition During Antibiotic Exposure Enhances Bacterial Survival. PMID:31849882
Differential Expression of Signaling Pathway Genes Associated With Aflatoxin Reduction Quantitative Trait Loci in Maize (Zea mays L.). PMID:31849861
Extracellular Vesicles From Auditory Cells as Nanocarriers for Anti-inflammatory Drugs and Pro-resolving Mediators. PMID:31849615
Defining and Evaluating Microbial Contributions to Metabolite Variation in Microbiome-Metabolome Association Studies. PMID:31848305
Identification of a novel regulatory pathway for PPARα by RNA-seq characterization of the endothelial cell lipid peroxidative injury transcriptome. PMID:31847785
RNA sequencing-based transcriptome profiling of cardiac tissue implicates novel putative disease mechanisms in FLNC-associated arrhythmogenic cardiomyopathy. PMID:31843279
Neuroprotectants attenuate hypobaric hypoxia-induced brain injuries in cynomolgus monkeys. PMID:31840949
Improving drug response prediction by integrating multiple data sources: matrix factorization, kernel and network-based approaches. PMID:31838491
Systematic expression analysis of WEE family kinases reveals the importance of PKMYT1 in breast carcinogenesis. PMID:31837068
Bacillus amyloliquefaciens MBI600 differentially induces tomato defense signaling pathways depending on plant part and dose of application. PMID:31836790
Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation. PMID:31836713
Transcriptome Analysis of Wheat Roots Reveals a Differential Regulation of Stress Responses Related to Arbuscular Mycorrhizal Fungi and Soil Disturbance. PMID:31835704
Metabolomics of Small Intestine Neuroendocrine Tumors and Related Hepatic Metastases. PMID:31835679
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Comparative iTRAQ proteomics revealed proteins associated with lobed fin regeneration in Bichirs. PMID:31832023
Role of Catalase in Oxidative Stress- and Age-Associated Degenerative Diseases. PMID:31827713
Long-term nutrient inputs shift soil microbial functional profiles of phosphorus cycling in diverse agroecosystems. PMID:31827246
Bioinformatic analysis of peripheral blood RNA-sequencing sensitively detects the cause of late graft loss following overt hyperglycemia in pig-to-nonhuman primate islet xenotransplantation. PMID:31827198
Blocks in Tricarboxylic Acid Cycle of Salmonella enterica Cause Global Perturbation of Carbon Storage, Motility, and Host-Pathogen Interaction. PMID:31826974
FOXA1 upregulation promotes enhancer and transcriptional reprogramming in endocrine-resistant breast cancer. PMID:31826955
Transcriptome analysis of human brain microvascular endothelial cells response to Neisseria meningitidis and its antigen MafA using RNA-seq. PMID:31822804
Manually curated genome-scale reconstruction of the metabolic network of Bacillus megaterium DSM319. PMID:31822710
Environmental Chemical Diethylhexyl Phthalate Alters Intestinal Microbiota Community Structure and Metabolite Profile in Mice. PMID:31822602
Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. PMID:31822585
Longitudinal linear combination test for gene set analysis. PMID:31822265
Discovery of genomic variations by whole-genome resequencing of the North American Araucana chicken. PMID:31821332
Genomic insights into mite phylogeny, fitness, development, and reproduction. PMID:31818245
Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions. PMID:31816986
RankerGUI: A Computational Framework to Compare Differential Gene Expression Profiles Using Rank Based Statistics. PMID:31816915
Extracellular Vesicles in the Forebrain Display Reduced miR-346 and miR-331-3p in a Rat Model of Chronic Temporal Lobe Epilepsy. PMID:31813125
Morpho-physiological and proteomic responses to water stress in two contrasting tobacco varieties. PMID:31811189
Lipopolysaccharide Stimulates the Growth of Bacteria That Contribute to Ruminal Acidosis. PMID:31811042
Phylogenomic Analyses of Members of the Widespread Marine Heterotrophic Genus Pseudovibrio Suggest Distinct Evolutionary Trajectories and a Novel Genus, Polycladidibacter gen. nov. PMID:31811036
Inflammation-Induced Alternative Pre-mRNA Splicing in Mouse Alveolar Macrophages. PMID:31810980
Association between breast cancer cell migration and radiosensitivity in vitro. PMID:31807191
Exploring the Pharmacological Mechanism of Quercetin-Resveratrol Combination for Polycystic Ovary Syndrome: A Systematic Pharmacological Strategy-Based Research. PMID:31804513
Integrative Omics Approach to Identifying Genes Associated With Atrial Fibrillation. PMID:31801406
Enhanced translation expands the endo-lysosome size and promotes antigen presentation during phagocyte activation. PMID:31800587
Analysis of Postdeployment Serum Samples Identifies Potential Biomarkers of Exposure to Burn Pits and Other Environmental Hazards. PMID:31800450
Metabolome-Wide Association Study of Deployment to Balad, Iraq or Bagram, Afghanistan. PMID:31800448
Identification of Breast Cancer Subtype Specific MicroRNAs Using Survival Analysis to Find Their Role in Transcriptomic Regulation. PMID:31798622
Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility. PMID:31798553
Nitric oxide modulating ion balance in Hylotelephium erythrostictum roots subjected to NaCl stress based on the analysis of transcriptome, fluorescence, and ion fluxes. PMID:31797954
Graph-based information diffusion method for prioritizing functionally related genes in protein-protein interaction networks. PMID:31797617
Potential Pathways and Genes Involved in Lac Synthesis and Secretion in Kerria chinensis (Hemiptera: Kerriidae) Based on Transcriptomic Analyses. PMID:31795150
Integrative In Silico and In Vitro Transcriptomics Analysis Revealed Gene Expression Changes and Oncogenic Features of Normal Cholangiocytes after Chronic Alcohol Exposure. PMID:31795085
Pathways That Synthesize Phosphatidylethanolamine Impact Candida albicans Hyphal Length and Cell Wall Composition through Transcriptional and Posttranscriptional Mechanisms. PMID:31792076
Evaluation of colorectal cancer subtypes and cell lines using deep learning. PMID:31792061
Electronic Cigarette (E-Cigarette) Vapor Exposure Alters the Streptococcus pneumoniae Transcriptome in a Nicotine-Dependent Manner without Affecting Pneumococcal Virulence. PMID:31791951
PhySpeTree: an automated pipeline for reconstructing phylogenetic species trees. PMID:31791235
A probabilistic method for leveraging functional annotations to enhance estimation of the temporal order of pathway mutations during carcinogenesis. PMID:31791231
A High-Content Screening Approach to Identify MicroRNAs Against Head and Neck Cancer Cell Survival and EMT in an Inflammatory Microenvironment. PMID:31788442
High gene expression levels of VEGFA and CXCL8 in the peritumoral brain zone are associated with the recurrence of glioblastoma: A bioinformatics analysis. PMID:31788092
Identification of core differentially methylated genes in glioma. PMID:31788078
Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways. PMID:31788075
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. PMID:31787983
Calorie restriction slows age-related microbiota changes in an Alzheimer's disease model in female mice. PMID:31784610
Type I Interferon Signaling Disrupts the Hepatic Urea Cycle and Alters Systemic Metabolism to Suppress T Cell Function. PMID:31784108
Development and verification of a nomogram for prediction of recurrence-free survival in clear cell renal cell carcinoma. PMID:31782902
Analysis of Metabolite Profiling in Human Endothelial Cells after Plasma Jet Treatment. PMID:31781609
Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism. PMID:31781066
Hypoxic Environment and Paired Hierarchical 3D and 2D Models of Pediatric H3.3-Mutated Gliomas Recreate the Patient Tumor Complexity. PMID:31779235
Ovarian cancer detection by DNA methylation in cervical scrapings. PMID:31775891
Molecular bases of responses to abiotic stress in trees. PMID:31768543
Evolution of placental invasion and cancer metastasis are causally linked. PMID:31768023
Genomic landscape and genetic manipulation of the black soldier fly Hermetia illucens, a natural waste recycler. PMID:31767972
Wolbachia supplement biotin and riboflavin to enhance reproduction in planthoppers. PMID:31767943
Sugar-Phosphate Metabolism Regulates Stationary-Phase Entry and Stalk Elongation in Caulobacter crescentus. PMID:31767777
Genomic Analysis of Spontaneous Abortion in Holstein Heifers and Primiparous Cows. PMID:31766405
Deciphering Molecular Mechanism of the Neuropharmacological Action of Fucosterol through Integrated System Pharmacology and In Silico Analysis. PMID:31766220
Analysis of the Indole Diterpene Gene Cluster for Biosynthesis of the Epoxy-Janthitrems in Epichloë Endophytes. PMID:31766147
GPCRs show widespread differential mRNA expression and frequent mutation and copy number variation in solid tumors. PMID:31765370
H2 Metabolism revealed by metagenomic analysis of subglacial sediment from East Antarctica. PMID:31758395
Candidate lncRNA-miRNA-mRNA network in predicting hepatocarcinogenesis with cirrhosis: an integrated bioinformatics analysis. PMID:31758243
Transcription modulation by CDK9 regulates inflammatory genes and RIPK3-MLKL-mediated necroptosis in periodontitis progression. PMID:31758083
Adipocyte epigenetic alterations and potential therapeutic targets in transgenerationally inherited lean and obese phenotypes following ancestral exposures. PMID:31755359
ENCORE: A Visualization Tool for Insight into Circadian Omics. PMID:31754663
Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis. PMID:31754224
Function-driven single-cell genomics uncovers cellulose-degrading bacteria from the rare biosphere. PMID:31754206
Mesenchymal stem cell-derived exosomes: a new therapeutic approach to osteoarthritis? PMID:31753036
The genomes of two parasitic wasps that parasitize the diamondback moth. PMID:31752718
Multi-tissue to whole plant metabolic modelling. PMID:31748916
Integrative analysis of mRNA and miRNA expression profiles reveals seven potential diagnostic biomarkers for non‑small cell lung cancer. PMID:31746439
17β‑estradiol‑induced mitochondrial dysfunction and Warburg effect in cervical cancer cells allow cell survival under metabolic stress. PMID:31746421
LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer. PMID:31746401
Construction and analysis of circular RNA molecular regulatory networks in clear cell renal cell carcinoma. PMID:31746384
A Bayesian machine learning approach for drug target identification using diverse data types. PMID:31745082
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. PMID:31742321
The orphan nuclear receptor estrogen-related receptor beta (ERRβ) in triple-negative breast cancer. PMID:31741180
Discovery of disease- and drug-specific pathways through community structures of a literature network. PMID:31738408
Protein Interactions Network of Hepatitis E Virus RNA and Polymerase With Host Proteins. PMID:31736926
Integrated Analysis of mRNA and miRNA Expression Profiles in the Ovary of Oryctolagus cuniculus in Response to Gonadotrophic Stimulation. PMID:31736880
Transcriptomic and metabolomic analyses reveal several critical metabolic pathways and candidate genes involved in resin biosynthesis in Pinus massoniana. PMID:31735985
Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. PMID:31730853
Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease. PMID:31730674
A therapeutic antibody targeting osteoprotegerin attenuates severe experimental pulmonary arterial hypertension. PMID:31729368
Integrated Counts of Carbohydrate-Active Protein Domains as Metabolic Readouts to Distinguish Probiotic Biology and Human Fecal Metagenomes. PMID:31727954
Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness. PMID:31727924
Complete Genome Sequence of Cellulomonas sp. Strain Y8, a High-GC-Content Plasmid-Free Heavy Metal-Resistant Bacterium Isolated from Farmland Soil. PMID:31727705
Restructured Lactococcus lactis strains with emergent properties constructed by a novel highly efficient screening system. PMID:31727072
The plasma metabolome of women in early pregnancy differs from that of non-pregnant women. PMID:31726468
Identifying candidate diagnostic markers for early stage of non-small cell lung cancer. PMID:31726467
Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. PMID:31725857
A network-based predictive gene expression signature for recurrence risks in stage II colorectal cancer. PMID:31724326
Transcriptome analysis during photostimulated recrudescence reveals distinct patterns of gene regulation in Siberian hamster ovaries†. PMID:31724051
Investigation of Proteomic and Phosphoproteomic Responses to Signaling Network Perturbations Reveals Functional Pathway Organizations in Yeast. PMID:31722220
Identification of the molecular mechanisms associated with acute type A aortic dissection through bioinformatics methods. PMID:31721906
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. PMID:31720216
Multi-ancestry sleep-by-SNP interaction analysis in 126,926 individuals reveals lipid loci stratified by sleep duration. PMID:31719535
Transcriptomic Signatures Predict Regulators of Drug Synergy and Clinical Regimen Efficacy against Tuberculosis. PMID:31719182
A New Lineage of Cryptococcus gattii (VGV) Discovered in the Central Zambezian Miombo Woodlands. PMID:31719178
Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community. PMID:31719174
Comparative Analysis of Whole-Genome and Methylome Profiles of a Smooth and a Rough Mycobacterium abscessus Clinical Strain. PMID:31719113
Identification of loci associated with conception rate in primiparous Holstein cows. PMID:31718557
Accurate and Efficient Determination of Unknown Metabolites in Metabolomics by NMR-Based Molecular Motif Identification. PMID:31718151
Creating a Reliable Mass Spectral-Retention Time Library for All Ion Fragmentation-Based Metabolomics. PMID:31717785
Hepatitis C Virus Downregulates Core Subunits of Oxidative Phosphorylation, Reminiscent of the Warburg Effect in Cancer Cells. PMID:31717433
A pan-inflammatory microRNA-cluster is associated with orbital non-Hodgkin lymphoma and idiopathic orbital inflammation. PMID:31713839
Environmental boundary conditions for the origin of life converge to an organo-sulfur metabolism. PMID:31712697
Draft genome assembly of Tenualosa ilisha, Hilsa shad, provides resource for osmoregulation studies. PMID:31712633
Long non-coding RNAs and latent HIV - A search for novel targets for latency reversal. PMID:31710657
Uncovering the subtype-specific temporal order of cancer pathway dysregulation. PMID:31710622
A High-Density Genetic Linkage Map and QTL Mapping for Sex and Growth-Related Traits of Large-Scale Loach (Paramisgurnus dabryanus). PMID:31708968
A Bioinformatics Guide to Plant Microbiome Analysis. PMID:31708944
Dual oxidase 1 and NADPH oxidase 2 exert favorable effects in cervical cancer patients by activating immune response. PMID:31706280
Induction of detrusor underactivity by extensive vascular endothelial damages of iliac arteries in a rat model and its pathophysiology in the genetic levels. PMID:31705030
Causal Inference Engine: a platform for directional gene set enrichment analysis and inference of active transcriptional regulators. PMID:31701125
Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population. PMID:31699813
Improved Draft Genome Sequence of Microbacterium sp. Strain LKL04, a Bacterial Endophyte Associated with Switchgrass Plants. PMID:31699756
CRUP: a comprehensive framework to predict condition-specific regulatory units. PMID:31699133
Physiological and genomic evidence that selection on the transcription factor Epas1 has altered cardiovascular function in high-altitude deer mice. PMID:31697676
Measurement of Conditional Relatedness Between Genes Using Fully Convolutional Neural Network. PMID:31695723
Extracellular vesicles from endothelial progenitor cells prevent steroid-induced osteoporosis by suppressing the ferroptotic pathway in mouse osteoblasts based on bioinformatics evidence. PMID:31695092
Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. PMID:31687376
A New Strategy for Identifying Mechanisms of Drug-drug Interaction Using Transcriptome Analysis: Compound Kushen Injection as a Proof of Principle. PMID:31685921
A comparative study of topology-based pathway enrichment analysis methods. PMID:31684881
Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations. PMID:31682807
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. PMID:31681953
T1000: a reduced gene set prioritized for toxicogenomic studies. PMID:31681519
Profiling Transcriptional Regulation and Functional Roles of Schistosoma mansoni c-Jun N-Terminal Kinase. PMID:31681440
An Integrated Pipeline for Annotation and Visualization of Metagenomic Contigs. PMID:31681429
Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response. PMID:31681427
Comprehensive Flux Modeling of Chlamydia trachomatis Proteome and qRT-PCR Data Indicate Biphasic Metabolic Differences Between Elementary Bodies and Reticulate Bodies During Infection. PMID:31681215
Decoding the complexities of human malaria through systems immunology. PMID:31680289
Comparative gene expression analysis in melanocytes driven by tumor cell-derived exosomes. PMID:31678172
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. PMID:31675502
Gene expression profile analysis of ileum transcriptomes in pigs fed Gelsemium elegans plants. PMID:31673142
Microplastics induce transcriptional changes, immune response and behavioral alterations in adult zebrafish. PMID:31673028
ColPortal, an integrative multiomic platform for analysing epigenetic interactions in colorectal cancer. PMID:31672979
Meta-Analysis of Gene Expression Changes in the Blood of Patients with Mild Cognitive Impairment and Alzheimer's Disease Dementia. PMID:31671574
Physiological and transcriptome analyses of photosynthesis and chlorophyll metabolism in variegated Citrus (Shiranuhi and Huangguogan) seedlings. PMID:31666652
Postmortem Cortex Samples Identify Distinct Molecular Subtypes of ALS: Retrotransposon Activation, Oxidative Stress, and Activated Glia. PMID:31665631
ProteomicsDB: a multi-omics and multi-organism resource for life science research. PMID:31665479
Network inference with ensembles of bi-clustering trees. PMID:31660848
Salicibibacter halophilus sp. nov., a moderately halophilic bacterium isolated from kimchi. PMID:31659686
Bioengineering tools for the production of pharmaceuticals: current perspective and future outlook. PMID:31656120
DNA methylation of antisense noncoding RNA in the INK locus (ANRIL) is associated with coronary artery disease in a Chinese population. PMID:31653960
Comparative Genomics of Rumen Butyrivibrio spp. Uncovers a Continuum of Polysaccharide-Degrading Capabilities. PMID:31653790
Taxonomical and Functional Assessment of the Endometrial Microbiota in A Context of Recurrent Reproductive Failure: A Case Report. PMID:31653041
Exploring lithium's transcriptional mechanisms of action in bipolar disorder: a multi-step study. PMID:31652432
Microbial Metabolic Capacity for Intestinal Folate Production and Modulation of Host Folate Receptors. PMID:31649646
Illumina-based Analysis of Endophytic Bacterial Diversity of four Allium species. PMID:31649302
Conservation of cell-intrinsic immune responses in diverse nonhuman primate species. PMID:31649152
Metagenomes from Late Pleistocene Ice Complex Sediments of the Siberian Arctic. PMID:31649080
Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. PMID:31647099
Aspergillus niger upregulated glycerolipid metabolism and ethanol utilization pathway under ethanol stress. PMID:31646764
A high-quality Actinidia chinensis (kiwifruit) genome. PMID:31645971
The microbiota regulate neuronal function and fear extinction learning. PMID:31645720
Multi-tissue network analysis for drug prioritization in knee osteoarthritis. PMID:31645614
Adult sox10+ Cardiomyocytes Contribute to Myocardial Regeneration in the Zebrafish. PMID:31644901
Elevated serum alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality. PMID:31644575
Transcriptional analysis of insect extreme freeze tolerance. PMID:31640516
HMNPPID-human malignant neoplasm protein-protein interaction database. PMID:31639057
Construction of a competing endogenous RNA network using differentially expressed lncRNAs, miRNAs and mRNAs in non‑small cell lung cancer. PMID:31638248
Tacrolimus increases the expression level of the chemokine receptor CXCR2 to promote renal fibrosis progression. PMID:31638188
ANLN and KDR Are Jointly Prognostic of Breast Cancer Survival and Can Be Modulated for Triple Negative Breast Cancer Control. PMID:31636652
Nitrates as a Potential N Supply for Microbial Ecosystems in a Hyperarid Mars Analog System. PMID:31635024
A chromosomal-level genome assembly for the giant African snail Achatina fulica. PMID:31634388
Identification of biomarker microRNA-mRNA regulatory pairs for predicting the docetaxel resistance in prostate cancer. PMID:31632491
Hepatic PKA inhibition accelerates the lipid accumulation in liver. PMID:31632452
Synergistic Combination of Polymyxin B and Enrofloxacin Induced Metabolic Perturbations in Extensive Drug-Resistant Pseudomonas aeruginosa. PMID:31632279
Druggable genome in attention deficit/hyperactivity disorder and its co-morbid conditions. New avenues for treatment. PMID:31628418
Integrated Bioinformatic Analyses and Immune Characterization of New Neisseria gonorrhoeae Vaccine Antigens Expressed during Natural Mucosal Infection. PMID:31627489
Spatial-Temporal Variation of Bacterial Communities in Sediments in Lake Chaohu, a Large, Shallow Eutrophic Lake in China. PMID:31627458
Optical Pooled Screens in Human Cells. PMID:31626775
Flux balance analysis of cyanobacteria reveals selective use of photosynthetic electron transport components under different spectral light conditions. PMID:31625072
Metabolomics of Eothenomys miletus from five Hengduan Mountains locations in summer. PMID:31624370
Identification of conserved and novel miRNAs responsive to heat stress in flowering Chinese cabbage using high-throughput sequencing. PMID:31624298
Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1T. PMID:31623351
Prenylquinones in Human Parasitic Protozoa: Biosynthesis, Physiological Functions, and Potential as Chemotherapeutic Targets. PMID:31623105
Stringent response regulators (p)ppGpp and DksA positively regulate virulence and host adaptation of Xanthomonas citri. PMID:31621195
Transcriptome Profiles of Strawberry (Fragaria vesca) Fruit Interacting With Botrytis cinerea at Different Ripening Stages. PMID:31620156
De novo transcriptome of Gymnema sylvestre identified putative lncRNA and genes regulating terpenoid biosynthesis pathway. PMID:31619732
GENAVi: a shiny web application for gene expression normalization, analysis and visualization. PMID:31619158
Identification of potential key genes in esophageal adenocarcinoma using bioinformatics. PMID:31616504
Embryonic mesothelial-derived hepatic lineage of quiescent and heterogenous scar-orchestrating cells defined but suppressed by WT1. PMID:31615982
Robust structure measures of metabolic networks that predict prokaryotic optimal growth temperature. PMID:31615420
Lomatogonium Rotatum for Treatment of Acute Liver Injury in Mice: A Metabolomics Study. PMID:31615066
Neglog: Homology-Based Negative Data Sampling Method for Genome-Scale Reconstruction of Human Protein-Protein Interaction Networks. PMID:31614890
Musclin, A Myokine Induced by Aerobic Exercise, Retards Muscle Atrophy During Cancer Cachexia in Mice. PMID:31614775
Bioinformatics for Marine Products: An Overview of Resources, Bottlenecks, and Perspectives. PMID:31614509
Association of a novel seven-gene expression signature with the disease prognosis in colon cancer patients. PMID:31612869
Changing expression profiles of lncRNAs, circRNAs and mRNAs in esophageal squamous carcinoma. PMID:31612046
Differential expression of miR-4492 and IL-10 is involved in chronic rhinosinusitis with nasal polyps. PMID:31611936
Experimental challenge with bovine respiratory syncytial virus in dairy calves: bronchial lymph node transcriptome response. PMID:31611566
A Japanese history of the Human Genome Project. PMID:31611500
Advances and Challenges in Metatranscriptomic Analysis. PMID:31608125
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Variation in Actinobacterial Community Composition and Potential Function in Different Soil Ecosystems Belonging to the Arid Heihe River Basin of Northwest China. PMID:31608036
Identification of Genes/Proteins Related to Submergence Tolerance by Transcriptome and Proteome Analyses in Soybean. PMID:31604973
Modulatory Effect of Protein and Carotene Dietary Levels on Pig gut Microbiota. PMID:31601914
Investigating the Multi-Target Pharmacological Mechanism of Hedyotis diffusa Willd Acting on Prostate Cancer: A Network Pharmacology Approach. PMID:31600936
Functional rare variants influence the clinical response to anti-TNF therapy in Crohn's disease. PMID:31598133
Identifying significantly impacted pathways: a comprehensive review and assessment. PMID:31597578
Retroelement-Linked H3K4me1 Histone Tags Uncover Regulatory Evolution Trends of Gene Enhancers and Feature Quickly Evolving Molecular Processes in Human Physiology. PMID:31597351
The U1 spliceosomal RNA is recurrently mutated in multiple cancers. PMID:31597163
Global gene expression analysis of Escherichia coli K-12 DH5α after exposure to 2.4 GHz wireless fidelity radiation. PMID:31595026
Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice. PMID:31591555
An Integrated Approach for Efficient Multi-Omics Joint Analysis. PMID:31588431
CAGEfightR: analysis of 5'-end data using R/Bioconductor. PMID:31585526
Pitavastatin slows tumor progression and alters urine-derived volatile organic compounds through the mevalonate pathway. PMID:31585508
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate. PMID:31583016
Changes of Gene Expression in Euglena gracilis Obtained During the 29th DLR Parabolic Flight Campaign. PMID:31582787
Unraveling the Heterogeneous Mutational Signature of Spontaneously Developing Tumors in MLH1-/- Mice. PMID:31581674
An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer. PMID:31581665
Transposon mutagenesis reveals Pseudomonas cannabina pv. alisalensis optimizes its virulence factors for pathogenicity on different hosts. PMID:31579596
Integrated analysis of quantitative proteome and transcriptional profiles reveals abnormal gene expression and signal pathway in bladder cancer. PMID:31576517
The sequencing and de novo assembly of the Larimichthys crocea genome using PacBio and Hi-C technologies. PMID:31575853
Distinct Drivers of Core and Accessory Components of Soil Microbial Community Functional Diversity under Environmental Changes. PMID:31575666
Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents. PMID:31573126
S‑allyl‑cysteine sulfoxide (alliin) alleviates myocardial infarction by modulating cardiomyocyte necroptosis and autophagy. PMID:31573046
ITRAQ-Based Proteomics Analysis Reveals the Effect of Neoliensinine on KCl-Induced Vascular Smooth Muscle Contraction by Inhibiting Regulatory Light Chain Phosphorylation. PMID:31572175
MicroRNA-424 regulates cisplatin resistance of gastric cancer by targeting SMURF1 based on GEO database and primary validation in human gastric cancer tissues. PMID:31571913
Early transcriptional responses to soybean cyst nematode HG Type 0 show genetic differences among resistant and susceptible soybeans. PMID:31570969
KCNH2-3.1 mediates aberrant complement activation and impaired hippocampal-medial prefrontal circuitry associated with working memory deficits. PMID:31570775
Transcriptomic comparison between beetle strains selected for short and long durations of death feigning. PMID:31570743
Expression of microRNA in human retinal pigment epithelial cells following infection with Zaire ebolavirus. PMID:31570108
Integration of Bioinformatics Resources Reveals the Therapeutic Benefits of Gemcitabine and Cell Cycle Intervention in SMAD4-Deleted Pancreatic Ductal Adenocarcinoma. PMID:31569425
Identification of key genes and pathways associated with different immune statuses of hepatitis B virus infection. PMID:31565863
Molecular phenotyping using networks, diffusion, and topology: soft tissue sarcoma. PMID:31562358
Expression Profile of Cell Cycle-Related Genes in Human Fibroblasts Exposed Simultaneously to Radiation and Simulated Microgravity. PMID:31561588
Molecular Mechanisms of Intranasal Insulin in SAMP8 Mice. PMID:31561374
Pathway Analysis Integrating Genome-Wide and Functional Data Identifies PLCG2 as a Candidate Gene for Age-Related Macular Degeneration. PMID:31560769
Decreased expression of microRNAs targeting type-2 diabetes susceptibility genes in peripheral blood of patients and predisposed individuals. PMID:31559537
Functional interpretation of single cell similarity maps. PMID:31558714
Circadian clock genes and the transcriptional architecture of the clock mechanism. PMID:31557726
Regulation of the Larval Transcriptome of Diatraea saccharalis (Lepidoptera: Crambidae) by Maternal and Other Factors of the Parasitoid Cotesia flavipes (Hymenoptera: Braconidae). PMID:31555143
Role of NF-kappaB2-p100 in regulatory T cell homeostasis and activation. PMID:31554891
Genome-wide analysis of methylation in giant pandas with cataract by methylation-dependent restriction-site associated DNA sequencing (MethylRAD). PMID:31553743
The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2. PMID:31551465
Cofactor Selectivity in Methylmalonyl Coenzyme A Mutase, a Model Cobamide-Dependent Enzyme. PMID:31551329
Persistent homology analysis of brain transcriptome data in autism. PMID:31551047
The pomegranate (Punica granatum L.) draft genome dissects genetic divergence between soft- and hard-seeded cultivars. PMID:31549477
SoyCSN: Soybean context-specific network analysis and prediction based on tissue-specific transcriptome data. PMID:31549018
The metaRbolomics Toolbox in Bioconductor and beyond. PMID:31548506
A precision medicine approach to defining the impact of doxorubicin on the bioenergetic-metabolite interactome in human platelets. PMID:31546171
Reconstruction and analysis of competitive endogenous RNA network reveals regulatory role of long non‑coding RNAs in hepatic fibrosis. PMID:31545470
Genome profiling revealed the activation of IL2RG/JAK3/STAT5 in peripheral T‑cell lymphoma expressing the ITK‑SYK fusion gene. PMID:31545408
A Hybrid Ensemble Approach for Identifying Robust Differentially Methylated Loci in Pan-Cancers. PMID:31543899
A Transcriptome Analysis Identifies Biological Pathways and Candidate Genes for Feed Efficiency in DLY Pigs. PMID:31540540
Genome-wide identification of DNA methylation QTLs in whole blood highlights pathways for cardiovascular disease. PMID:31537805
Discovering genetic interactions bridging pathways in genome-wide association studies. PMID:31537791
Reserve Flux Capacity in the Pentose Phosphate Pathway by NADPH Binding Is Conserved across Kingdoms. PMID:31536961
Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking. PMID:31536415
Distinct evolution of toll-like receptor signaling pathway genes in cetaceans. PMID:31535317
Spatial sorting enables comprehensive characterization of liver zonation. PMID:31535084
Exploring the Pathological Mechanism of Bladder Cancer Based on Tumor Mutational Burden Analysis. PMID:31534952
Temporal changes in transcriptome profile provide insights of White Spot Syndrome Virus infection in Litopenaeus vannamei. PMID:31534145
Antibody-Dependent Dengue Virus Entry Modulates Cell Intrinsic Responses for Enhanced Infection. PMID:31533998
Ontology based mining of pathogen-disease associations from literature. PMID:31533864
Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality. PMID:31533045
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Effects of a vinegar-based multi-micronutrient supplement in rats: a multi-pronged assessment of dietary impact. PMID:31531127
Dissection of Pharmacological Mechanism of Chinese Herbal Medicine Yihuo Huatan Formula on Chronic Obstructive Pulmonary Disease: A Systems Pharmacology-Based Study. PMID:31530860
Cold-induced lipid dynamics and transcriptional programs in white adipose tissue. PMID:31530289
Epigenetic transgenerational inheritance of testis pathology and Sertoli cell epimutations: generational origins of male infertility. PMID:31528361
Unified feature association networks through integration of transcriptomic and proteomic data. PMID:31527878
An integrated genome-wide multi-omics analysis of gene expression dynamics in the preimplantation mouse embryo. PMID:31527703
Expression of FGF8, FGF18, and FGFR4 in Gastroesophageal Adenocarcinomas. PMID:31527546
Synergistic Cytotoxicity of Renieramycin M and Doxorubicin in MCF-7 Breast Cancer Cells. PMID:31527453
HnRNPR-CCNB1/CENPF axis contributes to gastric cancer proliferation and metastasis. PMID:31527303
Genome-wide miRNA profiling and pivotal roles of miRs 125a-5p and 17-92 cluster in human neutrophil maturation and differentiation of acute myeloid leukemia cells. PMID:31523391
A comprehensive, multidisciplinary, precision medicine approach to discover effective therapy for an undiagnosed, progressive, fibroinflammatory disease. PMID:31520587
Exploratory analysis of covariation of microbiota-derived vitamin K and cognition in older adults. PMID:31518386
Effect of hyperoside on cervical cancer cells and transcriptome analysis of differentially expressed genes. PMID:31516392
Changes in the metabolic potential of the sponge microbiome under ocean acidification. PMID:31515490
Loss of DNA methyltransferase activity in primed human ES cells triggers increased cell-cell variability and transcriptional repression. PMID:31515224
The opportunistic pathogen Stenotrophomonas maltophilia utilizes a type IV secretion system for interbacterial killing. PMID:31513674
Sex-dependent and -independent transcriptional changes during haploid phase gametogenesis in the sugar kelp Saccharina latissima. PMID:31513596
Characteristics and Complete Genome Analysis of Bacillus asahii OM18, a Bacterium in Relation to Soil Fertility in Alkaline Soils Under Long-Term Organic Manure Amendment. PMID:31511964
A multi-omics analysis of the grapevine pathogen Lasiodiplodia theobromae reveals that temperature affects the expression of virulence- and pathogenicity-related genes. PMID:31511626
Comparative proteomic analysis provides new insights into the specialization of shoots and stolons in bermudagrass (Cynodon dactylon L.). PMID:31510936
DIFFUSE: predicting isoform functions from sequences and expression profiles via deep learning. PMID:31510699
Identification of a Specific Gene Module for Predicting Prognosis in Glioblastoma Patients. PMID:31508371
ePath: an online database towards comprehensive essential gene annotation for prokaryotes. PMID:31506471
In Vitro and In Silico Mechanistic Insights into miR-21-5p-Mediated Topoisomerase Drug Resistance in Human Colorectal Cancer Cells. PMID:31505885
Current and Promising Approaches to Identify Horizontal Gene Transfer Events in Metagenomes. PMID:31504488
RetSynth: determining all optimal and sub-optimal synthetic pathways that facilitate synthesis of target compounds in chassis organisms. PMID:31500573
The relevance between the immune response-related gene module and clinical traits in head and neck squamous cell carcinoma. PMID:31496804
Migratory Neural Crest Cells Phagocytose Dead Cells in the Developing Nervous System. PMID:31495570
Pseudomonas spp. are key players in agricultural biogas substrate degradation. PMID:31492882
Potential Interactions between Clade SUP05 Sulfur-Oxidizing Bacteria and Phages in Hydrothermal Vent Sponges. PMID:31492669
Multi-omics signature of brain amyloid deposition in asymptomatic individuals at-risk for Alzheimer's disease: The INSIGHT-preAD study. PMID:31492558
Analysis of widely targeted metabolites of the euhalophyte Suaeda salsa under saline conditions provides new insights into salt tolerance and nutritional value in halophytic species. PMID:31492100
H3K4me3, H3K9ac, H3K27ac, H3K27me3 and H3K9me3 Histone Tags Suggest Distinct Regulatory Evolution of Open and Condensed Chromatin Landmarks. PMID:31491936
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages. PMID:31490939
Transcriptome and gene expression analysis of three developmental stages of the coffee berry borer, Hypothenemus hampei. PMID:31488852
Hair follicle regeneration suppresses Ras-driven oncogenic growth. PMID:31488583
Challenges in the construction of knowledge bases for human microbiome-disease associations. PMID:31488215
Carbohydrate, glutathione, and polyamine metabolism are central to Aspergillus flavus oxidative stress responses over time. PMID:31488075
Dual RNA-Seq Analysis of the Pine-Fusarium circinatum Interaction in Resistant (Pinus tecunumanii) and Susceptible (Pinus patula) Hosts. PMID:31487786
Large scale evaluation of differences between network-based and pairwise sequence-alignment-based methods of dendrogram reconstruction. PMID:31487289
Structure to function analysis with antigenic characterization of a hypothetical protein,HPAG1_0576 from Helicobacter pylori HPAG1. PMID:31485131
Intestinal proteomic analysis of a novel non-human primate model of experimental colitis reveals signatures of mitochondrial and metabolic dysfunction. PMID:31481749
P2Y2 purinergic receptor modulates virus yield, calcium homeostasis, and cell motility in human cytomegalovirus-infected cells. PMID:31481624
A Carbonic Anhydrase Pseudogene Sensitizes Select Brucella Lineages to Low CO2 Tension. PMID:31481543
Yersiniabactin-Producing Adherent/Invasive Escherichia coli Promotes Inflammation-Associated Fibrosis in Gnotobiotic Il10-/- Mice. PMID:31481410
A Pathway-Based Kernel Boosting Method for Sample Classification Using Genomic Data. PMID:31480483
Drivers of human gut microbial community assembly: coadaptation, determinism and stochasticity. PMID:31477821
Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium. PMID:31477760
Sex-Specific Linkages Between Taxonomic and Functional Profiles of Tick Gut Microbiomes. PMID:31475121
Distinct Morphological, Physiological, and Biochemical Responses to Light Quality in Barley Leaves and Roots. PMID:31475023
Lysosome-Rich Enterocytes Mediate Protein Absorption in the Vertebrate Gut. PMID:31474562
Early Life Represents a Vulnerable Time Window for IL-33-Induced Peripheral Lung Pathology. PMID:31471525
MicroRNA regulation in colorectal cancer tissue and serum. PMID:31469874
P4HB, a Novel Hypoxia Target Gene Related to Gastric Cancer Invasion and Metastasis. PMID:31467922
Draft Genome Sequence of Dicyma pulvinata Strain 414-3, a Mycoparasite of Cladosporium fulvum, Causal Agent of Tomato Leaf Mold. PMID:31467096
Whole Genome Sequencing of Chinese White Dolphin (Sousa chinensis) for High-Throughput Screening of Antihypertensive Peptides. PMID:31466310
Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus) and High-Throughput Screening of Putative Antimicrobial Peptide Genes. PMID:31466296
LAS: A Lipid Annotation Service Capable of Explaining the Annotations It Generates. PMID:31462967
Vancomycin relieves mycophenolate mofetil-induced gastrointestinal toxicity by eliminating gut bacterial β-glucuronidase activity. PMID:31457102
Multi-study reanalysis of 2,213 acute myeloid leukemia patients reveals age- and sex-dependent gene expression signatures. PMID:31455838
High expression of EZR (ezrin) gene is correlated with the poor overall survival of breast cancer patients. PMID:31452341
Relevance of Non-Targeted Effects for Radiotherapy and Diagnostic Radiology; A Historical and Conceptual Analysis of Key Players. PMID:31450803
Target Genes of Autism Risk Loci in Brain Frontal Cortex. PMID:31447881
Glycine decarboxylase is a transcriptional target of MYCN required for neuroblastoma cell proliferation and tumorigenicity. PMID:31444411
Toward understanding the origin and evolution of cellular organisms. PMID:31441146
Health and Aging: Unifying Concepts, Scores, Biomarkers and Pathways. PMID:31440392
Identification of Rumen Microbial Genes Involved in Pathways Linked to Appetite, Growth, and Feed Conversion Efficiency in Cattle. PMID:31440274
MiR-190a potentially ameliorates postoperative cognitive dysfunction by regulating Tiam1. PMID:31438846
Differential gene expression and gene-set enrichment analysis in Caco-2 monolayers during a 30-day timeline with Dexamethasone exposure. PMID:31438773
Statistical genomics in rare cancer. PMID:31437624
Chlorella vulgaris genome assembly and annotation reveals the molecular basis for metabolic acclimation to high light conditions. PMID:31437318
A high-quality genome assembly for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). PMID:31437279
A SNP Mutation of SiCRC Regulates Seed Number Per Capsule and Capsule Length of cs1 Mutant in Sesame. PMID:31434218
Upregulation of MAPK10, TUBB2B and RASL11B may contribute to the development of neuroblastoma. PMID:31432180
MAP‑1B, PACS‑2 and AHCYL1 are regulated by miR‑34A/B/C and miR‑449 in neuroplasticity following traumatic spinal cord injury in rats: Preliminary explorative results from microarray data. PMID:31432119
Plasma metabolomics profiles suggest beneficial effects of a low-glycemic load dietary pattern on inflammation and energy metabolism. PMID:31432072
Screening of Microbial Volatile Organic Compounds for Detection of Disease in Cattle: Development of Lab-scale Method. PMID:31431630
The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities. PMID:31431193
A chromosome-level draft genome of the grain aphid Sitobion miscanthi. PMID:31430367
A differential transcriptional profile by Culex quinquefasciatus larvae resistant to Lysinibacillus sphaericus IAB59 highlights genes and pathways associated with the resistance phenotype. PMID:31429782
Using Large Datasets to Understand Nanotechnology. PMID:31429126
A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology. PMID:31428833
Large-scale identification of pathogen essential genes during coinfection with sympatric and allopatric microbes. PMID:31427504
A chromosomal-level genome assembly for the insect vector for Chagas disease, Triatoma rubrofasciata. PMID:31425588
KEGG Mapper for inferring cellular functions from protein sequences. PMID:31423653
DNA methylation profiling identifies potentially significant epigenetically-regulated genes in glioblastoma multiforme. PMID:31423235
Integrated bioinformatics analysis to identify 15 hub genes in breast cancer. PMID:31423162
Exploring the new horizons of drug repurposing: A vital tool for turning hard work into smart work. PMID:31421629
The endosomal sorting adaptor HD-PTP is required for ephrin-B:EphB signalling in cellular collapse and spinal motor axon guidance. PMID:31420572
Structural determination of the large photosystem II-light-harvesting complex II supercomplex of Chlamydomonas reinhardtii using nonionic amphipol. PMID:31420447
Transcriptome sequencing, de novo assembly, characterisation of wild accession of blackgram (Vigna mungo var. silvestris) as a rich resource for development of molecular markers and validation of SNPs by high resolution melting (HRM) analysis. PMID:31419947
Investigation into the underlying regulatory mechanisms shaping inflorescence architecture in Chenopodium quinoa. PMID:31419932
Chromosomal level assembly and population sequencing of the Chinese tree shrew genome. PMID:31418539
Disease classification via gene network integrating modules and pathways. PMID:31417727
Transcriptional alterations reveal Bacillus amyloliquefaciens-rice cooperation under salt stress. PMID:31417134
Genome-wide transcriptomic analysis of a desert willow, Salix psammophila, reveals the function of hub genes SpMDP1 and SpWRKY33 in drought tolerance. PMID:31416414
Antibiotic treatment of Chlamydia-induced cystitis in the koala is linked to expression of key inflammatory genes in reactive oxygen pathways. PMID:31415633
Effect of dietary fat and sucrose consumption on cardiac fibrosis in mice and rhesus monkeys. PMID:31415241
IRNdb: the database of immunologically relevant non-coding RNAs. PMID:31414702
Application of the High-throughput TAB-Array for the Discovery of Novel 5-Hydroxymethylcytosine Biomarkers in Pancreatic Ductal Adenocarcinoma. PMID:31413874
The liver proteome in a mouse model for Ascaris suum resistance and susceptibility: evidence for an altered innate immune response. PMID:31412915
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation. PMID:31409826
Prioritization of candidate cancer drugs based on a drug functional similarity network constructed by integrating pathway activities and drug activities. PMID:31408580
Metabolomics reveals a link between homocysteine and lipid metabolism and leukocyte telomere length: the ENGAGE consortium. PMID:31406173
The genome of Ensifer alkalisoli YIC4027 provides insights for host specificity and environmental adaptations. PMID:31405380
α-Tocopherol Modulates Non-Amyloidogenic Pathway and Autophagy in an In Vitro Model of Alzheimer's Disease: A Transcriptional Study. PMID:31405115
Network as a Biomarker: A Novel Network-Based Sparse Bayesian Machine for Pathway-Driven Drug Response Prediction. PMID:31405013
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
A Mixed Quantum Chemistry/Machine Learning Approach for the Fast and Accurate Prediction of Biochemical Redox Potentials and Its Large-Scale Application to 315 000 Redox Reactions. PMID:31404220
Clinical value of microRNA-198-5p downregulation in lung adenocarcinoma and its potential pathways. PMID:31402959
TDCIPP exposure affects Artemia franciscana growth and osmoregulation. PMID:31401516
Untargeted Metabolomics Reveals Molecular Effects of Ketogenic Diet on Healthy and Tumor Xenograft Mouse Models. PMID:31398922
Tumor Microbiome Diversity and Composition Influence Pancreatic Cancer Outcomes. PMID:31398337
Sex Differences in Adrenal Bmal1 Deletion-Induced Augmentation of Glucocorticoid Responses to Stress and ACTH in Mice. PMID:31398249
Analysis of Protein-Protein Functional Associations by Using Gene Ontology and KEGG Pathway. PMID:31396531
Single-Cell RNA Sequencing of Visceral Adipose Tissue Leukocytes Reveals that Caloric Restriction Following Obesity Promotes the Accumulation of a Distinct Macrophage Population with Features of Phagocytic Cells. PMID:31396408
Weighted Fused Pathway Graphical Lasso for Joint Estimation of Multiple Gene Networks. PMID:31396259
Elucidation of Galactomannan Biosynthesis Pathway Genes through Transcriptome Sequencing of Seeds Collected at Different Developmental Stages of Commercially Important Indian Varieties of Cluster Bean (Cyamopsis tetragonoloba L.). PMID:31395961
A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. PMID:31395883
Whole blood microRNA expression associated with stroke: Results from the Framingham Heart Study. PMID:31393881
Identification of significant gene and pathways involved in HBV-related hepatocellular carcinoma by bioinformatics analysis. PMID:31392101
IL-33 Is a Cell-Intrinsic Regulator of Fitness during Early B Cell Development. PMID:31391233
A systematic assessment of current genome-scale metabolic reconstruction tools. PMID:31391098
Effects of long-term feeding of rapeseed meal on skeletal muscle transcriptome, production efficiency and meat quality traits in Norwegian Landrace growing-finishing pigs. PMID:31390356
Finding MEMo: minimum sets of elementary flux modes. PMID:31388689
Metagenomics analysis of cocoa bean fermentation microbiome identifying species diversity and putative functional capabilities. PMID:31388591
Identifying miltefosine-resistant key genes in protein-protein interactions network and experimental verification in Iranian Leishmania major. PMID:31385238
Intraspecific Variation in Protists: Clues for Microevolution from Poteriospumella lacustris (Chrysophyceae). PMID:31384914
Characterization of the prognostic values of the NDRG family in gastric cancer. PMID:31384305
Phylogenetic, genomic, and biogeographic characterization of a novel and ubiquitous marine invertebrate-associated Rickettsiales parasite, Candidatus Aquarickettsia rohweri, gen. nov., sp. nov. PMID:31384012
Comparative transcriptomics reveals the selection patterns of domesticated ramie. PMID:31380033
Distribution, Function and Regulation of Type 6 Secretion Systems of Xanthomonadales. PMID:31379785
Uncovering the Transcriptional Correlates of Hub Connectivity in Neural Networks. PMID:31379515
De novo genome assembly and comparative annotation reveals metabolic versatility in cellulolytic bacteria from cropland and forest soils. PMID:31378834
Amino Acid Biosynthesis Regulation during Endoplasmic Reticulum Stress Is Coupled to Protein Expression Demands. PMID:31377665
Regulatory Network Analysis to Reveal Important miRNAs and Genes in Non-Small Cell Lung Cancer. PMID:31376328
Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery. PMID:31375809
RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes. PMID:31375064
Integrative omics of Lonicera japonica Thunb. Flower development unravels molecular changes regulating secondary metabolites. PMID:31374363
Spatial Regulation of Mitochondrial Heterogeneity by Stromal Confinement in Micropatterned Tumor Models. PMID:31371796
Detection of dynamic protein complexes through Markov Clustering based on Elephant Herd Optimization Approach. PMID:31366992
Metabolic diversification of nitrogen-containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis. PMID:31364191
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). PMID:31357931
The IDO Metabolic Trap Hypothesis for the Etiology of ME/CFS. PMID:31357483
A Systems Pharmacology-Based Study of the Molecular Mechanisms of San Cao Decoction for Treating Hypertension. PMID:31354853
RNA sequencing profiling of the retina in C57BL/6J and DBA/2J mice: Enhancing the retinal microarray data sets from GeneNetwork. PMID:31354228
DISPOT: a simple knowledge-based protein domain interaction statistical potential. PMID:31350874
Analysis of gene expression in rheumatoid arthritis and related conditions offers insights into sex-bias, gene biotypes and co-expression patterns. PMID:31344123
Differential responses of epithelial cells from urinary and biliary tract to eggs of Schistosoma haematobium and S. mansoni. PMID:31341177
Chromosome assembly of Collichthys lucidus, a fish of Sciaenidae with a multiple sex chromosome system. PMID:31341172
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
Functional properties of bacterial communities in water and sediment of the eutrophic river-lake system of Poyang Lake, China. PMID:31338262
Inactivation of Prostaglandin E2 as a Mechanism for UGT2B17-Mediated Adverse Effects in Chronic Lymphocytic Leukemia. PMID:31334126
Towards sex identification of Asian Palmyra palm (Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing. PMID:31333909
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures. PMID:31333598
Comparative Metabolomics Reveals Key Pathways Associated With the Synergistic Killing of Colistin and Sulbactam Combination Against Multidrug-Resistant Acinetobacter baumannii. PMID:31333468
Darkness-induced effects on gene expression in Cosmarium crenatum (Zygnematophyceae) from a polar habitat. PMID:31332253
GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis. PMID:31329248
The Subgingival Microbiome Relationship to Periodontal Disease in Older Women. PMID:31329044
Differential regulation of mycelial growth and aflatoxin biosynthesis by Aspergillus flavus under different temperatures as revealed by strand-specific RNA-Seq. PMID:31328901
A step-by-step guide to analyzing CAGE data using R/Bioconductor. PMID:31327999
Acute and short-term administrations of delta-9-tetrahydrocannabinol modulate major gut metabolomic regulatory pathways in C57BL/6 mice. PMID:31324830
The ilvGMEDA Operon Is Regulated by Transcription Attenuation in Vibrio alginolyticus ZJ-T. PMID:31324637
LATS1/2 suppress NFκB and aberrant EMT initiation to permit pancreatic progenitor differentiation. PMID:31323030
Identification and characterization of sexual dimorphism‑linked gene expression profile in hepatocellular carcinoma. PMID:31322260
Identiﬁcation of differentially expressed genes in hip cartilage with femoral head necrosis, based on genome‑wide expression proﬁles. PMID:31322206
Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value. PMID:31320697
Proteo-metabolomic investigation of transgenic rice unravels metabolic alterations and accumulation of novel proteins potentially involved in defence against Rhizoctonia solani. PMID:31320685
Draft Genome Sequence of Thermodesulfovibrio sp. Strain Kuro-1, a Thermophilic, Lactate-Degrading Anaerobe Isolated from a Thermophilic Anaerobic Digestion Reactor. PMID:31320437
De novo transcriptome sequencing and gene expression profiling of Magnolia wufengensis in response to cold stress. PMID:31319815
Functionally significant metabolic differences between B and T lymphocyte lineages. PMID:31318442
Circulating miR-141-3p, miR-143-3p and miR-200c-3p are differentially expressed in colorectal cancer and advanced adenomas. PMID:31316774
Insights into the transcriptomic response of the plant engineering bacterium Ensifer adhaerens OV14 during transformation. PMID:31316079
The genome assembly of asparagus bean, Vigna unguiculata ssp. sesquipedialis. PMID:31316072
Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences. PMID:31316056
Discovery of potential genes contributing to the biosynthesis of short-chain fatty acids and lactate in gut microbiota from systematic investigation in E. coli. PMID:31312512
Replication and transcriptionomic analysis of human noroviruses in human intestinal enteroids. PMID:31312350
A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis. PMID:31312201
Membrane protein-regulated networks across human cancers. PMID:31311925
Stress-induced Changes in the S-palmitoylation and S-nitrosylation of Synaptic Proteins. PMID:31311849
Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide. PMID:31309106
Poorly controlled diabetes during pregnancy and lactation activates the Foxo1 pathway and causes glucose intolerance in adult offspring. PMID:31308441
Mechanisms of vascular permeability and remodeling associated with hemarthrosis in factor VIII-deficient mice. PMID:31301687
Comparative transcriptome analysis reveals potential fruiting body formation mechanisms in Morchella importuna. PMID:31300949
Fungal canker pathogens trigger carbon starvation by inhibiting carbon metabolism in poplar stems. PMID:31300723
The splicing factor Sf3b1 regulates erythroid maturation and proliferation via TGFβ signaling in zebrafish. PMID:31300417
Simultaneous Enrichment Analysis of all Possible Gene-sets: Unifying Self-Contained and Competitive Methods. PMID:31297505
Topological integration of RPPA proteomic data with multi-omics data for survival prediction in breast cancer via pathway activity inference. PMID:31296204
Circular RNA Signature in Hepatocellular Carcinoma. PMID:31293639
BioNetStat: A Tool for Biological Networks Differential Analysis. PMID:31293621
The Transcriptome Landscape of Walnut Interspecies Hybrid (Juglans hindsii × Juglans regia) and Regulation of Cambial Activity in Relation to Grafting. PMID:31293615
Acceleration of Mechanistic Investigation of Plant Secondary Metabolism Based on Computational Chemistry. PMID:31293608
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
Study of Gene Expression Profiles of Breast Cancers in Indian Women. PMID:31292488
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease. PMID:31291905
Chromosomal-level assembly of the blood clam, Scapharca (Anadara) broughtonii, using long sequence reads and Hi-C. PMID:31289832
Identification of microRNA-92a and the related combination biomarkers as promising substrates in predicting risk, recurrence and poor survival of colorectal cancer. PMID:31289586
Investigation of differentially expressed genes in nasopharyngeal carcinoma by integrated bioinformatics analysis. PMID:31289570
Clostridioides difficile LuxS mediates inter-bacterial interactions within biofilms. PMID:31289293
A systematic approach to orient the human protein-protein interaction network. PMID:31289271
Quantitative proteomic analysis of sperm in unexplained recurrent pregnancy loss. PMID:31288842
Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks. PMID:31288752
Predictive Analysis Using Chemical-Gene Interaction Networks Consistent with Observed Endocrine Activity and Mutagenicity of U.S. Streams. PMID:31287672
iMet: A graphical user interface software tool to merge metabolic networks. PMID:31286073
Genome-scale metabolic model of the rat liver predicts effects of diet restriction. PMID:31285465
Canine Bone Marrow-derived Mesenchymal Stem Cells: Genomics, Proteomics and Functional Analyses of Paracrine Factors. PMID:31285283
TGF-β1-p53 cooperativity regulates a profibrotic genomic program in the kidney: molecular mechanisms and clinical implications. PMID:31284746
Moonlighting Proteins and Cardiopathy in the Spatial Response of MCF-7 Breast Cancer Cells to Tamoxifen. PMID:31282103
Sharing Programming Resources Between Bio* Projects. PMID:31278684
Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. PMID:31278252
Metabolomic profiles in yak mammary gland tissue during the lactation cycle. PMID:31276563
Characterizing semen abnormality male infertility using non-targeted blood plasma metabolomics. PMID:31276533
Whole-Genome Sequencing of the Giant Devil Catfish, Bagarius yarrelli. PMID:31274158
A draft genome for Spatholobus suberectus. PMID:31273216
The Route to 'Chemobrain' - Computational probing of neuronal LTP pathway. PMID:31270411
Comparative transcriptome analysis of pigeonpea, Cajanus cajan (L.) and one of its wild relatives Cajanus platycarpus (Benth.) Maesen. PMID:31269083
Integrating proteomics and transcriptomics for the identification of potential targets in early colorectal cancer. PMID:31268166
Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge. PMID:31266798
Biosynthetic Potential of a Novel Antarctic Actinobacterium Marisediminicola antarctica ZS314T Revealed by Genomic Data Mining and Pigment Characterization. PMID:31266176
Genomic ecology of Marine Group II, the most common marine planktonic Archaea across the surface ocean. PMID:31264806
Whole Genome Sequencing of the Blue Tilapia (Oreochromis aureus) Provides a Valuable Genetic Resource for Biomedical Research on Tilapias. PMID:31261751
The origin, diversification and adaptation of a major mangrove clade (Rhizophoreae) revealed by whole-genome sequencing. PMID:31258950
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Computational Systems Pharmacology-Target Mapping for Fentanyl-Laced Cocaine Overdose. PMID:31257858
Isatin inhibits the invasion of human neuroblastoma SH‑SY5Y cells, based on microarray analysis. PMID:31257543
Analysis of potential functional significance of microRNA‑3613‑3p in human umbilical vein endothelial cells affected by heat stress. PMID:31257536
Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach. PMID:31257484
Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach. PMID:31249629
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Trader as a new optimization algorithm predicts drug-target interactions efficiently. PMID:31249365
Tremorgenic effects and functional metabolomics analysis of lolitrem B and its biosynthetic intermediates. PMID:31249318
Expression profiling of immature florets of IR58025A, a wild-abortive cytoplasmic male sterile line of rice and its cognate, isonuclear maintainer line, IR58025B. PMID:31245242
A tropomyosin receptor kinase family protein, NTRK2 is a potential predictive biomarker for lung adenocarcinoma. PMID:31245181
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Can trophectoderm RNA analysis predict human blastocyst competency? PMID:31244343
Comparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host. PMID:31243442
Genome-driven cell engineering review: in vivo and in silico metabolic and genome engineering. PMID:31243142
A Systematic Review of MicroRNA Expression as Biomarker of Late-Onset Alzheimer's Disease. PMID:31240600
Prediction of hub genes associated with intramuscular fat content in Nelore cattle. PMID:31238883
Integrated analysis of microRNA regulation and its interaction with mechanisms of epigenetic regulation in the etiology of systemic lupus erythematosus. PMID:31237906
DNA methylome and transcriptome alterations and cancer prevention by triterpenoid ursolic acid in UVB-induced skin tumor in mice. PMID:31237383
Whole Genome Sequencing and Analysis of Chlorimuron-Ethyl Degrading Bacteria Klebsiella pneumoniae 2N3. PMID:31234527
Metabolomics of childhood exposure to perfluoroalkyl substances: a cross-sectional study. PMID:31227916
Whole blood microRNA levels associate with glycemic status and correlate with target mRNAs in pathways important to type 2 diabetes. PMID:31222113
Network-based prediction of polygenic disease genes involved in cell motility. PMID:31216978
Gradient Boosting Decision Tree-Based Method for Predicting Interactions Between Target Genes and Drugs. PMID:31214240
Differential Metabolism of Medium-Chain Fatty Acids in Differentiated Human-Induced Pluripotent Stem Cell-Derived Astrocytes. PMID:31214043
Natural Product Target Network Reveals Potential for Cancer Combination Therapies. PMID:31214023
Personalized medicine in breast cancer: pharmacogenomics approaches. PMID:31213877
Determination of an Interaction Network between an Extracellular Bacterial Pathogen and the Human Host. PMID:31213562
Metabolomics Studies on Cytoplasmic Male Sterility during Flower Bud Development in Soybean. PMID:31212804
Comparative genomics of chytrid fungi reveal insights into the obligate biotrophic and pathogenic lifestyle of Synchytrium endobioticum. PMID:31209237
Secretion of fibronectin by human pancreatic stellate cells promotes chemoresistance to gemcitabine in pancreatic cancer cells. PMID:31208372
The Influence of Modernization and Disease on the Gastric Microbiome of Orang Asli, Myanmars and Modern Malaysians. PMID:31208001
Pathway Interactions Based on Drug-Induced Datasets. PMID:31205412
Discovery and validation of temporal patterns involved in human brain ketometabolism in cerebral microdialysis fluids of traumatic brain injury patients. PMID:31202815
Association between the oral microbiome and brain resting state connectivity in smokers. PMID:31201984
Screening of differentially expressed genes and identification of NUF2 as a prognostic marker in breast cancer. PMID:31198978
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health. PMID:31196177
Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data. PMID:31196115
Clinical expression and antigenic profiles of a Plasmodium vivax vaccine candidate: merozoite surface protein 7 (PvMSP-7). PMID:31196098
Aspergillus fumigatus Challenged by Human Dendritic Cells: Metabolic and Regulatory Pathway Responses Testify a Tight Battle. PMID:31192161
IgG based immunome analyses of breast cancer patients reveal underlying signaling pathways. PMID:31191821
Determination of the Key Resistance Gene Analogs Involved in Ascochyta rabiei Recognition in Chickpea. PMID:31191572
Identification of key genes and pathways in seminoma by bioinformatics analysis. PMID:31190870
Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis. PMID:31190860
Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. PMID:31188086
Comparison of de-novo assembly tools for plasmid metagenome analysis. PMID:31187446
A multidimensional perspective on microbial interactions. PMID:31187139
Sperm epimutation biomarkers of obesity and pathologies following DDT induced epigenetic transgenerational inheritance of disease. PMID:31186947
Analysis of the role of DAMTC in lung adenocarcinoma cells based on the DNA microarrays. PMID:31186684
A novel electro-chemotactic approach to impact the directional migration of transplantable retinal progenitor cells. PMID:31185219
The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs. PMID:31184303
Differential gene expression analysis of human cumulus cells. PMID:31181875
Bioinformatics analysis of a long non‑coding RNA and mRNA regulation network in rats with middle cerebral artery occlusion based on RNA sequencing. PMID:31180537
Organelle Studies and Proteome Analyses of Mitochondria and Plastids Fractions from the Diatom Thalassiosira pseudonana. PMID:31179502
Identify CRNDE and LINC00152 as the key lncRNAs in age-related degeneration of articular cartilage through comprehensive and integrative analysis. PMID:31179196
Elucidation of Akkermansia muciniphila Probiotic Traits Driven by Mucin Depletion. PMID:31178843
Population structure, demographic history and local adaptation of the grass carp. PMID:31174480
Screening key genes and signaling pathways in colorectal cancer by integrated bioinformatics analysis. PMID:31173250
Identification of diagnostic long non‑coding RNA biomarkers in patients with hepatocellular carcinoma. PMID:31173205
Identification of key candidate genes involved in melanoma metastasis. PMID:31173190
Identification of core genes and clinical roles in pregnancy-associated breast cancer based on integrated analysis of different microarray profile datasets. PMID:31171715
What determines host specificity in hyperspecialized plant parasitic nematodes? PMID:31170914
Targeting BCAA Catabolism to Treat Obesity-Associated Insulin Resistance. PMID:31167878
Muscle fiber hypertrophy in response to 6 weeks of high-volume resistance training in trained young men is largely attributed to sarcoplasmic hypertrophy. PMID:31166954
Distinct Bacterial Communities in Wet and Dry Seasons During a Seasonal Water Level Fluctuation in the Largest Freshwater Lake (Poyang Lake) in China. PMID:31164883
Deep expression analysis reveals distinct cold-response strategies in rubber tree (Hevea brasiliensis). PMID:31164105
Negative regulation of miR-1275 by H3K27me3 is critical for glial induction of glioblastoma cells. PMID:31162799
Elucidating the endogenous synovial fluid proteome and peptidome of inflammatory arthritis using label-free mass spectrometry. PMID:31160890
Multi-omics analysis of the development and fracture resistance for maize internode. PMID:31160669
Understanding microbial community dynamics to improve optimal microbiome selection. PMID:31159875
Temporal Analysis of the Microbial Community from the Crystallizer Ponds in Cabo Rojo, Puerto Rico, Using Metagenomics. PMID:31159288
Network pharmacology-based identifcation of potential targets of the flower of Trollius chinensis Bunge acting on anti-inflammatory effectss. PMID:31147584
Towards an Internet of Science. PMID:31145694
A Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes. PMID:31143202
Time varying causal network reconstruction of a mouse cell cycle. PMID:31142274
Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging. PMID:31138672
Developmental origins for semilunar valve stenosis identified in mice harboring congenital heart disease-associated GATA4 mutation. PMID:31138536
Identify differential gene expressions in fatty infiltration process in rotator cuff. PMID:31138249
CODA-ML: context-specific biological knowledge representation for systemic physiology analysis. PMID:31138123
Tremorgenic Mycotoxins: Structure Diversity and Biological Activity. PMID:31137882
GC-MS method for metabolic profiling of mouse femoral head articular cartilage reveals distinct effects of tissue culture and development. PMID:31136803
Dual RNA-Seq Unveils Pseudomonas plecoglossicida htpG Gene Functions During Host-Pathogen Interactions With Epinephelus coioides. PMID:31130962
Effect of cold atmospheric plasma treatment on the metabolites of human leukemia cells. PMID:31130824
Molecular mechanisms of temperature acclimation and adaptation in marine diatoms. PMID:31127177
The antioxidant and DNA-repair enzyme apurinic/apyrimidinic endonuclease 1 limits the development of tubulointerstitial fibrosis partly by modulating the immune system. PMID:31127150
Sequencing of a Wild Apple (Malus baccata) Genome Unravels the Differences Between Cultivated and Wild Apple Species Regarding Disease Resistance and Cold Tolerance. PMID:31126974
New Microbial Lineages Capable of Carbon Fixation and Nutrient Cycling in Deep-Sea Sediments of the Northern South China Sea. PMID:31126943
Polybrominated Diphenyl Ethers and Gut Microbiome Modulate Metabolic Syndrome-Related Aqueous Metabolites in Mice. PMID:31123037
Phosphates as Energy Sources to Expand Metabolic Networks. PMID:31121973
Metabolome Wide Association Study of Serum Poly and Perfluoroalkyl Substances (PFASs) in Pregnancy and Early Postpartum. PMID:31121237
Transcriptomic responses of the clam Meretrix meretrix to the organophosphorus pesticide (dimethoate). PMID:31119591
Time-Resolved Systems Medicine Reveals Viral Infection-Modulating Host Targets. PMID:31119214
The genome resources for conservation of Indo-Pacific humpback dolphin, Sousa chinensis. PMID:31118413
Robust Transcriptional Response to Heat Shock Impacting Diverse Cellular Processes despite Lack of Heat Shock Factor in Microsporidia. PMID:31118302
Kinome-Wide RNA Interference Screening Identifies Mitogen-Activated Protein Kinases and Phosphatidylinositol Metabolism as Key Factors for Rabies Virus Infection. PMID:31118297
Linking aberrant chromatin features in chronic lymphocytic leukemia to transcription factor networks. PMID:31118277
Improvement of growth rates through nucleoside media supplementation of CHO clones. PMID:31115721
Transcriptomics analysis of sirolimus treatment in lupus nephritis. PMID:31115581
Geneshot: search engine for ranking genes from arbitrary text queries. PMID:31114885
An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa. PMID:31112559
Decoding microbial community intelligence through metagenomics for efficient wastewater treatment. PMID:31111267
Transcriptome analysis of Chelidonium majus elaiosomes and seeds provide insights into fatty acid biosynthesis. PMID:31110927
Proteomic and Metabolomic Profiling of Deinococcus radiodurans Recovering After Exposure to Simulated Low Earth Orbit Vacuum Conditions. PMID:31110498
Mediterranean grassland soil C-N compound turnover is dependent on rainfall and depth, and is mediated by genomically divergent microorganisms. PMID:31110364
Tubular cell and keratinocyte single-cell transcriptomics applied to lupus nephritis reveal type I IFN and fibrosis relevant pathways. PMID:31110316
Genome-wide identification of GhAAI genes reveals that GhAAI66 triggers a phase transition to induce early flowering. PMID:31106831
Systems Biology Analysis of the Effect and Mechanism of Qi-Jing-Sheng-Bai Granule on Leucopenia in Mice. PMID:31105563
Serum metabolic signatures of coronary and carotid atherosclerosis and subsequent cardiovascular disease. PMID:31102408
Transcriptional profiling of contrasting genotypes revealed key candidates and nucleotide variations for drought dissection in Camellia sinensis (L.) O. Kuntze. PMID:31097754
Transcriptomic Analysis of MAPK Signaling in NSC-34 Motor Neurons Treated with Vitamin E. PMID:31096690
An Investigation about Gene Modules Associated with hDPSC Differentiation for Adolescents. PMID:31089336
Glutamine to proline conversion is associated with response to glutaminase inhibition in breast cancer. PMID:31088535
-Omics biomarker identification pipeline for translational medicine. PMID:31088492
Identification of novel biomarkers and small molecule drugs in human colorectal cancer by microarray and bioinformatics analysis. PMID:31087508
Transcriptional changes associated with advancing stages of heart failure underlie atrial and ventricular arrhythmogenesis. PMID:31083689
Evolution of the gut microbiome following acute HIV-1 infection. PMID:31078141
A comprehensive analysis of the Lactuca sativa, L. transcriptome during different stages of the compatible interaction with Rhizoctonia solani. PMID:31076623
Predicting the decision making chemicals used for bacterial growth. PMID:31076576
modEnrichr: a suite of gene set enrichment analysis tools for model organisms. PMID:31069376
Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease. PMID:31068785
Microbiota alter metabolism and mediate neurodevelopmental toxicity of 17β-estradiol. PMID:31068624
Genomewide Profiling of the Enterococcus faecalis Transcriptional Response to Teixobactin Reveals CroRS as an Essential Regulator of Antimicrobial Tolerance. PMID:31068434
DNA Methylation Analysis of the Citrullus lanatus Response to Cucumber Green Mottle Mosaic Virus Infection by Whole-Genome Bisulfite Sequencing. PMID:31067797
Exploring Differential Transcriptome between Jejunal and Cecal Tissue of Broiler Chickens. PMID:31067716
Marine Natural Products from Microalgae: An -Omics Overview. PMID:31067655
Gene expression and DNA methylation as mechanisms of disturbed metabolism in offspring after exposure to a prenatal HF diet. PMID:31064776
PhyloToL: A Taxon/Gene-Rich Phylogenomic Pipeline to Explore Genome Evolution of Diverse Eukaryotes. PMID:31062861
Aspergillus niger citrate exporter revealed by comparison of two alternative citrate producing conditions. PMID:31062025
Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4+ T cells. PMID:31061531
Metabolic characterization of the chitinolytic bacterium Serratia marcescens using a genome-scale metabolic model. PMID:31060515
Signature microRNAs and long noncoding RNAs in laryngeal cancer recurrence identified using a competing endogenous RNA network. PMID:31059106
Bioinformatics identification of lncRNA biomarkers associated with the progression of esophageal squamous cell carcinoma. PMID:31059058
Structural and Proteomic Changes in Viable but Non-culturable Vibrio cholerae. PMID:31057510
Bacterial Community Succession, Transmigration, and Differential Gene Transcription in a Controlled Vertebrate Decomposition Model. PMID:31057499
A metabolomic approach to understand the solid-state fermentation of okara using Bacillus subtilis WX-17 for enhanced nutritional profile. PMID:31055712
Filamentation Regulatory Pathways Control Adhesion-Dependent Surface Responses in Yeast. PMID:31053593
MOSClip: multi-omic and survival pathway analysis for the identification of survival associated gene and modules. PMID:31049575
Non-monotonic auto-regulation in single gene circuits. PMID:31048872
Functional adaptations in the cecal and colonic metagenomes associated with the consumption of transglycosylated starch in a pig model. PMID:31046662
A genome-wide association study of bitter and sweet beverage consumption. PMID:31046077
Systematic elucidation of the mechanism of geraniol via network pharmacology. PMID:31040644
Systems biology in inflammatory bowel diseases: on the way to precision medicine. PMID:31040620
An integrated genomic and metabolomic approach for defining survival time in adult oligodendrogliomas patients. PMID:31037432
Fgf3 is crucial for the generation of monoaminergic cerebrospinal fluid contacting cells in zebrafish. PMID:31036752
Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies. PMID:31036036
Mapping Semaphorins and Netrins in the Pathogenesis of Human Thoracic Aortic Aneurysms. PMID:31035427
Use of faecal volatile organic compound analysis for ante-mortem discrimination between CWD-positive, -negative exposed, and -known negative white-tailed deer (Odocoileus virginianus). PMID:31032718
In Silico Integration Approach Reveals Key MicroRNAs and Their Target Genes in Follicular Thyroid Carcinoma. PMID:31032340
Bacterial communities within Phengaris (Maculinea) alcon caterpillars are shifted following transition from solitary living to social parasitism of Myrmica ant colonies. PMID:31031919
Quantitative Proteomic Analysis of the Response of Probiotic Putative Lactococcus lactis NCDO 2118 Strain to Different Oxygen Availability Under Temperature Variation. PMID:31031733
Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs. PMID:31031713
Divergent Fine-Scale Recombination Landscapes between a Freshwater and Marine Population of Threespine Stickleback Fish. PMID:31028697
Alterations in the gut microbiome and metabolism with coronary artery disease severity. PMID:31027508
Metabolome and Transcriptome Association Analysis Reveals Dynamic Regulation of Purine Metabolism and Flavonoid Synthesis in Transdifferentiation during Somatic Embryogenesis in Cotton. PMID:31027387
Response of Lactobacillus plantarum WCFS1 to the Gram-Negative Pathogen-Associated Quorum Sensing Molecule N-3-Oxododecanoyl Homoserine Lactone. PMID:31024494
Major Traditional Probiotics: Comparative Genomic Analyses and Roles in Gut Microbiome of Eight Cohorts. PMID:31024492
Complete Genome Sequence of Oxidase-Positive Stenotrophomonas maltophilia Strain SM7059. PMID:31023803
Benefits and Drawbacks of Harboring Plasmid pP32BP2, Identified in Arctic Psychrophilic Bacterium Psychrobacter sp. DAB_AL32B. PMID:31022896
Systematic identification of key genes and pathways in clear cell renal cell carcinoma on bioinformatics analysis. PMID:31019939
Understanding the regulation of overwintering diapause molecular mechanisms in Culex pipiens pallens through comparative proteomics. PMID:31019237
A context-based ABC model for literature-based discovery. PMID:31017923
DNAmod: the DNA modification database. PMID:31016417
Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat. PMID:31015528
A small molecule promotes cartilage extracellular matrix generation and inhibits osteoarthritis development. PMID:31015473
Gene expression changes associated with the evolutionary loss of a metabolic trait: lack of lipogenesis in parasitoids. PMID:31014246
Different gut microbiome composition in obese Guizhou minipigs between female and castrated male. PMID:31011890
Assessment of Glyphosate Induced Epigenetic Transgenerational Inheritance of Pathologies and Sperm Epimutations: Generational Toxicology. PMID:31011160
Structured Genome-Wide Association Studies with Bayesian Hierarchical Variable Selection. PMID:31010934
Natamycin and Voriconazole Exhibit Synergistic Interactions with Nonantifungal Ophthalmic Agents against Fusarium Species Ocular Isolates. PMID:31010869
Identification of significant genes with poor prognosis in ovarian cancer via bioinformatical analysis. PMID:31010415
Proteomics of intracellular Salmonella enterica reveals roles of Salmonella pathogenicity island 2 in metabolism and antioxidant defense. PMID:31009521
Integration of Multiple Data Sources for Gene Network Inference Using Genetic Perturbation Data. PMID:31009236
A multiplatform metabolomic approach to characterize fecal signatures of negative postnatal events in chicks: a pilot study. PMID:31007908
De novo Mutations From Whole Exome Sequencing in Neurodevelopmental and Psychiatric Disorders: From Discovery to Application. PMID:31001316
Opposite T3 Response of ACTG1-FOS Subnetwork Differentiate Tailfin Fate in Xenopus Tadpole and Post-hatching Axolotl. PMID:31001200
Alkylaminophenol Induces G1/S Phase Cell Cycle Arrest in Glioblastoma Cells Through p53 and Cyclin-Dependent Kinase Signaling Pathway. PMID:31001122
Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity - indications of immune cell activation. PMID:31000755
Whole genomes and transcriptomes reveal adaptation and domestication of pistachio. PMID:30999938
BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. PMID:30999927
Bacterial community structure and function distinguish gut sites in captive red-shanked doucs (Pygathrix nemaeus). PMID:30997937
The acute transcriptional response to resistance exercise: impact of age and contraction mode. PMID:30996129
Phosphoproteome Analysis of Cells Infected with Adapted and Nonadapted Influenza A Virus Reveals Novel Pro- and Antiviral Signaling Networks. PMID:30996098
Transcriptomic Responses to Ivacaftor and Prediction of Ivacaftor Clinical Responsiveness. PMID:30995102
Transcriptomic analysis reveals differences in the regulation of amino acid metabolism in asexual and sexual planarians. PMID:30992461
Unprecedented bacterial community richness in soybean nodules vary with cultivar and water status. PMID:30992078
Metabopolis: scalable network layout for biological pathway diagrams in urban map style. PMID:30991966
Identification of key pathways and genes in nasopharyngeal carcinoma using bioinformatics analysis. PMID:30988824
Myometrial Transcriptional Signatures of Human Parturition. PMID:30988671
A quantitative analysis of heterogeneities and hallmarks in acute myelogenous leukaemia. PMID:30988472
Highly efficient hypothesis testing methods for regression-type tests with correlated observations and heterogeneous variance structure. PMID:30987598
A cmap-enabled gene expression signature-matching approach identifies small-molecule inducers of accelerated cell senescence. PMID:30987592
Exosomal miRNAs as Novel Pharmacodynamic Biomarkers for Cancer Chemopreventive Agent Early Stage Treatments in Chemically Induced Mouse Model of Lung Squamous Cell Carcinoma. PMID:30987362
Sex differences in gene expression related to antipsychotic induced weight gain. PMID:30986260
MicroRNA-related transcription factor regulatory networks in human colorectal cancer. PMID:30985693
1,25-Dihydroxyvitamin D3 Restrains CD4+ T Cell Priming Ability of CD11c+ Dendritic Cells by Upregulating Expression of CD31. PMID:30984180
In Silico Investigation of the Anti-Tumor Mechanisms of Epigallocatechin-3-Gallate. PMID:30979098
The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis. PMID:30974826
Altered gene expression in antipsychotic-induced weight gain. PMID:30971689
Host-Microbiome Synergistic Control on Sphingolipid Metabolism by Mechanotransduction in Model Arthritis. PMID:30970641
Network and Pathway-Based Analysis of Single-Nucleotide Polymorphism of miRNA in Temporal Lobe Epilepsy. PMID:30968344
Diverse Environmental Microbiota as a Tool to Augment Biodiversity in Urban Landscaping Materials. PMID:30967847
A preliminary transcriptome analysis suggests a transitory effect of vitamin D on mitochondrial function in obese young Finnish subjects. PMID:30965285
Systems biology: perspectives on multiscale modeling in research on endocrine-related cancers. PMID:30965282
isoTar: Consensus Target Prediction with Enrichment Analysis for MicroRNAs Harboring Editing Sites and Other Variations. PMID:30963495
Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database. PMID:30963208
Integrated analysis of gene expression changes associated with coronary artery disease. PMID:30961613
Microbial iron metabolism as revealed by gene expression profiles in contrasted Southern Ocean regimes. PMID:30958628
New Zealand Tree and Giant Wētā (Orthoptera) Transcriptomics Reveal Divergent Selection Patterns in Metabolic Loci. PMID:30957857
Transcriptional factor regulation network and competitive endogenous RNA (ceRNA) network determining response of esophageal squamous cell carcinomas to neoadjuvant chemoradiotherapy. PMID:30956903
Colonic Mucosal Transcriptomic Changes in Patients with Long-Duration Ulcerative Colitis Revealed Colitis-Associated Cancer Pathways. PMID:30954025
Developmental expression and evolution of hexamerin and haemocyanin from Folsomia candida (Collembola). PMID:30953580
Boolean network modeling of β-cell apoptosis and insulin resistance in type 2 diabetes mellitus. PMID:30953496
Gene expression profiles between cystic and solid vestibular schwannoma indicate susceptible molecules and pathways in the cystic formation of vestibular schwannoma. PMID:30953268
Microbial community design: methods, applications, and opportunities. PMID:30952088
De novo genome assembly of the white-spotted flower chafer (Protaetia brevitarsis). PMID:30949689
Cell cycle genes are downregulated after adipogenic triggering in human adipose tissue-derived stem cells by regulation of mRNA abundance. PMID:30948750
Identification of Key Genes and Circular RNAs in Human Gastric Cancer. PMID:30948703
Alterations of the MEK/ERK, BMP, and Wnt/β-catenin pathways detected in the blood of individuals with lymphatic malformations. PMID:30947262
The complete chloroplast genome of the threatened Dipentodon sinicus (Dipentodontaceae). PMID:30945682
Candidate genes and potential mechanisms for chemoradiotherapy sensitivity in locally advanced rectal cancer. PMID:30944639
Using Bacterial Transcriptomics to Investigate Targets of Host-Bacterial Interactions in Caenorhabditis elegans. PMID:30944351
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
Rhodnius prolixus: Identification of missing components of the IMD immune signaling pathway and functional characterization of its role in eliminating bacteria. PMID:30943246
MGS-Fast: Metagenomic shotgun data fast annotation using microbial gene catalogs. PMID:30942867
A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures. PMID:30941158
Meta-path Based Prioritization of Functional Drug Actions with Multi-Level Biological Networks. PMID:30940832
Genome-wide association study for kernel composition and flour pasting behavior in wholemeal maize flour. PMID:30940081
Deciphering the Pharmacological Mechanism of the Herb Radix Ophiopogonis in the Treatment of Nasopharyngeal Carcinoma by Integrating iTRAQ-Coupled 2-D LC-MS/MS Analysis and Network Investigation. PMID:30936832
Prioritizing candidate genes for fertility in dairy cows using gene-based analysis, functional annotation and differential gene expression. PMID:30935378
Transcriptomic Sequencing and Co-Expression Network Analysis on Key Genes and Pathways Regulating Nitrogen Use Efficiency in Myriophyllum aquaticum. PMID:30934901
The First Transcriptome Assembly of Yenyuan Stream Salamander (Batrachuperus yenyuanensis) Provides Novel Insights into Its Molecular Evolution. PMID:30934682
"Redox lipidomics technology: Looking for a needle in a haystack". PMID:30928338
Long-Distance Transportation Causes Temperature Stress in the Honey Bee, Apis mellifera (Hymenoptera: Apidae). PMID:30927358
Electrotaxis of Glioblastoma and Medulloblastoma Spheroidal Aggregates. PMID:30926929
Translational and transcriptional responses in human primary hepatocytes under hypoxia. PMID:30920299
Just the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse into the Evolution of Large Mobile Elements. PMID:30918968
RNA-seq reveals the involvement of key genes for aerobic adaptation in rice. PMID:30918284
Identification of rfk-1, a Meiotic Driver Undergoing RNA Editing in Neurospora. PMID:30918007
Integrative Bioinformatics Analysis Reveals Potential Gene Biomarkers and Analysis of Function in Human Degenerative Disc Annulus Fibrosus Cells. PMID:30915367
Effects of sublethal doses of clothianidin and/or V. destructor on honey bee (Apis mellifera) self-grooming behavior and associated gene expression. PMID:30914660
Gene expression imputation across multiple brain regions provides insights into schizophrenia risk. PMID:30911161
Genome-wide Analysis Reveals DNA Methylation Alterations in Obesity Associated with High Risk of Colorectal Cancer. PMID:30911103
Deciphering the mechanism of Indirubin and its derivatives in the inhibition of Imatinib resistance using a "drug target prediction-gene microarray analysis-protein network construction" strategy. PMID:30909944
Variation of gene expression in plants is influenced by gene architecture and structural properties of promoters. PMID:30908494
Screening pathways and hub genes involved in osteoclastogenesis by gene expression analysis of circulating monocytes based on Gibbs sampling. PMID:30906441
Transcriptome Profiling and Genome-Wide Association Studies Reveal GSTs and Other Defense Genes Involved in Multiple Signaling Pathways Induced by Herbicide Safener in Grain Sorghum. PMID:30906302
High levels of PIWI-interacting RNAs are present in the small RNA landscape of prostate epithelium from vitamin D clinical trial specimens. PMID:30905091
Metaproteomic and 16S rRNA Gene Sequencing Analysis of the Infant Fecal Microbiome. PMID:30901843
Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation. PMID:30899329
Genome-wide analysis of long non-coding RNAs unveils the regulatory roles in the heat tolerance of Chinese cabbage (Brassica rapa ssp.chinensis). PMID:30899041
Identification and functional analysis of microRNAs in rats following focal cerebral ischemia injury. PMID:30896823
Differential gene expression in response to eCry3.1Ab ingestion in an unselected and eCry3.1Ab-selected western corn rootworm (Diabrotica virgifera virgifera LeConte) population. PMID:30894586
Genome of Crucihimalaya himalaica, a close relative of Arabidopsis, shows ecological adaptation to high altitude. PMID:30894495
Common miRNA Patterns of Alzheimer's Disease and Parkinson's Disease and Their Putative Impact on Commensal Gut Microbiota. PMID:30890906
Nuclear actin interactome analysis links actin to KAT14 histone acetyl transferase and mRNA splicing. PMID:30890647
Identifying and exploiting gene-pathway interactions from RNA-seq data for binary phenotype. PMID:30890140
Identification of evolutionarily conserved virulence factor by selective pressure analysis of Streptococcus pneumoniae. PMID:30886906
Adaptation of metal and antibiotic resistant traits in novel β-Proteobacterium Achromobacter xylosoxidans BHW-15. PMID:30886770
MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction. PMID:30885720
RNAi-based small molecule repositioning reveals clinically approved urea-based kinase inhibitors as broadly active antivirals. PMID:30883607
Neuronal Apolipoprotein E4 Expression Results in Proteome-Wide Alterations and Compromises Bioenergetic Capacity by Disrupting Mitochondrial Function. PMID:30883359
Metabolomics Analysis of L-Arginine Induced Gastrointestinal Motility Disorder in Rats Using UPLC-MS After Magnolol Treatment. PMID:30881305
Mitochondria in precision medicine; linking bioenergetics and metabolomics in platelets. PMID:30877854
Identifying miRNA-mRNA regulatory relationships in breast cancer with invariant causal prediction. PMID:30876399
The Toxic Effect of Herbicidal Ionic Liquids on Biogas-Producing Microbial Community. PMID:30875750
Transcriptome response of roots to salt stress in a salinity-tolerant bread wheat cultivar. PMID:30875373
New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. PMID:30873404
Integrative analysis of KIF4A, 9, 18A, and 23 and their clinical significance in low-grade glioma and glioblastoma. PMID:30872592
Production Phase Affects the Bioaerosol MicrobialComposition and Functional Potential in SwineConfinement Buildings. PMID:30871116
Loss of RNA-Binding Protein Sfpq Causes Long-Gene Transcriptopathy in Skeletal Muscle and Severe Muscle Mass Reduction with Metabolic Myopathy. PMID:30870781
Identification of Hfq-binding RNAs in Caulobacter crescentus. PMID:30870072
Identification of differentially expressed key genes between glioblastoma and low-grade glioma by bioinformatics analysis. PMID:30867991
Combined analysis and validation for DNA methylation and gene expression profiles associated with prostate cancer. PMID:30867653
New insights from uncultivated genomes of the global human gut microbiome. PMID:30867587
Metatranscriptomic exploration of microbial functioning in clouds. PMID:30867542
Roadmap of DNA methylation in breast cancer identifies novel prognostic biomarkers. PMID:30866861
In-depth transcriptome characterization uncovers distinct gene family expansions for Cupressus gigantea important to this long-lived species' adaptability to environmental cues. PMID:30866823
Both Peripheral Blood and Urinary miR-195-5p, miR-192-3p, miR-328-5p and Their Target Genes PPM1A, RAB1A and BRSK1 May Be Potential Biomarkers for Membranous Nephropathy. PMID:30865617
Identification of hub genes in chronically hypoxic myocardium using bioinformatics analysis. PMID:30864710
Studies Into β-Glucan Recognition in Fish Suggests a Key Role for the C-Type Lectin Pathway. PMID:30863400
Characterization of the rumen and fecal microbiome in bloated and non-bloated cattle grazing alfalfa pastures and subjected to bloat prevention strategies. PMID:30862851
Comparative Transcriptome and Methylome Analysis in Human Skeletal Muscle Anabolism, Hypertrophy and Epigenetic Memory. PMID:30862794
Characterisation of genes differentially expressed in macrophages by virulent and attenuated Mycobacterium tuberculosis through RNA-Seq analysis. PMID:30858471
PIMKL: Pathway-Induced Multiple Kernel Learning. PMID:30854223
Potential for Microbially Mediated Natural Attenuation of Diluted Bitumen on the Coast of British Columbia (Canada). PMID:30850431
In vitro expansion affects the response of human bone marrow stromal cells to irradiation. PMID:30850008
A microRNA profile of pediatric glioblastoma: The role of NUCKS1 upregulation. PMID:30847170
Metabolomic Insights into Human Arboviral Infections: Dengue, Chikungunya, and Zika Viruses. PMID:30845653
Gene expression profiling meta-analysis reveals novel gene signatures and pathways shared between tuberculosis and rheumatoid arthritis. PMID:30845171
Honey bee (Apis mellifera) exposomes and dysregulated metabolic pathways associated with Nosema ceranae infection. PMID:30845162
Liquid Chromatography-Mass Spectrometry-Based Metabolomics of Nonhuman Primates after 4 Gy Total Body Radiation Exposure: Global Effects and Targeted Panels. PMID:30843397
Transcriptome analysis of a rice cultivar reveals the differentially expressed genes in response to wild and mutant strains of Xanthomonas oryzae pv. oryzae. PMID:30842619
PAI-1 augments mucosal damage in colitis. PMID:30842312
Bacillus subtilis DSM 32315 Supplementation Attenuates the Effects of Clostridium perfringens Challenge on the Growth Performance and Intestinal Microbiota of Broiler Chickens. PMID:30841654
Compositional and Functional Differences between Microbiota and Cervical Carcinogenesis as Identified by Shotgun Metagenomic Sequencing. PMID:30841606
Does the Chemodiversity of Bacterial Exometabolomes Sustain the Chemodiversity of Marine Dissolved Organic Matter? PMID:30837961
Differential Sensitivity to Plasmodium yoelii Infection in C57BL/6 Mice Impacts Gut-Liver Axis Homeostasis. PMID:30837607
DAKB-GPCRs: An Integrated Computational Platform for Drug Abuse Related GPCRs. PMID:30835466
Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain. PMID:30835008
Identification of Key circRNAs/lncRNAs/miRNAs/mRNAs and Pathways in Preeclampsia Using Bioinformatics Analysis. PMID:30833538
Comparative Gene Expression Profiles in Parathyroid Adenoma and Normal Parathyroid Tissue. PMID:30832348
Genome Sequencing Illustrates the Genetic Basis of the Pharmacological Properties of Gloeostereum incarnatum. PMID:30832255
GC-MS metabolic profiling reveals fructose-2,6-bisphosphate regulates branched chain amino acid metabolism in the heart during fasting. PMID:30830475
An LC-MS-based lipidomics pre-processing framework underpins rapid hypothesis generation towards CHO systems biotechnology. PMID:30830409
Mitochondrial aconitase is a key regulator of energy production for growth and protein expression in Chinese hamster ovary cells. PMID:30830403
Global testing of shifts in metabolic phenotype. PMID:30830386
Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water. PMID:30830325
Prediction of Driver Modules via Balancing Exclusive Coverages of Mutations in Cancer Samples. PMID:30828525
Identification of Potential Genes Responsible for Thermotolerance in Wheat under High Temperature Stress. PMID:30823586
Genome‑wide DNA methylation profile of thymomas and potential epigenetic regulation of thymoma subtypes. PMID:30816514
Elevated atmospheric CO2 concentrations alter grapevine (Vitis vinifera) systemic transcriptional response to European grapevine moth (Lobesia botrana) herbivory. PMID:30816321
Rapalog resistance is associated with mesenchymal-type changes in Tsc2-null cells. PMID:30816188
The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury. PMID:30815016
Hydrogenotrophic methanogenesis in archaeal phylum Verstraetearchaeota reveals the shared ancestry of all methanogens. PMID:30814220
Identifying Windows of Susceptibility by Temporal Gene Analysis. PMID:30809014
FoPA: identifying perturbed signaling pathways in clinical conditions using formal methods. PMID:30808299
Draft genomic and transcriptome resources for marine chelicerate Tachypleus tridentatus. PMID:30806641
A comparison of the transcriptomes between diploid and autotetraploid Paulownia fortunei under salt stress. PMID:30804626
Circadian regulation in human white adipose tissue revealed by transcriptome and metabolic network analysis. PMID:30804433
Mammalian Target of Rapamycin: A Metabolic Rheostat for Regulating Adipose Tissue Function and Cardiovascular Health. PMID:30803496
Establishing synthesis pathway-host compatibility via enzyme solubility. PMID:30802311
Complete genome sequence of acetate-producing Klebsiella pneumoniae L5-2 isolated from infant feces. PMID:30800595
Genome analysis of the rice coral Montipora capitata. PMID:30796282
Pareto Optimality Explanation of the Glycolytic Alternatives in Nature. PMID:30796263
Evolutionary dynamics of the chromatophore genome in three photosynthetic Paulinella species. PMID:30796245
In-feed resin acids reduce matrix metalloproteinase activity in the ileal mucosa of healthy broilers without inducing major effects on the gut microbiota. PMID:30795808
A phthalimidoalkanamide derived novel DNMT inhibitor enhanced radiosensitivity of A549 cells by inhibition of homologous recombination of DNA damage. PMID:30793218
Differential effects, on oncogenic pathway signalling, by derivatives of the HNF4 α inhibitor BI6015. PMID:30792535
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0. PMID:30787451
Integrative Gene Selection on Gene Expression Data: Providing Biological Context to Traditional Approaches. PMID:30785707
A Novel Analysis of the Peptide Terminome Characterizes Dynamics of Proteolytic Regulation in Vertebrate Skeletal Muscle Under Severe Stress. PMID:30781840
A draft genome assembly of the solar-powered sea slug Elysia chlorotica. PMID:30778257
Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease. PMID:30778168
Barrett's esophagus network analysis revealed that arginine, alanine, aspartate, glutamate, valine, leucine and isoleucine can be biomarkers. PMID:30774814
Integrated Bioinformatics Analysis of Hub Genes and Pathways in Anaplastic Thyroid Carcinomas. PMID:30774662
Functional high-throughput screening reveals miR-323a-5p and miR-342-5p as new tumor-suppressive microRNA for neuroblastoma. PMID:30770954
Identification of novel candidate indicators for assessing zinc status during pregnancy in mice from microarray data. PMID:30770772
Alterations in tissue microRNA after heat stress in the conscious rat: potential biomarkers of organ-specific injury. PMID:30770735
Functional Heatmap: an automated and interactive pattern recognition tool to integrate time with multi-omics assays. PMID:30770734
Analysis of Topological Parameters of Complex Disease Genes Reveals the Importance of Location in a Biomolecular Network. PMID:30769902
Metabolomics Approaches for the Diagnosis and Understanding of Kidney Diseases. PMID:30769897
Proteomic Analysis of the Effect of Inorganic and Organic Chemicals on Silver Nanoparticles in Wheat. PMID:30769865
Protein Network Analysis of the Serum and Their Functional Implication in Patients Subjected to Traumatic Brain Injury. PMID:30766469
Integration of Imaging (epi)Genomics Data for the Study of Schizophrenia Using Group Sparse Joint Nonnegative Matrix Factorization. PMID:30762565
Gene expression atlas of embryo development in Arabidopsis. PMID:30762127
Exploring cold quarantine to mango fruit against fruit fly using artificial ripening. PMID:30760867
Neonicotinoid Insecticides Alter the Transcriptome of Soybean and Decrease Plant Resistance. PMID:30759791
A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine. PMID:30754631
Effect of plasma MicroRNA on antihypertensive response to beta blockers in the Pharmacogenomic Evaluation of Antihypertensive Responses (PEAR) studies. PMID:30753892
A combined computational strategy of sequence and structural analysis predicts the existence of a functional eicosanoid pathway in Drosophila melanogaster. PMID:30753230
Genetic algorithm as an optimization tool for the development of sponge cell culture media. PMID:30747414
Identification of critical genes associated with spinal cord injury based on the gene expression profile of spinal cord tissues from trkB.T1 knockout mice. PMID:30747207
Universal scaling across biochemical networks on Earth. PMID:30746442
Probabilistic Modeling of Microbial Metabolic Networks for Integrating Partial Quantitative Knowledge Within the Nitrogen Cycle. PMID:30745899
Dopaminergic Pathway Genes Influence Adverse Events Related to Dopaminergic Treatment in Parkinson's Disease. PMID:30745869
Identification of potential blood biomarkers for Parkinson's disease by gene expression and DNA methylation data integration analysis. PMID:30744671
Molecular signature of human bone marrow-derived mesenchymal stromal cell subsets. PMID:30742027
Amino acids and proteomic acclimation of Staphylococcus aureus when incubated in a defined minimal medium supplemented with 5% sodium chloride. PMID:30739392
A network biology approach to unraveling inherited axonopathies. PMID:30737464
Lymphocyte innateness defined by transcriptional states reflects a balance between proliferation and effector functions. PMID:30737409
Identification of epilepsy related pathways using genome-wide DNA methylation measures: A trio-based approach. PMID:30735541
Competitive Endogenous RNA (ceRNA) Regulation Network of lncRNA-miRNA-mRNA in Colorectal Carcinogenesis. PMID:30734239
Smp38 MAP Kinase Regulation in Schistosoma mansoni: Roles in Survival, Oviposition, and Protection Against Oxidative Stress. PMID:30733716
SqueezeMeta, A Highly Portable, Fully Automatic Metagenomic Analysis Pipeline. PMID:30733714
Murine trophoblast-derived and pregnancy-associated exosome-enriched extracellular vesicle microRNAs: Implications for placenta driven effects on maternal physiology. PMID:30730971
Genome sequence of the H2-producing Clostridium beijerinckii strain Br21 isolated from a sugarcane vinasse treatment plant. PMID:30730526
Pathway Based Analysis of Mutation Data Is Efficient for Scoring Target Cancer Drugs. PMID:30728774
Autophagy and Apoptosis Specific Knowledgebases-guided Systems Pharmacology Drug Research. PMID:30727895
Ocimum metabolomics in response to abiotic stresses: Cold, flood, drought and salinity. PMID:30726239
Comparative transcriptome analysis reveals new molecular pathways for cucumber genes related to sex determination. PMID:30719568
COMMD7 Regulates NF-κB Signaling Pathway in Hepatocellular Carcinoma Stem-like Cells. PMID:30719501
Ulcerative colitis: functional analysis of the in-depth proteome. PMID:30718987
1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses. PMID:30718868
Pancreatic adenocarcinomas with mature blood vessels have better overall survival. PMID:30718678
Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry. PMID:30715294
The genomic basis for colonizing the freezing Southern Ocean revealed by Antarctic toothfish and Patagonian robalo genomes. PMID:30715292
A unified approach for sparse dynamical system inference from temporal measurements. PMID:30715136
Conserved Disease Modules Extracted From Multilayer Heterogeneous Disease and Gene Networks for Understanding Disease Mechanisms and Predicting Disease Treatments. PMID:30713550
Gene2vec: distributed representation of genes based on co-expression. PMID:30712510
Integrative analysis of pooled CRISPR genetic screens using MAGeCKFlute. PMID:30710114
Host-hijacking and planktonic piracy: how phages command the microbial high seas. PMID:30709355
High-throughput RNAi screening reveals cancer-selective lethal targets in the RNA spliceosome. PMID:30705407
Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism. PMID:30705326
De Novo Transcriptome Assembly of Agave H11648 by Illumina Sequencing and Identification of Cellulose Synthase Genes in Agave Species. PMID:30704153
Identification of Early Salinity Stress-Responsive Proteins in Dunaliella salina by isobaric tags for relative and absolute quantitation (iTRAQ)-Based Quantitative Proteomic Analysis. PMID:30704074
Association of High miR-182 Levels with Low-Risk Prostate Cancer. PMID:30703341
Combined impacts of prolonged drought and warming on plant size and foliar chemistry. PMID:30698658
Transcriptomic Analysis Reveals Insights on Male Infertility in Octopus maya Under Chronic Thermal Stress. PMID:30697164
Isolation and characterization of Lactobacillus-derived membrane vesicles. PMID:30696852
Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells. PMID:30696696
iVikodak-A Platform and Standard Workflow for Inferring, Analyzing, Comparing, and Visualizing the Functional Potential of Microbial Communities. PMID:30692979
Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL. PMID:30692684
Expression of Immune Regulatory Genes in the Porcine Internal Genital Tract Is Differentially Triggered by Spermatozoa and Seminal Plasma. PMID:30691059
Genome sequence of Malania oleifera, a tree with great value for nervonic acid production. PMID:30689848
The Eucalyptus Cuticular Waxes Contribute in Preformed Defense Against Austropuccinia psidii. PMID:30687371
Stems cells, big data and compendium-based analyses for identifying cell types, signalling pathways and gene regulatory networks. PMID:30684132
The Short Chain Fatty Acid Butyrate Imprints an Antimicrobial Program in Macrophages. PMID:30683619
Tri-mannose grafting of chitosan nanocarriers remodels the macrophage response to bacterial infection. PMID:30683129
Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica. PMID:30682815
Metabolic reconstruction of the genome of candidate Desulfatiglans TRIP_1 and identification of key candidate enzymes for anaerobic phenanthrene degradation. PMID:30680888
A gene expression signature in developing Purkinje cells predicts autism and intellectual disability co-morbidity status. PMID:30679692
Susceptibility of Escherichia coli O157:H7 grown at low temperatures to the krypton-chlorine excilamp. PMID:30679621
Marine biogenics in sea spray aerosols interact with the mTOR signaling pathway. PMID:30679557
Transcriptome analysis identifies strong candidate genes for ginsenoside biosynthesis and reveals its underlying molecular mechanism in Panax ginseng C.A. Meyer. PMID:30679448
Identification of Key Candidate Genes and Pathways for Relationship between Ovarian Cancer and Diabetes Mellitus Using Bioinformatical Analysis. PMID:30678426
Genetic and genomic analyses of testicular hypoplasia in Nellore cattle. PMID:30677076
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism. PMID:30677028
Integrative analysis of gene expression profiles reveals distinct molecular characteristics in oral tongue squamous cell carcinoma. PMID:30675303
Periodontal pathogens are a risk factor of oral cavity squamous cell carcinoma, independent of tobacco and alcohol and human papillomavirus. PMID:30671943
Identification of Blood Biomarkers for Alzheimer's Disease Through Computational Prediction and Experimental Validation. PMID:30671019
Mechanistic Target of Rapamycin Complex 1 Promotes the Expression of Genes Encoding Electron Transport Chain Proteins and Stimulates Oxidative Phosphorylation in Primary Human Trophoblast Cells by Regulating Mitochondrial Biogenesis. PMID:30670706
Transcriptionally induced enhancers in the macrophage immune response to Mycobacterium tuberculosis infection. PMID:30669987
Real world scenarios in rare variant association analysis: the impact of imbalance and sample size on the power in silico. PMID:30669967
Mechanistic Computational Models of MicroRNA-Mediated Signaling Networks in Human Diseases. PMID:30669429
Contrasting Patterns of Rapid Molecular Evolution within the p53 Network across Mammal and Sauropsid Lineages. PMID:30668691
Ochrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains. PMID:30668584
Identification of key genes and pathways involved in microsatellite instability in colorectal cancer. PMID:30664178
Pathway Instability Is an Effective New Mutation-Based Type of Cancer Biomarkers. PMID:30662873
Identification of cordycepin biosynthesis-related genes through de novo transcriptome assembly and analysis in Cordyceps cicadae. PMID:30662735
EFNB2 acts as the target of miR-557 to facilitate cell proliferation, migration and invasion in pancreatic ductal adenocarcinoma by bioinformatics analysis and verification. PMID:30662604
Identification of Key Genes and Pathways in Female Lung Cancer Patients Who Never Smoked by a Bioinformatics Analysis. PMID:30662525
Identification of hub genes and pathways in glioblastoma by bioinformatics analysis. PMID:30655863
Identification of potential genes and pathways for response prediction of neoadjuvant chemoradiotherapy in patients with rectal cancer by systemic biological analysis. PMID:30655792
Identification of core genes and prediction of miRNAs associated with osteoporosis using a bioinformatics approach. PMID:30655789
Assessment of somatic single-nucleotide variation in brain tissue of cases with schizophrenia. PMID:30655504
Low-temperature-induced changes in the transcriptome reveal a major role of CgSVP genes in regulating flowering of Cymbidium goeringii. PMID:30654752
Organ-Specific Analysis of Morus alba Using a Gel-Free/Label-Free Proteomic Technique. PMID:30654535
Coexpression modules constructed by weighted gene co-expression network analysis indicate ubiquitin-mediated proteolysis as a potential biomarker of uveal melanoma. PMID:30651788
GLIS Rearrangement is a Genomic Hallmark of Hyalinizing Trabecular Tumor of the Thyroid Gland. PMID:30648929
Identification of wheat stress-responding genes and TaPR-1-1 function by screening a cDNA yeast library prepared following abiotic stress. PMID:30644420
Mature IgDlow/- B cells maintain tolerance by promoting regulatory T cell homeostasis. PMID:30643147
Investigation of the Underlying Genes and Mechanism of Macrophage-Enriched Ruptured Atherosclerotic Plaques Using Bioinformatics Method. PMID:30643084
Prognostic signature associated with radioresistance in head and neck cancer via transcriptomic and bioinformatic analyses. PMID:30642292
Identification of candidate diagnostic and prognostic biomarkers for pancreatic carcinoma. PMID:30639415
Comparative Metabolomics and Transcriptomics Reveal Multiple Pathways Associated with Polymyxin Killing in Pseudomonas aeruginosa. PMID:30637340
Inhibitor of DNA-Binding/Differentiation Proteins and Environmental Toxicants: Genomic Impact on the Onset of Depressive Dysfunction. PMID:30634536
Identification of key regulators of pancreatic ductal adenocarcinoma using bioinformatics analysis of microarray data. PMID:30633213
Leveraging Multilayered "Omics" Data for Atopic Dermatitis: A Road Map to Precision Medicine. PMID:30631320
Convergent evolution on the hypoxia-inducible factor (HIF) pathway genes EGLN1 and EPAS1 in high-altitude ducks. PMID:30631144
SREBP-dependent lipidomic reprogramming as a broad-spectrum antiviral target. PMID:30631056
Drug-Target Interaction Prediction via Dual Laplacian Graph Regularized Matrix Completion. PMID:30627536
Transcriptome network analysis identifies protective role of the LXR/SREBP-1c axis in murine pulmonary fibrosis. PMID:30626759
Variations in HPV function are associated with survival in squamous cell carcinoma. PMID:30626753
Breaking the paradigm: Dr Insight empowers signature-free, enhanced drug repurposing. PMID:30624606
Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and Nanomaterials. PMID:30622555
Maternal choline supplementation ameliorates Alzheimer's disease pathology by reducing brain homocysteine levels across multiple generations. PMID:30622336
The use of next generation sequencing for improving food safety: Translation into practice. PMID:30621881
Commonly Used Pancreatic Stellate Cell Cultures Differ Phenotypically and in Their Interactions with Pancreatic Cancer Cells. PMID:30621293
Personalized Prediction of Acquired Resistance to EGFR-Targeted Inhibitors Using a Pathway-Based Machine Learning Approach. PMID:30621238
Immune genes are hotspots of shared positive selection across birds and mammals. PMID:30620335
Detection of Foodborne Pathogens Using Proteomics and Metabolomics-Based Approaches. PMID:30619201
Toxic Indole Diterpenes from Endophyte-Infected Perennial Ryegrass Lolium perenne L.: Isolation and Stability. PMID:30609849
Network Profiling of Brain-Expressed X-Chromosomal MicroRNA Genes Implicates Shared Key MicroRNAs in Intellectual Disability. PMID:30604382
Epigenetic Alternations of MicroRNAs and DNA Methylation Contribute to Liver Metastasis of Colorectal Cancer. PMID:30604369
Alarmones as Vestiges of a Bygone RNA World. PMID:30604017
Transcriptome driven characterization of curly- and smooth-leafed endives reveals molecular differences in the sesquiterpenoid pathway. PMID:30603088
Random Forest Analysis of Untargeted Metabolomics Data Suggests Increased Use of Omega Fatty Acid Oxidation Pathway in Drosophila Melanogaster Larvae Fed a Medium Chain Fatty Acid Rich High-Fat Diet. PMID:30602659
Ovarian Cancer Prognostic Prediction Model Using RNA Sequencing Data. PMID:30602093
Comparison of serum and saliva miRNAs for identification and characterization of mTBI in adult mixed martial arts fighters. PMID:30601825
Constructing tissue-specific transcriptional regulatory networks via a Markov random field. PMID:30598101
Integrated molecular characterization of adult soft tissue sarcoma for therapeutic targets. PMID:30598078
Bayesian generalized biclustering analysis via adaptive structured shrinkage. PMID:30596887
Network spectra for drug-target identification in complex diseases: new guns against old foes. PMID:30596144
Time-lagged Ordered Lasso for network inference. PMID:30594121
Bioinformatic identification of key genes and pathways that may be involved in the pathogenesis of HBV-associated acute liver failure. PMID:30591937
In silico engineering of Pseudomonas metabolism reveals new biomarkers for increased biosurfactant production. PMID:30588397
A six-mRNA prognostic model to predict survival in head and neck squamous cell carcinoma. PMID:30588115
Plant stress RNA-seq Nexus: a stress-specific transcriptome database in plant cells. PMID:30587128
Harnessing formal concepts of biological mechanism to analyze human disease. PMID:30586388
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. PMID:30577795
Insights into Xylan Degradation and Haloalkaline Adaptation through Whole-Genome Analysis of Alkalitalea saponilacus, an Anaerobic Haloalkaliphilic Bacterium Capable of Secreting Novel Halostable Xylanase. PMID:30577500
MicroRNA-31 Reduces the Motility of Proinflammatory T Helper 1 Lymphocytes. PMID:30574141
Impact of Dietary Carbohydrate/Protein Ratio on Hepatic Metabolism in Land-Locked Atlantic Salmon (Salmo salar L.). PMID:30574094
Drug-target-disease network analysis of gene-phenotype connectivity for genistein in ovarian cancer. PMID:30573976
Enhanced cerebellar myelination with concomitant iron elevation and ultrastructural irregularities following prenatal exposure to ambient particulate matter in the mouse. PMID:30572762
Expression and potential molecular mechanisms of miR‑204‑5p in breast cancer, based on bioinformatics and a meta‑analysis of 2,306 cases. PMID:30569120
A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer. PMID:30568637
Physiological and proteomic analysis on long-term drought resistance of cassava (Manihot esculenta Crantz). PMID:30568257
Nuclear MET requires ARF and is inhibited by carbon nanodots through binding to phospho-tyrosine in prostate cancer. PMID:30568225
TriPOINT: a software tool to prioritize important genes in pathways and their non-coding regulators. PMID:30566622
Prenatal Bisphenol A Exposure in Mice Induces Multitissue Multiomics Disruptions Linking to Cardiometabolic Disorders. PMID:30566610
Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken. PMID:30565091
Identification of genes and pathways, including the CXCL2 axis, altered by DNA methylation in hepatocellular carcinoma. PMID:30564899
Genome Assembly for a Yunnan-Guizhou Plateau "3E" Fish, Anabarilius grahami (Regan), and Its Evolutionary and Genetic Applications. PMID:30564274
A Curated Resource for Phosphosite-specific Signature Analysis. PMID:30563849
Defining a Characteristic Gene Expression Set Responsible for Cancer Stem Cell-Like Features in a Sub-Population of Ewing Sarcoma Cells CADO-ES1. PMID:30563222
High Throughput Identification of Novel Conotoxins from the Vermivorous Oak Cone Snail (Conus quercinus) by Transcriptome Sequencing. PMID:30563163
Comparative Proteomic Analysis Reveals Elevated Capacity for Photosynthesis in Polyphenol Oxidase Expression-Silenced Clematis terniflora DC. Leaves. PMID:30563128
De Novo Analysis Reveals Transcriptomic Responses in Eriobotrya japonica Fruits during Postharvest Cold Storage. PMID:30563027
The Prognostic Value of Cell Cycle Gene Expression Signatures in Muscle Invasive, High-Grade Bladder Cancer. PMID:30561442
MicroRNA-150 down Regulation in Acute Myeloid Leukaemia Patients and Its Prognostic Implication. PMID:30559849
Liriodendron genome sheds light on angiosperm phylogeny and species-pair differentiation. PMID:30559417
Immunologic Pathways in Protective versus Maladaptive Host Responses to Attenuated and Pathogenic Strains of Mycoplasma gallisepticum. PMID:30559221
Genome-wide RNAseq study of the molecular mechanisms underlying microglia activation in response to pathological tau perturbation in the rTg4510 tau transgenic animal model. PMID:30558641
Integrating tumor genomics into studies of the microbiome in colorectal cancer. PMID:30556775
Elucidating the Role of Chromatin State and Transcription Factors on the Regulation of the Yeast Metabolic Cycle: A Multi-Omic Integrative Approach. PMID:30555512
Comparative Transcriptome and iTRAQ Proteome Analyses Reveal the Mechanisms of Diapause in Aphidius gifuensis Ashmead (Hymenoptera: Aphidiidae). PMID:30555341
Pan-cancer analysis of transcriptional metabolic dysregulation using The Cancer Genome Atlas. PMID:30552315
Interferon-gamma production in Lyme arthritis synovial tissue promotes differentiation of fibroblast-like synoviocytes into immune effector cells. PMID:30550623
Identification of key genes and pathways by bioinformatics analysis with TCGA RNA sequencing data in hepatocellular carcinoma. PMID:30546887
Let it RE:IN: integrating experimental observations to predict pluripotency network behaviour. PMID:30545825
The Antitumor Activity of a Lead Thioxanthone is Associated with Alterations in Cholesterol Localization. PMID:30545153
Clinical Significance of CUB and Sushi Multiple Domains 1 Inactivation in Head and Neck Squamous Cell Carcinoma. PMID:30545040
Search of Allosteric Inhibitors and Associated Proteins of an AKT-like Kinase from Trypanosoma cruzi. PMID:30544836
Rice Overexpressing OsNUC1-S Reveals Differential Gene Expression Leading to Yield Loss Reduction after Salt Stress at the Booting Stage. PMID:30544581
Lateral Gene Transfer Shapes the Distribution of RuBisCO among Candidate Phyla Radiation Bacteria and DPANN Archaea. PMID:30544151
A two‑circRNA signature predicts tumour recurrence in clinical non‑functioning pituitary adenoma. PMID:30542712
Transcriptome reprogramming during severe dehydration contributes to physiological and metabolic changes in the resurrection plant Haberlea rhodopensis. PMID:30541446
Changes in Transcriptome of Yersinia pseudotuberculosis IP32953 Grown at 3 and 28°C Detected by RNA Sequencing Shed Light on Cold Adaptation. PMID:30538955
Role of miRNAs in skeletal muscle aging. PMID:30538437
Differential regulation of cysteine oxidative post-translational modifications in high and low aerobic capacity. PMID:30538258
Metagenomic Sequencing of Wastewater from a South African Research Farm. PMID:30533733
Draft Genome Sequence of Dyella sp. Strain C9, Isolated from a Malaysian Tropical Peat Swamp Forest. PMID:30533674
Draft Genome Sequence of Streptomyces cavourensis YBQ59, an Endophytic Producer of Antibiotics Bafilomycin D, Nonactic Acid, Prelactone B, and 5,11-Epoxy-10-Cadinanol. PMID:30533639
A novel network-based approach for discovering dynamic metabolic biomarkers in cardiovascular disease. PMID:30533038
Transcriptome-wide responses of adult melon thrips (Thrips palmi) associated with capsicum chlorosis virus infection. PMID:30532222
Comparative shotgun metagenomic data of the silkworm Bombyx mori gut microbiome. PMID:30532085
Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. PMID:30531987
Microbiota and cancer immunotherapy: in search of microbial signals. PMID:30530851
Single-cell analyses demonstrate that a heme-GATA1 feedback loop regulates red cell differentiation. PMID:30530752
Practical considerations on performing and analyzing CLIP-seq experiments to identify transcriptomic-wide RNA-protein interactions. PMID:30527764
L-Fucose ameliorates high-fat diet-induced obesity and hepatic steatosis in mice. PMID:30526624
Flux Connections Between Gluconate Pathway, Glycolysis, and Pentose-Phosphate Pathway During Carbohydrate Metabolism in Bacillus megaterium QM B1551. PMID:30524402
Effects of acute exposures of 2,4,6-trinitrotoluene and inorganic lead on the fecal microbiome of the green anole (Anolis carolinensis). PMID:30521592
Derivation and Validation of the Potential Core Genes in Pancreatic Cancer for Tumor-Stroma Crosstalk. PMID:30519576
De novo sequencing and transcriptome assembly of Arisaema heterophyllum Blume and identification of genes involved in isoflavonoid biosynthesis. PMID:30518768
GhNAC83 inhibits corm dormancy release by regulating ABA signaling and cytokinin biosynthesis in Gladiolus hybridus. PMID:30517656
The Transcriptomic Landscape of Yaks Reveals Molecular Pathways for High Altitude Adaptation. PMID:30517636
Analysis of the transcriptome data in Litopenaeus vannamei reveals the immune basis and predicts the hub regulation-genes in response to high-pH stress. PMID:30517152
Glucose intake hampers PKA-regulated HSP90 chaperone activity. PMID:30516470
Pathway sensor-based functional genomics screening identifies modulators of neuronal activity. PMID:30514868
Automated generation of genome-scale metabolic draft reconstructions based on KEGG. PMID:30514205
Decoupling the Variances of Heterosis and Inbreeding Effects Is Evidenced in Yeast's Life-History and Proteomic Traits. PMID:30509954
Gene set enrichment analysis and meta-analysis to identify six key genes regulating and controlling the prognosis of esophageal squamous cell carcinoma. PMID:30505479
Metabolic Analyses Revealed Time-Dependent Synergistic Killing by Colistin and Aztreonam Combination Against Multidrug-Resistant Acinetobacter baumannii. PMID:30505298
Birth mode is associated with earliest strain-conferred gut microbiome functions and immunostimulatory potential. PMID:30504906
Developmental origins of transgenerational sperm DNA methylation epimutations following ancestral DDT exposure. PMID:30500333
Members of Marinobacter and Arcobacter Influence System Biogeochemistry During Early Production of Hydraulically Fractured Natural Gas Wells in the Appalachian Basin. PMID:30498478
Prognostic value of sorting nexin 10 weak expression in stomach adenocarcinoma revealed by weighted gene co-expression network analysis. PMID:30487700
Selective expansion of myeloid and NK cells in humanized mice yields human-like vaccine responses. PMID:30487575
High-throughput sequencing of small RNAs revealed the diversified cold-responsive pathways during cold stress in the wild banana (Musa itinerans). PMID:30486778
Semantic Multi-Classifier Systems Identify Predictive Processes in Heart Failure Models across Species. PMID:30486323
Rumen and plasma metabolomics profiling by UHPLC-QTOF/MS revealed metabolic alterations associated with a high-corn diet in beef steers. PMID:30485366
Interactive online application for the prediction, ranking and prioritisation of drug targets in Schistosoma haematobium. PMID:30482220
Comparison of Microbiota Variation in Korean Healthy Adolescents with Adults Suggests Notable Maturity Differences. PMID:30481125
Dissection of metabolic reprogramming in polycystic kidney disease reveals coordinated rewiring of bioenergetic pathways. PMID:30480096
Toxicity of Melaleuca alternifolia essential oil to the mitochondrion and NAD+/NADH dehydrogenase in Tribolium confusum. PMID:30479882
GC-MS metabolite profiling for specific detection of dwarf somaclonal variation in banana plants. PMID:30473940
Comparative analysis of nucleus-encoded plastid-targeting proteins in Rafflesia cantleyi against photosynthetic and non-photosynthetic representatives reveals orthologous systems with potentially divergent functions. PMID:30467394
Variant information systems for precision oncology. PMID:30463544
Endangered Père David's deer genome provides insights into population recovering. PMID:30459847
Identification of the Toxicity Pathways Associated With Thioacetamide-Induced Injuries in Rat Liver and Kidney. PMID:30459623
Transcriptomic analysis of Bifidobacterium longum subsp. longum BBMN68 in response to oxidative shock. PMID:30459453
Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD. PMID:30459441
Whole-Transcriptome Profiling of Canine and Human in Vitro Models Exposed to a G-Quadruplex Binding Small Molecule. PMID:30459395
Damage-responsive elements in Drosophila regeneration. PMID:30459214
Population sequencing reveals clonal diversity and ancestral inbreeding in the grapevine cultivar Chardonnay. PMID:30458008
Transcriptome Analysis of Cinnamomum chago: A Revelation of Candidate Genes for Abiotic Stress Response and Terpenoid and Fatty Acid Biosyntheses. PMID:30455715
Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants. PMID:30454555
Host genetic selection for cold tolerance shapes microbiome composition and modulates its response to temperature. PMID:30454554
Monensin Alters the Functional and Metabolomic Profile of Rumen Microbiota in Beef Cattle. PMID:30453603
Genetic variants influence on the placenta regulatory landscape. PMID:30452450
Periodic and Spatial Spreading of Alkanes and Alcanivorax Bacteria in Deep Waters of the Mariana Trench. PMID:30446553
Complete Genome Sequence of Massilia oculi sp. nov. CCUG 43427T (=DSM 26321T), the Type Strain of M. oculi, and Comparison with Genome Sequences of Other Massilia Strains. PMID:30443686
Soy-Induced Fecal Metabolome Changes in Ovariectomized and Intact Female Rats: Relationship with Cardiometabolic Health. PMID:30442926
Selective colonization ability of human fecal microbes in different mouse gut environments. PMID:30442907
Single-Cell Transcriptomics Reveals Heterogeneity and Drug Response of Human Colorectal Cancer Organoids. PMID:30440885
Bioinformatics-based study to detect chemical compounds that show potential as treatments for pulmonary thromboembolism. PMID:30431066
Transcriptomic changes with increasing algal symbiont reveal the detailed process underlying establishment of coral-algal symbiosis. PMID:30429501
Complement Inhibitor CRIg/FH Ameliorates Renal Ischemia Reperfusion Injury via Activation of PI3K/AKT Signaling. PMID:30429287
Soy supplementation: Impact on gene expression in different tissues of ovariectomized rats and evaluation of the rat model to predict (post)menopausal health effect. PMID:30425930
Transcriptomics Study on Staphylococcus aureus Biofilm Under Low Concentration of Ampicillin. PMID:30425687
Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces. PMID:30424821
piMGM: incorporating multi-source priors in mixed graphical models for learning disease networks. PMID:30423087
PSMD12 haploinsufficiency in a neurodevelopmental disorder with autistic features. PMID:30421579
Integrative analysis of differential genes and identification of a "2-gene score" associated with survival in esophageal squamous cell carcinoma. PMID:30421504
Born to Cry: A Genetic Dissection of Infant Vocalization. PMID:30420800
Novel protein signatures suggest progression to muscular invasiveness in bladder cancer. PMID:30419021
Assessment of 16S rRNA gene primers for studying bacterial community structure and function of aging flue-cured tobaccos. PMID:30415449
Unlocking conserved and diverged metabolic characteristics in cassava carbon assimilation via comparative genomics approach. PMID:30413726
The Overexpression of CD80 and ISG15 Are Associated with the Progression and Metastasis of Breast Cancer by a Meta-Analysis Integrating Three Microarray Datasets. PMID:30411299
Uracil moieties in Plasmodium falciparum genomic DNA. PMID:30410856
Identification of critically carcinogenesis-related genes in basal cell carcinoma. PMID:30410353
Effect of Early Calf-Hood Nutrition on the Transcriptional Regulation of the Hypothalamic-Pituitary-Testicular axis in Holstein-Friesian Bull Calves. PMID:30409985
Visualization-assisted binning of metagenome assemblies reveals potential new pathogenic profiles in idiopathic travelers' diarrhea. PMID:30409177
Resequencing of cv CRI-12 family reveals haplotype block inheritance and recombination of agronomically important genes in artificial selection. PMID:30407717
Endotoxemia by Porphyromonas gingivalis Injection Aggravates Non-alcoholic Fatty Liver Disease, Disrupts Glucose/Lipid Metabolism, and Alters Gut Microbiota in Mice. PMID:30405551
Maternal depression during pregnancy and cord blood DNA methylation: findings from the Avon Longitudinal Study of Parents and Children. PMID:30405117
Metabolic pathways synthesis based on ant colony optimization. PMID:30401873
Uncovering full-length transcript isoforms of sugarcane cultivar Khon Kaen 3 using single-molecule long-read sequencing. PMID:30397543
DrugThatGene: integrative analysis to streamline the identification of druggable genes, pathways and protein complexes from CRISPR screens. PMID:30395160
Dysregulation of NCAPG, KNL1, miR-148a-3p, miR-193b-3p, and miR-1179 may contribute to the progression of gastric cancer. PMID:30390708
Transcriptome analysis of Xenopus orofacial tissues deficient in retinoic acid receptor function. PMID:30390632
The relationship between substrate topography and stem cell differentiation in the musculoskeletal system. PMID:30390116
Strategies for Pathway Analysis Using GWAS and WGS Data. PMID:30387919
RNA-Seq-based transcriptome analysis of reproduction- and growth-related genes in Lateolabrax japonicus ovaries at four different ages. PMID:30386972
Interplay Between MicroRNAs and Targeted Genes in Cellular Homeostasis of Adult Zebrafish (Danio rerio). PMID:30386173
Disease-relevant transcriptional signatures identified in individual smooth muscle cells from healthy mouse vessels. PMID:30385745
Identification of highly connected and differentially expressed gene subnetworks in metastasizing endometrial cancer. PMID:30383835
Hunt for the tipping point during endocrine resistance process in breast cancer by dynamic network biomarkers. PMID:30383247
RNA-Seq transcriptomic profiling of primary murine microglia treated with LPS or LPS + IFNγ. PMID:30382133
Bacillus megaterium adapts to acid stress condition through a network of genes: Insight from a genome-wide transcriptome analysis. PMID:30382109
Long-term investigation of microbial community composition and transcription patterns in a biogas plant undergoing ammonia crisis. PMID:30381904
Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential. PMID:30379883
Genome sequence of the cauliflower mushroom Sparassis crispa (Hanabiratake) and its association with beneficial usage. PMID:30375506
New miRNA Signature Heralds Human NK Cell Subsets at Different Maturation Steps: Involvement of miR-146a-5p in the Regulation of KIR Expression. PMID:30374356
Comparative cochlear transcriptomics of echolocating bats provides new insights into different nervous activities of CF bat species. PMID:30374045
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data. PMID:30372442
Effects of sugarcane aphid herbivory on transcriptional responses of resistant and susceptible sorghum. PMID:30367619
Multiple model species selection for transcriptomics analysis of non-model organisms. PMID:30367568
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
A Cyclic Metabolic Network in Pseudomonas protegens Pf-5 Prioritizes the Entner-Doudoroff Pathway and Exhibits Substrate Hierarchy during Carbohydrate Co-Utilization. PMID:30366991
De Novo Hepatic Transcriptome Assembly and Systems Level Analysis of Three Species of Dietary Fish, Sardinops sagax, Scomber japonicus, and Pleuronichthys verticalis. PMID:30366465
ETCM: an encyclopaedia of traditional Chinese medicine. PMID:30365030
Identification of candidate genes or microRNAs associated with the lymph node metastasis of SCLC. PMID:30364292
Proteomic analysis of Lactobacillus casei GCRL163 cell-free extracts reveals a SecB homolog and other biomarkers of prolonged heat stress. PMID:30359441
Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNA. PMID:30356407
Quantum chemistry reveals thermodynamic principles of redox biochemistry. PMID:30356318
Comparative study of gut microbiota in wild and captive Malaysian Mahseer (Tor tambroides). PMID:30353678
Increased dynamin expression precedes proteinuria in glomerular disease. PMID:30350425
Cell-type specific RNA-Seq reveals novel roles and regulatory programs for terminally differentiated Dictyostelium cells. PMID:30348074
Complete Genome Sequence of Bacillus cereus CC-1, A Novel Marine Selenate/Selenite Reducing Bacterium Producing Metallic Selenides Nanomaterials. PMID:30343326
Comparative proteomic analysis of four biotechnological strains Lactococcus lactis through label-free quantitative proteomics. PMID:30341804
An integrated proteomic and metabolomic study to evaluate the effect of nucleus-cytoplasm interaction in a diploid citrus cybrid between sweet orange and lemon. PMID:30341661
Comamonadaceae OTU as a Remnant of an Ancient Microbial Community in Sulfidic Waters. PMID:30341500
Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates. PMID:30341451
Deep sequencing of primary human lung epithelial cells challenged with H5N1 influenza virus reveals a proviral role for CEACAM1. PMID:30341336
Indirubin attenuates mouse psoriasis-like skin lesion in a CD274-dependent manner: an achievement of RNA sequencing. PMID:30341238
Robust estimation of high-dimensional covariance and precision matrices. PMID:30337763
RNA sequencing and de novo assembly of Solanum trilobatum leaf transcriptome to identify putative transcripts for major metabolic pathways. PMID:30337583
Prediction of Target Genes and Pathways Associated With Cetuximab Insensitivity in Colorectal Cancer. PMID:30336768
Differential expression profiles of microRNAs in highly and weakly invasive/metastatic pancreatic cancer cells. PMID:30333874
Injury promotes sarcoma development in a genetically and temporally restricted manner. PMID:30333301
A dynamic transcriptomic atlas of cytokine-induced killer cells. PMID:30333226
A novel prognostic signature of seven genes for the prediction in patients with thymoma. PMID:30328513
Metabolic flux analysis in Ashbya gossypii using 13C-labeled yeast extract: industrial riboflavin production under complex nutrient conditions. PMID:30326916
A Prognostic 5-lncRNA Expression Signature for Head and Neck Squamous Cell Carcinoma. PMID:30323196
The Genomic Basis of Tumor Regression in Tasmanian Devils (Sarcophilus harrisii). PMID:30321343
An Increased Abundance of Clostridiaceae Characterizes Arthritis in Inflammatory Bowel Disease and Rheumatoid Arthritis: A Cross-sectional Study. PMID:30321331
Soil Viruses Are Underexplored Players in Ecosystem Carbon Processing. PMID:30320215
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
Transcriptome profiling of rubber tree (Hevea brasiliensis) discovers candidate regulators of the cold stress response. PMID:30315521
TargetScore used to reveal potential targets of miRNA203 and miRNA-146a in psoriasis by integrating microRNA overexpression and microarray data. PMID:30313058
Hydroxyurea Treated β-Thalassemia Children Demonstrate a Shift in Metabolism Towards Healthy Pattern. PMID:30310134
Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. PMID:30309961
Protective role of the vulture facial skin and gut microbiomes aid adaptation to scavenging. PMID:30309375
DNA methylation patterns in peripheral blood mononuclear cells from Holstein cattle with variable milk yield. PMID:30309336
Microbial Changes and Host Response in F344 Rat Colon Depending on Sex and Age Following a High-Fat Diet. PMID:30298061
Transcriptomic responses of Serratia liquefaciens cells grown under simulated Martian conditions of low temperature, low pressure, and CO2-enriched anoxic atmosphere. PMID:30297913
Candida albicans biofilm-induced vesicles confer drug resistance through matrix biogenesis. PMID:30296253
Transcriptome analysis reveals the molecular response to cadmium toxicity in P. pseudoannulata. PMID:30291617
Genome Sequence of Peacock Reveals the Peculiar Case of a Glittering Bird. PMID:30283495
FLIM-MAP: Gene Context Based Identification of Functional Modules in Bacterial Metabolic Pathways. PMID:30283416
Identification of key microRNAs and their targets in exosomes of pancreatic cancer using bioinformatics analysis. PMID:30278585
Deep analysis of immune response and metabolic signature in children with food protein induced enterocolitis to cow's milk. PMID:30275944
Gene expression differences between thyroid carcinoma, thyroid adenoma and normal thyroid tissue. PMID:30272326
Gene module analysis of juvenile myelomonocytic leukemia and screening of anticancer drugs. PMID:30272300
PlaD: A Transcriptomics Database for Plant Defense Responses to Pathogens, Providing New Insights into Plant Immune System. PMID:30266409
Bioinformatics analysis to identify action targets in NCI-N87 gastric cancer cells exposed to quercetin. PMID:30266078
Transcriptome analysis of Macrobrachium rosenbergii intestines under the white spot syndrome virus and poly (I:C) challenges. PMID:30265693
Metabolomics profiling of xenobiotics in elite athletes: relevance to supplement consumption. PMID:30261929
Multiscale analysis of autotroph-heterotroph interactions in a high-temperature microbial community. PMID:30260956
Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress. PMID:30258841
Meta-analysis of data from spaceflight transcriptome experiments does not support the idea of a common bacterial "spaceflight response". PMID:30258082
Methods and results from the genome-wide association group at GAW20. PMID:30255814
Integrative pathway-based survival prediction utilizing the interaction between gene expression and DNA methylation in breast cancer. PMID:30255812
Modification effect of fenofibrate therapy, a longitudinal epigenomic-wide methylation study of triglycerides levels in the GOLDN study. PMID:30255776
Comparative in depth RNA sequencing of P. tricornutum's morphotypes reveals specific features of the oval morphotype. PMID:30254372
Microenvironmental niche divergence shapes BRCA1-dysregulated ovarian cancer morphological plasticity. PMID:30254278
Single cell molecular alterations reveal target cells and pathways of concussive brain injury. PMID:30254269
Potential use of compounds from sea cucumbers as MDM2 and CXCR4 inhibitors to control cancer cell growth. PMID:30250516
GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. PMID:30250203
Computer-aided identification of protein targets of four polyphenols in Alzheimer's disease (AD) and validation in a mouse AD model. PMID:30249814
Comprehensive Transcriptome Profiling and Identification of Potential Genes Responsible for Salt Tolerance in Tall Fescue Leaves under Salinity Stress. PMID:30248970
OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. PMID:30248096
The genomic basis of environmental adaptation in house mice. PMID:30248095
In silico Prioritization of Transporter-Drug Relationships From Drug Sensitivity Screens. PMID:30245630
The intragenic mRNA-microRNA regulatory network during telogen-anagen hair follicle transition in the cashmere goat. PMID:30242252
Multimodal Meta-Analysis of 1,494 Hepatocellular Carcinoma Samples Reveals Significant Impact of Consensus Driver Genes on Phenotypes. PMID:30242023
Condition-adaptive fused graphical lasso (CFGL): An adaptive procedure for inferring condition-specific gene co-expression network. PMID:30240439
Chromosome-level genome assembly of the spotted sea bass, Lateolabrax maculatus. PMID:30239684
Direct-fed microbial supplementation influences the bacteria community composition of the gastrointestinal tract of pre- and post-weaned calves. PMID:30237565
Metabolite accumulation and metabolic network in developing roots of Rehmannia glutinosa reveals its root developmental mechanism and quality. PMID:30237415
Bioinformatics Analysis Identifies p53 as a Candidate Prognostic Biomarker for Neuropathic Pain. PMID:30233637
Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source. PMID:30233558
Global Profiling of Lysine Acetylation in Borrelia burgdorferi B31 Reveals Its Role in Central Metabolism. PMID:30233522
The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units. PMID:30232462
Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. PMID:30232199
The assembled transcriptome of the adult horn fly, Haematobia irritans. PMID:30229068
Analysis of Transcription Factor-Related Regulatory Networks Based on Bioinformatics Analysis and Validation in Hepatocellular Carcinoma. PMID:30228980
Cross-exchange of B-vitamins underpins a mutualistic interaction between Ostreococcus tauri and Dinoroseobacter shibae. PMID:30228381
Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes). PMID:30228118
An integrated methylation and gene expression microarray analysis reveals significant prognostic biomarkers in oral squamous cell carcinoma. PMID:30226546
ChIP-Seq reveals that QsMYB1 directly targets genes involved in lignin and suberin biosynthesis pathways in cork oak (Quercus suber). PMID:30223777
Network analysis of membranous glomerulonephritis based on metabolomics data. PMID:30221719
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. PMID:30219839
Robust interferon signature and suppressed tissue repair gene expression in synovial tissue from patients with postinfectious, Borrelia burgdorferi-induced Lyme arthritis. PMID:30218476
High-throughput sequencing revealed that microRNAs were involved in the development of superior and inferior grains in bread wheat. PMID:30218081
Identifying miRNA-mRNA regulation network of major depressive disorder in ovarian cancer patients. PMID:30214617
DECtp: Calling Differential Gene Expression Between Cancer and Normal Samples by Integrating Tumor Purity Information. PMID:30210526
Computational prediction of changes in brain metabolic fluxes during Parkinson's disease from mRNA expression. PMID:30208076
Environmental toxicant induced epigenetic transgenerational inheritance of ovarian pathology and granulosa cell epigenome and transcriptome alterations: ancestral origins of polycystic ovarian syndrome and primary ovarian insufiency. PMID:30207508
An exploration of microbial and associated functional diversity in the OMZ and non-OMZ areas in the Bay of Bengal. PMID:30207310
Transcriptomic analyses of cacao cell suspensions in light and dark provide target genes for controlled flavonoid production. PMID:30206304
Metagenomic Analysis of Fish-Associated Ca. Parilichlamydiaceae Reveals Striking Metabolic Similarities to the Terrestrial Chlamydiaceae. PMID:30202970
Metagenomic sequencing provides insights into microbial detoxification in the guts of small mammalian herbivores (Neotoma spp.). PMID:30202961
De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome. PMID:30202061
Comparative gene expression profile and DNA methylation status in diabetic patients of Kazak and Han people. PMID:30200077
Jinfukang induces cellular apoptosis through activation of Fas and DR4 in A549 cells. PMID:30197670
Muscle transcriptome resource for growth, lipid metabolism and immune system in Hilsa shad, Tenualosa ilisha. PMID:30196475
Differential Co-expression and Regulatory Network Analysis Uncover the Relapse Factor and Mechanism of T Cell Acute Leukemia. PMID:30195757
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities. PMID:30192979
The joint lasso: high-dimensional regression for group structured data. PMID:30192903
Prioritizing candidate genes post-GWAS using multiple sources of data for mastitis resistance in dairy cattle. PMID:30189836
De novo transcriptome sequencing and metabolite profiling analyses reveal the complex metabolic genes involved in the terpenoid biosynthesis in Blue Anise Sage (Salvia guaranitica L.). PMID:30188980
Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood. PMID:30186694
Microarray data analysis to identify differentially expressed genes and biological pathways associated with asthma. PMID:30186379
Detection of high-risk carbapenem-resistant Klebsiella pneumoniae and Enterobacter cloacae isolates using volatile molecular profiles. PMID:30185884
Progesterone and plasma metabolites in women with and in those without premenstrual dysphoric disorder. PMID:30184299
Identification of key pathways and genes in response to trastuzumab treatment in breast cancer using bioinformatics analysis. PMID:30181805
Integration of gene interaction information into a reweighted random survival forest approach for accurate survival prediction and survival biomarker discovery. PMID:30181543
Transcriptomic Insights Into the Growth Phase- and Sugar-Associated Changes in the Exopolysaccharide Production of a High EPS-Producing Streptococcus thermophilus ASCC 1275. PMID:30177921
Molecular mechanism of activated T cells in breast cancer. PMID:30174439
Sex dependent impact of gestational stress on predisposition to eating disorders and metabolic disease. PMID:30174229
Low nadir CD4+ T-cell counts predict gut dysbiosis in HIV-1 infection. PMID:30171206
CEA: Combination-based gene set functional enrichment analysis. PMID:30166636
A potential central role of Thaumarchaeota in N-Cycling in a semi-arid environment, Fort Stanton Cave, Snowy River passage, New Mexico, USA. PMID:30165514
Pathway-Based Drug Repositioning for Breast Cancer Molecular Subtypes. PMID:30158869
Differentially expressed proteins in positive versus negative HNSCC lymph nodes. PMID:30157864
An in-silico study examining the induction of apoptosis by Cryptotanshinone in metastatic melanoma cell lines. PMID:30157799
Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases. PMID:30157260
Mechanisms of Huangqi Decoction Granules () on Hepatitis B Cirrhosis Patients Based on RNA-Sequencing. PMID:30155678
Disruption of mesoderm formation during cardiac differentiation due to developmental exposure to 13-cis-retinoic acid. PMID:30154523
Circular RNAs hsa_circ_0032462, hsa_circ_0028173, hsa_circ_0005909 are predicted to promote CADM1 expression by functioning as miRNAs sponge in human osteosarcoma. PMID:30153287
Comparative transcriptome of neurons after oxygen-glucose deprivation: Potential differences in neuroprotection versus reperfusion. PMID:30152713
Narciclasine induces autophagy-dependent apoptosis in triple-negative breast cancer cells by regulating the AMPK-ULK1 axis. PMID:30152053
Identification of key genes and pathways using bioinformatics analysis in septic shock children. PMID:30147344
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma. PMID:30143675
Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions. PMID:30143657
Podocyte-Specific Induction of Krüppel-Like Factor 15 Restores Differentiation Markers and Attenuates Kidney Injury in Proteinuric Kidney Disease. PMID:30143559
Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans. PMID:30140739
Differential effects of selective and non-selective cyclooxygenase inhibitors on fecal microbiota in adult horses. PMID:30138339
Effects of bone marrow-derived mesenchymal stromal cells on gene expression in human alveolar type II cells exposed to TNF-α, IL-1β, and IFN-γ. PMID:30136410
Alterations of 63 hub genes during lingual carcinogenesis in C57BL/6J mice. PMID:30135512
MAIT cells protect against pulmonary Legionella longbeachae infection. PMID:30135490
Prediction of key genes and pathways involved in trastuzumab-resistant gastric cancer. PMID:30134903
Transcriptome analysis of Valsa mali reveals its response mechanism to the biocontrol actinomycete Saccharothrix yanglingensis Hhs.015. PMID:30134836
Bioinformatics analyses of significant genes, related pathways and candidate prognostic biomarkers in glioblastoma. PMID:30132538
Improved Brassica rapa reference genome by single-molecule sequencing and chromosome conformation capture technologies. PMID:30131865
Developmental effects of maternal smoking during pregnancy on the human frontal cortex transcriptome. PMID:30131587
Comprehensive analysis of the whole coding and non-coding RNA transcriptome expression profiles and construction of the circRNA-lncRNA co-regulated ceRNA network in laryngeal squamous cell carcinoma. PMID:30128795
A linked organ-on-chip model of the human neurovascular unit reveals the metabolic coupling of endothelial and neuronal cells. PMID:30125269
Sex-specific gene and pathway modeling of inherited glioma risk. PMID:30124908
Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma. PMID:30124166
Using Supervised Learning Methods for Gene Selection in RNA-Seq Case-Control Studies. PMID:30123241
Gene Expression Response to Sea Lice in Atlantic Salmon Skin: RNA Sequencing Comparison Between Resistant and Susceptible Animals. PMID:30123239
Genomic Analysis of the Insect-Killing Fungus Beauveria bassiana JEF-007 as a Biopesticide. PMID:30120392
Stearoly-CoA desaturase 1 differentiates early and advanced dengue virus infections and determines virus particle infectivity. PMID:30118512
Analysis of the miRNA and mRNA involved in osteogenesis of adipose-derived mesenchymal stem cells. PMID:30116362
PRSS8 suppresses colorectal carcinogenesis and metastasis. PMID:30115975
Photosynthetic Accumulation of Lutein in Auxenochlorella protothecoides after Heterotrophic Growth. PMID:30115823
Identification of key genes and pathways for esophageal squamous cell carcinoma by bioinformatics analysis. PMID:30112053
Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis). PMID:30111282
Transcriptome sequencing identifies key pathways and genes involved in gastric adenocarcinoma. PMID:30106143
Proteomics: Clinical and research applications in respiratory diseases. PMID:30105802
Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities. PMID:30105201
Transcriptome profiling of anti-müllerian hormone treated preantral/small antral mouse ovary follicles. PMID:30100987
Identification of prognostic risk factors for esophageal adenocarcinoma using bioinformatics analysis. PMID:30100738
Cooperative Metabolic Adaptations in the Host Can Favor Asymptomatic Infection and Select for Attenuated Virulence in an Enteric Pathogen. PMID:30100182
Machine learning and feature selection for drug response prediction in precision oncology applications. PMID:30097794
Autophagy upregulation as a possible mechanism of arsenic induced diabetes. PMID:30097599
Global metabolomic responses in urine from atm deficient mice in response to LD50/30 gamma irradiation doses. PMID:30095186
Genome-wide identification of lipoxygenase gene family in cotton and functional characterization in response to abiotic stresses. PMID:30092779
Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers. PMID:30092766
Prediction of Acquired Taxane Resistance Using a Personalized Pathway-Based Machine Learning Method. PMID:30092623
Genome wide association mapping of agro-morphological traits among a diverse collection of finger millet (Eleusine coracana L.) genotypes using SNP markers. PMID:30092057
BART: bioinformatics array research tool. PMID:30089462
Integrative analysis of the inter-tumoral heterogeneity of triple-negative breast cancer. PMID:30087365
SNP discovery of Korean short day onion inbred lines using double digest restriction site-associated DNA sequencing. PMID:30086138
Constructing disease onset signatures using multi-dimensional network-structured biomarkers. PMID:30084874
Long-Term Land Use Affects Phosphorus Speciation and the Composition of Phosphorus Cycling Genes in Agricultural Soils. PMID:30083148
Red fox genome assembly identifies genomic regions associated with tame and aggressive behaviours. PMID:30082739
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Contribution of Inhibitor of Differentiation and Estrogenic Endocrine Disruptors to Neurocognitive Disorders. PMID:30081481
Identification of transcription factors responsible for dysregulated networks in human osteoarthritis cartilage by global gene expression analysis. PMID:30081074
Gut Microbial Carbohydrate Metabolism Hinders Weight Loss in Overweight Adults Undergoing Lifestyle Intervention With a Volumetric Diet. PMID:30077203
Transcriptome analysis highlights key differentially expressed genes involved in cellulose and lignin biosynthesis of sugarcane genotypes varying in fiber content. PMID:30072760
Analysis of Candidate Idarubicin Drug Resistance Genes in MOLT-3 Cells Using Exome Nuclear DNA. PMID:30071629
Culture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size. PMID:30068938
A study on multi-omic oscillations in Escherichia coli metabolic networks. PMID:30066640
Effects of Diacetyl Flavoring Exposure in Mice Metabolism. PMID:30065948
Single-cell transcriptomic analyses reveal distinct dorsal/ventral pancreatic programs. PMID:30065074
Investigation on the Evolutionary Relation of Diverse Polyhydroxyalkanoate Gene Clusters in Betaproteobacteria. PMID:30062554
Integration of RNAi and RNA-seq Reveals the Immune Responses of Epinephelus coioides to sigX Gene of Pseudomonas plecoglossicida. PMID:30061893
Explaining cancer type specific mutations with transcriptomic and epigenomic features in normal tissues. PMID:30061703
A network pharmacology-based approach to analyse potential targets of traditional herbal formulas: An example of Yu Ping Feng decoction. PMID:30061691
Discovery and control of culturable and viable but non-culturable cells of a distinctive Lactobacillus harbinensis strain from spoiled beer. PMID:30061572
Elastic Net Constrained Stereotype Logit Model for Ordered Categorical Data. PMID:30058001
A comparison of computationally predicted functional metagenomes and microarray analysis for microbial P cycle genes in a unique basalt-soil forest. PMID:30057749
ADReCS-Target: target profiles for aiding drug safety research and application. PMID:30053268
Target enrichment sequencing of 307 germplasm accessions identified ancestry of ancient and modern hybrids and signatures of adaptation and selection in sugarcane (Saccharum spp.), a 'sweet' crop with 'bitter' genomes. PMID:30051590
Effect of Freeze-Thaw on a Midtemperate Soil Bacterial Community and the Correlation Network of Its Members. PMID:30050943
Machine Learning on Human Muscle Transcriptomic Data for Biomarker Discovery and Tissue-Specific Drug Target Identification. PMID:30050560
Glucose promotes cell growth by suppressing branched-chain amino acid degradation. PMID:30050148
Differentially expressed microRNAs in experimental cerebral malaria and their involvement in endocytosis, adherens junctions, FoxO and TGF-β signalling pathways. PMID:30050092
In silico identification and computational characterization of endogenous small interfering RNAs from diverse grapevine tissues and stages. PMID:30047108
Mitofusin2 Induces Cell Autophagy of Pancreatic Cancer through Inhibiting the PI3K/Akt/mTOR Signaling Pathway. PMID:30046371
Genome sequence and genetic transformation of a widely distributed and cultivated poplar. PMID:30044051
Neuronal activity induces glutathione metabolism gene expression in astrocytes. PMID:30043519
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Identification of genes associated with stress tolerance in moth bean [Vigna aconitifolia (Jacq.) Marechal], a stress hardy crop. PMID:30042612
Associations Between Nutrition, Gut Microbiome, and Health in A Novel Nonhuman Primate Model. PMID:30042392
Dynamics of Gut Microbiota Diversity During the Early Development of an Avian Host: Evidence From a Cross-Foster Experiment. PMID:30038608
Comparative transcriptome analysis of field- and chamber-grown samples of Colobanthus quitensis (Kunth) Bartl, an Antarctic flowering plant. PMID:30038328
Gene alterations in monocytes are pathogenic factors for immunoglobulin a nephropathy by bioinformatics analysis of microarray data. PMID:30029622
Exploring miRNA-mRNA regulatory network in cardiac pathology in Na+/H+ exchanger isoform 1 transgenic mice. PMID:30029588
Comparative Study of Different Diets-Induced NAFLD Models of Zebrafish. PMID:30026731
Co-expression network of transcription factors reveal ethylene-responsive element-binding factor as key regulator of wood phenotype in Eucalyptus tereticornis. PMID:30023147
InDePTH: detection of hub genes for developing gene expression networks under anticancer drug treatment. PMID:30018738
16S rRNA Long-Read Sequencing of the Granulation Tissue from Nonsmokers and Smokers-Severe Chronic Periodontitis Patients. PMID:30013983
Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome. PMID:30013164
Refining a steroidogenic model: an analysis of RNA-seq datasets from insect prothoracic glands. PMID:30005604
E47 Governs the MYC-CDKN1B/p27KIP1-RB Network to Growth Arrest PDA Cells Independent of CDKN2A/p16INK4A and Wild-Type p53. PMID:30003124
Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells. PMID:30001349
High-Throughput Metabolomics by 1D NMR. PMID:29999221
A Computational Systems Pharmacology Approach to Investigate Molecular Mechanisms of Herbal Formula Tian-Ma-Gou-Teng-Yin for Treatment of Alzheimer's Disease. PMID:29997503
Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. PMID:29997476
Molecular genetic overlap between migraine and major depressive disorder. PMID:29995844
Predicting Potential Drugs for Breast Cancer based on miRNA and Tissue Specificity. PMID:29989066
PathCORE-T: identifying and visualizing globally co-occurring pathways in large transcriptomic compendia. PMID:29988723
An integrated analysis of genome-wide DNA methylation and gene expression data in hepatocellular carcinoma. PMID:29988590
A vascular endothelial growth factor receptor gene variant is associated with susceptibility to acute respiratory distress syndrome. PMID:29987654
Comparative molecular characterization of typical and exceptional responders in glioblastoma. PMID:29983870
Comparison of metabolite networks from four German population-based studies. PMID:29982629
Transcriptional responses of soybean roots to colonization with the root endophytic fungus Piriformospora indica reveals altered phenylpropanoid and secondary metabolism. PMID:29980739
A transcriptome study on Macrobrachium nipponense hepatopancreas experimentally challenged with white spot syndrome virus (WSSV). PMID:29979781
KBase: The United States Department of Energy Systems Biology Knowledgebase. PMID:29979655
PASI: A novel pathway method to identify delicate group effects. PMID:29975740
Identification of Antifungal Targets Based on Computer Modeling. PMID:29973534
A novel gene-expression-signature-based model for prediction of response to Tripterysium glycosides tablet for rheumatoid arthritis patients. PMID:29973208
Development and validation of an updated computational model of Streptomyces coelicolor primary and secondary metabolism. PMID:29973148
Maternal obesity has sex-dependent effects on insulin, glucose and lipid metabolism and the liver transcriptome in young adult rat offspring. PMID:29972240
Viruses of the Nahant Collection, characterization of 251 marine Vibrionaceae viruses. PMID:29969110
Plasmids of Psychrotolerant Polaromonas spp. Isolated From Arctic and Antarctic Glaciers - Diversity and Role in Adaptation to Polar Environments. PMID:29967598
Identification of key pathways and genes in the progression of cervical cancer using bioinformatics analysis. PMID:29963176
cpubi4 Is Essential for Development and Virulence in Chestnut Blight Fungus. PMID:29963030
Bioinformatics analysis of aberrantly methylated-differentially expressed genes and pathways in hepatocellular carcinoma. PMID:29962817
Four Key Steps Control Glycolytic Flux in Mammalian Cells. PMID:29960885
Identification of a noncoding RNA‑mediated gene pair‑based regulatory module in Alzheimer's disease. PMID:29956760
Methanotrophy across a natural permafrost thaw environment. PMID:29955139
Single SNP- and pathway-based genome-wide association studies for beak deformity in chickens using high-density 600K SNP arrays. PMID:29954329
DynSig: Modelling Dynamic Signaling Alterations along Gene Pathways for Identifying Differential Pathways. PMID:29954150
Improved pathway reconstruction from RNA interference screens by exploiting off-target effects. PMID:29950000
Expression of the Circadian Clock Gene BMAL1 Positively Correlates With Antitumor Immunity and Patient Survival in Metastatic Melanoma. PMID:29946530
Time Series Analysis of the Microbiota of Children Suffering From Acute Infectious Diarrhea and Their Recovery After Treatment. PMID:29946306
Blood Serum From Head and Neck Squamous Cell Carcinoma Patients Induces Altered MicroRNA and Target Gene Expression Profile in Treated Cells. PMID:29942793
Analysis of Gene Expression Variance in Schizophrenia Using Structural Equation Modeling. PMID:29942251
Quantitative proteomic analysis using iTRAQ to identify salt-responsive proteins during the germination stage of two Medicago species. PMID:29934583
High-quality assembly of the reference genome for scarlet sage, Salvia splendens, an economically important ornamental plant. PMID:29931210
Potential candidate treatment agents for targeting of cholangiocarcinoma identified by gene expression profile analysis. PMID:29930804
Integrated multi-omics data analysis identifying novel drug sensitivity-associated molecular targets of hepatocellular carcinoma cells. PMID:29930714
Embracing the Blessing of Dimensionality in Factor Models. PMID:29930437
Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest. PMID:29930066
Draft Genome Sequence of Klebsiella sp. Strain C31 Isolated from a Malaysian Tropical Peat Swamp Forest. PMID:29930065
Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest. PMID:29930031
Exploring the molecular pathogenesis associated with T-cell prolymphocytic leukemia based on a comprehensive bioinformatics analysis. PMID:29928415
Dysregulated genes targeted by microRNAs and metabolic pathways in bladder cancer revealed by bioinformatics methods. PMID:29928337
Genome-wide methylomic and transcriptomic analyses identify subtype-specific epigenetic signatures commonly dysregulated in glioma stem cells and glioblastoma. PMID:29927689
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity. PMID:29925878
Molecular Characterization and Putative Pathogenic Pathways of Tuberous Sclerosis Complex-Associated Renal Cell Carcinoma. PMID:29925043
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PMID:29924794
Long-read sequencing and de novo genome assembly of Ammopiptanthus nanus, a desert shrub. PMID:29917074
Impaired β-cell glucokinase as an underlying mechanism in diet-induced diabetes. PMID:29915142
Dynamic elementary mode modelling of non-steady state flux data. PMID:29914483
CircadiOmics: circadian omic web portal. PMID:29912458
Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed. PMID:29912209
A Single-Cell Transcriptome Atlas of the Aging Drosophila Brain. PMID:29909982
Molecular chaperoning helps safeguarding mitochondrial integrity and motor functions in the Sahara silver ant Cataglyphis bombycina. PMID:29907755
The comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut. PMID:29906260
LncRNA expression profiling of BMSCs in osteonecrosis of the femoral head associated with increased adipogenic and decreased osteogenic differentiation. PMID:29904151
Deep Transcriptomic Analysis of Black Rockfish (Sebastes schlegelii) Provides New Insights on Responses to Acute Temperature Stress. PMID:29904092
MiR-374b Promotes Proliferation and Inhibits Apoptosis of Human GIST Cells by Inhibiting PTEN through Activation of the PI3K/Akt Pathway. PMID:29902839
Novel Metabolomic Comparison of Arterial and Jugular Venous Blood in Severe Adult Traumatic Brain Injury Patients and the Impact of Pentobarbital Infusion. PMID:29901425
Weighted gene co‑expression network analysis in identification of key genes and networks for ischemic‑reperfusion remodeling myocardium. PMID:29901145
Screening genes associated with elevated neutrophil‑to‑lymphocyte ratio in chronic heart failure. PMID:29901123
Metabolite extraction for high-throughput FTICR-MS-based metabolomics of grapevine leaves. PMID:29900113
Immunome differences between porcine ileal and jejunal Peyer's patches revealed by global transcriptome sequencing of gut-associated lymphoid tissues. PMID:29899562
Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. PMID:29899345
The microRNA expression signature of CD4+ T cells in the transition of brucellosis into chronicity. PMID:29897958
BioSankey: Visualization of Microbial Communities Over Time. PMID:29897884
A systematic approach to identify therapeutic effects of natural products based on human metabolite information. PMID:29897322
Metagenomics Reveals the Influence of Land Use and Rain on the Benthic Microbial Communities in a Tropical Urban Waterway. PMID:29896568
Comparative transcriptome analysis of dikaryotic mycelia and mature fruiting bodies in the edible mushroom Lentinula edodes. PMID:29895888
Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PMID:29894496
Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. PMID:29892840
Genetics of alternative splicing evolution during sunflower domestication. PMID:29891718
Blazing Signature Filter: a library for fast pairwise similarity comparisons. PMID:29890950
Tocotrienol-Rich Fraction of Palm Oil Improves Behavioral Impairments and Regulates Metabolic Pathways in AβPP/PS1 Mice. PMID:29889072
CATCH-KB: Establishing a Pharmacogenomics Variant Repository for Chemotherapy-Induced Cardiotoxicity. PMID:29888066
REDESIGN: RDF-based Differential Signaling Framework for Precision Medicine Analytics. PMID:29888036
CowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software. PMID:29887853
Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization. PMID:29878151
MetQy-an R package to query metabolic functions of genes and genomes. PMID:29878056
Data on genome sequencing, analysis and annotation of a pathogenic Bacillus cereus 062011msu. PMID:29876371
Influence of Glucose Availability and CRP Acetylation on the Genome-Wide Transcriptional Response of Escherichia coli: Assessment by an Optimized Factorial Microarray Analysis. PMID:29875739
Chemotypes and Biomarkers of Seven Species of New Caledonian Liverworts from the Bazzanioideae Subfamily. PMID:29874780
The proteome of neurofilament-containing protein aggregates in blood. PMID:29872749
Hypoxia-derived exosomes induce putative altered pathways in biosynthesis and ion regulatory channels in glioblastoma cells. PMID:29872742
Network-based machine learning and graph theory algorithms for precision oncology. PMID:29872707
Regulatory role of resveratrol, a microRNA-controlling compound, in HNRNPA1 expression, which is associated with poor prognosis in breast cancer. PMID:29872500
Construction of a specific SVM classifier and identification of molecular markers for lung adenocarcinoma based on lncRNA-miRNA-mRNA network. PMID:29872324
RNA Sequencing Reveals Novel Transcripts from Sympathetic Stellate Ganglia During Cardiac Sympathetic Hyperactivity. PMID:29872217
Multidrug resistant pathogens respond differently to the presence of co-pathogen, commensal, probiotic and host cells. PMID:29872152
HNRNPLL stabilizes mRNA for DNA replication proteins and promotes cell cycle progression in colorectal cancer cells. PMID:29869816
Proteomics Versus Clinical Data and Stochastic Local Search Based Feature Selection for Acute Myeloid Leukemia Patients' Classification. PMID:29869179
Global untargeted serum metabolomic analyses nominate metabolic pathways responsive to loss of expression of the orphan metallo β-lactamase, MBLAC1. PMID:29868674
ARMOUR - A Rice miRNA: mRNA Interaction Resource. PMID:29868062
Evaluating the Genetics of Common Variable Immunodeficiency: Monogenetic Model and Beyond. PMID:29867916
Metagenomic Approaches to Investigate the Contribution of the Vineyard Environment to the Quality of Wine Fermentation: Potentials and Difficulties. PMID:29867889
Metabolome changes are induced in the arbuscular mycorrhizal fungus Gigaspora margarita by germination and by its bacterial endosymbiont. PMID:29860608
Systematic Identification of Druggable Epithelial-Stromal Crosstalk Signaling Networks in Ovarian Cancer. PMID:29860390
Mechanism-based Pharmacovigilance over the Life Sciences Linked Open Data Cloud. PMID:29854169
p53 Mediates Vast Gene Expression Changes That Contribute to Poor Chemotherapeutic Response in a Mouse Model of Breast Cancer. PMID:29852458
Identification of key genes in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. PMID:29851858
Pathway-structured predictive modeling for multi-level drug response in multiple myeloma. PMID:29850860
Fermentative Spirochaetes mediate necromass recycling in anoxic hydrocarbon-contaminated habitats. PMID:29849169
Metabolic co-dependence drives the evolutionarily ancient Hydra-Chlorella symbiosis. PMID:29848439
Chytridiomycosis causes catastrophic organism-wide metabolic dysregulation including profound failure of cellular energy pathways. PMID:29844538
Reconstruction of a genome-scale metabolic model for Actinobacillus succinogenes 130Z. PMID:29843739
Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. PMID:29807988
Alternative splicing events implicated in carcinogenesis and prognosis of colorectal cancer. PMID:29805701
An ERK-Dependent Feedback Mechanism Prevents Hematopoietic Stem Cell Exhaustion. PMID:29804890
Comparative gene expression analysis after exposure to 123I-iododeoxyuridine, γ- and α-radiation-potential biomarkers for the discrimination of radiation qualities. PMID:29800458
eXpression2Kinases (X2K) Web: linking expression signatures to upstream cell signaling networks. PMID:29800326
Metabolic reconstruction and experimental verification of glucose utilization in Desulfurococcus amylolyticus DSM 16532. PMID:29797222
Association of increased primary breast tumor AGR2 with decreased disease-specific survival. PMID:29796176
Transcriptomic response of breast cancer cells to anacardic acid. PMID:29795261
Identification of differentially expressed genes in childhood asthma. PMID:29794786
Genes Activated by Vibrio cholerae upon Exposure to Caenorhabditis elegans Reveal the Mannose-Sensitive Hemagglutinin To Be Essential for Colonization. PMID:29794057
Putative vaccine candidates and drug targets identified by reverse vaccinology and subtractive genomics approaches to control Haemophilus ducreyi, the causative agent of chancroid. PMID:29792307
Interplay between gut microbiota metabolism and inflammation in HIV infection. PMID:29789624
Metabolic Footprinting of Fermented Milk Consumption in Serum of Healthy Men. PMID:29788433
WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update. PMID:29788377
Pharmacophore modeling for identification of anti-IGF-1R drugs and in-vitro validation of fulvestrant as a potential inhibitor. PMID:29787591
A Metabolomic Serum Signature from Nonhuman Primates Treated with a Radiation Countermeasure, Gamma-tocotrienol, and Exposed to Ionizing Radiation. PMID:29787425
Identification of potential crucial genes and pathways associated with vein graft restenosis based on gene expression analysis in experimental rabbits. PMID:29785339
A genome-wide cross-trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases. PMID:29785011
A workflow for the integrative transcriptomic description of molecular pathology and the suggestion of normalizing compounds, exemplified by Parkinson's disease. PMID:29784986
Differential Gene Expression in Prostate Tissue According to Ejaculation Frequency. PMID:29784192
Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model. PMID:29784056
Multi-omic network-based interrogation of rat liver metabolism following gastric bypass surgery featuring SWATH proteomics. PMID:29780857
Establishing an innovative carbohydrate metabolic pathway for efficient production of 2-keto-L-gulonic acid in Ketogulonicigenium robustum initiated by intronic promoters. PMID:29778095
p300-Mediated Lysine 2-Hydroxyisobutyrylation Regulates Glycolysis. PMID:29775581
RNA-Seq and UHPLC-Q-TOF/MS Based Lipidomics Study in Lysiphlebia japonica. PMID:29773840
Identification of novel drug targets in bovine respiratory disease: an essential step in applying biotechnologic techniques to develop more effective therapeutic treatments. PMID:29765203
Comprehensive and integrative analysis identifies microRNA-106 as a novel non-invasive biomarker for detection of gastric cancer. PMID:29764446
Ouroboros resembling competitive endogenous loop (ORCEL) in circular RNAs revealed through transcriptome sequencing dataset analysis. PMID:29764361
An intersection network based on combining SNP coassociation and RNA coexpression networks for feed utilization traits in Japanese Black cattle. PMID:29762780
MRMAssayDB: an integrated resource for validated targeted proteomics assays. PMID:29762640
The influence of diet and environment on the gut microbial community of field crickets. PMID:29760910
Identification of potential crucial genes and construction of microRNA-mRNA negative regulatory networks in osteosarcoma. PMID:29760609
Temperature regulates NF-κB dynamics and function through timing of A20 transcription. PMID:29760065
AlloFinder: a strategy for allosteric modulator discovery and allosterome analyses. PMID:29757429
Transcriptome based individualized therapy of refractory pediatric sarcomas: feasibility, tolerability and efficacy. PMID:29755686
The Algicidal Fungus Trametes versicolor F21a Eliminating Blue Algae via Genes Encoding Degradation Enzymes and Metabolic Pathways Revealed by Transcriptomic Analysis. PMID:29755442
Transcription Factor Co-expression Networks of Adipose RNA-Seq Data Reveal Regulatory Mechanisms of Obesity. PMID:29755291
Targeting TWIST1 through loss of function inhibits tumorigenicity of human glioblastoma. PMID:29754406
Starch content differences between two sweet potato accessions are associated with specific changes in gene expression. PMID:29754269
Discovering novel SNPs that are correlated with patient outcome in a Singaporean cancer patient cohort treated with gemcitabine-based chemotherapy. PMID:29751792
Green Tea Liquid Consumption Alters the Human Intestinal and Oral Microbiome. PMID:29750437
Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia. PMID:29749511
Differential plasma microvesicle and brain profiles of microRNA in experimental cerebral malaria. PMID:29747626
Predicting multi-level drug response with gene expression profile in multiple myeloma using hierarchical ordinal regression. PMID:29747599
Identification of novel drug targets for diamond-blackfan anemia based on RPS19 gene mutation using protein-protein interaction network. PMID:29745857
Automated transition analysis of activated gene regulation during diauxic nutrient shift in Escherichia coli and adipocyte differentiation in mouse cells. PMID:29745848
Multi-target drug repositioning by bipartite block-wise sparse multi-task learning. PMID:29745839
Gene expression profiles and pathway enrichment analysis of human osteosarcoma cells exposed to sorafenib. PMID:29744300
Transcriptomic analysis of crustacean molting gland (Y-organ) regulation via the mTOR signaling pathway. PMID:29743490
Scalable Bayesian variable selection for structured high-dimensional data. PMID:29738602
Plastid genome analysis of three Nemaliophycidae red algal species suggests environmental adaptation for iron limited habitats. PMID:29738547
Identifying Cancer Specific Driver Modules Using a Network-Based Method. PMID:29738475
Metabolic Reprogramming of Vibrio cholerae Impaired in Respiratory NADH Oxidation Is Accompanied by Increased Copper Sensitivity. PMID:29735761
Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes. PMID:29734356
Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease. PMID:29732173
Non-invasive tumor genotyping using radiogenomic biomarkers, a systematic review and oncology-wide pathway analysis. PMID:29732009
A Large-Scale Comparative Metagenomic Study Reveals the Functional Interactions in Six Bloom-Forming Microcystis-Epibiont Communities. PMID:29731741
Integration of Enhancer-Promoter Interactions with GWAS Summary Results Identifies Novel Schizophrenia-Associated Genes and Pathways. PMID:29728367
Whole-genome de novo sequencing reveals unique genes that contributed to the adaptive evolution of the Mikado pheasant. PMID:29722814
Histone acetylation maps in aged mice developmentally exposed to lead: epigenetic drift and Alzheimer-related genes. PMID:29722544
Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism. PMID:29721834
Identification of key gene modules for human osteosarcoma by co-expression analysis. PMID:29720180
Induced PTF1a expression in pancreatic ductal adenocarcinoma cells activates acinar gene networks, reduces tumorigenic properties, and sensitizes cells to gemcitabine treatment. PMID:29719936
Proteome-wide mapping of PQS-interacting proteins in Pseudomonas aeruginosa. PMID:29719702
PVCbase: an integrated web resource for the PVC bacterial proteomes. PMID:29718141
Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups. PMID:29717207
Bioinformatics-based identification of potential microRNA biomarkers in frequent and non-frequent exacerbators of COPD. PMID:29713155
Structural basis for energy transduction by respiratory alternative complex III. PMID:29712914
Characterization of miRNA and their target gene during chicken embryo skeletal muscle development. PMID:29707110
De novo Assembly of the Burying Beetle Nicrophorus orbicollis (Coleoptera: Silphidae) Transcriptome Across Developmental Stages with Identification of Key Immune Transcripts. PMID:29707046
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis. PMID:29706661
Necroptosis promotes cell-autonomous activation of proinflammatory cytokine gene expression. PMID:29703889
Cholesterol synthesis pathway genes in prostate cancer are transcriptionally downregulated when tissue confounding is minimized. PMID:29703166
Molecular mechanisms of an antimicrobial peptide piscidin (Lc-pis) in a parasitic protozoan, Cryptocaryon irritans. PMID:29703140
Complete Genome Sequence of Multiple-Antibiotic-Resistant Streptococcus parauberis Strain SPOF3K, Isolated from Diseased Olive Flounder (Paralichthys olivaceus). PMID:29700142
Integrative metabolomics and transcriptomics signatures of clinical tolerance to Plasmodium vivax reveal activation of innate cell immunity and T cell signaling. PMID:29698924
Mut2Vec: distributed representation of cancerous mutations. PMID:29697361
Oral microbiota reveals signs of acculturation in Mexican American women. PMID:29694348
Analysis of NFKB2‑mediated regulation of mechanisms underlying the development of Hodgkin's lymphoma. PMID:29693141
Metabolic characterization of isocitrate dehydrogenase (IDH) mutant and IDH wildtype gliomaspheres uncovers cell type-specific vulnerabilities. PMID:29692895
iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. PMID:29692801
Molecular basis of autotrophic vs mixotrophic growth in Chlorella sorokiniana. PMID:29691462
Adaptive response of neonatal sepsis-derived Group B Streptococcus to bilirubin. PMID:29691444
RNA-Seq analysis of interferon inducible p204-mediated network in anti-tumor immunity. PMID:29691417
The Gastrodia elata genome provides insights into plant adaptation to heterotrophy. PMID:29691383
Effect of early calf-hood nutrition on the transcriptomic profile of subcutaneous adipose tissue in Holstein-Friesian bulls. PMID:29690861
miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions. PMID:29688364
Chromosome-scale assembly of the Monopterus genome. PMID:29688346
Microarray Analysis of the Molecular Mechanism Involved in Parkinson's Disease. PMID:29686831
Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis. PMID:29686365
Transcriptomic insights into citrus segment membrane's cell wall components relating to fruit sensory texture. PMID:29685103
One for all and all for One: Improving replication of genetic studies through network diffusion. PMID:29684019
De Novo Sequencing of a Sparassis latifolia Genome and Its Associated Comparative Analyses. PMID:29682127
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs. PMID:29678199
An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. PMID:29677511
Systematic analysis and comparison of the PHD-Finger gene family in Chinese pear (Pyrus bretschneideri) and its role in fruit development. PMID:29675811
Comparative High-Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell-Line-Specific Pathway Dysregulation. PMID:29674676
Complete Genome Sequence of Agrobacterium tumefaciens 1D1609. PMID:29674541
Possible Molecular Markers for the Diagnosis of Pancreatic Ductal Adenocarcinoma. PMID:29671412
Discovery of Boolean metabolic networks: integer linear programming based approach. PMID:29671395
A Novel S100A8/A9 Induced Fingerprint of Mesenchymal Stem Cells associated with Enhanced Wound Healing. PMID:29670130
PPARγ Contributes to Immunity Induced by Cancer Cell Vaccines That Secrete GM-CSF. PMID:29669721
Pathways of topological rank analysis (PoTRA): a novel method to detect pathways involved in hepatocellular carcinoma. PMID:29666752
Pan-cancer analysis of somatic mutations and transcriptomes reveals common functional gene clusters shared by multiple cancer types. PMID:29662161
miR-148b-3p functions as a tumor suppressor in GISTs by directly targeting KIT. PMID:29661252
Transcriptomic Analysis of Flower Bud Differentiation in Magnolia sinostellata. PMID:29659525
Comparative microRNA-seq Analysis Depicts Candidate miRNAs Involved in Skin Color Differentiation in Red Tilapia. PMID:29659520
Analysis of potential genes and pathways associated with the colorectal normal mucosa-adenoma-carcinoma sequence. PMID:29659199
Key signaling pathways, genes and transcription factors associated with hepatocellular carcinoma. PMID:29658607
Screening for implicated genes in colorectal cancer using whole‑genome gene expression profiling. PMID:29658574
Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction. PMID:29658273
Genome Reduction in Psychromonas Species within the Gut of an Amphipod from the Ocean's Deepest Point. PMID:29657971
Detecting Disease Specific Pathway Substructures through an Integrated Systems Biology Approach. PMID:29657291
Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle. PMID:29654251
Dietary supplementation with flaxseed meal and oat hulls modulates intestinal histomorphometric characteristics, digesta- and mucosa-associated microbiota in pigs. PMID:29651010
Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro-inflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation. PMID:29649237
Bioinformatic analysis reveals the key pathways and genes in early-onset breast cancer. PMID:29644522
Proteomic profiling of human cancer pseudopodia for the identification of anti-metastatic drug candidates. PMID:29643415
A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition. PMID:29636512
Proteomic approach to understand the molecular physiology of symbiotic interaction between Piriformospora indica and Brassica napus. PMID:29636503
ACTH and PMX53 recover synaptic transcriptome alterations in a rat model of infantile spasms. PMID:29636502
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. PMID:29636439
The latent geometry of the human protein interaction network. PMID:29635317
The draft genome sequence of forest musk deer (Moschus berezovskii). PMID:29635287
Cox-nnet: An artificial neural network method for prognosis prediction of high-throughput omics data. PMID:29634719
Profiling expression of coding genes, long noncoding RNA, and circular RNA in lung adenocarcinoma by ribosomal RNA-depleted RNA sequencing. PMID:29632808
Oligotrophic wetland sediments susceptible to shifts in microbiomes and mercury cycling with dissolved organic matter addition. PMID:29632744
Oncogenic Signaling Pathways in The Cancer Genome Atlas. PMID:29625050
Performance comparison of three DNA extraction kits on human whole-exome data from formalin-fixed paraffin-embedded normal and tumor samples. PMID:29621323
Integrated analysis of the gene expression profile and DNA methylation profile of obese patients with type 2 diabetes. PMID:29620215
A multi-landing pad DNA integration platform for mammalian cell engineering. PMID:29617873
Liver regeneration during the associating liver partition and portal vein ligation for staged hepatectomy procedure in Sus scrofa is positively modulated by stem cells. PMID:29616108
The Skin Microbiome of the Neotropical Frog Craugastor fitzingeri: Inferring Potential Bacterial-Host-Pathogen Interactions From Metagenomic Data. PMID:29615997
Distinct Metabolic features differentiating FLT3-ITD AML from FLT3-WT childhood Acute Myeloid Leukemia. PMID:29615816
A comparative analysis of rod bipolar cell transcriptomes identifies novel genes implicated in night vision. PMID:29615777
Metabolomics coupled with pathway analysis characterizes metabolic changes in response to BDE-3 induced reproductive toxicity in mice. PMID:29615664
Lipid accumulation in human breast cancer cells injured by iron depletors. PMID:29615075
Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. PMID:29611031
A computational biology approach of a genome-wide screen connected miRNAs to obesity and type 2 diabetes. PMID:29605715
Transcriptomic analysis reveals inflammatory and metabolic pathways that are regulated by renal perfusion pressure in the outer medulla of Dahl-S rats. PMID:29602296
From Network Analysis to Functional Metabolic Modeling of the Human Gut Microbiota. PMID:29600286
Identification of key genes and miRNAs associated with carotid atherosclerosis based on mRNA-seq data. PMID:29595698
Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin. PMID:29593680
Pathway-Based Analysis of Genome-Wide Association Data Identified SNPs in HMMR as Biomarker for Chemotherapy- Induced Neutropenia in Breast Cancer Patients. PMID:29593529
Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites. PMID:29593303
Genomic epidemiology of the UK outbreak of the emerging human fungal pathogen Candida auris. PMID:29593275
Constraints on signaling network logic reveal functional subgraphs on Multiple Myeloma OMIC data. PMID:29589566
Transcriptome-wide mapping of signaling pathways and early immune responses in lumpfish leukocytes upon in vitro bacterial exposure. PMID:29588496
Comparative genome-wide analysis of extracellular small RNAs from the mucormycosis pathogen Rhizopus delemar. PMID:29588481
Confirmation of a metastasis-specific microRNA signature in primary colon cancer. PMID:29588449
Biosynthesis of redox-active metabolites in response to iron deficiency in plants. PMID:29581584
Pyruvate dehydrogenase complex and lactate dehydrogenase are targets for therapy of acute liver failure. PMID:29580866
Gene microarray analysis of lncRNA and mRNA expression profiles in patients with high‑grade ovarian serous cancer. PMID:29577163
Systematic Characterization of Stress-Induced RNA Granulation. PMID:29576526
Impact of spatial organization on a novel auxotrophic interaction among soil microbes. PMID:29572468
Key genes and regulatory networks involved in the initiation, progression and invasion of colorectal cancer. PMID:29568567
Sigmoid colon mucosal gene expression supports alterations of neuronal signaling in irritable bowel syndrome with constipation. PMID:29565640
Comparative transcriptome analysis reveals phytohormone signalings, heat shock module and ROS scavenger mediate the cold-tolerance of rubber tree. PMID:29563566
SPSNet: subpopulation-sensitive network-based analysis of heterogeneous gene expression data. PMID:29560831
A homologous mapping method for three-dimensional reconstruction of protein networks reveals disease-associated mutations. PMID:29560828
Transcriptome analysis of a taxol-producing endophytic fungus Cladosporium cladosporioides MD2. PMID:29556854
Gastric cancer biomarkers; A systems biology approach. PMID:29556568
Exploring the Mechanism of Dangguiliuhuang Decoction Against Hepatic Fibrosis by Network Pharmacology and Experimental Validation. PMID:29556199
The Pathway Coexpression Network: Revealing pathway relationships. PMID:29554099
Ranking Enzyme Structures in the PDB by Bound Ligand Similarity to Biological Substrates. PMID:29551288
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
BURRITO: An Interactive Multi-Omic Tool for Visualizing Taxa-Function Relationships in Microbiome Data. PMID:29545787
Discovery and validation of a glioblastoma co-expressed gene module. PMID:29541392
Expression of Hippo pathway genes and their clinical significance in colon adenocarcinoma. PMID:29541248
LINC00152 is a potential biomarker involved in the modulation of biological characteristics of residual colorectal cancer cells following chemoradiotherapy. PMID:29541183
Discriminate the response of Acute Myeloid Leukemia patients to treatment by using proteomics data and Answer Set Programming. PMID:29536824
Beyond Chloride Brines: Variable Metabolomic Responses in the Anaerobic Organism Yersinia intermedia MASE-LG-1 to NaCl and MgSO4 at Identical Water Activity. PMID:29535699
SMILE: a novel procedure for subcellular module identification with localisation expansion. PMID:29533218
Investigation of mechanisms of mesenchymal stem cells for treatment of diabetic nephropathy via construction of a miRNA-TF-mRNA network. PMID:29532746
TryTransDB: A web-based resource for transport proteins in Trypanosomatidae. PMID:29531295
Metabolomic and inflammatory mediator based biomarker profiling as a potential novel method to aid pediatric appendicitis identification. PMID:29529041
Pseudomonas rhizophila S211, a New Plant Growth-Promoting Rhizobacterium with Potential in Pesticide-Bioremediation. PMID:29527191
A Novel Five-Node Feed-Forward Loop Unravels miRNA-Gene-TF Regulatory Relationships in Ischemic Stroke. PMID:29524052
Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics. PMID:29524042
RNA sequencing of kidney distal tubule cells reveals multiple mediators of chronic aldosterone action. PMID:29521601
A proteomic landscape of diffuse-type gastric cancer. PMID:29520031
Allergen-induced activation of natural killer cells represents an early-life immune response in the development of allergic asthma. PMID:29518416
Evolution of heterotrophy in chrysophytes as reflected by comparative transcriptomics. PMID:29518196
Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. PMID:29515151
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
The mRNA, miRNA and lncRNA networks in hepatocellular carcinoma: An integrative transcriptomic analysis from Gene Expression Omnibus. PMID:29512731
Identification of COL4A1 as a potential gene conferring trastuzumab resistance in gastric cancer based on bioinformatics analysis. PMID:29512712
The chemokine receptor CCR1 is identified in mast cell-derived exosomes. PMID:29511430
The Use of Metabolomics and Inflammatory Mediator Profiling Provides a Novel Approach to Identifying Pediatric Appendicitis in the Emergency Department. PMID:29511263
Herbivorous turtle ants obtain essential nutrients from a conserved nitrogen-recycling gut microbiome. PMID:29511180
Investigating the molecular basis for heterophylly in the aquatic plant Potamogeton octandrus (Potamogetonaceae) with comparative transcriptomics. PMID:29507839
Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy. PMID:29506508
BRCA-Pathway: a structural integration and visualization system of TCGA breast cancer data on KEGG pathways. PMID:29504910
Gene expression in retinal ischemic post-conditioning. PMID:29504043
Taxa-function robustness in microbial communities. PMID:29499759
Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice. PMID:29497108
Landscape of the spliced leader trans-splicing mechanism in Schistosoma mansoni. PMID:29497070
Whole-exome sequencing reveals the origin and evolution of hepato-cholangiocarcinoma. PMID:29497050
Improving eukaryotic genome annotation using single molecule mRNA sequencing. PMID:29495964
Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease. PMID:29494619
Direct Reprogramming of Spiral Ganglion Non-neuronal Cells into Neurons: Toward Ameliorating Sensorineural Hearing Loss by Gene Therapy. PMID:29492404
Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes. PMID:29492402
Integrative functional analysis of super enhancer SNPs for coronary artery disease. PMID:29491472
Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men. PMID:29489876
Development of a Reverse Phase HPLC Retention Index Model for Nontargeted Metabolomics Using Synthetic Compounds. PMID:29489351
The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets. PMID:29487617
Meta- and cross-species analyses of insulin resistance based on gene expression datasets in human white adipose tissues. PMID:29487289
A Metagenome-Wide Association Study and Arrayed Mutant Library Confirm Acetobacter Lipopolysaccharide Genes Are Necessary for Association with Drosophila melanogaster. PMID:29487183
Competitive Traits Are More Important than Stress-Tolerance Traits in a Cadmium-Contaminated Rhizosphere: A Role for Trait Theory in Microbial Ecology. PMID:29483898
Comparative and integrative metabolomics reveal that S-nitrosation inhibits physiologically relevant metabolic enzymes. PMID:29483187
Alterations in sperm DNA methylation, non-coding RNA and histone retention associate with DDT-induced epigenetic transgenerational inheritance of disease. PMID:29482626
PhLeGrA: Graph Analytics in Pharmacology over the Web of Life Sciences Linked Open Data. PMID:29479581
The transcriptomic signature of different sexes in two protogynous hermaphrodites: Insights into the molecular network underlying sex phenotype in fish. PMID:29476120
RaMP: A Comprehensive Relational Database of Metabolomics Pathways for Pathway Enrichment Analysis of Genes and Metabolites. PMID:29470400
Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes. PMID:29468131
Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature. PMID:29468112
iTRAQ-Based Comparative Proteomic Analysis of Adult Schistosoma japonicum from Water Buffalo and Yellow Cattle. PMID:29467732
Proteome analysis of Aspergillus flavus isolate-specific responses to oxidative stress in relationship to aflatoxin production capability. PMID:29467403
PTEN deficiency promotes pathological vascular remodeling of human coronary arteries. PMID:29467331
Loss of epigenetic regulator TET2 and oncogenic KIT regulate myeloid cell transformation via PI3K pathway. PMID:29467326
Identification, isolation and characterization of human LGR5-positive colon adenoma cells. PMID:29467240
A novel heterogeneous network-based method for drug response prediction in cancer cell lines. PMID:29463808
Dietary Fiber Treatment Corrects the Composition of Gut Microbiota, Promotes SCFA Production, and Suppresses Colon Carcinogenesis. PMID:29462896
Common Deregulation of Seven Biological Processes by MicroRNAs in Gastrointestinal Cancers. PMID:29459716
Hologenomic adaptations underlying the evolution of sanguivory in the common vampire bat. PMID:29459707
Understanding the functional role of genistein in the bone differentiation in mouse osteoblastic cell line MC3T3-E1 by RNA-seq analysis. PMID:29459627
An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans. PMID:29456073
Neovasculature can be induced by patching an arterial graft into a vein: A novel in vivo model of spontaneous arteriovenous fistula formation. PMID:29453407
Anthropogenic N Deposition Alters the Composition of Expressed Class II Fungal Peroxidases. PMID:29453258
Potential Breast Anticancer Drug Targets Revealed by Differential Gene Regulatory Network Analysis and Molecular Docking: Neoadjuvant Docetaxel Drug as a Case Study. PMID:29449773
An in silico argument for mitochondrial microRNA as a determinant of primary non function in liver transplantation. PMID:29449571
Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation. PMID:29447276
FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks. PMID:29447218
Species-specific regulation of angiogenesis by glucocorticoids reveals contrasting effects on inflammatory and angiogenic pathways. PMID:29447208
A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts. PMID:29447159
Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma. PMID:29445139
Influence of Different Sugars and Initial pH on β-Glucan Formation by Lactobacillus brevis TMW 1.2112. PMID:29442149
Profiling of Human Molecular Pathways Affected by Retrotransposons at the Level of Regulation by Transcription Factor Proteins. PMID:29441061
Network Analyses in Plant Pathogens. PMID:29441045
Microarray profile of circular RNAs identifies hsa_circ_0014130 as a new circular RNA biomarker in non-small cell lung cancer. PMID:29440731
Analyzing the genes related to nicotine addiction or schizophrenia via a pathway and network based approach. PMID:29440730
Microarray analysis for the identification of specific proteins and functional modules involved in the process of hepatocellular carcinoma originating from cirrhotic liver. PMID:29436633
microRNA expression profiles of scar and normal tissue from patients with posterior urethral stricture caused by pelvic fracture urethral distraction defects. PMID:29436608
Bioinformatic analysis of gene expression profiles of pituitary gonadotroph adenomas. PMID:29434861
Identification of core pathways based on attractor and crosstalk in ischemic stroke. PMID:29434737
14q32 and let-7 microRNAs regulate transcriptional networks in fetal and adult human erythroblasts. PMID:29432581
Molecular Correlates of In Vitro Responses to Dacomitinib and Afatinib in Bladder Cancer. PMID:29430509
Identification of genomic expression differences between right-sided and left-sided colon cancer based on bioinformatics analysis. PMID:29430186
Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition. PMID:29426343
Genome-Wide Identification and Characterization of WD40 Protein Genes in the Silkworm, Bombyx mori. PMID:29425159
Integrated Systems Approach Reveals Sphingolipid Metabolism Pathway Dysregulation in Association with Late-Onset Alzheimer's Disease. PMID:29425116
Dietary Safety Assessment of Flk1-Transgenic Fish. PMID:29422865
Integrated Theory- and Data-driven Feature Selection in Gene Expression Data Analysis. PMID:29422764
HER kinase inhibition in patients with HER2- and HER3-mutant cancers. PMID:29420467
Transcriptome-wide identification and functional prediction of novel and flowering-related circular RNAs from trifoliate orange (Poncirus trifoliata L. Raf.). PMID:29417269
Metabolomic alterations in invasive ductal carcinoma of breast: A comprehensive metabolomic study using tissue and serum samples. PMID:29416801
Identification of human age-associated gene co-expressions in functional modules using liquid association. PMID:29416677
Proteome Data Improves Protein Function Prediction in the Interactome of Helicobacter pylori. PMID:29414760
Integrating eQTL data with GWAS summary statistics in pathway-based analysis with application to schizophrenia. PMID:29411426
Metatranscriptome Sequencing Reveals Insights into the Gene Expression and Functional Potential of Rumen Wall Bacteria. PMID:29410661
Intratumoral bacteria may elicit chemoresistance by metabolizing anticancer agents. PMID:29404397
Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet. PMID:29402949
Transcriptome sequence analysis and mining of SSRs in Jhar Ber (Ziziphus nummularia (Burm.f.) Wight & Arn) under drought stress. PMID:29402924
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. PMID:29402381
Investigation of the molecular mechanisms underlying postoperative recurrence in prostate cancer by gene expression profiling. PMID:29399083
Nitrogen supply influences photosynthesis establishment along the sugarcane leaf. PMID:29396510
Gene expression profile analysis of the bone microenvironment in patients with spinal metastases. PMID:29387210
PPARα-Target Gene Expression Requires TIS21/BTG2 Gene in Liver of the C57BL/6 Mice under Fasting Condition. PMID:29385670
The Glaciozyma antarctica genome reveals an array of systems that provide sustained responses towards temperature variations in a persistently cold habitat. PMID:29385175
Human Skeletal Muscle Possesses an Epigenetic Memory of Hypertrophy. PMID:29382913
Identification of regulatory role of DNA methylation in colon cancer gene expression via systematic bioinformatics analysis. PMID:29381923
New Targets for Zika Virus Determined by Human-Viral Interactomic: A Bioinformatics Approach. PMID:29379794
Genomic signal processing for DNA sequence clustering. PMID:29379686
Cardiac shock wave therapy promotes arteriogenesis of coronary micrangium, and ILK is involved in the biomechanical effects by proteomic analysis. PMID:29379038
Commensal microbiota modulate gene expression in the skin. PMID:29378633
Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. PMID:29378627
Integrated omics data of two annual ryegrass (Lolium multiflorum L.) genotypes reveals core metabolic processes under drought stress. PMID:29378511
Prediction of enzymatic pathways by integrative pathway mapping. PMID:29377793
Identification of key genes associated with bladder cancer using gene expression profiles. PMID:29375713
Scuba: scalable kernel-based gene prioritization. PMID:29370760
Integrated phenotypic-genotypic approach to understand the influence of ultrasound on metabolic response of Lactobacillus sakei. PMID:29370210
Binding and entry of peste des petits ruminants virus into caprine endometrial epithelial cells profoundly affect early cellular gene expression. PMID:29368634
Somatic APC mosaicism and oligogenic inheritance in genetically unsolved colorectal adenomatous polyposis patients. PMID:29367705
A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification. PMID:29363426
The Identification of Key Genes and Pathways in Glioma by Bioinformatics Analysis. PMID:29362722
Evolutionary loss and replacement of Buchnera, the obligate endosymbiont of aphids. PMID:29362506
Whole-exome sequencing identifies common and rare variant metabolic QTLs in a Middle Eastern population. PMID:29362361
Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome. PMID:29359195
Construction of an oesophageal cancer-specific ceRNA network based on miRNA, lncRNA, and mRNA expression data. PMID:29358879
Feature selection for high-dimensional temporal data. PMID:29357817
Regeneration in distantly related species: common strategies and pathways. PMID:29354283
Functional Characteristics of the Flying Squirrel's Cecal Microbiota under a Leaf-Based Diet, Based on Multiple Meta-Omic Profiling. PMID:29354108
Metabolic Adaptation of a C-Terminal Protease A-Deficient Rhizobium leguminosarum in Response to Loss of Nutrient Transport. PMID:29354107
Investigating the Mechanisms of Action of Depside Salt from Salvia miltiorrhiza Using Bioinformatic Analysis. PMID:29348768
Microarray analysis reveals Tmub1 as a cell cycle-associated protein in rat hepatocytes. PMID:29344642
Changes in contractile protein expression are linked to ventricular stiffness in infants with pulmonary hypertension or right ventricular hypertrophy due to congenital heart disease. PMID:29344379
Identification of differentially expressed molecular functions associated with breast cancer using Gibbs sampling. PMID:29344193
The protective role of DOT1L in UV-induced melanomagenesis. PMID:29343685
Ceratocystis cacaofunesta genome analysis reveals a large expansion of extracellular phosphatidylinositol-specific phospholipase-C genes (PI-PLC). PMID:29343217
Prediction of novel target genes and pathways involved in bevacizumab-resistant colorectal cancer. PMID:29342159
Structure Elucidation of Unknown Metabolites in Metabolomics by Combined NMR and MS/MS Prediction. PMID:29342073
RBiomirGS: an all-in-one miRNA gene set analysis solution featuring target mRNA mapping and expression profile integration. PMID:29340253
Identification of bladder cancer prognostic biomarkers using an ageing gene-related competitive endogenous RNA network. PMID:29340088
Differential gene expression profiles between two subtypes of ischemic stroke with blood stasis syndromes. PMID:29340078
Loss of disease tolerance during Citrobacter rodentium infection is associated with impaired epithelial differentiation and hyperactivation of T cell responses. PMID:29339782
Volatile molecules from bronchoalveolar lavage fluid can 'rule-in' Pseudomonas aeruginosa and 'rule-out' Staphylococcus aureus infections in cystic fibrosis patients. PMID:29339749
Genomic and transcriptomic analysis of the Asian honeybee Apis cerana provides novel insights into honeybee biology. PMID:29339745
Identification of differentially expressed genes and pathways for intramuscular fat metabolism between breast and thigh tissues of chickens. PMID:29338766
Semi-supervised identification of cancer subgroups using survival outcomes and overlapping grouping information. PMID:29336210
Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys. PMID:29335507
Transcriptome profiling during mangrove viviparity in response to abscisic acid. PMID:29335506
Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn's disease. PMID:29335008
Easy and efficient ensemble gene set testing with EGSEA. PMID:29333246
Mycobacterium tuberculosis Exploits a Molecular Off Switch of the Immune System for Intracellular Survival. PMID:29330469
Tissue and serum microRNA profile of oral squamous cell carcinoma patients. PMID:29330429
Bioinformatic analysis of gene expression profiling of intracranial aneurysm. PMID:29328431
Investigation into the underlying molecular mechanisms of hypertensive nephrosclerosis using bioinformatics analyses. PMID:29328390
Logistic regression analysis for the identification of the metastasis-associated signaling pathways of osteosarcoma. PMID:29328361
An Integrated Analysis of miRNAs and Methylated Genes Encoding mRNAs and lncRNAs in Sheep Breeds with Different Fecundity. PMID:29326596
Systematic target function annotation of human transcription factors. PMID:29325558
Filling gaps in bacterial amino acid biosynthesis pathways with high-throughput genetics. PMID:29324779
Electromagnetic Radiation Disturbed the Photosynthesis of Microcystis aeruginosa at the Proteomics Level. PMID:29323219
A census of P. longum's phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders. PMID:29320554
Genomic islands of differentiation in two songbird species reveal candidate genes for hybrid female sterility. PMID:29319911
Boolean network modeling in systems pharmacology. PMID:29307099
Comparative analysis of miRNA and mRNA abundance in determinate cucumber by high-throughput sequencing. PMID:29304061
A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers. PMID:29304003
The variome of pneumococcal virulence factors and regulators. PMID:29298677
De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II). PMID:29298661
The node-weighted Steiner tree approach to identify elements of cancer-related signaling pathways. PMID:29297291
Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. PMID:29297278
Perturbation-response genes reveal signaling footprints in cancer gene expression. PMID:29295995
Integrative analysis reveals disrupted pathways regulated by microRNAs in cancer. PMID:29294105
Photosynthetic functions of Synechococcus in the ocean microbiomes of diverse salinity and seasons. PMID:29293601
Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics data. PMID:29291722
Unique metabolomic signature associated with hepatorenal dysfunction and mortality in cirrhosis. PMID:29291380
Genomics-Driven Precision Medicine for Advanced Pancreatic Cancer: Early Results from the COMPASS Trial. PMID:29288237
Changes in microRNA expression in the brachial plexus avulsion model of neuropathic pain. PMID:29286067
Taxonomic differences of gut microbiomes drive cellulolytic enzymatic potential within hind-gut fermenting mammals. PMID:29281673
Novel associations between blood DNA methylation and body mass index in middle-aged and older adults. PMID:29278407
Genome sequence of the model plant pathogen Pectobacterium carotovorum SCC1. PMID:29276572
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host. PMID:29276507
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat. PMID:29272997
Missing value imputation for LC-MS metabolomics data by incorporating metabolic network and adduct ion relations. PMID:29272352
Developing a 'personalome' for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes. PMID:29272327
The pomegranate (Punica granatum L.) genome provides insights into fruit quality and ovule developmental biology. PMID:29271050
Adaptive Evolution of Energy Metabolism-Related Genes in Hypoxia-Tolerant Mammals. PMID:29270192
Super-delta: a new differential gene expression analysis procedure with robust data normalization. PMID:29268715
Sequential feature selection and inference using multi-variate random forests. PMID:29267851
Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. PMID:29267397
Tissue Tropism in Host Transcriptional Response to Members of the Bovine Respiratory Disease Complex. PMID:29263411
Isoprenoids responsible for protein prenylation modulate the biological effects of statins on pancreatic cancer cells. PMID:29262834
Dual blockade of the lipid kinase PIP4Ks and mitotic pathways leads to cancer-selective lethality. PMID:29259156
Computational antimicrobial peptide design and evaluation against multidrug-resistant clinical isolates of bacteria. PMID:29259134
Metabolomic Profiles of a Midge (Procladius villosimanus, Kieffer) Are Associated with Sediment Contamination in Urban Wetlands. PMID:29258276
Stability of Signaling Pathways during Aging-A Boolean Network Approach. PMID:29258225
Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. PMID:29257335
iDTI-ESBoost: Identification of Drug Target Interaction Using Evolutionary and Structural Features with Boosting. PMID:29255285
Enterotypes in the landscape of gut microbial community composition. PMID:29255284
Informatics for cancer immunotherapy. PMID:29253114
Computational identification of microRNAs and their targets in liver cirrhosis. PMID:29250171
Potential Diagnostic Power of Blood Circular RNA Expression in Active Pulmonary Tuberculosis. PMID:29248507
Subspecies in the global human gut microbiome. PMID:29242367
Orthogonality and Burdens of Heterologous AND Gate Gene Circuits in E. coli. PMID:29240998
Identiﬁcation of Key Genes and Pathways in Tongue Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:29240723
Identification of potential transcriptomic markers in developing pediatric sepsis: a weighted gene co-expression network analysis and a case-control validation study. PMID:29237456
Evaluation of epidermal growth factor receptor signaling effects in gastric cancer cell lines by detailed motility-focused phenotypic characterization linked with molecular analysis. PMID:29237412
Genetic adaptation of microbial populations present in high-intensity catfish production systems with therapeutic oxytetracycline treatment. PMID:29235508
Identification and validation of FaP1D7, a putative marker associated with the biosynthesis of methyl butanoate in cultivated strawberry (Fragaria x ananassa). PMID:29234071
Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. PMID:29229974
The genomic study of an environmental isolate of Scedosporium apiospermum shows its metabolic potential to degrade hydrocarbons. PMID:29225727
Differently expressed long noncoding RNAs and mRNAs in TK6 cells exposed to low dose hydroquinone. PMID:29221148
Plasma-derived extracellular vesicle proteins as a source of biomarkers for lung adenocarcinoma. PMID:29221141
In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. PMID:29220465
SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. PMID:29220461
New extension software modules to enhance searching and display of transcriptome data in Tripal databases. PMID:29220446
The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. PMID:29220445
LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. PMID:29220437
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease. PMID:29215193
Reprogramming of a defense signaling pathway in rough lemon and sweet orange is a critical element of the early response to 'Candidatus Liberibacter asiaticus'. PMID:29214028
A Comprehensive Assessment of the Genetic Determinants in Salmonella Typhimurium for Resistance to Hydrogen Peroxide Using Proteogenomics. PMID:29213059
Atmospheric trace gases support primary production in Antarctic desert surface soil. PMID:29211716
Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans. PMID:29206865
Annotation of nerve cord transcriptome in earthworm Eisenia fetida. PMID:29204349
Utilization of Host Polyamines in Alternatively Activated Macrophages Promotes Chronic Infection by Brucella abortus. PMID:29203548
Distribution and Evolution of Peroxisomes in Alveolates (Apicomplexa, Dinoflagellates, Ciliates). PMID:29202176
Protein-protein interaction analysis to identify biomarker networks for endometriosis. PMID:29201163
A time-course microarray data analysis reveals consistent dysregulated genes and upstream microRNAs in autoantibody-mediated arthritis. PMID:29197380
A novel Chromatiales bacterium is a potential sulfide oxidizer in multiple orders of marine sponges. PMID:29194919
Landscape of the regulatory elements for lysine 2-hydroxyisobutyrylation pathway. PMID:29192674
HIDEEP: a systems approach to predict hormone impacts on drug efficacy based on effect paths. PMID:29192270
Differential prioritization of therapies to subtypes of triple negative breast cancer using a systems medicine method. PMID:29190967
Silibinin suppresses bladder cancer through down-regulation of actin cytoskeleton and PI3K/Akt signaling pathways. PMID:29190895
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
Comparative Analysis of Soybean Root Proteome Reveals Molecular Basis of Differential Carboxylate Efflux under Low Phosphorus Stress. PMID:29189708
Stage-Specific Gene Profiling of Germinal Cells Helps Delineate the Mitosis/Meiosis Transition. PMID:29187566
Amyloid Accumulation Drives Proteome-wide Alterations in Mouse Models of Alzheimer's Disease-like Pathology. PMID:29186695
Semi-supervised network inference using simulated gene expression dynamics. PMID:29186340
Dysregulation of YAP by ARF Stimulated with Tea-derived Carbon Nanodots. PMID:29185453
Dietary energy drives the dynamic response of bovine rumen viral communities. PMID:29179741
Sugar Lego: gene composition of bacterial carbohydrate metabolism genomic loci. PMID:29178959
Gene and genome-centric analyses of koala and wombat fecal microbiomes point to metabolic specialization for Eucalyptus digestion. PMID:29177117
Shared genetic etiology of hypertension and stroke: evidence from bioinformatics analysis of genome-wide association studies. PMID:29176593
Identification and analysis of seven effector protein families with different adaptive and evolutionary histories in plant-associated members of the Xanthomonadaceae. PMID:29170530
An extracellular matrix-related prognostic and predictive indicator for early-stage non-small cell lung cancer. PMID:29170406
Transcriptome and metabolite analyses reveal the complex metabolic genes involved in volatile terpenoid biosynthesis in garden sage (Salvia officinalis). PMID:29167468
FMRFamide-like peptides expand the behavioral repertoire of a densely connected nervous system. PMID:29167374
ADAGE signature analysis: differential expression analysis with data-defined gene sets. PMID:29166858
Identification of molecular mechanisms of glutamine in pancreatic cancer. PMID:29163679
Metabolic Pathway Assignment of Plant Genes based on Phylogenetic Profiling-A Feasibility Study. PMID:29163570
Global Transcriptome Sequencing Reveals Molecular Profiles of Summer Diapause Induction Stage of Onion Maggot, Delia antiqua (Diptera: Anthomyiidae). PMID:29158334
Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa. PMID:29155802
Identification of key genes in glioma CpG island methylator phenotype via network analysis of gene expression data. PMID:29152649
Deep RNAseq indicates protective mechanisms of cold-tolerant indica rice plants during early vegetative stage. PMID:29151156
Decoding critical long non-coding RNA in ovarian cancer epithelial-to-mesenchymal transition. PMID:29150601
Early nutritional programming affects liver transcriptome in diploid and triploid Atlantic salmon, Salmo salar. PMID:29149845
Draft genome analysis provides insights into the fiber yield, crude protein biosynthesis, and vegetative growth of domesticated ramie (Boehmeria nivea L. Gaud). PMID:29149285
Knockdown of SIRT1 Suppresses Bladder Cancer Cell Proliferation and Migration and Induces Cell Cycle Arrest and Antioxidant Response through FOXO3a-Mediated Pathways. PMID:29147649
Generational comparisons (F1 versus F3) of vinclozolin induced epigenetic transgenerational inheritance of sperm differential DNA methylation regions (epimutations) using MeDIP-Seq. PMID:29147574
Migrainomics - identifying brain and genetic markers of migraine. PMID:29146952
ANAT 2.0: reconstructing functional protein subnetworks. PMID:29145805
Phosphorylation Dynamics Dominate the Regulated Proteome during Early Xenopus Development. PMID:29142207
Copy number gains at chr3p25 and chr11p11 are associated with lymph node involvement and survival in muscle-invasive bladder tumors. PMID:29140994
Transcriptomics-driven lipidomics (TDL) identifies the microbiome-regulated targets of ileal lipid metabolism. PMID:29138692
Predicted molecular targets and pathways for germacrone, curdione, and furanodiene in the treatment of breast cancer using a bioinformatics approach. PMID:29138518
New eight genes identified at the clinical multidrug-resistant Acinetobacter baumannii DMS06669 strain in a Vietnam hospital. PMID:29137647
Metabolic Profile of the Cellulolytic Industrial Actinomycete Thermobifida fusca. PMID:29137138
Genome sequence of the small brown planthopper, Laodelphax striatellus. PMID:29136191
Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism. PMID:29134060
Metabolomics identifies metabolite biomarkers associated with acute rejection after heart transplantation in rats. PMID:29133921
Animal multicellularity and polarity without Wnt signaling. PMID:29133828
Weighted gene co-expression network analysis of expression data of monozygotic twins identifies specific modules and hub genes related to BMI. PMID:29132311
Statistical Contributions to Bioinformatics: Design, Modeling, Structure Learning, and Integration. PMID:29129969
Identification of cancer biomarkers of prognostic value using specific gene regulatory networks (GRN): a novel role of RAD51AP1 for ovarian and lung cancers. PMID:29126163
Deep sequencing and comprehensive expression analysis identifies several molecules potentially related to human poorly differentiated hepatocellular carcinoma. PMID:29123978
miRNA profiling identifies deregulated miRNAs associated with osteosarcoma development and time to metastasis in two large cohorts. PMID:29120535
Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-β-xylanase activity. PMID:29118851
Combining membrane proteomics and computational three-way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs. PMID:29118436
Influences of anthropogenic land use on microbial community structure and functional potentials of stream benthic biofilms. PMID:29118402
Wild Silkworm Cocoon Contains More Metabolites Than Domestic Silkworm Cocoon to Improve Its Protection. PMID:29117380
General response of Salmonella enterica serovar Typhimurium to desiccation: A new role for the virulence factors sopD and sseD in survival. PMID:29117268
Genome-wide DNA methylome alterations in acute coronary syndrome. PMID:29115576
Abnormal DNA methylation may contribute to the progression of osteosarcoma. PMID:29115427
Gene expression profiles and protein‑protein interaction networks during tongue carcinogenesis in the tumor microenvironment. PMID:29115421
Predicting pathogenic genes for primary myelofibrosis based on a system‑network approach. PMID:29115418
Common mechanism of pathogenesis in various types of metastatic osteosarcoma. PMID:29113282
Bacterial colonization stimulates a complex physiological response in the immature human intestinal epithelium. PMID:29110754
Chemical Similarity Enrichment Analysis (ChemRICH) as alternative to biochemical pathway mapping for metabolomic datasets. PMID:29109515
Metabolic Mitigation of Staphylococcus aureus Vancomycin Intermediate-Level Susceptibility. PMID:29109158
Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes. PMID:29108274
The UCSC Genome Browser database: 2018 update. PMID:29106570
Orchid: a novel management, annotation and machine learning framework for analyzing cancer mutations. PMID:29106441
Human microbiome signatures of differential colorectal cancer drug metabolism. PMID:29104759
Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. PMID:29101370
Arabidopsis Novel Glycine-Rich Plasma Membrane PSS1 Protein Enhances Disease Resistance in Transgenic Soybean Plants. PMID:29101280
Cancer cell line specific co-factors modulate the FOXM1 cistrome. PMID:29100329
Genome-scale single-cell mechanical phenotyping reveals disease-related genes involved in mitotic rounding. PMID:29097687
Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. PMID:29097493
Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum. PMID:29093020
Systems Study on the Antirheumatic Mechanism of Tibetan Medicated-Bath Therapy Using Wuwei-Ganlu-Yaoyu-Keli. PMID:29090217
Inhibitory effect and mechanism of Tagetes erecta L. fungicide on Fusarium oxysporum f. sp. niveum. PMID:29089546
Comparative evaluation of atom mapping algorithms for balanced metabolic reactions: application to Recon 3D. PMID:29086112
Dorsal and Ventral Hippocampus Differentiate in Functional Pathways and Differentially Associate with Neurological Disease-Related Genes during Postnatal Development. PMID:29085281
Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax - a liver transcriptomics approach. PMID:29084988
Acquisition of the Phosphate Transporter NptA Enhances Staphylococcus aureus Pathogenesis by Improving Phosphate Uptake in Divergent Environments. PMID:29084897
Computational correction of copy number effect improves specificity of CRISPR-Cas9 essentiality screens in cancer cells. PMID:29083409
Cardiomyocyte proliferation prevents failure in pressure overload but not volume overload. PMID:29083322
Interactions of the Hindgut Mucosa-Associated Microbiome with Its Host Regulate Shedding of Escherichia coli O157:H7 by Cattle. PMID:29079612
Framework and resource for more than 11,000 gene-transcript-protein-reaction associations in human metabolism. PMID:29078384
Epigenetics and adaptive phenotypic variation between habitats in an asexual snail. PMID:29074962
Transcriptome Analysis Reveals Neuroprotective aspects of Human Reactive Astrocytes induced by Interleukin 1β. PMID:29070875
Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1α axis inhibition. PMID:29069732
MEBS, a software platform to evaluate large (meta)genomic collections according to their metabolic machinery: unraveling the sulfur cycle. PMID:29069412
Identification of key pathways and genes with aberrant methylation in prostate cancer using bioinformatics analysis. PMID:29066912
Periodontal pathogenic bacteria, Aggregatibacter actinomycetemcomitans affect non-alcoholic fatty liver disease by altering gut microbiota and glucose metabolism. PMID:29066788
Identification of polymorphisms in cancer patients that differentially affect survival with age. PMID:29064820
Draft Genome Sequence of Cyclohexylamine-Degrading Strain Acinetobacter sp. YT-02 Isolated. PMID:29063968
IL-17 Exerts Anti-Apoptotic Effect via miR-155-5p Downregulation in Experimental Autoimmune Encephalomyelitis. PMID:29063445
Transcriptomics and proteomics reveal genetic and biological basis of superior biomass crop Miscanthus. PMID:29062090
Genome-wide profiling of transcribed enhancers during macrophage activation. PMID:29061167
Low levels of lead and glutathione markers of redox status in human blood. PMID:29058203
Antibiotics ameliorate lupus-like symptoms in mice. PMID:29057975
Overexpression of COL3A1 confers a poor prognosis in human bladder cancer identified by co-expression analysis. PMID:29050298
An integrative in-silico approach for therapeutic target identification in the human pathogen Corynebacterium diphtheriae. PMID:29049350
Inferring gene and protein interactions using PubMed citations and consensus Bayesian networks. PMID:29049295
A probabilistic pathway score (PROPS) for classification with applications to inflammatory bowel disease. PMID:29048458
Epigenome-wide association study of asthma and wheeze in childhood and adolescence. PMID:29046734
Global Analysis of Small RNA Dynamics during Seed Development of Picea glauca and Arabidopsis thaliana Populations Reveals Insights on their Evolutionary Trajectories. PMID:29046688
Early Transcriptional Divergence Marks Virus-Specific Primary Human CD8+ T Cells in Chronic versus Acute Infection. PMID:29045899
Integrated mRNA and microRNA transcriptome analyses reveal regulation of thermal acclimation in Gymnocypris przewalskii: A case study in Tibetan Schizothoracine fish. PMID:29045433
Transcriptomic responses of Biomphalaria pfeifferi to Schistosoma mansoni: Investigation of a neglected African snail that supports more S. mansoni transmission than any other snail species. PMID:29045404
Exercise and high-fat feeding remodel transcript-metabolite interactive networks in mouse skeletal muscle. PMID:29044196
Dynamic and Modularized MicroRNA Regulation and Its Implication in Human Cancers. PMID:29042600
A plasma proteomics method reveals links between ischemic stroke and MTHFR C677T genotype. PMID:29042595
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. PMID:29042495
Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis. PMID:29042298
Gene expression profile identifies potential biomarkers for human intervertebral disc degeneration. PMID:29039500
Prokineticin receptor-1-dependent paracrine and autocrine pathways control cardiac tcf21+ fibroblast progenitor cell transformation into adipocytes and vascular cells. PMID:29038558
13C metabolic flux analysis of three divergent extremely thermophilic bacteria: Geobacillus sp. LC300, Thermus thermophilus HB8, and Rhodothermus marinus DSM 4252. PMID:29037779
TaxMapper: an analysis tool, reference database and workflow for metatranscriptome analysis of eukaryotic microorganisms. PMID:29037173
DISNOR: a disease network open resource. PMID:29036667
ScanGEO: parallel mining of high-throughput gene expression data. PMID:29036513
Quantitative proteomics of a B12 -dependent alga grown in coculture with bacteria reveals metabolic tradeoffs required for mutualism. PMID:29034959
Comparative Metabolomics of Mycoplasma bovis and Mycoplasma gallisepticum Reveals Fundamental Differences in Active Metabolic Pathways and Suggests Novel Gene Annotations. PMID:29034329
High-Fat Diet Changes Fungal Microbiomes and Interkingdom Relationships in the Murine Gut. PMID:29034327
Affected pathways and transcriptional regulators in gene expression response to an ultra-marathon trail: Global and independent activity approaches. PMID:29028836
The Plasticizer Bisphenol A Perturbs the Hepatic Epigenome: A Systems Level Analysis of the miRNome. PMID:29027980
Partitioning of functional gene expression data using principal points. PMID:29025390
High-resolution mass spectrometry of skin mucus for monitoring physiological impacts and contaminant biotransformation products in fathead minnows exposed to wastewater effluent. PMID:29023973
Human Parvovirus Infection of Human Airway Epithelia Induces Pyroptotic Cell Death by Inhibiting Apoptosis. PMID:29021400
The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. PMID:29020946
Dehydration induced transcriptomic responses in two Tibetan hulless barley (Hordeum vulgare var. nudum) accessions distinguished by drought tolerance. PMID:29020945
A novel network analysis approach reveals DNA damage, oxidative stress and calcium/cAMP homeostasis-associated biomarkers in frontotemporal dementia. PMID:29020091
A Massively Parallel Sequence Similarity Search for Metagenomic Sequencing Data. PMID:29019934
Global transcriptome‑wide analysis of the function of GDDR in acute gastric lesions. PMID:28990076
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. PMID:28988802
Transcriptional profiling of cork oak phellogenic cells isolated by laser microdissection. PMID:28988391
MicroRNA expression profiles and type 1 diabetes mellitus: systematic review and bioinformatic analysis. PMID:28986402
Caspase-8, association with Alzheimer's Disease and functional analysis of rare variants. PMID:28985224
Bacteria alone establish the chemical basis of the wood-fall chemosynthetic ecosystem in the deep-sea. PMID:28984846
Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer. PMID:28984209
System modeling reveals the molecular mechanisms of HSC cell cycle alteration mediated by Maff and Egr3 under leukemia. PMID:28984203
MD-Miner: a network-based approach for personalized drug repositioning. PMID:28984195
ScaPD: a database for human scaffold proteins. PMID:28984188
Dietary Heme Induces Gut Dysbiosis, Aggravates Colitis, and Potentiates the Development of Adenomas in Mice. PMID:28983289
OPATs: Omnibus P-value association tests. PMID:28981573
Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale. PMID:28981454
Microbial functional genes elucidate environmental drivers of biofilm metabolism in glacier-fed streams. PMID:28978929
Functional 5' UTR motif discovery with LESMoN: Local Enrichment of Sequence Motifs in biological Networks. PMID:28977652
Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score. PMID:28974751
Cytological Assessments and Transcriptome Profiling Demonstrate that Evodiamine Inhibits Growth and Induces Apoptosis in a Renal Carcinoma Cell Line. PMID:28974748
Anaconda: AN automated pipeline for somatic COpy Number variation Detection and Annotation from tumor exome sequencing data. PMID:28974218
A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis. PMID:28970579
RNA-seq based gene expression analysis of ovarian granulosa cells exposed to zearalenone in vitro: significance to steroidogenesis. PMID:28969048
RNA sequencing indicates that atrazine induces multiple detoxification genes in Daphnia magna and this is a potential source of its mixture interactions with other chemicals. PMID:28968576
IPI59: An Actionable Biomarker to Improve Treatment Response in Serous Ovarian Carcinoma Patients. PMID:28966695
Preliminary identification of key miRNAs, signaling pathways, and genes associated with Hirschsprung's disease by analysis of tissue microRNA expression profiles. PMID:28965333
Plasma bioavailability and changes in PBMC gene expression after treatment of ovariectomized rats with a commercial soy supplement. PMID:28962364
MWASTools: an R/bioconductor package for metabolome-wide association studies. PMID:28961702
miR-181d-5p promotes neurite outgrowth in PC12 Cells via PI3K/Akt pathway. PMID:28961370
Lipid Metabolic Versatility in Malassezia spp. Yeasts Studied through Metabolic Modeling. PMID:28959251
A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect. PMID:28957320
BARHL1 Is Downregulated in Alzheimer's Disease and May Regulate Cognitive Functions through ESR1 and Multiple Pathways. PMID:28956815
iTRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves. PMID:28953898
Exception to the Rule: Genomic Characterization of Naturally Occurring Unusual Vibrio cholerae Strains with a Single Chromosome. PMID:28951866
Transcriptome reprogramming during developmental switching in Physarum polycephalum involves extensive remodeling of intracellular signaling networks. PMID:28951552
Temporal dynamics in microbial soil communities at anthrax carcass sites. PMID:28950879
Screening of potential genes contributing to the macrocycle drug resistance of C. albicans via microarray analysis. PMID:28944888
Exploring the key genes and pathways of osteosarcoma with pulmonary metastasis using a gene expression microarray. PMID:28944885
Gene expression analysis: Regulation of key genes associated with mycophenolate mofetil treatment of symptomatic carotid artery stenosis. PMID:28944878
A Statistical Framework for Pathway and Gene Identification from Integrative Analysis. PMID:28943673
The draft genome sequence of a desert tree Populus pruinosa. PMID:28938721
Integrative Systems Biology Investigation of Fabry Disease. PMID:28933415
A computational method using the random walk with restart algorithm for identifying novel epigenetic factors. PMID:28932904
Atrazine induced epigenetic transgenerational inheritance of disease, lean phenotype and sperm epimutation pathology biomarkers. PMID:28931070
Screening of candidate key genes associated with human osteosarcoma using bioinformatics analysis. PMID:28928828
Affected energy metabolism under manganese stress governs cellular toxicity. PMID:28928443
Host modification of a bacterial quorum-sensing signal induces a phenotypic switch in bacterial symbionts. PMID:28923926
Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. PMID:28922347
Nε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains: Proteins Involved in Bioenergetics, Virulence, and Antimicrobial Resistance Are Acetylated. PMID:28920697
Digging into the low molecular weight peptidome with the OligoNet web server. PMID:28916823
Detecting the genetic link between Alzheimer's disease and obesity using bioinformatics analysis of GWAS data. PMID:28915562
Large-scale cross-species chemogenomic platform proposes a new drug discovery strategy of veterinary drug from herbal medicines. PMID:28915268
Bioinformatics-Based Identification of Methylated-Differentially Expressed Genes and Related Pathways in Gastric Cancer. PMID:28914394
Histological and Transcriptomic Analysis during Bulbil Formation in Lilium lancifolium. PMID:28912794
Systematic review and meta-analysis of differentially expressed miRNAs in experimental and human temporal lobe epilepsy. PMID:28912503
Deconvolution of DNA methylation identifies differentially methylated gene regions on 1p36 across breast cancer subtypes. PMID:28912426
Potential role of intratumor bacteria in mediating tumor resistance to the chemotherapeutic drug gemcitabine. PMID:28912244
Microarray Analysis and Detection of MicroRNAs Associated with Chronic Thromboembolic Pulmonary Hypertension. PMID:28904974
RNA-Seq of Human Neural Progenitor Cells Exposed to Lead (Pb) Reveals Transcriptome Dynamics, Splicing Alterations and Disease Risk Associations. PMID:28903495
Transcriptome analysis and identification of significantly differentially expressed genes in Holstein calves subjected to severe thermal stress. PMID:28900747
Molecular Resources from Transcriptomes in the Brassicaceae Family. PMID:28900436
Metagenomic insight into the microbial networks and metabolic mechanism in anaerobic digesters for food waste by incorporating activated carbon. PMID:28900280
Evolution and genome specialization of Brucella suis biovar 2 Iberian lineages. PMID:28899413
Identification of genes associated with primary open-angle glaucoma by bioinformatics approach. PMID:28894971
Isolation and Characterization of Phenanthrene Degrading Bacteria from Diesel Fuel-Contaminated Antarctic Soils. PMID:28894442
A mouse model for embryonal tumors with multilayered rosettes uncovers the therapeutic potential of Sonic-hedgehog inhibitors. PMID:28892064
A meta-analysis of genome-wide association studies identifies 17 new Parkinson's disease risk loci. PMID:28892059
Metabolomics differences between silkworms (Bombyx mori) reared on fresh mulberry (Morus) leaves or artificial diets. PMID:28887546
Evidence-based gene models for structural and functional annotations of the oil palm genome. PMID:28886750
PP2A-B' holoenzyme substrate recognition, regulation and role in cytokinesis. PMID:28884018
Quantitative proteomics of Sf21 cells during Baculovirus infection reveals progressive host proteome changes and its regulation by viral miRNA. PMID:28883418
Multiple network-constrained regressions expand insights into influenza vaccination responses. PMID:28881994
DextMP: deep dive into text for predicting moonlighting proteins. PMID:28881966
Integrating Imaging Genomic Data in the Quest for Biomarkers of Schizophrenia Disease. PMID:28880187
MicroRNA Profiling in Aging Brain of PSEN1/PSEN2 Double Knockout Mice. PMID:28879407
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PMID:28879061
Comparative proteomic analysis of autotetraploid and diploid Paulownia tomentosa reveals proteins associated with superior photosynthetic characteristics and stress adaptability in autotetraploid Paulownia. PMID:28878499
A Protocol for Generating and Exchanging (Genome-Scale) Metabolic Resource Allocation Models. PMID:28878200
Perilipin-2 modulates dietary fat-induced microbial global gene expression profiles in the mouse intestine. PMID:28877764
The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq. PMID:28877263
In vivo therapeutic effect of combination treatment with metformin and Scutellaria baicalensis on maintaining bile acid homeostasis. PMID:28877164
Using Accurate Mass Gas Chromatography-Mass Spectrometry with the MINE Database for Epimetabolite Annotation. PMID:28876899
Integrated Analysis of Copy Number Variations and Gene Expression Profiling in Hepatocellular carcinoma. PMID:28874807
BUFET: boosting the unbiased miRNA functional enrichment analysis using bitsets. PMID:28874117
Transcriptome analysis of the response of Burmese python to digestion. PMID:28873961
Chronic obstructive pulmonary disease candidate gene prioritization based on metabolic networks and functional information. PMID:28873096
A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research. PMID:28872130
A strategy for the identification of patterns in the biosynthesis of nonribosomal peptides by Betaproteobacteria species. PMID:28871139
Phylo_dCor: distance correlation as a novel metric for phylogenetic profiling. PMID:28870256
Single-Base Resolution Mapping of 5-Hydroxymethylcytosine Modifications in Hippocampus of Alzheimer's Disease Subjects. PMID:28866733
Members of the Candidate Phyla Radiation are functionally differentiated by carbon- and nitrogen-cycling capabilities. PMID:28865481
Gut microbiome in ADHD and its relation to neural reward anticipation. PMID:28863139
Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis. PMID:28861277
miR-96 attenuates status epilepticus-induced brain injury by directly targeting Atg7 and Atg16L1. PMID:28860495
Learning Microbial Community Structures with Supervised and Unsupervised Non-negative Matrix Factorization. PMID:28859695
Functional Analogy in Human Metabolism: Enzymes with Different Biological Roles or Functional Redundancy? PMID:28854631
Investigation of host-pathogen interaction between Burkholderia pseudomallei and autophagy-related protein LC3 using hydrophobic chromatography-based technique. PMID:28852470
Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. PMID:28852099
Comparative RNA-Seq Analysis Uncovers a Complex Regulatory Network for Soybean Cyst Nematode Resistance in Wild Soybean (Glycine soja). PMID:28852059
Analysis of gene expression profiling variations induced by hsa‑miR‑145‑5p‑overexpression in laryngeal squamous cell carcinoma cell line Tu‑177. PMID:28849105
The effect of Bu Zhong Yi Qi decoction on simulated weightlessness‑induced muscle atrophy and its mechanisms. PMID:28849026
Personalized identification of differentially expressed pathways in pediatric sepsis. PMID:28849000
Uncovering Male Fertility Transition Responsive miRNA in a Wheat Photo-Thermosensitive Genic Male Sterile Line by Deep Sequencing and Degradome Analysis. PMID:28848574
Conservation of Species- and Trait-Based Modeling Network Interactions in Extremely Acidic Microbial Community Assembly. PMID:28848508
The Essential Genome of Burkholderia cenocepacia H111. PMID:28847919
Integration of Metabolomics and Transcriptomics Reveals a Complex Diet of Mycobacterium tuberculosis during Early Macrophage Infection. PMID:28845460
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. PMID:28841418
Untargeted metabolomic analysis and pathway discovery in perinatal asphyxia and hypoxic-ischaemic encephalopathy. PMID:28840775
Comparative Transcriptome Analysis Identified Candidate Genes Related to Bailinggu Mushroom Formation and Genetic Markers for Genetic Analyses and Breeding. PMID:28839254
Logic programming reveals alteration of key transcription factors in multiple myeloma. PMID:28835615
Epigenetic variation between urban and rural populations of Darwin's finches. PMID:28835203
Bioinformatics analysis of gene expression profiling for identification of potential key genes among ischemic stroke. PMID:28834871
Influence of CNTRENE® C100LM carbon nanotube material on the growth and regulation of Escherichia coli. PMID:28828284
Protein microarray analysis identifies key cytokines associated with malignant middle cerebral artery infarction. PMID:28828208
Long-term taxonomic and functional divergence from donor bacterial strains following fecal microbiota transplantation in immunocompromised patients. PMID:28827811
Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis. PMID:28827734
Metabolic Reconstruction and Modeling Microbial Electrosynthesis. PMID:28827682
A Serum Small Molecule Biosignature of Radiation Exposure from Total Body Irradiated Patients. PMID:28825479
Sniffing out the hypoxia volatile metabolic signature of Aspergillus fumigatus. PMID:28825403
Aspergillus niger Secretes Citrate to Increase Iron Bioavailability. PMID:28824560
Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica. PMID:28824553
The heat shock response and humoral immune response are mutually antagonistic in honey bees. PMID:28821863
Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics. PMID:28821734
Space-type radiation induces multimodal responses in the mouse gut microbiome and metabolome. PMID:28821301
A computational method for the identification of candidate drugs for non-small cell lung cancer. PMID:28820893
Silencing of HJURP induces dysregulation of cell cycle and ROS metabolism in bladder cancer cells via PPARγ-SIRT1 feedback loop. PMID:28819432
Interleukin-17 receptor A (IL-17RA) as a central regulator of the protective immune response against Giardia. PMID:28819174
Comparative Genome Analysis of Rathayibacter tritici NCPPB 1953 with Rathayibacter toxicus Strains Can Facilitate Studies on Mechanisms of Nematode Association and Host Infection. PMID:28811754
Identification of key genes and pathways associated with obesity in children. PMID:28810559
Effect of HA330 resin-directed hemoadsorption on a porcine acute respiratory distress syndrome model. PMID:28808944
Identification of Staphylococcus aureus Factors Required for Pathogenicity and Growth in Human Blood. PMID:28808156
Toxoplasma gondii and Neospora caninum induce different host cell responses at proteome-wide phosphorylation events; a step forward for uncovering the biological differences between these closely related parasites. PMID:28803361
RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PMID:28800607
Transcriptional hallmarks of cancer cell lines reveal an emerging role of branched chain amino acid catabolism. PMID:28798381
ODG: Omics database generator - a tool for generating, querying, and analyzing multi-omics comparative databases to facilitate biological understanding. PMID:28797229
Network design and analysis for multi-enzyme biocatalysis. PMID:28797226
The Adaptive Evolution Database (TAED): A New Release of a Database of Phylogenetically Indexed Gene Families from Chordates. PMID:28795237
Aberrantly methylated-differentially expressed genes and pathways in colorectal cancer. PMID:28794688
Identification of key genes and pathways associated with classical Hodgkin lymphoma by bioinformatics analysis. PMID:28791394
Molecular mechanisms of breast cancer metastasis by gene expression profile analysis. PMID:28791367
Identification of the anticancer effects of a novel proteasome inhibitor, ixazomib, on colorectal cancer using a combined method of microarray and bioinformatics analysis. PMID:28790851
A clinician's guide to microbiome analysis. PMID:28790452
Gene and transcript abundances of bacterial type III secretion systems from the rumen microbiome are correlated with methane yield in sheep. PMID:28789673
A network-based method using a random walk with restart algorithm and screening tests to identify novel genes associated with Menière's disease. PMID:28787010
Commensal microbiota maintains alveolar macrophages with a low level of CCL24 production to generate anti-metastatic tumor activity. PMID:28785009
Improving the phenotype predictions of a yeast genome-scale metabolic model by incorporating enzymatic constraints. PMID:28779005
Identification of an early transcriptomic signature of insulin resistance and related diseases in lymphomonocytes of healthy subjects. PMID:28777829
Genome-wide signatures of complex introgression and adaptive evolution in the big cats. PMID:28776029
OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development. PMID:28775143
Comparative genome-wide methylation analysis of longissimus dorsi muscles between Japanese black (Wagyu) and Chinese Red Steppes cattle. PMID:28771560
2-Hydroxyisobutyrylation on histone H4K8 is regulated by glucose homeostasis in Saccharomyces cerevisiae. PMID:28768809
PiiL: visualization of DNA methylation and gene expression data in gene pathways. PMID:28768481
Low-level maternal exposure to nicotine associates with significant metabolic perturbations in second-trimester amniotic fluid. PMID:28759762
Effects of aqueous extract of Arctium lappa L. roots on serum lipid metabolism. PMID:28758851
Transcriptome profiling of monocytes from XLA patients revealed the innate immune function dysregulation due to the BTK gene expression deficiency. PMID:28754963
Krüppel-like factor 4 acts as a potential therapeutic target of Sijunzi decoction for treatment of colorectal cancer. PMID:28752861
Quantifying Gene Regulatory Relationships with Association Measures: A Comparative Study. PMID:28751908
Circulating microRNAs and association with methacholine PC20 in the Childhood Asthma Management Program (CAMP) cohort. PMID:28749975
Prediction of novel target genes and pathways involved in irinotecan-resistant colorectal cancer. PMID:28749961
Unraveling Key Metabolomic Alterations in Wheat Embryos Derived from Freshly Harvested and Water-Imbibed Seeds of Two Wheat Cultivars with Contrasting Dormancy Status. PMID:28747920
Linking the morphological and metabolomic response of Lactuca sativa L exposed to emerging contaminants using GC × GC-MS and chemometric tools. PMID:28747703
Sphingolipid metabolism potential in fecal microbiome and bronchiolitis in infants: a case-control study. PMID:28747215
Combining Genome-Scale Experimental and Computational Methods To Identify Essential Genes in Rhodobacter sphaeroides. PMID:28744485
The Protein Interactome of Streptococcus pneumoniae and Bacterial Meta-interactomes Improve Function Predictions. PMID:28744484
Deficient glutamate biosynthesis triggers a concerted upregulation of ribosomal protein genes in Arabidopsis. PMID:28733652
Inferring microbial interactions in thermophilic and mesophilic anaerobic digestion of hog waste. PMID:28732056
A Simple Representation of Three-Dimensional Molecular Structure. PMID:28731335
Investigation of the molecular mechanisms underlying myotonic dystrophy types 1 and 2 cataracts using microRNA‑target gene networks. PMID:28731161
Microbiome of Trichodesmium Colonies from the North Pacific Subtropical Gyre. PMID:28729854
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
Not just a colourful metaphor: modelling the landscape of cellular development using Hopfield networks. PMID:28725466
Engineering microbial cell factories for the production of plant natural products: from design principles to industrial-scale production. PMID:28724386
Microbial Community Structure and Function Decoupling Across a Phosphorus Gradient in Streams. PMID:28721504
Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia. PMID:28719003
A Transcriptomic Survey of Ion Channel-Based Conotoxins in the Chinese Tubular Cone Snail (Conus betulinus). PMID:28718820
Clinical Significance and Effect of lncRNA HOXA11-AS in NSCLC: A Study Based on Bioinformatics, In Vitro and in Vivo Verification. PMID:28717185
Two microRNA signatures for malignancy and immune infiltration predict overall survival in advanced epithelial ovarian cancer. PMID:28716985
Cryptic oxygen cycling in anoxic marine zones. PMID:28716941
Transcriptome analysis of the sea cucumber (Apostichopus japonicus) with variation in individual growth. PMID:28715451
Microarray analysis reveals key genes and pathways in Tetralogy of Fallot. PMID:28713939
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. PMID:28711280
Clonal competition in BcrAbl-driven leukemia: how transplantations can accelerate clonal conversion. PMID:28709463
Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle. PMID:28706200
Comparative transcriptome combined with morpho-physiological analyses revealed key factors for differential cadmium accumulation in two contrasting sweet sorghum genotypes. PMID:28703450
Metagenomic Analysis of Subtidal Sediments from Polar and Subpolar Coastal Environments Highlights the Relevance of Anaerobic Hydrocarbon Degradation Processes. PMID:28702706
Long noncoding RNA expression profile changes associated with dietary energy in the sheep testis during sexual maturation. PMID:28701734
Integrated analysis of zone-specific protein and metabolite profiles within nitrogen-fixing Medicago truncatula-Sinorhizobium medicae nodules. PMID:28700717
Screening for the protective effect target of deproteinized extract of calf blood and its mechanisms in mice with CCl4-induced acute liver injury. PMID:28700704
Excavation of attractor modules for nasopharyngeal carcinoma via integrating systemic module inference with attract method. PMID:28700035
Insight into synergetic mechanisms of tetracycline and the selective serotonin reuptake inhibitor, sertraline, in a tetracycline-resistant strain of Escherichia coli. PMID:28698674
A Novel Dual Eigen-Analysis of Mouse Multi-Tissues' Expression Profiles Unveils New Perspectives into Type 2 Diabetes. PMID:28698587
Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions. PMID:28698277
Incorporating biological information in sparse principal component analysis with application to genomic data. PMID:28697740
The metabolic analysis of psoriasis identifies the associated metabolites while providing computational models for the monitoring of the disease. PMID:28695330
Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia. PMID:28694917
Screening of potentially crucial genes and regulatory factors involved in epithelial ovarian cancer using microarray analysis. PMID:28693226
The self-inhibitory nature of metabolic networks and its alleviation through compartmentalization. PMID:28691704
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Chinese Herbal Medicine Meets Biological Networks of Complex Diseases: A Computational Perspective. PMID:28690664
Reduced Circulating Levels of miR-433 and miR-133b Are Potential Biomarkers for Parkinson's Disease. PMID:28690499
Transcriptomic analysis identifies a role of PI3K-Akt signalling in the responses of skeletal muscle to acute hypoxia in vivo. PMID:28688178
Transcriptome and metabolome analysis of Ferula gummosa Boiss. to reveal major biosynthetic pathways of galbanum compounds. PMID:28687892
A global evolutionary and metabolic analysis of human obesity gene risk variants. PMID:28687331
Strength of functional signature correlates with effect size in autism. PMID:28687074
Use of fecal volatile organic compound analysis to discriminate between non-vaccinated and BCG-Vaccinated cattle prior to and after Mycobacterium bovis challenge. PMID:28686691
The viable but nonculturable state induction and genomic analyses of Lactobacillus casei BM-LC14617, a beer-spoilage bacterium. PMID:28685978
Metabolomics Applications in Precision Medicine: An Oncological Perspective. PMID:28685691
Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. PMID:28685384
Tumoral expression of drug and xenobiotic metabolizing enzymes in breast cancer patients of different ethnicities with implications to personalized medicine. PMID:28684774
Microarray expression profile of circular RNAs in chronic thromboembolic pulmonary hypertension. PMID:28682884
Logic Modeling in Quantitative Systems Pharmacology. PMID:28681552
Transcriptional response to West Nile virus infection in the zebra finch (Taeniopygia guttata). PMID:28680683
Perspectives and Challenges in Microbial Communities Metabolic Modeling. PMID:28680442
A Novel Unsupervised Algorithm for Biological Process-based Analysis on Cancer. PMID:28680165
Preexisting antibodies can protect against congenital cytomegalovirus infection in monkeys. PMID:28679960
Shaping functional gut microbiota using dietary bioactives to reduce colon cancer risk. PMID:28676459
A statistical framework for biomedical literature mining. PMID:28675924
Pathway-related modules involved in the application of sevoflurane or propofol in off-pump coronary artery bypass graft surgery. PMID:28672899
Interactome analysis of gene expression profiles of cervical cancer reveals dysregulated mitotic gene clusters. PMID:28670392
The Stress-Responding miR-132-3p Shows Evolutionarily Conserved Pathway Interactions. PMID:28667373
Comparative genomic analysis of Mycobacterium neoaurum MN2 and MN4 substrate and product tolerance. PMID:28664368
Altered miRNA expression network in locus coeruleus of depressed suicide subjects. PMID:28663595
Frontline Science: c-Myc regulates P-selectin glycoprotein ligand-1 expression in monocytes during HIV-1 infection. PMID:28663244
Relating genomic characteristics to environmental preferences and ubiquity in different microbial taxa. PMID:28662636
RBM10 promotes transformation-associated processes in small cell lung cancer and is directly regulated by RBM5. PMID:28662214
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. PMID:28661399
Computational Methods for Characterizing Cancer Mutational Heterogeneity. PMID:28659971
Unravelling the relationship between the tsetse fly and its obligate symbiont Wigglesworthia: transcriptomic and metabolomic landscapes reveal highly integrated physiological networks. PMID:28659447
16S sequencing and functional analysis of the fecal microbiome during treatment of newly diagnosed pediatric inflammatory bowel disease. PMID:28658154
Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica. PMID:28655556
Dysfunction of PLA2G6 and CYP2C44-associated network signals imminent carcinogenesis from chronic inflammation to hepatocellular carcinoma. PMID:28655161
A data analysis framework for biomedical big data: Application on mesoderm differentiation of human pluripotent stem cells. PMID:28654683
Alterations of expression of inflammation/immune-related genes in the dorsal and ventral striatum of adult C57BL/6J mice following chronic oxycodone self-administration: a RNA sequencing study. PMID:28653080
Flipping between Polycomb repressed and active transcriptional states introduces noise in gene expression. PMID:28652613
Downregulation of PKCζ/Pard3/Pard6b is responsible for lung adenocarcinoma cell EMT and invasion. PMID:28652146
A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq. PMID:28646208
High expression of Collagen Triple Helix Repeat Containing 1 (CTHRC1) facilitates progression of oesophageal squamous cell carcinoma through MAPK/MEK/ERK/FRA-1 activation. PMID:28645305
Quantitative Phosphoproteomics Reveals a Role for Collapsin Response Mediator Protein 2 in PDGF-Induced Cell Migration. PMID:28638064
Exploring Wound-Healing Genomic Machinery with a Network-Based Approach. PMID:28635674
Proteomic analysis reveals large amounts of decomposition enzymes and major metabolic pathways involved in algicidal process of Trametes versicolor F21a. PMID:28634367
Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis. PMID:28633446
Protein expression in tension wood formation monitored at high tissue resolution in Populus. PMID:28633298
The islet-resident macrophage is in an inflammatory state and senses microbial products in blood. PMID:28630088
Exposure of Induced Pluripotent Stem Cell-Derived Vascular Endothelial and Smooth Muscle Cells in Coculture to Hemodynamics Induces Primary Vascular Cell-Like Phenotypes. PMID:28628273
Gut microbiome and serum metabolome alterations in obesity and after weight-loss intervention. PMID:28628112
Data mining and pathway analysis of glucose-6-phosphate dehydrogenase with natural language processing. PMID:28627690
Bioinformatics analysis of transcription profiling of solid pseudopapillary neoplasm of the pancreas. PMID:28627654
Complete genome sequence and description of Lactococcus garvieae M14 isolated from Algerian fermented milk. PMID:28626583
DUSP1 and KCNJ2 mRNA upregulation can serve as a biomarker of mechanical asphyxia-induced death in cardiac tissue. PMID:28624985
Dysbiosis in chronic periodontitis: Key microbial players and interactions with the human host. PMID:28623321
A knowledge-based T2-statistic to perform pathway analysis for quantitative proteomic data. PMID:28622336
Proteome profiling in IL-1β and VEGF-activated human umbilical vein endothelial cells delineates the interlink between inflammation and angiogenesis. PMID:28617818
Drug repositioning for enzyme modulator based on human metabolite-likeness. PMID:28617219
RNAseq based transcriptomics study of SMCs from carotid atherosclerotic plaque: BMP2 and IDs proteins are crucial regulators of plaque stability. PMID:28615715
Improving the detection of pathways in genome-wide association studies by combined effects of SNPs from Linkage Disequilibrium blocks. PMID:28615668
Dammarane Sapogenins Ameliorates Neurocognitive Functional Impairment Induced by Simulated Long-Duration Spaceflight. PMID:28611667
A Systems Biology Approach Identifies FUT8 as a Driver of Melanoma Metastasis. PMID:28609658
Transcriptome of Pterospermum kingtungense provides implications on the mechanism underlying its rapid vegetative growth and limestone adaption. PMID:28600559
Functional dissection of human targets for KSHV-encoded miRNAs using network analysis. PMID:28600495
Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data. PMID:28598965
Label-free quantitative proteomics of Corynebacterium pseudotuberculosis isolates reveals differences between Biovars ovis and equi strains. PMID:28595597
Sequencing, de novo assembling, and annotating the genome of the endangered Chinese crocodile lizard Shinisaurus crocodilurus. PMID:28595343
Identification of key microRNAs and genes in preeclampsia by bioinformatics analysis. PMID:28594854
An analysis of gene expression data involving examination of signaling pathways activation reveals new insights into the mechanism of action of minoxidil topical foam in men with androgenetic alopecia. PMID:28594262
The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples. PMID:28592326
Metabolomic Profiling of Soybeans (Glycine max L.) Reveals the Importance of Sugar and Nitrogen Metabolism under Drought and Heat Stress. PMID:28587097
Comparative proteomic analysis of eggplant (Solanum melongena L.) heterostylous pistil development. PMID:28586360
A novel approach to select differential pathways associated with hypertrophic cardiomyopathy based on gene co‑expression analysis. PMID:28586052
Identification and functional analysis of the risk microRNAs associated with cerebral low-grade glioma prognosis. PMID:28586047
JDINAC: joint density-based non-parametric differential interaction network analysis and classification using high-dimensional sparse omics data. PMID:28582486
Liquid Chromatography Mass Spectrometry-Based Metabolite Pathway Analyses of Myeloma and Non-Hodgkin's Lymphoma Patients. PMID:28580307
RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. PMID:28577019
Monitoring of the spatial and temporal dynamics of BER/SSBR pathway proteins, including MYH, UNG2, MPG, NTH1 and NEIL1-3, during DNA replication. PMID:28575236
Downregulation of TRPM7 suppressed migration and invasion by regulating epithelial-mesenchymal transition in prostate cancer cells. PMID:28573641
Databases, Repositories, and Other Data Resources in Structural Biology. PMID:28573593
Understanding the mechanisms of dormancy in an invasive alien Sycamore lace bug, Corythucha ciliata through transcript and metabolite profiling. PMID:28572631
Genetic subclone architecture of tumor clone-initiating cells in colorectal cancer. PMID:28572216
The replicative lifespan-extending deletion of SGF73 results in altered ribosomal gene expression in yeast. PMID:28568901
Establishment of the model system between phytochemicals and gene expression profiles in Macrosclereid cells of Medicago truncatula. PMID:28566751
Identification of potential biomarkers of sepsis using bioinformatics analysis. PMID:28565754
Identification of Differentially Expressed Micrornas Associate with Glucose Metabolism in Different Organs of Blunt Snout Bream (Megalobrama amblycephala). PMID:28561770
Systematic discovery of mutation-specific synthetic lethals by mining pan-cancer human primary tumor data. PMID:28561042
Prediction of marker genes associated with hypertension by bioinformatics analyses. PMID:28560446
pathVar: a new method for pathway-based interpretation of gene expression variability. PMID:28560097
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype. PMID:28559929
Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments. PMID:28559911
Bactericidal potential of silver nanoparticles synthesized using cell-free extract of Comamonas acidovorans: in vitro and in silico approaches. PMID:28555428
Time-Resolved Transcriptomics and Constraint-Based Modeling Identify System-Level Metabolic Features and Overexpression Targets to Increase Spiramycin Production in Streptomyces ambofaciens. PMID:28553270
Lysine Acetylome Analysis Reveals Photosystem II Manganese-stabilizing Protein Acetylation is Involved in Negative Regulation of Oxygen Evolution in Model Cyanobacterium Synechococcus sp. PCC 7002. PMID:28550166
GLADIATOR: a global approach for elucidating disease modules. PMID:28549478
Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. PMID:28549454
Different adaptation strategies of two citrus scion/rootstock combinations in response to drought stress. PMID:28545114
CD44 deletion leading to attenuation of experimental autoimmune encephalomyelitis results from alterations in gut microbiome in mice. PMID:28543188
Genome-wide association and pathway analysis of left ventricular function after anthracycline exposure in adults. PMID:28542097
Comprehensive whole genome sequence analyses yields novel genetic and structural insights for Intellectual Disability. PMID:28539120
Identifying CpG sites with different differential methylation frequencies in colorectal cancer tissues based on individualized differential methylation analysis. PMID:28537885
Fipronil-induced enantioselective developmental toxicity to zebrafish embryo-larvae involves changes in DNA methylation. PMID:28536466
The draft genome of blunt snout bream (Megalobrama amblycephala) reveals the development of intermuscular bone and adaptation to herbivorous diet. PMID:28535200
Unique identifiers for small molecules enable rigorous labeling of their atoms. PMID:28534867
Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris. PMID:28534062
Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes. PMID:28533961
Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug. PMID:28530702
SCENERY: a web application for (causal) network reconstruction from cytometry data. PMID:28525568
Candidate miRNAs and pathogenesis investigation for hepatocellular carcinoma based on bioinformatics analysis. PMID:28521446
From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics. PMID:28520864
A Study of the Microbial Spatial Heterogeneity of Bahamian Thrombolites Using Molecular, Biochemical, and Stable Isotope Analyses. PMID:28520472
Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms. PMID:28518075
De novo Transcriptome Profiling of Flowers, Flower Pedicels and Pods of Lupinus luteus (Yellow Lupine) Reveals Complex Expression Changes during Organ Abscission. PMID:28512462
Using an Event-History with Risk-Free Model to Study the Genetics of Alcoholism. PMID:28512340
Clone temporal centrality measures for incomplete sequences of graph snapshots. PMID:28511665
Network modelling of gene regulation. PMID:28510232
Application of a systems approach to study developmental gene regulation. PMID:28510076
Tracing the Enterococci from Paleozoic Origins to the Hospital. PMID:28502769
Thermal adaptation strategies of the extremophile bacterium Thermus filiformis based on multi-omics analysis. PMID:28500387
Bovis Bacillus Calmette-Guerin (BCG) infection induces exosomal miRNA release by human macrophages. PMID:28499455
Metabolomics analysis: Finding out metabolic building blocks. PMID:28493998
Identification of Long Noncoding RNAs Deregulated in Papillary Thyroid Cancer and Correlated with BRAFV600E Mutation by Bioinformatics Integrative Analysis. PMID:28490781
NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation. PMID:28487382
Transcriptome profiling of litchi leaves in response to low temperature reveals candidate regulatory genes and key metabolic events during floral induction. PMID:28486930
Stratification of clear cell renal cell carcinoma (ccRCC) genomes by gene-directed copy number alteration (CNA) analysis. PMID:28486536
Investigating the neuroimmunogenic architecture of schizophrenia. PMID:28485405
De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge. PMID:28484475
Effects of cold-acclimation on gene expression in Fall field cricket (Gryllus pennsylvanicus) ionoregulatory tissues. PMID:28482796
Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. PMID:28482794
Metabolic reprogramming in clear cell renal cell carcinoma. PMID:28480903
An Integrating Approach for Genome-Wide Screening of MicroRNA Polymorphisms Mediated Drug Response Alterations. PMID:28480217
A review of metabolomics approaches and their application in identifying causal pathways of childhood asthma. PMID:28479327
Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. PMID:28478508
Personalized Drug Analysis in B Cell Chronic Lymphocytic Leukemia Patients. PMID:28477439
Using scale and feather traits for module construction provides a functional approach to chicken epidermal development. PMID:28477104
Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata. PMID:28475810
Metabolic Dysregulation after Neutron Exposures Expected from an Improvised Nuclear Device. PMID:28475424
Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler. PMID:28473720
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. PMID:28472271
Identifying novel fruit-related genes in Arabidopsis thaliana based on the random walk with restart algorithm. PMID:28472169
Gene expression profiling in Pekin duck embryonic breast muscle. PMID:28472139
PAIRS: Prediction of Activation/Inhibition Regulation Signaling Pathway. PMID:28469669
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. PMID:28469601
Graphical Modeling Meets Systems Pharmacology. PMID:28469411
Lipidomics and RNA-Seq Study of Lipid Regulation in Aphis gossypii parasitized by Lysiphlebia japonica. PMID:28465512
Mercury-induced epigenetic transgenerational inheritance of abnormal neurobehavior is correlated with sperm epimutations in zebrafish. PMID:28464002
The Response to 2-Aminoacrylate Differs in Escherichia coli and Salmonella enterica, despite Shared Metabolic Components. PMID:28461448
The physical characteristics of human proteins in different biological functions. PMID:28459865
Predictive Genomic Analyses Inform the Basis for Vitamin Metabolism and Provisioning in Bacteria-Arthropod Endosymbioses. PMID:28455417
Microarray based analysis of gene regulation by mesenchymal stem cells in breast cancer. PMID:28454465
Variable habitat conditions drive species covariation in the human microbiota. PMID:28448493
PARP3 is a promoter of chromosomal rearrangements and limits G4 DNA. PMID:28447610
Transcriptome analysis of creeping bentgrass exposed to drought stress and polyamine treatment. PMID:28445484
Unveiling differentially expressed genes upon regulation of transcription factors in sepsis. PMID:28444588
Draft genome of the lined seahorse, Hippocampus erectus. PMID:28444302
Biological Aging and the Human Gut Microbiota. PMID:28444190
Insight into the evolution of microbial metabolism from the deep-branching bacterium, Thermovibrio ammonificans. PMID:28436819
Hierarchical Feature Selection Incorporating Known and Novel Biological Information: Identifying Genomic Features Related to Prostate Cancer Recurrence. PMID:28435175
Genome characteristics of the proteorhodopsin-containing marine flavobacterium Polaribacter dokdonensis DSW-5. PMID:28432541
Disease biomarker identification from gene network modules for metastasized breast cancer. PMID:28432361
A microRNA-mRNA expression network during oral siphon regeneration in Ciona. PMID:28432214
Bioinformatics analysis of key genes and latent pathway interactions based on the anaplastic thyroid carcinoma gene expression profile. PMID:28428828
Genome Sequence of Microbacterium sp. Strain TPU 3598, a Lumichrome Producer. PMID:28428303
Transcriptional landscape of human cancers. PMID:28427185
Multiple components of PKA and TGF-β pathways are mutated in pseudomyxoma peritonei. PMID:28426742
Unified Alignment of Protein-Protein Interaction Networks. PMID:28424527
Exome Analysis of Rare and Common Variants within the NOD Signaling Pathway. PMID:28422189
Transcriptomic and Metabolomics Profiling of Phage-Host Interactions between Phage PaP1 and Pseudomonas aeruginosa. PMID:28421049
Global gene expression profiling of healthy human brain and its application in studying neurological disorders. PMID:28420888
Transcriptional changes in litchi (Litchi chinensis Sonn.) inflorescences treated with uniconazole. PMID:28419137
The E. coli molecular phenotype under different growth conditions. PMID:28417974
L1000CDS2: LINCS L1000 characteristic direction signatures search engine. PMID:28413689
Comparison of different cell type correction methods for genome-scale epigenetics studies. PMID:28410574
Exploring the key genes and pathways in enchondromas using a gene expression microarray. PMID:28410203
Ecology of cold environments: new insights of bacterial metabolic adaptation through an integrated genomic-phenomic approach. PMID:28404986
Determining the presence of asthma-related molecules and salivary contamination in exhaled breath condensate. PMID:28403875
An oil containing EPA and DHA from transgenic Camelina sativa to replace marine fish oil in feeds for Atlantic salmon (Salmo salar L.): Effects on intestinal transcriptome, histology, tissue fatty acid profiles and plasma biochemistry. PMID:28403232
Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce. PMID:28401891
Study of intra-inter species protein-protein interactions for potential drug targets identification and subsequent drug design for Escherichia coli O104:H4 C277-11. PMID:28401513
Rare copy number variants in patients with congenital conotruncal heart defects. PMID:28398664
Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. PMID:28396410
Inhibition of expression of the circadian clock gene Period causes metabolic abnormalities including repression of glycometabolism in Bombyx mori cells. PMID:28393918
Identification of Biomarkers for Schistosoma-Associated Pulmonary Arterial Hypertension Based on RNA-Seq Data of Mouse Whole Lung Tissues. PMID:28393260
Genotype Correlation Analysis Reveals Pathway-Based Functional Disequilibrium and Potential Epistasis in the Human Interactome. PMID:28393142
High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice. PMID:28390422
RNA sequence analysis of rat acute experimental pancreatitis with and without fatty liver: a gene expression profiling comparative study. PMID:28389636
Establishment of apoptotic regulatory network for genetic markers of colorectal cancer and optimal selection of traditional Chinese medicine target. PMID:28386190
Establishment of apoptotic regulatory network for genetic markers of colorectal cancer. PMID:28386169
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PMID:28384184
Comparative proteomics of Rhizopus delemar ATCC 20344 unravels the role of amino acid catabolism in fumarate accumulation. PMID:28382234
Linkages between changes in the 3D organization of the genome and transcription during myotube differentiation in vitro. PMID:28381300
Whole transcriptome profiling of the human hippocampus suggests an involvement of the KIBRA rs17070145 polymorphism in differential activation of the MAPK signaling pathway. PMID:28380666
Gracob: a novel graph-based constant-column biclustering method for mining growth phenotype data. PMID:28379298
The Transcriptome of Leishmania major Developmental Stages in Their Natural Sand Fly Vector. PMID:28377524
Evolutionary gradient of predicted nuclear localization signals (NLS)-bearing proteins in genomes of family Planctomycetaceae. PMID:28376722
Omics Approaches to Identify Potential Biomarkers of Inflammatory Diseases in the Focal Adhesion Complex. PMID:28373027
Genome sequence of a rice pest, the white-backed planthopper (Sogatella furcifera). PMID:28369349
Genome-wide sequencing of longan (Dimocarpus longan Lour.) provides insights into molecular basis of its polyphenol-rich characteristics. PMID:28368449
Genetic variation in the exome: Associations with alcohol and tobacco co-use. PMID:28368157
Transcriptome Analysis of the Melon-Fusarium oxysporum f. sp. melonis Race 1.2 Pathosystem in Susceptible and Resistant Plants. PMID:28367157
miRnalyze: an interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways. PMID:28365733
A Cell-Surface Membrane Protein Signature for Glioblastoma. PMID:28365151
Interrogating the topological robustness of gene regulatory circuits by randomization. PMID:28362798
Transcriptomics and proteomic studies reveal acaricidal mechanism of octadecanoic acid-3, 4 - tetrahydrofuran diester against Sarcoptes scabiei var. cuniculi. PMID:28361965
SNP by SNP by environment interaction network of alcoholism. PMID:28361705
Plant miRNAs found in human circulating system provide evidences of cross kingdom RNAi. PMID:28361700
Prior knowledge guided active modules identification: an integrated multi-objective approach. PMID:28361699
PINTnet: construction of condition-specific pathway interaction network by computing shortest paths on weighted PPI. PMID:28361687
Identifying miRNA sponge modules using biclustering and regulatory scores. PMID:28361682
Towards targeted combinatorial therapy design for the treatment of castration-resistant prostate cancer. PMID:28361666
Combinatorial Ranking of Gene Sets to Predict Disease Relapse: The Retinoic Acid Pathway in Early Prostate Cancer. PMID:28361034
24h-gene variation effect of combined bevacizumab/erlotinib in advanced non-squamous non-small cell lung cancer using exon array blood profiling. PMID:28359318
Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. PMID:28356768
Comparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation. PMID:28356072
Microbial community and metabolic pathway succession driven by changed nutrient inputs in tailings: effects of different nutrients on tailing remediation. PMID:28352108
Tissue and time specific expression pattern of interferon regulated genes in the chicken. PMID:28351377
Molecular, phenotypic, and sample-associated data to describe pluripotent stem cell lines and derivatives. PMID:28350385
Spatial transcriptome analysis provides insights of key gene(s) involved in steroidal saponin biosynthesis in medicinally important herb Trillium govanianum. PMID:28349986
Comparative genomics and evolution of transcriptional regulons in Proteobacteria. PMID:28348857
Polysaccharide utilization loci and nutritional specialization in a dominant group of butyrate-producing human colonic Firmicutes. PMID:28348841
Proteogenomic integration reveals therapeutic targets in breast cancer xenografts. PMID:28348404
Genome Reduction and Microbe-Host Interactions Drive Adaptation of a Sulfur-Oxidizing Bacterium Associated with a Cold Seep Sponge. PMID:28345060
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite. PMID:28340554
Expression of Yes-associated protein 1 and its clinical significance in ovarian serous cystadenocarcinoma. PMID:28339095
EXPath tool-a system for comprehensively analyzing regulatory pathways and coexpression networks from high-throughput transcriptome data. PMID:28338930
Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium. PMID:28337181
Induction of apoptosis and ganoderic acid biosynthesis by cAMP signaling in Ganoderma lucidum. PMID:28336949
Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles. PMID:28336542
Lung function associated gene Integrator Complex subunit 12 regulates protein synthesis pathways. PMID:28335732
Testing the Ret and Sema3d genetic interaction in mouse enteric nervous system development. PMID:28334784
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. PMID:28334094
Epigenomic annotation of noncoding mutations identifies mutated pathways in primary liver cancer. PMID:28333948
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. PMID:28333345
Transcriptome analysis of endometrial tissues following GnRH agonist treatment in a mouse adenomyosis model. PMID:28331289
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis. PMID:28330499
The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis. PMID:28329862
Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q. PMID:28327996
Draft genome of the honey bee ectoparasitic mite, Tropilaelaps mercedesae, is shaped by the parasitic life history. PMID:28327890
BCIP: a gene-centered platform for identifying potential regulatory genes in breast cancer. PMID:28327601
metaX: a flexible and comprehensive software for processing metabolomics data. PMID:28327092
Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores. PMID:28326099
Dietary emulsifiers directly alter human microbiota composition and gene expression ex vivo potentiating intestinal inflammation. PMID:28325746
On DNA numerical representations for genomic similarity computation. PMID:28323839
Association between fatty acid metabolism in the brain and Alzheimer disease neuropathology and cognitive performance: A nontargeted metabolomic study. PMID:28323825
Age-associated DNA methylation changes in naive CD4+ T cells suggest an evolving autoimmune epigenotype in aging T cells. PMID:28322571
Reconstruction and signal propagation analysis of the Syk signaling network in breast cancer cells. PMID:28306714
Draft Genome Sequence of Rhizobium sp. Strain TBD182, an Antagonist of the Plant-Pathogenic Fungus Fusarium oxysporum, Isolated from a Novel Hydroponics System Using Organic Fertilizer. PMID:28302768
Simulated herbivory in chickpea causes rapid changes in defense pathways and hormonal transcription networks of JA/ethylene/GA/auxin within minutes of wounding. PMID:28300183
Identification of lymph node metastasis-related microRNAs in lung adenocarcinoma and analysis of the underlying mechanisms using a bioinformatics approach. PMID:28299977
Apoptosis, Toll-like, RIG-I-like and NOD-like Receptors Are Pathways Jointly Induced by Diverse Respiratory Bacterial and Viral Pathogens. PMID:28298903
Weaning age influences the severity of gastrointestinal microbiome shifts in dairy calves. PMID:28298634
Metabolomics approaches in pancreatic adenocarcinoma: tumor metabolism profiling predicts clinical outcome of patients. PMID:28298227
CATTLE (CAncer treatment treasury with linked evidence): An integrated knowledge base for personalized oncology research and practice. PMID:28296354
Integrating miRNA and mRNA Expression Profiling Uncovers miRNAs Underlying Fat Deposition in Sheep. PMID:28293627
Novel aromatase inhibitors selection using induced fit docking and extra precision methods: Potential clinical use in ER-alpha-positive breast cancer. PMID:28293075
Comprehensive discovery of subsample gene expression components by information explanation: therapeutic implications in cancer. PMID:28292312
Understanding Physiology in the Continuum: Integration of Information from Multiple -Omics Levels. PMID:28289389
MiR-153 Regulates Amelogenesis by Targeting Endocytotic and Endosomal/lysosomal Pathways-Novel Insight into the Origins of Enamel Pathologies. PMID:28287144
Support for phosphoinositol 3 kinase and mTOR inhibitors as treatment for lupus using in-silico drug-repurposing analysis. PMID:28284231
The essential and downstream common proteins of amyotrophic lateral sclerosis: A protein-protein interaction network analysis. PMID:28282387
Variability in statin-induced changes in gene expression profiles of pancreatic cancer. PMID:28276528
Protein Kinase CK2: Intricate Relationships within Regulatory Cellular Networks. PMID:28273877
Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle. PMID:28272430
Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome. PMID:28267153
IODNE: An integrated optimization method for identifying the deregulated subnetwork for precision medicine in cancer. PMID:28266149
High quality draft genome sequence of an extremely halophilic archaeon Natrinema altunense strain AJ2T. PMID:28265340
GeneAnalytics Pathway Analysis and Genetic Overlap among Autism Spectrum Disorder, Bipolar Disorder and Schizophrenia. PMID:28264500
Parvovirus B19 NS1 protein induces cell cycle arrest at G2-phase by activating the ATR-CDC25C-CDK1 pathway. PMID:28264028
Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients. PMID:28263955
Whole-genome sequencing identifies common-to-rare variants associated with human blood metabolites. PMID:28263315
Data-Driven Discovery of Extravasation Pathway in Circulating Tumor Cells. PMID:28262832
Impact of Westernized Diet on Gut Microbiota in Children on Leyte Island. PMID:28261164
Subgingival dysbiosis in smoker and non‑smoker patients with chronic periodontitis. PMID:28260061
Identifying and Analyzing Novel Epilepsy-Related Genes Using Random Walk with Restart Algorithm. PMID:28255556
Transgenic expression of fungal accessory hemicellulases in Arabidopsis thaliana triggers transcriptional patterns related to biotic stress and defense response. PMID:28253318
Bioresources inner-recycling between bioflocculation of Microcystis aeruginosa and its reutilization as a substrate for bioflocculant production. PMID:28252111
A taxonomy of visualization tasks for the analysis of biological pathway data. PMID:28251869
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution. PMID:28250803
Transcriptomic analyses reveal biosynthetic genes related to rosmarinic acid in Dracocephalum tanguticum. PMID:28250432
Challenges and Strategies for Proteome Analysis of the Interaction of Human Pathogenic Fungi with Host Immune Cells. PMID:28248281
Leaf transcriptome analysis of a subtropical evergreen broadleaf plant, wild oil-tea camellia (Camellia oleifera), revealing candidate genes for cold acclimation. PMID:28241790
Impact of Exercise and Aging on Rat Urine and Blood Metabolome. An LC-MS Based Metabolomics Longitudinal Study. PMID:28241477
Cyclin Y-mediated transcript profiling reveals several important functional pathways regulated by Cyclin Y in hippocampal neurons. PMID:28241067
Effects upon metabolic pathways and energy production by Sb(III) and As(III)/Sb(III)-oxidase gene aioA in Agrobacterium tumefaciens GW4. PMID:28241045
Comparative pan genome analysis of oral Prevotella species implicated in periodontitis. PMID:28236274
Metabolic anchor reactions for robust biorefining. PMID:28232136
A Comprehensive Analysis of Metabolomics and Transcriptomics in Cervical Cancer. PMID:28225065
Identification of novel cancer therapeutic targets using a designed and pooled shRNA library screen. PMID:28223711
Identification of host cellular proteins that interact with the M protein of a highly pathogenic porcine reproductive and respiratory syndrome virus vaccine strain. PMID:28222748
Pathway-wide association study identifies five shared pathways associated with schizophrenia in three ancestral distinct populations. PMID:28221366
Individual Signatures Define Canine Skin Microbiota Composition and Variability. PMID:28220148
Differential Gene Expression Analysis in Polygonum minus Leaf upon 24 h of Methyl Jasmonate Elicitation. PMID:28220135
Temporal Stability and the Effect of Transgenerational Transfer on Fecal Microbiota Structure in a Long Distance Migratory Bird. PMID:28220109
A Lipidomic and Metabolomic Serum Signature from Nonhuman Primates Exposed to Ionizing Radiation. PMID:28220056
Genomic Characterization of Dairy Associated Leuconostoc Species and Diversity of Leuconostocs in Undefined Mixed Mesophilic Starter Cultures. PMID:28217118
An In Silico Identification of Common Putative Vaccine Candidates against Treponema pallidum: A Reverse Vaccinology and Subtractive Genomics Based Approach. PMID:28216574
Genome-wide identification of direct HBx genomic targets. PMID:28212627
RNA-Seq of Guar (Cyamopsis tetragonoloba, L. Taub.) Leaves: De novo Transcriptome Assembly, Functional Annotation and Development of Genomic Resources. PMID:28210265
Altered hepatic lipid metabolism in mice lacking both the melanocortin type 4 receptor and low density lipoprotein receptor. PMID:28207798
Using predictive specificity to determine when gene set analysis is biologically meaningful. PMID:28204549
Exploring targeted therapy of osteosarcoma using proteomics data. PMID:28203090
An integrative metabolomics and transcriptomics study to identify metabolic alterations in aged skin of humans in vivo. PMID:28201987
An approach to infer putative disease-specific mechanisms using neighboring gene networks. PMID:28200075
Systematic analyses of drugs and disease indications in RepurposeDB reveal pharmacological, biological and epidemiological factors influencing drug repositioning. PMID:28200013
β-Thalassemia Patients Revealed a Significant Change of Untargeted Metabolites in Comparison to Healthy Individuals. PMID:28198811
Electroacupuncture induces acute changes in cerebral cortical miRNA profile, improves cerebral blood flow and alleviates neurological deficits in a rat model of stroke. PMID:28197190
Metatranscriptomics Reveals the Active Bacterial and Eukaryotic Fibrolytic Communities in the Rumen of Dairy Cow Fed a Mixed Diet. PMID:28197133
The transcriptional activity of hepatocyte nuclear factor 4 alpha is inhibited via phosphorylation by ERK1/2. PMID:28196117
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods. PMID:28194174
The post-genomic era of biological network alignment. PMID:28194172
Optimal cancer prognosis under network uncertainty. PMID:28194170
Incorporating prior biological knowledge for network-based differential gene expression analysis using differentially weighted graphical LASSO. PMID:28187708
Doxycycline directly targets PAR1 to suppress tumor progression. PMID:28187433
Transcriptome analysis reveals a complex interplay between resistance and effector genes during the compatible lentil-Colletotrichum lentis interaction. PMID:28186158
Var2GO: a web-based tool for gene variants selection. PMID:28185576
Comparative Transcriptomics Reveals Discrete Survival Responses of S. aureus and S. epidermidis to Sapienic Acid. PMID:28179897
Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome. PMID:28179006
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. PMID:28178989
Comparative transcriptomic analysis of mice liver treated with different AMPK activators in a mice model of atherosclerosis. PMID:28178661
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. PMID:28176778
Integrative analysis of copy number and transcriptional expression profiles in esophageal cancer to identify a novel driver gene for therapy. PMID:28169357
A novel signal transduction protein: Combination of solute binding and tandem PAS-like sensor domains in one polypeptide chain. PMID:28168783
Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet. PMID:28167213
The PeptideAtlas of the Domestic Laying Hen. PMID:28166638
Single-cell spatial reconstruction reveals global division of labour in the mammalian liver. PMID:28166538
Genetic loci associated with chronic obstructive pulmonary disease overlap with loci for lung function and pulmonary fibrosis. PMID:28166215
Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells. PMID:28159795
Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes. PMID:28158295
Deep-proteome mapping of WM-266-4 human metastatic melanoma cells: From oncogenic addiction to druggable targets. PMID:28158294
Alteration of Multiple Leukocyte Gene Expression Networks is Linked with Magnetic Resonance Markers of Prognosis After Acute ST-Elevation Myocardial Infarction. PMID:28155873
The extraction of drug-disease correlations based on module distance in incomplete human interactome. PMID:28155709
Prioritizing biological pathways by recognizing context in time-series gene expression data. PMID:28155707
Global inference of disease-causing single nucleotide variants from exome sequencing data. PMID:28155632
Mining the Proteome of Fusobacterium nucleatum subsp. nucleatum ATCC 25586 for Potential Therapeutics Discovery: An In Silico Approach. PMID:28154519
Genomic variants in mouse model induced by azoxymethane and dextran sodium sulfate improperly mimic human colorectal cancer. PMID:28154415
Draft Genome Sequence of Staphylococcus hominis BHG17 Isolated from Wild Bar-Headed Goose (Anser indicus) Feces. PMID:28153901
Differentially expressed miR-3680-5p is associated with parathyroid hormone regulation in peritoneal dialysis patients. PMID:28152049
Breed and adaptive response modulate bovine peripheral blood cells' transcriptome. PMID:28149510
Meta-analytic support vector machine for integrating multiple omics data. PMID:28149325
Survey of (Meta)genomic Approaches for Understanding Microbial Community Dynamics. PMID:28148977
Differential DNA Methylation Regions in Adult Human Sperm following Adolescent Chemotherapy: Potential for Epigenetic Inheritance. PMID:28146567
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. PMID:28143596
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Regulation of miR-29b-1/a transcription and identification of target mRNAs in CHO-K1 cells. PMID:28137615
Microbial production of vitamin B12: a review and future perspectives. PMID:28137297
Global Proteome Changes in the Rat Diaphragm Induced by Endurance Exercise Training. PMID:28135290
Identification of Entry Factors Involved in Hepatitis C Virus Infection Based on Host-Mimicking Short Linear Motifs. PMID:28129350
Differential methylation of genes in individuals exposed to maternal diabetes in utero. PMID:28127622
Linking Peripartal Dynamics of Ruminal Microbiota to Dietary Changes and Production Parameters. PMID:28127294
Identification of the molecular mechanisms underlying dilated cardiomyopathy via bioinformatic analysis of gene expression profiles. PMID:28123501
Metabolite Profiling of adh1 Mutant Response to Cold Stress in Arabidopsis. PMID:28123394
CD99 is a therapeutic target on disease stem cells in myeloid malignancies. PMID:28123069
Fast and simple protein-alignment-guided assembly of orthologous gene families from microbiome sequencing reads. PMID:28122610
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. PMID:28122605
Range expansion underlies historical introgressive hybridization in the Iberian hare. PMID:28120863
GSAR: Bioconductor package for Gene Set analysis in R. PMID:28118818
Dataset on differential gene expression analysis for splenic transcriptome profiling and the transcripts related to six immune pathways in grass carp. PMID:28116337
A systematic comparative evaluation of biclustering techniques. PMID:28114903
Scalable Parameter Estimation for Genome-Scale Biochemical Reaction Networks. PMID:28114351
Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae. PMID:28106722
The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. PMID:28106101
Shigatoxin encoding Bacteriophage ϕ24B modulates bacterial metabolism to raise antimicrobial tolerance. PMID:28106081
Phenotype-Specific Association of Single-Nucleotide Polymorphisms with Heart Failure and Preserved Ejection Fraction: a Genome-Wide Association Analysis of the Cardiovascular Health Study. PMID:28105587
Metagenomic Analysis of Hot Springs in Central India Reveals Hydrocarbon Degrading Thermophiles and Pathways Essential for Survival in Extreme Environments. PMID:28105025
Screening and analysis of breast cancer genes regulated by the human mammary microenvironment in a humanized mouse model. PMID:28101242
Transcriptomic response of wolf spider, Pardosa pseudoannulata, to transgenic rice expressing Bacillus thuringiensis Cry1Ab protein. PMID:28100213
Conserved gene expression in sperm reservoirs between birds and mammals in response to mating. PMID:28100167
On joint estimation of Gaussian graphical models for spatial and temporal data. PMID:28099997
Systematic analysis of microarray datasets to identify Parkinson's disease‑associated pathways and genes. PMID:28098893
Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes. PMID:28097055
Nutrition, microRNAs, and Human Health. PMID:28096131
Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D. PMID:28094339
A transcriptome analysis focusing on inflammation-related genes of grass carp intestines following infection with Aeromonas hydrophila. PMID:28094307
Urinary Exosomes Contain MicroRNAs Capable of Paracrine Modulation of Tubular Transporters in Kidney. PMID:28094285
Global open data management in metabolomics. PMID:28092796
microRNAs and DICER1 are regulated by 1,25-dihydroxyvitamin D in prostate stroma. PMID:28089917
A genome-wide scan for genes under balancing selection in Drosophila melanogaster. PMID:28086750
Transcriptomic Analysis of Laribacter hongkongensis Reveals Adaptive Response Coupled with Temperature. PMID:28085929
Combining Chemical Profiling and Network Analysis to Investigate the Pharmacology of Complex Prescriptions in Traditional Chinese Medicine. PMID:28084407
Altered Pathway Analyzer: A gene expression dataset analysis tool for identification and prioritization of differentially regulated and network rewired pathways. PMID:28084397
Landscape of Fluid Sets of Hairpin-Derived 21-/24-nt-Long Small RNAs at Seed Set Uncovers Special Epigenetic Features in Picea glauca. PMID:28082604
Complete Genome Sequence of Spiroplasma sp. TU-14. PMID:28082500
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
Integrated omics analyses reveal the details of metabolic adaptation of Clostridium thermocellum to lignocellulose-derived growth inhibitors released during the deconstruction of switchgrass. PMID:28077967
Transcriptomic evidence for the control of soybean root isoflavonoid content by regulation of overlapping phenylpropanoid pathways. PMID:28077078
The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes. PMID:28076790
Transcriptome and Gene Expression Analysis of Cylas formicarius (Coleoptera: Brentidae) During Different Development Stages. PMID:28076281
Horizontally Transferred Genetic Elements in the Tsetse Fly Genome: An Alignment-Free Clustering Approach Using Batch Learning Self-Organising Map (BLSOM). PMID:28074180
Redox crisis underlies conditional light-dark lethality in cyanobacterial mutants that lack the circadian regulator, RpaA. PMID:28074036
Is the average shortest path length of gene set a reflection of their biological relatedness? PMID:28073302
A Survey of Computational Tools to Analyze and Interpret Whole Exome Sequencing Data. PMID:28070503
Metabolic phenotype of clinical and environmental Mycobacterium avium subsp. hominissuis isolates. PMID:28070460
A few sequence polymorphisms among isolates of Maize bushy stunt phytoplasma associate with organ proliferation symptoms of infected maize plants. PMID:28069632
Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis. PMID:28068432
Unusual respiratory capacity and nitrogen metabolism in a Parcubacterium (OD1) of the Candidate Phyla Radiation. PMID:28067254
Large-scale DNA methylation expression analysis across 12 solid cancers reveals hypermethylation in the calcium-signaling pathway. PMID:28060724
Genome-Wide DNA Methylation Patterns Analysis of Noncoding RNAs in Temporal Lobe Epilepsy Patients. PMID:28058582
Omics for understanding synergistic action of validamycin A and Trichoderma asperellum GDFS1009 against maize sheath blight pathogen. PMID:28057927
Immune adaptation to chronic intense exercise training: new microarray evidence. PMID:28056786
Novel Rosaceae plant elicitor peptides as sustainable tools to control Xanthomonas arboricola pv. pruni in Prunus spp. PMID:28056495
Quantitative Proteomics Reveals Ecophysiological Effects of Light and Silver Stress on the Mixotrophic Protist Poterioochromonas malhamensis. PMID:28056027
Functional constraints on adaptive evolution of protein ubiquitination sites. PMID:28054638
Network pharmacology-based identification of key pharmacological pathways of Yin-Huang-Qing-Fei capsule acting on chronic bronchitis. PMID:28053519
Deep Transcriptomic Profiling of M1 Macrophages Lacking Trpc3. PMID:28051144
Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw. PMID:28050853
Pathway-Structured Predictive Model for Cancer Survival Prediction: A Two-Stage Approach. PMID:28049703
Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening. PMID:28049426
Changes of Ovarian microRNA Profile in Long-Living Ames Dwarf Mice during Aging. PMID:28046124
Transcriptome Profiling Identifies Ribosome Biogenesis as a Target of Alcohol Teratogenicity and Vulnerability during Early Embryogenesis. PMID:28046103
Gene-based analyses reveal novel genetic overlap and allelic heterogeneity across five major psychiatric disorders. PMID:28035465
Characterisation of the genomic landscape of CRLF2-rearranged acute lymphoblastic leukemia. PMID:28033648
Brain transcriptomes of harbor seals demonstrate gene expression patterns of animals undergoing a metabolic disease and a viral infection. PMID:28028481
Unique Transcriptional Programs Identify Subtypes of AKI. PMID:28028135
Evolution of Chemosensory Gene Families in Arthropods: Insight from the First Inclusive Comparative Transcriptome Analysis across Spider Appendages. PMID:28028122
Red Algal Phylogenomics Provides a Robust Framework for Inferring Evolution of Key Metabolic Pathways. PMID:28018750
Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns. PMID:28018379
Network Analysis-Based Approach for Exploring the Potential Diagnostic Biomarkers of Acute Myocardial Infarction. PMID:28018242
Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli. PMID:28013396
MetaboSignal: a network-based approach for topological analysis of metabotype regulation via metabolic and signaling pathways. PMID:28011775
Long-term propagation of tree shrew spermatogonial stem cells in culture and successful generation of transgenic offspring. PMID:28008926
Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers. PMID:28000768
RNA-seq for comparative transcript profiling of kenaf under salinity stress. PMID:27999968
Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus). PMID:27998035
Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells. PMID:27997581
Metabolic engineering of Corynebacterium crenatium for enhancing production of higher alcohols. PMID:27996038
Characterization of an Abiraterone Ultraresponsive Phenotype in Castration-Resistant Prostate Cancer Patient-Derived Xenografts. PMID:27993966
Comparative metagenomics reveals taxonomically idiosyncratic yet functionally congruent communities in periodontitis. PMID:27991530
Community metabolic modeling approaches to understanding the gut microbiome: Bridging biochemistry and ecology. PMID:27989793
IMP: a pipeline for reproducible reference-independent integrated metagenomic and metatranscriptomic analyses. PMID:27986083
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota. PMID:27984592
Co-expression analysis and identification of fecundity-related long non-coding RNAs in sheep ovaries. PMID:27982099
The role of tumor metabolism as a driver of prostate cancer progression and lethal disease: results from a nested case-control study. PMID:27980733
A childhood acute lymphoblastic leukemia-specific lncRNA implicated in prednisolone resistance, cell proliferation, and migration. PMID:27980230
A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. PMID:27976707
Microbial Communities of Lycaenid Butterflies Do Not Correlate with Larval Diet. PMID:27965647
Genome Sequencing of Sulfolobus sp. A20 from Costa Rica and Comparative Analyses of the Putative Pathways of Carbon, Nitrogen, and Sulfur Metabolism in Various Sulfolobus Strains. PMID:27965637
KRAS mutant colorectal cancer gene signatures identified angiotensin II receptor blockers as potential therapies. PMID:27965461
Identification of Risk Pathways and Functional Modules for Coronary Artery Disease Based on Genome-wide SNP Data. PMID:27965104
Mobile-phone radiation-induced perturbation of gene-expression profiling, redox equilibrium and sporadic-apoptosis control in the ovary of Drosophila melanogaster. PMID:27960592
Phage-inducible islands in the Gram-positive cocci. PMID:27959343
RBM5 reduces small cell lung cancer growth, increases cisplatin sensitivity and regulates key transformation-associated pathways. PMID:27957556
Development of an in vitro human liver system for interrogating nonalcoholic steatohepatitis. PMID:27942596
Quantification of Microbial Phenotypes. PMID:27941694
Robust multi-group gene set analysis with few replicates. PMID:27938331
Insecticidal Activity of Melaleuca alternifolia Essential Oil and RNA-Seq Analysis of Sitophilus zeamais Transcriptome in Response to Oil Fumigation. PMID:27936192
Genome maintenance and bioenergetics of the long-lived hypoxia-tolerant and cancer-resistant blind mole rat, Spalax: a cross-species analysis of brain transcriptome. PMID:27934892
De Novo Sequencing and Comparative Analysis of Schima superba Seedlings to Explore the Response to Drought Stress. PMID:27930677
Human adipose mesenchymal stem cell-derived exosomal-miRNAs are critical factors for inducing anti-proliferation signalling to A2780 and SKOV-3 ovarian cancer cells. PMID:27929108
Network analysis of human post-mortem microarrays reveals novel genes, microRNAs, and mechanistic scenarios of potential importance in fighting huntington's disease. PMID:27924190
Identification of key genes induced by platelet-rich plasma in human dermal papilla cells using bioinformatics methods. PMID:27922680
Identification of functional pathways associated with the conditional ablation of serum response factor in Dstncorn1 mice. PMID:27922676
Cephalosporin-3'-Diazeniumdiolate NO Donor Prodrug PYRRO-C3D Enhances Azithromycin Susceptibility of Nontypeable Haemophilus influenzae Biofilms. PMID:27919896
STON: exploring biological pathways using the SBGN standard and graph databases. PMID:27919219
Distinct and Shared Determinants of Cardiomyocyte Contractility in Multi-Lineage Competent Ethnically Diverse Human iPSCs. PMID:27917881
Global Deletion of TSPO Does Not Affect the Viability and Gene Expression Profile. PMID:27907096
In Silico Knockout Studies of Xenophagic Capturing of Salmonella. PMID:27906974
Persistent microbiome alterations modulate the rate of post-dieting weight regain. PMID:27906159
Identification of biomarker microRNAs for predicting the response of colorectal cancer to neoadjuvant chemoradiotherapy based on microRNA regulatory network. PMID:27903980
miRTar2GO: a novel rule-based model learning method for cell line specific microRNA target prediction that integrates Ago2 CLIP-Seq and validated microRNA-target interaction data. PMID:27903911
THD-Module Extractor: An Application for CEN Module Extraction and Interesting Gene Identification for Alzheimer's Disease. PMID:27901073
Microarray analysis of differentially-expressed genes and linker genes associated with the molecular mechanism of colorectal cancer. PMID:27899990
Analysis of the molecular mechanism of osteosarcoma using a bioinformatics approach. PMID:27899966
YMDB 2.0: a significantly expanded version of the yeast metabolome database. PMID:27899612
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. PMID:27899593
Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model. PMID:27898737
Identification and Characterization of MicroRNAs in the Liver of Blunt Snout Bream (Megalobrama amblycephala) Infected by Aeromonas hydrophila. PMID:27898025
HUMAN KINASES DISPLAY MUTATIONAL HOTSPOTS AT COGNATE POSITIONS WITHIN CANCER. PMID:27896994
MICRORNA-AUGMENTED PATHWAYS (mirAP) AND THEIR APPLICATIONS TO PATHWAY ANALYSIS AND DISEASE SUBTYPING. PMID:27896992
Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool. PMID:27895636
Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. PMID:27893735
Biomolecular Network-Based Synergistic Drug Combination Discovery. PMID:27891522
Complete Genome Sequence of Clostridium estertheticum DSM 8809, a Microbe Identified in Spoiled Vacuum Packed Beef. PMID:27891116
A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism. PMID:27883890
Environmental Intervention as a Therapy for Adverse Programming by Ancestral Stress. PMID:27883060
MathIOmica: An Integrative Platform for Dynamic Omics. PMID:27883025
Loss of p300 accelerates MDS-associated leukemogenesis. PMID:27881875
Inhibition of mTOR induces a paused pluripotent state. PMID:27880763
Insights into the Sesquiterpenoid Pathway by Metabolic Profiling and De novo Transcriptome Assembly of Stem-Chicory (Cichorium intybus Cultigroup "Catalogna"). PMID:27877190
Family-wide Structural Characterization and Genomic Comparisons Decode the Diversity-oriented Biosynthesis of Thalassospiramides by Marine Proteobacteria. PMID:27875306
Genomic Contributors to Rhythm Outcome of Atrial Fibrillation Catheter Ablation - Pathway Enrichment Analysis of GWAS Data. PMID:27870913
Advances on plant-pathogen interactions from molecular toward systems biology perspectives. PMID:27870294
Titin-truncating variants affect heart function in disease cohorts and the general population. PMID:27869827
Circulating microRNA levels predict residual beta cell function and glycaemic control in children with type 1 diabetes mellitus. PMID:27866223
Differentiated regulation of immune-response related genes between LUAD and LUSC subtypes of lung cancers. PMID:27863400
Computational approaches for the identification of cancer genes and pathways. PMID:27863091
Transcriptome Profiling of Watermelon Root in Response to Short-Term Osmotic Stress. PMID:27861528
A framework for the use of single-chemical transcriptomics data in predicting the hazards associated with complex mixtures of polycyclic aromatic hydrocarbons. PMID:27858113
Genomic contributors to atrial electroanatomical remodeling and atrial fibrillation progression: Pathway enrichment analysis of GWAS data. PMID:27857207
Immunosenescence-Related Transcriptomic and Immunologic Changes in Older Individuals Following Influenza Vaccination. PMID:27853459
Transcriptome analysis revealed the dynamic oil accumulation in Symplocos paniculata fruit. PMID:27852215
Identification of potential genes for human ischemic cardiomyopathy based on RNA-Seq data. PMID:27852050
Whole-Genome Sequence Analysis of Bombella intestini LMG 28161T, a Novel Acetic Acid Bacterium Isolated from the Crop of a Red-Tailed Bumble Bee, Bombus lapidarius. PMID:27851750
Nitrogen-induced metabolic changes and molecular determinants of carbon allocation in Dunaliella tertiolecta. PMID:27849022
Characterization of genes and pathways that respond to heat stress in Holstein calves through transcriptome analysis. PMID:27848120
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
Analysis of the enzyme network involved in cattle milk production using graph theory. PMID:27844001
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. PMID:27842596
Identfication of key miRNAs in pancreatitis using bioinformatics analysis of microarray data. PMID:27840954
Using GWAS to identify novel therapeutic targets for osteoporosis. PMID:27837649
Leaf transcriptome of two highly divergent genotypes of Urochloa humidicola (Poaceae), a tropical polyploid forage grass adapted to acidic soils and temporary flooding areas. PMID:27835957
Mass Spectrometry Based Metabolomics Comparison of Liver Grafts from Donors after Circulatory Death (DCD) and Donors after Brain Death (DBD) Used in Human Orthotopic Liver Transplantation. PMID:27835640
Systemic Approach to Virulence Gene Network Analysis for Gaining New Insight into Cryptococcal Virulence. PMID:27833589
Comparative transcriptomics enlarges the toolkit of known developmental genes in mollusks. PMID:27832738
MinePath: Mining for Phenotype Differential Sub-paths in Molecular Pathways. PMID:27832067
CASTIN: a system for comprehensive analysis of cancer-stromal interactome. PMID:27829362
Activation of the basal cell carcinoma pathway in a patient with CNS HGNET-BCOR diagnosis: consequences for personalized targeted therapy. PMID:27825128
MicroRNA Expression Patterns of CD8+ T Cells in Acute and Chronic Brucellosis. PMID:27824867
Diversity and Activity of Communities Inhabiting Plastic Debris in the North Pacific Gyre. PMID:27822538
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. PMID:27822528
ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa Gene Expression Data with Denoising Autoencoders Illuminates Microbe-Host Interactions. PMID:27822512
Pyrimidine Salvage Enzymes Are Essential for De Novo Biosynthesis of Deoxypyrimidine Nucleotides in Trypanosoma brucei. PMID:27820863
Multi-label ℓ2-regularized logistic regression for predicting activation/inhibition relationships in human protein-protein interaction networks. PMID:27819359
Transcriptomic analysis on the formation of the viable putative non-culturable state of beer-spoilage Lactobacillus acetotolerans. PMID:27819317
Metagenomic Analysis of Genes Encoding Nutrient Cycling Pathways in the Microbiota of Deep-Sea and Shallow-Water Sponges. PMID:27819120
Inferring propagation paths for sparsely observed perturbations on complex networks. PMID:27819038
EphA2 proteomics in human keratinocytes reveals a novel association with afadin and epidermal tight junctions. PMID:27815408
Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations. PMID:27814717
Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. PMID:27814671
A Novel Murine Model of Parvovirus Associated Dilated Cardiomyopathy Induced by Immunization with VP1-Unique Region of Parvovirus B19. PMID:27812527
Comparative Gene Expression Profiling of Primary and Metastatic Renal Cell Carcinoma Stem Cell-Like Cancer Cells. PMID:27812180
Elucidation of Relevant Neuroinflammation Mechanisms Using Gene Expression Profiling in Patients with Amyotrophic Lateral Sclerosis. PMID:27812125
Proteomes and Ubiquitylomes Analysis Reveals the Involvement of Ubiquitination in Protein Degradation in Petunias. PMID:27810942
Unsupervised gene set testing based on random matrix theory. PMID:27809777
Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. PMID:27809776
Perplexing Metabolomes in Fungal-Insect Trophic Interactions: A Terra Incognita of Mycobiocontrol Mechanisms. PMID:27807434
Transcriptome Analysis and Comparison of Marmota monax and Marmota himalayana. PMID:27806133
A Novel Method for Pathway Identification Based on Attractor and Crosstalk in Polyarticular Juvenile Idiopathic Arthritis. PMID:27804927
Comparative Profiling of miRNAs and Target Gene Identification in Distant-Grafting between Tomato and Lycium (Goji Berry). PMID:27803702
An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography. PMID:27803195
ATR maintains chromosomal integrity during postnatal cerebellar neurogenesis and is required for medulloblastoma formation. PMID:27803059
An Integrative Analysis of Preeclampsia Based on the Construction of an Extended Composite Network Featuring Protein-Protein Physical Interactions and Transcriptional Relationships. PMID:27802351
A YY1-dependent increase in aerobic metabolism is indispensable for intestinal organogenesis. PMID:27802136
Path2enet: generation of human pathway-derived networks in an expression specific context. PMID:27801297
Identification of Binding Targets of a Pyrrole-Imidazole Polyamide KR12 in the LS180 Colorectal Cancer Genome. PMID:27798693
Expression Variations of miRNAs and mRNAs in Rice (Oryza sativa). PMID:27797952
Cancer driver gene discovery through an integrative genomics approach in a non-parametric Bayesian framework. PMID:27797769
Identifying reproducible cancer-associated highly expressed genes with important functional significances using multiple datasets. PMID:27796338
Shedding light on cell compartmentation in the candidate phylum Poribacteria by high resolution visualisation and transcriptional profiling. PMID:27796326
A network-biology perspective of microRNA function and dysfunction in cancer. PMID:27795564
Complete Genome Sequence of Spiroplasma helicoides TABS-2T (DSM 22551), a Bacterium Isolated from a Horsefly (Tabanus abactor). PMID:27795290
Genome sequence of Phormia regina Meigen (Diptera: Calliphoridae): implications for medical, veterinary and forensic research. PMID:27793085
FOXA1 overexpression mediates endocrine resistance by altering the ER transcriptome and IL-8 expression in ER-positive breast cancer. PMID:27791031
Application of RNAi-induced gene expression profiles for prognostic prediction in breast cancer. PMID:27788678
Novel equine tissue miRNAs and breed-related miRNA expressed in serum. PMID:27782799
Transcriptome Sequencing and De Novo Assembly of Golden Cuttlefish Sepia esculenta Hoyle. PMID:27782082
Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer. PMID:27781158
Identification of potential biomarkers and drugs for papillary thyroid cancer based on gene expression profile analysis. PMID:27779685
Systems biology analysis reveals role of MDM2 in diabetic nephropathy. PMID:27777973
Enhanced metabolic process to indole alkaloids in Clematis terniflora DC. after exposure to high level of UV-B irradiation followed by the dark. PMID:27776479
Capsaicin Suppresses Cell Proliferation, Induces Cell Cycle Arrest and ROS Production in Bladder Cancer Cells through FOXO3a-Mediated Pathways. PMID:27775662
Knowledge-guided fuzzy logic modeling to infer cellular signaling networks from proteomic data. PMID:27774993
Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. PMID:27774985
A computational interactome and functional annotation for the human proteome. PMID:27770567
De novo transcriptome sequencing of black pepper (Piper nigrum L.) and an analysis of genes involved in phenylpropanoid metabolism in response to Phytophthora capsici. PMID:27769171
Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model. PMID:27766938
Integrating Candida albicans metabolism with biofilm heterogeneity by transcriptome mapping. PMID:27765942
Attractor landscape analysis of colorectal tumorigenesis and its reversion. PMID:27765040
Chromatin accessibility contributes to simultaneous mutations of cancer genes. PMID:27762310
The promises of quantitative systems pharmacology modelling for drug development. PMID:27761201
Combined Use of Genome-Wide Association Data and Correlation Networks Unravels Key Regulators of Primary Metabolism in Arabidopsis thaliana. PMID:27760136
Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure. PMID:27758847
miR-145 and miR20a-5p Potentially Mediate Pleiotropic Effects of Interferon-Beta Through Mitogen-Activated Protein Kinase Signaling Pathway in Multiple Sclerosis Patients. PMID:27752929
miRPathDB: a new dictionary on microRNAs and target pathways. PMID:27742822
Heat Stress and Lipopolysaccharide Stimulation of Chicken Macrophage-Like Cell Line Activates Expression of Distinct Sets of Genes. PMID:27736938
Leaf Transcriptome Sequencing for Identifying Genic-SSR Markers and SNP Heterozygosity in Crossbred Mango Variety 'Amrapali' (Mangifera indica L.). PMID:27736892
Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis. PMID:27736793
A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum. PMID:27732672
Ovarian transcriptomic study reveals the differential regulation of miRNAs and lncRNAs related to fecundity in different sheep. PMID:27731399
Nuclear receptors control pro-viral and antiviral metabolic responses to hepatitis C virus infection. PMID:27723751
Altered Expressions of miR-1238-3p, miR-494, miR-6069, and miR-139-3p in the Formation of Chronic Brucellosis. PMID:27722176
A decision analysis model for KEGG pathway analysis. PMID:27716040
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells. PMID:27713552
Self-Contained Statistical Analysis of Gene Sets. PMID:27711232
Transcriptome Analysis of Stem and Globally Comparison with Other Tissues in Brassica napus. PMID:27708656
Hyperoxaluria leads to dysbiosis and drives selective enrichment of oxalate metabolizing bacterial species in recurrent kidney stone endures. PMID:27708409
A Thymic Epithelial Stem Cell Pool Persists throughout Ontogeny and Is Modulated by TGF-β. PMID:27705793
Divergent Isoprenoid Biosynthesis Pathways in Staphylococcus Species Constitute a Drug Target for Treating Infections in Companion Animals. PMID:27704053
Repeatability of cortisol stress response in the European sea bass (Dicentrarchus labrax) and transcription differences between individuals with divergent responses. PMID:27703277
Transcriptome and Metabolite analysis reveal candidate genes of the cardiac glycoside biosynthetic pathway from Calotropis procera. PMID:27703261
Elimination of p19ARF-expressing cells enhances pulmonary function in mice. PMID:27699227
Molecular Characterization and Enhancement of Anticancer Activity of Caffeic Acid Phenethyl Ester by γ Cyclodextrin. PMID:27698914
Sample Level Enrichment Analysis of KEGG Pathways Identifies Clinically Relevant Subtypes of Glioblastoma. PMID:27698907
Bioinformatics analysis of the molecular mechanism of diffuse intrinsic pontine glioma. PMID:27698822
Identification of genes involved in Epstein-Barr virus-associated nasopharyngeal carcinoma. PMID:27698802
Celecoxib exhibits an anti-gastric cancer effect by targeting focal adhesion and leukocyte transendothelial migration-associated genes. PMID:27698798
Proteome-wide Structural Analysis of PTM Hotspots Reveals Regulatory Elements Predicted to Impact Biological Function and Disease. PMID:27697855
Probing the diversity of healthy oral microbiome with bioinformatics approaches. PMID:27697111
Production of the Bioactive Compounds Violacein and Indolmycin Is Conditional in a maeA Mutant of Pseudoalteromonas luteoviolacea S4054 Lacking the Malic Enzyme. PMID:27695447
Genomic Survey of a Hyperparasitic Microsporidian Amphiamblys sp. (Metchnikovellidae). PMID:27694476
Listeria monocytogenes in Stone Fruits Linked to a Multistate Outbreak: Enumeration of Cells and Whole-Genome Sequencing. PMID:27694232
Combining multiple tools outperforms individual methods in gene set enrichment analyses. PMID:27694195
Aberrant LncRNA Expression Profile in a Contusion Spinal Cord Injury Mouse Model. PMID:27689092
Draft Genome Sequence of Bacillus litoralis C44, Isolated from Chinese Scholar Tree (Sophora japonica) Forest Soil. PMID:27688317
K-Ras Activation Induces Differential Sensitivity to Sulfur Amino Acid Limitation and Deprivation and to Oxidative and Anti-Oxidative Stress in Mouse Fibroblasts. PMID:27685888
Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice. PMID:27683878
Acinetobacter baumannii Coordinates Urea Metabolism with Metal Import To Resist Host-Mediated Metal Limitation. PMID:27677795
Differential network analysis from cross-platform gene expression data. PMID:27677586
De novo Assembly and Analysis of the Chilean Pencil Catfish Trichomycterus areolatus Transcriptome. PMID:27672404
TrpM, a Small Protein Modulating Tryptophan Biosynthesis and Morpho-Physiological Differentiation in Streptomyces coelicolor A3(2). PMID:27669158
Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. PMID:27667984
Breast cancer genome and transcriptome integration implicates specific mutational signatures with immune cell infiltration. PMID:27666519
In silico structural characterization of protein targets for drug development against Trypanosoma cruzi. PMID:27665464
Assessing the Association of Mitochondrial Genetic Variation With Primary Open-Angle Glaucoma Using Gene-Set Analyses. PMID:27661856
Complete Genome Sequence of Spiroplasma turonicum Tab4cT, a Bacterium Isolated from Horse Flies (Haematopota sp.). PMID:27660788
Circulating microRNA-192 as a diagnostic biomarker in human chronic lymphocytic leukemia. PMID:27659777
A deep sequencing analysis of transcriptomes and the development of EST-SSR markers in mungbean (Vigna radiata). PMID:27659323
modPDZpep: a web resource for structure based analysis of human PDZ-mediated interaction networks. PMID:27655048
Systems Analysis of Early Host Gene Expression Provides Clues for Transient Mycobacterium avium ssp avium vs. Persistent Mycobacterium avium ssp paratuberculosis Intestinal Infections. PMID:27653506
Perturbation Detection Through Modeling of Gene Expression on a Latent Biological Pathway Network: A Bayesian hierarchical approach. PMID:27647944
Transcriptome Profiling in Rat Inbred Strains and Experimental Cross Reveals Discrepant Genetic Architecture of Genome-Wide Gene Expression. PMID:27646706
Quantitative metabolomics of photoreceptor degeneration and the effects of stem cell-derived retinal pigment epithelium transplantation. PMID:27644974
Identification of 2-oxohistidine Interacting Proteins Using E. coli Proteome Chips. PMID:27644758
StemCellCKB: An Integrated Stem Cell-Specific Chemogenomics KnowledgeBase for Target Identification and Systems-Pharmacology Research. PMID:27643925
Effects of Elevated Tropospheric Ozone Concentration on the Bacterial Community in the Phyllosphere and Rhizoplane of Rice. PMID:27643794
Lactobacillus plantarum attenuates anxiety-related behavior and protects against stress-induced dysbiosis in adult zebrafish. PMID:27641717
Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses. PMID:27641516
Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms. PMID:27634898
Computational Metabolomics: A Framework for the Million Metabolome. PMID:27629808
Enhanced T cell responses to IL-6 in type 1 diabetes are associated with early clinical disease and increased IL-6 receptor expression. PMID:27629486
Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression. PMID:27626693
Bidirectional Expression of Metabolic, Structural, and Immune Pathways in Early Myopia and Hyperopia. PMID:27625591
Comparative proteomic analysis reveals alterations in development and photosynthesis-related proteins in diploid and triploid rice. PMID:27619227
The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice. PMID:27618555
PGD: a pangolin genome hub for the research community. PMID:27616775
Transcriptome assessment of the Pompe (Gaa-/-) mouse spinal cord indicates widespread neuropathology. PMID:27614205
Mergeomics: a web server for identifying pathological pathways, networks, and key regulators via multidimensional data integration. PMID:27612452
EPRS is a critical regulator of cell proliferation and estrogen signaling in ER+ breast cancer. PMID:27612429
Comparative Genomics of Acetobacterpasteurianus Ab3, an Acetic Acid Producing Strain Isolated from Chinese Traditional Rice Vinegar Meiguichu. PMID:27611790
Integrated Analysis of DNA Methylation and mRNA Expression Profiles Data to Identify Key Genes in Lung Adenocarcinoma. PMID:27610375
24-hour-restraint stress induces long-term depressive-like phenotypes in mice. PMID:27609090
Hsa-miR-137, hsa-miR-520e and hsa-miR-590-3p perform crucial roles in Lynch syndrome. PMID:27602130
Candida albicans triggers the expression of inflammatory genes in human umbilical vein endothelial cells. PMID:27602073
Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM 1313 implementing an adjustable cellulosome. PMID:27602057
Post-translational modifications are enriched within protein functional groups important to bacterial adaptation within a deep-sea hydrothermal vent environment. PMID:27600525
Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array. PMID:27600348
Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. PMID:27600081
NEAT: an efficient network enrichment analysis test. PMID:27597310
Systems Pharmacology Dissection of the Integrated Treatment for Cardiovascular and Gastrointestinal Disorders by Traditional Chinese Medicine. PMID:27597117
Viruses-to-mobile genetic elements skew in the deep Atlantis II brine pool sediments. PMID:27596223
Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments. PMID:27594854
Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity. PMID:27592001
Draft Genome Sequence of Methanohalophilus mahii Strain DAL1 Reconstructed from a Hydraulic Fracturing-Produced Water Metagenome. PMID:27587817
Inferring metabolic pathway activity levels from RNA-Seq data. PMID:27585456
An Untargeted Metabolomics Approach to Characterize Short-Term and Long-Term Metabolic Changes after Bariatric Surgery. PMID:27584017
RNAseq Transcriptional Profiling following Whip Development in Sugarcane Smut Disease. PMID:27583836
Diversity of Gut Microbiota Metabolic Pathways in 10 Pairs of Chinese Infant Twins. PMID:27583441
TP53 mutation hits energy metabolism and increases glycolysis in breast cancer. PMID:27582538
Aiptasia sp. larvae as a model to reveal mechanisms of symbiont selection in cnidarians. PMID:27582179
Identification of key pathways and genes in colorectal cancer using bioinformatics analysis. PMID:27581154
A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence. PMID:27579370
A pathway-centric approach to rare variant association analysis. PMID:27577545
Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands. PMID:27576083
Overexpression of CD44 is associated with the occurrence and migration of non-small cell lung cancer. PMID:27573351
Analysis of gene expression profile identifies potential biomarkers for atherosclerosis. PMID:27573188
Identification of hub genes and regulatory factors of glioblastoma multiforme subgroups by RNA-seq data analysis. PMID:27572852
Global microbialization of coral reefs. PMID:27572833
Sexually Dimorphic Gene Expression Associated with Growth and Reproduction of Tongue Sole (Cynoglossus semilaevis) Revealed by Brain Transcriptome Analysis. PMID:27571066
DRUG-DRUG INTERACTION PROFILES OF MEDICATION REGIMENS EXTRACTED FROM A DE-IDENTIFIED ELECTRONIC MEDICAL RECORDS SYSTEM. PMID:27570646
Identification of DNA Methyltransferase Genes in Human Pathogenic Bacteria by Comparative Genomics. PMID:27570304
EpCAM-Regulated Transcription Exerts Influences on Nanomechanical Properties of Endometrial Cancer Cells That Promote Epithelial-to-Mesenchymal Transition. PMID:27569206
Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism. PMID:27565352
Identification of miRNAs Potentially Involved in Bronchiolitis Obliterans Syndrome: A Computational Study. PMID:27564214
A validated metabolomic signature for colorectal cancer: exploration of the clinical value of metabolomics. PMID:27560555
Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis. PMID:27560381
Data Mining and Pattern Recognition Models for Identifying Inherited Diseases: Challenges and Implications. PMID:27559342
Properties of Boolean dynamics by node classification using feedback loops in a network. PMID:27558408
A comprehensive draft genome sequence for lupin (Lupinus angustifolius), an emerging health food: insights into plant-microbe interactions and legume evolution. PMID:27557478
Whole genomic sequence analysis of Bacillus infantis: defining the genetic blueprint of strain NRRL B-14911, an emerging cardiopathogenic microbe. PMID:27557119
A developmental coordinate of pluripotency among mice, monkeys and humans. PMID:27556940
High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium. PMID:27555890
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. PMID:27553427
Comparison of Collection Methods for Fecal Samples for Discovery Metabolomics in Epidemiologic Studies. PMID:27543620
Resolvin E1 Reverses Experimental Periodontitis and Dysbiosis. PMID:27543615
Metabolic requirements for cancer cell proliferation. PMID:27540483
Robust de novo pathway enrichment with KeyPathwayMiner 5. PMID:27540470
Shifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma. PMID:27538953
Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. PMID:27535938
Systematic analysis of the regulatory functions of microRNAs in chicken hepatic lipid metabolism. PMID:27535581
Topic model-based mass spectrometric data analysis in cancer biomarker discovery studies. PMID:27535232
Integrated analysis of omics data using microRNA-target mRNA network and PPI network reveals regulation of Gnai1 function in the spinal cord of Ews/Ewsr1 KO mice. PMID:27534535
Whole genome sequencing of a banana wild relative Musa itinerans provides insights into lineage-specific diversification of the Musa genus. PMID:27531320
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. PMID:27530928
A Skyline Plugin for Pathway-Centric Data Browsing. PMID:27530777
Interaction Between Peroxisome Proliferator Activated Receptor δ and Epithelial Membrane Protein 2 Polymorphisms Influences HDL-C Levels in the Chinese Population. PMID:27530449
The interplay between chromosome stability and cell cycle control explored through gene-gene interaction and computational simulation. PMID:27530428
Colonic Transit Time Is a Driven Force of the Gut Microbiota Composition and Metabolism: In Vitro Evidence. PMID:27530163
Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination. PMID:27529750
Myeloid cell expressed proprotein convertase FURIN attenuates inflammation. PMID:27527873
Identification of candidate genes related to calanolide biosynthesis by transcriptome sequencing of Calophyllum brasiliense (Calophyllaceae). PMID:27527830
Identification of crucial microRNAs and genes in hypoxia-induced human lung adenocarcinoma cells. PMID:27524914
Reprogramming of Strawberry (Fragaria vesca) Root Transcriptome in Response to Phytophthora cactorum. PMID:27518577
Highlighting the Need for Systems-Level Experimental Characterization of Plant Metabolic Enzymes. PMID:27516767
Identification of conserved and novel microRNAs in Porphyridium purpureum via deep sequencing and bioinformatics. PMID:27516065
Late-Exponential Gene Expression in codY-Deficient Bacillus anthracis in a Host-Like Environment. PMID:27515669
COMAN: a web server for comprehensive metatranscriptomics analysis. PMID:27515514
Transcriptomics of liver and muscle in Holstein cows genetically divergent for fertility highlight differences in nutrient partitioning and inflammation processes. PMID:27514375
High-resolution characterization of the human microbiome. PMID:27513210
Evaluation of artificial selection in Standard Poodles using whole-genome sequencing. PMID:27510710
Phenome-Wide Association Study to Explore Relationships between Immune System Related Genetic Loci and Complex Traits and Diseases. PMID:27508393
Identification of Drought Tolerant Mechanisms in Maize Seedlings Based on Transcriptome Analysis of Recombination Inbred Lines. PMID:27507977
Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. PMID:27506548
De novo assembly of the blunt snout bream (Megalobrama amblycephala) gill transcriptome to identify ammonia exposure associated microRNAs and their targets. PMID:27504260
Modeling central metabolism and energy biosynthesis across microbial life. PMID:27502787
Databases and tools for constructing signal transduction networks in cancer. PMID:27502015
Transcriptome analysis of seed dormancy after rinsing and chilling in ornamental peaches (Prunus persica (L.) Batsch). PMID:27501791
Genome-Wide Transcriptome and Binding Sites Analyses Identify Early FOX Expressions for Enhancing Cardiomyogenesis Efficiency of hESC Cultures. PMID:27501774
MicroRNAs as Novel Biomarkers of Deployment Status and Exposure to Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans. PMID:27501109
Detection of Serum microRNAs From Department of Defense Serum Repository: Correlation With Cotinine, Cytokine, and Polycyclic Aromatic Hydrocarbon Levels. PMID:27501106
High-Resolution Metabolomics Assessment of Military Personnel: Evaluating Analytical Strategies for Chemical Detection. PMID:27501105
Asymptotically Normal and Efficient Estimation of Covariate-Adjusted Gaussian Graphical Model. PMID:27499564
Distinct interacting core taxa in co-occurrence networks enable discrimination of polymicrobial oral diseases with similar symptoms. PMID:27499042
Draft Genome Sequence of Escherichia coli S51, a Chicken Isolate Harboring a Chromosomally Encoded mcr-1 Gene. PMID:27491979
Wnt signal transduction pathways: modules, development and evolution. PMID:27490822
Prediction of scaffold proteins based on protein interaction and domain architectures. PMID:27490120
A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model. PMID:27490109
Context-specific functional module based drug efficacy prediction. PMID:27490093
Transcriptomic analysis of mouse liver reveals a potential hepato-enteric pathogenic mechanism in acute Toxoplasma gondii infection. PMID:27488578
Thermal fluctuations affect the transcriptome through mechanisms independent of average temperature. PMID:27487917
Draft genome sequence of Mycobacterium rufum JS14(T), a polycyclic-aromatic-hydrocarbon-degrading bacterium from petroleum-contaminated soil in Hawaii. PMID:27486485
Genome-wide characterization of non-reference transposons in crops suggests non-random insertion. PMID:27485608
MicroRNAs as biomarkers for major depression: a role for let-7b and let-7c. PMID:27483380
GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering. PMID:27482905
Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome. PMID:27482299
Neuraminidase A-Exposed Galactose Promotes Streptococcus pneumoniae Biofilm Formation during Colonization. PMID:27481242
Deep genome sequencing and variation analysis of 13 inbred mouse strains defines candidate phenotypic alleles, private variation and homozygous truncating mutations. PMID:27480531
Characterisation of the Whole Blood mRNA Transcriptome in Holstein-Friesian and Jersey Calves in Response to Gradual Weaning. PMID:27479136
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
Identification of differentially expressed genes in salivary adenoid cystic carcinoma cells associated with metastasis. PMID:27478471
A Catalogue of Altered Salivary Proteins Secondary to Invasive Ductal Carcinoma: A Novel In Vivo Paradigm to Assess Breast Cancer Progression. PMID:27477923
Metabolites: messengers between the microbiota and the immune system. PMID:27474437
Joint sparse canonical correlation analysis for detecting differential imaging genetics modules. PMID:27466625
Transcriptome Analysis Reveals Candidate Genes involved in Blister Blight defense in Tea (Camellia sinensis (L) Kuntze). PMID:27465480
Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis. PMID:27465117
Loss of Renal Tubular PGC-1α Exacerbates Diet-Induced Renal Steatosis and Age-Related Urinary Sodium Excretion in Mice. PMID:27463191
Proteotyping of biogas plant microbiomes separates biogas plants according to process temperature and reactor type. PMID:27462366
Systems genetics identifies Hp1bp3 as a novel modulator of cognitive aging. PMID:27460150
Modelling with ANIMO: between fuzzy logic and differential equations. PMID:27460034
Mannitol Stress Directs Flavonoid Metabolism toward Synthesis of Flavones via Differential Regulation of Two Cytochrome P450 Monooxygenases in Coleus forskohlii. PMID:27458469
Characterization of Microbial Mat Microbiomes in the Modern Thrombolite Ecosystem of Lake Clifton, Western Australia Using Shotgun Metagenomics. PMID:27458453
Integrative Analysis of Microarray Data to Reveal Regulation Patterns in the Pathogenesis of Hepatocellular Carcinoma. PMID:27458175
Metatranscriptome analysis of active microbial communities in produced water samples from the Marcellus Shale. PMID:27457653
Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function. PMID:27456714
Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery. PMID:27455329
RichMind: A Tool for Improved Inference from Large-Scale Neuroimaging Results. PMID:27455041
Nutritional Evaluation of an EPA-DHA Oil from Transgenic Camelina sativa in Feeds for Post-Smolt Atlantic Salmon (Salmo salar L.). PMID:27454884
Kupffer Cells Undergo Fundamental Changes during the Development of Experimental NASH and Are Critical in Initiating Liver Damage and Inflammation. PMID:27454866
Mutations of the Sonic Hedgehog Pathway Underlie Hypothalamic Hamartoma with Gelastic Epilepsy. PMID:27453577
Deep Proteome Analysis Identifies Age-Related Processes in C. elegans. PMID:27453442
MicroRNA expression and gene regulation drive breast cancer progression and metastasis in PyMT mice. PMID:27449149
Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia. PMID:27447987
Molecular mechanisms of OLIG2 transcription factor in brain cancer. PMID:27447975
Transcriptome of the Australian Mollusc Dicathais orbita Provides Insights into the Biosynthesis of Indoles and Choline Esters. PMID:27447649
Identification of key target genes and pathways in laryngeal carcinoma. PMID:27446427
Predicting associations between microRNAs and target genes in breast cancer by bioinformatics analyses. PMID:27446395
Single-cell Sequencing of Thiomargarita Reveals Genomic Flexibility for Adaptation to Dynamic Redox Conditions. PMID:27446006
Draft Genome Sequence of Rhizobium sp. GHKF11, Isolated from Farmland Soil in Pecan Grove, Texas. PMID:27445376
Draft Genome Sequence of Exiguobacterium sp. KKBO11, Isolated Downstream of a Wastewater Treatment Plant in Houston, Texas. PMID:27445375
A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes. PMID:27442864
Changes in the Cytoplasmic Composition of Amino Acids and Proteins Observed in Staphylococcus aureus during Growth under Variable Growth Conditions Representative of the Human Wound Site. PMID:27442022
Integration and Visualization of Translational Medicine Data for Better Understanding of Human Diseases. PMID:27441714
The nonessentiality of essential genes in yeast provides therapeutic insights into a human disease. PMID:27440870
Time-Course Study of the Transcriptome of Peripheral Blood Mononuclear Cells (PBMCs) from Sheep Infected with Fasciola hepatica. PMID:27438474
Low-coverage, whole-genome sequencing of Artocarpus camansi (Moraceae) for phylogenetic marker development and gene discovery. PMID:27437173
Reciprocal genomic evolution in the ant-fungus agricultural symbiosis. PMID:27436133
Genic and Intergenic SSR Database Generation, SNPs Determination and Pathway Annotations, in Date Palm (Phoenix dactylifera L.). PMID:27434138
Coordinate Regulation of Metabolite Glycosylation and Stress Hormone Biosynthesis by TT8 in Arabidopsis. PMID:27432888
Germinants and Their Receptors in Clostridia. PMID:27432831
Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources. PMID:27432472
Comparative Genomics of Syntrophic Branched-Chain Fatty Acid Degrading Bacteria. PMID:27431485
Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. PMID:27429547
Mesenchymal Tumors Can Derive from Ng2/Cspg4-Expressing Pericytes with β-Catenin Modulating the Neoplastic Phenotype. PMID:27425618
Isoprenoid-Based Biofuels: Homologous Expression and Heterologous Expression in Prokaryotes. PMID:27422837
Draft Genome Sequence of Pseudomonas putida CBF10-2, a Soil Isolate with Bioremediation Potential in Agricultural and Industrial Environmental Settings. PMID:27417844
Comorbid Analysis of Genes Associated with Autism Spectrum Disorders Reveals Differential Evolutionary Constraints. PMID:27414027
Analyses of Compact Trichinella Kinomes Reveal a MOS-Like Protein Kinase with a Unique N-Terminal Domain. PMID:27412987
Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. PMID:27403564
Screening Driving Transcription Factors in the Processing of Gastric Cancer. PMID:27403158
Piriformospora indica Stimulates Root Metabolism of Arabidopsis thaliana. PMID:27399695
Transcriptome Analysis of Capsicum Chlorosis Virus-Induced Hypersensitive Resistance Response in Bell Capsicum. PMID:27398596
Investigating Evolutionary Dynamics of RHA1 Operons. PMID:27398020
MAIT, MR1, microbes and riboflavin: a paradigm for the co-evolution of invariant TCRs and restricting MHCI-like molecules? PMID:27393664
Draft Genome Sequence of Paecilomyces hepiali, Isolated from Cordyceps sinensis. PMID:27389266
Expression and methylation patterns partition luminal-A breast tumors into distinct prognostic subgroups. PMID:27386846
Biomonitoring in the Era of the Exposome. PMID:27385067
Drug Target Identification and Prioritization for Treatment of Ovine Foot Rot: An In Silico Approach. PMID:27379247
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. PMID:27379244
An automated system for evaluation of the potential functionome: MAPLE version 2.1.0. PMID:27374611
The Genome of a Southern Hemisphere Seagrass Species (Zostera muelleri). PMID:27373688
A Combinatorial Algorithm for Microbial Consortia Synthetic Design. PMID:27373593
The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles. PMID:27368709
Comparative genomics reveals multiple pathways to mutualism for tick-borne pathogens. PMID:27368698
Pathway analysis of expression-related SNPs on genome-wide association study of basal cell carcinoma. PMID:27367190
Data set for diet specific differential gene expression analysis in three Spodoptera moths. PMID:27366783
A De-Novo Genome Analysis Pipeline (DeNoGAP) for large-scale comparative prokaryotic genomics studies. PMID:27363390
Conservation in Mammals of Genes Associated with Aggression-Related Behavioral Phenotypes in Honey Bees. PMID:27359102
Genome-wide transcriptome analysis of female-sterile rice ovule shed light on its abortive mechanism. PMID:27357232
Network-based pathway enrichment analysis with incomplete network information. PMID:27357170
Screening of gene signatures for rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. PMID:27356888
Transcriptome comparison reveals a genetic network regulating the lower temperature limit in fish. PMID:27356472
Transcriptome Alterations In X-Irradiated Human Gingiva Fibroblasts. PMID:27356049
Genome wide analysis of protein production load in Trichoderma reesei. PMID:27354857
A metagenomic-based survey of microbial (de)halogenation potential in a German forest soil. PMID:27353292
Integrated microRNA, gene expression and transcription factors signature in papillary thyroid cancer with lymph node metastasis. PMID:27350898
Pharmacometabonomic Prediction of Busulfan Clearance in Hematopoetic Cell Transplant Recipients. PMID:27350098
Use of RNA-seq to identify cardiac genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy. PMID:27347821
Concerted changes in transcriptional regulation of genes involved in DNA methylation, demethylation, and folate-mediated one-carbon metabolism pathways in the NCI-60 cancer cell line panel in response to cancer drug treatment. PMID:27347216
Identification of novel biomarkers for preeclampsia on the basis of differential expression network analysis. PMID:27347039
p62/Sqstm1 promotes malignancy of HCV-positive hepatocellular carcinoma through Nrf2-dependent metabolic reprogramming. PMID:27345495
Uncovering Notch pathway in the parasitic flatworm Schistosoma mansoni. PMID:27344453
A data-driven network model of primary myelofibrosis: transcriptional and post-transcriptional alterations in CD34+ cells. PMID:27341078
The Impact of Intramammary Escherichia coli Challenge on Liver and Mammary Transcriptome and Cross-Talk in Dairy Cows during Early Lactation Using RNAseq. PMID:27336699
Cytochrome P450 metabolism of the post-lanosterol intermediates explains enigmas of cholesterol synthesis. PMID:27334049
Assessment of Saliva as a Potential Biofluid for Biodosimetry: A Pilot Metabolomics Study in Mice. PMID:27332953
De novo Transcriptome Analysis of Chinese Citrus Fly, Bactrocera minax (Diptera: Tephritidae), by High-Throughput Illumina Sequencing. PMID:27331903
BioTriangle: a web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions. PMID:27330567
Comprehensive analysis of high-throughput screens with HiTSeekR. PMID:27330136
MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data. PMID:27327495
Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors. PMID:27324944
Identification of the key regulating genes of diminished ovarian reserve (DOR) by network and gene ontology analysis. PMID:27324248
Integrated gene set analysis for microRNA studies. PMID:27324197
Systematic protein interactome analysis of glycosaminoglycans revealed YcbS as a novel bacterial virulence factor. PMID:27323865
Metatranscriptomics reveals the molecular mechanism of large granule formation in granular anammox reactor. PMID:27319320
Transcriptional signatures of influenza A/H1N1-specific IgG memory-like B cell response in older individuals. PMID:27317456
Identification of key genes in glioblastoma-associated stromal cells using bioinformatics analysis. PMID:27313730
Comparative Proteomic Analysis of the Response of Maize (Zea mays L.) Leaves to Long Photoperiod Condition. PMID:27313588
Molecular classification based on apomorphic amino acids (Arthropoda, Hexapoda): Integrative taxonomy in the era of phylogenomics. PMID:27312960
Whole Genome Re-Sequencing and Characterization of Powdery Mildew Disease-Associated Allelic Variation in Melon. PMID:27311063
BioASF: a framework for automatically generating executable pathway models specified in BioPAX. PMID:27307645
Influence maximization in time bounded network identifies transcription factors regulating perturbed pathways. PMID:27307609
Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota. PMID:27306058
Molecular and genetic inflammation networks in major human diseases. PMID:27303926
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". PMID:27303384
When Genome-Based Approach Meets the "Old but Good": Revealing Genes Involved in the Antibacterial Activity of Pseudomonas sp. P482 against Soft Rot Pathogens. PMID:27303376
Antimicrobial Resistance Prediction in PATRIC and RAST. PMID:27297683
Structural and functional analysis of the finished genome of the recently isolated toxic Anabaena sp. WA102. PMID:27296936
Transcriptome profiling of the salt-stress response in Triticum aestivum cv. Kharchia Local. PMID:27293111
The Landscape of microRNA Targeting in Prostate Cancer Defined by AGO-PAR-CLIP. PMID:27292025
Analysis of the metatranscriptome of microbial communities of an alkaline hot sulfur spring revealed different gene encoding pathway enzymes associated with energy metabolism. PMID:27290724
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PMID:27286824
Identification of nondiabetic heart failure-associated genes by bioinformatics approaches in patients with dilated ischemic cardiomyopathy. PMID:27284354
Non-small-cell lung cancer cells combat epidermal growth factor receptor tyrosine kinase inhibition through immediate adhesion-related responses. PMID:27284246
The Drosophila ETV5 Homologue Ets96B: Molecular Link between Obesity and Bipolar Disorder. PMID:27280443
Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis. PMID:27280288
DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies. PMID:27276067
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. PMID:27275538
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. PMID:27274991
Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches. PMID:27273017
Linking Bacillus cereus Genotypes and Carbohydrate Utilization Capacity. PMID:27272929
Shedding light on Aspergillus niger volatile exometabolome. PMID:27264696
The Importance of the Biological Impact of Exposure to the Concept of the Exposome. PMID:27258438
Development of Database Assisted Structure Identification (DASI) Methods for Nontargeted Metabolomics. PMID:27258318
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
De novo assembly and characterization of the Chinese three-keeled pond turtle (Mauremys reevesii) transcriptome: presence of longevity-related genes. PMID:27257545
Challenges in structural approaches to cell modeling. PMID:27255863
Metagenomic Reconstruction of Key Anaerobic Digestion Pathways in Municipal Sludge and Industrial Wastewater Biogas-Producing Systems. PMID:27252693
Key genes and pathways predicted in papillary thyroid carcinoma based on bioinformatics analysis. PMID:27250077
Identification of differentially expressed genes associated with the enhancement of X-ray susceptibility by RITA in a hypopharyngeal squamous cell carcinoma cell line (FaDu). PMID:27247549
Development and clinical application of an integrative genomic approach to personalized cancer therapy. PMID:27245685
Label-Free Proteomics Assisted by Affinity Enrichment for Elucidating the Chemical Reactivity of the Liver Mitochondrial Proteome toward Adduction by the Lipid Electrophile 4-hydroxy-2-nonenal (HNE). PMID:27242993
Different Gene Expression Patterns between Leaves and Flowers in Lonicera japonica Revealed by Transcriptome Analysis. PMID:27242839
Induction of Subacute Ruminal Acidosis Affects the Ruminal Microbiome and Epithelium. PMID:27242724
Tricking Arthrinium malaysianum into Producing Industrially Important Enzymes Under 2-Deoxy D-Glucose Treatment. PMID:27242677
Metabolomic Profiling of Bradyrhizobium diazoefficiens-Induced Root Nodules Reveals Both Host Plant-Specific and Developmental Signatures. PMID:27240350
Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation. PMID:27239563
Genomic Analysis Unravels Reduced Inorganic Sulfur Compound Oxidation of Heterotrophic Acidophilic Acidicaldus sp. Strain DX-1. PMID:27239474
In Silico Modeling of Liver Metabolism in a Human Disease Reveals a Key Enzyme for Histidine and Histamine Homeostasis. PMID:27239044
Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor. PMID:27235586
Genomic and transcriptomic predictors of response levels to endurance exercise training. PMID:27234805
Applications of Fourier Transform Ion Cyclotron Resonance (FT-ICR) and Orbitrap Based High Resolution Mass Spectrometry in Metabolomics and Lipidomics. PMID:27231903
Genome-wide identification of microRNAs in pomegranate (Punica granatum L.) by high-throughput sequencing. PMID:27230657
Genetic heterogeneity in primary and relapsed mantle cell lymphomas: Impact of recurrent CARD11 mutations. PMID:27224912
Peeping into genomic architecture by re-sequencing of Ochrobactrum intermedium M86 strain during laboratory adapted conditions. PMID:27222803
Comparative genomics explains the evolutionary success of reef-forming corals. PMID:27218454
Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis. PMID:27217061
RNA-seq analysis of virR and revR mutants of Clostridium perfringens. PMID:27216822
Identification of Maturation-Specific Proteins by Single-Cell Proteomics of Human Oocytes. PMID:27215607
A de novo transcriptome analysis shows that modulation of the JAK-STAT signaling pathway by salmonid alphavirus subtype 3 favors virus replication in macrophage/dendritic-like TO-cells. PMID:27215196
Integrated Analysis of Expression Profile Based on Differentially Expressed Genes in Middle Cerebral Artery Occlusion Animal Models. PMID:27213359
Transcriptome analysis revealed the drought-responsive genes in Tibetan hulless barley. PMID:27207260
Reprogramming human A375 amelanotic melanoma cells by catalase overexpression: Upregulation of antioxidant genes correlates with regression of melanoma malignancy and with malignant progression when downregulated. PMID:27206673
The Yeast Cyclin-Dependent Kinase Routes Carbon Fluxes to Fuel Cell Cycle Progression. PMID:27203178
The Classification of Sini Decoction Pattern in Traditional Chinese Medicine by Gene Expression Profiling. PMID:27200105
A High-resolution Typing Assay for Uropathogenic Escherichia coli Based on Fimbrial Diversity. PMID:27199951
Development of Ruminal and Fecal Microbiomes Are Affected by Weaning But Not Weaning Strategy in Dairy Calves. PMID:27199916
Metagenomics, Metatranscriptomics, and Metabolomics Approaches for Microbiome Analysis. PMID:27199545
Prevention of antipsychotic-induced hyperglycaemia by vitamin D: a data mining prediction followed by experimental exploration of the molecular mechanism. PMID:27199286
Nanofiber Alignment Regulates NIH3T3 Cell Orientation and Cytoskeletal Gene Expression on Electrospun PCL+Gelatin Nanofibers. PMID:27196306
Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution. PMID:27196065
Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis. PMID:27193824
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. PMID:27191992
Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts. PMID:27190004
The effect of growth rate on pyrazinamide activity in Mycobacterium tuberculosis - insights for early bactericidal activity? PMID:27184366
Systems-level analysis of human aging genes shed new light on mechanisms of aging. PMID:27179790
Membrane proteome profiling of Mentha arvensis leaves in response to Alternaria alternata infection identifies crucial candidates for defense response. PMID:27177294
Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women. PMID:27176052
Filtering large-scale event collections using a combination of supervised and unsupervised learning for event trigger classification. PMID:27175227
Draft Genome Sequence of Stenotrophomonas maltophilia CBF10-1, an Organophosphate-Degrading Bacterium Isolated from Ranch Soil in Fairchilds, Texas. PMID:27174285
Draft Genome Sequence of Lampenflora Chlorobium limicola Strain Frasassi in a Sulfidic Cave System. PMID:27174272
Draft Genome Sequence of Bacillus megaterium BHG1.1, a Strain Isolated from Bar-Headed Goose (Anser indicus) Feces on the Qinghai-Tibet Plateau. PMID:27174262
An Improved Genome Assembly of Azadirachta indica A. Juss. PMID:27172223
Identification of genetic interaction networks via an evolutionary algorithm evolved Bayesian network. PMID:27168765
Elucidation of the Mode of Action of a New Antibacterial Compound Active against Staphylococcus aureus and Pseudomonas aeruginosa. PMID:27167126
Identification of a new gene regulatory circuit involving B cell receptor activated signaling using a combined analysis of experimental, clinical and global gene expression data. PMID:27166259
Evaluating techniques for metagenome annotation using simulated sequence data. PMID:27162180
Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes - a genome comparison. PMID:27162150
Model-based contextualization of in vitro toxicity data quantitatively predicts in vivo drug response in patients. PMID:27161439
Comparative Genomics of Pathogens Causing Brown Spot Disease of Tobacco: Alternaria longipes and Alternaria alternata. PMID:27159564
A New Approach for Identification of Cancer-related Pathways using Protein Networks and Genomic Data. PMID:27158220
Genome-scale prediction of moonlighting proteins using diverse protein association information. PMID:27153604
Comparative Analysis of Transcriptomes among Bombyx mori Strains and Sexes Reveals the Genes Regulating Melanic Morph and the Related Phenotypes. PMID:27153103
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. PMID:27151405
One step beyond a ribosome: The ancient anaerobic core. PMID:27150504
Small RNA Profiles of the Rice PTGMS Line Wuxiang S Reveal miRNAs Involved in Fertility Transition. PMID:27148335
Fermentation Conditions that Affect Clavulanic Acid Production in Streptomyces clavuligerus: A Systematic Review. PMID:27148211
Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis. PMID:27148207
Ligand cluster-based protein network and ePlatton, a multi-target ligand finder. PMID:27143991
Modeling Doxorubicin-Induced Cardiotoxicity in Human Pluripotent Stem Cell Derived-Cardiomyocytes. PMID:27142468
The first de novo transcriptome of pepino (Solanum muricatum): assembly, comprehensive analysis and comparison with the closely related species S. caripense, potato and tomato. PMID:27142449
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. PMID:27137126
Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota. PMID:27136381
Profiling and Validation of the Circular RNA Repertoire in Adult Murine Hearts. PMID:27132142
MANORAA (Mapping Analogous Nuclei Onto Residue And Affinity) for identifying protein-ligand fragment interaction, pathways and SNPs. PMID:27131358
Evolutionary redesign of the Atlantic cod (Gadus morhua L.) Toll-like receptor repertoire by gene losses and expansions. PMID:27126702
A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus. PMID:27116338
Steroid-induced Deficiency of Mucosal-associated Invariant T Cells in the Chronic Obstructive Pulmonary Disease Lung. Implications for Nontypeable Haemophilus influenzae Infection. PMID:27115408
The myogenic electric organ of Sternopygus macrurus: a non-contractile tissue with a skeletal muscle transcriptome. PMID:27114860
Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production. PMID:27114075
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons. PMID:27113915
Diverse human extracellular RNAs are widely detected in human plasma. PMID:27112789
Network-driven plasma proteomics expose molecular changes in the Alzheimer's brain. PMID:27112350
The effects of PPO activity on the proteome of ingested red clover and implications for improving the nutrition of grazing cattle. PMID:27109346
Transcriptome analysis and molecular marker discovery in Solanum incanum and S. aethiopicum, two close relatives of the common eggplant (Solanum melongena) with interest for breeding. PMID:27108408
Activation of an Otherwise Silent Xylose Metabolic Pathway in Shewanella oneidensis. PMID:27107127
Draft Genome Sequence of Organophosphate-Degrading Ochrobactrum anthropi FRAF13. PMID:27103720
Analysis of proteome dynamics inside the silk gland lumen of Bombyx mori. PMID:27102218
The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes. PMID:27099620
GAM: a web-service for integrated transcriptional and metabolic network analysis. PMID:27098040
Interferon-α signaling promotes embryonic HSC maturation. PMID:27095787
Altered oncomodules underlie chromatin regulatory factors driver mutations. PMID:27095575
Ultrastructure of the liver microcirculation influences hepatic and systemic insulin activity and provides a mechanism for age-related insulin resistance. PMID:27095270
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
Gene-set Analysis with CGI Information for Differential DNA Methylation Profiling. PMID:27090937
Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile. PMID:27090785
The Asian arowana (Scleropages formosus) genome provides new insights into the evolution of an early lineage of teleosts. PMID:27089831
Whole-transcriptome analyses of the Sapsaree, a Korean natural monument, before and after exercise-induced stress. PMID:27087983
Transcriptome changes in apple peel tissues during CO2 injury symptom development under controlled atmosphere storage regimens. PMID:27087982
Epigenetic Profiling of H3K4Me3 Reveals Herbal Medicine Jinfukang-Induced Epigenetic Alteration Is Involved in Anti-Lung Cancer Activity. PMID:27087825
Draft Genome Sequence of Pseudomonas stutzeri ODKF13, Isolated from Farmland Soil in Alvin, Texas. PMID:27081147
Draft Genome Sequence of Alkane-Degrading Acinetobacter venetianus JKSF02, Isolated from Contaminated Sediment of the San Jacinto River in Houston, Texas. PMID:27081144
Draft Genome Sequence of the Broad-Spectrum Xenobiotic Degrader Achromobacter xylosoxidans ADAF13. PMID:27081123
Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PMID:27078856
Whole transcriptome data analysis of mouse embryonic hematopoietic stem and progenitor cells that lack Geminin expression. PMID:27077091
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
Opposite activation of the Hedgehog pathway in CD138+ plasma cells and CD138-CD19+ B cells identifies two subgroups of patients with multiple myeloma and different prognosis. PMID:27074969
MicroRNAs in Hyperglycemia Induced Endothelial Cell Dysfunction. PMID:27070575
Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). PMID:27065985
The Features of Fecal and Ileal Mucosa-Associated Microbiota in Dairy Calves during Early Infection with Mycobacterium avium Subspecies paratuberculosis. PMID:27065983
Evidence of a broad histamine footprint on the human exercise transcriptome. PMID:27061420
Studying the Genetics of Complex Disease With Ancestry-Specific Human Phenotype Networks: The Case of Type 2 Diabetes in East Asian Populations. PMID:27061195
A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources. PMID:27050304
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PMID:27050193
iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate. PMID:27048574
Identification of downstream target genes regulated by the nitric oxide-soluble guanylate cyclase-cyclic guanosine monophosphate signal pathway in pulmonary hypertension. PMID:27048385
Evidence for embryonic stem-like signature and epithelial-mesenchymal transition features in the spheroid cells derived from lung adenocarcinoma. PMID:27048287
Mucus Sugar Content Shapes the Bacterial Community Structure in Thermally Stressed Acropora muricata. PMID:27047481
Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo. PMID:27044921
Implications of genotypic differences in the generation of a urinary metabolomics radiation signature. PMID:27040378
Metabolomic network analysis of estrogen-stimulated MCF-7 cells: a comparison of overrepresentation analysis, quantitative enrichment analysis and pathway analysis versus metabolite network analysis. PMID:27039105
Metabolomics by Gas Chromatography-Mass Spectrometry: Combined Targeted and Untargeted Profiling. PMID:27038389
Novel personalized pathway-based metabolomics models reveal key metabolic pathways for breast cancer diagnosis. PMID:27036109
Using biological networks to integrate, visualize and analyze genomics data. PMID:27036106
Gene expression profile analysis of pancreatic cancer based on microarray data. PMID:27035876
Impact of the Type I Interferon Receptor on the Global Gene Expression Program During the Course of Dendritic Cell Maturation Induced by Polyinosinic Polycytidylic Acid. PMID:27035059
Network Biomarkers of Bladder Cancer Based on a Genome-Wide Genetic and Epigenetic Network Derived from Next-Generation Sequencing Data. PMID:27034531
Skeletal muscle phosphatidylcholine and phosphatidylethanolamine are related to insulin sensitivity and respond to acute exercise in humans. PMID:27032901
Identification of Multiple Stress Responsive Genes by Sequencing a Normalized cDNA Library from Sea-Land Cotton (Gossypium barbadense L.). PMID:27031331
Analysis of gene expression in mouse brain regions after exposure to 1.9 GHz radiofrequency fields. PMID:27028625
Pathway Analysis Revealed Potential Diverse Health Impacts of Flavonoids that Bind Estrogen Receptors. PMID:27023590
Differences down-under: alcohol-fueled methanogenesis by archaea present in Australian macropodids. PMID:27022996
Transcriptome Analysis of an Insecticide Resistant Housefly Strain: Insights about SNPs and Regulatory Elements in Cytochrome P450 Genes. PMID:27019205
Maternal genome-wide DNA methylation profiling in gestational diabetes shows distinctive disease-associated changes relative to matched healthy pregnancies. PMID:27019060
Partial Decay of Thiamine Signal Transduction Pathway Alters Growth Properties of Candida glabrata. PMID:27015653
Mycobacterium bovis BCG Interferes with miR-3619-5p Control of Cathepsin S in the Process of Autophagy. PMID:27014637
Transcriptome Analyses Reveal the Involvement of Both C and N Termini of Cryptochrome 1 in Its Regulation of Phytohormone-Responsive Gene Expression in Arabidopsis. PMID:27014317
Proteomic Responses of Switchgrass and Prairie Cordgrass to Senescence. PMID:27014316
Genomic Insight into the Host-Endosymbiont Relationship of Endozoicomonas montiporae CL-33(T) with its Coral Host. PMID:27014194
A novel metabolomic approach used for the comparison of Staphylococcus aureus planktonic cells and biofilm samples. PMID:27013931
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. PMID:27013077
Role of MicroRNAs in carcinogenesis that potential for biomarker of endometrial cancer. PMID:27006767
Inside the Pan-genome - Methods and Software Overview. PMID:27006628
An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection. PMID:27006471
Transcriptome analyses reveal molecular mechanism underlying tapping panel dryness of rubber tree (Hevea brasiliensis). PMID:27005401
Proteomic Profiling of Mouse Liver following Acute Toxoplasma gondii Infection. PMID:27003162
Identification and functional analyses of sex determination genes in the sexually dimorphic stag beetle Cyclommatus metallifer. PMID:27001106
Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. PMID:27000948
miTALOS v2: Analyzing Tissue Specific microRNA Function. PMID:26998997
Comparative Proteomic Analysis of Advanced Ovarian Cancer Tissue to Identify Potential Biomarkers of Responders and Nonresponders to First-Line Chemotherapy of Carboplatin and Paclitaxel. PMID:26997873
BRG1/SMARCA4 is essential for neuroblastoma cell viability through modulation of cell death and survival pathways. PMID:26996667
Two Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura). PMID:26994086
New features of desiccation tolerance in the lichen photobiont Trebouxia gelatinosa are revealed by a transcriptomic approach. PMID:26992400
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves. PMID:26990967
The Transcript Profile of a Traditional Chinese Medicine, Atractylodes lancea, Revealing Its Sesquiterpenoid Biosynthesis of the Major Active Components. PMID:26990438
Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)classes. PMID:26989424
DASPfind: new efficient method to predict drug-target interactions. PMID:26985240
Pipeline for the identification and classification of ion channels in parasitic flatworms. PMID:26983991
Genetic Evidence of Human Adaptation to a Cooked Diet. PMID:26979798
Data for global lysine-acetylation analysis in rice (Oryza sativa). PMID:26977447
Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection. PMID:26975510
Long genes and genes with multiple splice variants are enriched in pathways linked to cancer and other multigenic diseases. PMID:26968808
Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases. PMID:26966660
Expression Profiles of miRNA Subsets Distinguish Human Colorectal Carcinoma and Normal Colonic Mucosa. PMID:26963002
How special is the biochemical function of native proteins? PMID:26962440
Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes. PMID:26960548
Characterization of the Kenaf (Hibiscus cannabinus) Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers. PMID:26960153
Comparative Transcriptomic Analysis of Rectal Tissue from Beef Steers Revealed Reduced Host Immunity in Escherichia coli O157:H7 Super-Shedders. PMID:26959367
Translational Meta-analytical Methods to Localize the Regulatory Patterns of Neurological Disorders in the Human Brain. PMID:26958307
De novo assembly and analysis of the transcriptome of Ocimum americanum var. pilosum under cold stress. PMID:26955811
Delta-proteobacterial SAR324 group in hydrothermal plumes on the South Mid-Atlantic Ridge. PMID:26953077
Discovery and dissection of metabolic oscillations in the microaerobic nitric oxide response network of Escherichia coli. PMID:26951670
Distribution of CpG Motifs in Upstream Gene Domains in a Reef Coral and Sea Anemone: Implications for Epigenetics in Cnidarians. PMID:26950882
Acquisition of exogenous haem is essential for tick reproduction. PMID:26949258
Melatonin Pathway and Atenolol-Related Glucose Dysregulation: Is There a Correlation? PMID:26946962
Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. PMID:26944061
De Novo Transcriptome Analysis of Medicinally Important Plantago ovata Using RNA-Seq. PMID:26943165
Transcriptomic analysis of human breast cancer cells reveals differentially expressed genes and related cellular functions and pathways in response to gold nanorods. PMID:26942225
Identification of biological targets of therapeutic intervention for clear cell renal cell carcinoma based on bioinformatics approach. PMID:26941587
Pathway Analysis of Genome-wide Association Study in Childhood Leukemia among Hispanics. PMID:26941364
High throughput sequencing of small RNAs transcriptomes in two Crassostrea oysters identifies microRNAs involved in osmotic stress response. PMID:26940974
Multidimensional Screening Platform for Simultaneously Targeting Oncogenic KRAS and Hypoxia-Inducible Factors Pathways in Colorectal Cancer. PMID:26938486
Network Analysis of Metabolite GWAS Hits: Implication of CPS1 and the Urea Cycle in Weight Maintenance. PMID:26938218
Comparing Alzheimer's and Parkinson's diseases networks using graph communities structure. PMID:26935435
Differential root transcriptomics in a polyploid non-model crop: the importance of respiration during osmotic stress. PMID:26935041
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. PMID:26932197
De Novo Transcriptome Assembly in Shiraia bambusicola to Investigate Putative Genes Involved in the Biosynthesis of Hypocrellin A. PMID:26927096
Transcriptome Analysis for Identification of Genes Related to Gonad Differentiation, Growth, Immune Response and Marker Discovery in The Turbot (Scophthalmus maximus). PMID:26925843
Transcriptome sequencing revealed differences in the response of renal cancer cells to hypoxia and CoCl 2 treatment. PMID:26925226
KENeV: A web-application for the automated reconstruction and visualization of the enriched metabolic and signaling super-pathways deriving from genomic experiments. PMID:26925206
Cognitive impairment by antibiotic-induced gut dysbiosis: Analysis of gut microbiota-brain communication. PMID:26923630
Correlation of Metabolic Variables with the Number of ORFs in Human Pathogenic and Phylogenetically Related Non- or Less-Pathogenic Bacteria. PMID:26920870
PKCδ regulates integrin αVβ3 expression and transformed growth of K-ras dependent lung cancer cells. PMID:26918447
New insights into virulence mechanisms of rice pathogen Acidovorax avenae subsp. avenae strain RS-1 following exposure to ß-lactam antibiotics. PMID:26915352
Integrative Analysis of Multi-omics Data for Discovery and Functional Studies of Complex Human Diseases. PMID:26915271
RDIS: The Rabies Disease Information System. PMID:26912951
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. PMID:26912667
Novel loci and pathways significantly associated with longevity. PMID:26912274
Human genetic variation database, a reference database of genetic variations in the Japanese population. PMID:26911352
Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae). PMID:26907245
Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau. PMID:26906946
Antipsychotic pharmacogenomics in first episode psychosis: a role for glutamate genes. PMID:26905411
Genetic features of Mycobacterium tuberculosis modern Beijing sublineage. PMID:26905026
Analysis of Sensitive CO2 Pathways and Genes Related to Carbon Uptake and Accumulation in Chlamydomonas reinhardtii through Genomic Scale Modeling and Experimental Validation. PMID:26904035
Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. PMID:26903887
Quantitative proteomic analyses of mammary organoids reveals distinct signatures after exposure to environmental chemicals. PMID:26903627
An interactive web-based application for Comprehensive Analysis of RNAi-screen Data. PMID:26902267
Featured Article: Genotation: Actionable knowledge for the scientific reader. PMID:26900164
Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. PMID:26898953
Identification of genes and pathways associated with pancreatic ductal adenocarcinoma by bioinformatics analyses. PMID:26893748
Identification of genes and signaling pathways associated with squamous cell carcinoma by bioinformatics analysis. PMID:26893747
Revealing the role of VEGFA in clear cell sarcoma of the kidney by protein-protein interaction network and significant pathway analysis. PMID:26893674
Antibiotic binding of STY3178, a yfdX protein from Salmonella Typhi. PMID:26892637
Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. PMID:26887814
Individual Differences in Scotopic Visual Acuity and Contrast Sensitivity: Genetic and Non-Genetic Influences. PMID:26886100
Integrative analysis of genome-wide association studies and gene expression analysis identifies pathways associated with rheumatoid arthritis. PMID:26885899
Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials. PMID:26885455
Computationally expanding infinium HumanMethylation450 BeadChip array data to reveal distinct DNA methylation patterns of rheumatoid arthritis. PMID:26883487
Discovery of candidate tumor biomarkers for treatment with intraperitoneal chemotherapy for ovarian cancer. PMID:26883286
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Transcriptomic changes associated with DKK4 overexpression in pancreatic cancer cells detected by RNA-Seq. PMID:26880586
Major remodeling of brain microvessels during neonatal period in the mouse: A proteomic and transcriptomic study. PMID:26873886
Missense Variant in MAPK Inactivator PTPN5 Is Associated with Decreased Severity of Post-Burn Hypertrophic Scarring. PMID:26872063
Signal transduction by M3 muscarinic acetylcholine receptor in prostate cancer. PMID:26870222
Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges. PMID:26870081
Filtering genetic variants and placing informative priors based on putative biological function. PMID:26866982
Transcriptomic, proteomic and metabolic changes in Arabidopsis thaliana leaves after the onset of illumination. PMID:26865323
Comparative Transcriptomic Exploration Reveals Unique Molecular Adaptations of Neuropathogenic Trichobilharzia to Invade and Parasitize Its Avian Definitive Host. PMID:26863542
ApoCanD: Database of human apoptotic proteins in the context of cancer. PMID:26861916
Effects of Oxygen Limitation on the Biosynthesis of Photo Pigments in the Red Microalgae Galdieria sulphuraria Strain 074G. PMID:26859750
Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform. PMID:26858723
The Global Reciprocal Reprogramming between Mycobacteriophage SWU1 and Mycobacterium Reveals the Molecular Strategy of Subversion and Promotion of Phage Infection. PMID:26858712
Resistance related metabolic pathways for drug target identification in Mycobacterium tuberculosis. PMID:26856535
Colorectal cancer characterization and therapeutic target prediction based on microRNA expression profile. PMID:26852921
Transcriptome Analysis of an Anthracnose-Resistant Tea Plant Cultivar Reveals Genes Associated with Resistance to Colletotrichum camelliae. PMID:26849553
Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria. PMID:26849311
Vikodak--A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets. PMID:26848568
Non-Coding RNAs in Thyroid Cancer. PMID:26847830
An integrated in silico approach for functional and structural impact of non- synonymous SNPs in the MYH1 gene in Jeju Native Pigs. PMID:26847462
Genome-Wide Analysis of Acute Endurance Exercise-Induced Translational Regulation in Mouse Skeletal Muscle. PMID:26845575
Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum. PMID:26844018
Prime, Shock, and Kill: Priming CD4 T Cells from HIV Patients with a BCL-2 Antagonist before HIV Reactivation Reduces HIV Reservoir Size. PMID:26842479
Grain-rich diets altered the colonic fermentation and mucosa-associated bacterial communities and induced mucosal injuries in goats. PMID:26841945
Recruitment of the Mammalian Histone-modifying EMSY Complex to Target Genes Is Regulated by ZNF131. PMID:26841866
iTRAQ-Based Quantitative Proteomic Analysis of Cotton Roots and Leaves Reveals Pathways Associated with Salt Stress. PMID:26841024
Gene expression profiling analysis of lung adenocarcinoma. PMID:26840709
Use of De Novo Transcriptome Libraries to Characterize a Novel Oleaginous Marine Chlorella Species during the Accumulation of Triacylglycerols. PMID:26840425
An individualized prognostic signature for gastric cancer patients treated with 5-Fluorouracil-based chemotherapy and distinct multi-omics characteristics of prognostic groups. PMID:26840027
Major bacterial lineages are essentially devoid of CRISPR-Cas viral defence systems. PMID:26837824
Transcriptional Profiles from Paired Normal Samples Offer Complementary Information on Cancer Patient Survival--Evidence from TCGA Pan-Cancer Data. PMID:26837275
Development of the Chick Microbiome: How Early Exposure Influences Future Microbial Diversity. PMID:26835461
MetFrag relaunched: incorporating strategies beyond in silico fragmentation. PMID:26834843
Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle. PMID:26833409
Characterization of parasite-specific indels and their proposed relevance for selective anthelminthic drug targeting. PMID:26829384
Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. PMID:26826224
Candidate Antimetastasis Drugs Suppress the Metastatic Capacity of Breast Cancer Cells by Reducing Membrane Fluidity. PMID:26825169
Glutamate Dehydrogenase Is Required by Mycobacterium bovis BCG for Resistance to Cellular Stress. PMID:26824899
Detailed Mechanistic Study of the Non-enzymatic Formation of the Discoipyrrole Family of Natural Products. PMID:26824832
Genomes and virulence difference between two physiological races of Phytophthora nicotianae. PMID:26823972
Genomic Analyses Reveal Demographic History and Temperate Adaptation of the Newly Discovered Honey Bee Subspecies Apis mellifera sinisxinyuan n. ssp. PMID:26823447
High yield 1,3-propanediol production by rational engineering of the 3-hydroxypropionaldehyde bottleneck in Citrobacter werkmanii. PMID:26822953
Prognostic Molecular Subtypes of Low-Grade Cancer of the Appendix. PMID:26821970
Correlation between Gene Variants, Signaling Pathways, and Efficacy of Chemotherapy Drugs against Colon Cancers. PMID:26819545
Missing value imputation for microRNA expression data by using a GO-based similarity measure. PMID:26818962
Generalized logical model based on network topology to capture the dynamical trends of cellular signaling pathways. PMID:26818802
Gene expression profiling identifies candidate biomarkers for active and latent tuberculosis. PMID:26818387
Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. PMID:26818233
Prediction of drugs having opposite effects on disease genes in a directed network. PMID:26818006
Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen. PMID:26817455
Identification of miRNA-mRNA regulatory modules by exploring collective group relationships. PMID:26817421
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Integrating mutation and gene expression cross-sectional data to infer cancer progression. PMID:26810975
Cascade: an RNA-seq visualization tool for cancer genomics. PMID:26810393
Transcriptional response to heat shock in liver of snow trout (Schizothorax richardsonii)--a vulnerable Himalayan Cyprinid fish. PMID:26810178
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PMID:26808278
Improvement and transcriptome analysis of root architecture by overexpression of Fraxinus pennsylvanica DREB2A transcription factor in Robinia pseudoacacia L. 'Idaho'. PMID:26806173
A multiple kernel learning algorithm for drug-target interaction prediction. PMID:26801218
Advanced Running Performance by Genetic Predisposition in Male Dummerstorf Marathon Mice (DUhTP) Reveals Higher Sterol Regulatory Element-Binding Protein (SREBP) Related mRNA Expression in the Liver and Higher Serum Levels of Progesterone. PMID:26799318
Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis. PMID:26794841
In vivo Cigarette Smoke Exposure Decreases CCL20, SLPI, and BD-1 Secretion by Human Primary Nasal Epithelial Cells. PMID:26793127
Unique pioneer microbial communities exposed to volcanic sulfur dioxide. PMID:26791101
Insight into the Salivary Gland Transcriptome of Lygus lineolaris (Palisot de Beauvois). PMID:26789269
Gene set enrichment and topological analyses based on interaction networks in pediatric acute lymphoblastic leukemia. PMID:26788135
Transcriptome analysis reveals the molecular mechanisms underlying growth superiority in a novel grouper hybrid (Epinephelus fuscogutatus♀ × E. lanceolatus♂). PMID:26785614
Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis. PMID:26784944
Network Topology Analysis of Post-Mortem Brain Microarrays Identifies More Alzheimer's Related Genes and MicroRNAs and Points to Novel Routes for Fighting with the Disease. PMID:26784894
Core level regulatory network of osteoblast as molecular mechanism for osteoporosis and treatment. PMID:26783964
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates. PMID:26783758
Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data. PMID:26779252
SEPARATING THE CAUSES AND CONSEQUENCES IN DISEASE TRANSCRIPTOME. PMID:26776202
AN INTEGRATED NETWORK APPROACH TO IDENTIFYING BIOLOGICAL PATHWAYS AND ENVIRONMENTAL EXPOSURE INTERACTIONS IN COMPLEX DISEASES. PMID:26776169
Combinatorial Cis-regulation in Saccharomyces Species. PMID:26772747
Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis. PMID:26769582
Data set for transcriptome analysis of the Chinese giant salamander (Andrias davidianus ). PMID:26759822
Slowed aging during reproductive dormancy is reflected in genome-wide transcriptome changes in Drosophila melanogaster. PMID:26758761
Metatranscriptomic analysis of diverse microbial communities reveals core metabolic pathways and microbiome-specific functionality. PMID:26757703
Transcriptomic analysis reveals the gene expression profile that specifically responds to IBA during adventitious rooting in mung bean seedlings. PMID:26755210
Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024. PMID:26754974
Global Transcriptomic Analysis of Interactions between Pseudomonas aeruginosa and Bacteriophage PaP3. PMID:26750429
PBX3 and MEIS1 Cooperate in Hematopoietic Cells to Drive Acute Myeloid Leukemias Characterized by a Core Transcriptome of the MLL-Rearranged Disease. PMID:26747896
Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus. PMID:26747700
Microbial and Functional Diversity within the Phyllosphere of Espeletia Species in an Andean High-Mountain Ecosystem. PMID:26746719
Computational Identification of Tumor Anatomic Location Associated with Survival in 2 Large Cohorts of Human Primary Glioblastomas. PMID:26744442
The Floating (Pathogenicity) Island: A Genomic Dessert. PMID:26744223
Exome arrays capture polygenic rare variant contributions to schizophrenia. PMID:26740555
The cytomegalovirus protein UL138 induces apoptosis of gastric cancer cells by binding to heat shock protein 70. PMID:26735338
Year-Long Metagenomic Study of River Microbiomes Across Land Use and Water Quality. PMID:26733955
Adaptive Genetic Robustness of Escherichia coli Metabolic Fluxes. PMID:26733489
Transcriptional profiling revealed the anti-proliferative effect of MFN2 deficiency and identified risk factors in lung adenocarcinoma. PMID:26733181
A transcriptome-wide, organ-specific regulatory map of Dendrobium officinale, an important traditional Chinese orchid herb. PMID:26732614
Selecting Superior De Novo Transcriptome Assemblies: Lessons Learned by Leveraging the Best Plant Genome. PMID:26731733
Differentially expressed genes and microRNAs in bladder carcinoma cell line 5637 and T24 detected by RNA sequencing. PMID:26722457
Proteomics and bioinformatics analysis of mouse hypothalamic neurogenesis with or without EPHX2 gene deletion. PMID:26722453
Construction and analysis of three networks of genes and microRNAs in adenocarcinoma. PMID:26722320
Role of NSC319726 in ovarian cancer based on the bioinformatics analyses. PMID:26719703
De novo characterization of the liver transcriptome of javelin goby Synechogobius hasta and analysis of its transcriptomic profile following waterborne copper exposure. PMID:26719065
Multi-label multi-instance transfer learning for simultaneous reconstruction and cross-talk modeling of multiple human signaling pathways. PMID:26718335
Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis. PMID:26717154
miRLAB: An R Based Dry Lab for Exploring miRNA-mRNA Regulatory Relationships. PMID:26716983
Linking short tandem repeat polymorphisms with cytosine modifications in human lymphoblastoid cell lines. PMID:26714498
Using RNA-seq to Profile Gene Expression of Spikelet Development in Response to Temperature and Nitrogen during Meiosis in Rice (Oryza sativa L.). PMID:26714321
In Silico Comparative Transcriptome Analysis of Two Color Morphs of the Common Coral Trout (Plectropomus Leopardus). PMID:26713756
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris. PMID:26712940
Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models. PMID:26709835
Regionally Smoothed Meta-Analysis Methods for GWAS Datasets. PMID:26707090
Expression of microRNAs in human post-mortem amyotrophic lateral sclerosis spinal cords provides insight into disease mechanisms. PMID:26704906
Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. PMID:26699225
Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PMID:26698123
Differential Expression of Hepatic Genes of the Greater Horseshoe Bat (Rhinolophus ferrumequinum) between the Summer Active and Winter Torpid States. PMID:26698122
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. PMID:26695483
Investigation of a Quadruplex-Forming Repeat Sequence Highly Enriched in Xanthomonas and Nostoc sp. PMID:26695179
A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. PMID:26694930
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. PMID:26693857
A Computational Pipeline for Cross-Species Analysis of RNA-seq Data Using R and Bioconductor. PMID:26692761
A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants. PMID:26691988
De Novo Transcriptome Sequencing of Oryza officinalis Wall ex Watt to Identify Disease-Resistance Genes. PMID:26690414
Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection. PMID:26690385
The Tasmanian devil microbiome-implications for conservation and management. PMID:26689946
Network-Based Integration of Disparate Omic Data To Identify "Silent Players" in Cancer. PMID:26683094
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PMID:26682918
Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. PMID:26680552
Consistent gene expression profiles in MexTAg transgenic mouse and wild type mouse asbestos-induced mesothelioma. PMID:26680231
LENS: web-based lens for enrichment and network studies of human proteins. PMID:26680011
Screening of potential biomarkers for cholangiocarcinoma by integrated analysis of microarray data sets. PMID:26679756
Genome-wide transcriptomic analyses provide insights into the lifestyle transition and effector repertoire of Leptosphaeria maculans during the colonization of Brassica napus seedlings. PMID:26679637
Draft Genome Sequence of Francisella tularensis Strain 410108 from Tibet, China. PMID:26679594
A computational method for drug repositioning using publicly available gene expression data. PMID:26679199
De novo assembly and characterization of root transcriptome in two distinct morphotypes of vetiver, Chrysopogon zizaniodes (L.) Roberty. PMID:26679063
Understanding Metabolomics in Biomedical Research. PMID:26676338
Circulating microRNA 132-3p and 324-3p Profiles in Patients after Acute Aneurysmal Subarachnoid Hemorrhage. PMID:26675167
Identifying gene-gene interactions that are highly associated with Body Mass Index using Quantitative Multifactor Dimensionality Reduction (QMDR). PMID:26674805
Comparative transcriptomics reveals similarities and differences between astrocytoma grades. PMID:26673168
Pathway-Based Genome-Wide Association Studies for Two Meat Production Traits in Simmental Cattle. PMID:26672757
Comparative Transcriptome Analysis in the Hepatopancreas Tissue of Pacific White Shrimp Litopenaeus vannamei Fed Different Lipid Sources at Low Salinity. PMID:26670122
Quantitative proteomics identifies 38 proteins that are differentially expressed in cucumber in response to cucumber green mottle mosaic virus infection. PMID:26666291
Draft genome sequence of Halopiger salifodinae KCY07-B2(T), an extremly halophilic archaeon isolated from a salt mine. PMID:26664653
Identification of Th1/Th2 regulatory switch to promote healing response during leishmaniasis: a computational approach. PMID:26660865
Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples. PMID:26659691
A Longitudinal Study of the Feline Faecal Microbiome Identifies Changes into Early Adulthood Irrespective of Sexual Development. PMID:26659594
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
Whole Transcriptome Analysis Provides Insights into Molecular Mechanisms for Molting in Litopenaeus vannamei. PMID:26650402
A simple feature construction method for predicting upstream/downstream signal flow in human protein-protein interaction networks. PMID:26648121
Identification of key genes in hepatocellular carcinoma and validation of the candidate gene, cdc25a, using gene set enrichment analysis, meta-analysis and cross-species comparison. PMID:26647881
De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome. PMID:26647312
Identification of Major Signaling Pathways in Prion Disease Progression Using Network Analysis. PMID:26646948
Wind and sunlight shape microbial diversity in surface waters of the North Pacific Subtropical Gyre. PMID:26645474
A human 3'UTR clone collection to study post-transcriptional gene regulation. PMID:26645212
Disulfide-Bond-Forming Pathways in Gram-Positive Bacteria. PMID:26644434
Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction. PMID:26640947
Enhanced reproducibility of SADI web service workflows with Galaxy and Docker. PMID:26640691
Cross-species Transcriptomic Comparison of In Vitro and In Vivo Mammalian Neural Cells. PMID:26640375
Gene Expression Switching of Receptor Subunits in Human Brain Development. PMID:26636753
RNA Sequence Analysis of Human Huntington Disease Brain Reveals an Extensive Increase in Inflammatory and Developmental Gene Expression. PMID:26636579
Evaluation of Oxidative Stress Response Related Genetic Variants, Pro-oxidants, Antioxidants and Prostate Cancer. PMID:26636131
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast. PMID:26635866
Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets. PMID:26635209
Functional overlap of the Arabidopsis leaf and root microbiota. PMID:26633631
Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). PMID:26633323
Consistency Analysis of Genome-Scale Models of Bacterial Metabolism: A Metamodel Approach. PMID:26629901
Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells. PMID:26627478
Pathogenic mechanisms of lung adenocarcinoma in smokers and non-smokers determined by gene expression interrogation. PMID:26622675
Variation in Rural African Gut Microbiota Is Strongly Correlated with Colonization by Entamoeba and Subsistence. PMID:26619199
Differential abundance analysis of mesocarp protein from high- and low-yielding oil palms associates non-oil biosynthetic enzymes to lipid biosynthesis. PMID:26617468
Database resources of the National Center for Biotechnology Information. PMID:26615191
Preadult life history variation determines adult transcriptome expression. PMID:26615085
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Mining for Candidate Genes Related to Pancreatic Cancer Using Protein-Protein Interactions and a Shortest Path Approach. PMID:26613085
Large-scale transcriptome sequencing reveals novel expression patterns for key sex-related genes in a sex-changing fish. PMID:26613014
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories. PMID:26609052
SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships. PMID:26607947
Draft Genome Sequence of a 16SrII-A Subgroup Phytoplasma Associated with Purple Coneflower (Echinacea purpurea) Witches' Broom Disease in Taiwan. PMID:26607900
Gonadal transcriptomic analysis and differentially expressed genes in the testis and ovary of the Pacific white shrimp (Litopenaeus vannamei). PMID:26607692
Development and validation of a mixed-tissue oligonucleotide DNA microarray for Atlantic bluefin tuna, Thunnus thynnus (Linnaeus, 1758). PMID:26607231
Transcriptome analysis of GVHD reveals aurora kinase A as a targetable pathway for disease prevention. PMID:26606970
De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. PMID:26602763
Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks. PMID:26597226
Comparative genomics and metabolic profiling of the genus Lysobacter. PMID:26597042
An Examination of Dynamic Gene Expression Changes in the Mouse Brain During Pregnancy and the Postpartum Period. PMID:26596646
Testing for Ancient Selection Using Cross-population Allele Frequency Differentiation. PMID:26596347
NDEx, the Network Data Exchange. PMID:26594663
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources. PMID:26589635
Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis. PMID:26589282
Sensing Small Changes in Protein Abundance: Stimulation of Caco-2 Cells by Human Whey Proteins. PMID:26586228
enviPath--The environmental contaminant biotransformation pathway resource. PMID:26582924
Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA. PMID:26581084
Digital Gene Expression Analysis Based on De Novo Transcriptome Assembly Reveals New Genes Associated with Floral Organ Differentiation of the Orchid Plant Cymbidium ensifolium. PMID:26580566
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India. PMID:26579081
Bioinformatic tools for microRNA dissection. PMID:26578605
A method for developing regulatory gene set networks to characterize complex biological systems. PMID:26576648
RNA-seq reveals differentially expressed genes of rice (Oryza sativa) spikelet in response to temperature interacting with nitrogen at meiosis stage. PMID:26576634
An Effective Method to Identify Shared Pathways and Common Factors among Neurodegenerative Diseases. PMID:26575483
Transcription analysis of neonicotinoid resistance in Mediterranean (MED) populations of B. tabaci reveal novel cytochrome P450s, but no nAChR mutations associated with the phenotype. PMID:26573457
NRP1 is targeted by miR-130a and miR-130b, and is associated with multidrug resistance in epithelial ovarian cancer based on integrated gene network analysis. PMID:26573160
Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis. PMID:26573092
Identification of genes related to learning and memory in the brain transcriptome of the mollusc, Hermissenda crassicornis. PMID:26572652
Deep sequencing of the uterine immune response to bacteria during the equine oestrous cycle. PMID:26572250
High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1. PMID:26566420
Codon Bias Patterns of E. coli's Interacting Proteins. PMID:26566157
Temporal protein expression pattern in intracellular signalling cascade during T-cell activation: a computational study. PMID:26564978
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PMID:26561344
Effectiveness and Usability of Bioinformatics Tools to Analyze Pathways Associated with miRNA Expression. PMID:26560461
Radiation and SN38 treatments modulate the expression of microRNAs, cytokines and chemokines in colon cancer cells in a p53-directed manner. PMID:26556872
A network-based method to evaluate quality of reproducibility of differential expression in cancer genomics studies. PMID:26556852
Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. PMID:26556590
WITHDRAWN--a resource for withdrawn and discontinued drugs. PMID:26553801
Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(Δexon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. PMID:26552589
Pathway-based variant enrichment analysis on the example of dilated cardiomyopathy. PMID:26547721
Adaptation to High Ethanol Reveals Complex Evolutionary Pathways. PMID:26545090
Transcriptome analysis and characterisation of gill-expressed carbonic anhydrase and other key osmoregulatory genes in freshwater crayfish Cherax quadricarinatus. PMID:26543880
Correlation of clinical features and genetic profiles of stromal interaction molecule 1 (STIM1) in colorectal cancers. PMID:26543234
MetAnnotate: function-specific taxonomic profiling and comparison of metagenomes. PMID:26541816
Changes in the NMR Metabolic Profile of Live Human Neuron-Like SH-SY5Y Cells Exposed to Interferon-α2. PMID:26541470
Structural Characterisation of FabG from Yersinia pestis, a Key Component of Bacterial Fatty Acid Synthesis. PMID:26539719
Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations. PMID:26539502
De Novo Assembly and Characterization of the Invasive Northern Pacific Seastar Transcriptome. PMID:26529321
Effects of Controlled Cortical Impact on the Mouse Brain Vasculome. PMID:26528928
Characterising the bacterial microbiota across the gastrointestinal tracts of dairy cattle: membership and potential function. PMID:26527325
Subtractive assembly for comparative metagenomics, and its application to type 2 diabetes metagenomes. PMID:26527161
Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. PMID:26526746
Systematic Tracking of Disrupted Modules Identifies Altered Pathways Associated with Congenital Heart Defects in Down Syndrome. PMID:26524729
The discordant method: a novel approach for differential correlation. PMID:26520855
Identification of CD146 as a marker enriched for tumor-propagating capacity reveals targetable pathways in primary human sarcoma. PMID:26517673
Whole Genome Sequence of the Soybean Aphid Endosymbiont Buchnera aphidicola and Genetic Differentiation among Biotype-Specific Strains. PMID:26516375
Mutations in the TLR3 signaling pathway and beyond in adult patients with herpes simplex encephalitis. PMID:26513235
A survey of computational tools for downstream analysis of proteomic and other omic datasets. PMID:26510531
Metabolic profiling reveals potential metabolic markers associated with Hypoxia Inducible Factor-mediated signalling in hypoxic cancer cells. PMID:26508589
Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa. PMID:26507235
MicroRNAs-mRNAs Expression Profile and Their Potential Role in Malignant Transformation of Human Bronchial Epithelial Cells Induced by Cadmium. PMID:26504844
Identification of SSRs and differentially expressed genes in two cultivars of celery (Apium graveolens L.) by deep transcriptome sequencing. PMID:26504532
Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach. PMID:26504486
Comparative analysis of molecular mechanism of spinal cord injury with time based on bioinformatics data. PMID:26503224
The combination of thymoquinone and paclitaxel shows anti-tumor activity through the interplay with apoptosis network in triple-negative breast cancer. PMID:26500095
Role of estrogen receptor alpha in human cervical cancer-associated fibroblasts: a transcriptomic study. PMID:26499945
Further insight into molecular mechanism underlying thoracic spinal cord injury using bioinformatics methods. PMID:26497545
Mapping Proteome-Wide Targets of Environmental Chemicals Using Reactivity-Based Chemoproteomic Platforms. PMID:26496688
Cellular metabolic network analysis: discovering important reactions in Treponema pallidum. PMID:26495292
Overexpression of mitochondrial uncoupling protein 1 (UCP1) induces a hypoxic response in Nicotiana tabacum leaves. PMID:26494730
Complete Genome Sequence of Spiroplasma cantharicola CC-1T (DSM 21588), a Bacterium Isolated from Soldier Beetle (Cantharis carolinus). PMID:26494686
A Glimpse to Background and Characteristics of Major Molecular Biological Networks. PMID:26491677
Identification of novel and conserved microRNAs in Panax notoginseng roots by high-throughput sequencing. PMID:26490136
The human skin double-stranded DNA virome: topographical and temporal diversity, genetic enrichment, and dynamic associations with the host microbiome. PMID:26489866
Integrative Genomics-Based Discovery of Novel Regulators of the Innate Antiviral Response. PMID:26485378
Digital gene-expression of alfalfa saponin extract on laying hens. PMID:26484156
Deep sequencing of the microRNA expression in fall dormant and non-dormant alfalfa. PMID:26484115
Computational identification of microRNAs and their targets in Catharanthus roseus expressed sequence tags. PMID:26484050
Genome sequence of the Asian Tiger mosquito, Aedes albopictus, reveals insights into its biology, genetics, and evolution. PMID:26483478
Transcriptome sequencing of a thalloid bryophyte; Dumortiera hirsuta (Sw) Nees: assembly, annotation, and marker discovery. PMID:26481431
Spatially extensive microbial biogeography of the Indian Ocean provides insights into the unique community structure of a pristine coral atoll. PMID:26481089
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Structural and Functional Analysis of Murine Polyomavirus Capsid Proteins Establish the Determinants of Ligand Recognition and Pathogenicity. PMID:26474293
Draft Genome Sequence of Burkholderia pseudomallei Strain 350105, Isolated in Hainan, China, in 1976. PMID:26472827
Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis. PMID:26472343
The mixed lineage kinase-3 inhibitor URMC-099 improves therapeutic outcomes for long-acting antiretroviral therapy. PMID:26472049
A novel bi-level meta-analysis approach: applied to biological pathway analysis. PMID:26471455
Predicting Pharmacodynamic Drug-Drug Interactions through Signaling Propagation Interference on Protein-Protein Interaction Networks. PMID:26469276
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
Gene expression underlying enhanced, steroid-dependent auditory sensitivity of hair cell epithelium in a vocal fish. PMID:26466782
Prioritization Of Nonsynonymous Single Nucleotide Variants For Exome Sequencing Studies Via Integrative Learning On Multiple Genomic Data. PMID:26459872
Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes. PMID:26459834
Comparative genome analysis of the candidate functional starter culture strains Lactobacillus fermentum 222 and Lactobacillus plantarum 80 for controlled cocoa bean fermentation processes. PMID:26459565
Personalised pathway analysis reveals association between DNA repair pathway dysregulation and chromosomal instability in sporadic breast cancer. PMID:26456802
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data. PMID:26454280
Indexing a protein-protein interaction network expedites network alignment. PMID:26453444
Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis. PMID:26453433
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
The early immune response to infection of chickens with Infectious Bronchitis Virus (IBV) in susceptible and resistant birds. PMID:26452558
Genome Analysis of Pseudomonas fluorescens PCL1751: A Rhizobacterium that Controls Root Diseases and Alleviates Salt Stress for Its Plant Host. PMID:26452056
An Independent Filter for Gene Set Testing Based on Spectral Enrichment. PMID:26451820
Intrastrand triplex DNA repeats in bacteria: a source of genomic instability. PMID:26450966
Dynamic Changes in the Transcriptome and Methylome of Chlamydomonas reinhardtii throughout Its Life Cycle. PMID:26450704
Aberrant DNA methylation in non-small cell lung cancer-associated fibroblasts. PMID:26449251
Bioinformatics analyses of differentially expressed genes associated with bisphosphonate-related osteonecrosis of the jaw in patients with multiple myeloma. PMID:26445550
Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening. PMID:26444490
Giving Time Purpose: The Synechococcus elongatus Clock in a Broader Network Context. PMID:26442846
Physicochemical characteristics of structurally determined metabolite-protein and drug-protein binding events with respect to binding specificity. PMID:26442281
Long-term survival of Borrelia burgdorferi lacking the hibernation promotion factor homolog in the unfed tick vector. PMID:26438790
Interlog protein network: an evolutionary benchmark of protein interaction networks for the evaluation of clustering algorithms. PMID:26437714
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types. PMID:26436532
Entropy-scaling search of massive biological data. PMID:26436140
Illuminating the dark matter in metabolomics. PMID:26430243
Complete Genome Sequence of Spiroplasma litorale TN-1T (DSM 21781), a Bacterium Isolated from a Green-Eyed Horsefly (Tabanus nigrovittatus). PMID:26430038
De Novo Transcriptome Assembly in Firmiana danxiaensis, a Tree Species Endemic to the Danxia Landform. PMID:26427005
Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance. PMID:26426997
Transcriptome sequencing and analysis of major genes involved in calcium signaling pathways in pear plants (Pyrus calleryana Decne.). PMID:26424153
MGDB: a comprehensive database of genes involved in melanoma. PMID:26424083
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse. PMID:26424082
Bioinformatics Analyses of the Role of Vascular Endothelial Growth Factor in Patients with Non-Small Cell Lung Cancer. PMID:26422603
mmnet: An R Package for Metagenomics Systems Biology Analysis. PMID:26421278
Pan-genomic analysis to redefine species and subspecies based on quantum discontinuous variation: the Klebsiella paradigm. PMID:26420254
Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. PMID:26418914
Race Does Not Predict Melanocyte Heterogeneous Responses to Dermal Fibroblast-Derived Mediators. PMID:26418010
Quantitative analysis of the murine lipid droplet-associated proteome during diet-induced hepatic steatosis. PMID:26416795
Analysis of the miRNA-mRNA-lncRNA networks in ER+ and ER- breast cancer cell lines. PMID:26416600
Diversity in Compartmental Dynamics of Gene Regulatory Networks: The Immune Response in Primary Influenza A Infection in Mice. PMID:26413862
Covariance-based analyses of biological pathways. PMID:26412865
De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development. PMID:26406914
Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel. PMID:26406373
DAPPER: a data-mining resource for protein-protein interactions. PMID:26405458
(13)C Tracers for Glucose Degrading Pathway Discrimination in Gluconobacter oxydans 621H. PMID:26404385
Phenotypic and Transcriptomic Analyses of Autotetraploid and Diploid Mulberry (Morus alba L.). PMID:26402678
Recent findings and technological advances in phosphoproteomics for cells and tissues. PMID:26400465
Integrative analysis of human protein, function and disease networks. PMID:26399914
A fast and high performance multiple data integration algorithm for identifying human disease genes. PMID:26399620
Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores. PMID:26393325
Extracellular vesicle-mediated transfer of processed and functional RNY5 RNA. PMID:26392588
Whole-Genome Resequencing Reveals Extensive Natural Variation in the Model Green Alga Chlamydomonas reinhardtii. PMID:26392080
Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. PMID:26391404
Metabolome and proteome changes with aging in Caenorhabditis elegans. PMID:26390854
FOXC2 and fluid shear stress stabilize postnatal lymphatic vasculature. PMID:26389677
Ascaris lumbricoides β carbonic anhydrase: a potential target enzyme for treatment of ascariasis. PMID:26385556
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME. PMID:26384374
SimiRa: A tool to identify coregulation between microRNAs and RNA-binding proteins. PMID:26383775
Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485. PMID:26379770
The Role of ARF6 in Biliary Atresia. PMID:26379158
Meta-Analysis of Microarray Data of Rainbow Trout Fry Gonad Differentiation Modulated by Ethynylestradiol. PMID:26379055
Comparative transcriptomic analyses to scrutinize the assumption that genotoxic PAHs exert effects via a common mode of action. PMID:26377693
Identification of Gene-Expression Signatures and Protein Markers for Breast Cancer Grading and Staging. PMID:26375396
Identification of four functionally important microRNA families with contrasting differential expression profiles between drought-tolerant and susceptible rice leaf at vegetative stage. PMID:26369665
Embryonic Lethality Due to Arrested Cardiac Development in Psip1/Hdgfrp2 Double-Deficient Mice. PMID:26367869
Assessing the Metabolic Diversity of Streptococcus from a Protein Domain Point of View. PMID:26366735
Expansion of the tetracycline-dependent regulation toolbox for Helicobacter pylori. PMID:26362986
Overexpression and knockout of miR-126 both promote leukemogenesis. PMID:26361793
A new approach for investigating venom function applied to venom calreticulin in a parasitoid wasp. PMID:26359852
A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. PMID:26354861
An eigenvalue transformation technique for predicting drug-target interaction. PMID:26350590
Discovery of Intermediary Genes between Pathways Using Sparse Regression. PMID:26348038
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. PMID:26346536
Transcriptomic Signatures Mirror the Lack of the Fecundity/Longevity Trade-Off in Ant Queens. PMID:26341296
Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. PMID:26340901
Screening key genes associated with congenital heart defects in Down syndrome based on differential expression network. PMID:26339408
Cell type-selective disease-association of genes under high regulatory load. PMID:26338775
Less pronounced response to exercise in healthy relatives to type 2 diabetic subjects compared with controls. PMID:26338460
Identification of genes associated with methotrexate resistance in methotrexate-resistant osteosarcoma cell lines. PMID:26337976
Complete Genome Sequence of Strain H5989 of a Novel Devosia Species. PMID:26337876
Composition, taxonomy and functional diversity of the oropharynx microbiome in individuals with schizophrenia and controls. PMID:26336637
Cross-tissue and cross-species analysis of gene expression in skeletal muscle and electric organ of African weakly-electric fish (Teleostei; Mormyridae). PMID:26335922
Implications of ethylene biosynthesis and signaling in soybean drought stress tolerance. PMID:26335593
In silico analyses of metagenomes from human atherosclerotic plaque samples. PMID:26334731
Transcriptome analysis in Coffea eugenioides, an Arabica coffee ancestor, reveals differentially expressed genes in leaves and fruits. PMID:26334613
Integration of 'omics' data in aging research: from biomarkers to systems biology. PMID:26331998
De novo sequencing and analysis of Lophophora williamsii transcriptome, and searching for putative genes involved in mescaline biosynthesis. PMID:26330142
In silico analysis of the molecular mechanism of postmenopausal osteoporosis. PMID:26329309
Metabolic diversity and ecological niches of Achromatium populations revealed with single-cell genomic sequencing. PMID:26322031
Proteomic and Biochemical Studies of Lysine Malonylation Suggest Its Malonic Aciduria-associated Regulatory Role in Mitochondrial Function and Fatty Acid Oxidation. PMID:26320211
Oxidative stress and ROS metabolism via down-regulation of sirtuin 3 expression in Cmah-null mice affect hearing loss. PMID:26319214
Modeling and Classification of Kinetic Patterns of Dynamic Metabolic Biomarkers in Physical Activity. PMID:26317529
Gene expression profiling in adipose tissue from growing broiler chickens. PMID:26317054
NETWORK-REGULARIZED HIGH-DIMENSIONAL COX REGRESSION FOR ANALYSIS OF GENOMIC DATA. PMID:26316678
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community. PMID:26315217
Comparative Genomics Including the Early-Diverging Smut Fungus Ceraceosorus bombacis Reveals Signatures of Parallel Evolution within Plant and Animal Pathogens of Fungi and Oomycetes. PMID:26314305
A Rich-Club Organization in Brain Ischemia Protein Interaction Network. PMID:26310627
Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales. PMID:26309130
Transcriptional dysregulation of inflammatory/immune pathways after active vaccination against Huntington's disease. PMID:26307082
Disease Comorbidity Network Guides the Detection of Molecular Evidence for the Link Between Colorectal Cancer and Obesity. PMID:26306270
Detecting Cancer Pathway Crosstalk with Distance Correlation. PMID:26306231
A Catalog of Proteins Expressed in the AG Secreted Fluid during the Mature Phase of the Chinese Mitten Crabs (Eriocheir sinensis). PMID:26305468
Novel insights into the molecular events linking to cell death induced by tetracycline in the amitochondriate protozoan Trichomonas vaginalis. PMID:26303799
Phosphotyrosine Substrate Sequence Motifs for Dual Specificity Phosphatases. PMID:26302245
Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis. PMID:26299571
A thiol-disulfide oxidoreductase of the Gram-positive pathogen Corynebacterium diphtheriae is essential for viability, pilus assembly, toxin production and virulence. PMID:26294390
MicroRNA-142-3p and microRNA-142-5p are downregulated in hepatocellular carcinoma and exhibit synergistic effects on cell motility. PMID:26293610
Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi. PMID:26293353
Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression. PMID:26288239
Microbial Communities Can Be Described by Metabolic Structure: A General Framework and Application to a Seasonally Variable, Depth-Stratified Microbial Community from the Coastal West Antarctic Peninsula. PMID:26285202
Diversified Control Paths: A Significant Way Disease Genes Perturb the Human Regulatory Network. PMID:26284649
Identification of in vitro and in vivo disconnects using transcriptomic data. PMID:26282683
Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in endothelial cells. PMID:26278786
Deciphering the Correlation between Breast Tumor Samples and Cell Lines by Integrating Copy Number Changes and Gene Expression Profiles. PMID:26273658
Directional migration and transcriptional analysis of oligodendrocyte precursors subjected to stimulation of electrical signal. PMID:26269459
Dissecting ancestry genomic background in substance dependence genome-wide association studies. PMID:26267224
Genetic architecture of cyst nematode resistance revealed by genome-wide association study in soybean. PMID:26263897
A "footprint" of plant carbon fixation cycle functions during the development of a heterotrophic fungus. PMID:26263551
Serum Dyslipidemia Is Induced by Internal Exposure to Strontium-90 in Mice, Lipidomic Profiling Using a Data-Independent Liquid Chromatography-Mass Spectrometry Approach. PMID:26262552
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets. PMID:26261215
Integrated miRNA-mRNA analysis in the habenula nuclei of mice intravenously self-administering nicotine. PMID:26260614
An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. PMID:26256211
Aberrant splicing of genes involved in haemoglobin synthesis and impaired terminal erythroid maturation in SF3B1 mutated refractory anaemia with ring sideroblasts. PMID:26255870
MESSI: metabolic engineering target selection and best strain identification tool. PMID:26255308
Found and Lost: The Fates of Horizontally Acquired Genes in Arthropod-Symbiotic Spiroplasma. PMID:26254485
Algorithms for modeling global and context-specific functional relationship networks. PMID:26254431
Structural analysis of Clostridium acetobutylicum ATCC 824 glycoside hydrolase from CAZy family GH105. PMID:26249707
Genetic underpinnings of left superior temporal gyrus thickness in patients with schizophrenia. PMID:26249676
Transcriptomes That Confer to Plant Defense against Powdery Mildew Disease in Lagerstroemia indica. PMID:26247009
Molecular Architecture of Spinal Cord Injury Protein Interaction Network. PMID:26241741
Functional and protein‑protein interaction network analysis of colorectal cancer induced by ulcerative colitis. PMID:26239378
Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq. PMID:26236320
IscR of Rhodobacter sphaeroides functions as repressor of genes for iron-sulfur metabolism and represents a new type of iron-sulfur-binding protein. PMID:26235649
Identification of the key genes connected with plasma cells of multiple myeloma using expression profiles. PMID:26229487
Computer aided gene mining for gingerol biosynthesis. PMID:26229293
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder. PMID:26228432
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Biological processes and pathway changes in isoflurane-induced anesthesia revealed by bioinformatics analysis of gene expression profiles. PMID:26223573
An Integrative Approach for Mapping Differentially Expressed Genes and Network Components Using Novel Parameters to Elucidate Key Regulatory Genes in Colorectal Cancer. PMID:26222778
Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans. PMID:26221956
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1. PMID:26220682
Deep sequencing-based characterization of transcriptome of trifoliate orange (Poncirus trifoliata (L.) Raf.) in response to cold stress. PMID:26219960
Longevity Genes Revealed by Integrative Analysis of Isoform-Specific daf-16/FoxO Mutants of Caenorhabditis elegans. PMID:26219299
Pathway Relevance Ranking for Tumor Samples through Network-Based Data Integration. PMID:26217958
Data in support of enhancing metabolomics research through data mining. PMID:26217737
Data for iTRAQ-based quantitative proteomics analysis of Brassica napus leaves in response to chlorophyll deficiency. PMID:26217696
A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes. PMID:26217230
Analytical strategies for studying stem cell metabolism. PMID:26213533
Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. PMID:26208504
A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis. PMID:26207740
Microarray Analysis of the Major Depressive Disorder mRNA Profile Data. PMID:26207134
Knowledge transfer via classification rules using functional mapping for integrative modeling of gene expression data. PMID:26202217
Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing. PMID:26199343
Empirical comparison of structure-based pathway methods. PMID:26197809
Functional Classification of Uncultured "Candidatus Caldiarchaeum subterraneum" Using the Maple System. PMID:26196861
An Interactive Cluster Heat Map to Visualize and Explore Multidimensional Metabolomic Data. PMID:26195918
Network-Based Analysis of Schizophrenia Genome-Wide Association Data to Detect the Joint Functional Association Signals. PMID:26193471
A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. PMID:26189680
Adaptation of a Bioinformatics Microarray Analysis Workflow for a Toxicogenomic Study in Rainbow Trout. PMID:26186543
Screening of potential diagnostic markers and therapeutic targets against colorectal cancer. PMID:26185457
Draft Genome Sequence of a Novel Nicotine-Degrading Bacterium, Pseudomonas plecoglossicida TND35. PMID:26184952
Evolutionary Influenced Interaction Pattern as Indicator for the Investigation of Natural Variants Causing Nephrogenic Diabetes Insipidus. PMID:26180540
De Novo Characterization of the Mung Bean Transcriptome and Transcriptomic Analysis of Adventitious Rooting in Seedlings Using RNA-Seq. PMID:26177103
swDMR: A Sliding Window Approach to Identify Differentially Methylated Regions Based on Whole Genome Bisulfite Sequencing. PMID:26176536
Transfer of energy pathway genes in microbial enhanced biological phosphorus removal communities. PMID:26173980
Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments. PMID:26173481
Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. PMID:26170900
Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle. PMID:26169777
Targeted plasma metabolome response to variations in dietary glycemic load in a randomized, controlled, crossover feeding trial in healthy adults. PMID:26165375
Genome Sequence of Arthrobacter sp. YC-RL1, an Aromatic Compound-Degrading Bacterium. PMID:26159532
Heterogeneous Network Edge Prediction: A Data Integration Approach to Prioritize Disease-Associated Genes. PMID:26158728
PAND: A Distribution to Identify Functional Linkage from Networks with Preferential Attachment Property. PMID:26158709
Comparative analysis of tissue-specific transcriptomes in the funnel-web spider Macrothele calpeiana (Araneae, Hexathelidae). PMID:26157629
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PMID:26157614
Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. PMID:26157422
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L. PMID:26157330
Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase: A potential case of cytonuclear cointrogression. PMID:26155926
Proteome profiling of heat, oxidative, and salt stress responses in Thermococcus kodakarensis KOD1. PMID:26150806
Known structure, unknown function: An inquiry-based undergraduate biochemistry laboratory course. PMID:26148241
Transcriptome and Molecular Pathway Analysis of the Hepatopancreas in the Pacific White Shrimp Litopenaeus vannamei under Chronic Low-Salinity Stress. PMID:26147449
Thermodynamics and H2 Transfer in a Methanogenic, Syntrophic Community. PMID:26147299
Phenome-Wide Association Studies: Leveraging Comprehensive Phenotypic and Genotypic Data for Discovery. PMID:26146598
Evaluation of a high-EPA oil from transgenic Camelina sativa in feeds for Atlantic salmon (Salmo salar L.): Effects on tissue fatty acid composition, histology and gene expression. PMID:26146421
Time-course gene profiling and networks in demethylated retinoblastoma cell line. PMID:26143641
Transcriptional response of Atlantic salmon families to Piscirickettsia salmonis infection highlights the relevance of the iron-deprivation defence system. PMID:26141111
The antigenic landscape of multiple myeloma: mass spectrometry (re)defines targets for T-cell-based immunotherapy. PMID:26138685
Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome. PMID:26137199
Bioinformatics analysis to identify the differentially expressed genes of glaucoma. PMID:26135629
Identification of Chemical Inhibitors of β-Catenin-Driven Liver Tumorigenesis in Zebrafish. PMID:26134322
Drug-Path: a database for drug-induced pathways. PMID:26130661
Dual Transcriptomic Profiling of Host and Microbiota during Health and Disease in Pediatric Asthma. PMID:26125632
Identification of enhanced hydrogen and ethanol Escherichia coli producer strains in a glycerol-based medium by screening in single-knock out mutant collections. PMID:26122736
Metabolome progression during early gut microbial colonization of gnotobiotic mice. PMID:26118551
Ensemble Methods for MiRNA Target Prediction from Expression Data. PMID:26114448
Time-Course Gene Set Analysis for Longitudinal Gene Expression Data. PMID:26111374
Metabolomics Analysis Reveals that AICAR Affects Glycerolipid, Ceramide and Nucleotide Synthesis Pathways in INS-1 Cells. PMID:26107620
Identifying Highly Penetrant Disease Causal Mutations Using Next Generation Sequencing: Guide to Whole Process. PMID:26106619
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. PMID:26102287
Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis. PMID:26100984
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes. PMID:26100352
Systems analysis of gene ontology and biological pathways involved in post-myocardial infarction responses. PMID:26100218
Application of a hierarchical enzyme classification method reveals the role of gut microbiome in human metabolism. PMID:26099921
An integrated approach to reveal miRNAs' impacts on the functional consequence of copy number alterations in cancer. PMID:26099552
Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. PMID:26097471
Gene Expression Associated with Early and Late Chronotypes in Drosophila melanogaster. PMID:26097463
A Conserved Circular Network of Coregulated Lipids Modulates Innate Immune Responses. PMID:26095250
Using quantitative PCR with retrotransposon-based insertion polymorphisms as markers in sugarcane. PMID:26093024
Nitrite-Oxidizing Bacterium Nitrobacter winogradskyi Produces N-Acyl-Homoserine Lactone Autoinducers. PMID:26092466
Asian Citrus Psyllid Expression Profiles Suggest Candidatus Liberibacter Asiaticus-Mediated Alteration of Adult Nutrition and Metabolism, and of Nymphal Development and Immunity. PMID:26091106
Metatranscriptome Analysis of Fig Flowers Provides Insights into Potential Mechanisms for Mutualism Stability and Gall Induction. PMID:26090817
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
Extensive rewiring of epithelial-stromal co-expression networks in breast cancer. PMID:26087699
Unusual biology across a group comprising more than 15% of domain Bacteria. PMID:26083755
Measuring information flow in cellular networks by the systems biology method through microarray data. PMID:26082788
Circulating microRNA Signatures in Rodent Models of Pain. PMID:26081151
Suppression of cell division-associated genes by Helicobacter pylori attenuates proliferation of RAW264.7 monocytic macrophage cells. PMID:26078204
High-Throughput Sequencing Identifies Novel and Conserved Cucumber (Cucumis sativus L.) microRNAs in Response to Cucumber Green Mottle Mosaic Virus Infection. PMID:26076360
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway. PMID:26075876
Genome-wide association study identifies novel genetic variants contributing to variation in blood metabolite levels. PMID:26068415
Draft Genome Sequence of Microbacterium profundi Shh49T, an Actinobacterium Isolated from Deep-Sea Sediment of a Polymetallic Nodule Environment. PMID:26067975
Systems biology of neurodegenerative diseases. PMID:26065845
Prediction of Metabolic Gene Biomarkers for Neurodegenerative Disease by an Integrated Network-Based Approach. PMID:26064912
Lysosome and Cytoskeleton Pathways Are Robustly Enriched in the Blood of Septic Patients: A Meta-Analysis of Transcriptomic Data. PMID:26063982
Next-generation transcriptome analysis in transgenic birch overexpressing and suppressing APETALA1 sheds lights in reproduction development and diterpenoid biosynthesis. PMID:26063613
Investigation of Gene Regulatory Networks Associated with Autism Spectrum Disorder Based on MiRNA Expression in China. PMID:26061495
Novel Drug Targets for Food-Borne Pathogen Campylobacter jejuni: An Integrated Subtractive Genomics and Comparative Metabolic Pathway Study. PMID:26061459
Cyclic Rhamnosylated Elongation Factor P Establishes Antibiotic Resistance in Pseudomonas aeruginosa. PMID:26060278
Gene set analysis: A step-by-step guide. PMID:26059482
Comparative genomic and phenomic analysis of Clostridium difficile and Clostridium sordellii, two related pathogens with differing host tissue preference. PMID:26059449
Identification of New Candidate Genes and Chemicals Related to Esophageal Cancer Using a Hybrid Interaction Network of Chemicals and Proteins. PMID:26058041
Discrete Logic Modelling Optimization to Contextualize Prior Knowledge Networks Using PRUNET. PMID:26058016
DksA and (p)ppGpp have unique and overlapping contributions to Haemophilus ducreyi pathogenesis in humans. PMID:26056381
A knowledge base for Vitis vinifera functional analysis. PMID:26050794
DeCoaD: determining correlations among diseases using protein interaction networks. PMID:26047952
The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer. PMID:26047514
Analysis of the transcriptional regulation of cancer-related genes by aberrant DNA methylation of the cis-regulation sites in the promoter region during hepatocyte carcinogenesis caused by arsenic. PMID:26046465
Context-based resolution of semantic conflicts in biological pathways. PMID:26045143
Reference genome of wild goat (capra aegagrus) and sequencing of goat breeds provide insight into genic basis of goat domestication. PMID:26044654
Complete Genome Sequence of Agrobacterium tumefaciens Ach5. PMID:26044425
Combined analysis of gene regulatory network and SNV information enhances identification of potential gene markers in mouse knockout studies with small number of samples. PMID:26044212
Detection and analysis of disease-associated single nucleotide polymorphism influencing post-translational modification. PMID:26043787
De novo Transcriptome Analysis of Portunus trituberculatus Ovary and Testis by RNA-Seq: Identification of Genes Involved in Gonadal Development. PMID:26042806
Transcriptome Characterization of Cymbidium sinense 'Dharma' Using 454 Pyrosequencing and Its Application in the Identification of Genes Associated with Leaf Color Variation. PMID:26042676
De novo Assembly, Characterization of Immature Seed Transcriptome and Development of Genic-SSR Markers in Black Gram [Vigna mungo (L.) Hepper]. PMID:26042595
Microbial community structure and function on sinking particles in the North Pacific Subtropical Gyre. PMID:26042105
An integrated structural proteomics approach along the druggable genome of Corynebacterium pseudotuberculosis species for putative druggable targets. PMID:26041381
Signatures of host/symbiont genome coevolution in insect nutritional endosymbioses. PMID:26039986
PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data. PMID:26038725
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PMID:26035711
Defining bacterial regulons using ChIP-seq. PMID:26032817
Extracellular matrix-associated proteins form an integral and dynamic system during Pseudomonas aeruginosa biofilm development. PMID:26029669
Elucidation of the recognition mechanisms for hemicellulose and pectin in Clostridium cellulovorans using intracellular quantitative proteome analysis. PMID:26020016
Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci†. PMID:26019233
miRNA proxy approach reveals hidden functions of glycosylation. PMID:26015571
Reanalysis of mGWAS results and in vitro validation show that lactate dehydrogenase interacts with branched-chain amino acid metabolism. PMID:26014429
Fostering synergy between cell biology and systems biology. PMID:26013981
The prognostic factors and multiple biomarkers in young patients with colorectal cancer. PMID:26013439
Systematic Genome-wide Screening and Prediction of microRNAs in EBOV During the 2014 Ebolavirus Outbreak. PMID:26011078
A Comprehensive Metabolomic Investigation in Urine of Mice Exposed to Strontium-90. PMID:26010713
Translational regulation shapes the molecular landscape of complex disease phenotypes. PMID:26007203
NetworkPainter: dynamic intracellular pathway animation in Cytobank. PMID:26003204
Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2. PMID:26002892
Identification of cold tolerance genes from leaves of mangrove plant Kandelia obovata by suppression subtractive hybridization. PMID:26002218
Pan-phylum Comparison of Nematode Metabolic Potential. PMID:26000881
Genome Sequence of Bacillus coagulans P38, an Efficient Polymer-Grade l-Lactate Producer from Cellulosic Substrates. PMID:25999580
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. PMID:25999509
Gene expression studies of a human monocyte cell line identify dissimilarities between differently manufactured glatiramoids. PMID:25998228
Identification of genes associated with laryngeal squamous cell carcinoma samples based on bioinformatic analysis. PMID:25997441
Multi-omic profiling -of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production. PMID:25995028
Transcriptional (ChIP-Chip) Analysis of ELF1, ETS2, RUNX1 and STAT5 in Human Abdominal Aortic Aneurysm. PMID:25993293
Immunohistochemical analysis of the natural killer cell cytotoxicity pathway in human abdominal aortic aneurysms. PMID:25993291
Integrative genomic signatures of hepatocellular carcinoma derived from nonalcoholic Fatty liver disease. PMID:25993042
Metabolic energy-based modelling explains product yielding in anaerobic mixed culture fermentations. PMID:25992959
A network flow-based method to predict anticancer drug sensitivity. PMID:25992881
Rapid molecular evolution across amniotes of the IIS/TOR network. PMID:25991861
Gut microbial succession follows acute secretory diarrhea in humans. PMID:25991682
MyProteinNet: build up-to-date protein interaction networks for organisms, tissues and user-defined contexts. PMID:25990735
FOXO target gene CTDSP2 regulates cell cycle progression through Ras and p21(Cip1/Waf1). PMID:25990325
PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool. PMID:25989388
PathRings: a web-based tool for exploration of ortholog and expression data in biological pathways. PMID:25982732
Genetic alterations of JAK/STAT cascade and histone modification in extranodal NK/T-cell lymphoma nasal type. PMID:25980440
NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. PMID:25980407
Gap junctions modulate glioma invasion by direct transfer of microRNA. PMID:25978028
Flow-dependent regulation of genome-wide mRNA and microRNA expression in endothelial cells in vivo. PMID:25977794
Draft Genome Sequence of Anaeromyxobacter sp. Strain PSR-1, an Arsenate-Respiring Bacterium Isolated from Arsenic-Contaminated Soil. PMID:25977440
Dissection of the style's response to pollination using transcriptome profiling in self-compatible (Solanum pimpinellifolium) and self-incompatible (Solanum chilense) tomato species. PMID:25976872
Integrating transcriptome and genome re-sequencing data to identify key genes and mutations affecting chicken eggshell qualities. PMID:25974068
Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange. PMID:25972851
Inference of Evolutionary Forces Acting on Human Biological Pathways. PMID:25971280
A de novo floral transcriptome reveals clues into Phalaenopsis orchid flower development. PMID:25970572
Peripheral blood mononuclear cell proteome changes in patients with myelodysplastic syndrome. PMID:25969835
ClustVis: a web tool for visualizing clustering of multivariate data using Principal Component Analysis and heatmap. PMID:25969447
Function of cancer associated genes revealed by modern univariate and multivariate association tests. PMID:25965968
Screening of candidate genes in fibroblasts derived from patients with Dupuytren's contracture using bioinformatics analysis. PMID:25963801
Pathway-based personalized analysis of breast cancer expression data. PMID:25963740
Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. PMID:25957781
Mutations in Nature Conferred a High Affinity Phosphatidylinositol 4,5-Bisphosphate-binding Site in Vertebrate Inwardly Rectifying Potassium Channels. PMID:25957411
Energy Conservation Model Based on Genomic and Experimental Analyses of a Carbon Monoxide-Utilizing, Butyrate-Forming Acetogen, Eubacterium limosum KIST612. PMID:25956767
Analysis of Cynandione A's Anti-Ischemic Stroke Effects from Pathways and Protein-Protein Interactome. PMID:25955557
Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. PMID:25954263
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. PMID:25953818
Gene Ontology and KEGG Pathway Enrichment Analysis of a Drug Target-Based Classification System. PMID:25951454
ErbB2-intronic microRNA-4728: a novel tumor suppressor and antagonist of oncogenic MAPK signaling. PMID:25950472
SELPHI: correlation-based identification of kinase-associated networks from global phospho-proteomics data sets. PMID:25948583
Assembly of a comprehensive regulatory network for the mammalian circadian clock: a bioinformatics approach. PMID:25945798
The goose genome sequence leads to insights into the evolution of waterfowl and susceptibility to fatty liver. PMID:25943208
Metabolic dependencies drive species co-occurrence in diverse microbial communities. PMID:25941371
Genetic Basis of Common Human Disease: Insight into the Role of Missense SNPs from Genome-Wide Association Studies. PMID:25937569
Pathways with PathWhiz. PMID:25934797
Temperament type specific metabolite profiles of the prefrontal cortex and serum in cattle. PMID:25927228
PolySearch2: a significantly improved text-mining system for discovering associations between human diseases, genes, drugs, metabolites, toxins and more. PMID:25925572
Visual analysis of biological data-knowledge networks. PMID:25925016
Insights from the metagenome of an acid salt lake: the role of biology in an extreme depositional environment. PMID:25923206
RNA-seq analysis of Macrobrachium rosenbergii hepatopancreas in response to Vibrio parahaemolyticus infection. PMID:25922623
Protein expression profiles characterize distinct features of mouse cerebral cortices at different developmental stages. PMID:25915664
Multiset Statistics for Gene Set Analysis. PMID:25914887
Inferring data-specific micro-RNA function through the joint ranking of micro-RNA and pathways from matched micro-RNA and gene expression data. PMID:25910695
Co-regulation of translation in protein complexes. PMID:25909184
The genetic basis of peripheral arterial disease: current knowledge, challenges, and future directions. PMID:25908728
Bioinformatics analyses of significant prognostic risk markers for thyroid papillary carcinoma. PMID:25908172
Differential gene expression in liver tissues of streptozotocin-induced diabetic rats in response to resveratrol treatment. PMID:25905778
The resurrection genome of Boea hygrometrica: A blueprint for survival of dehydration. PMID:25902549
Global transcriptional dynamics of diapause induction in non-blood-fed and blood-fed Aedes albopictus. PMID:25897664
Metatranscriptomic profiles of Eastern subterranean termites, Reticulitermes flavipes (Kollar) fed on second generation feedstocks. PMID:25896921
Poplar trees reconfigure the transcriptome and metabolome in response to drought in a genotype- and time-of-day-dependent manner. PMID:25895923
Exome analysis of patients with concurrent pediatric inflammatory bowel disease and autoimmune disease. PMID:25895113
High-resolution metabolomics to discover potential parasite-specific biomarkers in a Plasmodium falciparum erythrocytic stage culture system. PMID:25889340
Plasmodium vivax inhibits erythroid cell growth through altered phosphorylation of the cytoskeletal protein ezrin. PMID:25889165
DomSign: a top-down annotation pipeline to enlarge enzyme space in the protein universe. PMID:25888481
New insights into the genetic networks affecting seed fatty acid concentrations in Brassica napus. PMID:25888376
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Whole-genome assembly of Akkermansia muciniphila sequenced directly from human stool. PMID:25888298
The genome of the basal agaricomycete Xanthophyllomyces dendrorhous provides insights into the organization of its acetyl-CoA derived pathways and the evolution of Agaricomycotina. PMID:25887949
MeSH ORA framework: R/Bioconductor packages to support MeSH over-representation analysis. PMID:25887539
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. PMID:25887162
MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. PMID:25885687
Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver. PMID:25885344
ACTN4 and the pathways associated with cell motility and adhesion contribute to the process of lung cancer metastasis to the brain. PMID:25885339
Phenome-wide Association Study Relating Pretreatment Laboratory Parameters With Human Genetic Variants in AIDS Clinical Trials Group Protocols. PMID:25884002
Epithelial Plasticity in Cancer: Unmasking a MicroRNA Network for TGF-β-, Notch-, and Wnt-Mediated EMT. PMID:25883651
Nourishment level affects caste-related gene expression in Polistes wasps. PMID:25880983
Spectral gene set enrichment (SGSE). PMID:25879888
Inorganic Arsenic-induced cellular transformation is coupled with genome wide changes in chromatin structure, transcriptome and splicing patterns. PMID:25879800
NEMix: single-cell nested effects models for probabilistic pathway stimulation. PMID:25879530
The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation. PMID:25879418
Metaproteomics of complex microbial communities in biogas plants. PMID:25874383
Identification of novel thyroid cancer-related genes and chemicals using shortest path algorithm. PMID:25874234
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. PMID:25873626
GWAS for executive function and processing speed suggests involvement of the CADM2 gene. PMID:25869804
SIRT3 mediates multi-tissue coupling for metabolic fuel switching. PMID:25863253
Applying stability selection to consistently estimate sparse principal components in high-dimensional molecular data. PMID:25861969
A microarray study of middle cerebral occlusion rat brain with acupuncture intervention. PMID:25861363
Identifying overlapping mutated driver pathways by constructing gene networks in cancer. PMID:25859819
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. PMID:25853934
The composition of the global and feature specific cyanobacterial core-genomes. PMID:25852675
Transcriptome analyses to investigate symbiotic relationships between marine protists. PMID:25852650
Transposon mutagenesis identifies genetic drivers of Braf(V600E) melanoma. PMID:25848750
Multivariate analysis of subjective responses to d-amphetamine in healthy volunteers finds novel genetic pathway associations. PMID:25843748
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. PMID:25840044
Dietary nitrate is a modifier of vascular gene expression in old male mice. PMID:25838870
Transcriptome analysis and its application in identifying genes associated with fruiting body development in basidiomycete Hypsizygus marmoreus. PMID:25837428
Transcriptomic analysis revealed the mechanism of oil dynamic accumulation during developing Siberian apricot (Prunus sibirica L.) seed kernels for the development of woody biodiesel. PMID:25834637
Complete genome-wide screening and subtractive genomic approach revealed new virulence factors, potential drug targets against bio-war pathogen Brucella melitensis 16M. PMID:25834405
BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies. PMID:25833955
MicroRNA profiling of CD3+ CD56+ cytokine-induced killer cells. PMID:25826780
iPathCase(KEGG): An iPad interface for KEGG metabolic pathways. PMID:25825656
Module-based association analysis for omics data with network structure. PMID:25822417
Prediction of drug indications based on chemical interactions and chemical similarities. PMID:25821813
Colorectal cancer drug target prediction using ontology-based inference and network analysis. PMID:25818893
Gene expression changes in human mesenchymal stem cells from patients with osteoporosis. PMID:25815782
Phenotype and transcriptome analysis reveals chloroplast development and pigment biosynthesis together influenced the leaf color formation in mutants of Anthurium andraeanum 'Sonate'. PMID:25814997
Genome Sequence of Organophosphorus Pesticide-Degrading Bacterium Pseudomonas stutzeri Strain YC-YH1. PMID:25814604
Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network. PMID:25809411
Analysis of pharmacogenomic variants associated with population differentiation. PMID:25807276
An epigenetic map of age-associated autosomal loci in northern European families at high risk for the metabolic syndrome. PMID:25806089
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. PMID:25806041
Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR. PMID:25799583
De novo characterization of fall dormant and nondormant alfalfa (Medicago sativa L.) leaf transcriptome and identification of candidate genes related to fall dormancy. PMID:25799491
De novo transcriptome assembly of pummelo and molecular marker development. PMID:25799271
Developmental exposure to estrogen alters differentiation and epigenetic programming in a human fetal prostate xenograft model. PMID:25799167
Personal genomes, quantitative dynamic omics and personalized medicine. PMID:25798291
Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. PMID:25797143
A genomic comparison of two termites with different social complexity. PMID:25788900
Translational arrest due to cytoplasmic redox stress delays adaptation to growth on methanol and heterologous protein expression in a typical fed-batch culture of Pichia pastoris. PMID:25785713
A meta-analysis of gene expression signatures of blood pressure and hypertension. PMID:25785607
Simultaneous inference of cancer pathways and tumor progression from cross-sectional mutation data. PMID:25785493
Identification of B cells participated in the mechanism of postmenopausal women osteoporosis using microarray analysis. PMID:25785089
The beta-3 adrenergic agonist (CL-316,243) restores the expression of down-regulated fatty acid oxidation genes in type 2 diabetic mice. PMID:25784953
Performance of case-control rare copy number variation annotation in classification of autism. PMID:25783485
Gene networks underlying convergent and pleiotropic phenotypes in a large and systematically-phenotyped cohort with heterogeneous developmental disorders. PMID:25781962
Analysis of expressed sequence tags from cDNA library of Fusarium culmorum infected barley (Hordeum vulgare L.) roots. PMID:25780278
MetaNET--a web-accessible interactive platform for biological metabolic network analysis. PMID:25779921
Social networks predict gut microbiome composition in wild baboons. PMID:25774601
A Bayesian model for the identification of differentially expressed genes in Daphnia magna exposed to munition pollutants. PMID:25771699
Comparing Mycobacterium tuberculosis genomes using genome topology networks. PMID:25766780
High correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains. PMID:25766446
A statistical framework for revealing signaling pathways perturbed by DNA variants. PMID:25765646
Comparative genome analysis of Prevotella intermedia strain isolated from infected root canal reveals features related to pathogenicity and adaptation. PMID:25765460
Serum biomarkers of habitual coffee consumption may provide insight into the mechanism underlying the association between coffee consumption and colorectal cancer. PMID:25762808
Transcriptome analysis reveals the potential mechanism of the albino skin development in pufferfish Takifugu obscurus. PMID:25761722
Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation. PMID:25761715
Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response. PMID:25758009
Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses. PMID:25750594
Dietary methionine restriction in mice elicits an adaptive cardiovascular response to hyperhomocysteinemia. PMID:25744495
Mango (Mangifera indica L.) cv. Kent fruit mesocarp de novo transcriptome assembly identifies gene families important for ripening. PMID:25741352
A metagenomic approach to characterize temperate bacteriophage populations from Cystic Fibrosis and non-Cystic Fibrosis bronchiectasis patients. PMID:25741327
Genetically modified bacteria as a tool to detect microscopic solid tumor masses with triggered release of a recombinant biomarker. PMID:25737274
Meta-analysis of gene expression profiles indicates genes in spliceosome pathway are up-regulated in hepatocellular carcinoma (HCC). PMID:25731616
Cancer based pharmacogenomics network supported with scientific evidences: from the view of drug repurposing. PMID:25729430
Protein complexes in bacteria. PMID:25723151
The gut bacterium Bacteroides thetaiotaomicron influences the virulence potential of the enterohemorrhagic Escherichia coli O103:H25. PMID:25719195
Expression profiling analysis of the microRNA response of Cynoglossus semilaevis to Vibrio anguillarum and other stimuli. PMID:25715708
Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome. PMID:25715653
Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle. PMID:25714999
YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research. PMID:25712262
Pinpointing disease genes through phenomic and genomic data fusion. PMID:25708473
Accurate multiple network alignment through context-sensitive random walk. PMID:25707987
IIIDB: a database for isoform-isoform interactions and isoform network modules. PMID:25707505
Whole transcriptome analysis using next-generation sequencing of sterile-cultured Eisenia andrei for immune system research. PMID:25706644
Diversity in gut bacterial community of school-age children in Asia. PMID:25703686
Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.). PMID:25700980
Comparative genomic analysis of seven Mycoplasma hyosynoviae strains. PMID:25693846
CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing. PMID:25692681
Pilot dietary intervention with heat-stabilized rice bran modulates stool microbiota and metabolites in healthy adults. PMID:25690418
Identification of potential transcriptomic markers in developing ankylosing spondylitis: a meta-analysis of gene expression profiles. PMID:25688367
Mitofusin 2 is required to maintain mitochondrial coenzyme Q levels. PMID:25688136
Dispensability of zinc and the putative zinc-binding domain in bacterial glutamyl-tRNA synthetase. PMID:25686371
Computing smallest intervention strategies for multiple metabolic networks in a boolean model. PMID:25684199
Proteome analysis of pear reveals key genes associated with fruit development and quality. PMID:25682102
Comparative transcriptome analysis reveals that lactose acts as an inducer and provides proper carbon sources for enhancing exopolysaccharide yield in the deep-sea bacterium Zunongwangia profunda SM-A87. PMID:25679965
Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly. PMID:25674789
New genetic loci link adipose and insulin biology to body fat distribution. PMID:25673412
Environmental genes and genomes: understanding the differences and challenges in the approaches and software for their analyses. PMID:25673291
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PMID:25670818
Modulation of macrophage activities in proliferation, lysosome, and phagosome by the nonspecific immunostimulator, mica. PMID:25668030
Antimicrobial peptides expressed in medicinal maggots of the blow fly Lucilia sericata show combinatorial activity against bacteria. PMID:25666157
Crystallization and preliminary X-ray diffraction analysis of a putative carbon-carbon bond hydrolase from Mycobacterium abscessus 103. PMID:25664803
Untargeted UPLC-MS profiling pipeline to expand tissue metabolome coverage: application to cardiovascular disease. PMID:25664760
HPOSim: an R package for phenotypic similarity measure and enrichment analysis based on the human phenotype ontology. PMID:25664462
Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. PMID:25663508
Differential gene expression in Aspergillus fumigatus induced by human platelets in vitro. PMID:25661519
Regulation of toll-like receptor signaling by the SF3a mRNA splicing complex. PMID:25658809
Retrospective review using targeted deep sequencing reveals mutational differences between gastroesophageal junction and gastric carcinomas. PMID:25656989
Regulation of ICAM-1 in cells of the monocyte/macrophage system in microgravity. PMID:25654110
Genome analysis of Flaviramulus ichthyoenteri Th78(T) in the family Flavobacteriaceae: insights into its quorum quenching property and potential roles in fish intestine. PMID:25652846
A visual review of the interactome of LRRK2: Using deep-curated molecular interaction data to represent biology. PMID:25648416
Fetal-adult cardiac transcriptome analysis in rats with contrasting left ventricular mass reveals new candidates for cardiac hypertrophy. PMID:25646840
Methylated microRNA genes of the developing murine palate. PMID:25642850
Establishing Chlamydomonas reinhardtii as an industrial biotechnology host. PMID:25641561
miRNA-target gene regulatory networks: A Bayesian integrative approach to biomarker selection with application to kidney cancer. PMID:25639276
Complete Genome Sequence of "Candidatus Sulcia muelleri" ML, an Obligate Nutritional Symbiont of Maize Leafhopper (Dalbulus maidis). PMID:25635014
Draft Genome Sequence of Geobacter sp. Strain OR-1, an Arsenate-Respiring Bacterium Isolated from Japanese Paddy Soil. PMID:25635012
Genome-wide analysis of alternative splicing landscapes modulated during plant-virus interactions in Brachypodium distachyon. PMID:25634987
Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction. PMID:25634120
Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G. PMID:25628353
Metabolome profiling by HRMAS NMR spectroscopy of pheochromocytomas and paragangliomas detects SDH deficiency: clinical and pathophysiological implications. PMID:25622899
Inferring biological tasks using Pareto analysis of high-dimensional data. PMID:25622107
Organization of enzyme concentration across the metabolic network in cancer cells. PMID:25621879
Directed evolution combined with synthetic biology strategies expedite semi-rational engineering of genes and genomes. PMID:25621864
Draft Genome Sequence of Marine Bacterium Streptomyces sp. Strain CNQ431, a Producer of the Cytokine Inhibitor Splenocin. PMID:25614558
Bias in microRNA functional enrichment analysis. PMID:25609791
Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation. PMID:25609551
RNA-Seq analysis and transcriptome assembly for blackberry (Rubus sp. Var. Lochness) fruit. PMID:25608670
De novo assembly and characterization of narrow-ridged finless porpoise renal transcriptome and identification of candidate genes involved in osmoregulation. PMID:25608655
Transcriptome analysis reveals in vitro cultured Withania somnifera leaf and root tissues as a promising source for targeted withanolide biosynthesis. PMID:25608483
Acquisition of docetaxel resistance in breast cancer cells reveals upregulation of ABCB1 expression as a key mediator of resistance accompanied by discrete upregulation of other specific genes and pathways. PMID:25596703
Effects of copy number variable regions on local gene expression in white blood cells of Mexican Americans. PMID:25585699
Galacto-oligosaccharides and Colorectal Cancer: Feeding our Intestinal Probiome. PMID:25584074
The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau. PMID:25583503
Reconstruction and analysis of a genome-scale metabolic model of the oleaginous fungus Mortierella alpina. PMID:25582171
Methods of integrating data to uncover genotype-phenotype interactions. PMID:25582081
The RIG-I-like helicase receptor MDA5 (IFIH1) is involved in the host defense against Candida infections. PMID:25579795
Identification of hub subnetwork based on topological features of genes in breast cancer. PMID:25573623
Comparative exomics of Phalaris cultivars under salt stress. PMID:25573273
Proteome scale comparative modeling for conserved drug and vaccine targets identification in Corynebacterium pseudotuberculosis. PMID:25573232
Cabut/dTIEG associates with the transcription factor Yorkie for growth control. PMID:25572844
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. PMID:25572802
Proceedings of the Thirteenth Annual UT- KBRIN Bioinformatics Summit 2014. PMID:25571995
Insight in genome-wide association of metabolite quantitative traits by exome sequence analyses. PMID:25569235
The majority of transcripts in the squid nervous system are extensively recoded by A-to-I RNA editing. PMID:25569156
Global coordination in adaptation to gene rewiring. PMID:25564530
Analysis of signaling networks distributed over intracellular compartments based on protein-protein interactions. PMID:25564293
Genetic determinants of depression: recent findings and future directions. PMID:25563565
Time-course human urine proteomics in space-flight simulation experiments. PMID:25563515
Impulsivity and comorbid traits: a multi-step approach for finding putative responsible microRNAs in the amygdala. PMID:25561905
A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. PMID:25559748
Identification of genes and pathways involved in kidney renal clear cell carcinoma. PMID:25559354
Exploration of molecular pathways mediating electric field-directed Schwann cell migration by RNA-seq. PMID:25557037
Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells. PMID:25555159
Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing. PMID:25553907
A field guide to whole-genome sequencing, assembly and annotation. PMID:25553065
Drosophila melanogaster show a threshold effect in response to radiation. PMID:25552957
Regulation of gene expression in HBV- and HCV-related hepatocellular carcinoma: integrated GWRS and GWGS analyses. PMID:25550913
Loss of ion transporters and increased unfolded protein response in Fuchs' dystrophy. PMID:25548511
HLA ligandome analysis identifies the underlying specificities of spontaneous antileukemia immune responses in chronic lymphocytic leukemia (CLL). PMID:25548167
Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state. PMID:25545155
ReNE: a cytoscape plugin for regulatory network enhancement. PMID:25541727
UProC: tools for ultra-fast protein domain classification. PMID:25540185
Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor. PMID:25539760
Persistence of furan-induced epigenetic aberrations in the livers of F344 rats. PMID:25539665
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PMID:25536074
Sequence search and analysis of gene products containing RNA recognition motifs in the human genome. PMID:25534245
Integrative view of α2,3-sialyltransferases (ST3Gal) molecular and functional evolution in deuterostomes: significance of lineage-specific losses. PMID:25534026
A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont. PMID:25527092
Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions. PMID:25523622
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes. PMID:25523484
A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. PMID:25523208
Assessment of cancer cell line representativeness using microarrays for Merkel cell carcinoma. PMID:25521454
Assessment of subnetwork detection methods for breast cancer. PMID:25520555
Comparative proteomics analysis of global cellular stress responses to hydroxyurea-induced DNA damage in HeLa cells. PMID:25519465
PROGgeneV2: enhancements on the existing database. PMID:25518851
Identification of differentially expressed genes regulated by transcription factors in glioblastomas by bioinformatics analysis. PMID:25514975
Genome-based metabolic mapping and 13C flux analysis reveal systematic properties of an oleaginous microalga Chlorella protothecoides. PMID:25511434
Subcellular metabolite and lipid analysis of Xenopus laevis eggs by LAESI mass spectrometry. PMID:25506922
A chemical proteomics approach for global analysis of lysine monomethylome profiling. PMID:25505155
Modelling the spatial heterogeneity and molecular correlates of lymphocytic infiltration in triple-negative breast cancer. PMID:25505134
Analysis of the early immune response to infection by infectious bursal disease virus in chickens differing in their resistance to the disease. PMID:25505077
Visnagin protects against doxorubicin-induced cardiomyopathy through modulation of mitochondrial malate dehydrogenase. PMID:25504881
Browning of human adipocytes requires KLF11 and reprogramming of PPARγ superenhancers. PMID:25504365
Comparative proteomic analysis of midgut proteins from male and female Bombyx mori (Lepidoptera: Bombycidae). PMID:25502033
Metatranscriptomic analyses of plant cell wall polysaccharide degradation by microorganisms in the cow rumen. PMID:25501482
Apoplastic venom allergen-like proteins of cyst nematodes modulate the activation of basal plant innate immunity by cell surface receptors. PMID:25500833
Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species. PMID:25496777
Standardised animal models of host microbial mutualism. PMID:25492472
Finding gene regulatory network candidates using the gene expression knowledge base. PMID:25490885
Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase. PMID:25487798
Fetal lung and placental methylation is associated with in utero nicotine exposure. PMID:25482056
Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums. PMID:25481640
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. PMID:25480530
Accounting for eXentricities: analysis of the X chromosome in GWAS reveals X-linked genes implicated in autoimmune diseases. PMID:25479423
MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens. PMID:25476604
Detection of pleiotropy through a Phenome-wide association study (PheWAS) of epidemiologic data as part of the Environmental Architecture for Genes Linked to Environment (EAGLE) study. PMID:25474351
Genome update of the dimorphic human pathogenic fungi causing paracoccidioidomycosis. PMID:25474325
Potential mechanism of action of meso-dihydroguaiaretic acid on Mycobacterium tuberculosis H37Rv. PMID:25474289
Transcriptomic survey of the midgut of Anthonomus grandis (Coleoptera: Curculionidae). PMID:25473064
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. PMID:25471253
Pathway-based analysis tools for complex diseases: a review. PMID:25462153
Diffusion of information throughout the host interactome reveals gene expression variations in network proximity to target proteins of hepatitis C virus. PMID:25461596
Characterization of the usage of the serine metabolic network in human cancer. PMID:25456139
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. PMID:25453034
Deciphering life history transcriptomes in different environments. PMID:25442828
Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. PMID:25433708
LigDig: a web server for querying ligand-protein interactions. PMID:25433696
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
A set-based association test identifies sex-specific gene sets associated with type 2 diabetes. PMID:25429300
Computational strategies for a system-level understanding of metabolism. PMID:25427076
ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis. PMID:25426929
Prolonged use of a proton pump inhibitor reduces microbial diversity: implications for Clostridium difficile susceptibility. PMID:25426290
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
Gene duplication of type-B ARR transcription factors systematically extends transcriptional regulatory structures in Arabidopsis. PMID:25425016
Transcriptome analysis of neonatal larvae after hyperthermia-induced seizures in the contractile silkworm, Bombyx mori. PMID:25423472
CONSTRICTOR: constraint modification provides insight into design of biochemical networks. PMID:25422896
Novel transcriptome assembly and improved annotation of the whiteleg shrimp (Litopenaeus vannamei), a dominant crustacean in global seafood mariculture. PMID:25420880
Synergy: a web resource for exploring gene regulation in Synechocystis sp. PCC6803. PMID:25420108
De novo amino acid biosynthesis contributes to salmonella enterica growth in Alfalfa seedling exudates. PMID:25416761
Tree shrew database (TreeshrewDB): a genomic knowledge base for the Chinese tree shrew. PMID:25413576
Comparative transcriptomic analysis of the response to cold acclimation in Eucalyptus dunnii. PMID:25412179
Comparative genomics of transcriptional regulation of methionine metabolism in Proteobacteria. PMID:25411846
Predicting the functional repertoire of an organism from unassembled RNA-seq data. PMID:25409897
De novo assembly of the grass carp Ctenopharyngodon idella transcriptome to identify miRNA targets associated with motile aeromonad septicemia. PMID:25409340
Global gene expression profiling identifies ALDH2, CCNE1 and SMAD3 as potential prognostic markers in upper tract urothelial carcinoma. PMID:25408144
Heterogeneous DNA methylation contributes to tumorigenesis through inducing the loss of coexpression connectivity in colorectal cancer. PMID:25407423
Flavonoid supplementation affects the expression of genes involved in cell wall formation and lignification metabolism and increases sugar content and saccharification in the fast-growing eucalyptus hybrid E. urophylla x E. grandis. PMID:25407319
Anatomo-proteomic characterization of human basal ganglia: focus on striatum and globus pallidus. PMID:25406675
Chemotactic signal transduction and phosphate metabolism as adaptive strategies during citrus canker induction by Xanthomonas citri. PMID:25403594
Fast and sensitive protein alignment using DIAMOND. PMID:25402007
Database resources of the National Center for Biotechnology Information. PMID:25398906
MethHC: a database of DNA methylation and gene expression in human cancer. PMID:25398901
Proteomics informed by transcriptomics reveals Hendra virus sensitizes bat cells to TRAIL-mediated apoptosis. PMID:25398248
Complete Genome Sequence of Dyella japonica Strain A8 Isolated from Malaysian Tropical Soil. PMID:25395638
Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study. PMID:25395096
Suppression of microbial metabolic pathways inhibits the generation of the human body odor component diacetyl by Staphylococcus spp. PMID:25390046
Exploring the genetic basis of adaptation to high elevations in reptiles: a comparative transcriptome analysis of two toad-headed agamas (genus Phrynocephalus). PMID:25386640
Identification of genes associated with the differentiation potential of adipose-derived stem cells to osteocytes or myocytes. PMID:25385480
A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia). PMID:25380694
Proteomics for systems toxicology. PMID:25379146
The exometabolome of Clostridium thermocellum reveals overflow metabolism at high cellulose loading. PMID:25379055
Proteomic analysis of human plasma in chronic rheumatic mitral stenosis reveals proteins involved in the complement and coagulation cascade. PMID:25379033
The role of cis regulatory evolution in maize domestication. PMID:25375861
Network based meta-analysis prediction of microenvironmental relays involved in stemness of human embryonic stem cells. PMID:25374775
Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods. PMID:25374614
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PMID:25369077
Gene regulatory networks and their applications: understanding biological and medical problems in terms of networks. PMID:25364745
Long-term phenotypic evolution of bacteria. PMID:25363780
Analysis of clock-regulated genes in Neurospora reveals widespread posttranscriptional control of metabolic potential. PMID:25362047
Near-isogenic lines of Triticum aestivum with distinct modes of resistance exhibit dissimilar transcriptional regulation during Diuraphis noxia feeding. PMID:25361582
Relating diseases by integrating gene associations and information flow through protein interaction network. PMID:25360770
Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. PMID:25352861
The complex jujube genome provides insights into fruit tree biology. PMID:25350882
Identifying disease genes by integrating multiple data sources. PMID:25350511
Ketogenesis prevents diet-induced fatty liver injury and hyperglycemia. PMID:25347470
New insights into regulation of proteome and polysaccharide in cell wall of Elsholtzia splendens in response to copper stress. PMID:25340800
Comparative and mechanistic genotoxicity assessment of nanomaterials via a quantitative toxicogenomics approach across multiple species. PMID:25338269
Fine-mapping the 2q37 and 17q11.2-q22 loci for novel genes and sequence variants associated with a genetic predisposition to prostate cancer. PMID:25335771
Metabolomic and lipidomic analysis of serum from mice exposed to an internal emitter, cesium-137, using a shotgun LC-MS(E) approach. PMID:25333951
Phylogenomic reconstruction indicates mitochondrial ancestor was an energy parasite. PMID:25333787
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PMID:25330313
Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses. PMID:25330259
De novo transcriptome sequencing of the Octopus vulgaris hemocytes using Illumina RNA-Seq technology: response to the infection by the gastrointestinal parasite Aggregata octopiana. PMID:25329466
De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China. PMID:25329319
Identification and monitoring of nitrification and denitrification genes in Klebsiella pneumoniae EGD-HP19-C for its ability to perform heterotrophic nitrification and aerobic denitrification. PMID:25326064
Hidden treasures in "ancient" microarrays: gene-expression portrays biology and potential resistance pathways of major lung cancer subtypes and normal tissue. PMID:25325012
On dynamically generating relevant elementary flux modes in a metabolic network using optimization. PMID:25323319
De novo assembly and transcriptome characterization: novel insights into catechins biosynthesis in Camellia sinensis. PMID:25316555
A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14-3-3 orthologs and associated effects of rapamycin. PMID:25315811
Translation of genomics-guided RNA-based personalised cancer vaccines: towards the bedside. PMID:25314223
MicroRNA expression profiling altered by variant dosage of radiation exposure. PMID:25313363
Organ system heterogeneity DB: a database for the visualization of phenotypes at the organ system level. PMID:25313158
RNA-seq reveals the pan-transcriptomic impact of attenuating the gliotoxin self-protection mechanism in Aspergillus fumigatus. PMID:25311525
Executing SADI services in Galaxy. PMID:25309716
Electro-acupuncture at Neiguan pretreatment alters genome-wide gene expressions and protects rat myocardium against ischemia-reperfusion. PMID:25302705
Divergence of RNA localization between rat and mouse neurons reveals the potential for rapid brain evolution. PMID:25301173
FungiFun2: a comprehensive online resource for systematic analysis of gene lists from fungal species. PMID:25294921
Single amino acid substitution in homogentisate 1,2-dioxygenase is responsible for pigmentation in a subset of Burkholderia cepacia complex isolates. PMID:25294803
Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam. PMID:25293379
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Comparative network analysis via differential graphlet communities. PMID:25283527
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. PMID:25281301
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. PMID:25280501
Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. PMID:25280473
Biogeography and individuality shape function in the human skin metagenome. PMID:25279917
Complete Genome Sequence of Vibrio vulnificus 93U204, a Bacterium Isolated from Diseased Tilapia in Taiwan. PMID:25278541
Systematic expression profiling analysis identifies specific microRNA-gene interactions that may differentiate between active and latent tuberculosis infection. PMID:25276827
Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs. PMID:25276232
Integrated analysis of miRNA and mRNA expression profiles in response to Cd exposure in rice seedlings. PMID:25273267
Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis. PMID:25268590
An online system for metabolic network analysis. PMID:25267793
Dynamics of gut microbiota in autoimmune lupus. PMID:25261516
Contrasting nitrogen fertilization treatments impact xylem gene expression and secondary cell wall lignification in Eucalyptus. PMID:25260963
Transcriptome profiling in imipenem-selected Acinetobacter baumannii. PMID:25260865
In-vivo fusion of human cancer and hamster stromal cells permanently transduces and transcribes human DNA. PMID:25259521
De novo transcriptome analysis of an aerial microalga Trentepohlia jolithus: pathway description and gene discovery for carbon fixation and carotenoid biosynthesis. PMID:25254555
Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis. PMID:25253284
Proteomic study reveals a functional network of cancer markers in the G1-Stage of the breast cancer cell cycle. PMID:25252636
Identification and characterization of a new erythromycin biosynthetic gene cluster in Actinopolyspora erythraea YIM90600, a novel erythronolide-producing halophilic actinomycete isolated from salt field. PMID:25250723
Non-metastatic 2 (NME2)-mediated suppression of lung cancer metastasis involves transcriptional regulation of key cell adhesion factor vinculin. PMID:25249619
Identification of copy number variations in Qinchuan cattle using BovineHD Genotyping Beadchip array. PMID:25248638
Complementary symbiont contributions to plant decomposition in a fungus-farming termite. PMID:25246537
Protein-protein interaction analysis of distinct molecular pathways in two subtypes of colorectal carcinoma. PMID:25242495
A novel model to combine clinical and pathway-based transcriptomic information for the prognosis prediction of breast cancer. PMID:25233347
Allele-specific network reveals combinatorial interaction that transcends small effects in psoriasis GWAS. PMID:25233071
Members of the human gut microbiota involved in recovery from Vibrio cholerae infection. PMID:25231861
Gene expression and pathway analysis of effects of the CMAH deactivation on mouse lung, kidney and heart. PMID:25229777
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection. PMID:25220818
The clinicopathological and gene expression patterns associated with ulceration of primary melanoma. PMID:25220403
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits. PMID:25218520
Genomic analysis of the Pacific oyster (Crassostrea gigas) reveals possible conservation of vertebrate sex determination in a mollusc. PMID:25213692
Evidence for the plasticity of arthropod signal transduction pathways. PMID:25213332
Co-regulated transcripts associated to cooperating eSNPs define Bi-fan motifs in human gene networks. PMID:25210734
Systems biology and brain activity in neuronal pathways by smart device and advanced signal processing. PMID:25206359
Network signatures link hepatic effects of anti-diabetic interventions with systemic disease parameters. PMID:25204982
Phylogenetic and metagenomic analyses of substrate-dependent bacterial temporal dynamics in microbial fuel cells. PMID:25202990
Evolutionary conservation and expression of human RNA-binding proteins and their role in human genetic disease. PMID:25201102
Comparative transcriptomic characterization of the early development in Pacific white shrimp Litopenaeus vannamei. PMID:25197823
Data mining of atherosclerotic plaque transcriptomes predicts STAT1-dependent inflammatory signal integration in vascular disease. PMID:25196434
Deep RNA-Seq to unlock the gene bank of floral development in Sinapis arvensis. PMID:25192023
The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice. PMID:25190456
MYCN repression of Lifeguard/FAIM2 enhances neuroblastoma aggressiveness. PMID:25188511
Small non-coding RNA profiling and the role of piRNA pathway genes in the protection of chicken primordial germ cells. PMID:25185950
De novo assembly and characterization of the fruit transcriptome of Chinese jujube (Ziziphus jujuba Mill.) Using 454 pyrosequencing and the development of novel tri-nucleotide SSR markers. PMID:25184704
FSim: a novel functional similarity search algorithm and tool for discovering functionally related gene products. PMID:25184141
esyN: network building, sharing and publishing. PMID:25181461
The mRNAs associated to a zinc finger protein from Trypanosoma cruzi shift during stress conditions. PMID:25180711
A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest. PMID:25180633
A systematic investigation of computation models for predicting Adverse Drug Reactions (ADRs). PMID:25180585
MYLK and MYL9 expression in non-small cell lung cancer identified by bioinformatics analysis of public expression data. PMID:25179839
Synergistic effects of combined DNA methyltransferase inhibition and MBD2 depletion on breast cancer cells; MBD2 depletion blocks 5-aza-2'-deoxycytidine-triggered invasiveness. PMID:25178277
PSEA-Quant: a protein set enrichment analysis on label-free and label-based protein quantification data. PMID:25177766
Developmentally-Dynamic Murine Brain Proteomes and Phosphoproteomes Revealed by Quantitative Proteomics. PMID:25177544
Diet-induced obesity modulates epigenetic responses to ionizing radiation in mice. PMID:25171162
Construction and analysis of the protein-protein interaction networks based on gene expression profiles of Parkinson's disease. PMID:25170921
Gene ontology and KEGG enrichment analyses of genes related to age-related macular degeneration. PMID:25165703
Broad-Enrich: functional interpretation of large sets of broad genomic regions. PMID:25161225
Dynamic gene expression patterns in animal models of early and late heart failure reveal biphasic-bidirectional transcriptional activation of signaling pathways. PMID:25159852
Making proteomics data accessible and reusable: current state of proteomics databases and repositories. PMID:25158685
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
Comparative analysis of false discovery rate methods in constructing metabolic association networks. PMID:25152043
Global proteome analysis identifies active immunoproteasome subunits in human platelets. PMID:25146974
Defining the estimated core genome of bacterial populations using a Bayesian decision model. PMID:25144616
The genome of Eimeria falciformis--reduction and specialization in a single host apicomplexan parasite. PMID:25142335
Genome-wide mutant fitness profiling identifies nutritional requirements for optimal growth of Yersinia pestis in deep tissue. PMID:25139902
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. PMID:25127889
Primary transcriptome map of the hyperthermophilic archaeon Thermococcus kodakarensis. PMID:25127548
A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers. PMID:25126847
MIR125B1 represses the degradation of the PML-RARA oncoprotein by an autophagy-lysosomal pathway in acute promyelocytic leukemia. PMID:25126724
ABCD2 alters peroxisome proliferator-activated receptor α signaling in vitro, but does not impair responses to fenofibrate therapy in a mouse model of diet-induced obesity. PMID:25123288
A novel eliminase from a marine bacterium that degrades hyaluronan and chondroitin sulfate. PMID:25122756
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. PMID:25122667
SNP identification by transcriptome sequencing and candidate gene-based association analysis for heat tolerance in the bay scallop Argopecten irradians. PMID:25121601
Identification of collaboration patterns of dysfunctional pathways in breast cancer. PMID:25120762
Alzheimer's disease: relevant molecular and physiopathological events affecting amyloid-β brain balance and the putative role of PPARs. PMID:25120477
Identifying a polymorphic 'switch' that influences miRNAs' regulation of a myasthenia gravis risk pathway. PMID:25118158
Grouping annotations on the subcellular layered interactome demonstrates enhanced autophagy activity in a recurrent experimental autoimmune uveitis T cell line. PMID:25116327
Proteomics-based metabolic modeling and characterization of the cellulolytic bacterium Thermobifida fusca. PMID:25115351
KiMoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems. PMID:25115331
The gene expression profile of cumulus cells reveals altered pathways in patients with endometriosis. PMID:25113618
Extremely low-frequency electromagnetic fields cause G1 phase arrest through the activation of the ATM-Chk2-p21 pathway. PMID:25111195
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Global transcriptome-wide analysis of CIK cells identify distinct roles of IL-2 and IL-15 in acquisition of cytotoxic capacity against tumor. PMID:25108500
Pathway-based association analysis of two genome-wide screening data identifies rheumatoid arthritis-related pathways. PMID:25101796
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. PMID:25099887
Expression analysis of miRNA and target mRNAs in esophageal cancer. PMID:25098614
Molecular analysis of the cold tolerant Antarctic nematode, Panagrolaimus davidi. PMID:25098249
Novel entries in a fungal biofilm matrix encyclopedia. PMID:25096878
Wnt pathway activation increases hypoxia tolerance during development. PMID:25093834
Depth-stratified functional and taxonomic niche specialization in the 'core' and 'flexible' Pacific Ocean Virome. PMID:25093636
Gene set enrichment analysis for multiple continuous phenotypes. PMID:25086605
Effect of histone deacetylase inhibitor JNJ-26481585 in pain. PMID:25085711
Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. PMID:25079003
Integrative genomics of chronic obstructive pulmonary disease. PMID:25078622
PRKCZ methylation is associated with sunlight exposure in a North American but not a Mediterranean population. PMID:25075435
Storing red blood cells with vitamin C and N-acetylcysteine prevents oxidative stress-related lesions: a metabolomics overview. PMID:25074788
The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal. PMID:25071079
Genome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen. PMID:25070509
Differential hippocampal gene expression and pathway analysis in an etiology-based mouse model of major depressive disorder. PMID:25059218
An intronic microRNA links Rb/E2F and EGFR signaling. PMID:25058496
Functional gene groups are concentrated within chromosomes, among chromosomes and in the nuclear space of the human genome. PMID:25056310
Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks. PMID:25055984
Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis. PMID:25052024
Differentially expressed genes and interacting pathways in bladder cancer revealed by bioinformatic analysis. PMID:25050631
Paradigm of Time-sequence Development of the Intestine of Suckling Piglets with Microarray. PMID:25049506
Metabolic pathways for the whole community. PMID:25048541
De novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways. PMID:25048025
The effect of low dose rate on metabolomic response to radiation in mice. PMID:25047638
Identifying plausible adverse drug reactions using knowledge extracted from the literature. PMID:25046831
Accurate in silico identification of species-specific acetylation sites by integrating protein sequence-derived and functional features. PMID:25042424
Functional characterization of breast cancer using pathway profiles. PMID:25041817
Hypothesis-independent pathway analysis implicates GABA and acetyl-CoA metabolism in primary open-angle glaucoma and normal-pressure glaucoma. PMID:25037249
Cheese rind communities provide tractable systems for in situ and in vitro studies of microbial diversity. PMID:25036636
SpliceNet: recovering splicing isoform-specific differential gene networks from RNA-Seq data of normal and diseased samples. PMID:25034693
Transcriptome analysis of a petal anthocyanin polymorphism in the arctic mustard, Parrya nudicaulis. PMID:25033465
Bioinformatic analysis of proteomics data. PMID:25033288
The common ground of genomics and systems biology. PMID:25033072
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Transcriptome analysis of Acidovorax avenae subsp. avenae cultivated in vivo and co-culture with Burkholderia seminalis. PMID:25027476
De novo transcriptome assembly from inflorescence of Orchis italica: analysis of coding and non-coding transcripts. PMID:25025767
Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. PMID:25024357
Pathway-centric integrative analysis identifies RRM2 as a prognostic marker in breast cancer associated with poor survival and tamoxifen resistance. PMID:25016594
Set-based joint test of interaction between SNPs in the VEGF pathway and exogenous estrogen finds association with age-related macular degeneration. PMID:25015356
Oil accumulation mechanisms of the oleaginous microalga Chlorella protothecoides revealed through its genome, transcriptomes, and proteomes. PMID:25012212
Deep Illumina-based shotgun sequencing reveals dietary effects on the structure and function of the fecal microbiome of growing kittens. PMID:25010839
Fumaric acid esters can block pro-inflammatory actions of human CRP and ameliorate metabolic disturbances in transgenic spontaneously hypertensive rats. PMID:25010431
Identification of a core miRNA-pathway regulatory network in glioma by therapeutically targeting miR-181d, miR-21, miR-23b, β-Catenin, CBP, and STAT3. PMID:25007077
Metabolomics for biomarker discovery in gastroenterological cancer. PMID:25003943
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. PMID:25003081
eXamine: exploring annotated modules in networks. PMID:25002203
Developmental cell fate and virulence are linked to trehalose homeostasis in Cryptococcus neoformans. PMID:25001408
Quantitative mass spectrometry reveals plasticity of metabolic networks in Mycobacterium smegmatis. PMID:24997995
An integrated catalog of reference genes in the human gut microbiome. PMID:24997786
Partial least squares based gene expression analysis in renal failure. PMID:24997640
Identification and expression analysis of salt-responsive genes using a comparative microarray approach in Salix matsudana. PMID:24993115
Integrated analysis of mutation data from various sources identifies key genes and signaling pathways in hepatocellular carcinoma. PMID:24988079
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Simulated annealing based algorithm for identifying mutated driver pathways in cancer. PMID:24982873
Transcriptome analysis of the Bombyx mori fat body after constant high temperature treatment shows differences between the sexes. PMID:24972568
Cytokine (IL16) and tyrphostin actions on ovarian primordial follicle development. PMID:24970835
Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer. PMID:24968068
Colony-live--a high-throughput method for measuring microbial colony growth kinetics--reveals diverse growth effects of gene knockouts in Escherichia coli. PMID:24964927
Correlating information contents of gene ontology terms to infer semantic similarity of gene products. PMID:24963342
High-throughput transcriptome sequencing identifies candidate genetic modifiers of vulnerability to fetal alcohol spectrum disorders. PMID:24962712
Glycerophosphoglycerol, Beta-alanine, and pantothenic Acid as metabolic companions of glycolytic activity and cell migration in breast cancer cell lines. PMID:24958267
On functional module detection in metabolic networks. PMID:24958145
Metabolite Identification through Machine Learning- Tackling CASMI Challenge Using FingerID. PMID:24958002
Systematic applications of metabolomics in metabolic engineering. PMID:24957776
Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. PMID:24955762
Adolescent mouse takes on an active transcriptomic expression during postnatal cerebral development. PMID:24953867
A controlled vocabulary for pathway entities and events. PMID:24951798
Investigating bacterial populations in styrene-degrading biofilters by 16S rDNA tag pyrosequencing. PMID:24950754
Comparative transcriptome profiling of two Tibetan wild barley genotypes in responses to low potassium. PMID:24949953
Proteomics analysis of the non-muscle myosin heavy chain IIa-enriched actin-myosin complex reveals multiple functions within the podocyte. PMID:24949636
Pathway bridge based multiobjective optimization approach for lurking pathway prediction. PMID:24949437
Complete Genome Sequence of the p-Nitrophenol-Degrading Bacterium Pseudomonas putida DLL-E4. PMID:24948765
Predicting targeted drug combinations based on Pareto optimal patterns of coexpression network connectivity. PMID:24944582
Recovery of the gut microbiome following fecal microbiota transplantation. PMID:24939885
A rare sequence variant in intron 1 of THAP1 is associated with primary dystonia. PMID:24936516
Multicilin drives centriole biogenesis via E2f proteins. PMID:24934224
In silico identification of plant miRNAs in mammalian breast milk exosomes--a small step forward? PMID:24933019
Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum. PMID:24932683
New directions for diffusion-based network prediction of protein function: incorporating pathways with confidence. PMID:24931987
Metabolite identification through multiple kernel learning on fragmentation trees. PMID:24931979
Cardiac extracellular proteome profiling and membrane topology analysis using glycoproteomics. PMID:24920555
Extracellular matrix and cytochrome P450 gene expression can distinguish steatohepatitis from steatosis in mice. PMID:24913135
Pathway and network analysis in proteomics. PMID:24911777
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Methane yield phenotypes linked to differential gene expression in the sheep rumen microbiome. PMID:24907284
Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. PMID:24906912
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. PMID:24906883
Whole-genome sequencing of Mesorhizobium huakuii 7653R provides molecular insights into host specificity and symbiosis island dynamics. PMID:24906389
Profiling the orphan enzymes. PMID:24906382
Quantitative temporal viromics: an approach to investigate host-pathogen interaction. PMID:24906157
Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families. PMID:24906019
Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia. PMID:24901509
Interactome profile of the host cellular proteins and the nonstructural protein 2 of porcine reproductive and respiratory syndrome virus. PMID:24901321
Integration of residue attributes for sequence diversity characterization of terpenoid enzymes. PMID:24900985
Exploring the substrate range of wild-type aminoacyl-tRNA synthetases. PMID:24890918
Metabolomics and proteomics reveal impacts of chemically mediated competition on marine plankton. PMID:24889616
Merging metagenomics and geochemistry reveals environmental controls on biological diversity and evolution. PMID:24886397
TGF-β stimulation in human and murine cells reveals commonly affected biological processes and pathways at transcription level. PMID:24886091
Investigating perturbed pathway modules from gene expression data via structural equation models. PMID:24885496
Lactobacillus delbrueckii ssp. lactis and ssp. bulgaricus: a chronicle of evolution in action. PMID:24884896
Complete sequencing of Novosphingobium sp. PP1Y reveals a biotechnologically meaningful metabolic pattern. PMID:24884518
A community effort to assess and improve drug sensitivity prediction algorithms. PMID:24880487
Transcriptome assembly and analysis of Tibetan Hulless Barley (Hordeum vulgare L. var. nudum) developing grains, with emphasis on quality properties. PMID:24871534
Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation. PMID:24865352
The ctenophore genome and the evolutionary origins of neural systems. PMID:24847885
The polycyclic aromatic hydrocarbon degradation potential of Gulf of Mexico native coastal microbial communities after the Deepwater Horizon oil spill. PMID:24847320
Update on abdominal aortic aneurysm research: from clinical to genetic studies. PMID:24834361
Analysis pipeline for the epistasis search - statistical versus biological filtering. PMID:24817878
Fetal alcohol syndrome, chemo-biology and OMICS: ethanol effects on vitamin metabolism during neurodevelopment as measured by systems biology analysis. PMID:24816220
The plasmid complement of Lactococcus lactis UC509.9 encodes multiple bacteriophage resistance systems. PMID:24814781
Promise and reality in the expanding field of network interaction analysis: metabolic networks. PMID:24812497
fastGapFill: efficient gap filling in metabolic networks. PMID:24812336
Identification of miRNA-mediated core gene module for glioma patient prediction by integrating high-throughput miRNA, mRNA expression and pathway structure. PMID:24809850
The Longissimus and Semimembranosus muscles display marked differences in their gene expression profiles in pig. PMID:24809746
categoryCompare, an analytical tool based on feature annotations. PMID:24808906
Transport proteins of parasitic protists and their role in nutrient salvage. PMID:24808897
Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production. PMID:24808102
Isolation and characterization of mammalian cells expressing the Arf promoter during eye development. PMID:24806224
Wiring miRNAs to pathways: a topological approach to integrate miRNA and mRNA expression profiles. PMID:24803669
How the mountain pine beetle (Dendroctonus ponderosae) breached the Canadian Rocky Mountains. PMID:24803641
Modeling genome-wide dynamic regulatory network in mouse lungs with influenza infection using high-dimensional ordinary differential equations. PMID:24802016
Functional characterization of the Xanthophyllomyces dendrorhous farnesyl pyrophosphate synthase and geranylgeranyl pyrophosphate synthase encoding genes that are involved in the synthesis of isoprenoid precursors. PMID:24796858
SDS, a structural disruption score for assessment of missense variant deleteriousness. PMID:24795746
Exo-metabolome of Pseudovibrio sp. FO-BEG1 analyzed by ultra-high resolution mass spectrometry and the effect of phosphate limitation. PMID:24787987
Characterization of changes in gene expression and biochemical pathways at low levels of benzene exposure. PMID:24786086
Mining a database of single amplified genomes from Red Sea brine pool extremophiles-improving reliability of gene function prediction using a profile and pattern matching algorithm (PPMA). PMID:24778629
Label-Free LC-MS Profiling of Skeletal Muscle Reveals Heart-Type Fatty Acid Binding Protein as a Candidate Biomarker of Aerobic Capacity. PMID:24772389
Assessment of the Deepwater Horizon oil spill impact on Gulf coast microbial communities. PMID:24772107
Conditional independence mapping of DIGE data reveals PDIA3 protein species as key nodes associated with muscle aerobic capacity. PMID:24769234
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. PMID:24767249
Constraint-based modeling of carbon fixation and the energetics of electron transfer in Geobacter metallireducens. PMID:24762737
Differential expression analysis of transcripts related to oil metabolism in maturing seeds of Jatropha curcas L. PMID:24757322
Effects of silver nitrate and silver nanoparticles on a planktonic community: general trends after short-term exposure. PMID:24755991
Overrepresentation of glutamate signaling in Alzheimer's disease: network-based pathway enrichment using meta-analysis of genome-wide association studies. PMID:24755620
Amoebal endosymbiont Neochlamydia genome sequence illuminates the bacterial role in the defense of the host amoebae against Legionella pneumophila. PMID:24747986
Microarray analysis of cell cycle gene expression in adult human corneal endothelial cells. PMID:24747418
Genome Sequence of Streptomyces albulus PD-1, a Productive Strain for Epsilon-Poly-L-Lysine and Poly-L-Diaminopropionic Acid. PMID:24744334
Genome and transcriptome analysis of the fungal pathogen Fusarium oxysporum f. sp. cubense causing banana vascular wilt disease. PMID:24743270
Microarray analysis of differentially expressed genes engaged in fruit development between table and wine grape. PMID:24728608
No large-effect low-frequency coding variation found for myocardial infarction. PMID:24728188
Transcriptome analysis of the Portunus trituberculatus: de novo assembly, growth-related gene identification and marker discovery. PMID:24722690
Module-based functional pathway enrichment analysis of a protein-protein interaction network to study the effects of intestinal microbiota depletion in mice. PMID:24718810
Alteration of protein levels during influenza virus H1N1 infection in host cells: a proteomic survey of host and virus reveals differential dynamics. PMID:24718678
Improving clustering with metabolic pathway data. PMID:24717120
KEGGViewer, a BioJS component to visualize KEGG Pathways. PMID:24715980
An insight into the genes involved in secoiridoid biosynthesis in Gentiana macrophylla by RNA-seq. PMID:24706059
REGEN: Ancestral Genome Reconstruction for Bacteria. PMID:24704978
The recA operon: A novel stress response gene cluster in Bacteroides fragilis. PMID:24703997
Molecular profiles of pyramidal neurons in the superior temporal cortex in schizophrenia. PMID:24702465
Transcriptional profile of Paracoccidioides spp. in response to itraconazole. PMID:24690401
Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PMID:24688832
A network view on Parkinson's disease. PMID:24688734
Chemical structure identification in metabolomics: computational modeling of experimental features. PMID:24688698
Integrated LC-MS/MS system for plant metabolomics. PMID:24688692
Statistical methods for the analysis of high-throughput metabolomics data. PMID:24688690
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
Applying mass spectrometry-based qualitative proteomics to human amygdaloid complex. PMID:24688456
Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. PMID:24677424
Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri. PMID:24676796
High throughput sequencing of two celery varieties small RNAs identifies microRNAs involved in temperature stress response. PMID:24673837
Metatranscriptome analysis of fungal strains Penicillium camemberti and Geotrichum candidum reveal cheese matrix breakdown and potential development of sensory properties of ripened Camembert-type cheese. PMID:24670012
Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis. PMID:24666644
Differential transcriptome analysis between Paulownia fortunei and its synthesized autopolyploid. PMID:24663058
Remodeling of the sarcomeric cytoskeleton in cardiac ventricular myocytes during heart failure and after cardiac resynchronization therapy. PMID:24657727
The metabolic potential of Escherichia coli BL21 in defined and rich medium. PMID:24656150
INsPeCT: INtegrative Platform for Cancer Transcriptomics. PMID:24653643
Integer programming-based method for designing synthetic metabolic networks by Minimum Reaction Insertion in a Boolean model. PMID:24651476
The global landscape of intron retentions in lung adenocarcinoma. PMID:24646369
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. PMID:24643865
Transcriptomic analysis of the rice white tip nematode, Aphelenchoides besseyi (Nematoda: Aphelenchoididae). PMID:24637831
Dysbiosis in the inflamed intestine: chance favors the prepared microbe. PMID:24637596
Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. PMID:24635915
Integration of gene expression data with network-based analysis to identify signaling and metabolic pathways regulated during the development of osteoarthritis. PMID:24630964
AlgaePath: comprehensive analysis of metabolic pathways using transcript abundance data from next-generation sequencing in green algae. PMID:24628857
Western corn rootworm (Diabrotica virgifera virgifera) transcriptome assembly and genomic analysis of population structure. PMID:24628835
Molecular profiles of parvalbumin-immunoreactive neurons in the superior temporal cortex in schizophrenia. PMID:24628518
De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification. PMID:24626227
Whole Genome Sequence of the Probiotic Strain Lactobacillus paracasei N1115, Isolated from Traditional Chinese Fermented Milk. PMID:24625864
A method for predicting protein-protein interaction types. PMID:24625764
Discrimination of conventional and organic white cabbage from a long-term field trial study using untargeted LC-MS-based metabolomics. PMID:24618989
An integrative modeling framework reveals plasticity of TGF-β signaling. PMID:24618419
Childhood abuse is associated with methylation of multiple loci in adult DNA. PMID:24618023
Extracellular vesicles in luminal fluid of the ovine uterus. PMID:24614226
Shedding some light over the floral metabolism by arum lily (Zantedeschia aethiopica) spathe de novo transcriptome assembly. PMID:24614014
New approach for phylogenetic tree recovery based on genome-scale metabolic networks. PMID:24611553
Translational research platforms integrating clinical and omics data: a review of publicly available solutions. PMID:24608524
Transcriptomic analysis of differentially expressed genes in the Ras1(CA)-overexpressed and wildtype posterior silk glands. PMID:24606580
Vascular tone pathway polymorphisms in relation to primary open-angle glaucoma. PMID:24603425
DAWN: a framework to identify autism genes and subnetworks using gene expression and genetics. PMID:24602502
Modulation of neuronal proteome profile in response to Japanese encephalitis virus infection. PMID:24599148
Single cell genomic study of Dehalococcoidetes species from deep-sea sediments of the Peruvian Margin. PMID:24599070
Broad phenotypic changes associated with gain of radiation resistance in head and neck squamous cell cancer. PMID:24597745
Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer. PMID:24597571
Identifying gene expression profile of spinal cord injury in rat by bioinformatics strategy. PMID:24595446
Mapping posttranscriptional regulation of the human glycome uncovers microRNA defining the glycocode. PMID:24591635
MULTI-WAY BLOCKMODELS FOR ANALYZING COORDINATED HIGH-DIMENSIONAL RESPONSES. PMID:24587846
RANKING RELATIONS USING ANALOGIES IN BIOLOGICAL AND INFORMATION NETWORKS. PMID:24587838
Effect of bodily fluids from honey bee (Apis mellifera) larvae on growth and genome-wide transcriptional response of the causal agent of American Foulbrood disease (Paenibacillus larvae). PMID:24586572
RNA-seq analysis of transcriptome and glucosinolate metabolism in seeds and sprouts of broccoli (Brassica oleracea var. italic). PMID:24586398
Systems kinomics for characterizing host responses to high-consequence pathogens at the NIH/NIAID Integrated Research Facility-Frederick. PMID:24585711
Increased interaction with insulin receptor substrate 1, a novel abnormality in insulin resistance and type 2 diabetes. PMID:24584551
Potential epigenetic dysregulation of genes associated with MODY and type 2 diabetes in humans exposed to a diabetic intrauterine environment: an analysis of genome-wide DNA methylation. PMID:24582139
Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions. PMID:24576339
Optimization of gene set annotations via entropy minimization over variable clusters (EMVC). PMID:24574114
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. PMID:24573880
Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases. PMID:24571091
Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets. PMID:24569707
Chemogenomics knowledgebased polypharmacology analyses of drug abuse related G-protein coupled receptors and their ligands. PMID:24567719
ppiPre: predicting protein-protein interactions by combining heterogeneous features. PMID:24565177
A scalable method for discovering significant subnetworks. PMID:24565174
Weighted set enrichment of gene expression data. PMID:24565001
Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods. PMID:24564962
GeneTopics--interpretation of gene sets via literature-driven topic models. PMID:24564875
Towards integrative gene functional similarity measurement. PMID:24564710
Quantitative proteomics by SWATH-MS reveals altered expression of nucleic acid binding and regulatory proteins in HIV-1-infected macrophages. PMID:24564501
Analysis of the intestinal microbiota using SOLiD 16S rRNA gene sequencing and SOLiD shotgun sequencing. PMID:24564472
Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma. PMID:24564407
Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse. PMID:24558413
DanQi Pill protects against heart failure through the arachidonic acid metabolism pathway by attenuating different cyclooxygenases and leukotrienes B4. PMID:24555740
Statistical hypothesis testing of factor loading in principal component analysis and its application to metabolite set enrichment analysis. PMID:24555693
Utility of network integrity methods in therapeutic target identification. PMID:24550933
The structural pathway of interleukin 1 (IL-1) initiated signaling reveals mechanisms of oncogenic mutations and SNPs in inflammation and cancer. PMID:24550720
Molecular evolution of the substrate utilization strategies and putative virulence factors in mosquito-associated Spiroplasma species. PMID:24534435
Importance of collection in gene set enrichment analysis of drug response in cancer cell lines. PMID:24522610
Genome sequence and comparative analysis of a Vibrio cholerae O139 strain E306 isolated from a cholera case in China. PMID:24517211
Growth factor priming differentially modulates components of the extracellular matrix proteome in chondrocytes and synovium-derived stem cells. PMID:24516581
Evolutionary comparisons of miRNA regulation system in six model organisms. PMID:24515651
Whole genome analyses of a well-differentiated liposarcoma reveals novel SYT1 and DDR2 rearrangements. PMID:24505276
Draft Genome Sequence of Amphibacillus jilinensis Y1(T), a Facultatively Anaerobic, Alkaliphilic and Halotolerant Bacterium. PMID:24501633
The phylogenetic distribution and evolution of enzymes within the thymidine kinase 2-like gene family in metazoa. PMID:24500774
Prediction of cancer drugs by chemical-chemical interactions. PMID:24498372
Insights into naturally minimised Streptomyces albus J1074 genome. PMID:24495463
Genomic evolution of 11 type strains within family Planctomycetaceae. PMID:24489782
Integrative gene set analysis of multi-platform data with sample heterogeneity. PMID:24489370
Analysis of the transcriptome of adult Dictyocaulus filaria and comparison with Dictyocaulus viviparus, with a focus on molecules involved in host-parasite interactions. PMID:24487001
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions. PMID:24478989
Clinical insights from metagenomic analysis of sputum samples from patients with cystic fibrosis. PMID:24478471
Composition of Archaea in seawater, sediment, and sponges in the Kepulauan Seribu reef system, Indonesia. PMID:24477923
The role of viral and host microRNAs in the Aujeszky's disease virus during the infection process. PMID:24475202
Unveiling the mechanism by which microsporidian parasites prevent locust swarm behavior. PMID:24474758
Microbial sulfur cycle in two hydrothermal chimneys on the Southwest Indian Ridge. PMID:24473131
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. PMID:24468196
Grimontia indica AK16(T), sp. nov., isolated from a seawater sample reports the presence of pathogenic genes similar to Vibrio genus. PMID:24465608
Robust prognostic gene expression signatures in bladder cancer and lung adenocarcinoma depend on cell cycle related genes. PMID:24465512
Review of biological network data and its applications. PMID:24465231
Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics. PMID:24463735
Insights into miRNA regulation of the human glycome. PMID:24463102
TP53 mutation-correlated genes predict the risk of tumor relapse and identify MPS1 as a potential therapeutic kinase in TP53-mutated breast cancers. PMID:24462521
A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool. PMID:24453985
Proliferation and cilia dynamics in neural stem cells prospectively isolated from the SEZ. PMID:24448162
Interplay of choline metabolites and genes in patient-derived breast cancer xenografts. PMID:24447408
Improvement of experimental testing and network training conditions with genome-wide microarrays for more accurate predictions of drug gene targets. PMID:24444313
Is serotonin transporter genotype associated with epigenetic susceptibility or vulnerability? Examination of the impact of socioeconomic status risk on African American youth. PMID:24438855
DBM-DB: the diamondback moth genome database. PMID:24434032
A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility. PMID:24430173
Induction of Wnt-inducible signaling protein-1 correlates with invasive breast cancer oncogenesis and reduced type 1 cell-mediated cytotoxic immunity: a retrospective study. PMID:24426833
Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter. PMID:24416233
Complete Genome Sequence of Spiroplasma apis B31T (ATCC 33834), a Bacterium Associated with May Disease of Honeybees (Apis mellifera). PMID:24407648
A data integration and visualization resource for the metabolic network of Synechocystis sp. PCC 6803. PMID:24402049
Evolution of human longevity uncoupled from caloric restriction mechanisms. PMID:24400080
Regulatory networks and complex interactions between the insulin and angiotensin II signalling systems: models and implications for hypertension and diabetes. PMID:24400038
Transcriptome analysis of Houttuynia cordata Thunb. by Illumina paired-end RNA sequencing and SSR marker discovery. PMID:24392108
Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PMID:24392013
Strategic genome-scale prioritization of unique drug targets: A case study of Streptococcus gordonii. PMID:24391362
Microarray gene expression analysis of tumorigenesis and regional lymph node metastasis in laryngeal squamous cell carcinoma. PMID:24386425
A novel role for an ECF sigma factor in fatty acid biosynthesis and membrane fluidity in Pseudomonas aeruginosa. PMID:24386415
Genetic interaction networks: better understand to better predict. PMID:24381582
Development of urinary biomarkers for internal exposure by cesium-137 using a metabolomics approach in mice. PMID:24377719
Galaxy tools to study genome diversity. PMID:24377391
Multistrain probiotic modulation of intestinal epithelial cells' immune response to a double-stranded RNA ligand, poly(i·c). PMID:24375132
The contribution of the glycine cleavage system to the pathogenesis of Francisella tularensis. PMID:24374051
Genome Sequence of Sporolactobacillus laevolacticus DSM442, an Efficient Polymer-Grade D-Lactate Producer from Agricultural Waste Cottonseed as a Nitrogen Source. PMID:24371202
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. PMID:24369854
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. PMID:24369052
The role of glutamine oxoglutarate aminotransferase and glutamate dehydrogenase in nitrogen metabolism in Mycobacterium bovis BCG. PMID:24367660
The draft genome of a socially polymorphic halictid bee, Lasioglossum albipes. PMID:24359881
Obligate mutualism within a host drives the extreme specialization of a fig wasp genome. PMID:24359812
A p53-like transcription factor similar to Ndt80 controls the response to nutrient stress in the filamentous fungus, Aspergillus nidulans. PMID:24358888
Draft genome sequence of pseudomonas strain p818, isolated from glyphosate-polluted soil. PMID:24356842
Early transcriptional response of soybean contrasting accessions to root dehydration. PMID:24349513
Bioinformatics analysis for the antirheumatic effects of huang-lian-jie-du-tang from a network perspective. PMID:24348693
The atypical mechanosensitive microRNA-712 derived from pre-ribosomal RNA induces endothelial inflammation and atherosclerosis. PMID:24346612
Investigation of the hub genes and related mechanism in ovarian cancer via bioinformatics analysis. PMID:24341673
Transcriptome analysis of Pinus monticola primary needles by RNA-seq provides novel insight into host resistance to Cronartium ribicola. PMID:24341615
Network-based differential gene expression analysis suggests cell cycle related genes regulated by E2F1 underlie the molecular difference between smoker and non-smoker lung adenocarcinoma. PMID:24341432
Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects. PMID:24339888
Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography. PMID:24339887
Diet rapidly and reproducibly alters the human gut microbiome. PMID:24336217
Determining molecular predictors of adverse drug reactions with causality analysis based on structure learning. PMID:24334612
A genome-wide association study identifies major loci affecting the immune response against infectious bronchitis virus in chicken. PMID:24333371
Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks. PMID:24330590
A phylogenomic approach to bacterial subspecies classification: proof of concept in Mycobacterium abscessus. PMID:24330254
Computational prediction of human salivary proteins from blood circulation and application to diagnostic biomarker identification. PMID:24324552
Up-regulation of CLDN1 in gastric cancer is correlated with reduced survival. PMID:24321518
A Bayesian extension of the hypergeometric test for functional enrichment analysis. PMID:24320951
De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes. PMID:24314324
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. PMID:24314206
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. PMID:24308365
Transcriptomic responses provide a new mechanistic basis for the chemopreventive effects of folic acid and tributyrin in rat liver carcinogenesis. PMID:24302446
Dissection of complex gene expression using the combined analysis of pleiotropy and epistasis. PMID:24297548
Screening preeclamptic cord plasma for proteins associated with decreased breast cancer susceptibility. PMID:24296084
Transcriptome characterization and sequencing-based identification of drought-responsive genes in potato. PMID:24293150
Analysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition. PMID:24289474
Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid. PMID:24289302
Being Aquifex aeolicus: Untangling a hyperthermophile's checkered past. PMID:24281050
De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. PMID:24279309
Development of reference transcriptomes for the major field insect pests of cowpea: a toolbox for insect pest management approaches in west Africa. PMID:24278221
Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. PMID:24274140
Minke whale genome and aquatic adaptation in cetaceans. PMID:24270359
Towards human-computer synergetic analysis of large-scale biological data. PMID:24267485
Breast cancer prediction using genome wide single nucleotide polymorphism data. PMID:24266904
MetaboLyzer: a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data. PMID:24266674
Transcriptome analysis of leaf tissue of Raphanus sativus by RNA sequencing. PMID:24265813
Genome Sequence of Dyella ginsengisoli Strain LA-4, an Efficient Degrader of Aromatic Compounds. PMID:24265495
Widespread sex differences in gene expression and splicing in the adult human brain. PMID:24264146
Comparative proteomic and bioinformatic analysis of the effects of a high-grain diet on the hepatic metabolism in lactating dairy goats. PMID:24260456
Database resources of the National Center for Biotechnology Information. PMID:24259429
Profiling post-transcriptionally networked mRNA subsets using RIP-Chip and RIP-Seq. PMID:24257445
Gene expression profiling analysis of the putamen for the investigation of compensatory mechanisms in Parkinson's disease. PMID:24256571
TTG2-regulated development is related to expression of putative AUXIN RESPONSE FACTOR genes in tobacco. PMID:24252253
De novo assembly and characterization of tissue specific transcriptomes in the emerald notothen, Trematomus bernacchii. PMID:24252228
Identification of phenylpropanoid biosynthetic genes and phenylpropanoid accumulation by transcriptome analysis of Lycium chinense. PMID:24252158
Do plants contain g protein-coupled receptors? PMID:24246381
De novo assembly, gene annotation, and marker discovery in stored-product pest Liposcelis entomophila (Enderlein) using transcriptome sequences. PMID:24244605
Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response. PMID:24244133
Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. PMID:24243932
Global gene expression and focused knockout analysis reveals genes associated with fungal fruiting body development in Neurospora crassa. PMID:24243796
Toward better drug repositioning: prioritizing and integrating existing methods into efficient pipelines. PMID:24239728
UniCarbKB: building a knowledge platform for glycoproteomics. PMID:24234447
Mercury alters B-cell protein phosphorylation profiles. PMID:24224561
Adaptation of intertidal biofilm communities is driven by metal ion and oxidative stresses. PMID:24212283
Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways. PMID:24209716
CellFateScout - a bioinformatics tool for elucidating small molecule signaling pathways that drive cells in a specific direction. PMID:24206562
Metabolic proximity in the order of colonization of a microbial community. PMID:24204896
A comprehensive survey of small-molecule binding pockets in proteins. PMID:24204237
Integrative gene set analysis: application to platinum pharmacogenomics. PMID:24199607
MicroRNA-Mediated Down-Regulation of M-CSF Receptor Contributes to Maturation of Mouse Monocyte-Derived Dendritic Cells. PMID:24198819
The semantic web in translational medicine: current applications and future directions. PMID:24197933
Catabolite control protein E (CcpE) is a LysR-type transcriptional regulator of tricarboxylic acid cycle activity in Staphylococcus aureus. PMID:24194525
Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. PMID:24192039
Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically. PMID:24191963
Expression levels of DNA replication and repair genes predict regional somatic repeat instability in the brain but are not altered by polyglutamine disease protein expression or age. PMID:24191263
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Mitochondrial-related proteomic changes during obesity and fasting in mice are greater in the liver than skeletal muscles. PMID:24178926
MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. PMID:24177720
Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli. PMID:24176774
Solving gap metabolites and blocked reactions in genome-scale models: application to the metabolic network of Blattabacterium cuenoti. PMID:24176055
Characterization of microRNA expression profiles in patients with intervertebral disc degeneration. PMID:24173697
Hypoxia and human genome stability: downregulation of BRCA2 expression in breast cancer cell lines. PMID:24171172
High contents of very long-chain polyunsaturated fatty acids in different moss species. PMID:24170342
Baiji genomes reveal low genetic variability and new insights into secondary aquatic adaptations. PMID:24169659
Comparative metabolic systems analysis of pathogenic Burkholderia. PMID:24163337
A primer to frequent itemset mining for bioinformatics. PMID:24162173
A systematic analysis of a mi-RNA inter-pathway regulatory motif. PMID:24152805
Multi-dimensional prioritization of dental caries candidate genes and its enriched dense network modules. PMID:24146904
Identification and characterization of a repertoire of genes differentially expressed in developing top ear shoots between a superior hybrid and its parental inbreds in Zea mays L. PMID:24146224
Establishment of a CpG island microarray for analyses of genome-wide DNA methylation in Chinese hamster ovary cells. PMID:24146078
Riboswitches in eubacteria sense the second messenger c-di-AMP. PMID:24141192
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. PMID:24137540
microRNA and gene networks in human pancreatic cancer. PMID:24137477
Reconstructing targetable pathways in lung cancer by integrating diverse omics data. PMID:24135919
Sexually transmitted diseases putative drug target database: a comprehensive database of putative drug targets of pathogens identified by comparative genomics. PMID:24130375
Analytical tools and databases for metagenomics in the next-generation sequencing era. PMID:24124405
Two novel pathway analysis methods based on a hierarchical model. PMID:24123673
Application of machine learning to proteomics data: classification and biomarker identification in postgenomics biology. PMID:24116388
Antibacterial mechanisms identified through structural systems pharmacology. PMID:24112686
Soft truncation thresholding for gene set analysis of RNA-seq data: application to a vaccine study. PMID:24104466
Identification of miRNAs and their targets in tea (Camellia sinensis). PMID:24101208
Analysis of nonlinear gene expression progression reveals extensive pathway and age-specific transitions in aging human brains. PMID:24098339
Selective anticancer agents suppress aging in Drosophila. PMID:24096697
Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an Invasive Isolate That Caused Necrotizing Myositis. PMID:24092777
Unsupervised automated high throughput phenotyping of RNAi time-lapse movies. PMID:24090185
A comprehensive map of the influenza A virus replication cycle. PMID:24088197
CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation. PMID:24086311
Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways. PMID:24083237
Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions. PMID:24078917
Recommendations for the design and analysis of epigenome-wide association studies. PMID:24076989
Transcriptome profile of the green odorous frog (Odorrana margaretae). PMID:24073255
Gene expression rate comparison for multiple high-throughput datasets. PMID:24067413
Single nucleotide polymorphisms and haplotypes associated with feed efficiency in beef cattle. PMID:24066663
Transcriptome-wide single nucleotide polymorphisms (SNPs) for abalone (Haliotis midae): validation and application using GoldenGate medium-throughput genotyping assays. PMID:24065109
Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome. PMID:24063311
BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. PMID:24058887
Doping control using high and ultra-high resolution mass spectrometry based non-targeted metabolomics-a case study of salbutamol and budesonide abuse. PMID:24058591
Transcriptome profiling of Gossypium barbadense inoculated with Verticillium dahliae provides a resource for cotton improvement. PMID:24053558
An integrated transcriptome and epigenome analysis identifies a novel candidate gene for pancreatic cancer. PMID:24053169
Characterization of microRNA expression profiles in 3T3-L1 adipocytes overexpressing C10orf116. PMID:24052233
Polymorphisms in metabolism/antioxidant genes may mediate the effect of dietary intake on pancreatic cancer risk. PMID:24051964
Multicellular bacteria deploy the type VI secretion system to preemptively strike neighboring cells. PMID:24039579
Detecting and removing inconsistencies between experimental data and signaling network topologies using integer linear programming on interaction graphs. PMID:24039561
Human SNP links differential outcomes in inflammatory and infectious disease to a FOXO3-regulated pathway. PMID:24035192
Structural and Functional Analysis of Giant Strong Component of Bacillus thuringiensis Metabolic Network. PMID:24031381
High-fat diet alters gut microbiota physiology in mice. PMID:24030595
Stress-induced isoforms of MDM2 and MDM4 correlate with high-grade disease and an altered splicing network in pediatric rhabdomyosarcoma. PMID:24027430
A genetical genomics approach reveals new candidates and confirms known candidate genes for drip loss in a porcine resource population. PMID:24026665
Genetic interactions found between calcium channel genes modulate amyloid load measured by positron emission tomography. PMID:24026422
Differential inhibition of ex-vivo tumor kinase activity by vemurafenib in BRAF(V600E) and BRAF wild-type metastatic malignant melanoma. PMID:24023633
Functional diversity of genes for the biosynthesis of paeoniflorin and its derivatives in Paeonia. PMID:24022687
De novo assembly of the Indo-Pacific humpback dolphin leucocyte transcriptome to identify putative genes involved in the aquatic adaptation and immune response. PMID:24015242
A genome-wide identification and characterization of mircoRNAs and their targets in 'Suli' pear (Pyrus pyrifolia white pear group). PMID:24013795
Analyzing LC/MS metabolic profiling data in the context of existing metabolic networks. PMID:24010053
How microRNA and transcription factor co-regulatory networks affect osteosarcoma cell proliferation. PMID:24009496
Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma. PMID:24007313
In silico enzymatic synthesis of a 400,000 compound biochemical database for nontargeted metabolomics. PMID:23991755
Transcriptome analysis of Litopenaeus vannamei in response to white spot syndrome virus infection. PMID:23991181
Bovine mammary gene expression profiling during the onset of lactation. PMID:23990904
Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen. PMID:23990803
Predicting disease risk using bootstrap ranking and classification algorithms. PMID:23990773
Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins. PMID:23988573
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. PMID:23984715
The Tarenaya hassleriana genome provides insight into reproductive trait and genome evolution of crucifers. PMID:23983221
A combined omics study on activated macrophages--enhanced role of STATs in apoptosis, immunity and lipid metabolism. PMID:23981351
Combinatorial drug screening identifies synergistic co-targeting of Bruton's tyrosine kinase and the proteasome in mantle cell lymphoma. PMID:23979520
Dynamic regulation of Ero1α and peroxiredoxin 4 localization in the secretory pathway. PMID:23979138
Vitamin B6 reduces hippocampal apoptosis in experimental pneumococcal meningitis. PMID:23977941
Quantitative Proteomics Identifies Activation of Hallmark Pathways of Cancer in Patient Melanoma. PMID:23976835
HOMO: A novel script for data mining of microarrays. PMID:23976833
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. PMID:23975765
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria. PMID:23975204
Deamination of 6-aminodeoxyfutalosine in menaquinone biosynthesis by distantly related enzymes. PMID:23972005
Structure-guided discovery of new deaminase enzymes. PMID:23968233
Association signals unveiled by a comprehensive gene set enrichment analysis of dental caries genome-wide association studies. PMID:23967329
Regulatory and metabolic networks for the adaptation of Pseudomonas aeruginosa biofilms to urinary tract-like conditions. PMID:23967252
The effect of simvastatin on lipid droplets accumulation in human embryonic kidney cells and pancreatic cancer cells. PMID:23961716
Identification of interconnected markers for T-cell acute lymphoblastic leukemia. PMID:23956970
Adhesion to carbon nanotube conductive scaffolds forces action-potential appearance in immature rat spinal neurons. PMID:23951361
A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication. PMID:23950709
Genome Sequence of a Novel Polymer-Grade L-Lactate-Producing Alkaliphile, Exiguobacterium sp. Strain 8-11-1. PMID:23950124
Molecular fingerprinting reflects different histotypes and brain region in low grade gliomas. PMID:23947815
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
Integrative mechanisms of oriented neuronal migration in the developing brain. PMID:23937349
Reconstruction of cellular signal transduction networks using perturbation assays and linear programming. PMID:23935958
The embedding problem for markov models of nucleotide substitution. PMID:23935949
A moonlighting enzyme links Escherichia coli cell size with central metabolism. PMID:23935518
A graphical model method for integrating multiple sources of genome-scale data. PMID:23934610
Genome Sequence of the 2,4,5-Trichlorophenoxyacetate-Degrading Bacterium Burkholderia phenoliruptrix Strain AC1100. PMID:23929488
Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea. PMID:23929464
Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations. PMID:23921631
A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. PMID:23915218
RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus. PMID:23913949
A decision-theory approach to interpretable set analysis for high-dimensional data. PMID:23909925
Bioinformatics and Gene Network Analyses of the Swine Mammary Gland Transcriptome during Late Gestation. PMID:23908586
Global gene expression response of a population exposed to benzene: a pilot study exploring the use of RNA-sequencing technology. PMID:23907980
Gene-smoking interactions in multiple Rho-GTPase pathway genes in an early-onset coronary artery disease cohort. PMID:23907653
Investigation of endogenous compounds for assessing the drug interactions in the urinary excretion involving multidrug and toxin extrusion proteins. PMID:23907530
Functional profiling of the gut microbiome in disease-associated inflammation. PMID:23906180
Genome-wide analysis of 3'-untranslated regions supports the existence of post-transcriptional regulons controlling gene expression in trypanosomes. PMID:23904995
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. PMID:23902988
Complete genome sequence and comparative analysis of Acetobacter pasteurianus 386B, a strain well-adapted to the cocoa bean fermentation ecosystem. PMID:23902333
Identification of a missense variant in LNPEP that confers psoriasis risk. PMID:23897274
A new approach for prediction of tumor sensitivity to targeted drugs based on functional data. PMID:23890326
An analysis of a 'community-driven' reconstruction of the human metabolic network. PMID:23888127
Analysis of the genomic response of human prostate cancer cells to histone deacetylase inhibitors. PMID:23880963
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. PMID:23875761
Sequential waves of gene expression in patients with clinically defined dengue illnesses reveal subtle disease phases and predict disease severity. PMID:23875036
ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells. PMID:23874979
Tracing the transcriptomic changes in synthetic Trigenomic allohexaploids of Brassica using an RNA-Seq approach. PMID:23874799
RMOD: a tool for regulatory motif detection in signaling network. PMID:23874612
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
Comparison of metabolic capacities and inference of gene content evolution in mosquito-associated Spiroplasma diminutum and S. taiwanense. PMID:23873917
Estrogen pathway polymorphisms in relation to primary open angle glaucoma: an analysis accounting for gender from the United States. PMID:23869166
Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules. PMID:23858463
The genome sequence of Leishmania (Leishmania) amazonensis: functional annotation and extended analysis of gene models. PMID:23857904
Insights into TREM2 biology by network analysis of human brain gene expression data. PMID:23855984
Protein-protein interaction network prediction by using rigid-body docking tools: application to bacterial chemotaxis. PMID:23855669
A latent capacity for evolutionary innovation through exaptation in metabolic systems. PMID:23851393
Variants in exons and in transcription factors affect gene expression in trans. PMID:23844908
Transient exposure to low levels of insecticide affects metabolic networks of honeybee larvae. PMID:23844170
Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy. PMID:23840633
The Embryonic Transcriptome of the Red-Eared Slider Turtle (Trachemys scripta). PMID:23840449
Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics. PMID:23840410
PhosphoChain: a novel algorithm to predict kinase and phosphatase networks from high-throughput expression data. PMID:23832245
Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. PMID:23828894
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. PMID:23828783
Towards systematic discovery of signaling networks in budding yeast filamentous growth stress response using interventional phosphorylation data. PMID:23825934
Bcl2-associated athanogene 3 interactome analysis reveals a new role in modulating proteasome activity. PMID:23824909
Network-based penalized regression with application to genomic data. PMID:23822182
Identifying proteins controlling key disease signaling pathways. PMID:23812988
Simple topological properties predict functional misannotations in a metabolic network. PMID:23812979
The transition from a phytopathogenic smut ancestor to an anamorphic biocontrol agent deciphered by comparative whole-genome analysis. PMID:23800965
MetaPathways: a modular pipeline for constructing pathway/genome databases from environmental sequence information. PMID:23800136
Microarray gene expression profiling of neural tissues in bovine spastic paresis. PMID:23782433
Human immunodeficiency virus protease inhibitors interact with ATP binding cassette transporter 4/multidrug resistance protein 4: a basis for unanticipated enhanced cytotoxicity. PMID:23775562
PathAct: a novel method for pathway analysis using gene expression profiles. PMID:23750088
Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern. PMID:23750079
Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome. PMID:23748443
Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach. PMID:23738659
Biological networks for predicting chemical hepatocarcinogenicity using gene expression data from treated mice and relevance across human and rat species. PMID:23737943
Gene set enrichment analysis of RNA-Seq data: integrating differential expression and splicing. PMID:23734663
Functional diversity and structural disorder in the human ubiquitination pathway. PMID:23734257
Transcriptome and proteome data reveal candidate genes for pollinator attraction in sexually deceptive orchids. PMID:23734209
Activation of CpxRA in Haemophilus ducreyi primarily inhibits the expression of its targets, including major virulence determinants. PMID:23729647
Suppression and activation of the malignant phenotype by extracellular matrix in xenograft models of bladder cancer: a model for tumor cell "dormancy". PMID:23717563
HGPGD: the human gene population genetic difference database. PMID:23717556
Proteomic analysis of Oesophagostomum dentatum (Nematoda) during larval transition, and the effects of hydrolase inhibitors on development. PMID:23717515
A genome-wide screen indicates correlation between differentiation and expression of metabolism related genes. PMID:23717462
Microarray analyses reveal novel targets of exercise-induced stress resistance in the dorsal raphe nucleus. PMID:23717271
Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma. PMID:23711669
Untargeted metabolomics from biological sources using ultraperformance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS). PMID:23711563
Global alignment of pairwise protein interaction networks for maximal common conserved patterns. PMID:23710435
Behavioral and neurogenomic transcriptome changes in wild-derived zebrafish with fluoxetine treatment. PMID:23706039
Proteomic signatures of acquired letrozole resistance in breast cancer: suppressed estrogen signaling and increased cell motility and invasiveness. PMID:23704778
Transcriptional profiling by RNA-Seq of peri-attachment porcine embryos generated by a variety of assisted reproductive technologies. PMID:23695885
Metazoan innovation: from aromatic amino acids to extracellular signaling. PMID:23690137
IR/IGF1R signaling as potential target for treatment of high-grade osteosarcoma. PMID:23688189
Complete Genome Sequence of Marinobacter sp. BSs20148. PMID:23682144
DrugMap Central: an on-line query and visualization tool to facilitate drug repositioning studies. PMID:23681121
Protein-protein interaction and pathway analyses of top schizophrenia genes reveal schizophrenia susceptibility genes converge on common molecular networks and enrichment of nucleosome (chromatin) assembly genes in schizophrenia susceptibility loci. PMID:23671194
Computational meta'omics for microbial community studies. PMID:23670539
A fast workflow for identification and quantification of proteomes. PMID:23669031
Transcriptome sequencing of Zhikong scallop (Chlamys farreri) and comparative transcriptomic analysis with Yesso scallop (Patinopecten yessoensis). PMID:23667690
INCORPORATING BIOLOGICAL INFORMATION INTO LINEAR MODELS: A BAYESIAN APPROACH TO THE SELECTION OF PATHWAYS AND GENES. PMID:23667412
The endosymbiont Amoebophilus asiaticus encodes an S-adenosylmethionine carrier that compensates for its missing methylation cycle. PMID:23667233
A bi-Poisson model for clustering gene expression profiles by RNA-seq. PMID:23665510
Genome-wide association study of antibody response to Newcastle disease virus in chicken. PMID:23663563
Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum. PMID:23658685
A poor man's BLASTX--high-throughput metagenomic protein database search using PAUDA. PMID:23658416
Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations. PMID:23651669
Complete Genome Sequence of Glaciecola psychrophila Strain 170T. PMID:23640379
Transcriptome analysis of buds and leaves using 454 pyrosequencing to discover genes associated with the biosynthesis of active ingredients in Lonicera japonica Thunb. PMID:23638167
Toxicological effects of the different substances in tobacco smoke on human embryonic development by a systems chemo-biology approach. PMID:23637898
miRNA biogenesis enzyme Drosha is required for vascular smooth muscle cell survival. PMID:23637774
Chapter 15: disease gene prioritization. PMID:23633938
Glycolytic strategy as a tradeoff between energy yield and protein cost. PMID:23630264
Comparative analysis of the peanut witches'-broom phytoplasma genome reveals horizontal transfer of potential mobile units and effectors. PMID:23626855
Autotrophic microbe metagenomes and metabolic pathways differentiate adjacent Red Sea brine pools. PMID:23624511
Role of central metabolism in the osmoadaptation of the halophilic bacterium Chromohalobacter salexigens. PMID:23615905
Large-scale event extraction from literature with multi-level gene normalization. PMID:23613707
Cytochrome P450 CYP78A9 is involved in Arabidopsis reproductive development. PMID:23610218
Use of a global metabolic network to curate organismal metabolic networks. PMID:23603845
Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum. PMID:23593322
De novo sequence assembly and characterization of Lycoris aurea transcriptome using GS FLX titanium platform of 454 pyrosequencing. PMID:23593220
Maternal coding variants in complement receptor 1 and spontaneous idiopathic preterm birth. PMID:23591632
Exploiting conformational ensembles in modeling protein-protein interactions on the proteome scale. PMID:23590674
hLGDB: a database of human lysosomal genes and their regulation. PMID:23584836
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. PMID:23580552
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
Structural and functional characterization of a phosphatase domain within yeast general transcription factor IIIC. PMID:23569204
Finding type 2 diabetes causal single nucleotide polymorphism combinations and functional modules from genome-wide association data. PMID:23566118
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. PMID:23559334
Complete Genome Sequence of Serratia marcescens WW4. PMID:23558532
RNA-Seq analysis of Cocos nucifera: transcriptome sequencing and de novo assembly for subsequent functional genomics approaches. PMID:23555859
Probabilistic inference of biochemical reactions in microbial communities from metagenomic sequences. PMID:23555216
Transcription factor-microRNA-target gene networks associated with ovarian cancer survival and recurrence. PMID:23554906
Developmental profiles of the murine palatal methylome. PMID:23554260
Transcriptome Profiling Following Neuronal and Glial Expression of ALS-Linked SOD1 in Drosophila. PMID:23550139
Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling. PMID:23549481
Pathway-based personalized analysis of cancer. PMID:23547110
New insights on the reorganization of gene transcription in Pseudomonas putida KT2440 at elevated pressure. PMID:23537069
Proteomic analysis of elite soybean Jidou17 and its parents using iTRAQ-based quantitative approaches. PMID:23531047
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
Universal distribution of component frequencies in biological and technological systems. PMID:23530195
Transcriptome analysis on Chinese shrimp Fenneropenaeus chinensis during WSSV acute infection. PMID:23527000
Transcriptional analysis of the innate immune response of ducks to different species-of-origin low pathogenic H7 avian influenza viruses. PMID:23521892
Xylem transcription profiles indicate potential metabolic responses for economically relevant characteristics of Eucalyptus species. PMID:23521840
Leveraging biodiversity knowledge for potential phyto-therapeutic applications. PMID:23518859
Identifying gene set association enrichment using the coefficient of intrinsic dependence. PMID:23516564
Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. PMID:23516243
Genome Sequence of Avirulent Riemerella anatipestifer Strain RA-SG. PMID:23516232
In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment. PMID:23514353
A novel metatranscriptomic approach to identify gene expression dynamics during extracellular electron transfer. PMID:23511466
The human gene connectome as a map of short cuts for morbid allele discovery. PMID:23509278
Towards a metagenomic understanding on enhanced biomethane production from waste activated sludge after pH 10 pretreatment. PMID:23506434
Dissection of regulatory networks that are altered in disease via differential co-expression. PMID:23505361
Moving H5N1 studies into the era of systems biology. PMID:23499671
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations. PMID:23497449
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus). PMID:23497389
Empirical Bayes estimation of posterior probabilities of enrichment: a comparative study of five estimators of the local false discovery rate. PMID:23497228
New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis. PMID:23497205
Transcriptional analysis of genes involved in nodulation in soybean roots inoculated with Bradyrhizobium japonicum strain CPAC 15. PMID:23497193
Characterization of expressed sequence tags from developing fibers of Gossypium barbadense and evaluation of insertion-deletion variation in tetraploid cultivated cotton species. PMID:23497047
Sequential binary gene ratio tests define a novel molecular diagnostic strategy for malignant pleural mesothelioma. PMID:23493352
A Bayesian Approach to Pathway Analysis by Integrating Gene-Gene Functional Directions and Microarray Data. PMID:23482678
Coordinate changes in histone modifications, mRNA levels, and metabolite profiles in clonal INS-1 832/13 β-cells accompany functional adaptations to lipotoxicity. PMID:23476019
Transcriptome analysis of Pacific white shrimp (Litopenaeus vannamei) hepatopancreas in response to Taura syndrome Virus (TSV) experimental infection. PMID:23469011
A genome-scale modeling approach to study inborn errors of liver metabolism: toward an in silico patient. PMID:23464878
Genes, environments, and developmental research: methods for a multi-site study of early substance abuse. PMID:23461817
Canonical correlation analysis for RNA-seq co-expression networks. PMID:23460206
Prenatal metformin exposure in mice programs the metabolic phenotype of the offspring during a high fat diet at adulthood. PMID:23457588
Microarray gene expression profiling analysis combined with bioinformatics in multiple sclerosis. PMID:23456643
Role of Gα(olf) in familial and sporadic adult-onset primary dystonia. PMID:23449625
A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation. PMID:23445355
Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes. PMID:23442822
Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation. PMID:23442222
De novo assembly and characterization of transcriptome using Illumina paired-end sequencing and identification of CesA gene in ramie (Boehmeria nivea L. Gaud). PMID:23442184
Recreational Music-Making alters gene expression pathways in patients with coronary heart disease. PMID:23435350
Precise generation of systems biology models from KEGG pathways. PMID:23433509
Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. PMID:23433184
Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry. PMID:23431327
Proteomics as a tool for understanding schizophrenia. PMID:23430140
Comparison of host cell gene expression in cowpox, monkeypox or vaccinia virus-infected cells reveals virus-specific regulation of immune response genes. PMID:23425254
A role for more axillary growth1 (MAX1) in evolutionary diversity in strigolactone signaling upstream of MAX2. PMID:23424248
Spectral clustering strategies for heterogeneous disease expression data. PMID:23424126
Transcriptome and proteome exploration to provide a resource for the study of Agrocybe aegerita. PMID:23418592
Microarray analysis reveals novel features of the muscle aging process in men and women. PMID:23418191
Linking genome-scale metabolic modeling and genome annotation. PMID:23417799
Characterization of the global transcriptome for Pyropia haitanensis (Bangiales, Rhodophyta) and development of cSSR markers. PMID:23414227
Genome Sequence of Sphingomonas xenophaga QYY, an Anthraquinone-Degrading Strain. PMID:23405319
Complete Genome of Lactococcus lactis subsp. cremoris UC509.9, Host for a Model Lactococcal P335 Bacteriophage. PMID:23405300
Molecular signature of cancer at gene level or pathway level? Case studies of colorectal cancer and prostate cancer microarray data. PMID:23401724
A survey of protein interaction data and multigenic inherited disorders. PMID:23398688
Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome. PMID:23394930
Discovery of glycoside hydrolase enzymes in an avicel-adapted forest soil fungal community by a metatranscriptomic approach. PMID:23393585
BIRS - Bioterrorism Information Retrieval System. PMID:23390356
Ensuring the statistical soundness of competitive gene set approaches: gene filtering and genome-scale coverage are essential. PMID:23389952
Network-based analysis of multivariate gene expression data. PMID:23385535
Differences in X-chromosome transcriptional activity and cholesterol metabolism between placentae from swine breeds from Asian and Western origins. PMID:23383161
Combining functional and structural genomics to sample the essential Burkholderia structome. PMID:23382856
Exoproteome and secretome derived broad spectrum novel drug and vaccine candidates in Vibrio cholerae targeted by Piper betel derived compounds. PMID:23382822
The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PMID:23382650
FANTOM: Functional and taxonomic analysis of metagenomes. PMID:23375020
miRNA expression profile analysis in kidney of different porcine breeds. PMID:23372853
Statistical assessment of crosstalk enrichment between gene groups in biological networks. PMID:23372799
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Genomic diversity and evolution of the head crest in the rock pigeon. PMID:23371554
Widespread evidence of viral miRNAs targeting host pathways. PMID:23369080
Visualization of protein interaction networks: problems and solutions. PMID:23368786
Reconstruction of phyletic trees by global alignment of multiple metabolic networks. PMID:23368411
Gene expression alterations in bipolar disorder postmortem brains. PMID:23360497
Sequencing and de novo assembly of the western tarnished plant bug (Lygus hesperus) transcriptome. PMID:23357950
DNA damage and transcriptional changes in the gills of mytilus galloprovincialis exposed to nanomolar doses of combined metal salts (Cd, Cu, Hg). PMID:23355883
De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PMID:23349770
Identification and functional annotation of genome-wide ER-regulated genes in breast cancer based on ChIP-Seq data. PMID:23346221
Association analysis of reactive oxygen species-hypertension genes discovered by literature mining. PMID:23346037
Pattern and synchrony of gene expression among sympatric marine microbial populations. PMID:23345438
Impact of constitutional copy number variants on biological pathway evolution. PMID:23342974
Comparative transcriptome analysis of the accessory sex gland and testis from the Chinese mitten crab (Eriocheir sinensis). PMID:23342039
From QTL to QTN: candidate gene set approach and a case study in porcine IGF1-FoxO pathway. PMID:23341942
Database resources for the tuberculosis community. PMID:23332401
Identification of Dirofilaria immitis miRNA using illumina deep sequencing. PMID:23331513
The ClpP protease is required for the stress tolerance and biofilm formation in Actinobacillus pleuropneumoniae. PMID:23326465
Comparative genomic analysis of the microbiome [corrected] of herbivorous insects reveals eco-environmental adaptations: biotechnology applications. PMID:23326236
Comparative genome analysis of Spiroplasma melliferum IPMB4A, a honeybee-associated bacterium. PMID:23324436
The B cell transcription program mediates hypomethylation and overexpression of key genes in Epstein-Barr virus-associated proliferative conversion. PMID:23320978
Exome sequencing identified NRG3 as a novel susceptible gene of Hirschsprung's disease in a Chinese population. PMID:23315268
Effects of warm ischemic time on gene expression profiling in colorectal cancer tissues and normal mucosa. PMID:23308215
Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. PMID:23307621
Metabolism and the circadian clock converge. PMID:23303907
Interactions of miR-323/miR-326/miR-329 and miR-130a/miR-155/miR-210 as prognostic indicators for clinical outcome of glioblastoma patients. PMID:23302469
Overexpressing 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) in the lactococcal mevalonate pathway for heterologous plant sesquiterpene production. PMID:23300671
Global gene transcriptome analysis in vaccinated cattle revealed a dominant role of IL-22 for protection against bovine tuberculosis. PMID:23300440
Chapter 2: Data-driven view of disease biology. PMID:23300408
MmPalateMiRNA, an R package compendium illustrating analysis of miRNA microarray data. PMID:23298515
Genetic heterogeneity of diffuse large B-cell lymphoma. PMID:23292937
Gene expression profiling combined with bioinformatics analysis identify biomarkers for Parkinson disease. PMID:23284986
Pathway correlation profile of gene-gene co-expression for identifying pathway perturbation. PMID:23284898
Genome-wide discovery of small RNAs in Mycobacterium tuberculosis. PMID:23284830
Transcriptome analysis suggests that starch synthesis may proceed via multiple metabolic routes in high yielding potato cultivars. PMID:23284672
Systematic identification of rhythmic genes reveals camk1gb as a new element in the circadian clockwork. PMID:23284293
Potential metabolic mechanism of girls' central precocious puberty: a network analysis on urine metabonomics data. PMID:23282096
Cliques for the identification of gene signatures for colorectal cancer across population. PMID:23282040
Localization of Wolbachia-like gene transcripts and peptides in adult Onchocerca flexuosa worms indicates tissue specific expression. PMID:23281896
MycoProtease-DB: Useful resource for Mycobacterium tuberculosis complex and nontuberculous mycobacterial proteases. PMID:23275726
Docking studies and network analyses reveal capacity of compounds from Kandelia rheedii to strengthen cellular immunity by interacting with host proteins during tuberculosis infection. PMID:23275699
Signalling network construction for modelling plant defence response. PMID:23272172
The genome of Prunus mume. PMID:23271652
Autoantibody signatures involving glycolysis and splicesome proteins precede a diagnosis of breast cancer among postmenopausal women. PMID:23269276
RIDDLE: reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. PMID:23268829
TEAK: topology enrichment analysis framework for detecting activated biological subpathways. PMID:23268448
Pathway analysis of the human brain transcriptome in disease. PMID:23263795
Clinical application of development of nonantibiotic macrolides that correct inflammation-driven immune dysfunction in inflammatory skin diseases. PMID:23258954
Genome-wide transcriptome and proteome analysis on different developmental stages of Cordyceps militaris. PMID:23251642
Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing. PMID:23251396
Analysis of omics data with genome-scale models of metabolism. PMID:23247105
TGF-β upregulates miR-181a expression to promote breast cancer metastasis. PMID:23241956
CINPER: an interactive web system for pathway prediction for prokaryotes. PMID:23236458
Architecture for interoperable software in biology. PMID:23235920
Evaluation method for the potential functionome harbored in the genome and metagenome. PMID:23234305
Boolean model of yeast apoptosis as a tool to study yeast and human apoptotic regulations. PMID:23233838
MetaboID: a graphical user interface package for assignment of 1H NMR spectra of bodyfluids and tissues. PMID:23232331
Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset. PMID:23232071
Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing. PMID:23231371
Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods. PMID:23227854
Non Linear Programming (NLP) formulation for quantitative modeling of protein signal transduction pathways. PMID:23226239
Identification and analysis of biomarkers for mismatch repair proteins: A bioinformatic approach. PMID:23225975
Genome-level transcription data of Yersinia pestis analyzed with a new metabolic constraint-based approach. PMID:23216785
Network-based regularization for matched case-control analysis of high-dimensional DNA methylation data. PMID:23212810
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
Network analysis of a Pkd1-mouse model of autosomal dominant polycystic kidney disease identifies HNF4α as a disease modifier. PMID:23209428
PolA1, a putative DNA polymerase I, is coexpressed with PerR and contributes to peroxide stress defenses of group A Streptococcus. PMID:23204468
Whole-organism screening for gluconeogenesis identifies activators of fasting metabolism. PMID:23201900
Regulon controlled by the GppX hybrid two component system in Porphyromonas gingivalis. PMID:23194602
Gut Pharmacomicrobiomics: the tip of an iceberg of complex interactions between drugs and gut-associated microbes. PMID:23194438
MIRAGE: a functional genomics-based approach for metabolic network model reconstruction and its application to cyanobacteria networks. PMID:23194418
Database resources of the National Center for Biotechnology Information. PMID:23193264
Myosinome: a database of myosins from select eukaryotic genomes to facilitate analysis of sequence-structure-function relationships. PMID:23189029
Cancer pharmacogenomics: strategies and challenges. PMID:23183705
Development of a gene expression database and related analysis programs for evaluation of anticancer compounds. PMID:23176546
Knowledge-based analysis of proteomics data. PMID:23176192
Reconciliation of metabolites and biochemical reactions for metabolic networks. PMID:23172809
Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PMID:23166587
Adipocytokine signaling is altered in Flinders sensitive line rats, and adiponectin correlates in humans with some symptoms of depression. PMID:23153628
Effects of protein interaction data integration, representation and reliability on the use of network properties for drug target prediction. PMID:23146171
Whole genome analysis of Leptospira licerasiae provides insight into leptospiral evolution and pathogenicity. PMID:23145189
A targeted glycan-related gene screen reveals heparan sulfate proteoglycan sulfation regulates WNT and BMP trans-synaptic signaling. PMID:23144627
Distinct neurogenomic states in basal ganglia subregions relate differently to singing behavior in songbirds. PMID:23144607
Genome sequence of Halorubrum sp. strain T3, an extremely halophilic archaeon harboring a virus-like element. PMID:23144373
Unravelling the enigma of selective vulnerability in neurodegeneration: motor neurons resistant to degeneration in ALS show distinct gene expression characteristics and decreased susceptibility to excitotoxicity. PMID:23143228
VANTED v2: a framework for systems biology applications. PMID:23140568
Adaptation of the black yeast Wangiella dermatitidis to ionizing radiation: molecular and cellular mechanisms. PMID:23139812
Transcriptome sequencing of the Antarctic vascular plant Deschampsia antarctica Desv. under abiotic stress. PMID:23135329
Assessing the gain of biological data integration in gene networks inference. PMID:23134775
Phenomenological model for predicting the catabolic potential of an arbitrary nutrient. PMID:23133365
A travel guide to Cytoscape plugins. PMID:23132118
Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria. PMID:23122209
Identification of new differentially methylated genes that have potential functional consequences in prostate cancer. PMID:23119026
Non-gaussian distributions affect identification of expression patterns, functional annotation, and prospective classification in human cancer genomes. PMID:23118863
A Neuronal Transcriptome Response Involving Stress Pathways is Buffered by Neuronal microRNAs. PMID:23115547
The signature of maternal rearing in the methylome in rhesus macaque prefrontal cortex and T cells. PMID:23115197
A de novo sSMC(22) Characterized by High-Resolution Arrays in a Girl with Cat-Eye Syndrome without Coloboma. PMID:23112755
Performance Comparison of Two Gene Set Analysis Methods for Genome-wide Association Study Results: GSA-SNP vs i-GSEA4GWAS. PMID:23105940
Comparing the reconstruction of regulatory pathways with distinct Bayesian networks inference methods. PMID:23095805
Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information. PMID:23093944
De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing. PMID:23091603
Cytotoxic necrotizing factor 1 and hemolysin from uropathogenic Escherichia coli elicit different host responses in the murine bladder. PMID:23090961
Adaptive elastic-net sparse principal component analysis for pathway association testing. PMID:23089825
A functional selection model explains evolutionary robustness despite plasticity in regulatory networks. PMID:23089682
Genome analysis of a highly virulent serotype 1 strain of Streptococcus pneumoniae from West Africa. PMID:23082106
Potential tumorigenic programs associated with TP53 mutation status reveal role of VEGF pathway. PMID:23079576
Functional modules, structural topology, and optimal activity in metabolic networks. PMID:23071431
MetNet Online: a novel integrated resource for plant systems biology. PMID:23066841
Tissue-based Alzheimer gene expression markers-comparison of multiple machine learning approaches and investigation of redundancy in small biomarker sets. PMID:23066814
Ribosomal protein L17, RpL17, is an inhibitor of vascular smooth muscle growth and carotid intima formation. PMID:23065385
Linking the signaling cascades and dynamic regulatory networks controlling stress responses. PMID:23064748
Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource. PMID:23061897
Transcriptomic and proteomic analyses of a Wolbachia-free filarial parasite provide evidence of trans-kingdom horizontal gene transfer. PMID:23049857
Tracing dynamic biological processes during phase transition. PMID:23046764
Insights into the pathogenesis of axial spondyloarthropathy from network and pathway analysis. PMID:23046677
The preservation of bidirectional promoter architecture in eukaryotes: what is the driving force? PMID:23046569
Toward allotetraploid cotton genome assembly: integration of a high-density molecular genetic linkage map with DNA sequence information. PMID:23046547
Gene set analysis for self-contained tests: complex null and specific alternative hypotheses. PMID:23044539
Genome sequence of the bacterium Streptomyces davawensis JCM 4913 and heterologous production of the unique antibiotic roseoflavin. PMID:23043000
MolFind: a software package enabling HPLC/MS-based identification of unknown chemical structures. PMID:23039714
Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network. PMID:23031817
MESSA: MEta-Server for protein Sequence Analysis. PMID:23031578
Profiling the anaerobic response of C. elegans using GC-MS. PMID:23029411
Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins. PMID:23029334
Therapeutic effects of astragaloside IV on myocardial injuries: multi-target identification and network analysis. PMID:23028693
Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans. PMID:23028371
Genome-wide metabolic (re-) annotation of Kluyveromyces lactis. PMID:23025710
A comparative analysis of the intestinal metagenomes present in guinea pigs (Cavia porcellus) and humans (Homo sapiens). PMID:23020652
MetR-regulated Vibrio cholerae metabolism is required for virulence. PMID:23015737
Genome sequence of a nicotine-degrading strain of Arthrobacter. PMID:23012289
Reconstructing dynamic gene regulatory networks from sample-based transcriptional data. PMID:23002138
Gap detection for genome-scale constraint-based models. PMID:22997515
Comparative Genome Sequence Analysis Reveals the Extent of Diversity and Conservation for Glycan-Associated Proteins in Burkholderia spp. PMID:22991502
Controlled reoxygenation cardiopulmonary bypass is associated with reduced transcriptomic changes in cyanotic tetralogy of Fallot patients undergoing surgery. PMID:22991208
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
Genomic landscape of non-small cell lung cancer in smokers and never-smokers. PMID:22980976
Sex peptide of Drosophila melanogaster males is a global regulator of reproductive processes in females. PMID:22977156
Notch signaling is activated in human hepatocellular carcinoma and induces tumor formation in mice. PMID:22974708
Convergent evolution of modularity in metabolic networks through different community structures. PMID:22974099
Distinct functional patterns of gene promoter hypomethylation and hypermethylation in cancer genomes. PMID:22970311
miRNA expression profile in primary gastric cancers and paired lymph node metastases indicates that miR-10a plays a role in metastasis from primary gastric cancer to lymph nodes. PMID:22969895
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Metagenomic analysis reveals a functional signature for biomass degradation by cecal microbiota in the leaf-eating flying squirrel (Petaurista alborufus lena). PMID:22963241
Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. PMID:22962473
Alcohol-induced alterations in maternal uterine endothelial proteome: a quantitative iTRAQ mass spectrometric approach. PMID:22960358
HYST: a hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis. PMID:22958900
A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. PMID:22958331
Shrinking the metabolic solution space using experimental datasets. PMID:22956899
Kinetic modelling of GlmU reactions - prioritization of reaction for therapeutic application. PMID:22952829
Importance of the latex-clearing protein (Lcp) for poly(cis-1,4-isoprene) rubber cleavage in Streptomyces sp. K30. PMID:22950008
Identification of unknown protein function using metabolite cocktail screening. PMID:22940582
Sequencing and analysis of the gastrula transcriptome of the brittle star Ophiocoma wendtii. PMID:22938175
Network-based assessment of the selectivity of metabolic drug targets in Plasmodium falciparum with respect to human liver metabolism. PMID:22937810
Evolution of domain architectures and catalytic functions of enzymes in metabolic systems. PMID:22936075
Complete genome sequence of the naphthalene-degrading Pseudomonas putida strain ND6. PMID:22933774
CardioNet: a human metabolic network suited for the study of cardiomyocyte metabolism. PMID:22929619
Deep sequencing of Porphyromonas gingivalis and comparative transcriptome analysis of a LuxS mutant. PMID:22919670
Analysis of gene expression from the Wolbachia genome of a filarial nematode supports both metabolic and defensive roles within the symbiosis. PMID:22919073
Prioritizing cancer therapeutic small molecules by integrating multiple OMICS datasets. PMID:22917481
VARIABLE SELECTION AND REGRESSION ANALYSIS FOR GRAPH-STRUCTURED COVARIATES WITH AN APPLICATION TO GENOMICS. PMID:22916087
A network-based approach for predicting missing pathway interactions. PMID:22916002
A network synthesis model for generating protein interaction network families. PMID:22912671
Novel insights into the transcriptome of Dirofilaria immitis. PMID:22911833
Identifying the genetic variation of gene expression using gene sets: application of novel gene Set eQTL approach to PharmGKB and KEGG. PMID:22905253
The chordate proteome history database. PMID:22904610
Systems biology for molecular life sciences and its impact in biomedicine. PMID:22903296
Genetic signatures shared in embryonic liver development and liver cancer define prognostically relevant subgroups in HCC. PMID:22891627
Characterization of microRNA expression profiles in normal and osteoarthritic human chondrocytes. PMID:22883423
Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals. PMID:22879444
GSA-PCA: gene set generation by principal component analysis of the Laplacian matrix of a metabolic network. PMID:22876834
Evaluating the consistency of gene sets used in the analysis of bacterial gene expression data. PMID:22873695
De novo transcriptome assembly and SNP discovery in the wing polymorphic salt marsh beetle Pogonus chalceus (Coleoptera, Carabidae). PMID:22870338
Detection of biomarkers for hepatocellular carcinoma using a hybrid univariate gene selection methods. PMID:22867264
Whole-genome microarray analysis and functional characterization reveal distinct gene expression profiles and patterns in two mouse models of ileal inflammation. PMID:22866923
Hal Is a Bacillus anthracis heme acquisition protein. PMID:22865843
Solution NMR and X-ray crystal structures of Pseudomonas syringae Pspto_3016 from protein domain family PF04237 (DUF419) adopt a "double wing" DNA binding motif. PMID:22865330
Comparison of methods for competitive tests of pathway analysis. PMID:22859961
Using bioinformatic approaches to identify pathways targeted by human leukemogens. PMID:22851955
CircadiOmics: integrating circadian genomics, transcriptomics, proteomics and metabolomics. PMID:22847108
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
Genome sequence of a novel indigo-producing strain, Pseudomonas monteilii QM. PMID:22843591
Patterns and architecture of genomic islands in marine bacteria. PMID:22839777
Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-interaction. PMID:22838966
Design and characterization of auxotrophy-based amino acid biosensors. PMID:22829942
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PMID:22829753
Parasites, proteomes and systems: has Descartes' clock run out of time? PMID:22828391
Transcriptional changes associated with lack of lipid synthesis in parasitoids. PMID:22820524
Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. PMID:22817809
atBioNet--an integrated network analysis tool for genomics and biomarker discovery. PMID:22817640
Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome. PMID:22815919
MassTRIX reloaded: combined analysis and visualization of transcriptome and metabolome data. PMID:22815716
[Screening key genes associated with the development and progression of non-small cell lung cancer based on gene-enrichment analysis and meta-analysis]. PMID:22814261
Wnt-pathway activation in two molecular classes of hepatocellular carcinoma and experimental modulation by sorafenib. PMID:22811581
Subtractive libraries for prospecting differentially expressed genes in the soybean under water deficit. PMID:22802715
A web-based bioinformatics interface applied to the GENOSOJA Project: Databases and pipelines. PMID:22802706
Network-enabled gene expression analysis. PMID:22799258
Identification of common and distinctive mechanisms of resistance to different anti-IGF-IR agents in Ewing's sarcoma. PMID:22798295
Novel pathways in the pathobiology of human abdominal aortic aneurysms. PMID:22797469
Integration of biological networks and pathways with genetic association studies. PMID:22777728
Transcriptome analysis of head kidney in grass carp and discovery of immune-related genes. PMID:22776770
De novo transcriptome sequencing in a songbird, the dark-eyed junco (Junco hyemalis): genomic tools for an ecological model system. PMID:22776250
Tissue-specific temporal exome capture revealed muscle-specific genes and SNPs in Indian buffalo (Bubalus bubalis). PMID:22768984
Transcriptome analysis of the Octopus vulgaris central nervous system. PMID:22768275
Design constraints on a synthetic metabolism. PMID:22768162
Transcriptome sequencing and comparative analysis of Saccharina japonica (Laminariales, Phaeophyceae) under blue light induction. PMID:22761876
In silico method for modelling metabolism and gene product expression at genome scale. PMID:22760628
Text-mining applied to autoimmune disease research: the Sjögren's syndrome knowledge base. PMID:22759918
MuSiC: identifying mutational significance in cancer genomes. PMID:22759861
The yak genome and adaptation to life at high altitude. PMID:22751099
Draft genome sequence of salt-tolerant yeast Debaryomyces hansenii var. hansenii MTCC 234. PMID:22744717
Integration analysis of quantitative proteomics and transcriptomics data identifies potential targets of frizzled-8 protein-related antiproliferative factor in vivo. PMID:22738385
Genome-wide profiling of peroxisome proliferator-activated receptor γ in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression. PMID:22733994
NetWalker: a contextual network analysis tool for functional genomics. PMID:22732065
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
A cooperative strategy for parameter estimation in large scale systems biology models. PMID:22727112
Regulation of alternative splicing by the circadian clock and food related cues. PMID:22721557
De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus. PMID:22721448
AlignNemo: a local network alignment method to integrate homology and topology. PMID:22719866
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. PMID:22718037
Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. PMID:22713133
Divergent gene expression in the conserved dauer stage of the nematodes Pristionchus pacificus and Caenorhabditis elegans. PMID:22712530
Global Approaches to the Role of miRNAs in Drug-Induced Changes in Gene Expression. PMID:22707957
Prioritizing cancer-related key miRNA-target interactions by integrative genomics. PMID:22705797
PathCase-SB: integrating data sources and providing tools for systems biology research. PMID:22697505
Network-induced classification kernels for gene expression profile analysis. PMID:22697242
MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells. PMID:22691140
Genome sequence of a novel nicotine-degrading strain, Pseudomonas geniculata N1. PMID:22689240
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PMID:22675498
Identification of functional differences in metabolic networks using comparative genomics and constraint-based models. PMID:22666308
Repertoire of Protein Kinases Encoded in the Genome of Takifugu rubripes. PMID:22666085
Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts. PMID:22665442
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. PMID:22651983
Identification of differentially expressed genes and pathways for intramuscular fat deposition in pectoralis major tissues of fast-and slow-growing chickens. PMID:22646994
Exploring the evolution of protein function in Archaea. PMID:22646318
Gene expression profiling of Mycobacterium avium subsp. paratuberculosis in simulated multi-stress conditions and within THP-1 cells reveals a new kind of interactive intramacrophage behaviour. PMID:22646160
Invariants and other structural properties of biochemical models as a constraint satisfaction problem. PMID:22642806
Application of systems biology principles to protein biomarker discovery: urinary exosomal proteome in renal transplantation. PMID:22641613
Genome-wide gene-environment interaction analysis for asbestos exposure in lung cancer susceptibility. PMID:22637743
Computational tools for metabolic engineering. PMID:22629572
Assessment method for a power analysis to identify differentially expressed pathways. PMID:22629411
High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes. PMID:22629298
Sex-specific gene expression during asexual development of Neurospora crassa. PMID:22626843
Variations in target gene expression and pathway profiles in the mouse hippocampus following treatment with different effective compounds for ischemia-reperfusion injury. PMID:22622953
Transcriptome profiling and in silico analysis of somatic embryos in Japanese larch (Larix leptolepis). PMID:22622308
Proteins differentially expressed in elicited cell suspension culture of Podophyllum hexandrum with enhanced podophyllotoxin content. PMID:22621772
MAGIA²: from miRNA and genes expression data integrative analysis to microRNA-transcription factor mixed regulatory circuits (2012 update). PMID:22618880
NetAligner--a network alignment server to compare complexes, pathways and whole interactomes. PMID:22618871
Phosphosignature predicts dasatinib response in non-small cell lung cancer. PMID:22617229
Comparative proteomic analysis of Aedes aegypti larval midgut after intoxication with Cry11Aa toxin from Bacillus thuringiensis. PMID:22615881
Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes. PMID:22615549
Molecular signaling network complexity is correlated with cancer patient survivability. PMID:22615392
Subchronic oral exposure to benzo(a)pyrene leads to distinct transcriptomic changes in the lungs that are related to carcinogenesis. PMID:22610609
Genetic variation and metabolic pathway intricacy govern the active compound content and quality of the Chinese medicinal plant Lonicera japonica thunb. PMID:22607188
De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). PMID:22607098
Cis-acting polymorphisms affect complex traits through modifications of microRNA regulation pathways. PMID:22606281
The genome characteristics and predicted function of methyl-group oxidation pathway in the obligate aceticlastic methanogens, Methanosaeta spp. PMID:22590603
NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems. PMID:22589706
Bioinformatics opportunities for identification and study of medicinal plants. PMID:22589384
Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. PMID:22587966
Predicted Relative Metabolomic Turnover (PRMT): determining metabolic turnover from a coastal marine metagenomic dataset. PMID:22587810
A two-stage random forest-based pathway analysis method. PMID:22586488
miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations. PMID:22583976
Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico. PMID:22583864
Proteomics and systems biology for understanding diabetic nephropathy. PMID:22581264
Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. PMID:22580950
From genome-wide association studies to disease mechanisms: celiac disease as a model for autoimmune diseases. PMID:22580835
GHOSTM: a GPU-accelerated homology search tool for metagenomics. PMID:22574135
Inferring high-confidence human protein-protein interactions. PMID:22558947
A Bayesian variable selection procedure to rank overlapping gene sets. PMID:22554182
Categorization of metabolome in bacterial systems. PMID:22553387
MarVis-Filter: ranking, filtering, adduct and isotope correction of mass spectrometry data. PMID:22550397
Interaction among apoptosis-associated sequence variants and joint effects on aggressive prostate cancer. PMID:22546513
Nutritional metabolomics: progress in addressing complexity in diet and health. PMID:22540256
CMRF: analyzing differential gene regulation in two group perturbation experiments. PMID:22537297
THINK Back: KNowledge-based Interpretation of High Throughput data. PMID:22536867
Complete genome sequence of Paenibacillus mucilaginosus 3016, a bacterium functional as microbial fertilizer. PMID:22535950
Comparison of large-insert, small-insert and pyrosequencing libraries for metagenomic analysis. PMID:22534608
Dynamic interactions between Bombyx mori nucleopolyhedrovirus and its host cells revealed by transcriptome analysis. PMID:22532689
Symbiodinium transcriptomes: genome insights into the dinoflagellate symbionts of reef-building corals. PMID:22529998
Genome-scale modeling of light-driven reductant partitioning and carbon fluxes in diazotrophic unicellular cyanobacterium Cyanothece sp. ATCC 51142. PMID:22529767
Bioinformatic evidence and characterization of novel putative large conjugative transposons residing in genomes of genera Bacteroides and Prevotella. PMID:22528303
Development of a pharmaceutical hepatotoxicity biomarker panel using a discovery to targeted proteomics approach. PMID:22527513
Deep RNA sequencing reveals novel cardiac transcriptomic signatures for physiological and pathological hypertrophy. PMID:22523601
A systems biology approach to characterize the regulatory networks leading to trabectedin resistance in an in vitro model of myxoid liposarcoma. PMID:22523595
Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities. PMID:22514724
Downregulation of miR-31, miR-155, and miR-564 in chronic myeloid leukemia cells. PMID:22511990
Superessential reactions in metabolic networks. PMID:22509034
Identification and characterization of a novel diterpene gene cluster in Aspergillus nidulans. PMID:22506079
The Chlamydia psittaci genome: a comparative analysis of intracellular pathogens. PMID:22506068
A model-based analysis to infer the functional content of a gene list. PMID:22499692
Systematic identification of edited microRNAs in the human brain. PMID:22499667
Pathway-directed weighted testing procedures for the integrative analysis of gene expression and metabolomic data. PMID:22497771
Genome-wide association analysis for feed efficiency in Angus cattle. PMID:22497295
Functional annotation of hierarchical modularity. PMID:22496762
De novo assembly and characterization of the root transcriptome of Aegilops variabilis during an interaction with the cereal cyst nematode. PMID:22494814
Nkx3.1 and Myc crossregulate shared target genes in mouse and human prostate tumorigenesis. PMID:22484818
Gram-negative and Gram-positive bacterial infections give rise to a different metabolic response in a mouse model. PMID:22483232
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Comparative analysis of gene content evolution in phytoplasmas and mycoplasmas. PMID:22479625
Identification of chromosomal genes in Yersinia pestis that influence type III secretion and delivery of Yops into target cells. PMID:22479512
Metabolic profiling of a mapping population exposes new insights in the regulation of seed metabolism and seed, fruit, and plant relations. PMID:22479206
Drug target prediction based on the herbs components: the study on the multitargets pharmacological mechanism of qishenkeli acting on the coronary heart disease. PMID:22474514
Functional repertoire, molecular pathways and diseases associated with 3D domain swapping in the human proteome. PMID:22472218
Comparison of muscle transcriptome between pigs with divergent meat quality phenotypes identifies genes related to muscle metabolism and structure. PMID:22470472
Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. PMID:22469835
Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa. PMID:22465851
Prioritization of SNPs for genome-wide association studies using an interaction model of genetic variation, gene expression, and trait variation. PMID:22460606
Comparative genomics of the apicomplexan parasites Toxoplasma gondii and Neospora caninum: Coccidia differing in host range and transmission strategy. PMID:22457617
Proteomic analysis of microvesicles released by the human prostate cancer cell line PC-3. PMID:22457534
Understanding communication signals during mycobacterial latency through predicted genome-wide protein interactions and boolean modeling. PMID:22448278
Transcriptional profiling of ESTs from the biocontrol fungus Chaetomium cupreum. PMID:22448129
A previously unknown oxalyl-CoA synthetase is important for oxalate catabolism in Arabidopsis. PMID:22447686
Inference of modules associated to eQTLs. PMID:22447449
The complete genome sequence of the acarbose producer Actinoplanes sp. SE50/110. PMID:22443545
Transcriptome profiling of testis during sexual maturation stages in Eriocheir sinensis using Illumina sequencing. PMID:22442720
Coordination of the transcriptome and metabolome by the circadian clock. PMID:22431615
Metabolic modeling of Chlamydomonas reinhardtii: energy requirements for photoautotrophic growth and maintenance. PMID:22427720
Congenital nephrogenic diabetes insipidus: the current state of affairs. PMID:22427315
Personal omics profiling reveals dynamic molecular and medical phenotypes. PMID:22424236
Associations with early-life socio-economic position in adult DNA methylation. PMID:22422449
The application of selective reaction monitoring confirms dysregulation of glycolysis in a preclinical model of schizophrenia. PMID:22420779
Proteomic analysis of acquired tamoxifen resistance in MCF-7 cells reveals expression signatures associated with enhanced migration. PMID:22417809
Large-scale functional RNAi screen in C. elegans identifies genes that regulate the dysfunction of mutant polyglutamine neurons. PMID:22413862
Statistical inference and reverse engineering of gene regulatory networks from observational expression data. PMID:22408642
The automatic annotation of bacterial genomes. PMID:22408191
Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase. PMID:22395897
iCanPlot: visual exploration of high-throughput omics data using interactive Canvas plotting. PMID:22393367
Identification of potential drug targets implicated in Parkinson's disease from human genome: insights of using fused domains in hypothetical proteins as probes. PMID:22389811
High-performance metabolic profiling of plasma from seven mammalian species for simultaneous environmental chemical surveillance and bioeffect monitoring. PMID:22387982
Ten years of pathway analysis: current approaches and outstanding challenges. PMID:22383865
Vru (Sub0144) controls expression of proven and putative virulence determinants and alters the ability of Streptococcus uberis to cause disease in dairy cattle. PMID:22383474
Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation. PMID:22383037
Metagenomic analysis of a stable trichloroethene-degrading microbial community. PMID:22378537
Methods for Determining the Statistical Significance of Enrichment or Depletion of Gene Ontology Classifications under Weighted Membership. PMID:22375144
Genome sequence of Comamonas testosteroni ATCC 11996, a representative strain involved in steroid degradation. PMID:22374961
Bi-directional semantic similarity for gene ontology to optimize biological and clinical analyses. PMID:22374934
Rare variant collapsing in conjunction with mean log p-value and gradient boosting approaches applied to Genetic Analysis Workshop 17 data. PMID:22373203
Comparative analysis and assessment of M. tuberculosis H37Rv protein-protein interaction datasets. PMID:22369691
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. PMID:22369646
In silico secretome analysis approach for next generation sequencing transcriptomic data. PMID:22369360
Preimplantation development regulatory pathway construction through a text-mining approach. PMID:22369103
Analysis of the transcriptome of Panax notoginseng root uncovers putative triterpene saponin-biosynthetic genes and genetic markers. PMID:22369100
A novel framework for the comparative analysis of biological networks. PMID:22363585
The capsicum transcriptome DB: a "hot" tool for genomic research. PMID:22359434
Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis. PMID:22356827
Identifying neighborhoods of coordinated gene expression and metabolite profiles. PMID:22355360
Assignment of putative functions to membrane "hypothetical proteins" from the Trypanosoma cruzi genome. PMID:22354180
Identification of genes potentially related to biomineralization and immunity by transcriptome analysis of pearl sac in pearl oyster Pinctada martensii. PMID:22351046
Enriching the human apoptosis pathway by predicting the structures of protein-protein complexes. PMID:22349545
miR-10a is aberrantly overexpressed in Nucleophosmin1 mutated acute myeloid leukaemia and its suppression induces cell death. PMID:22348345
Identification of potential apicoplast associated therapeutic targets in human and animal pathogen Toxoplasma gondii ME49. PMID:22347778
Identification of prostate-enriched proteins by in-depth proteomic analyses of expressed prostatic secretions in urine. PMID:22339264
Insight into the transmission biology and species-specific functional capabilities of tsetse (Diptera: glossinidae) obligate symbiont Wigglesworthia. PMID:22334516
The transcriptome of compatible and incompatible interactions of potato (Solanum tuberosum) with Phytophthora infestans revealed by DeepSAGE analysis. PMID:22328937
Global changes in gene expression by the opportunistic pathogen Burkholderia cenocepacia in response to internalization by murine macrophages. PMID:22321740
Integrating the Alzheimer's disease proteome and transcriptome: a comprehensive network model of a complex disease. PMID:22321014
Pericellular pH homeostasis is a primary function of the Warburg effect: inversion of metabolic systems to control lactate steady state in tumor cells. PMID:22320183
Identification of candidate genes underlying an iron efficiency quantitative trait locus in soybean. PMID:22319075
Structure-based function discovery of an enzyme for the hydrolysis of phosphorylated sugar lactones. PMID:22313111
Non-housekeeping genes expressed in human trabecular meshwork cell cultures. PMID:22312193
Polycomb associates genome-wide with a specific RNA polymerase II variant, and regulates metabolic genes in ESCs. PMID:22305566
When one and one gives more than two: challenges and opportunities of integrative omics. PMID:22303399
Gene set analysis of survival following ovarian cancer implicates macrolide binding and intracellular signaling genes. PMID:22302016
Markov Chain Ontology Analysis (MCOA). PMID:22300537
Large-scale elucidation of drug response pathways in humans. PMID:22300318
Genetic polymorphisms in fatty acid metabolism genes and colorectal cancer. PMID:22294764
miRDeepFinder: a miRNA analysis tool for deep sequencing of plant small RNAs. PMID:22290409
FAME, the Flux Analysis and Modeling Environment. PMID:22289213
The combination of a genome-wide association study of lymphocyte count and analysis of gene expression data reveals novel asthma candidate genes. PMID:22286170
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. PMID:22277925
Do crystal structures obviate the need for theoretical models of GPCRs for structure-based virtual screening? PMID:22275072
Comparative genomic analysis of the genus Staphylococcus including Staphylococcus aureus and its newly described sister species Staphylococcus simiae. PMID:22272658
De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome. PMID:22270559
Computational tools for the synthetic design of biochemical pathways. PMID:22266781
Inflammatory pathway genes belong to major targets of persistent organic pollutants in adipose cells. PMID:22262711
Core module biomarker identification with network exploration for breast cancer metastasis. PMID:22257533
Comparison of Chloroflexus aurantiacus strain J-10-fl proteomes of cells grown chemoheterotrophically and photoheterotrophically. PMID:22249883
Altered miRNA expression patterns in Tff2 knock-out mice correlate with cellular pathways of neoplastic development and caloric metabolism. PMID:22245972
QTL/microarray approach using pathway information. PMID:22244197
Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis. PMID:22243521
Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. PMID:22233149
Predicting biological functions of compounds based on chemical-chemical interactions. PMID:22220213
Genetic co-occurrence network across sequenced microbes. PMID:22219725
Bacterial niche-specific genome expansion is coupled with highly frequent gene disruptions in deep-sea sediments. PMID:22216192
Fusion of the subunits α and β of succinyl-CoA synthetase as a phylogenetic marker for Pezizomycotina fungi. PMID:22215972
Stable isotope-resolved metabolomics and applications for drug development. PMID:22212615
Modeling community-wide molecular networks of multicellular systems. PMID:22210865
An integer linear programming approach for finding deregulated subgraphs in regulatory networks. PMID:22210863
Candidate gene analysis of spontaneous preterm delivery: new insights from re-analysis of a case-control study using case-parent triads and control-mother dyads. PMID:22208904
Interrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera. PMID:22208880
MotifMap: integrative genome-wide maps of regulatory motif sites for model species. PMID:22208852
Development of ESTs and data mining of pineapple EST-SSRs. PMID:22207174
Advanced stoichiometric analysis of metabolic networks of mammalian systems. PMID:22196224
Similarity-based disease risk assessment for personal genomes: proof of concept. PMID:22195217
Exploring schizophrenia drug-gene interactions through molecular network and pathway modeling. PMID:22195173
An integrated framework to model cellular phenotype as a component of biochemical networks. PMID:22190923
Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach. PMID:22185641
Reconstruction of Arabidopsis metabolic network models accounting for subcellular compartmentalization and tissue-specificity. PMID:22184215
Profiling the human response to physical exercise: a computational strategy for the identification and kinetic analysis of metabolic biomarkers. PMID:22182709
Methods, challenges, and promise of next-generation sequencing in cancer biology. PMID:22180681
MicroRNA miR-451 downregulates the PI3K/AKT pathway through CAB39 in human glioma. PMID:22179124
A meta-analysis of array-CGH studies implicates antiviral immunity pathways in the development of hepatocellular carcinoma. PMID:22174799
Enhancing the accuracy of HMM-based conserved pathway prediction using global correspondence scores. PMID:22165903
Neuroglobin-deficiency exacerbates Hif1A and c-FOS response, but does not affect neuronal survival during severe hypoxia in vivo. PMID:22164238
Metabolic routes affecting rubber biosynthesis in Hevea brasiliensis latex. PMID:22162870
Using the gene ontology to scan multilevel gene sets for associations in genome wide association studies. PMID:22161999
The production of conjugated α-linolenic, γ-linolenic and stearidonic acids by strains of bifidobacteria and propionibacteria. PMID:22160449
Array-based identification of common DNA methylation alterations in ulcerative colitis. PMID:22159500
Mutation of the sensor kinase chvG in Rhizobium leguminosarum negatively impacts cellular metabolism, outer membrane stability, and symbiosis. PMID:22155778
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Functional bias of positively selected genes in Streptococcus genomes. PMID:22155358
Human proteome-scale structural modeling of E2-E3 interactions exploiting interface motifs. PMID:22149024
Identifying highly conserved and highly differentiated gene ontology categories in human populations. PMID:22140477
Database resources of the National Center for Biotechnology Information. PMID:22140104
Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools. PMID:22138362
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles. PMID:22133144
A statistical method for region-based meta-analysis of genome-wide association studies in genetically diverse populations. PMID:22126751
Genome sequence of Halobiforma lacisalsi AJ5, an extremely halophilic archaeon which harbors a bop gene. PMID:22123770
hiPathDB: a human-integrated pathway database with facile visualization. PMID:22123737
Integrative set enrichment testing for multiple omics platforms. PMID:22118224
Multiple-input multiple-output causal strategies for gene selection. PMID:22118187
Xanthusbase after five years expands to become Openmods. PMID:22116063
Solution NMR structure of Asl3597 from Nostoc sp. PCC7120, the first structure from protein domain family PF12095, reveals a novel fold. PMID:22113821
Gene set analysis of GWAS data for human longevity highlights the relevance of the insulin/IGF-1 signaling and telomere maintenance pathways. PMID:22113349
Phytozome: a comparative platform for green plant genomics. PMID:22110026
MicroRNA expression in abdominal and gluteal adipose tissue is associated with mRNA expression levels and partly genetically driven. PMID:22102887
Capture of microRNA-bound mRNAs identifies the tumor suppressor miR-34a as a regulator of growth factor signaling. PMID:22102825
Identification of biochemical network modules based on shortest retroactive distances. PMID:22102800
Average rank-based score to measure deregulation of molecular pathway gene sets. PMID:22096597
Role of SPI-1 secreted effectors in acute bovine response to Salmonella enterica Serovar Typhimurium: a systems biology analysis approach. PMID:22096503
Functional genomic analysis unravels a metabolic-inflammatory interplay in adrenoleukodystrophy. PMID:22095690
Time-resolved transcriptomics and bioinformatic analyses reveal intrinsic stress responses during batch culture of Bacillus subtilis. PMID:22087258
Genome-wide functional analysis of the cotton transcriptome by creating an integrated EST database. PMID:22087239
Analysis of the Asian seabass transcriptome based on expressed sequence tags. PMID:22086997
Transcriptome analysis of orange-spotted grouper (Epinephelus coioides) spleen in response to Singapore grouper iridovirus. PMID:22078027
Prediction of disease and phenotype associations from genome-wide association studies. PMID:22076134
Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquens AM1. PMID:22074569
Genome sequence of Pseudomonas putida strain B6-2, a superdegrader of polycyclic aromatic hydrocarbons and dioxin-like compounds. PMID:22072645
ApoptoProteomics, an integrated database for analysis of proteomics data obtained from apoptotic cells. PMID:22067098
eQuilibrator--the biochemical thermodynamics calculator. PMID:22064852
Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. PMID:22057054
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. PMID:22056985
Resistance exercise training influences skeletal muscle immune activation: a microarray analysis. PMID:22052873
Software for systems biology: from tools to integrated platforms. PMID:22048662
The evolution of metabolic networks of E. coli. PMID:22044664
A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology. PMID:22041191
Proteomic analysis of Col11a1-associated protein complexes. PMID:22038862
Mechanisms of stable lipid loss in a social insect. PMID:22031746
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. PMID:22030749
SegMine workflows for semantic microarray data analysis in Orange4WS. PMID:22029475
The draft genome of the carcinogenic human liver fluke Clonorchis sinensis. PMID:22023798
Pattern specification and immune response transcriptional signatures of pericardial and subcutaneous adipose tissue. PMID:22022522
attract: A method for identifying core pathways that define cellular phenotypes. PMID:22022396
Dynamic gene network reconstruction from gene expression data in mice after influenza A (H1N1) infection. PMID:22017961
Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. PMID:22015969
Cancer associated epigenetic transitions identified by genome-wide histone methylation binding profiles in human colorectal cancer samples and paired normal mucosa. PMID:22011431
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. PMID:22006843
Genetic screening of functional properties of lactic acid bacteria in a fermented pearl millet slurry and in the metagenome of fermented starchy foods. PMID:22003019
Pathos: a web facility that uses metabolic maps to display experimental changes in metabolites identified by mass spectrometry. PMID:22002696
An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. PMID:22000015
Horizontal and vertical growth of S. cerevisiae metabolic network. PMID:21999464
A novel method to quantify gene set functional association based on gene ontology. PMID:21998111
An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92. PMID:21995956
Gene Cluster Profile Vectors: a method to infer functionally related gene sets by grouping proximity-based gene clusters. PMID:21989079
Translational analysis of mouse and human placental protein and mRNA reveals distinct molecular pathologies in human preeclampsia. PMID:21986993
Proteomic and phosphoproteomic comparison of human ES and iPS cells. PMID:21983960
Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PMID:21980418
Similarities and differences in peripheral blood gene-expression signatures of individuals with schizophrenia and their first-degree biological relatives. PMID:21972136
Proteomic profiling of the influence of iron availability on Cryptococcus gattii. PMID:21970549
A metagenomic study of methanotrophic microorganisms in Coal Oil Point seep sediments. PMID:21970369
Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS). PMID:21968429
Silencing of p130cas in ovarian carcinoma: a novel mechanism for tumor cell death. PMID:21957230
Peroxide stimulon and role of PerR in group A Streptococcus. PMID:21949080
EnzymeDetector: an integrated enzyme function prediction tool and database. PMID:21943292
Multi-membership gene regulation in pathway based microarray analysis. PMID:21939531
Bioinformatics and systems biology of the lipidome. PMID:21939287
BioMart Central Portal: an open database network for the biological community. PMID:21930507
International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data. PMID:21930502
Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. PMID:21929789
Quantification of protein group coherence and pathway assignment using functional association. PMID:21929787
Efficient de novo assembly of single-cell bacterial genomes from short-read data sets. PMID:21926975
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. PMID:21923952
Using blood gene signatures for assessing effects of exposure to perfluoroalkyl acids (PFAAs) in humans: the NOWAC postgenome study. PMID:21915359
Disease gene interaction pathways: a potential framework for how disease genes associate by disease-risk modules. PMID:21915342
Complete genome sequence of Alicyclobacillus acidocaldarius strain Tc-4-1. PMID:21914900
Complete genome analysis of Sulfobacillus acidophilus strain TPY, isolated from a hydrothermal vent in the Pacific Ocean. PMID:21914875
Complete genome sequence of the nicotine-degrading Pseudomonas putida strain S16. PMID:21914868
Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach. PMID:21912686
Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns. PMID:21910886
Phospholipase C isozymes are deregulated in colorectal cancer--insights gained from gene set enrichment analysis of the transcriptome. PMID:21909432
Identification of single- and multiple-class specific signature genes from gene expression profiles by group marker index. PMID:21909426
Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus. PMID:21909270
Structure of 3-ketoacyl-(acyl-carrier-protein) reductase from Rickettsia prowazekii at 2.25 Å resolution. PMID:21904060
Toward the blood-borne miRNome of human diseases. PMID:21892151
Dominating biological networks. PMID:21887225
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. PMID:21886097
Gene- or region-based association study via kernel principal component analysis. PMID:21871061
Systems analysis of immune responses in Marek's disease virus-infected chickens identifies a gene involved in susceptibility and highlights a possible novel pathogenicity mechanism. PMID:21865384
Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network. PMID:21865350
Environmental versatility promotes modularity in genome-scale metabolic networks. PMID:21864340
Gene expression analysis of the embryonic subplate. PMID:21862448
BLProt: prediction of bioluminescent proteins based on support vector machine and relieff feature selection. PMID:21849049
Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052. PMID:21846360
Identification and categorization of liver toxicity markers induced by a related pair of drugs. PMID:21845099
Exploring pathway interactions in insulin resistant mouse liver. PMID:21843341
Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states. PMID:21838295
Gene expression profiling in human high-grade astrocytomas. PMID:21836821
Novel insights into the structural requirements for the design of selective and specific aldose reductase inhibitors. PMID:21833829
Bacteriocyte-associated gammaproteobacterial symbionts of the Adelges nordmannianae/piceae complex (Hemiptera: Adelgidae). PMID:21833037
Why is there a lack of consensus on molecular subgroups of glioblastoma? Understanding the nature of biological and statistical variability in glioblastoma expression data. PMID:21829433
Reciprocal transcriptional regulation of metabolic and signaling pathways correlates with disease severity in heart failure. PMID:21828333
Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. PMID:21824427
Discovery of a cytokinin deaminase. PMID:21823622
Soy food supplementation, dietary fat reduction and peripheral blood gene expression in postmenopausal women--a randomized, controlled trial. PMID:21823222
RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. PMID:21811850
Improved genome annotation through untargeted detection of pathway-specific metabolites. PMID:21810208
Synergistic use of plant-prokaryote comparative genomics for functional annotations. PMID:21810204
Systems-biology approaches for predicting genomic evolution. PMID:21808261
Systems biology of bacterial nitrogen fixation: high-throughput technology and its integrative description with constraint-based modeling. PMID:21801415
Exploiting publicly available biological and biochemical information for the discovery of novel short linear motifs. PMID:21799808
Dynamic evolution of pathogenicity revealed by sequencing and comparative genomics of 19 Pseudomonas syringae isolates. PMID:21799664
GO Trimming: Systematically reducing redundancy in large Gene Ontology datasets. PMID:21798041
VISTA Region Viewer (RViewer)--a computational system for prioritizing genomic intervals for biomedical studies. PMID:21791533
Learning biomarkers of pluripotent stem cells in mouse. PMID:21791477
Network-based prediction for sources of transcriptional dysregulation using latent pathway identification analysis. PMID:21788508
Online nanoflow multidimensional fractionation for high efficiency phosphopeptide analysis. PMID:21788404
Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis. PMID:21781297
Randomizing genome-scale metabolic networks. PMID:21779409
Distinct spatio-temporal extracellular matrix accumulation within demyelinated spinal cord lesions in Theiler's murine encephalomyelitis. PMID:21767322
PGAT: a multistrain analysis resource for microbial genomes. PMID:21765097
Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. PMID:21764968
Transcriptome sequencing, and rapid development and application of SNP markers for the legume pod borer Maruca vitrata (Lepidoptera: Crambidae). PMID:21754987
A novel method to identify cooperative functional modules: study of module coordination in the Saccharomyces cerevisiae cell cycle. PMID:21749690
Systematic approaches towards the development of host-directed antiviral therapeutics. PMID:21747723
Differences in lateral gene transfer in hypersaline versus thermal environments. PMID:21740576
From SNPs to genes: disease association at the gene level. PMID:21738570
Therapy-, gender- and race-specific microRNA markers, target genes and networks related to glioblastoma recurrence and survival. PMID:21737610
Interferon regulatory factor 8 regulates pathways for antigen presentation in myeloid cells and during tuberculosis. PMID:21731497
Global transcriptome changes underlying colony growth in the opportunistic human pathogen Aspergillus fumigatus. PMID:21724936
Assessment of hepatocyte growth factor in ovarian cancer mortality. PMID:21724856
Transcriptome sequencing and de novo analysis for Yesso scallop (Patinopecten yessoensis) using 454 GS FLX. PMID:21720557
The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. PMID:21719571
Network-based group variable selection for detecting expression quantitative trait loci (eQTL). PMID:21718480
Metatranscriptomic analysis of autonomously collected and preserved marine bacterioplankton. PMID:21716310
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. PMID:21715386
ncFANs: a web server for functional annotation of long non-coding RNAs. PMID:21715382
General metabolism of Laribacter hongkongensis: a genome-wide analysis. PMID:21711917
Regulation of gene expression in ovarian cancer cells by luteinizing hormone receptor expression and activation. PMID:21711548
High-throughput mapping of the promoters of the mouse olfactory receptor genes reveals a new type of mammalian promoter and provides insight into olfactory receptor gene regulation. PMID:21705439
On the origins of Mendelian disease genes in man: the impact of gene duplication. PMID:21705381
In vivo versus in vitro protein abundance analysis of Shigella dysenteriae type 1 reveals changes in the expression of proteins involved in virulence, stress and energy metabolism. PMID:21702961
KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. PMID:21700675
Proteomic patterns of cervical cancer cell lines, a network perspective. PMID:21696634
Stromal upregulation of lateral epithelial adhesions: gene expression analysis of signalling pathways in prostate epithelium. PMID:21696611
Fusion of metabolomics and proteomics data for biomarkers discovery: case study on the experimental autoimmune encephalomyelitis. PMID:21696593
Systems biology of the qa gene cluster in Neurospora crassa. PMID:21695121
Integrative analysis of environmental sequences using MEGAN4. PMID:21690186
Mining metabolites: extracting the yeast metabolome from the literature. PMID:21687783
An integrative clustering and modeling algorithm for dynamical gene expression data. PMID:21685097
Small sets of interacting proteins suggest functional linkage mechanisms via Bayesian analogical reasoning. PMID:21685095
Generation and analysis of expressed sequence tags from the bone marrow of Chinese Sika deer. PMID:21681423
Nutritional regulation of bile acid metabolism is associated with improved pathological characteristics of the metabolic syndrome. PMID:21680746
Regional regulation of transcription in the bovine genome. PMID:21673989
A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. PMID:21663690
Rare de novo variants associated with autism implicate a large functional network of genes involved in formation and function of synapses. PMID:21658583
Genome-wide association study of severity in multiple sclerosis. PMID:21654844
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
Multiple preconditioning paradigms converge on interferon regulatory factor-dependent signaling to promote tolerance to ischemic brain injury. PMID:21653850
The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways. PMID:21653523
Integrated proteomic profiling of cell line conditioned media and pancreatic juice for the identification of pancreatic cancer biomarkers. PMID:21653254
De novo discovery of mutated driver pathways in cancer. PMID:21653252
Enhancing the role of veterinary vaccines reducing zoonotic diseases of humans: linking systems biology with vaccine development. PMID:21651944
Analysis of a viral metagenomic library from 200 m depth in Monterey Bay, California constructed by direct shotgun cloning. PMID:21651822
Cell cycle and aging, morphogenesis, and response to stimuli genes are individualized biomarkers of glioblastoma progression and survival. PMID:21649900
Common peptides study of aminoacyl-tRNA synthetases. PMID:21647378
In silico analysis of candidate genes associated with humoral innate immune response in chicken. PMID:21645317
The plasma membrane of the cyanobacterium Gloeobacter violaceus contains segregated bioenergetic domains. PMID:21642550
Transcriptomics and molecular evolutionary rate analysis of the bladderwort (Utricularia), a carnivorous plant with a minimal genome. PMID:21639913
Pathway analysis of expression data: deciphering functional building blocks of complex diseases. PMID:21637797
LinkinPath: from sequence to interconnected pathway. PMID:21636594
Protein expression dynamics during Escherichia coli glucose-lactose diauxie. PMID:21631920
A toolbox model of evolution of metabolic pathways on networks of arbitrary topology. PMID:21625566
GLAMM: Genome-Linked Application for Metabolic Maps. PMID:21624891
Effect of PITX2 knockdown on transcriptome of primary human trabecular meshwork cell cultures. PMID:21617755
Génie: literature-based gene prioritization at multi genomic scale. PMID:21609954
GiSAO.db: a database for ageing research. PMID:21609420
Improved functional overview of protein complexes using inferred epistatic relationships. PMID:21605386
Label-free protein profiling of adipose-derived human stem cells under hyperosmotic treatment. PMID:21604804
Gitools: analysis and visualisation of genomic data using interactive heat-maps. PMID:21602921
Diet drives convergence in gut microbiome functions across mammalian phylogeny and within humans. PMID:21596990
Knowledge-driven multi-locus analysis reveals gene-gene interactions influencing HDL cholesterol level in two independent EMR-linked biobanks. PMID:21589926
Atmospheric reaction systems as null-models to identify structural traces of evolution in metabolism. PMID:21573072
In silico identification of common putative drug targets in Leptospira interrogans. PMID:21572503
Crystal structures of a halophilic archaeal malate synthase from Haloferax volcanii and comparisons with isoforms A and G. PMID:21569248
Characterizing the diversity and biological relevance of the MLPCN assay manifold and screening set. PMID:21568288
Virtual screening for potential inhibitors of homology modeled Leptospira interrogans MurD ligase. PMID:21566738
Characterization of Betula platyphylla gene transcripts associated with early development of male inflorescence. PMID:21559830
The strength of chemical linkage as a criterion for pruning metabolic graphs. PMID:21551141
Mixture models for analysis of the taxonomic composition of metagenomes. PMID:21546400
Molecular signatures database (MSigDB) 3.0. PMID:21546393
Canonical NF-kappaB activation is essential for Epstein-Barr virus latent membrane protein 1 TES2/CTAR2 gene regulation. PMID:21543491
NOA: a novel Network Ontology Analysis method. PMID:21543451
Properties of metabolic graphs: biological organization or representation artifacts? PMID:21542923
A central metabolic circuit controlled by QseC in pathogenic Escherichia coli. PMID:21542868
Proteomic analyses of nucleoid-associated proteins in Escherichia coli, Pseudomonas aeruginosa, Bacillus subtilis, and Staphylococcus aureus. PMID:21541338
Differential growth-related gene expression in abalone (Haliotis midae). PMID:21533523
Alternatively Spliced Genes as Biomarkers for Schizophrenia, Bipolar Disorder and Psychosis: A Blood-Based Spliceome-Profiling Exploratory Study. PMID:21532980
Hydrothermally generated aromatic compounds are consumed by bacteria colonizing in Atlantis II Deep of the Red Sea. PMID:21525946
Characterization of the genomic structure and function of regions influencing renin and angiogenesis in the SS rat. PMID:21521778
Human induced pluripotent stem cells derived under feeder-free conditions display unique cell cycle and DNA replication gene profiles. PMID:21506733
Gene expression patterns in four brain areas associate with quantitative measure of estrous behavior in dairy cows. PMID:21504592
Pulsed stable isotope labeling of amino acids in cell culture uncovers the dynamic interactions between HIV-1 and the monocyte-derived macrophage. PMID:21500866
PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic. PMID:21499864
Analysis of the human pancreatic stellate cell secreted proteome. PMID:21499210
SNP-based pathway enrichment analysis for genome-wide association studies. PMID:21496265
A qualitative and quantitative proteomic study of human microdialysate and the cutaneous response to injury. PMID:21494910
Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PMID:21494657
Prioritization and evaluation of depression candidate genes by combining multidimensional data resources. PMID:21494644
Role of complement cascade in abdominal aortic aneurysms. PMID:21493888
Incorporating biological pathways via a Markov random field model in genome-wide association studies. PMID:21490723
Genome-wide meta-analysis identifies regions on 7p21 (AHR) and 15q24 (CYP1A2) as determinants of habitual caffeine consumption. PMID:21490707
Gene set analysis of SNP data: benefits, challenges, and future directions. PMID:21487444
454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng. PMID:21484331
Consensus-phenotype integration of transcriptomic and metabolomic data implies a role for metabolism in the chemosensitivity of tumour cells. PMID:21483477
Statistical Test of Expression Pattern (STEPath): a new strategy to integrate gene expression data with genomic information in individual and meta-analysis studies. PMID:21481242
Effects of homologous phosphoenolpyruvate-carbohydrate phosphotransferase system proteins on carbohydrate uptake and poly(3-Hydroxybutyrate) accumulation in Ralstonia eutropha H16. PMID:21478317
Metabolic characterization of volume overload heart failure due to aorto-caval fistula in rats. PMID:21465236
Response to adverse conditions in two strains of the extremely halophilic species Salinibacter ruber. PMID:21461978
Histidine protects against zinc and nickel toxicity in Caenorhabditis elegans. PMID:21455490
A systems biology approach for the investigation of the heparin/heparan sulfate interactome. PMID:21454685
Sex hormones and gene expression signatures in peripheral blood from postmenopausal women - the NOWAC postgenome study. PMID:21453500
Stochastic variation of transcript abundance in C57BL/6J mice. PMID:21450099
A new approach to assess and predict the functional roles of proteins across all known structures. PMID:21445639
Complete genome sequence of the pathogenic bacterium Riemerella anatipestifer strain RA-GD. PMID:21441509
Metalloproteins and the pyrite-based origin of life: a critical assessment. PMID:21431891
Predicting protein phenotypes based on protein-protein interaction network. PMID:21423698
A topological map of the compartmentalized Arabidopsis thaliana leaf metabolome. PMID:21423574
Genome-wide analysis reveals gene expression and metabolic network dynamics during embryo development in Arabidopsis. PMID:21402797
Cranberry proanthocyanidins mediate growth arrest of lung cancer cells through modulation of gene expression and rapid induction of apoptosis. PMID:21399574
The expanded human disease network combining protein-protein interaction information. PMID:21386875
The microRNA cluster miR-106b~25 regulates adult neural stem/progenitor cell proliferation and neuronal differentiation. PMID:21386132
Genotype networks, innovation, and robustness in sulfur metabolism. PMID:21385333
Identification of potential Leptospira phosphoheptose isomerase inhibitors through virtual high-throughput screening. PMID:21382593
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
NAViGaTing the micronome--using multiple microRNA prediction databases to identify signalling pathway-associated microRNAs. PMID:21364759
Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis research. PMID:21360826
The wMelPop strain of Wolbachia interferes with dopamine levels in Aedes aegypti. PMID:21356077
Epistatic interaction maps relative to multiple metabolic phenotypes. PMID:21347328
Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG. PMID:21342551
Defining an informativeness metric for clustering gene expression data. PMID:21330289
Comparative transcriptional pathway bioinformatic analysis of dietary restriction, Sir2, p53 and resveratrol life span extension in Drosophila. PMID:21325893
Complete genome sequence of Mycoplasma haemofelis, a hemotropic mycoplasma. PMID:21317334
A comparative transcriptomic analysis of uveal melanoma and normal uveal melanocyte. PMID:21305041
Complete genome sequence of Archaeoglobus profundus type strain (AV18). PMID:21304717
New detection systems of bacteria using highly selective media designed by SMART: selective medium-design algorithm restricted by two constraints. PMID:21304596
De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum. PMID:21303537
Amplification of the 20q chromosomal arm occurs early in tumorigenic transformation and may initiate cancer. PMID:21297939
Differential gene expression in liver and small intestine from lactating rats compared to age-matched virgin controls detects increased mRNA of cholesterol biosynthetic genes. PMID:21291544
Essential metabolites of Mycobacterium tuberculosis and their mimics. PMID:21285434
Transcriptomics of the bed bug (Cimex lectularius). PMID:21283830
Is my network module preserved and reproducible? PMID:21283776
Transcriptomic signatures of ash (Fraxinus spp.) phloem. PMID:21283712
Gender-associated genes in filarial nematodes are important for reproduction and potential intervention targets. PMID:21283610
Aphid genome expression reveals host-symbiont cooperation in the production of amino acids. PMID:21282658
Dengue-2 structural proteins associate with human proteins to produce a coagulation and innate immune response biased interactome. PMID:21281507
Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. PMID:21281499
Genetic analysis of biological pathway data through genomic randomization. PMID:21279722
Modular analysis of the probabilistic genetic interaction network. PMID:21278184
Enzymatic deamination of the epigenetic base N-6-methyladenine. PMID:21275375
Systems-wide temporal proteomic profiling in glucose-starved Bacillus subtilis. PMID:21266987
Experimental selection of hypoxia-tolerant Drosophila melanogaster. PMID:21262834
Investigating the effect of paralogs on microarray gene-set analysis. PMID:21261946
Caries induced cytokine network in the odontoblast layer of human teeth. PMID:21261944
Uracil influences quorum sensing and biofilm formation in Pseudomonas aeruginosa and fluorouracil is an antagonist. PMID:21261882
Molecular and structural basis of ESCRT-III recruitment to membranes during archaeal cell division. PMID:21255729
Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma. PMID:21253009
ePlant and the 3D data display initiative: integrative systems biology on the world wide web. PMID:21249219
Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PMID:21249183
Analysis of positional candidate genes in the AAA1 susceptibility locus for abdominal aortic aneurysms on chromosome 19. PMID:21247474
Catalytic mechanism and three-dimensional structure of adenine deaminase. PMID:21247091
Nicotiana tabacum overexpressing γ-ECS exhibits biotic stress tolerance likely through NPR1-dependent salicylic acid-mediated pathway. PMID:21234598
Increased mRNA Levels of TCF7L2 and MYC of the Wnt Pathway in Tg-ArcSwe Mice and Alzheimer's Disease Brain. PMID:21234373
A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation. PMID:21232107
Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. PMID:21226959
Metabolic fate of fumarate, a side product of the purine salvage pathway in the intraerythrocytic stages of Plasmodium falciparum. PMID:21209090
Concerted changes in gene expression and cell physiology of the cyanobacterium Synechocystis sp. strain PCC 6803 during transitions between nitrogen and light-limited growth. PMID:21205618
The annotation of the asparagine N-linked glycosylation pathway in the Reactome database. PMID:21199820
Adaptation of cells to new environments. PMID:21197660
Principal network analysis: identification of subnetworks representing major dynamics using gene expression data. PMID:21193522
A systems biological approach to identify key transcription factors and their genomic neighborhoods in human sarcomas. PMID:21192842
The annotation and the usage of scientific databases could be improved with public issue tracker software. PMID:21186182
De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweet potato (Ipomoea batatas). PMID:21182800
The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications. PMID:21179244
Checks and balances: the ocular response to infection. PMID:21178447
mESAdb: microRNA expression and sequence analysis database. PMID:21177657
From RNA-seq reads to differential expression results. PMID:21176179
Phenocopy--a strategy to qualify chemical compounds during hit-to-lead and/or lead optimization. PMID:21170314
Rapid evolutionary innovation during an Archaean genetic expansion. PMID:21170026
Transcriptomic analysis of cell-free fetal RNA suggests a specific molecular phenotype in trisomy 18. PMID:21152935
Homocysteine suppresses the expression of the collagen cross-linker lysyl oxidase involving IL-6, Fli1, and epigenetic DNA methylation. PMID:21148317
Global gene expression profiling of a population exposed to a range of benzene levels. PMID:21147609
POVME: an algorithm for measuring binding-pocket volumes. PMID:21147010
Extending pathways and processes using molecular interaction networks to analyse cancer genome data. PMID:21144022
PETALS: Proteomic Evaluation and Topological Analysis of a mutated Locus' Signaling. PMID:21144021
Integrative analysis of cancer pathway progression and coherence. PMID:21136972
GOAPhAR: An Integrative Discovery Tool for Annotation, Pathway Analysis. PMID:21132056
Simultaneous genome-wide inference of physical, genetic, regulatory, and functional pathway components. PMID:21124865
Mining functionally relevant gene sets for analyzing physiologically novel clinical expression data. PMID:21121032
Theoretical and experimental characterization of the scope of protein O-glycosylation in Bacteroides fragilis. PMID:21115495
Software that goes with the flow in systems biology. PMID:21114874
Discovering pathways by orienting edges in protein interaction networks. PMID:21109539
Skeletal muscle gene expression in response to resistance exercise: sex specific regulation. PMID:21106073
Database resources of the National Center for Biotechnology Information. PMID:21097890
Extending CATH: increasing coverage of the protein structure universe and linking structure with function. PMID:21097779
In silico gene expression analysis in Codonopsis lanceolata root. PMID:21088900
Analysing biological pathways in genome-wide association studies. PMID:21085203
Sequencing, de novo annotation and analysis of the first Anguilla anguilla transcriptome: EeelBase opens new perspectives for the study of the critically endangered European eel. PMID:21080939
Analysis of protein pathway networks using hybrid properties. PMID:21076385
Patterns of human gene expression variance show strong associations with signaling network hierarchy. PMID:21073694
MicroRNA profile indicates downregulation of the TGFβ pathway in sporadic non-functioning pituitary adenomas. PMID:21063788
A genome-wide association scan on estrogen receptor-negative breast cancer. PMID:21062454
Tissue-specific transcriptomics of the exotic invasive insect pest emerald ash borer (Agrilus planipennis). PMID:21060843
MicroRNA-221/222 confers breast cancer fulvestrant resistance by regulating multiple signaling pathways. PMID:21057537
P2CS: a database of prokaryotic two-component systems. PMID:21051349
Integrative systems biology for data-driven knowledge discovery. PMID:21044756
Parameter balancing in kinetic models of cell metabolism. PMID:21038890
starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data. PMID:21037263
Uncovering genes and regulatory pathways related to urinary albumin excretion. PMID:21030601
Literature-based discovery of diabetes- and ROS-related targets. PMID:20979611
The vascular cambium: molecular control of cellular structure. PMID:20978810
DEGAS: de novo discovery of dysregulated pathways in human diseases. PMID:20976054
Generalized random set framework for functional enrichment analysis using primary genomics datasets. PMID:20971985
PubChem as a public resource for drug discovery. PMID:20970519
Metabolomics and malaria biology. PMID:20970461
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways. PMID:20964848
Chronic high-fat diet in fathers programs β-cell dysfunction in female rat offspring. PMID:20962845
Human functional genetic studies are biased against the medically most relevant primate-specific genes. PMID:20961448
Evidence of aberrant lipid metabolism in hepatitis C and hepatocellular carcinoma. PMID:20961371
Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis. PMID:20959420
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. PMID:20959003
Dynamics of protein damage in yeast frataxin mutant exposed to oxidative stress. PMID:20958246
Temporal gene expression profiling during rat femoral marrow ablation-induced intramembranous bone regeneration. PMID:20957030
Critical reasoning on causal inference in genome-wide linkage and association studies. PMID:20951462
Time lagged information theoretic approaches to the reverse engineering of gene regulatory networks. PMID:20946602
Next generation models for storage and representation of microbial biological annotation. PMID:20946598
Discovering gene functional relationships using FAUN (Feature Annotation Using Nonnegative matrix factorization). PMID:20946597
Mitogen-activated protein kinase-activated protein kinase 2 (MK2) contributes to secondary damage after spinal cord injury. PMID:20943915
Gene regulatory network reveals oxidative stress as the underlying molecular mechanism of type 2 diabetes and hypertension. PMID:20942928
Genome-wide expression patterns in physiological cardiac hypertrophy. PMID:20937113
Multi-species integrative biclustering. PMID:20920250
Gene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana. PMID:20890965
A QUICK screen for Lrrk2 interaction partners--leucine-rich repeat kinase 2 is involved in actin cytoskeleton dynamics. PMID:20876399
ATHENA: A knowledge-based hybrid backpropagation-grammatical evolution neural network algorithm for discovering epistasis among quantitative trait Loci. PMID:20875103
Gene set enrichment; a problem of pathways. PMID:20861160
Molecular phylogeny and functional genomics of beta-galactoside alpha2,6-sialyltransferases that explain ubiquitous expression of st6gal1 gene in amniotes. PMID:20855889
Data-driven assessment of eQTL mapping methods. PMID:20849587
Transferase activity function and system development process are critical in cattle embryo development. PMID:20844914
Global transcriptional profiles of beating clusters derived from human induced pluripotent stem cells and embryonic stem cells are highly similar. PMID:20843318
Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function. PMID:20838587
In silico models of cancer. PMID:20836040
Computational modeling of mammalian signaling networks. PMID:20836022
Auxin carriers localization drives auxin accumulation in plant cells infected by Frankia in Casuarina glauca actinorhizal nodules. PMID:20826704
Functional genome annotation by combined analysis across microarray studies of Trypanosoma brucei. PMID:20824174
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Emergent cooperation in microbial metabolism. PMID:20823845
Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. PMID:20823844
Transcript analysis of stem cells. PMID:20816160
Characterizing the metabolism of Dehalococcoides with a constraint-based model. PMID:20811585
Enhancing interdisciplinary mathematics and biology education: a microarray data analysis course bridging these disciplines. PMID:20810954
Circadian control of global gene expression patterns. PMID:20809800
Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PMID:20808879
High-throughput generation, optimization and analysis of genome-scale metabolic models. PMID:20802497
*omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants. PMID:20796314
In situ dynamics of O2, pH and cyanobacterial transcripts associated with CCM, photosynthesis and detoxification of ROS. PMID:20740024
Structured digital tables on the Semantic Web: toward a structured digital literature. PMID:20739925
Integration of metabolic reactions and gene regulation. PMID:20737299
Characterization of macaque pulmonary fluid proteome during monkeypox infection: dynamics of host response. PMID:20736407
Analysis of the signaling pathways regulating Src-dependent remodeling of the actin cytoskeleton. PMID:20719402
Multi-targeted priming for genome-wide gene expression assays. PMID:20716356
Distinct choline metabolic profiles are associated with differences in gene expression for basal-like and luminal-like breast cancer xenograft models. PMID:20716336
Survival associated pathway identification with group Lp penalized global AUC maximization. PMID:20712896
A comparative analysis of extra-embryonic endoderm cell lines. PMID:20711519
A genome-wide gene function prediction resource for Drosophila melanogaster. PMID:20711346
Ranked retrieval of Computational Biology models. PMID:20701772
Mass spectrometry-based metabolomics, analysis of metabolite-protein interactions, and imaging. PMID:20701590
Spliced leader trapping reveals widespread alternative splicing patterns in the highly dynamic transcriptome of Trypanosoma brucei. PMID:20700444
Evolution of an adenocarcinoma in response to selection by targeted kinase inhibitors. PMID:20696054
The glycobiome of the rumen bacterium Butyrivibrio proteoclasticus B316(T) highlights adaptation to a polysaccharide-rich environment. PMID:20689770
Monitoring the Effect of Docetaxel Treatment in MCF7 Xenografts Using Multimodal In Vivo and Ex Vivo Magnetic Resonance Methods, Histopathology, and Gene Expression. PMID:20689767
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Co-expressed immune and metabolic genes in visceral and subcutaneous adipose tissue from severely obese individuals are associated with plasma HDL and glucose levels: a microarray study. PMID:20687939
Patterns of HIV-1 protein interaction identify perturbed host-cellular subsystems. PMID:20686668
The CoFactor database: organic cofactors in enzyme catalysis. PMID:20679331
Comprehensive transcriptome analysis of mouse embryonic stem cell adipogenesis unravels new processes of adipocyte development. PMID:20678241
Recombinant avian leukosis viruses of subgroup J isolated from field infected commercial layer chickens with hemangioma and myeloid leukosis possess an insertion in the E element. PMID:20676760
Functional analysis of multiple genomic signatures demonstrates that classification algorithms choose phenotype-related genes. PMID:20676069
Comparative Membranome expression analysis in primary tumors and derived cell lines. PMID:20668533
Publishing Chinese medicine knowledge as Linked Data on the Web. PMID:20663193
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. PMID:20663121
The Trypanosoma brucei MitoCarta and its regulation and splicing pattern during development. PMID:20660476
MicroRNAs control intestinal epithelial differentiation, architecture, and barrier function. PMID:20659473
Statistical methods for integrating multiple types of high-throughput data. PMID:20652519
MZmine 2: modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data. PMID:20650010
Metagenomics: Facts and Artifacts, and Computational Challenges*. PMID:20648230
DNA repair and recombination in higher plants: insights from comparative genomics of Arabidopsis and rice. PMID:20646326
Integration and visualization of systems biology data in context of the genome. PMID:20642854
Gene expression analysis of forskolin treated basilar papillae identifies microRNA181a as a mediator of proliferation. PMID:20634979
Optimal network alignment with graphlet degree vectors. PMID:20628593
MicroRNA 320a functions as a novel endogenous modulator of aquaporins 1 and 4 as well as a potential therapeutic target in cerebral ischemia. PMID:20628061
Elevation of sulfatides in ovarian cancer: an integrated transcriptomic and lipidomic analysis including tissue-imaging mass spectrometry. PMID:20624317
Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq. PMID:20617162
The metabolic network of Synechocystis sp. PCC 6803: systemic properties of autotrophic growth. PMID:20616194
Combining next-generation sequencing strategies for rapid molecular resource development from an invasive aphid species, Aphis glycines. PMID:20614011
High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. PMID:20610602
Genomic similarity and kernel methods II: methods for genomic information. PMID:20606458
Fragile regions and not functional constraints predominate in shaping gene organization in the genus Drosophila. PMID:20601587
Multiple ontologies in action: composite annotations for biosimulation models. PMID:20601121
Systematizing the generation of missing metabolic knowledge. PMID:20589842
Mining metabolic pathways through gene expression. PMID:20587705
Pathway analysis comparison using Crohn's disease genome wide association studies. PMID:20584322
Identifying differentially regulated subnetworks from phosphoproteomic data. PMID:20584295
Tracking the transcriptional host response from the acute to the regenerative phase of experimental pneumococcal meningitis. PMID:20565785
Powerful SNP-set analysis for case-control genome-wide association studies. PMID:20560208
Environmental and genetic factors that contribute to Escherichia coli K-12 biofilm formation. PMID:20559621
Neuronal microRNA deregulation in response to Alzheimer's disease amyloid-beta. PMID:20552018
Protein interaction network topology uncovers melanogenesis regulatory network components within functional genomics datasets. PMID:20550706
Proteome-wide profiling of the MCF10AT breast cancer progression model. PMID:20543960
Automated identification of pathways from quantitative genetic interaction data. PMID:20531408
Computational tools for the interactive exploration of proteomic and structural data. PMID:20525940
A novel gene network inference algorithm using predictive minimum description length approach. PMID:20522257
A genome-wide map of human genetic interactions inferred from radiation hybrid genotypes. PMID:20508145
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. PMID:20507895
An information-flow-based model with dissipation, saturation and direction for active pathway inference. PMID:20504374
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. PMID:20500821
Genes encoding hub and bottleneck enzymes of the Arabidopsis metabolic network preferentially retain homeologs through whole genome duplication. PMID:20478072
The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways. PMID:20478018
Identification and characterization of microRNAs and their targets in the bioenergy plant switchgrass (Panicum virgatum). PMID:20461402
Metabolic pathway relationships revealed by an integrative analysis of the transcriptional and metabolic temperature stress-response dynamics in yeast. PMID:20455750
A Large-scale genetic association study of esophageal adenocarcinoma risk. PMID:20453000
Dealing with the unknown: metabolomics and metabolite atlases. PMID:20452782
Dynamics and control of the central carbon metabolism in hepatoma cells. PMID:20426867
Loss of lipid synthesis as an evolutionary consequence of a parasitic lifestyle. PMID:20421492
Adaptive evolution of energy metabolism genes and the origin of flight in bats. PMID:20421465
Comprehensive mapping of the human kinome to epidermal growth factor receptor signaling. PMID:20421302
Global transcriptome analysis of spore formation in Myxococcus xanthus reveals a locus necessary for cell differentiation. PMID:20420673
Comparative transcriptomic and proteomic profiling of industrial wine yeast strains. PMID:20418425
De novo sequencing and analysis of the American ginseng root transcriptome using a GS FLX Titanium platform to discover putative genes involved in ginsenoside biosynthesis. PMID:20416102
Flanking region sequence information to refine microRNA target predictions. PMID:20413915
Design and analysis of synthetic carbon fixation pathways. PMID:20410460
Meta-analysis for pathway enrichment analysis when combining multiple genomic studies. PMID:20410053
OptFlux: an open-source software platform for in silico metabolic engineering. PMID:20403172
Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. PMID:20398412
Increased expression of angiogenic genes in the brains of mouse meg3-null embryos. PMID:20392836
Genome-wide dissection of microRNA functions and cotargeting networks using gene set signatures. PMID:20385095
PRPS1 mutations: four distinct syndromes and potential treatment. PMID:20380929
Whole transcriptome analysis of the hippocampus: toward a molecular portrait of epileptogenesis. PMID:20377889
Growth delay of human bladder cancer cells by Prostate Stem Cell Antigen downregulation is associated with activation of immune signaling pathways. PMID:20374648
Differential transcript expression between the microfilariae of the filarial nematodes, Brugia malayi and B. pahangi. PMID:20370932
Coupled amino acid deamidase-transport systems essential for Helicobacter pylori colonization. PMID:20368342
Metabolic switching of human myotubes is improved by n-3 fatty acids. PMID:20363834
Mutation@A Glance: an integrative web application for analysing mutations from human genetic diseases. PMID:20360267
Mining connections between chemicals, proteins, and diseases extracted from Medline annotations. PMID:20348023
Integrating pathway analysis and genetics of gene expression for genome-wide association studies. PMID:20346437
Prediction of novel synthetic pathways for the production of desired chemicals. PMID:20346180
TimeDelay-ARACNE: Reverse engineering of gene networks from time-course data by an information theoretic approach. PMID:20338053
Reciprocal regulation of metabolic and signaling pathways. PMID:20334672
Network-based empirical Bayes methods for linear models with applications to genomic data. PMID:20309755
Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. PMID:20307315
Genotype networks in metabolic reaction spaces. PMID:20302636
Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence. PMID:20300646
Deciphering normal blood gene expression variation--The NOWAC postgenome study. PMID:20300640
Gene regulatory networks modelling using a dynamic evolutionary hybrid. PMID:20298548
Topological network alignment uncovers biological function and phylogeny. PMID:20236959
Genetic and functional analysis of the soluble oxaloacetate decarboxylase from Corynebacterium glutamicum. PMID:20233922
The embryonic genes Dkk3, Hoxd8, Hoxd9 and Tbx1 identify muscle types in a diet-independent and fiber-type unrelated way. PMID:20230627
Methods for optimizing statistical analyses in pharmacogenomics research. PMID:20221410
Homozygous deletion mapping in myeloma samples identifies genes and an expression signature relevant to pathogenesis and outcome. PMID:20215539
High-fat diet leads to tissue-specific changes reflecting risk factors for diseases in DBA/2J mice. PMID:20215417
Genomics and bioinformatics resources for crop improvement. PMID:20208064
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The DIANA-mirExTra web server: from gene expression data to microRNA function. PMID:20161787
Genomic approaches in the identification of hypoxia biomarkers in model fish species. PMID:20161383
Feedback between p21 and reactive oxygen production is necessary for cell senescence. PMID:20160708
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Differential gene expression in the developing human macula: microarray analysis using rare tissue samples. PMID:20157359
Cellular processes of v-Src transformation revealed by gene profiling of primary cells--implications for human cancer. PMID:20152043
Systems metabolic engineering: genome-scale models and beyond. PMID:20151446
A metabolic signature of long life in Caenorhabditis elegans. PMID:20146810
Simulation of a Petri net-based model of the terpenoid biosynthesis pathway. PMID:20144236
Genomic and evolutionary comparisons of diazotrophic and pathogenic bacteria of the order Rhizobiales. PMID:20144182
Global regulation of food supply by Pseudomonas putida DOT-T1E. PMID:20139187
Expander: from expression microarrays to networks and functions. PMID:20134430
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Comparison of PGH2 binding site in prostaglandin synthases. PMID:20122226
Detection of characteristic sub pathway network for angiogenesis based on the comprehensive pathway network. PMID:20122205
Simulating plant metabolic pathways with enzyme-kinetic models. PMID:20118273
A critical role for ceramide synthase 2 in liver homeostasis: II. insights into molecular changes leading to hepatopathy. PMID:20110366
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Oncogenes and pathway identification using filter-based approaches between various carcinoma types in lung. PMID:20090162
Modulation of hepatic PPAR expression during Ft LVS LPS-induced protection from Francisella tularensis LVS infection. PMID:20082697
Temperature increase prevails over acidification in gene expression modulation of amastigote differentiation in Leishmania infantum. PMID:20074347
A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI). PMID:20071747
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Network-free inference of knockout effects in yeast. PMID:20066032
Deciphering chemotaxis pathways using cross species comparisons. PMID:20064255
Toward the dynamic interactome: it's about time. PMID:20061351
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Next generation transcriptomes for next generation genomes using est2assembly. PMID:20034392
The filamentous fungal gene expression database (FFGED). PMID:20025988
Gene expression relationship between prostate cancer cells of Gleason 3, 4 and normal epithelial cells as revealed by cell type-specific transcriptomes. PMID:20021671
Evolutionary plasticity and innovations in complex metabolic reaction networks. PMID:20019795
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Francisella tularensis T-cell antigen identification using humanized HLA-DR4 transgenic mice. PMID:20016043
Gene, region and pathway level analyses in whole-genome studies. PMID:20013942
Human cancer protein-protein interaction network: a structural perspective. PMID:20011507
Proteome bioprofiles distinguish between M1 priming and activation states in human macrophages. PMID:20007246
Transcriptional profiling of trait deterioration in the insect pathogenic nematode Heterorhabditis bacteriophora. PMID:20003534
Effective identification of conserved pathways in biological networks using hidden Markov models. PMID:19997609
Network-based Identification of novel cancer genes. PMID:19959820
A multi-factor model for caspase degradome prediction. PMID:19958504
PutidaNET: interactome database service and network analysis of Pseudomonas putida KT2440. PMID:19958481
High-throughput behavioral phenotyping in the expanded panel of BXD recombinant inbred strains. PMID:19958391
A genome-wide survey for host response of silkworm, Bombyx mori during pathogen Bacillus bombyseptieus infection. PMID:19956592
Proteome of Salmonella Enterica Serotype Typhimurium Grown in a Low Mg/pH Medium. PMID:19953200
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The use of neuroproteomics in drug abuse research. PMID:19926406
Protosappanin A induces immunosuppression of rats heart transplantation targeting T cells in grafts via NF-kappaB pathway. PMID:19924402
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Database resources of the National Center for Biotechnology Information. PMID:19910364
Diet-induced gene expression of isolated pancreatic islets from a polygenic mouse model of the metabolic syndrome. PMID:19902174
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Localized plasticity in the streamlined genomes of vinyl chloride respiring Dehalococcoides. PMID:19893622
Phenopedia and Genopedia: disease-centered and gene-centered views of the evolving knowledge of human genetic associations. PMID:19864262
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XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
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Brugia malayi gene expression in response to the targeting of the Wolbachia endosymbiont by tetracycline treatment. PMID:19806204
Recombination and insertion events involving the botulinum neurotoxin complex genes in Clostridium botulinum types A, B, E and F and Clostridium butyricum type E strains. PMID:19804621
Prediction of candidate primary immunodeficiency disease genes using a support vector machine learning approach. PMID:19801557
An editor for pathway drawing and data visualization in the Biopathways Workbench. PMID:19799790
Coexpression network based on natural variation in human gene expression reveals gene interactions and functions. PMID:19797678
Functionally guided alignment of protein interaction networks for module detection. PMID:19797409
The pathogenic properties of a novel and conserved gene product, KerV, in proteobacteria. PMID:19779606
Robust extraction of functional signals from gene set analysis using a generalized threshold free scoring function. PMID:19775443
Differential secreted proteome approach in murine model for candidate biomarker discovery in colon cancer. PMID:19769411
A novel regulatory protein involved in motility of Vibrio cholerae. PMID:19767434
Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses. PMID:19761607
Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function. PMID:19758432
Molecular cloning, sequencing, and expression analysis of presenilin cDNA from Schistosoma mansoni. PMID:19756746
Systemic delivery of synthetic microRNA-16 inhibits the growth of metastatic prostate tumors via downregulation of multiple cell-cycle genes. PMID:19738602
Context-driven discovery of gene cassettes in mobile integrons using a computational grammar. PMID:19735578
Identity of the growth-limiting nutrient strongly affects storage carbohydrate accumulation in anaerobic chemostat cultures of Saccharomyces cerevisiae. PMID:19734328
Ontological Discovery Environment: a system for integrating gene-phenotype associations. PMID:19733230
Comparison of structure-based and threading-based approaches to protein functional annotation. PMID:19731377
The FunGenES database: a genomics resource for mouse embryonic stem cell differentiation. PMID:19727443
Computational reasoning across multiple models. PMID:19717801
Streptococcus pneumoniae nasopharyngeal colonization induces type I interferons and interferon-induced gene expression. PMID:19712482
Metabolite and reaction inference based on enzyme specificities. PMID:19696044
Statistical methods for gene set co-expression analysis. PMID:19689953
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Cell cycle control at the first restriction point and its effect on tissue growth. PMID:19685243
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Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data. PMID:19661283
Systems biology approach to identification of biomarkers for metastatic progression in gastric cancer. PMID:19649653
Mining biological pathways using WikiPathways web services. PMID:19649250
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Local network topology in human protein interaction data predicts functional association. PMID:19641626
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Host sequence motifs shared by HIV predict response to antiretroviral therapy. PMID:19627600
Systems-level cancer gene identification from protein interaction network topology applied to melanogenesis-related functional genomics data. PMID:19625303
Missing in action: enzyme functional annotations in biological databases. PMID:19620987
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Methods for interpreting lists of affected genes obtained in a DNA microarray experiment. PMID:19615118
Shotgun proteomics in neuroscience. PMID:19607789
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Porcine muscle sensory attributes associate with major changes in gene networks involving CAPZB, ANKRD1, and CTBP2. PMID:19597856
Cytotoxic effect of recombinant Mycobacterium tuberculosis CFP-10/ESAT-6 protein on the crucial pathways of WI-38 cells. PMID:19584916
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Clique-based data mining for related genes in a biomedical database. PMID:19566964
Error control variability in pathway-based microarray analysis. PMID:19561020
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Transcriptomes and pathways associated with infectivity, survival and immunogenicity in Brugia malayi L3. PMID:19527522
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PSI-2: structural genomics to cover protein domain family space. PMID:19523904
Directed mammalian gene regulatory networks using expression and comparative genomic hybridization microarray data from radiation hybrids. PMID:19521529
Proteome-wide prediction of signal flow direction in protein interaction networks based on interacting domains. PMID:19502588
Coastal strains of marine Synechococcus species exhibit increased tolerance to copper shock and a distinctive transcriptional response relative to those of open-ocean strains. PMID:19502430
Metabolic-network-driven analysis of bacterial ecological strategies. PMID:19500338
Response and recovery in the plasma metabolome tracks the acute LCMV-induced immune response. PMID:19496611
Quantifying biogenic bias in screening libraries. PMID:19483698
Toolbox model of evolution of prokaryotic metabolic networks and their regulation. PMID:19482938
The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. PMID:19480664
Involvement of serine proteases in the excystation and metacystic development of Entamoeba invadens. PMID:19479279
IsoRankN: spectral methods for global alignment of multiple protein networks. PMID:19477996
Network-based prediction of metabolic enzymes' subcellular localization. PMID:19477995
Domain-oriented edge-based alignment of protein interaction networks. PMID:19477994
Fewer permutations, more accurate P-values. PMID:19477983
Probabilistic retrieval and visualization of biologically relevant microarray experiments. PMID:19477980
Mitochondrial proteomics on human fibroblasts for identification of metabolic imbalance and cellular stress. PMID:19476632
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways. PMID:19474337
Functional genomic analysis of amniotic fluid cell-free mRNA suggests that oxidative stress is significant in Down syndrome fetuses. PMID:19474297
Immunological profiles of Bos taurus and Bos indicus cattle infested with the cattle tick, Rhipicephalus (Boophilus) microplus. PMID:19474263
Integrative analysis of gene expression data including an assessment of pathway enrichment for predicting prostate cancer. PMID:19458772
Databases and QSAR for cancer research. PMID:19458762
Antioxidants used by Deinococcus radiodurans and implications for antioxidant drug discovery. PMID:19444250
Metatranscriptomics reveals unique microbial small RNAs in the ocean's water column. PMID:19444216
Inferring novel disease indications for known drugs by semantically linking drug action and disease mechanism relationships. PMID:19426461
Database resources in metabolomics: an overview. PMID:19418229
Owner controlled data exchange in nutrigenomic collaborations: the NuGO information network. PMID:19408032
Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription. PMID:19406940
DIANA-microT web server: elucidating microRNA functions through target prediction. PMID:19406924
Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PMID:19402753
FMM: a web server for metabolic pathway reconstruction and comparative analysis. PMID:19401437
Microarray and bioinformatics analysis of gene expression in experimental membranous nephropathy. PMID:19390219
A general map of iron metabolism and tissue-specific subnetworks. PMID:19381358
SysPTM: a systematic resource for proteomic research on post-translational modifications. PMID:19366988
The W, X, Y and Z of sex-chromosome dosage compensation. PMID:19359064
Evaluation of genome-wide association study results through development of ontology fingerprints. PMID:19349285
The transcriptomes of the cattle parasitic nematode Ostertagia ostartagi. PMID:19346077
Genome-wide functional divergence after the symbiosis of proteobacteria with insects unraveled through a novel computational approach. PMID:19343224
Network-based multiple locus linkage analysis of expression traits. PMID:19336446
KEGG for integration and interpretation of large-scale molecular data sets PubMed citations: 2143.

2143 articles citing: KEGG for integration and interpretation of large-scale molecular data sets

Epigenetically silenced apoptosis-associated tyrosine kinase (AATK) facilitates a decreased expression of Cyclin D1 and WEE1, phosphorylates TP53 and reduces cell proliferation in a kinase-dependent manner. PMID:35902728
Analysis of Alternative mRNA Splicing in Vemurafenib-Resistant Melanoma Cells. PMID:35883549
Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. PMID:35818398
Supplementation of xylo-oligosaccharides to suckling piglets promotes the growth of fiber-degrading gut bacterial populations during the lactation and nursery periods. PMID:35804098
SperoPredictor: An Integrated Machine Learning and Molecular Docking-Based Drug Repurposing Framework With Use Case of COVID-19. PMID:35784208
Clioquinol as an inhibitor of JmjC-histone demethylase exhibits common and unique histone methylome and transcriptome between clioquinol and hypoxia. PMID:35754713
Full-Length Transcriptome Sequencing Analysis of Differentially Expressed Genes and Pathways After Treatment of Psoriasis With Oxymatrine. PMID:35721124
Identification of an Endoplasmic Reticulum Stress-Related Gene Signature to Evaluate the Immune Status and Predict the Prognosis of Hepatocellular Carcinoma. PMID:35711939
Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants. PMID:35695455
Species- and site-specific circulating bacterial DNA in Subantarctic sentinel mussels Aulacomya atra and Mytilus platensis. PMID:35681072
Physiological and biochemical characterization and genome analysis of Rhodococcus qingshengii strain 7B capable of crude oil degradation and plant stimulation. PMID:35665370
Evansella halocellulosilytica sp. nov., an alkali-halotolerant and cellulose-dissolving bacterium isolated from bauxite residue. PMID:35661272
Synergy of Dietary Quercetin and Vitamin E Improves Cecal Microbiota and Its Metabolite Profile in Aged Breeder Hens. PMID:35656004
Fasciola hepatica Gastrodermal Cells Selectively Release Extracellular Vesicles via a Novel Atypical Secretory Mechanism. PMID:35628335
Distinct structural groups of histone H3 and H4 residues have divergent effects on chronological lifespan in Saccharomyces cerevisiae. PMID:35622816
Single-molecule long-read sequencing analysis improves genome annotation and sheds new light on the transcripts and splice isoforms of Zoysia japonica. PMID:35614434
Biotechnological Combination for Co-contaminated Soil Remediation: Focus on Tripartite "Meta-Enzymatic" Activity. PMID:35599908
Comparative Metabolomics Analysis Reveals the Taste Variations among Three Selected Wampee Cultivars. PMID:35583707
DPYSL2 interacts with JAK1 to mediate breast cancer cell migration. PMID:35575798
METTL3 Is Associated With the Malignancy of Esophageal Squamous Cell Carcinoma and Serves as a Potential Immunotherapy Biomarker. PMID:35574315
Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Nicotiana tabacum L.). PMID:35574122
Dietary ε-Polylysine Affects on Gut Microbiota and Plasma Metabolites Profiling in Mice. PMID:35571901
Adaptation of gut microbiome and host metabolic systems to lignocellulosic degradation in bamboo rats. PMID:35568757
Driver gene detection through Bayesian network integration of mutation and expression profiles. PMID:35561191
RNA methylation-mediated LINC01559 suppresses colorectal cancer progression by regulating the miR-106b-5p/PTEN axis. PMID:35541914
Non-canonical Wnt signaling participates in Jagged1-induced osteo/odontogenic differentiation in human dental pulp stem cells. PMID:35534526
Selection Signature Analyses Revealed Genes Associated With Adaptation, Production, and Reproduction in Selected Goat Breeds in Kenya. PMID:35528543
Analysis of bacterial and fungal communities in fermented fish (pla-ra) from Northeast Thailand. PMID:35524014
A Bayesian network structure learning approach to identify genes associated with stress in spleens of chickens. PMID:35523843
Multi-staged gene expression profiling reveals potential genes and the critical pathways in kidney cancer. PMID:35508649
Identification and verification of key taste components in wampee using widely targeted metabolomics. PMID:35499032
Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida. PMID:35486731
The clinical value of miRNA-21 in cervical cancer: A comprehensive investigation based on microarray datasets. PMID:35486636
Protein N-glycosylation aberrations and glycoproteomic network alterations in osteoarthritis and osteoarthritis with type 2 diabetes. PMID:35484284
The genome of hibiscus hamabo reveals its adaptation to saline and waterlogged habitat. PMID:35480957
Global Gene Expression and Docking Profiling of COVID-19 Infection. PMID:35480316
Transcriptional Regulation of Reproductive Diapause in the Convergent Lady Beetle, Hippodamia convergens. PMID:35447785
The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass. PMID:35435140
Acupuncture Effect Assessment in APP/PS1 Transgenic Mice: On Regulating Learning-Memory Abilities, Gut Microbiota, and Microbial Metabolites. PMID:35432583
Analysis on quality differences associated with metabolomics of rambutan during different temperature storage. PMID:35415667
A genome-wide screen for variants influencing certolizumab pegol response in a moderate to severe rheumatoid arthritis population. PMID:35413058
Label-Free LC-MS/MS Analysis Reveals Different Proteomic Profiles between Egg Yolks of Silky Fowl and Ordinary Chickens. PMID:35407122
Comparative Metabolomics Study of Chaenomeles speciosa (Sweet) Nakai from Different Geographical Regions. PMID:35407106
The chromosome-level genome assembly of Gentiana dahurica (Gentianaceae) provides insights into gentiopicroside biosynthesis. PMID:35380665
Oviducal gland transcriptomics of Octopus maya through physiological stages and the negative effects of temperature on fertilization. PMID:35378931
Host Immunity Influences the Composition of Murine Gut Microbiota. PMID:35371073
Characterization of polyhydroxyalkanoate production capacity, composition and weight synthesized by Burkholderia cepacia JC-1 from various carbon sources. PMID:35368536
Proteome profiling reveals changes in energy metabolism, transport and antioxidation during drought stress in Nostoc flagelliforme. PMID:35365086
A Method of Optimizing Weight Allocation in Data Integration Based on Q-Learning for Drug-Target Interaction Prediction. PMID:35356288
Integrated transcriptomic and proteomic analyses for the characterization of parathyroid oxyphil cells in uremic patients. PMID:35348903
Genome-wide Analysis Reflects Novel 5-Hydroxymethylcytosines Implicated in Diabetic Nephropathy and the Biomarker Potential. PMID:35342902
Identification of differentially expressed genes and signaling pathways with Candida infection by bioinformatics analysis. PMID:35314002
Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia. PMID:35295737
Integrated Bioinformatics Analysis and Validation of the Prognostic Value of RBM10 Expression in Hepatocellular Carcinoma. PMID:35283645
Altered Gut Microbiome and Fecal Immune Phenotype in Early Preterm Infants With Leaky Gut. PMID:35280991
Exploring genetic variation among Jordanian Solanum lycopersicon L. landraces and their performance under salt stress using SSR markers. PMID:35275332
Effects of Dietary Astragalus Polysaccharide Supplementation on the Th17/Treg Balance and the Gut Microbiota of Broiler Chickens Challenged With Necrotic Enteritis. PMID:35265068
Necroptosis-driving genes RIPK1, RIPK3 and MLKL-p are associated with intratumoral CD3+ and CD8+ T cell density and predict prognosis in hepatocellular carcinoma. PMID:35264437
Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule. PMID:35241789
Investigation of miR-21-5p Key Target Genes and Pathways in Head and Neck Squamous Cell Carcinoma Based on TCGA Database and Bioinformatics Analysis. PMID:35235474
Pathway Analysis for Cancer Research and Precision Oncology Applications. PMID:35230687
Low-Cost Algorithms for Metabolic Pathway Pairwise Comparison. PMID:35225919
Identification of Hub Genes in Pancreatic Ductal Adenocarcinoma Using Bioinformatics Analysis. PMID:35223598
Identifying individualized risk subpathways reveals pan-cancer molecular classification based on multi-omics data. PMID:35222843
Glutamine-dependent signaling controls pluripotent stem cell fate. PMID:35216682
Quorum Sensing Controls the CRISPR and Type VI Secretion Systems in Aliivibrio wodanis 06/09/139. PMID:35211539
Haplotype-Resolved Genome Analyses Reveal Genetically Distinct Nuclei within a Commercial Cultivar of Lentinula edodes. PMID:35205921
Molecular Details of Actinomycin D-Treated MRSA Revealed via High-Dimensional Data. PMID:35200643
Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium. PMID:35190553
Proteome-defined changes in cellular pathways for decidua and trophoblast tissues associated with location and viability of early-stage pregnancy. PMID:35189928
Genome assembly of the JD17 soybean provides a new reference genome for comparative genomics. PMID:35188189
De Novo Transcriptome of Mammillaria bombycina (Cactaceae) under In Vitro Conditions and Identification of Glyoxalase Genes. PMID:35161380
T-SIGn tumor reengineering therapy and CAR T cells synergize in combination therapy to clear human lung tumor xenografts and lung metastases in NSG mice. PMID:35154906
Physiological and Multi-Omics Approaches for Explaining Drought Stress Tolerance and Supporting Sustainable Production of Rice. PMID:35154193
Maternal microbiota-derived metabolic profile in fetal murine intestine, brain and placenta. PMID:35130835
Carbohydrate active enzymes (CAZy) regulate cellulolytic and pectinolytic enzymes in Colletotrichum falcatum causing red rot in sugarcane. PMID:35127303
Systems-based approaches to study immunometabolism. PMID:35121805
Disentangling glial diversity in peripheral nerves at single-nuclei resolution. PMID:35115729
Spatio-temporal variation of bacterioplankton community structure in the Pearl River: impacts of artificial fishery habitat and physicochemical factors. PMID:35114951
De novo and comparative transcriptomic analysis explain morphological differences in Panax notoginseng taproots. PMID:35100996
A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation. PMID:35094078
Profiling Signal Transduction in Global Marine Biofilms. PMID:35069473
Strong and widespread cycloheximide resistance in Stichococcus-like eukaryotic algal taxa. PMID:35058560
Capture of Essential Trace Elements and Phosphate Accumulation as a Basis for the Antimicrobial Activity of a New Ultramicrobacterium-Microbacterium lacticum Str. F2E. PMID:35056577
In Vitro Probiotic Characteristics and Whole Genome Sequence Analysis of Lactobacillus Strains Isolated from Cattle-Yak Milk. PMID:35053042
Chromosomal-level genome and multi-omics dataset of Pueraria lobata var. thomsonii provide new insights into legume family and the isoflavone and puerarin biosynthesis pathways. PMID:35043180
Maternal-fetal immune responses in pregnant women infected with SARS-CoV-2. PMID:35042863
Association between Arsenic Level, Gene Expression in Asian Population, and In Vitro Carcinogenic Bladder Tumor. PMID:35039759
Exploiting protein family and protein network data to identify novel drug targets for bladder cancer. PMID:35035776
Transcriptome analysis of Auricularia fibrillifera fruit-body responses to drought stress and rehydration. PMID:35033026
Chromosome-level genome assembly of Bactrocera dorsalis reveals its adaptation and invasion mechanisms. PMID:35017661
G3bp1 - microRNA-1 axis regulates cardiomyocyte hypertrophy. PMID:35017014
Circulating inflammatory cytokines and risk of five cancers: a Mendelian randomization analysis. PMID:35012533
PathwayMultiomics: An R Package for Efficient Integrative Analysis of Multi-Omics Datasets With Matched or Un-matched Samples. PMID:35003218
Multi-scale mechanism of antiviral drug-alike phytoligands from Ayurveda in managing COVID-19 and associated metabolic comorbidities: insights from network pharmacology. PMID:34993740
Gene regulation network analyses of pistil development in papaya. PMID:34983382
Intermittent compressive force induces cell cycling and reduces apoptosis in embryoid bodies of mouse induced pluripotent stem cells. PMID:34980892
Mosaic PKHD1 in Polycystic Kidneys Caused Aberrant Protein Expression in the Mitochondria and Lysosomes. PMID:34977057
Preconditioning With Intermittent Hypobaric Hypoxia Attenuates Stroke Damage and Modulates Endocytosis in Residual Neurons. PMID:34975719
Assessing Causal Relationship Between Human Blood Metabolites and Five Neurodegenerative Diseases With GWAS Summary Statistics. PMID:34955704
Plasma Cell-Free DNA Methylomics of Bipolar Disorder With and Without Rapid Cycling. PMID:34916903
Catecholamines are key modulators of ventricular repolarization patterns in the ball python (Python regius). PMID:34910097
Potential Novel Modules and Hub Genes as Prognostic Candidates of Thyroid Cancer by Weighted Gene Co-Expression Network Analysis. PMID:34908870
Proteomic analysis of a plastid gene encoding RPS4 mutant in Chinese cabbage (Brassica campestris L. ssp. pekinensis). PMID:34881421
Microbial Response to Fungal Infection in a Fungus-Growing Termite, Odontotermes formosanus (Shiraki). PMID:34880836
Novel cancer subtyping method based on patient-specific gene regulatory network. PMID:34880275
A computational approach for the discovery of significant cancer genes by weighted mutation and asymmetric spreading strength in networks. PMID:34876593
Single-cell genomics-based analysis reveals a vital ecological role of Thiocapsa sp. LSW in the meromictic Lake Shunet, Siberia. PMID:34860152
Serum Untargeted Metabolism Reveals the Mechanism of L. plantarum ZDY2013 in Alleviating Kidney Injury Induced by High-Salt Diet. PMID:34836175
Novel Mechanisms of Tumor Promotion by the Insulin Receptor Isoform A in Triple-Negative Breast Cancer Cells. PMID:34831367
Translation stalling proline motifs are enriched in slow-growing, thermophilic, and multicellular bacteria. PMID:34824398
d-Alanine Metabolism via d-Ala Aminotransferase by a Marine Gammaproteobacterium, Pseudoalteromonas sp. Strain CF6-2. PMID:34818098
Methylome and transcriptome analyses of soybean response to bean pyralid larvae. PMID:34794392
Vitamin A Deficiency Exacerbates Gut Microbiota Dysbiosis and Cognitive Deficits in Amyloid Precursor Protein/Presenilin 1 Transgenic Mice. PMID:34790112
MGEnrichment: A web application for microglia gene list enrichment analysis. PMID:34788279
Gut microbiota-a positive contributor in the process of intermittent fasting-mediated obesity control. PMID:34786501
Iron Accumulation and Changes in Cellular Organelles in WDR45 Mutant Fibroblasts. PMID:34769084
TopoFun: a machine learning method to improve the functional similarity of gene co-expression modules. PMID:34761220
Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis. PMID:34749661
Metabolic and Neural Mechanisms Underlying the Associations Between Gut Bacteroides and Cognition: A Large-Scale Functional Network Connectivity Study. PMID:34733135
Laxative use and mortality in patients on haemodialysis: a prospective cohort study. PMID:34732171
Genetic variations for the eggshell crystal structure revealed by genome-wide association study in chickens. PMID:34727889
Evaluating Causal Relationship Between Metabolites and Six Cardiovascular Diseases Based on GWAS Summary Statistics. PMID:34721534
Salivary microbiome profiling reveals a dysbiotic schizophrenia-associated microbiota. PMID:34711862
Prediction of bacterial functional diversity in clay microcosms. PMID:34703919
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. PMID:34686726
The Effect of Impaired Polyamine Transport on Pneumococcal Transcriptome. PMID:34684271
The Characteristics of Intestinal Bacterial Community in Three Omnivorous Fishes and Their Interaction with Microbiota from Habitats. PMID:34683446
MPA_Pathway_Tool: User-Friendly, Automatic Assignment of Microbial Community Data on Metabolic Pathways. PMID:34681649
Exploring Semi-Quantitative Metagenomic Studies Using Oxford Nanopore Sequencing: A Computational and Experimental Protocol. PMID:34680891
Transcriptome profiling of pepper leaves by RNA-Seq during an incompatible and a compatible pepper-tobamovirus interaction. PMID:34667194
SysInflam HuDB, a Web Resource for Mining Human Blood Cells Transcriptomic Data Associated with Systemic Inflammatory Responses to Sepsis. PMID:34663591
Nutrition, Inflammation, and the Gut Microbiota among Outpatients with Active Tuberculosis Disease in India. PMID:34662867
Characterization and genomic analysis of Exiguobacterium alkaliphilum B-3531D, an efficient crude oil degrading strain. PMID:34660213
Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings. PMID:34659286
Integrated Microbiome-Metabolome Analysis Reveals Stage-Dependent Alterations in Bacterial Degradation of Aromatics in Leptinotarsa decemlineata. PMID:34658924
GNG7 and ADCY1 as diagnostic and prognostic biomarkers for pancreatic adenocarcinoma through bioinformatic-based analyses. PMID:34650124
Gut microbiota dysbiosis of type 2 diabetic mice impairs the intestinal daily rhythms of GLP-1 sensitivity. PMID:34648088
NCATS Inxight Drugs: a comprehensive and curated portal for translational research. PMID:34648031
BCL-2 Inhibitor ABT-737 Effectively Targets Leukemia-Initiating Cells with Differential Regulation of Relevant Genes Leading to Extended Survival in a NRAS/BCL-2 Mouse Model of High Risk-Myelodysplastic Syndrome. PMID:34638998
Proteomics: Concepts and applications in human medicine. PMID:34630910
Metabolomic Profiling of Dongxiang Wild Rice Under Salinity Demonstrates the Significant Role of Amino Acids in Rice Salt Stress. PMID:34630473
Whole Genome Sequence of Alternaria alternata, the Causal Agent of Black Spot of Kiwifruit. PMID:34616379
METTL3 Is Involved in the Development of Graves' Disease by Inducing SOCS mRNA m6A Modification. PMID:34616359
Glioblastoma patient-derived cell-based phenotypic drug screening and identification of possible action mechanisms through proteomic analysis. PMID:34611628
Metabolome-wide association study of occupational exposure to benzene. PMID:34606590
Cell type-specific potential pathogenic genes and functional pathways in Alzheimer's Disease. PMID:34600516
Understanding the role of potential pathways and its components including hypoxia and immune system in case of oral cancer. PMID:34599215
Transcriptional Landscapes of Long Non-coding RNAs and Alternative Splicing in Pyricularia oryzae Revealed by RNA-Seq. PMID:34589103
BiG-MAP: an Automated Pipeline To Profile Metabolic Gene Cluster Abundance and Expression in Microbiomes. PMID:34581602
Dosage-Dependent Gynoecium Development and Gene Expression in Brassica napus-Orychophragmus violaceus Addition Lines. PMID:34579298
Microbial Composition and Genes for Key Metabolic Attributes in the Gut Digesta of Sea Urchins Lytechinus variegatus and Strongylocentrotus purpuratus Using Shotgun Metagenomics. PMID:34563039
AprGPD: the apricot genomic and phenotypic database. PMID:34556150
Physiological, proteomic, and metabolomic analysis provide insights into Bacillus sp.-mediated salt tolerance in wheat. PMID:34546426
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. PMID:34531741
Platelet transcriptome profiles provide potential therapeutic targets for elderly acute myelocytic leukemia patients. PMID:34507566
Inferring Functional Epigenetic Modules by Integrative Analysis of Multiple Heterogeneous Networks. PMID:34504516
A high-quality chromosome-level genome of wild Rosa rugosa. PMID:34499118
Gut microbiota alterations in response to sleep length among African-origin adults. PMID:34495955
Autoimmunity affecting the biliary tract fuels the immunosurveillance of cholangiocarcinoma. PMID:34495298
Proteomic Analysis of Copper Toxicity in Human Fungal Pathogen Cryptococcus neoformans. PMID:34485169
Microbial signatures in the lower airways of mechanically ventilated COVID-19 patients associated with poor clinical outcome. PMID:34465900
CIRP promotes the progression of non-small cell lung cancer through activation of Wnt/β-catenin signaling via CTNNB1. PMID:34465343
Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. PMID:34445339
Hepatic Proteomic Analysis of Selenoprotein T Knockout Mice by TMT: Implications for the Role of Selenoprotein T in Glucose and Lipid Metabolism. PMID:34445217
Using Functional Annotations to Study Pairwise Interactions in Urinary Tract Infection Communities. PMID:34440394
How to Achieve Therapeutic Response in Erlotinib-Resistant Head and Neck Squamous Cell Carcinoma? New Insights from Stable Isotope Labeling with Amino Acids in Cell Culture-Based Quantitative Tyrosine Phosphoproteomics. PMID:34432535
Identification of Key Functional Modules and Immunomodulatory Regulators of Hepatocellular Carcinoma. PMID:34423049
Identification of significant alteration genes, pathways and TFs induced by LPS in ARDS via bioinformatical analysis. PMID:34418997
Bioinformatics analysis of constructing a HCV-related hepatocellular carcinoma miRNA-mRNA regulation network. PMID:34414965
Integrated bioinformatics analysis of differentially expressed genes and immune cell infiltration characteristics in Esophageal Squamous cell carcinoma. PMID:34404882
Capabilities of bioinformatics tools for optimizing physicochemical features of proteins used in Nano biosensors: A short overview of the tools related to bioinformatics. PMID:34401530
Data on the first functionally-annotated de novo transcriptome assembly for North American flying squirrels (genus Glaucomys). PMID:34381854
Clusters of hairpins induce intrinsic transcription termination in bacteria. PMID:34376740
Genomic characterization of three marine fungi, including Emericellopsis atlantica sp. nov. with signatures of a generalist lifestyle and marine biomass degradation. PMID:34372938
Fecal Bacteria Implicated in Biofilm Production Are Enriched and Associate to Gastrointestinal Symptoms in Patients With APECED - A Pilot Study. PMID:34367134
Male Differentiation in the Marine Copepod Oithona nana Reveals the Development of a New Nervous Ganglion and Lin12-Notch-Repeat Protein-Associated Proteolysis. PMID:34356512
Reelin Alleviates Mesenchymal Stem Cell Senescence and Reduces Pathological α-Synuclein Expression in an In Vitro Model of Parkinson's Disease. PMID:34356083
Antimicrobial susceptibilities and comparative whole genome analysis of two isolates of the probiotic bacterium Lactiplantibacillus plantarum, strain ATCC 202195. PMID:34354117
In Silico Analysis of Potential Outer Membrane Beta-Barrel Proteins in Aeromonas hydrophila Pangenome. PMID:34335123
Public good exploitation in natural bacterioplankton communities. PMID:34321201
Rapid ecosystem-scale consequences of acute deoxygenation on a Caribbean coral reef. PMID:34312399
Bioinformatics analysis of epigenetic and SNP-related molecular markers in systemic lupus erythematosus. PMID:34306371
Functional dissection and modulation of the BirA protein for improved autotrophic growth of gas-fermenting Clostridium ljungdahlii. PMID:34291572
DysPIA: A Novel Dysregulated Pathway Identification Analysis Method. PMID:34290733
Bioinformatic Analysis of Temporal and Spatial Proteome Alternations During Infections. PMID:34276775
Insights Into Transcriptome Profiles Associated With Wooden Breast Myopathy in Broilers Slaughtered at the Age of 6 or 7 Weeks. PMID:34262480
Trajectories of Homoeolog-Specific Expression in Allotetraploid Tragopogon castellanus Populations of Independent Origins. PMID:34249049
Rhamnan sulphate from green algae Monostroma nitidum improves constipation with gut microbiome alteration in double-blind placebo-controlled trial. PMID:34226572
Composition and diversity of gut microbiota in Pomacea canaliculata in sexes and between developmental stages. PMID:34210255
Clinicopathological-Associated Regulatory Network of Deregulated circRNAs in Hepatocellular Carcinoma. PMID:34199580
Marinobacter atlanticus electrode biofilms differentially regulate gene expression depending on electrode potential and lifestyle. PMID:34195607
Specific phytochemicals in floral nectar up-regulate genes involved in longevity regulation and xenobiotic metabolism, extending mosquito life span. PMID:34188892
Searching for essential genes and drug discovery in breast cancer and periodontitis via text mining and bioinformatics analysis. PMID:34183495
Caloric restriction disrupts the microbiota and colonization resistance. PMID:34163067
In Silico Repositioning of Dopamine Modulators with Possible Application to Schizophrenia: Pharmacophore Mapping, Molecular Docking and Molecular Dynamics Analysis. PMID:34151057
Evaluating the lettuce metatranscriptome with MinION sequencing for future spaceflight food production applications. PMID:34140518
Proteomic analysis of chicken bone marrow-derived dendritic cells in response to an inactivated IBV + NDV poultry vaccine. PMID:34135356
A case of peritoneal dialysis-associated peritonitis caused by Rhodococcus kroppenstedtii. PMID:34120601
Binary Metabolic Phenotypes and Phenotype Diversity Metrics for the Functional Characterization of Microbial Communities. PMID:34113324
Identification of microRNAs and gene regulatory networks in cleft lip common in humans and mice. PMID:34104955
Advances in the Study of Metabolomics and Metabolites in Some Species Interactions. PMID:34072976
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
Transcriptome analysis of MBD5-associated neurodevelopmental disorder (MAND) neural progenitor cells reveals dysregulation of autism-associated genes. PMID:34050248
Precocious Metamorphosis of Silkworm Larvae Infected by BmNPV in the Latter Half of the Fifth Instar. PMID:34040541
Predicting phosphorylation sites using machine learning by integrating the sequence, structure, and functional information of proteins. PMID:34030700
Insights into the taxonomic and functional characterization of agricultural crop core rhizobiomes and their potential microbial drivers. PMID:33980901
Highly deregulated lncRNA LOC is associated with overall worse prognosis in Hepatocellular Carcinoma patients. PMID:33976720
Anaerobe-enriched gut microbiota predicts pro-inflammatory responses in pulmonary tuberculosis. PMID:33975252
Structural variations in papaya genomes. PMID:33971825
System biology and bioinformatics pipeline to identify comorbidities risk association: Neurodegenerative disorder case study. PMID:33956862
Performance assessment of sample-specific network control methods for bulk and single-cell biological data analysis. PMID:33956788
High biodiversity in a benzene-degrading nitrate-reducing culture is sustained by a few primary consumers. PMID:33953314
Genetic network and gene set enrichment analyses identify MND1 as potential diagnostic and therapeutic target gene for lung adenocarcinoma. PMID:33941804
Whole-genome resequencing of Osmanthus fragrans provides insights into flower color evolution. PMID:33931610
In-Silico Study of Immune System Associated Genes in Case of Type-2 Diabetes With Insulin Action and Resistance, and/or Obesity. PMID:33927693
Targeting the tumor stroma: integrative analysis reveal GATA2 and TORYAIP1 as novel prognostic targets in breast and ovarian cancer. PMID:33907495
Urine proteomics for profiling of mouse toxoplasmosis using liquid chromatography tandem mass spectrometry analysis. PMID:33879238
Subtypes identification on heart failure with preserved ejection fraction via network enhancement fusion using multi-omics data. PMID:33868594
Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge. PMID:33861732
Transcriptional profile in rat muscle: down-regulation networks in acute strenuous exercise. PMID:33859869
Temporal transcriptome profiling of developing seeds reveals candidate genes involved in oil accumulation in safflower (Carthamus tinctorius L.). PMID:33858333
Bioinformatics analysis of the expression and role of microRNA-221-3p in head and neck squamous cell carcinoma. PMID:33845800
The chromosome-level Hemerocallis citrina Borani genome provides new insights into the rutin biosynthesis and the lack of colchicine. PMID:33828071
Up-regulation of Key Glycolysis Proteins in Cancer Development. PMID:33817128
Characterization of Haemophilus Parasuis Serovar 2 CL120103, a Moderately Virulent Strain in China. PMID:33817086
Cuprizone and EAE mouse frontal cortex proteomics revealed proteins altered in multiple sclerosis. PMID:33785790
Crop Rotation With Cress Increases Cucumber Yields by Regulating the Composition of the Rhizosphere Soil Microbial Community. PMID:33776961
Elevated glucose represses lysosomal and mTOR-related genes in renal epithelial cells composed of progenitor CD133+ cells. PMID:33764985
Evolution of Sequence Type 4821 Clonal Complex Hyperinvasive and Quinolone-Resistant Meningococci. PMID:33754991
Targeting of FK506 binding protein 5 by miR-203 affects the progression of breast cancer via regulating the fatty acid degradation pathway and potential drug-repurposing. PMID:33747203
Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. PMID:33741065
Liraglutide targets the gut microbiota and the intestinal immune system to regulate insulin secretion. PMID:33723651
Transcriptome Expression of Biomineralization Genes in Littoraria flava Gastropod in Brazilian Rocky Shore Reveals Evidence of Local Adaptation. PMID:33720344
MetaPrism: A versatile toolkit for joint taxa/gene analysis of metagenomic sequencing data. PMID:33713107
Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. PMID:33712615
PreDTIs: prediction of drug-target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. PMID:33709119
Phytochrome regulates cellular response plasticity and the basic molecular machinery of leaf development. PMID:33693822
Primary Metabolism co-Opted for Defensive Chemical Production in the Carabid Beetle, Harpalus pensylvanicus. PMID:33689113
Intestinal Dysbiosis in Young Cystic Fibrosis Rabbits. PMID:33669429
Oral seeding and niche-adaptation of middle ear biofilms in health. PMID:33665609
Identification of theranostic factors for patients developing metastasis after surgery for early-stage lung adenocarcinoma. PMID:33664854
Combined LC-MS/MS and 16S rDNA analysis on mice under high temperature and humidity and Herb Yinchen protection mechanism. PMID:33658635
Human Chorionic Gonadotropin Modulates the Transcriptome of the Myometrium and Cervix in Late Gestation. PMID:33650091
Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. PMID:33648559
Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease. PMID:33626128
Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis. PMID:33620038
The draft genome sequence of the grove snail Cepaea nemoralis. PMID:33604668
Antidepressants fluoxetine and amitriptyline induce alterations in intestinal microbiota and gut microbiome function in rats exposed to chronic unpredictable mild stress. PMID:33602895
Improvement of Gut Diversity and Composition After Direct-Acting Antivirals in Hepatitis C Virus-Infected Patients With or Without Human Immunodeficiency Virus Coinfection. PMID:33598686
Is Sharing Datasets the Answer to the New Challenges of Reproductive Biology Research? PMID:33594650
Targeting critical kinases and anti-apoptotic molecules overcomes steroid resistance in MLL-rearranged leukaemia. PMID:33581643
Causal relationships between genetically determined metabolites and human intelligence: a Mendelian randomization study. PMID:33563321
RNA Sequencing Reveals Distinct Immune Responses in the Chorioamniotic Membranes of Women with Preterm Labor and Microbial or Sterile Intra-amniotic Inflammation. PMID:33558326
B. adolescentis ameliorates chronic colitis by regulating Treg/Th2 response and gut microbiota remodeling. PMID:33557671
Host Transcriptomic Response Following Administration of Rotavirus Vaccine in Infants' Mimics Wild Type Infection. PMID:33552046
Protuberances are organized distinct regions of long-term callus: histological and transcriptomic analyses in kiwifruit. PMID:33544186
microRNA let-7i-5p mediates the relationship between muscle fat infiltration and neck pain disability following motor vehicle collision: a preliminary study. PMID:33542428
Finding branched pathways in metabolic network via atom group tracking. PMID:33529200
Machine Learning Analysis of Longevity-Associated Gene Expression Landscapes in Mammals. PMID:33499037
Proliferation Genes Repressed by TGF-β Are Downstream of Slug/Snail2 in Normal Bronchial Epithelial Progenitors and Are Deregulated in COPD. PMID:33495975
Comparative analysis on the anti-inflammatory/immune effect of mesenchymal stem cell therapy for the treatment of pulmonary arterial hypertension. PMID:33479312
Microbiome Search Engine 2: a Platform for Taxonomic and Functional Search of Global Microbiomes on the Whole-Microbiome Level. PMID:33468706
Prediction and analysis of metagenomic operons via MetaRon: a pipeline for prediction of Metagenome and whole-genome opeRons. PMID:33468056
Changes on proteomic and metabolomic profile in serum of mice induced by chronic exposure to tramadol. PMID:33446901
The Gut Microbiota Profile According to Glycemic Control in Type 1 Diabetes Patients Treated with Personal Insulin Pumps. PMID:33445500
Network controllability-based algorithm to target personalized driver genes for discovering combinatorial drugs of individual patients. PMID:33434272
Identifying intracellular signaling modules and exploring pathways associated with breast cancer recurrence. PMID:33432018
Tomato Spotted Wilt Virus Benefits Its Thrips Vector by Modulating Metabolic and Plant Defense Pathways in Tomato. PMID:33424878
Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function. PMID:33407112
Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates. PMID:33378680
Integrative Multi-omics Analyses of Barley Rootzones under Salinity Stress Reveal Two Distinctive Salt Tolerance Mechanisms. PMID:33367236
A Comparative Evaluation of Tools to Predict Metabolite Profiles From Microbiome Sequencing Data. PMID:33343536
Microbial community composition in the rhizosphere of Larix decidua under different light regimes with additional focus on methane cycling microorganisms. PMID:33339837
Expression and Possible Molecular Mechanisms of microRNA-205-5p in Patients With Head and Neck Squamous Cell Carcinoma. PMID:33327871
Gut-Liver Immune Response and Gut Microbiota Profiling Reveal the Pathogenic Mechanisms of Vibrio harveyi in Pearl Gentian Grouper (Epinephelus lanceolatus ♂ × E. fuscoguttatus ♀). PMID:33324424
Comparative transcriptome profiling of pomegranate genotypes having resistance and susceptible reaction to Xanthomonas axonopodis pv. punicae. PMID:33304163
Geochemical transition zone powering microbial growth in subsurface sediments. PMID:33288718
β-catenin regulates FOXP2 transcriptional activity via multiple binding sites. PMID:33284517
Exploring the Influence of Signal Molecules on Marine Biofilms Development. PMID:33281767
Altitude influences microbial diversity and herbage fermentation in the rumen of yaks. PMID:33276718
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Impact of culture condition modulation on the high-yield, high-specificity and cost-effective production of terpenoids from microbial sources: A review. PMID:33257314
Dietary Emulsifiers Alter Composition and Activity of the Human Gut Microbiota in vitro, Irrespective of Chemical or Natural Emulsifier Origin. PMID:33250870
Sampling interstitial fluid from human skin using a microneedle patch. PMID:33239384
The Urine Metabolome of Young Autistic Children Correlates with Their Clinical Profile Severity. PMID:33238400
Development and validation of an RNA binding protein-associated prognostic model for hepatocellular carcinoma. PMID:33228611
Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis. PMID:33219248
Construction and validation of an immunity-related prognostic signature for breast cancer. PMID:33216733
A "Lymphocyte MicroRNA Signature" as Predictive Biomarker of Immunotherapy Response and Plasma PD-1/PD-L1 Expression Levels in Patients with Metastatic Renal Cell Carcinoma: Pointing towards Epigenetic Reprogramming. PMID:33207823
Involvement of the Wnt/β-Catenin signaling pathway in the heterogenous nuclear ribonucleoprotein K-driven inhibition of proliferation and migration in head and neck squamous cell carcinoma. PMID:33193854
A Qualitative Transcriptional Signature for Predicting CpG Island Methylator Phenotype Status of the Right-Sided Colon Cancer. PMID:33193579
A transcriptome profile in gallbladder cancer based on annotation analysis of microarray studies. PMID:33179115
Lower Airway Dysbiosis Affects Lung Cancer Progression. PMID:33177060
Inhibition of AURKB, regulated by pseudogene MTND4P12, confers synthetic lethality to PARP inhibition in skin cutaneous melanoma. PMID:33163283
RNA Sequencing Reveals Diverse Functions of Amniotic Fluid Neutrophils and Monocytes/Macrophages in Intra-Amniotic Infection. PMID:33152737
In-depth transcriptome reveals the potential biotechnological application of Bothrops jararaca venom gland. PMID:33149734
A review on drug repurposing applicable to COVID-19. PMID:33147623
miRNA profiles of canine cutaneous mast cell tumours with early nodal metastasis and evaluation as potential biomarkers. PMID:33144602
Uncovering the genomic potential of the Amazon River microbiome to degrade rainforest organic matter. PMID:33126925
Unravelling the gut bacteriome of Ips (Coleoptera: Curculionidae: Scolytinae): identifying core bacterial assemblage and their ecological relevance. PMID:33122700
Checkpoint therapeutic target database (CKTTD): the first comprehensive database for checkpoint targets and their modulators in cancer immunotherapy. PMID:33109630
Haplotype Block Analysis Reveals Candidate Genes and QTLs for Meat Quality and Disease Resistance in Chinese Jiangquhai Pig Breed. PMID:33101353
Gut microbiome in Schizophrenia: Altered functional pathways related to immune modulation and atherosclerotic risk. PMID:33098964
The FAM171A2 gene is a key regulator of progranulin expression and modifies the risk of multiple neurodegenerative diseases. PMID:33087363
Exploration of ovine milk whey proteome during postnatal development using an iTRAQ approach. PMID:33083141
Free Wanderer Powder regulates AMPA receptor homeostasis in chronic restraint stress-induced rat model of depression with liver-depression and spleen-deficiency syndrome. PMID:33052137
Integrated omics unveil the secondary metabolic landscape of a basal dinoflagellate. PMID:33050904
Transcriptome Analysis of Different Tissues Reveals Key Genes Associated With Galanthamine Biosynthesis in Lycoris longituba. PMID:33042169
The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans. PMID:33037220
The Differential Composition of Whey Proteomes in Hu Sheep Colostrum and Milk during Different Lactation Periods. PMID:33019658
High-quality nuclear genome for Sarcoptes scabiei-A critical resource for a neglected parasite. PMID:33001992
Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts. PMID:32994284
iTRAQ-based comparative proteomic analysis of differences in the protein profiles of stems and leaves from two alfalfa genotypes. PMID:32993512
Comparison of Gut Microbiota Diversity and Predicted Functions Between Healthy and Diseased Captive Rana dybowskii. PMID:32983063
Sappanone A Prevents Left Ventricular Dysfunction in a Rat Myocardial Ischemia Reperfusion Injury Model. PMID:32967328
Rational drug design, synthesis, and biological evaluation of novel chiral tetrahydronaphthalene-fused spirooxindole as MDM2-CDK4 dual inhibitor against glioblastoma. PMID:32963945
Viral Perturbation of Alternative Splicing of a Host Transcript Benefits Infection. PMID:32958561
Rps27a might act as a controller of microglia activation in triggering neurodegenerative diseases. PMID:32941527
Exhaled volatile organic compounds analysis in clinical pediatrics: a systematic review. PMID:32919397
Altered Gut Microbiota and Shift in Bacteroidetes between Young Obese and Normal-Weight Korean Children: A Cross-Sectional Observational Study. PMID:32908903
Identification of microRNA-451a as a Novel Circulating Biomarker for Colorectal Cancer Diagnosis. PMID:32908896
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome. PMID:32895427
Prediction of drug-target interactions from multi-molecular network based on LINE network representation method. PMID:32894154
Pregnancy-specific transcriptional changes upon endotoxin exposure in mice. PMID:32866128
Integrated Bioinformatics Analysis Reveals Key Candidate Genes and Pathways Associated With Clinical Outcome in Hepatocellular Carcinoma. PMID:32849813
Genetically Determined Levels of Serum Metabolites and Risk of Neuroticism: A Mendelian Randomization Study. PMID:32808022
Systemically-delivered biodegradable PLGA alters gut microbiota and induces transcriptomic reprogramming in the liver in an obesity mouse model. PMID:32796856
A Novel Network Pharmacology Strategy to Decode Metabolic Biomarkers and Targets Interactions for Depression. PMID:32760300
Application of Transcriptional Gene Modules to Analysis of Caenorhabditis elegans' Gene Expression Data. PMID:32759329
BMP2 signalling activation enhances bone metastases of non-small cell lung cancer. PMID:32750747
Identification of key genes of human bone marrow stromal cells adipogenesis at an early stage. PMID:32742785
Fungus-growing insects host a distinctive microbiota apparently adapted to the fungiculture environment. PMID:32709946
Shedding the Light on Litopenaeus vannamei Differential Muscle and Hepatopancreas Immune Responses in White Spot Syndrome Virus (WSSV) Exposure. PMID:32708590
An Integrative Analysis of Transcriptome, Proteome and Hormones Reveals Key Differentially Expressed Genes and Metabolic Pathways Involved in Flower Development in Loquat. PMID:32698310
Scoring Species for Synthetic Community Design: Network Analyses of Functional Core Microbiomes. PMID:32676061
Diversity of a bacterial community associated with Cliona lobata Hancock and Gelliodes pumila (Lendenfeld, 1887) sponges on the South-East coast of India. PMID:32665602
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. PMID:32663284
Identification of Differentially Expressed Hematopoiesis-associated Genes in Term Low Birth Weight Newborns by Systems Genomics Approach. PMID:32655286
Comparative analysis of single-cell transcriptomics in human and Zebrafish oocytes. PMID:32640983
Network of clinically-relevant lncRNAs-mRNAs associated with prognosis of hepatocellular carcinoma patients. PMID:32636408
Shared up-regulation and contrasting down-regulation of gene expression distinguish desiccation-tolerant from intolerant green algae. PMID:32636259
Breath Metabolomics Provides an Accurate and Noninvasive Approach for Screening Cirrhosis, Primary, and Secondary Liver Tumors. PMID:32626836
Transcriptional Profiles of Skeletal Muscle Associated With Increasing Severity of White Striping in Commercial Broilers. PMID:32612536
The emerging roles of GCN5L1 in mitochondrial and vacuolar organelle biology. PMID:32599084
Macronutrient, Energy, and Bile Acid Metabolism Pathways Altered Following a Physiological Meal Challenge, Relative to Fasting, among Guatemalan Adults. PMID:32597983
Transcriptome Profiling of Pacu (Piaractus mesopotamicus) Challenged With Pathogenic Aeromonas hydrophila: Inference on Immune Gene Response. PMID:32582300
Genome-wide transcriptome architecture in a mouse model of Gulf War Illness. PMID:32574576
Trametenolic Acid B Triggers HSP90AA4P and Autophagy in HepG2/2.2.15 Cells by Proteomic Analysis. PMID:32548489
Identification of Altered miRNAs in Cerumen of Dogs Affected by Otitis Externa. PMID:32547539
Construction and Analysis of a Long Non-Coding RNA-Associated Competing Endogenous RNA Network Identified Potential Prognostic Biomarkers in Luminal Breast Cancer. PMID:32547061
Shifting evolutionary sands: transcriptome characterization of the Aptostichus atomarius species complex. PMID:32539685
Fatty acid bioconversion in harpacticoid copepods in a changing environment: a transcriptomic approach. PMID:32536309
Transcriptional regulation of strigolactone signalling in Arabidopsis. PMID:32528176
Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage. PMID:32508885
dBMHCC: A comprehensive hepatocellular carcinoma (HCC) biomarker database provides a reliable prediction system for novel HCC phosphorylated biomarkers. PMID:32497121
Intrinsic Abnormalities of Cystic Fibrosis Airway Connective Tissue Revealed by an In Vitro 3D Stromal Model. PMID:32492951
Spatial Variation in Bacterioplankton Communities in the Pearl River, South China: Impacts of Land Use and Physicochemical Factors. PMID:32485891
PICRUSt2 for prediction of metagenome functions. PMID:32483366
Gene Expression Profiling to Delineate the Anticancer Potential of a New Alkaloid Isopicrinine From Rhazya stricta. PMID:32463309
Mining the Biosynthetic Potential for Specialized Metabolism of a Streptomyces Soil Community. PMID:32456220
Thaumarchaea Genome Sequences from a High Arctic Active Layer. PMID:32439668
PathwayPCA: an R/Bioconductor Package for Pathway Based Integrative Analysis of Multi-Omics Data. PMID:32430990
Identification of population-level differentially expressed genes in one-phenotype data. PMID:32428201
Identification of conditionally essential genes for Streptococcus suis infection in pigs. PMID:32419603
Association between SNAP25 and human glioblastoma multiform: a comprehensive bioinformatic analysis. PMID:32412599
Prioritizing Cancer Genes Based on an Improved Random Walk Method. PMID:32411180
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
Lung Development Genes and Adult Lung Function. PMID:32392078
Carbon monoxide-dependent transcriptional changes in a thermophilic, carbon monoxide-utilizing, hydrogen-evolving bacterium Calderihabitans maritimus KKC1 revealed by transcriptomic analysis. PMID:32388815
An improved high-quality genome assembly and annotation of Tibetan hulless barley. PMID:32385314
Knowledge-based structural models of SARS-CoV-2 proteins and their complexes with potential drugs. PMID:32379896
Large-Scale Differential Gene Expression Transcriptomic Analysis Identifies a Metabolic Signature Shared by All Cancer Cells. PMID:32365991
SHOGUN: a modular, accurate and scalable framework for microbiome quantification. PMID:32365167
Serum Metabolomics Revealed the Differential Metabolic Pathway in Calves with Severe Clinical Diarrhea Symptoms. PMID:32354125
Comparative transcriptomics characterized the distinct biosynthetic abilities of terpenoid and paeoniflorin biosynthesis in herbaceous peony strains. PMID:32341893
A comparative chemogenic analysis for predicting Drug-Target Pair via Machine Learning Approaches. PMID:32322011
Dual graph convolutional neural network for predicting chemical networks. PMID:32321421
The Computational Diet: A Review of Computational Methods Across Diet, Microbiome, and Health. PMID:32318028
Exploring potential biomarkers for lung adenocarcinoma using LC-MS/MS metabolomics. PMID:32316791
Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases. PMID:32316560
BioHackathon 2015: Semantics of data for life sciences and reproducible research. PMID:32308977
Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost. PMID:32301987
Novel insight into theacrine metabolism revealed by transcriptome analysis in bitter tea (Kucha, Camellia sinensis). PMID:32286351
Peruvian chicha: A Focus on the Microbial Populations of This Ancient Maize-Based Fermented Beverage. PMID:32284502
Acetylation of Phenylalanine Hydroxylase and Tryptophan 2,3-Dioxygenase Alters Hepatic Aromatic Amino Acid Metabolism in Weaned Piglets. PMID:32283695
eXplainable Artificial Intelligence (XAI) for the identification of biologically relevant gene expression patterns in longitudinal human studies, insights from obesity research. PMID:32275707
Quantitative Proteomic Analyses Identify STO/BBX24 -Related Proteins Induced by UV-B. PMID:32260266
Identifying Small Molecule-miRNA Associations Based on Credible Negative Sample Selection and Random Walk. PMID:32258003
A Systematic Bioinformatics Workflow With Meta-Analytics Identified Potential Pathogenic Factors of Alzheimer's Disease. PMID:32231518
Urine metabolomic analysis for monitoring internal load in professional football players. PMID:32222832
Understanding of Zaire ebolavirus-human protein interaction for drug repurposing. PMID:32206696
The Changes in the Frog Gut Microbiome and Its Putative Oxygen-Related Phenotypes Accompanying the Development of Gastrointestinal Complexity and Dietary Shift. PMID:32194513
Virtual screening web servers: designing chemical probes and drug candidates in the cyberspace. PMID:32187356
Genome Analysis and Physiological Characterization of Four Streptococcus thermophilus Strains Isolated From Chinese Traditional Fermented Milk. PMID:32184766
ICAM1 Regulates the Development of Gastric Cancer and May Be a Potential Biomarker for the Early Diagnosis and Prognosis of Gastric Cancer. PMID:32184657
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. PMID:32183716
Microecological Koch's postulates reveal that intestinal microbiota dysbiosis contributes to shrimp white feces syndrome. PMID:32156316
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Changes in the Intestinal Microbiota Are Seen Following Treatment with Infliximab in Children with Crohn's Disease. PMID:32143438
Identification and Validation of Metabolic Markers for Adulteration Detection of Edible Oils Using Metabolic Networks. PMID:32121379
Identification of Blood Circular RNAs as Potential Biomarkers for Acute Ischemic Stroke. PMID:32116524
In-depth Understanding of Camellia oleifera Self-incompatibility by Comparative Transcriptome, Proteome and Metabolome. PMID:32111089
Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length. PMID:32109421
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina. PMID:32103005
Proteogenomic analysis of pitaya reveals cold stress-related molecular signature. PMID:32095361
Proteomic analysis of the antimicrobial effects of sublethal concentrations of thymol on Salmonella enterica serovar Typhimurium. PMID:32072194
Brassinosteroid signaling may regulate the germination of axillary buds in ratoon rice. PMID:32059642
Enhancing reproducibility of gene expression analysis with known protein functional relationships: The concept of well-associated protein. PMID:32058996
A Novel Approach for Drug-Target Interactions Prediction Based on Multimodal Deep Autoencoder. PMID:32047432
Active sulfur cycling in the terrestrial deep subsurface. PMID:32047278
A Network-Based Bioinformatics Approach to Identify Molecular Biomarkers for Type 2 Diabetes that Are Linked to the Progression of Neurological Diseases. PMID:32041280
Genome-wide association study reveals that different pathways contribute to grain quality variation in sorghum (Sorghum bicolor). PMID:32005168
Diversity of D-Amino Acid Utilizing Bacteria From Kongsfjorden, Arctic and the Metabolic Pathways for Seven D-Amino Acids. PMID:31998270
Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure. PMID:31981004
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. PMID:31964916
Genome-wide scan identifies novel genetic loci regulating salivary metabolite levels. PMID:31960908
Eighty-eight variants highlight the role of T cell regulation and airway remodeling in asthma pathogenesis. PMID:31959851
The differential distribution of bacteria between cancerous and noncancerous ovarian tissues in situ. PMID:31954395
Drug-target interaction prediction using Multi Graph Regularized Nuclear Norm Minimization. PMID:31945078
Identification of genes associated with SiHa cell sensitivity to paclitaxel by CRISPR-Cas9 knockout screening. PMID:31938303
VAMPr: VAriant Mapping and Prediction of antibiotic resistance via explainable features and machine learning. PMID:31929521
Assessing the Causal Effects of Human Serum Metabolites on 5 Major Psychiatric Disorders. PMID:31919502
Transcriptomic analysis reveals recovery strategies in strawberry roots after using a soil amendment in continuous cropping soil. PMID:31900117
RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. PMID:31881735
Metagenome sequencing of fingermillet-associated microbial consortia provides insights into structural and functional diversity of endophytes. PMID:31879579
Transcriptome, Phenotypic, and Virulence Analysis of Streptococcus sanguinis SK36 Wild Type and Its CcpA-Null Derivative (ΔCcpA). PMID:31867286
Transcriptome Analysis of Wheat Roots Reveals a Differential Regulation of Stress Responses Related to Arbuscular Mycorrhizal Fungi and Soil Disturbance. PMID:31835704
Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27. PMID:31835347
Exploring thematic structure and predicted functionality of 16S rRNA amplicon data. PMID:31825995
Identification Of Novel lncRNAs For Detection Of HBV-Associated Hepatocellular Carcinoma. PMID:31819509
iTRAQ-Based Quantitative Proteomic Analysis of Digestive Juice across the First 48 Hours of the Fifth Instar in Silkworm Larvae. PMID:31817210
Integrated Proteomics and Lipidomics Reveal That the Swarming Motility of Paenibacillus polymyxa Is Characterized by Phospholipid Modification, Surfactant Deployment, and Flagellar Specialization Relative to Swimming Motility. PMID:31798553
Analysis of Centranthera grandiflora Benth Transcriptome Explores Genes of Catalpol, Acteoside and Azafrin Biosynthesis. PMID:31795510
Identification for Exploring Underlying Pathogenesis and Therapy Strategy of Oral Squamous Cell Carcinoma by Bioinformatics Analysis. PMID:31794546
Topological properties and in vitro identification of essential nodes of the Paclitaxel and Vincristine interactomes in PC-3 cells. PMID:31783991
Transcriptome profiling of posterior kidney of brown trout, Salmo trutta, during proliferative kidney disease. PMID:31783772
Transcriptome profiling of resistance response to Meloidogyne chitwoodi introgressed from wild species Solanum bulbocastanum into cultivated potato. PMID:31779600
A novel network control model for identifying personalized driver genes in cancer. PMID:31765387
Analysis of metabolomics associated with quality differences between room-temperature- and low-temperature-stored litchi pulps. PMID:31763006
Comparison of the intestinal microbiota composition and function in healthy and diseased Yunlong Grouper. PMID:31754862
Comparative Proteomic Analysis Reveals Immune Competence in Hemolymph of Bombyx mori Pupa Parasitized by Silkworm Maggot Exorista sorbillans. PMID:31752209
Indole-3-Acetic Acid in Burkholderia pyrrocinia JK-SH007: Enzymatic Identification of the Indole-3-Acetamide Synthesis Pathway. PMID:31749788
Genomic Signatures for Sedimentary Microbial Utilization of Phytoplankton Detritus in a Fast-Flowing Estuary. PMID:31749780
Phosphoproteomics Profiling of Cotton (Gossypium hirsutum L.) Roots in Response to Verticillium dahliae Inoculation. PMID:31720547
RNA sequencing of identical twins discordant for autism reveals blood-based signatures implicating immune and transcriptional dysregulation. PMID:31719968
Comparative Proteomic Analysis Reveals Key Proteins Linked to the Accumulation of Soluble Sugars and Organic Acids in the Mature Fruits of the Wild Malus Species. PMID:31717908
Metabolomic Analysis of Radiation-Induced Lung Injury in Rats: The Potential Radioprotective Role of Taurine. PMID:31700502
Metabolomic Analysis of Influenza A Virus A/WSN/1933 (H1N1) Infected A549 Cells during First Cycle of Viral Replication. PMID:31683654
Nodosilinea signiensis sp. nov. (Leptolyngbyaceae, Synechococcales), a new terrestrial cyanobacterium isolated from mats collected on Signy Island, South Orkney Islands, Antarctica. PMID:31682631
Loss of Lkb1 impairs Treg function and stability to aggravate graft-versus-host disease after bone marrow transplantation. PMID:31664223
Genome-Wide Identification and Functional Prediction of Long Non-coding RNAs Involved in the Heat Stress Response in Metarhizium robertsii. PMID:31649657
A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures. PMID:31641119
Sequence variants with large effects on cardiac electrophysiology and disease. PMID:31641117
Comparative Microbiome Profiles of Sympatric Tick Species from the Far-Western United States. PMID:31635285
Host plants influence the composition of the gut bacteria in Henosepilachna vigintioctopunctata. PMID:31626674
Depth-dependent transcriptomic response of diatoms during spring bloom in the western subarctic Pacific Ocean. PMID:31601926
Temporal evolution of the microbiome, immune system and epigenome with disease progression in ALS mice. PMID:31597644
A qualitative transcriptional signature for determining the grade of colorectal adenocarcinoma. PMID:31595030
Differential proteomic analysis of serum exosomes reveals alterations in progression of Parkinson disease. PMID:31593110
Critical microRNAs and regulatory motifs in cleft palate identified by a conserved miRNA-TF-gene network approach in humans and mice. PMID:31589286
Transcriptome analysis of the effect of GA3 in sugarcane culm. PMID:31588400
A novel miRNA-4484 is up-regulated on microarray and associated with increased MMP-21 expression in serum of systemic sclerosis patients. PMID:31582779
Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau. PMID:31579584
Genome-resolved metagenomics and metatranscriptomics reveal niche differentiation in functionally redundant microbial communities at deep-sea hydrothermal vents. PMID:31573126
Polyamine Synthesis Effects Capsule Expression by Reduction of Precursors in Streptococcus pneumoniae. PMID:31555234
Association study identified biologically relevant receptor genes with synergistic functions in celiac disease. PMID:31554915
Integrated Analysis of Multiple Microarray Studies to Identify Novel Gene Signatures in Non-alcoholic Fatty Liver Disease. PMID:31551930
Untargeted Metabolomics for Autism Spectrum Disorders: Current Status and Future Directions. PMID:31551836
Discovering genetic interactions bridging pathways in genome-wide association studies. PMID:31537791
Transposons played a major role in the diversification between the closely related almond and peach genomes: results from the almond genome sequence. PMID:31529539
Casiopeina II‑gly acts on lncRNA MALAT1 by miR‑17‑5p to inhibit FZD2 expression via the Wnt signaling pathway during the treatment of cervical carcinoma. PMID:31524268
Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome. PMID:31523007
Identifying protein complexes based on an edge weight algorithm and core-attachment structure. PMID:31521132
Exome Sequencing Reveals Immune Genes as Susceptibility Modifiers in Individuals with α1-Antitrypsin Deficiency. PMID:31511551
Cell-type-specific profiling of brain mitochondria reveals functional and molecular diversity. PMID:31501572
Genome-wide association studies identify polygenic effects for completed suicide in the Japanese population. PMID:31476763
Transcription Profiling Reveals Cooperative Metabolic Interactions in a Microbial Cheese-Ripening Community Composed of Debaryomyces hansenii, Brevibacterium aurantiacum, and Hafnia alvei. PMID:31474970
High-resolution 13C metabolic flux analysis. PMID:31471597
Gut microbiota and their putative metabolic functions in fragmented Bengal tiger population of Nepal. PMID:31465520
Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. PMID:31453412
Identification and characterization of biomarkers and their functions for docetaxel-resistant prostate cancer cells. PMID:31452801
Dietary Oligosaccharides Attenuate Stress-Induced Disruptions in Immune Reactivity and Microbial B-Vitamin Metabolism. PMID:31417554
Complete Genome Sequence of Azoarcus sp. Strain DD4, a Gram-Negative Propanotroph That Degrades 1,4-Dioxane and 1,1-Dichloroethylene. PMID:31416874
S-Adenosylmethionine Affects Cell Cycle Pathways and Suppresses Proliferation in Liver Cells. PMID:31413757
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation. PMID:31409826
Transcriptomic analysis of Pacific white shrimp (Litopenaeus vannamei, Boone 1931) in response to acute hepatopancreatic necrosis disease caused by Vibrio parahaemolyticus. PMID:31408485
Differential Proteomics Based on TMT and PRM Reveal the Resistance Response of Bambusa pervariabilis × Dendrocalamopisis grandis Induced by AP-Toxin. PMID:31405188
Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression. PMID:31396463
A seed-extended algorithm for detecting protein complexes based on density and modularity with topological structure and GO annotations. PMID:31390979
Taking insight into the gut microbiota of three spider species: No characteristic symbiont was found corresponding to the special feeding style of spiders. PMID:31380078
RITAN: rapid integration of term annotation and network resources. PMID:31355053
Drivers and patterns of microbial community assembly in a Lyme disease vector. PMID:31346439
Benchmark and integration of resources for the estimation of human transcription factor activities. PMID:31340985
The human microbiota is associated with cardiometabolic risk across the epidemiologic transition. PMID:31339887
Label-Free Proteomic Analysis of Molecular Effects of 2-Methoxy-1,4-naphthoquinone on Penicillium italicum. PMID:31337149
Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome. PMID:31333721
Position-Specific Metabolic Probing and Metagenomics of Microbial Communities Reveal Conserved Central Carbon Metabolic Network Activities at High Temperatures. PMID:31333598
Identification of gene co-expression modules and hub genes associated with lymph node metastasis of papillary thyroid cancer. PMID:31332712
Probing early wheat grain development via transcriptomic and proteomic approaches. PMID:31332594
Insights about multi-targeting and synergistic neuromodulators in Ayurvedic herbs against epilepsy: integrated computational studies on drug-target and protein-protein interaction networks. PMID:31332210
Transcriptome profiling of Gerbera hybrida reveals that stem bending is caused by water stress and regulation of abscisic acid. PMID:31331262
Large-scale Discovery of Substrates of the Human Kinome. PMID:31324866
Radiogenomics of breast cancer using dynamic contrast enhanced MRI and gene expression profiling. PMID:31307537
Royal jelly-derived proteins enhance proliferation and migration of human epidermal keratinocytes in an in vitro scratch wound model. PMID:31299973
The three-legged stool of understanding metabolism: integrating metabolomics with biochemical genetics and computational modeling. PMID:31294216
SCIA: A Novel Gene Set Analysis Applicable to Data With Different Characteristics. PMID:31293623
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases. PMID:31290545
Trait-based analysis of the human skin microbiome. PMID:31277701
Modulation of Growth Performance and Intestinal Microbiota in Chickens Fed Plant Extracts or Virginiamycin. PMID:31275268
Characterization and analysis of the transcriptome in Gymnocypris selincuoensis on the Qinghai-Tibetan Plateau using single-molecule long-read sequencing and RNA-seq. PMID:31274170
Time Series Genome-Centric Analysis Unveils Bacterial Response to Operational Disturbance in Activated Sludge. PMID:31266798
The effects of perineal disinfection on infant's oral microflora after transvaginal examination during delivery. PMID:31234808
Metagenomic analysis of bile salt biotransformation in the human gut microbiome. PMID:31234773
Partial defoliation of Brachypodium distachyon plants grown in petri dishes under low light increases P and other nutrient levels concomitantly with transcriptional changes in the roots. PMID:31223535
Identification and characterization of Populus microRNAs in response to plant growth-promoting endophytic Streptomyces sp. SSD49. PMID:31222457
Histopathological and proteomic analyses identify integrin-β1 as a potential mediator of phlebosclerosis in uremic patients. PMID:31214872
Genomic Diversity of Two Hydrocarbon-Degrading and Plant Growth-Promoting Pseudomonas Species Isolated from the Oil Field of Bóbrka (Poland). PMID:31212674
Fall armyworm (Spodoptera frugiperda Smith) feeding elicits differential defense responses in upland and lowland switchgrass. PMID:31194847
Astragalus alters gut-microbiota composition in type 2 diabetes mice: clues to its pharmacology. PMID:31190935
A Two-Enzyme Adaptive Unit within Bacterial Folate Metabolism. PMID:31189117
Genetic Predisposition for Immune System, Hormone, and Metabolic Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome: A Pilot Study. PMID:31179255
Temporal proteome dynamics of Clostridium cellulovorans cultured with major plant cell wall polysaccharides. PMID:31159733
Multi-Omic Data Interpretation to Repurpose Subtype Specific Drug Candidates for Breast Cancer. PMID:31134131
Horizontal Gene Transfer as an Indispensable Driver for Evolution of Neocallimastigomycota into a Distinct Gut-Dwelling Fungal Lineage. PMID:31126947
Identification of potential therapeutic target genes in mouse mesangial cells associated with diabetic nephropathy using bioinformatics analysis. PMID:31105790
Proteomics analysis reveals heat shock proteins involved in caprine parainfluenza virus type 3 infection. PMID:31101113
Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease. PMID:31092280
OsbZIP81, A Homologue of Arabidopsis VIP1, May Positively Regulate JA Levels by Directly Targetting the Genes in JA Signaling and Metabolism Pathway in Rice. PMID:31086007
Genetic mechanism underlying sexual plasticity and its association with colour patterning in zebrafish (Danio rerio). PMID:31060508
The genomes of pecan and Chinese hickory provide insights into Carya evolution and nut nutrition. PMID:31049561
Efficient proximal gradient algorithm for inference of differential gene networks. PMID:31046666
Matrix Metalloproteinase 11 Is a Potential Therapeutic Target in Lung Adenocarcinoma. PMID:31024988
Reverting Metabolic Dysfunction in Cortex and Cerebellum of APP/PS1 Mice, a Model for Alzheimer's Disease by Pioglitazone, a Peroxisome Proliferator-Activated Receptor Gamma (PPARγ) Agonist. PMID:31016475
Transcriptomic analysis of differential gene expression during chick periocular neural crest differentiation into corneal cells. PMID:31004457
[Role of miR-106b-5p in the regulation of gene profiles in endothelial cells]. PMID:30996357
Identification of atherosclerosis-related prioritizing metabolites based on a multi-omics composite network. PMID:30988716
ITLNI identified by comprehensive bioinformatic analysis as a hub candidate biological target in human epithelial ovarian cancer. PMID:30988639
Simultaneous Interrogation of Cancer Omics to Identify Subtypes With Significant Clinical Differences. PMID:30984238
Reconciling high-throughput gene essentiality data with metabolic network reconstructions. PMID:30973869
Network-based characterization of drug-protein interaction signatures with a space-efficient approach. PMID:30953486
Proteomic analysis of the similarities and differences of soil drought and polyethylene glycol stress responses in wheat (Triticum aestivum L.). PMID:30953278
Efficacy and safety assessment of a TRAF6-targeted nanoimmunotherapy in atherosclerotic mice and non-human primates. PMID:30936448
Pyrosequencing Uncovers a Shift in Bacterial Communities Across Life Stages of Octodonta nipae (Coleoptera: Chrysomelidae). PMID:30930872
"Redox lipidomics technology: Looking for a needle in a haystack". PMID:30928338
Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. PMID:30914504
MetaboAnalystR 2.0: From Raw Spectra to Biological Insights. PMID:30909447
A novel transcriptome-derived SNPs array for tench (Tinca tinca L.). PMID:30889192
Genome-wide genotyping uncovers genetic diversity, phylogeny, signatures of selection, and population structure of Chinese Jiangquhai pigs in a global perspective1. PMID:30882885
De novo structure determination of 3-((3-aminopropyl)amino)-4-hydroxybenzoic acid, a novel and abundant metabolite in Acinetobacter baylyi ADP1. PMID:30874951
Integrative analysis of KIF4A, 9, 18A, and 23 and their clinical significance in low-grade glioma and glioblastoma. PMID:30872592
Decorin as a prognostic biomarker in patients with malignant peripheral nerve sheath tumors. PMID:30867792
Post-transcriptional regulatory patterns revealed by protein-RNA interactions. PMID:30867517
Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome. PMID:30866812
Comparative transcriptome analysis uncovers the regulatory functions of long noncoding RNAs in fruit development and color changes of Fragaria pentaphylla. PMID:30854215
Transcriptome Sequencing and Analysis of Changes Associated with Insecticide Resistance in the Dengue Mosquito (Aedes aegypti) in Vietnam. PMID:30834881
Comparative transcriptome analysis reveals significant differences in the regulation of gene expression between hydrogen cyanide- and ethylene-treated Arabidopsis thaliana. PMID:30832566
Identification of bioactive metabolites using activity metabolomics. PMID:30814649
Man-made microbial resistances in built environments. PMID:30814504
Transcriptome analysis reveals the impact of arbuscular mycorrhizal symbiosis on Sesbania cannabina expose to high salinity. PMID:30808908
Genetic variants differentially associated with rheumatoid arthritis and systemic lupus erythematosus reveal the disease-specific biology. PMID:30804378
Multigenerational metabolic profiling in the Michigan PBB registry. PMID:30782538
Sequence and cultivation study of Muribaculaceae reveals novel species, host preference, and functional potential of this yet undescribed family. PMID:30782206
Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids. PMID:30781503
A Novel Discovery: Holistic Efficacy at the Special Organ Level of Pungent Flavored Compounds from Pungent Traditional Chinese Medicine. PMID:30754631
Hypersensitive IFN Responses in Lupus Keratinocytes Reveal Key Mechanistic Determinants in Cutaneous Lupus. PMID:30745462
Imaging-Genomic Study of Head and Neck Squamous Cell Carcinoma: Associations Between Radiomic Phenotypes and Genomic Mechanisms via Integration of The Cancer Genome Atlas and The Cancer Imaging Archive. PMID:30730765
'Candidatus Ornithobacterium hominis': insights gained from draft genomes obtained from nasopharyngeal swabs. PMID:30720420
Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices. PMID:30718727
Coupled changes of bacterial community and function in the gut of mud crab (Scylla Paramamosain) in response to Baimang disease. PMID:30712137
Network-based identification of critical regulators as putative drivers of human cleft lip. PMID:30704473
Genome-wide analysis of circular RNAs in goat skin fibroblast cells in response to Orf virus infection. PMID:30697481
Comparative analysis of microsatellite, SNP, and InDel markers in four Rhododendron species based on RNA-seq. PMID:30697114
Microbiome Alteration in Type 2 Diabetes Mellitus Model of Zebrafish. PMID:30696861
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. PMID:30695998
Fibroblast activation and abnormal extracellular matrix remodelling as common hallmarks in three cancer-prone genodermatoses. PMID:30693469
AutophagySMDB: a curated database of small molecules that modulate protein targets regulating autophagy. PMID:30669929
Pathway enrichment analysis and visualization of omics data using g:Profiler, GSEA, Cytoscape and EnrichmentMap. PMID:30664679
In Silico Prediction of Small Molecule-miRNA Associations Based on the HeteSim Algorithm. PMID:30654189
Alterations in PD-L1 Expression Associated with Acquisition of Resistance to ALK Inhibitors in ALK-Rearranged Lung Cancer. PMID:30653748
Comparative metagenomic and metatranscriptomic analyses reveal the breed effect on the rumen microbiome and its associations with feed efficiency in beef cattle. PMID:30642389
Immune genes are hotspots of shared positive selection across birds and mammals. PMID:30620335
The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation. PMID:30619486
Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells. PMID:30609717
Quantification of enterohemorrhagic Escherichia coli O157:H7 protein abundance by high-throughput proteome. PMID:30596662
Modeling human prostate cancer progression in vitro. PMID:30590461
FELLA: an R package to enrich metabolomics data. PMID:30577788
Antimicrobial Chemicals Associate with Microbial Function and Antibiotic Resistance Indoors. PMID:30574558
Bacterial diversity and community in Qula from the Qinghai-Tibetan Plateau in China. PMID:30568858
Transcriptomic Characterization of the South American Freshwater Stingray Potamotrygon motoro Venom Apparatus. PMID:30567320
A genome-scale metabolic model of potato late blight suggests a photosynthesis suppression mechanism. PMID:30537923
Building an octaploid genome and transcriptome of the medicinal plant Pogostemon cablin from Lamiales. PMID:30532075
Metabolome-wide association study of anti-epileptic drug treatment during pregnancy. PMID:30521819
Altered expression of K13 disrupts DNA replication and repair in Plasmodium falciparum. PMID:30486796
Nuclear genome sequence of the plastid-lacking cryptomonad Goniomonas avonlea provides insights into the evolution of secondary plastids. PMID:30482201
Chi-miR-3031 regulates beta-casein via the PI3K/AKT-mTOR signaling pathway in goat mammary epithelial cells (GMECs). PMID:30482199
Metabolomics and transcriptomics pathway approach reveals outcome-specific perturbations in COPD. PMID:30459441
Combinational Biomarkers for Atrial Fibrillation Derived from Atrial Appendage and Plasma Metabolomics Analysis. PMID:30446671
Evaluating the Information Content of Shallow Shotgun Metagenomics. PMID:30443602
Born to Cry: A Genetic Dissection of Infant Vocalization. PMID:30420800
Gastric Cancer Cell Lines Have Different MYC-Regulated Expression Patterns but Share a Common Core of Altered Genes. PMID:30410872
Systemic neurotransmitter responses to clinically approved and experimental neuropsychiatric drugs. PMID:30410047
Network and Pathway Analysis of Toxicogenomics Data. PMID:30405693
Comparative genomics of the major parasitic worms. PMID:30397333
Proteomic analysis of human prostate cancer PC-3M-1E8 cells and PC-3M-2B4 cells of same origin but with different metastatic potential. PMID:30379883
Analysis of the Trichuris suis excretory/secretory proteins as a function of life cycle stage and their immunomodulatory properties. PMID:30374177
Feature related multi-view nonnegative matrix factorization for identifying conserved functional modules in multiple biological networks. PMID:30373534
Rhazyaminine from Rhazya stricta Inhibits Metastasis and Induces Apoptosis by Downregulating Bcl-2 Gene in MCF7 Cell Line. PMID:30373413
From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology. PMID:30373182
The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. PMID:30371894
Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics. PMID:30368244
Protective Effect of Pediococcus pentosaceus LI05 Against Clostridium difficile Infection in a Mouse Model. PMID:30356740
Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem. PMID:30356154
High-throughput sequencing analysis of Euphorbia fischeriana Steud provides insights into the molecular mechanism of pharmaceutical ingredient biosynthesis. PMID:30333951
A phylogenomic and ecological analysis of the globally abundant Marine Group II archaea (Ca. Poseidoniales ord. nov.). PMID:30323263
Complete genome sequence of the halophile bacterium Kushneria konosiri X49T, isolated from salt-fermented Konosirus punctatus. PMID:30305867
Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice. PMID:30297755
Tripal Developer Toolkit. PMID:30295719
Efficient multi-task chemogenomics for drug specificity prediction. PMID:30286165
Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus. PMID:30285612
Analysis of Time-Series Gene Expression Data to Explore Mechanisms of Chemical-Induced Hepatic Steatosis Toxicity. PMID:30279702
Quantitative Proteomics Analysis of Lettuce (Lactuca sativa L.) Reveals Molecular Basis-Associated Auxin and Photosynthesis with Bolting Induced by High Temperature. PMID:30274198
Cellular stress and redox activity proteins are involved in gastric carcinogenesis associated with Helicobacter pylori infection expressing high levels of thioredoxin-1. PMID:30269443
Progress of analytical tools and techniques for human gut microbiome research. PMID:30267313
Widespread Antibiotic, Biocide, and Metal Resistance in Microbial Communities Inhabiting a Municipal Waste Environment and Anthropogenically Impacted River. PMID:30258036
Comparative genome analysis provides deep insights into Aeromonas hydrophila taxonomy and virulence-related factors. PMID:30257645
Synthesizing Signaling Pathways from Temporal Phosphoproteomic Data. PMID:30257219
Potential use of compounds from sea cucumbers as MDM2 and CXCR4 inhibitors to control cancer cell growth. PMID:30250516
Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater. PMID:30245678
A compendium of physical exercise-related human genes: an 'omic scale analysis. PMID:30237656
Bioprospecting for Genes Encoding Hydrocarbon-Degrading Enzymes from Metagenomic Samples Isolated from Northern Adriatic Sea Sediments. PMID:30228802
Modeling and Simulating the Aerobic Carbon Metabolism of a Green Microalga Using Petri Nets and New Concepts of VANESA. PMID:30218605
A Robust Methodology for Assessing Differential Homeolog Contributions to the Transcriptomes of Allopolyploids. PMID:30213855
A comprehensive investigation using meta-analysis and bioinformatics on miR-34a-5p expression and its potential role in head and neck squamous cell carcinoma. PMID:30210668
Modified LDL Particles Activate Inflammatory Pathways in Monocyte-derived Macrophages: Transcriptome Analysis. PMID:30205792
Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress. PMID:30205432
Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function. PMID:30204780
Gut Bacterial Communities of Dendroctonus valens and D. mexicanus (Curculionidae: Scolytinae): A Metagenomic Analysis across Different Geographical Locations in Mexico. PMID:30200218
Copy Number Alterations in Tumor Genomes Deleting Antineoplastic Drug Targets Partially Compensated by Complementary Amplifications. PMID:30194077
miR-324-5p is up regulated in end-stage osteoarthritis and regulates Indian Hedgehog signalling by differing mechanisms in human and mouse. PMID:30193893
Somatic inactivating PTPRJ mutations and dysregulated pathways identified in canine malignant melanoma by integrated comparative genomic analysis. PMID:30188888
Compositional and predicted functional analysis of the gut microbiota of Radix auricularia (Linnaeus) via high-throughput Illumina sequencing. PMID:30186698
Comparison of gene expression profiles between human erythroid cells derived from fetal liver and adult peripheral blood. PMID:30186694
Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia. PMID:30177915
The variation profile of intestinal microbiota in blunt snout bream (Megalobrama amblycephala) during feeding habit transition. PMID:30176798
Exploring the Mechanism of Flavonoids Through Systematic Bioinformatics Analysis. PMID:30158870
Genome-Wide Characterization of Selection Signatures and Runs of Homozygosity in Ugandan Goat Breeds. PMID:30154830
Integrated proteomic and phosphoproteomic analyses of cisplatin-sensitive and resistant bladder cancer cells reveal CDK2 network as a key therapeutic target. PMID:30145203
The impact of Helicobacter pylori infection, eradication therapy and probiotic supplementation on gut microenvironment homeostasis: An open-label, randomized clinical trial. PMID:30145102
Loss of the E3 ubiquitin ligase MKRN1 represses diet-induced metabolic syndrome through AMPK activation. PMID:30143610
Identification of biomarkers for Barcelona Clinic Liver Cancer staging and overall survival of patients with hepatocellular carcinoma. PMID:30138346
Biases in Prokaryotic Community Amplicon Sequencing Affected by DNA Extraction Methods in Both Saline and Non-saline Soil. PMID:30127778
PARP1 Is Up-Regulated in Non-small Cell Lung Cancer Tissues in the Presence of the Cyanobacterial Toxin Microcystin. PMID:30127774
Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory. PMID:30127461
Identifying the druggable interactome of EWS-FLI1 reveals MCL-1 dependent differential sensitivities of Ewing sarcoma cells to apoptosis inducers. PMID:30123424
Dietary l-arginine Supplementation Alleviates the Intestinal Injury and Modulates the Gut Microbiota in Broiler Chickens Challenged by Clostridium perfringens. PMID:30108569
The genome of the golden apple snail Pomacea canaliculata provides insight into stress tolerance and invasive adaptation. PMID:30107526
Multi-Scale Network Model Supported by Proteomics for Analysis of Combined Gemcitabine and Birinapant Effects in Pancreatic Cancer Cells. PMID:30084546
Transcriptomic Profiles in Zebrafish Liver Permit the Discrimination of Surface Water with Pollution Gradient and Different Discharges. PMID:30081495
Biobank-driven genomic discovery yields new insight into atrial fibrillation biology. PMID:30061737
Transcriptomic Analysis of Hepatic Cells in Multicellular Organotypic Liver Models. PMID:30054499
KampoDB, database of predicted targets and functional annotations of natural medicines. PMID:30046160
MoDentify: phenotype-driven module identification in metabolomics networks at different resolutions. PMID:30032270
Co-expression network of transcription factors reveal ethylene-responsive element-binding factor as key regulator of wood phenotype in Eucalyptus tereticornis. PMID:30023147
Identification of SNPs potentially related to immune responses and growth performance in Litopenaeus vannamei by RNA-seq analyses. PMID:30013834
Identification of potential target genes in pancreatic ductal adenocarcinoma by bioinformatics analysis. PMID:30013637
Body Mass Index Differences in the Gut Microbiota Are Gender Specific. PMID:29988340
Combining Targeted Metabolites Analysis and Transcriptomics to Reveal Chemical Composition Difference and Underlying Transcriptional Regulation in Maca (Lepidium Meyenii Walp.) Ecotypes. PMID:29970867
Upregulation of Immune Process-Associated Genes in RAW264.7 Macrophage Cells in Response to Burkholderia pseudomallei Infection. PMID:29967766
Transcriptome and Expression Profiling Analysis of Recalcitrant Tea (Camellia sinensis L.) Seeds Sensitive to Dehydration. PMID:29967765
Identification of Biomarkers Based on Differentially Expressed Genes in Papillary Thyroid Carcinoma. PMID:29967488
Genome-Wide Association Analyses Reveal the Importance of Alternative Splicing in Diversifying Gene Function and Regulating Phenotypic Variation in Maize. PMID:29967286
A taxonomic signature of obesity in a large study of American adults. PMID:29950689
Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea. PMID:29946801
Inferring potential small molecule-miRNA association based on triple layer heterogeneous network. PMID:29943160
Identification of endothelial selectin as a potential prognostic marker in breast cancer. PMID:29928363
Multi-omics "upstream analysis" of regulatory genomic regions helps identifying targets against methotrexate resistance of colon cancer. PMID:29900117
Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05. PMID:29892946
Differentially Expressed Genes in Osteomyelitis Induced by Staphylococcus aureus Infection. PMID:29887852
LOLAweb: a containerized web server for interactive genomic locus overlap enrichment analysis. PMID:29878235
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
Comparative transcriptome analysis reveals the regulatory networks of cytokinin in promoting the floral feminization in the oil plant Sapium sebiferum. PMID:29848288
In silico design of novel proton-pump inhibitors with reduced adverse effects. PMID:29845582
PAM-OBG: A monoamine oxidase B specific prodrug that inhibits MGMT and generates DNA interstrand crosslinks, potentiating temozolomide and chemoradiation therapy in intracranial glioblastoma. PMID:29844863
Identification and bioinformatics analysis of overlapping differentially expressed genes in depression, papillary thyroid cancer and uterine fibroids. PMID:29805500
Raphidocelis subcapitata (=Pseudokirchneriella subcapitata) provides an insight into genome evolution and environmental adaptations in the Sphaeropleales. PMID:29795299
Embryonic transcriptome and proteome analyses on hepatic lipid metabolism in chickens divergently selected for abdominal fat content. PMID:29792171
Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS. PMID:29789581
Mapping the HLA Ligandome of Colorectal Cancer Reveals an Imprint of Malignant Cell Transformation. PMID:29789417
A Computational Approach Using Bioinformatics to Screening Drug Targets for Leishmania infantum Species. PMID:29785196
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. PMID:29780371
Pathway-based approach using hierarchical components of rare variants to analyze multiple phenotypes. PMID:29745849
Identifying Cancer Specific Driver Modules Using a Network-Based Method. PMID:29738475
Proteomics integrated with metabolomics: analysis of the internal causes of nutrient changes in alfalfa at different growth stages. PMID:29728056
Ca. Endozoicomonas cretensis: A Novel Fish Pathogen Characterized by Genome Plasticity. PMID:29726925
Shared liver-like transcriptional characteristics in liver metastases and corresponding primary colorectal tumors. PMID:29721060
Sex Determination in Ceratopteris richardii Is Accompanied by Transcriptome Changes That Drive Epigenetic Reprogramming of the Young Gametophyte. PMID:29720393
Metabolome Integrated Analysis of High-Temperature Response in Pinus radiata. PMID:29719546
Regularized Multi-View Subspace Clustering for Common Modules Across Cancer Stages. PMID:29701681
Individualized predictive signatures for 5-fluorouracil-based chemotherapy in right- and left-sided colon cancer. PMID:29700901
Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines. PMID:29698445
Litopenaeus vannamei Transcriptome Profile of Populations Evaluated for Growth Performance and Exposed to White Spot Syndrome Virus (WSSV). PMID:29692800
Continuously Monocropped Jerusalem Artichoke Changed Soil Bacterial Community Composition and Ammonia-Oxidizing and Denitrifying Bacteria Abundances. PMID:29692769
Signalling maps in cancer research: construction and data analysis. PMID:29688383
dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication. PMID:29688359
The phosphorylated redox proteome of Chlamydomonas reinhardtii: Revealing novel means for regulation of protein structure and function. PMID:29673699
Hospitalized Premature Infants Are Colonized by Related Bacterial Strains with Distinct Proteomic Profiles. PMID:29636439
Alterations of Metabolic and Lipid Profiles in Polymyxin-Resistant Pseudomonas aeruginosa. PMID:29632014
Liver regeneration during the associating liver partition and portal vein ligation for staged hepatectomy procedure in Sus scrofa is positively modulated by stem cells. PMID:29616108
Genome and evolution of the shade-requiring medicinal herb Panax ginseng. PMID:29604169
Transcriptome-wide mapping of signaling pathways and early immune responses in lumpfish leukocytes upon in vitro bacterial exposure. PMID:29588496
Proteomic analysis of melatonin-mediated osmotic tolerance by improving energy metabolism and autophagy in wheat (Triticum aestivum L.). PMID:29564630
Studying microbial functionality within the gut ecosystem by systems biology. PMID:29556373
The Pathway Coexpression Network: Revealing pathway relationships. PMID:29554099
Identification of lncRNAs by microarray analysis reveals the potential role of lncRNAs in cervical cancer pathogenesis. PMID:29552195
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
Minority stress and leukocyte gene expression in sexual minority men living with treated HIV infection. PMID:29548994
A graphical and computational modeling platform for biological pathways. PMID:29543794
Expression of Hippo pathway genes and their clinical significance in colon adenocarcinoma. PMID:29541248
A benzene-degrading nitrate-reducing microbial consortium displays aerobic and anaerobic benzene degradation pathways. PMID:29540736
Identification of Discriminating Metabolic Pathways and Metabolites in Human PBMCs Stimulated by Various Pathogenic Agents. PMID:29535640
FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects. PMID:29533703
Proteomic Analysis of Combined Gemcitabine and Birinapant in Pancreatic Cancer Cells. PMID:29520231
Proteomic profiling of lung immune cells reveals dysregulation of phagocytotic pathways in female-dominated molecular COPD phenotype. PMID:29514663
Long-term smoking alters abundance of over half of the proteome in bronchoalveolar lavage cell in smokers with normal spirometry, with effects on molecular pathways associated with COPD. PMID:29514648
Metabolic Profiling of Dendrobium officinale in Response to Precursors and Methyl Jasmonate. PMID:29510516
Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activator Nutlin-3. PMID:29504919
From correlation to causation: analysis of metabolomics data using systems biology approaches. PMID:29503602
Compatible Solute Synthesis and Import by the Moderate Halophile Spiribacter salinus: Physiology and Genomics. PMID:29497403
Human milk oligosaccharides protect against the development of autoimmune diabetes in NOD-mice. PMID:29497108
Core Microbiome of Medicinal Plant Salvia miltiorrhiza Seed: A Rich Reservoir of Beneficial Microbes for Secondary Metabolism? PMID:29495531
Data processing, multi-omic pathway mapping, and metabolite activity analysis using XCMS Online. PMID:29494574
Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes. PMID:29492402
Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia. PMID:29486796
GCN5L1/BLOS1 Links Acetylation, Organelle Remodeling, and Metabolism. PMID:29477615
Genomewide Transcriptional Responses of Iron-Starved Chlamydia trachomatis Reveal Prioritization of Metabolic Precursor Synthesis over Protein Translation. PMID:29468197
Quantitative Viral Community DNA Analysis Reveals the Dominance of Single-Stranded DNA Viruses in Offshore Upper Bathyal Sediment from Tohoku, Japan. PMID:29467725
Calycosin Orchestrates Osteogenesis of Danggui Buxue Tang in Cultured Osteoblasts: Evaluating the Mechanism of Action by Omics and Chemical Knock-out Methodologies. PMID:29449812
Dynamic network biomarker indicates pulmonary metastasis at the tipping point of hepatocellular carcinoma. PMID:29445139
Identification of gene expression models for laryngeal squamous cell carcinoma using co-expression network analysis. PMID:29443735
Genomewide Identification of Essential Genes and Fitness Determinants of Streptococcus mutans UA159. PMID:29435491
Dysbiosis of Inferior Turbinate Microbiota Is Associated with High Total IgE Levels in Patients with Allergic Rhinitis. PMID:29426044
Human Suction Blister Fluid Composition Determined Using High-Resolution Metabolomics. PMID:29425024
A high-throughput study on endothelial cell adhesion and growth mediated by adsorbed serum protein via signaling pathway PCR array. PMID:29423265
RNA-seq transcriptome analysis of breast cancer cell lines under shikonin treatment. PMID:29422643
circRNA_0046366 inhibits hepatocellular steatosis by normalization of PPAR signaling. PMID:29391755
Transcriptome profiling of lentil (Lens culinaris) through the first 24 hours of Ascochyta lentis infection reveals key defence response genes. PMID:29385986
Vgll3 and the Hippo pathway are regulated in Sertoli cells upon entry and during puberty in Atlantic salmon testis. PMID:29382956
iTRAQ-based proteomics analysis of autophagy-mediated immune responses against the vascular fungal pathogen Verticillium dahliae in Arabidopsis. PMID:29369001
Plasma proteomic study of acute mountain sickness susceptible and resistant individuals. PMID:29352170
Identify Down syndrome transcriptome associations using integrative analysis of microarray database and correlation-interaction network. PMID:29351810
Preventive Effect and Safety of a Follicle Stimulating Hormone Inhibitory Formulation Containing a Mixture of Coicis Semen and Artemisia capillaris for Precocious Puberty: A Preliminary Experimental Study Using Female Rats. PMID:29348765
Multiple losses of photosynthesis and convergent reductive genome evolution in the colourless green algae Prototheca. PMID:29343788
Comparative Transcriptome Analysis Identifies Putative Genes Involved in Steroid Biosynthesis in Euphorbia tirucalli. PMID:29342957
Genome-Wide Methylation Patterns in Androgen-Independent Prostate Cancer Cells: A Comprehensive Analysis Combining MeDIP-Bisulfite, RNA, and microRNA Sequencing Data. PMID:29324665
Molecular processes underlying synergistic linuron mineralization in a triple-species bacterial consortium biofilm revealed by differential transcriptomics. PMID:29314727
Identification and validation long non-coding RNAs of oral squamous cell carcinoma by bioinformatics method. PMID:29296179
Genome-wide Study of Atrial Fibrillation Identifies Seven Risk Loci and Highlights Biological Pathways and Regulatory Elements Involved in Cardiac Development. PMID:29290336
Comparative analysis of phosphoethanolamine transferases involved in polymyxin resistance across 10 clinically relevant Gram-negative bacteria. PMID:29288722
In Silico Analysis of the Small Molecule Content of Outer Membrane Vesicles Produced by Bacteroides thetaiotaomicron Indicates an Extensive Metabolic Link between Microbe and Host. PMID:29276507
Identification of the Sex-Biased Gene Expression and Putative Sex-Associated Genes in Eucommia ulmoides Oliver Using Comparative Transcriptome Analyses. PMID:29258253
Interactome Analysis of Microtubule-targeting Agents Reveals Cytotoxicity Bases in Normal Cells. PMID:29246518
Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections. PMID:29221465
Differently expressed long noncoding RNAs and mRNAs in TK6 cells exposed to low dose hydroquinone. PMID:29221148
Mountain hare transcriptome and diagnostic markers as resources to monitor hybridization with European hares. PMID:29206218
Validity and clinical impact of glucose transporter 1 expression in colorectal cancer. PMID:29205188
Remodelling of the gut microbiota by hyperactive NLRP3 induces regulatory T cells to maintain homeostasis. PMID:29196621
Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers. PMID:29196415
Systems Bioinformatics: increasing precision of computational diagnostics and therapeutics through network-based approaches. PMID:29186305
The bacterial interlocked process ONtology (BiPON): a systemic multi-scale unified representation of biological processes in prokaryotes. PMID:29169408
Systemic Responses of Multidrug-Resistant Pseudomonas aeruginosa and Acinetobacter baumannii Following Exposure to the Antimicrobial Peptide Cathelicidin-BF Imply Multiple Intracellular Targets. PMID:29164074
A Review of Pathway-Based Analysis Tools That Visualize Genetic Variants. PMID:29163640
Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. PMID:29156751
Comparative Transcriptome Analysis Provides Insights into Differentially Expressed Genes and Long Non-Coding RNAs between Ovary and Testis of the Mud Crab (Scylla paramamosain). PMID:29152671
Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and compositional characterization. PMID:29145496
Copy number gains at chr3p25 and chr11p11 are associated with lymph node involvement and survival in muscle-invasive bladder tumors. PMID:29140994
SuperDRUG2: a one stop resource for approved/marketed drugs. PMID:29140469
Composition, diversity and function of intestinal microbiota in pacific white shrimp (Litopenaeus vannamei) at different culture stages. PMID:29134144
Combining membrane proteomics and computational three-way pathway analysis revealed signalling pathways preferentially regulated in human iPSCs and human ESCs. PMID:29118436
Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data. PMID:29110491
PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database. PMID:29106626
Signatures of adaptation and symbiosis in genomes and transcriptomes of Symbiodinium. PMID:29101370
RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole. PMID:29099835
Nonpher: computational method for design of hard-to-synthesize structures. PMID:29086122
Cereal products derived from wheat, sorghum, rice and oats alter the infant gut microbiota in vitro. PMID:29085002
Hypoxia tolerance, longevity and cancer-resistance in the mole rat Spalax - a liver transcriptomics approach. PMID:29084988
Comparative genomics reveals cotton-specific virulence factors in flexible genomic regions in Verticillium dahliae and evidence of horizontal gene transfer from Fusarium. PMID:29084346
The circulating microbiome signature and inferred functional metagenomics in alcoholic hepatitis. PMID:29083504
Role of the luxS gene in bacteriocin biosynthesis by Lactobacillus plantarum KLDS1.0391: A proteomic analysis. PMID:29066774
The Enigmatic Genome of an Obligate Ancient Spiroplasma Symbiont in a Hadal Holothurian. PMID:29054873
Meta-analysis approaches to combine multiple gene set enrichment studies. PMID:29052247
Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome. PMID:29042495
Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis. PMID:29042298
13C metabolic flux analysis of three divergent extremely thermophilic bacteria: Geobacillus sp. LC300, Thermus thermophilus HB8, and Rhodothermus marinus DSM 4252. PMID:29037779
The transcriptome of the developing grain: a resource for understanding seed development and the molecular control of the functional and nutritional properties of wheat. PMID:29020946
The gut microbiome in atherosclerotic cardiovascular disease. PMID:29018189
Pathway Analysis with Signaling Hypergraphs. PMID:28991726
Hybrid Sequencing of Full-Length cDNA Transcripts of Stems and Leaves in Dendrobium officinale. PMID:28981454
Multi-dimensional histone methylations for coordinated regulation of gene expression under hypoxia. PMID:28977425
LncRNA plasmacytoma variant translocation 1 is an oncogene in bladder urothelial carcinoma. PMID:28969069
Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants. PMID:28968757
Phenotype-driven identification of modules in a hierarchical map of multifluid metabolic correlations. PMID:28948040
Comparative proteomic analysis of pituitary glands from Huoyan geese between pre-laying and laying periods using an iTRAQ-based approach. PMID:28945779
Network-based analysis of the molecular mechanisms of multiple myeloma and monoclonal gammopathy of undetermined significance. PMID:28943924
Prognostic value of DNA repair genes based on stratification of glioblastomas. PMID:28938550
Three-way interaction model to trace the mechanisms involved in Alzheimer's disease transgenic mice. PMID:28934252
Screening of miRNA profiles and construction of regulation networks in early and late lactation of dairy goat mammary glands. PMID:28931951
Comparative Genomic Analysis of the Human Gut Microbiome Reveals a Broad Distribution of Metabolic Pathways for the Degradation of Host-Synthetized Mucin Glycans and Utilization of Mucin-Derived Monosaccharides. PMID:28912798
In silico prediction of drug-target interaction networks based on drug chemical structure and protein sequences. PMID:28894115
Ecological and genomic profiling of anaerobic methane-oxidizing archaea in a deep granitic environment. PMID:28885627
Tau exacerbates excitotoxic brain damage in an animal model of stroke. PMID:28883427
A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog. PMID:28879061
Transcriptome analysis of the response of Burmese python to digestion. PMID:28873961
Comparative Proteomic Analysis Provides insight into the Key Proteins as Possible Targets Involved in Aspirin Inhibiting Biofilm Formation of Staphylococcus xylosus. PMID:28871227
MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for the Construction of Sequence Data Warehouses. PMID:28867956
The respiratory tract microbial biogeography in alcohol use disorder. PMID:28860145
Conserved Transcription Factors Steer Growth-Related Genomic Programs in Daphnia. PMID:28854641
Unraveling the gut microbiome of the long-lived naked mole-rat. PMID:28852094
Proteome dynamics and physiological responses to short-term salt stress in Leymus chinensis leaves. PMID:28846722
Contrasting effects of copper limitation on the photosynthetic apparatus in two strains of the open ocean diatom Thalassiosira oceanica. PMID:28837661
Elucidation of the molecular responses to waterlogging in Sesbania cannabina roots by transcriptome profiling. PMID:28835646
Genomic analysis of methanogenic archaea reveals a shift towards energy conservation. PMID:28826405
Maternal obesity is associated with gut microbial metabolic potential in offspring during infancy. PMID:28819768
Morphologic, phenotypic, and transcriptomic characterization of classically and alternatively activated canine blood-derived macrophages in vitro. PMID:28817687
Effect of barley supplementation on the fecal microbiota, caecal biochemistry, and key biomarkers of obesity and inflammation in obese db/db mice. PMID:28815303
Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria. PMID:28813680
Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. PMID:28800327
Perturbed human sub-networks by Fusobacterium nucleatum candidate virulence proteins. PMID:28793925
The Cyanobacteria-Dominated Sponge Dactylospongia elegans in the South China Sea: Prokaryotic Community and Metagenomic Insights. PMID:28790992
Identification of SNPs associated with muscle yield and quality traits using allelic-imbalance analyses of pooled RNA-Seq samples in rainbow trout. PMID:28784089
PhosphoPredict: A bioinformatics tool for prediction of human kinase-specific phosphorylation substrates and sites by integrating heterogeneous feature selection. PMID:28761071
Integrated regulatory network reveals the early salt tolerance mechanism of Populus euphratica. PMID:28754917
Validation of a novel Mho microarray for a comprehensive characterisation of the Mycoplasma hominis action in HeLa cell infection. PMID:28753664
Novel Gene and Network Associations Found for Acute Lymphoblastic Leukemia Using Case-Control and Family-Based Studies in Multiethnic Populations. PMID:28751478
Genetic variants including markers from the exome chip and metabolite traits of type 2 diabetes. PMID:28729637
High throughput sequencing of small RNAs reveals dynamic microRNAs expression of lipid metabolism during Camellia oleifera and C. meiocarpa seed natural drying. PMID:28728593
ProtozoaDB 2.0: A Trypanosoma Brucei Case Study. PMID:28726736
Pathways on demand: automated reconstruction of human signaling networks. PMID:28725467
iTRAQ-based quantitative proteomic analysis reveals alterations in the metabolism of Actinidia arguta. PMID:28720800
Pharmacogenomics study of thiazide diuretics and QT interval in multi-ethnic populations: the cohorts for heart and aging research in genomic epidemiology. PMID:28719597
Gene microarray analysis of expression profiles in liver ischemia and reperfusion. PMID:28713993
Complete Chloroplast Genome Sequence of Coptis chinensis Franch. and Its Evolutionary History. PMID:28698879
Enriching plausible new hypothesis generation in PubMed. PMID:28678852
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. PMID:28652349
On the performance of de novo pathway enrichment. PMID:28649433
Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis. PMID:28649415
Pattern of Protein Expression in Developing Wheat Grains Identified through Proteomic Analysis. PMID:28649254
Identification of a novel fungus, Trichoderma asperellum GDFS1009, and comprehensive evaluation of its biocontrol efficacy. PMID:28644879
Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta. PMID:28644839
Computational dynamic approaches for temporal omics data with applications to systems medicine. PMID:28638442
Protein expression in tension wood formation monitored at high tissue resolution in Populus. PMID:28633298
Data mining and pathway analysis of glucose-6-phosphate dehydrogenase with natural language processing. PMID:28627690
Identifying drug-pathway association pairs based on L1L2,1-integrative penalized matrix decomposition. PMID:28624800
Differential effects of a post-anthesis heat stress on wheat (Triticum aestivum L.) grain proteome determined by iTRAQ. PMID:28615669
Visualization and Analysis of MicroRNAs within KEGG Pathways using VANESA. PMID:28609293
Workflow and web application for annotating NCBI BioProject transcriptome data. PMID:28605765
Proteomic analysis by iTRAQ-MRM of soybean resistance to Lamprosema Indicate. PMID:28587595
Integrative gene set enrichment analysis utilizing isoform-specific expression. PMID:28580727
RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. PMID:28577019
The replicative lifespan-extending deletion of SGF73 results in altered ribosomal gene expression in yeast. PMID:28568901
Metabolomic profiling in a Hedgehog Interacting Protein (Hhip) murine model of chronic obstructive pulmonary disease. PMID:28566717
Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype. PMID:28559929
SiGNet: A signaling network data simulator to enable signaling network inference. PMID:28545060
GLANET: genomic loci annotation and enrichment tool. PMID:28541490
Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment. PMID:28538171
Differences in Microbiota Membership along the Gastrointestinal Tract of Piglets and Their Differential Alterations Following an Early-Life Antibiotic Intervention. PMID:28536561
Fipronil-induced enantioselective developmental toxicity to zebrafish embryo-larvae involves changes in DNA methylation. PMID:28536466
Insights into the prevalence and underlying causes of clonal variation through transcriptomic analysis in Pichia pastoris. PMID:28534062
Label-Free Quantitative Proteomic Analysis of Chitosan Oligosaccharide-Treated Rice Infected with Southern Rice Black-Streaked Dwarf Virus. PMID:28524115
Bioinformatics analysis of dysregulated microRNAs in the nipple discharge of patients with breast cancer. PMID:28521415
Emergence of microbial diversity due to cross-feeding interactions in a spatial model of gut microbial metabolism. PMID:28511646
Whole genome analysis of a schistosomiasis-transmitting freshwater snail. PMID:28508897
A Systemic Analysis of Transcriptomic and Epigenomic Data To Reveal Regulation Patterns for Complex Disease. PMID:28500050
De novo Sequencing and Transcriptome Analysis Reveal Key Genes Regulating Steroid Metabolism in Leaves, Roots, Adventitious Roots and Calli of Periploca sepium Bunge. PMID:28484475
Pathview Web: user friendly pathway visualization and data integration. PMID:28482075
The Unwanted Cell Migration in the Brain: Glioma Metastasis. PMID:28478595
QueryOR: a comprehensive web platform for genetic variant analysis and prioritization. PMID:28454514
Genome-Wide Analyses of MicroRNA Profiling in Interleukin-27 Treated Monocyte-Derived Human Dendritic Cells Using Deep Sequencing: A Pilot Study. PMID:28452924
1000 Genomes-based meta-analysis identifies 10 novel loci for kidney function. PMID:28452372
Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment. PMID:28440294
LncRNAs2Pathways: Identifying the pathways influenced by a set of lncRNAs of interest based on a global network propagation method. PMID:28425476
Transcriptome Sequencing of Dianthus spiculifolius and Analysis of the Genes Involved in Responses to Combined Cold and Drought Stress. PMID:28420173
Analysis of Sub-Lethal Toxicity of Perfluorooctane Sulfonate (PFOS) to Daphnia magna Using ¹H Nuclear Magnetic Resonance-Based Metabolomics. PMID:28420092
Identification of driver modules in pan-cancer via coordinating coverage and exclusivity. PMID:28415609
NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. PMID:28415074
Identification of miRNA biomarkers of pneumonia using RNA-sequencing and bioinformatics analysis. PMID:28413462
Determining the presence of asthma-related molecules and salivary contamination in exhaled breath condensate. PMID:28403875
Systemic evaluation of cellular reprogramming processes exploiting a novel R-tool: eegc. PMID:28398503
Role of Stro1+/CD44+ stem cells in myometrial physiology and uterine remodeling during pregnancy. PMID:28395335
Bioinformatics analysis of gene expression alterations in microRNA‑122 knockout mice with hepatocellular carcinoma. PMID:28393247
Sex-specific differences in transcriptome profiles of brain and muscle tissue of the tropical gar. PMID:28388875
Using structural knowledge in the protein data bank to inform the search for potential host-microbe protein interactions in sequence space: application to Mycobacterium tuberculosis. PMID:28376709
Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease. PMID:28373841
Multi-Omics Analysis Reveals a Correlation between the Host Phylogeny, Gut Microbiota and Metabolite Profiles in Cyprinid Fishes. PMID:28367147
Bacterial Signatures of "Red-Operculum" Disease in the Gut of Crucian Carp (Carassius auratus). PMID:28364130
Drug-screening and genomic analyses of HER2-positive breast cancer cell lines reveal predictors for treatment response. PMID:28356768
Potential for microbial H2 and metal transformations associated with novel bacteria and archaea in deep terrestrial subsurface sediments. PMID:28350393
Gene Expression, Protein Function and Pathways of Arabidopsis thaliana Responding to Silver Nanoparticles in Comparison to Silver Ions, Cold, Salt, Drought, and Heat. PMID:28347022
Transcriptome analysis of molecular mechanisms responsible for light-stress response in Mythimna separata (Walker). PMID:28345615
Expression of Yes-associated protein 1 and its clinical significance in ovarian serous cystadenocarcinoma. PMID:28339095
Inhibition of fat cell differentiation in 3T3-L1 pre-adipocytes by all-trans retinoic acid: Integrative analysis of transcriptomic and phenotypic data. PMID:28331816
metaX: a flexible and comprehensive software for processing metabolomics data. PMID:28327092
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
Joint Estimation of Multiple High-dimensional Precision Matrices. PMID:28316451
NFP: An R Package for Characterizing and Comparing of Annotated Biological Networks. PMID:28280740
Gene-set meta-analysis of lung cancer identifies pathway related to systemic lupus erythematosus. PMID:28273134
The Role of Lipid Droplets in Mortierella alpina Aging Revealed by Integrative Subcellular and Whole-Cell Proteome Analysis. PMID:28266581
Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis. PMID:28266498
Social network architecture of human immune cells unveiled by quantitative proteomics. PMID:28263321
Pathway‑based detection of idiopathic pulmonary fibrosis at an early stage. PMID:28260097
MicroRNA-34c is regulated by p53 and is involved in sevoflurane-induced apoptosis in the developing rat brain potentially via the mitochondrial pathway. PMID:28259954
De novo transcriptome assembly reveals high transcriptional complexity in Pisum sativum axillary buds and shows rapid changes in expression of diurnally regulated genes. PMID:28253862
The Pivotal Role of Protein Phosphorylation in the Control of Yeast Central Metabolism. PMID:28250014
Nutrient starvation leading to triglyceride accumulation activates the Entner Doudoroff pathway in Rhodococcus jostii RHA1. PMID:28241831
Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle. PMID:28235871
Semi-quantitative proteomics of mammalian cells upon short-term exposure to non-ionizing electromagnetic fields. PMID:28234898
Genome-wide primary transcriptome analysis of H2-producing archaeon Thermococcus onnurineus NA1. PMID:28216628
Discovery of genes coding for carbohydrate-active enzyme by metagenomic analysis of lignocellulosic biomasses. PMID:28198423
Comparative RNA-Sequence Transcriptome Analysis of Phenolic Acid Metabolism in Salvia miltiorrhiza, a Traditional Chinese Medicine Model Plant. PMID:28194403
Exploring soybean metabolic pathways based on probabilistic graphical model and knowledge-based methods. PMID:28194174
Transcriptome analysis reveals a complex interplay between resistance and effector genes during the compatible lentil-Colletotrichum lentis interaction. PMID:28186158
Natural formulas and the nature of formulas: Exploring potential therapeutic targets based on traditional Chinese herbal formulas. PMID:28182702
Comparative Transcriptomics Reveals Discrete Survival Responses of S. aureus and S. epidermidis to Sapienic Acid. PMID:28179897
Revised computational metagenomic processing uncovers hidden and biologically meaningful functional variation in the human microbiome. PMID:28179006
Genome-scale analysis identifies GJB2 and ERO1LB as prognosis markers in patients with pancreatic cancer. PMID:28177904
Protein-Induced Pluripotent Stem Cells Ameliorate Cognitive Dysfunction and Reduce Aβ Deposition in a Mouse Model of Alzheimer's Disease. PMID:28170178
Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells. PMID:28159795
Drug-target interaction prediction via class imbalance-aware ensemble learning. PMID:28155697
The use of gene interaction networks to improve the identification of cancer driver genes. PMID:28149674
Metabox: A Toolbox for Metabolomic Data Analysis, Interpretation and Integrative Exploration. PMID:28141874
De novo transcriptome assemblies of four accessions of the metal hyperaccumulator plant Noccaea caerulescens. PMID:28140388
Protein biomarker druggability profiling. PMID:28131723
Identification of protein complexes by integrating multiple alignment of protein interaction networks. PMID:28130237
Stably Expressed Genes Involved in Basic Cellular Functions. PMID:28125669
Heat Stress Regulates the Expression of Genes at Transcriptional and Post-Transcriptional Levels, Revealed by RNA-seq in Brachypodium distachyon. PMID:28119730
Tissue Non-Specific Genes and Pathways Associated with Diabetes: An Expression Meta-Analysis. PMID:28117714
Novel adverse outcome pathways revealed by chemical genetics in a developing marine fish. PMID:28117666
Tensor Factorization for Precision Medicine in Heart Failure with Preserved Ejection Fraction. PMID:28116551
The choreography of the chemical defensome response to insecticide stress: insights into the Anopheles stephensi transcriptome using RNA-Seq. PMID:28112252
Systematic Characterization and Analysis of the Taxonomic Drivers of Functional Shifts in the Human Microbiome. PMID:28111203
A compendium of human genes regulating feeding behavior and body weight, its functional characterization and identification of GWAS genes involved in brain-specific PPI network. PMID:28105929
Genomewide landscape of gene-metabolome associations in Escherichia coli. PMID:28093455
Divergent functional isoforms drive niche specialisation for nutrient acquisition and use in rumen microbiome. PMID:28085156
Nitrosothiol-Trapping-Based Proteomic Analysis of S-Nitrosylation in Human Lung Carcinoma Cells. PMID:28081246
Parallel-META 3: Comprehensive taxonomical and functional analysis platform for efficient comparison of microbial communities. PMID:28079128
Metabolomic profiles as reliable biomarkers of dietary composition. PMID:28077380
Predicting the Metabolic Sites by Flavin-Containing Monooxygenase on Drug Molecules Using SVM Classification on Computed Quantum Mechanics and Circular Fingerprints Molecular Descriptors. PMID:28072829
Transcriptome analysis of the oriental melon (Cucumis melo L. var. makuwa) during fruit development. PMID:28070461
Integration of MicroRNA, mRNA, and Protein Expression Data for the Identification of Cancer-Related MicroRNAs. PMID:28056026
Differential expression and miRNA regulation of the GSTP1 gene in the regenerating liver of Chiloscyllium plagiosum. PMID:28054243
Epigenomics alternations and dynamic transcriptional changes in responses to 5-fluorouracil stimulation reveal mechanisms of acquired drug resistance of colorectal cancer cells. PMID:28045128
iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes. PMID:28007024
Systematic Understanding of Mechanisms of a Chinese Herbal Formula in Treatment of Metabolic Syndrome by an Integrated Pharmacology Approach. PMID:27999264
Modeling Rice Metabolism: From Elucidating Environmental Effects on Cellular Phenotype to Guiding Crop Improvement. PMID:27965696
Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. PMID:27964752
Comparative analysis of hepatocellular carcinoma and cirrhosis gene expression profiles. PMID:27959423
Profiling bacterial communities associated with sediment-based aquaculture bioremediation systems under contrasting redox regimes. PMID:27941918
Identification of Potential Biomarkers for Rhegmatogenous Retinal Detachment Associated with Choroidal Detachment by Vitreous iTRAQ-Based Proteomic Profiling. PMID:27941623
Aligning Metabolic Pathways Exploiting Binary Relation of Reactions. PMID:27936108
Analysis of the intestinal microbial community and inferred functional capacities during the host response to Pneumocystis pneumonia. PMID:27925857
Function-driven discovery of disease genes in zebrafish using an integrated genomics big data resource. PMID:27903883
ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm. PMID:27893733
iTRAQ-Based Comparative Proteomics Analysis of the Fruiting Dikaryon and the Non-fruiting Monokaryon of Flammulina velutipes. PMID:27866250
Discriminating cancer-related and cancer-unrelated chemoradiation-response genes for locally advanced rectal cancers. PMID:27845363
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PMID:27843720
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. PMID:27842596
Characterization of the Verticillium dahliae Exoproteome Involves in Pathogenicity from Cotton-Containing Medium. PMID:27840627
Potential molecular characteristics in situ in response to repetitive UVB irradiation. PMID:27829444
Whole Genome Sequencing Reveals Potential New Targets for Improving Nitrogen Uptake and Utilization in Sorghum bicolor. PMID:27826302
Identification of novel and differentially expressed MicroRNAs in goat enzootic nasal adenocarcinoma. PMID:27825300
Elucidation of Relevant Neuroinflammation Mechanisms Using Gene Expression Profiling in Patients with Amyotrophic Lateral Sclerosis. PMID:27812125
Chemogenomics knowledgebase and systems pharmacology for hallucinogen target identification-Salvinorin A as a case study. PMID:27810775
snpGeneSets: An R Package for Genome-Wide Study Annotation. PMID:27807048
DrugCentral: online drug compendium. PMID:27789690
Complete Genome Sequence of Aerococcus urinaeequi Strain AV208. PMID:27789648
Genomic resources for a unique, low-virulence Babesia taxon from China. PMID:27784333
Proteomic and phosphoproteomic analysis of renal cortex in a salt-load rat model of advanced kidney damage. PMID:27775022
Diet-Dependent Modular Dynamic Interactions of the Equine Cecal Microbiota. PMID:27773914
Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PMID:27761329
Pathway Analysis Based on Attractor and Cross Talk in Colon Cancer. PMID:27746583
Microbiome and Exudates of the Root and Rhizosphere of Brachypodium distachyon, a Model for Wheat. PMID:27727301
Genome sequence of the basal haplorrhine primate Tarsius syrichta reveals unusual insertions. PMID:27708261
High-resolution metabolomics of occupational exposure to trichloroethylene. PMID:27707868
Sample Level Enrichment Analysis of KEGG Pathways Identifies Clinically Relevant Subtypes of Glioblastoma. PMID:27698907
Co-acclimation of bacterial communities under stresses of hydrocarbons with different structures. PMID:27698451
Unconventional secretory processing diversifies neuronal ion channel properties. PMID:27677849
De novo transcriptomic analysis of Chlorella sorokiniana reveals differential genes expression in photosynthetic carbon fixation and lipid production. PMID:27669744
Inferences of drug responses in cancer cells from cancer genomic features and compound chemical and therapeutic properties. PMID:27645580
De Novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation Using Contrasting Genotypes. PMID:27627679
inFRank: a ranking-based identification of influential genes in biological networks. PMID:27623074
Pathway Analysis Incorporating Protein-Protein Interaction Networks Identified Candidate Pathways for the Seven Common Diseases. PMID:27622767
Conservation and diversification of the transcriptomes of adult Paragonimus westermani and P. skrjabini. PMID:27619014
DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions. PMID:27618709
Blood pressure regulation by CD4+ lymphocytes expressing choline acetyltransferase. PMID:27617738
Metagenomic analysis of an ecological wastewater treatment plant's microbial communities and their potential to metabolize pharmaceuticals. PMID:27610223
Urine metabolome profiling of immune-mediated inflammatory diseases. PMID:27609333
Comprehensive Proteome Profiling of Platelet Identified a Protein Profile Predictive of Responses to An Antiplatelet Agent Sarpogrelate. PMID:27601597
"Upstream Analysis": An Integrated Promoter-Pathway Analysis Approach to Causal Interpretation of Microarray Data. PMID:27600225
Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer. PMID:27597120
Chronic psychological stress and high-fat high-fructose diet disrupt metabolic and inflammatory gene networks in the brain, liver, and gut and promote behavioral deficits in mice. PMID:27592562
A biologically informed method for detecting rare variant associations. PMID:27582876
Long noncoding RNA linc00598 regulates CCND2 transcription and modulates the G1 checkpoint. PMID:27572135
Identification of rifampin-regulated functional modules and related microRNAs in human hepatocytes based on the protein interaction network. PMID:27557147
Functional characterization of EI24-induced autophagy in the degradation of RING-domain E3 ligases. PMID:27541728
NLDB: a database for 3D protein-ligand interactions in enzymatic reactions. PMID:27530928
Integration of targeted metabolomics and transcriptomics identifies deregulation of phosphatidylcholine metabolism in Huntington's disease peripheral blood samples. PMID:27524956
Identification of conserved and novel microRNAs in Porphyridium purpureum via deep sequencing and bioinformatics. PMID:27516065
Analysis of ethanol fermentation mechanism of ethanol producing white-rot fungus Phlebia sp. MG-60 by RNA-seq. PMID:27515927
Modelling the Structure and Dynamics of Biological Pathways. PMID:27509052
An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes. PMID:27507169
Suppression of ischemia in arterial occlusive disease by JNK-promoted native collateral artery development. PMID:27504807
A transcriptional blueprint for a spiral-cleaving embryo. PMID:27496340
Investigation of glycan evolution based on a comprehensive analysis of glycosyltransferases using phylogenetic profiling. PMID:27493855
LigandBox: A database for 3D structures of chemical compounds. PMID:27493549
Gene and Network Analysis of Common Variants Reveals Novel Associations in Multiple Complex Diseases. PMID:27489002
Comprehensive Identification of Meningococcal Genes and Small Noncoding RNAs Required for Host Cell Colonization. PMID:27486197
A high-resolution map of the gut microbiota in Atlantic salmon (Salmo salar): A basis for comparative gut microbial research. PMID:27485205
GPU-Acceleration of Sequence Homology Searches with Database Subsequence Clustering. PMID:27482905
On the study of microbial transcriptomes using second- and third-generation sequencing technologies. PMID:27480632
MiRSEA: Discovering the pathways regulated by dysfunctional MicroRNAs. PMID:27474169
Immune competence assessment in marine medaka (Orzyias melastigma)-a holistic approach for immunotoxicology. PMID:27473621
Construction of co-expression network based on natural expression variation of xylogenesis-related transcripts in Eucalyptus tereticornis. PMID:27465117
Small-molecule binding sites to explore protein-protein interactions in the cancer proteome. PMID:27452673
The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus. PMID:27442123
Impact of Helminth Infections and Nutritional Constraints on the Small Intestine Microbiota. PMID:27438701
Time-Course Study of the Transcriptome of Peripheral Blood Mononuclear Cells (PBMCs) from Sheep Infected with Fasciola hepatica. PMID:27438474
Identifying Aspects of the Post-Transcriptional Program Governing the Proteome of the Green Alga Micromonas pusilla. PMID:27434306
Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. PMID:27429074
A Tetrahydrofolate-Dependent Methyltransferase Catalyzing the Demethylation of Dicamba in Sphingomonas sp. Strain Ndbn-20. PMID:27422839
Isoprenoid-Based Biofuels: Homologous Expression and Heterologous Expression in Prokaryotes. PMID:27422837
Permanent draft genome sequence of sulfoquinovose-degrading Pseudomonas putida strain SQ1. PMID:27408681
Transcriptional profiling reveals intrinsic mRNA alterations in multipotent mesenchymal stromal cells isolated from bone marrow of newly-diagnosed type 1 diabetes patients. PMID:27406064
Investigating Evolutionary Dynamics of RHA1 Operons. PMID:27398020
Metagenomics and Bioinformatics in Microbial Ecology: Current Status and Beyond. PMID:27383682
From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model. PMID:27379044
miR-155 in the progression of lung fibrosis in systemic sclerosis. PMID:27377409
Enterocyte-Associated Microbiome of the Hadza Hunter-Gatherers. PMID:27375586
Identification of disease-associated pathways in pancreatic cancer by integrating genome-wide association study and gene expression data. PMID:27347177
Feedback Regulation of ABA Signaling and Biosynthesis by a bZIP Transcription Factor Targets Drought-Resistance-Related Genes. PMID:27325665
OncoScape: Exploring the cancer aberration landscape by genomic data fusion. PMID:27321817
Meta-Analysis of Differential Connectivity in Gene Co-Expression Networks in Multiple Sclerosis. PMID:27314336
Approaches to uncovering cancer diagnostic and prognostic molecular signatures. PMID:27308330
Integrative analysis of transcriptomics and proteomics of skeletal muscles of the Chinese indigenous Shaziling pig compared with the Yorkshire breed. PMID:27296698
Programmed death ligand-1 expression on donor T cells drives graft-versus-host disease lethality. PMID:27294527
Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity. PMID:27286824
Insights into Sexual Precocity of Female Oriental River Prawn Macrobrachium nipponense through Transcriptome Analysis. PMID:27280288
Genomic expression profiling and bioinformatics analysis on diabetic nephrology with ginsenoside Rg3. PMID:27279428
Environmental Breviatea harbour mutualistic Arcobacter epibionts. PMID:27279223
Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T)). PMID:27274784
Transcriptome sequences spanning key developmental states as a resource for the study of the cestode Schistocephalus solidus, a threespine stickleback parasite. PMID:27259971
Review on Graph Clustering and Subgraph Similarity Based Analysis of Neurological Disorders. PMID:27258269
Metabolomic Analysis in Brain Research: Opportunities and Challenges. PMID:27252656
Methyltransferase Dnmt3a upregulates HDAC9 to deacetylate the kinase TBK1 for activation of antiviral innate immunity. PMID:27240213
Genomic features of uncultured methylotrophs in activated-sludge microbiomes grown under different enrichment procedures. PMID:27221669
Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study. PMID:27220822
Characterization of the bacterial and fungal microbiome in indoor dust and outdoor air samples: a pilot study. PMID:27213188
Reprogramming human A375 amelanotic melanoma cells by catalase overexpression: Upregulation of antioxidant genes correlates with regression of melanoma malignancy and with malignant progression when downregulated. PMID:27206673
Genome-wide analysis of gene expression reveals gene regulatory networks that regulate chasmogamous and cleistogamous flowering in Pseudostellaria heterophylla (Caryophyllaceae). PMID:27206349
Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis. PMID:27198881
Evolutionary assembly patterns of prokaryotic genomes. PMID:27197212
Degradation of Swainsonine by the NADP-Dependent Alcohol Dehydrogenase A1R6C3 in Arthrobacter sp. HW08. PMID:27196926
Identification and Characterization of miRNAs in Chondrus crispus by High-Throughput Sequencing and Bioinformatics Analysis. PMID:27193824
The genome and transcriptome of Phalaenopsis yield insights into floral organ development and flowering regulation. PMID:27190718
Host-Associated Genomic Features of the Novel Uncultured Intracellular Pathogen Ca. Ichthyocystis Revealed by Direct Sequencing of Epitheliocysts. PMID:27190004
Transcription Analysis of the Myometrium of Labouring and Non-Labouring Women. PMID:27176052
Global Metabolic Regulation of the Snow Alga Chlamydomonas nivalis in Response to Nitrate or Phosphate Deprivation by a Metabolome Profile Analysis. PMID:27171077
RNA-Seq of Huntington's disease patient myeloid cells reveals innate transcriptional dysregulation associated with proinflammatory pathway activation. PMID:27170315
Proliferation and Migration of Peripheral Retinal Pigment Epithelial Cells Are Associated with the Upregulation of Wingless-Related Integration and Bone Morphogenetic Protein Signaling in Dark Agouti Rats. PMID:27165129
Specific microbiome-dependent mechanisms underlie the energy harvest efficiency of ruminants. PMID:27152936
Modulation of gut microbiota dysbioses in type 2 diabetic patients by macrobiotic Ma-Pi 2 diet. PMID:27151248
Global Transcriptome Profiling Analysis of Inhibitory Effects of Paclobutrazol on Leaf Growth in Lily (Lilium Longiflorum-Asiatic Hybrid). PMID:27148316
Investigation of the Activity of the Microorganisms in a Reblochon-Style Cheese by Metatranscriptomic Analysis. PMID:27148224
Alterations in human milk leptin and insulin are associated with early changes in the infant intestinal microbiome. PMID:27140533
RubisCO of a nucleoside pathway known from Archaea is found in diverse uncultivated phyla in bacteria. PMID:27137126
systemsDock: a web server for network pharmacology-based prediction and analysis. PMID:27131384
Identification of key genes for laryngeal squamous cell carcinoma using weighted co-expression network analysis. PMID:27123111
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. PMID:27114494
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Evaluation of Circulatory RNA-Based Biomarker Panel in Hepatocellular Carcinoma. PMID:27113935
Identifying Reproducible Molecular Biomarkers for Gastric Cancer Metastasis with the Aid of Recurrence Information. PMID:27109211
Network-Based Protein Biomarker Discovery Platforms. PMID:27103885
Can the microRNA expression profile help to identify novel targets for zoledronic acid in breast cancer? PMID:27081088
Drug Repurposing Is a New Opportunity for Developing Drugs against Neuropsychiatric Disorders. PMID:27073698
A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. PMID:27071721
De novo transcriptome sequencing and gene expression analysis reveal potential mechanisms of seed abortion in dove tree (Davidia involucrata Baill.). PMID:27068221
Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus. PMID:27065959
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PMID:27050193
Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant. PMID:27047386
Comprehensive Genome-Wide Transcriptomic Analysis of Immature Articular Cartilage following Ischemic Osteonecrosis of the Femoral Head in Piglets. PMID:27045355
Screening for genes and subnetworks associated with pancreatic cancer based on the gene expression profile. PMID:27035224
Prediction and verification of novel peptide targets of protein tyrosine phosphatase 1B. PMID:27025565
Cigarette smoking and the oral microbiome in a large study of American adults. PMID:27015003
BRG1/SMARCA4 is essential for neuroblastoma cell viability through modulation of cell death and survival pathways. PMID:26996667
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. PMID:26989150
LmSmdB: an integrated database for metabolic and gene regulatory network in Leishmania major and Schistosoma mansoni. PMID:26981382
Heat-treated high-fat diet modifies gut microbiota and metabolic markers in apoe-/- mice. PMID:26973703
Transcriptome analysis reveals differentially expressed genes associated with germ cell and gonad development in the Southern bluefin tuna (Thunnus maccoyii). PMID:26965070
Drug Repositioning for Cancer Therapy Based on Large-Scale Drug-Induced Transcriptional Signatures. PMID:26954019
Metagenomic evidence for taxonomic dysbiosis and functional imbalance in the gastrointestinal tracts of children with cystic fibrosis. PMID:26940651
Influence of whole-wheat consumption on fecal microbial community structure of obese diabetic mice. PMID:26925326
The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. PMID:26921407
Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes. PMID:26911872
Role of Protein Phosphorylation in the Regulation of Cell Cycle and DNA-Related Processes in Bacteria. PMID:26909079
Carbon Monoxide Gas Is Not Inert, but Global, in Its Consequences for Bacterial Gene Expression, Iron Acquisition, and Antibiotic Resistance. PMID:26907100
Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis. PMID:26904004
The genome of the miiuy croaker reveals well-developed innate immune and sensory systems. PMID:26902509
Systematic Analysis of Intracellular-targeting Antimicrobial Peptides, Bactenecin 7, Hybrid of Pleurocidin and Dermaseptin, Proline-Arginine-rich Peptide, and Lactoferricin B, by Using Escherichia coli Proteome Microarrays. PMID:26902206
Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development. PMID:26887814
BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine. PMID:26879404
Uncovering the pathways underlying whole body regeneration in a chordate model, Botrylloides leachi using de novo transcriptome analysis. PMID:26879048
ChemProt-3.0: a global chemical biology diseases mapping. PMID:26876982
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. PMID:26876889
Mechanisms and pharmacogenetic signals underlying thiazide diuretics blood pressure response. PMID:26874237
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction. PMID:26872142
Metagenomic Analysis Reveals Symbiotic Relationship among Bacteria in Microcystis-Dominated Community. PMID:26870018
Mechanisms Underlying Adaptation to Life in Hydrogen Sulfide-Rich Environments. PMID:26861137
A network-based analysis of colon cancer splicing changes reveals a tumorigenesis-favoring regulatory pathway emanating from ELK1. PMID:26860615
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. PMID:26856411
Effect of cerulenin on fatty acid composition and gene expression pattern of DHA-producing strain Colwellia psychrerythraea strain 34H. PMID:26852325
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Emerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria. PMID:26849311
Models of human core transcriptional regulatory circuitries. PMID:26843070
Exploring the chemistry and evolution of the isomerases. PMID:26842835
iTRAQ-Based Quantitative Proteomic Analysis of Cotton Roots and Leaves Reveals Pathways Associated with Salt Stress. PMID:26841024
Characterising Complex Enzyme Reaction Data. PMID:26840640
Association of Forced Vital Capacity with the Developmental Gene NCOR2. PMID:26836265
Genome-Wide Analysis of the Lysine Biosynthesis Pathway Network during Maize Seed Development. PMID:26829553
Glutamate Dehydrogenase Is Required by Mycobacterium bovis BCG for Resistance to Cellular Stress. PMID:26824899
Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments. PMID:26823996
Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. PMID:26820137
Transcriptome sequencing based annotation and homologous evidence based scaffolding of Anguilla japonica draft genome. PMID:26818233
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. PMID:26818115
Transcriptomic Determinants of Scrapie Prion Propagation in Cultured Ovine Microglia. PMID:26807844
Integrated analysis of microRNA regulatory network in nasopharyngeal carcinoma with deep sequencing. PMID:26795575
ConceptMetab: exploring relationships among metabolite sets to identify links among biomedical concepts. PMID:26794319
Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis. PMID:26791995
Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs. PMID:26787827
An evaluation of the accuracy and speed of metagenome analysis tools. PMID:26778510
KNOWLEDGE DRIVEN BINNING AND PHEWAS ANALYSIS IN MARSHFIELD PERSONALIZED MEDICINE RESEARCH PROJECT USING BIOBIN. PMID:26776191
Comprehensive analysis of schizophrenia-associated loci highlights ion channel pathways and biologically plausible candidate causal genes. PMID:26755824
Label-Free, In-Solution Screening of Peptide Libraries for Binding to Protein Targets Using Hydrogen Exchange Mass Spectrometry. PMID:26741284
A Multilayer Network Approach for Guiding Drug Repositioning in Neglected Diseases. PMID:26735851
The TIM Barrel Architecture Facilitated the Early Evolution of Protein-Mediated Metabolism. PMID:26733481
Thrombospondin-1 differentially regulates microRNAs in vascular smooth muscle cells. PMID:26728995
Identification and characterization of microRNAs in Eucheuma denticulatum by high-throughput sequencing and bioinformatics analysis. PMID:26717154
Iron Acquisition in Mycobacterium avium subsp. paratuberculosis. PMID:26712939
Comparative Analysis of Transcriptomes from Secondary Reproductives of Three Reticulitermes Termite Species. PMID:26698123
The Drosophila Chitinase-Like Protein IDGF3 Is Involved in Protection against Nematodes and in Wound Healing. PMID:26694862
MicroRNA-Target Network Inference and Local Network Enrichment Analysis Identify Two microRNA Clusters with Distinct Functions in Head and Neck Squamous Cell Carcinoma. PMID:26694379
Bioinformatics identification of potentially involved microRNAs in Tibetan with gastric cancer based on microRNA profiling. PMID:26692821
Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events. PMID:26679379
A comprehensive comparison of general RNA-RNA interaction prediction methods. PMID:26673718
Genomic and transcriptomic analyses of the Chinese Maotai-flavored liquor yeast MT1 revealed its unique multi-carbon co-utilization. PMID:26666414
Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks. PMID:26657352
De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome. PMID:26647312
ALCOdb: Gene Coexpression Database for Microalgae. PMID:26644461
Deciphering Genomic Underpinnings of Quantitative MRI-based Radiomic Phenotypes of Invasive Breast Carcinoma. PMID:26639025
The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. PMID:26634818
MERAV: a tool for comparing gene expression across human tissues and cell types. PMID:26626150
Exploring molecular variation in Schistosoma japonicum in China. PMID:26621075
Profile of microRNA in Giant Panda Blood: A Resource for Immune-Related and Novel microRNAs. PMID:26599861
Global Prioritization of Disease Candidate Metabolites Based on a Multi-omics Composite Network. PMID:26598063
Genome sequencing reveals mechanisms for heavy metal resistance and polycyclic aromatic hydrocarbon degradation in Delftia lacustris strain LZ-C. PMID:26589947
Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities. PMID:26579098
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. PMID:26578565
Psychiatric gene discoveries shape evidence on ADHD's biology. PMID:26573769
A potential endophenotype for Alzheimer's disease: cerebrospinal fluid clusterin. PMID:26545630
Identifying Novel Candidate Genes Related to Apoptosis from a Protein-Protein Interaction Network. PMID:26543496
Impact of Statins on Gene Expression in Human Lung Tissues. PMID:26535575
Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors. PMID:26527717
Genotypic and phenotypic analyses of a Pseudomonas aeruginosa chronic bronchiectasis isolate reveal differences from cystic fibrosis and laboratory strains. PMID:26519161
BioDB extractor: customized data extraction system for commonly used bioinformatics databases. PMID:26516349
Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. PMID:26515599
Comparative Proteomic Analysis of Gossypium thurberi in Response to Verticillium dahliae Inoculation. PMID:26506344
MicroRNA circulating in the early aftermath of motor vehicle collision predict persistent pain development and suggest a role for microRNA in sex-specific pain differences. PMID:26498117
Dereplication, sequencing and identification of peptidic natural products: from genome mining to peptidogenomics to spectral networks. PMID:26497201
GREM1 and POLE variants in hereditary colorectal cancer syndromes. PMID:26493165
Methods for biological data integration: perspectives and challenges. PMID:26490630
Copy number variations in the genome of the Qatari population. PMID:26490036
Genome sequencing and annotation of Laceyella sacchari strain GS 1-1, isolated from hot spring, Chumathang, Leh, India. PMID:26484058
Genome sequencing and annotation of Amycolatopsis vancoresmycina strain DSM 44592(T). PMID:26484057
The human gene damage index as a gene-level approach to prioritizing exome variants. PMID:26483451
Weevil endosymbiont dynamics is associated with a clamping of immunity. PMID:26482132
Computational Systems Biology of Psoriasis: Are We Ready for the Age of Omics and Systems Biomarkers? PMID:26480058
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Gene-Set Local Hierarchical Clustering (GSLHC)--A Gene Set-Based Approach for Characterizing Bioactive Compounds in Terms of Biological Functional Groups. PMID:26473729
Fundamental Roles of the Golgi-Associated Toxoplasma Aspartyl Protease, ASP5, at the Host-Parasite Interface. PMID:26473595
An Integrated Multiomics Approach to Identify Candidate Antigens for Serodiagnosis of Human Onchocerciasis. PMID:26472727
Virtual pathway explorer (viPEr) and pathway enrichment analysis tool (PEANuT): creating and analyzing focus networks to identify cross-talk between molecules and pathways. PMID:26467653
A survey about methods dedicated to epistasis detection. PMID:26442103
Phylogenetic approaches to microbial community classification. PMID:26437943
Dietary Modulation of Gut Microbiota Contributes to Alleviation of Both Genetic and Simple Obesity in Children. PMID:26425705
The eNanoMapper database for nanomaterial safety information. PMID:26425413
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs. PMID:26424084
Repertoires: How to Transform a Project into a Research Community. PMID:26412866
PanFP: pangenome-based functional profiles for microbial communities. PMID:26409790
De Novo Assembly of the Whole Transcriptome of the Wild Embryo, Preleptocephalus, Leptocephalus, and Glass Eel of Anguilla japonica and Deciphering the Digestive and Absorptive Capacities during Early Development. PMID:26406914
Suppression of Aflatoxin Biosynthesis in Aspergillus flavus by 2-Phenylethanol Is Associated with Stimulated Growth and Decreased Degradation of Branched-Chain Amino Acids. PMID:26404375
Xtalk: a path-based approach for identifying crosstalk between signaling pathways. PMID:26400040
Genomic, Proteomic, and Metabolomic Data Integration Strategies. PMID:26396492
Transcriptome Analysis Revealed the Embryo-Induced Gene Expression Patterns in the Endometrium from Meishan and Yorkshire Pigs. PMID:26393584
Experimental validation of in silico model-predicted isocitrate dehydrogenase and phosphomannose isomerase from Dehalococcoides mccartyi. PMID:26374290
Host genetic variation impacts microbiome composition across human body sites. PMID:26374288
Abundant toxin-related genes in the genomes of beneficial symbionts from deep-sea hydrothermal vent mussels. PMID:26371554
ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. PMID:26365237
The metabolic response of marine copepods to environmental warming and ocean acidification in the absence of food. PMID:26364855
Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PMID:26332409
Phylogenetic Co-Occurrence of ExoR, ExoS, and ChvI, Components of the RSI Bacterial Invasion Switch, Suggests a Key Adaptive Mechanism Regulating the Transition between Free-Living and Host-Invading Phases in Rhizobiales. PMID:26309130
In vivo hematopoietic Myc activation directs a transcriptional signature in endothelial cells within the bone marrow microenvironment. PMID:26308666
Network fingerprint: a knowledge-based characterization of biomedical networks. PMID:26307246
Structure and function of the healthy pre-adolescent pediatric gut microbiome. PMID:26306392
Phosphotyrosine Substrate Sequence Motifs for Dual Specificity Phosphatases. PMID:26302245
Deciphering common and specific transcriptional immune responses in pea towards the oomycete pathogens Aphanomyces euteiches and Phytophthora pisi. PMID:26293353
The effect of antibiotic exposure on eicosanoid generation from arachidonic acid and gene expression in a primitive chordate, Branchiostoma belcheri. PMID:26288743
Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe. PMID:26283343
Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice. PMID:26274050
Potential anti-cancer effect of curcumin in human lung squamous cell carcinoma. PMID:26273408
Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones. PMID:26272068
DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts. PMID:26271256
Circulating microRNAs as Potential Biomarkers of Endothelial Dysfunction in Obese Children. PMID:26270249
Integrative systems analysis of diet-induced obesity identified a critical transition in the transcriptomes of the murine liver and epididymal white adipose tissue. PMID:26268884
ESEA: Discovering the Dysregulated Pathways based on Edge Set Enrichment Analysis. PMID:26267116
Genomic analysis reveals the biotechnological and industrial potential of levan producing halophilic extremophile, Halomonas smyrnensis AAD6T. PMID:26251777
Transcriptomic and phytochemical analysis of the biosynthesis of characteristic constituents in tea (Camellia sinensis) compared with oil tea (Camellia oleifera). PMID:26245644
miRegulome: a knowledge-base of miRNA regulomics and analysis. PMID:26243198
In-depth analysis of the critical genes and pathways in colorectal cancer. PMID:26239303
RNA-seq for gene identification and transcript profiling in relation to root growth of bermudagrass (Cynodon dactylon) under salinity stress. PMID:26238595
Characterization of pH dependent Mn(II) oxidation strategies and formation of a bixbyite-like phase by Mesorhizobium australicum T-G1. PMID:26236307
The EGF receptor ligand amphiregulin controls cell division via FoxM1. PMID:26234682
Longitudinal Survey of Microbiota in Hospitalized Preterm Very-Low-Birth-Weight Infants. PMID:26230901
Genome-wide association study revealed a promising region and candidate genes for eggshell quality in an F2 resource population. PMID:26228268
Data in support of comparative proteomics analysis of superior and inferior spikelets in hybrid rice during grain filling and response of inferior spikelets to drought stress using isobaric tags for relative and absolute quantification. PMID:26217686
CovRS-Regulated Transcriptome Analysis of a Hypervirulent M23 Strain of Group A Streptococcus pyogenes Provides New Insights into Virulence Determinants. PMID:26216843
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. PMID:26205660
Genomic variations of the mevalonate pathway in porokeratosis. PMID:26202976
Partitioning of genomic variance reveals biological pathways associated with udder health and milk production traits in dairy cattle. PMID:26169777
Lymphangioleiomyomatosis Biomarkers Linked to Lung Metastatic Potential and Cell Stemness. PMID:26167915
GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks. PMID:26165520
Genome-wide pharmacologic unmasking identifies tumor suppressive microRNAs in multiple myeloma. PMID:26164366
The Enterobacterium Trabulsiella odontotermitis Presents Novel Adaptations Related to Its Association with Fungus-Growing Termites. PMID:26162887
MicroRNA Expression Profile in Penile Cancer Revealed by Next-Generation Small RNA Sequencing. PMID:26158897
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PMID:26157614
Metabolomics and transcriptomics identify pathway differences between visceral and subcutaneous adipose tissue in colorectal cancer patients: the ColoCare study. PMID:26156741
Using gene expression signatures to identify novel treatment strategies in gulf war illness. PMID:26156520
Genome Scan for Selection in Structured Layer Chicken Populations Exploiting Linkage Disequilibrium Information. PMID:26151449
Arsenophonus and Sodalis Symbionts in Louse Flies: an Analogy to the Wigglesworthia and Sodalis System in Tsetse Flies. PMID:26150448
Dynamic transcriptome analysis and volatile profiling of Gossypium hirsutum in response to the cotton bollworm Helicoverpa armigera. PMID:26148847
Perilipin-2 Modulates Lipid Absorption and Microbiome Responses in the Mouse Intestine. PMID:26147095
Pathway and network analysis of cancer genomes. PMID:26125594
A de novo Assembly of the Common Frog (Rana temporaria) Transcriptome and Comparison of Transcription Following Exposure to Ranavirus and Batrachochytrium dendrobatidis. PMID:26111016
Vitamin B12 modulates the transcriptome of the skin microbiota in acne pathogenesis. PMID:26109103
Metabolomics Analysis Reveals that AICAR Affects Glycerolipid, Ceramide and Nucleotide Synthesis Pathways in INS-1 Cells. PMID:26107620
Transcriptome response signatures associated with the overexpression of a mitochondrial uncoupling protein (AtUCP1) in tobacco. PMID:26106890
Randomised clinical trial: gut microbiome biomarkers are associated with clinical response to a low FODMAP diet in children with the irritable bowel syndrome. PMID:26104013
Cross-organism analysis using InterMine. PMID:26097192
A Comparative Proteomic Analysis of the Buds and the Young Expanding Leaves of the Tea Plant (Camellia sinensis L.). PMID:26096006
Metatranscriptome Analysis of Fig Flowers Provides Insights into Potential Mechanisms for Mutualism Stability and Gall Induction. PMID:26090817
An interactive web application for the dissemination of human systems immunology data. PMID:26088622
Evolutionary genomics of Culex pipiens: global and local adaptations associated with climate, life-history traits and anthropogenic factors. PMID:26085592
Genome-wide analysis of the gene families of resistance gene analogues in cotton and their response to Verticillium wilt. PMID:26084488
Unusual biology across a group comprising more than 15% of domain Bacteria. PMID:26083755
Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PMID:26083688
Deciphering Signaling Pathway Networks to Understand the Molecular Mechanisms of Metformin Action. PMID:26083494
Tools for visualization and analysis of molecular networks, pathways, and -omics data. PMID:26082651
Microbial bioinformatics for food safety and production. PMID:26082168
Functional Operons in Secondary Metabolic Gene Clusters in Glarea lozoyensis (Fungi, Ascomycota, Leotiomycetes). PMID:26081635
Many InChIs and quite some feat. PMID:26081259
Association of Protein Translation and Extracellular Matrix Gene Sets with Breast Cancer Metastasis: Findings Uncovered on Analysis of Multiple Publicly Available Datasets Using Individual Patient Data Approach. PMID:26080057
Bayesian Inference of Multiple Gaussian Graphical Models. PMID:26078481
Fibronectin induction abrogates the BRAF inhibitor response of BRAF V600E/PTEN-null melanoma cells. PMID:26073081
The Up-Regulation of Ribosomal Proteins Further Regulates Protein Expression Profile in Female Schistosoma japonicum after Pairing. PMID:26070205
Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing. PMID:26067561
Empirical inference of circuitry and plasticity in a kinase signaling network. PMID:26060313
Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis. PMID:26059548
PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data. PMID:26038725
Genome and Transcriptome of Clostridium phytofermentans, Catalyst for the Direct Conversion of Plant Feedstocks to Fuels. PMID:26035711
Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. PMID:26035208
Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock. PMID:26026709
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. PMID:26026612
A Comprehensive Profile of ChIP-Seq-Based Olig2 Target Genes in Motor Neuron Progenitor Cells Suggests the Possible Involvement of Olig2 in the Pathogenesis of Amyotrophic Lateral Sclerosis. PMID:26023283
Direct estimation of differential networks. PMID:26023240
Different Astrocytic Activation between Adult Gekko japonicus and Rats during Wound Healing In Vitro. PMID:26020931
De novo transcriptome characterization and gene expression profiling of the desiccation tolerant moss Bryum argenteum following rehydration. PMID:26016800
A less-biased analysis of metalloproteins reveals novel zinc coordination geometries. PMID:26009987
Whole-Genome Sequence Analysis and Genome-Wide Virulence Gene Identification of Riemerella anatipestifer Strain Yb2. PMID:26002892
Pan-phylum Comparison of Nematode Metabolic Potential. PMID:26000881
GraP: platform for functional genomics analysis of Gossypium raimondii. PMID:25982315
A comprehensive map of genome-wide gene regulation in Mycobacterium tuberculosis. PMID:25977815
Comparative Meta-Analysis of Transcriptomics Data during Cellular Senescence and In Vivo Tissue Ageing. PMID:25977747
Quantitative proteomic analysis reveals that anti-cancer effects of selenium-binding protein 1 in vivo are associated with metabolic pathways. PMID:25974208
Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach. PMID:25972988
Transcriptional activity of the giant barrel sponge, Xestospongia muta Holobiont: molecular evidence for metabolic interchange. PMID:25972851
MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data. PMID:25972773
Hybrid-controlled neurofuzzy networks analysis resulting in genetic regulatory networks reconstruction. PMID:25969749
Lactococcus garvieae: a small bacteria and a big data world. PMID:25960872
Deciphering the therapeutic mechanisms of Xiao-Ke-An in treatment of type 2 diabetes in mice by a Fangjiomics approach. PMID:25960133
NaviCell Web Service for network-based data visualization. PMID:25958393
ProtPhylo: identification of protein-phenotype and protein-protein functional associations via phylogenetic profiling. PMID:25956654
Zodiac: A Comprehensive Depiction of Genetic Interactions in Cancer by Integrating TCGA Data. PMID:25956356
De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress. PMID:25938968
MicroRNA-Seq Data Analysis Pipeline to Identify Blood Biomarkers for Alzheimer's Disease from Public Data. PMID:25922570
Discerning mechanistically rewired biological pathways by cumulative interaction heterogeneity statistics. PMID:25921728
Predicting drug metabolism: experiment and/or computation? PMID:25907346
The metabolome profiling and pathway analysis in metabolic healthy and abnormal obesity. PMID:25907313
SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering. PMID:25903787
The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits. PMID:25898945
Global transcriptional dynamics of diapause induction in non-blood-fed and blood-fed Aedes albopictus. PMID:25897664
ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. PMID:25897127
Inter-individual differences in the gene content of human gut bacterial species. PMID:25896518
Poplar trees reconfigure the transcriptome and metabolome in response to drought in a genotype- and time-of-day-dependent manner. PMID:25895923
Genomic data assimilation using a higher moment filtering technique for restoration of gene regulatory networks. PMID:25890175
Mimoza: web-based semantic zooming and navigation in metabolic networks. PMID:25889977
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems. PMID:25887162
Meloidogyne javanica fatty acid- and retinol-binding protein (Mj-FAR-1) regulates expression of lipid-, cell wall-, stress- and phenylpropanoid-related genes during nematode infection of tomato. PMID:25886179
MUSiCC: a marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome. PMID:25885687
Transcriptional analysis identifies key genes involved in metabolism, fibrosis/tissue repair and the immune response against Fasciola hepatica in sheep liver. PMID:25885344
GraphSAW: a web-based system for graphical analysis of drug interactions and side effects using pharmaceutical and molecular data. PMID:25881043
KPP: KEGG Pathway Painter. PMID:25879163
Overview of a surface-ripened cheese community functioning by meta-omics analyses. PMID:25867897
Genome-wide Analysis of Body Proportion Classifies Height-Associated Variants by Mechanism of Action and Implicates Genes Important for Skeletal Development. PMID:25865494
AVIA v2.0: annotation, visualization and impact analysis of genomic variants and genes. PMID:25861966
Systemic Metabolomic Changes in Blood Samples of Lung Cancer Patients Identified by Gas Chromatography Time-of-Flight Mass Spectrometry. PMID:25859693
Abiotic stress and genome dynamics: specific genes and transposable elements response to iron excess in rice. PMID:25844118
Dietary nitrate is a modifier of vascular gene expression in old male mice. PMID:25838870
Combinatorial proteomic analysis of intercellular signaling applied to the CD28 T-cell costimulatory receptor. PMID:25829543
iPathCase(KEGG): An iPad interface for KEGG metabolic pathways. PMID:25825656
Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice. PMID:25820259
Characterization of the Xylella fastidiosa PD1671 gene encoding degenerate c-di-GMP GGDEF/EAL domains, and its role in the development of Pierce's disease. PMID:25811864
CO-Releasing Molecules Have Nonheme Targets in Bacteria: Transcriptomic, Mathematical Modeling and Biochemical Analyses of CORM-3 [Ru(CO)3Cl(glycinate)] Actions on a Heme-Deficient Mutant of Escherichia coli. PMID:25811604
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. PMID:25806041
Developmental exposure to estrogen alters differentiation and epigenetic programming in a human fetal prostate xenograft model. PMID:25799167
Analytical methods in untargeted metabolomics: state of the art in 2015. PMID:25798438
Gene-based mapping and pathway analysis of metabolic traits in dairy cows. PMID:25789767
Translational arrest due to cytoplasmic redox stress delays adaptation to growth on methanol and heterologous protein expression in a typical fed-batch culture of Pichia pastoris. PMID:25785713
The beta-3 adrenergic agonist (CL-316,243) restores the expression of down-regulated fatty acid oxidation genes in type 2 diabetic mice. PMID:25784953
Analysis of protein expression changes of the Vero E6 cells infected with classic PEDV strain CV777 by using quantitative proteomic technique. PMID:25783682
Phylogenetic and functional alterations in bacterial community compositions in broiler ceca as a result of mannan oligosaccharide supplementation. PMID:25769823
Diabetes Associated Metabolomic Perturbations in NOD Mice. PMID:25755629
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. PMID:25750602
A systems approach to traditional oriental medicine. PMID:25748918
Integration of metabolomics data into metabolic networks. PMID:25741348
Network-assisted genetic dissection of pathogenicity and drug resistance in the opportunistic human pathogenic fungus Cryptococcus neoformans. PMID:25739925
Pathways associated with lignin biosynthesis in lignomaniac jute fibres. PMID:25724692
Analysis of long non-coding RNAs highlights tissue-specific expression patterns and epigenetic profiles in normal and psoriatic skin. PMID:25723451
Genetic basis and detection of unintended effects in genetically modified crop plants. PMID:25716164
Genome-Wide Profiling of TRACK Kidneys Shows Similarity to the Human ccRCC Transcriptome. PMID:25715653
Biological databases for human research. PMID:25712261
Integration of untargeted metabolomics with transcriptomics reveals active metabolic pathways. PMID:25705145
Substrate-dependent activation of the Vibrio cholerae vexAB RND efflux system requires vexR. PMID:25695834
Selective paired ion contrast analysis: a novel algorithm for analyzing postprocessed LC-MS metabolomics data possessing high experimental noise. PMID:25683158
New genetic loci link adipose and insulin biology to body fat distribution. PMID:25673412
Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network. PMID:25670818
De novo assembly and characterization of Muscovy duck liver transcriptome and analysis of differentially regulated genes in response to heat stress. PMID:25663538
Sequence variation, differential expression, and divergent evolution in starch-related genes among accessions of Arabidopsis thaliana. PMID:25663508
Inferring active and prognostic ligand-receptor pairs with interactions in survival regression models. PMID:25657571
Metabolomic markers of altered nucleotide metabolism in early stage adenocarcinoma. PMID:25657018
Quantitative proteomics analysis of CaMKII phosphorylation and the CaMKII interactome in the mouse forebrain. PMID:25650780
Aquifer environment selects for microbial species cohorts in sediment and groundwater. PMID:25647349
Quantitative and logic modelling of molecular and gene networks. PMID:25645874
Effects of the diet on the microbiota of the red palm weevil (Coleoptera: Dryophthoridae). PMID:25635833
Network representations of immune system complexity. PMID:25625853
Metabolic Profiling and Phenotyping of Central Nervous System Diseases: Metabolites Bring Insights into Brain Dysfunctions. PMID:25616565
Evolutionary constraint and disease associations of post-translational modification sites in human genomes. PMID:25611800
A computational approach to identifying gene-microRNA modules in cancer. PMID:25611546
Functional and phylogenetic characterization of proteins detected in various nematode intestinal compartments. PMID:25609831
Chemometric evaluation of Saccharomyces cerevisiae metabolic profiles using LC-MS. PMID:25598766
Biological interpretation of genome-wide association studies using predicted gene functions. PMID:25597830
Interleukin polymorphisms associated with overall survival, disease-free survival, and recurrence in non-small cell lung cancer patients. PMID:25597281
Acquisition of docetaxel resistance in breast cancer cells reveals upregulation of ABCB1 expression as a key mediator of resistance accompanied by discrete upregulation of other specific genes and pathways. PMID:25596703
Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors. PMID:25592566
Amyloid precursor protein interaction network in human testis: sentinel proteins for male reproduction. PMID:25591988
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis. PMID:25590628
Metabolomics in psoriatic disease: pilot study reveals metabolite differences in psoriasis and psoriatic arthritis. PMID:25580230
Single-cell-level spatial gene expression in the embryonic neural differentiation niche. PMID:25575549
Divergence across diet, time and populations rules out parallel evolution in the gut microbiomes of Trinidadian guppies. PMID:25575311
A Comprehensive Profile of ChIP-Seq-Based PU.1/Spi1 Target Genes in Microglia. PMID:25574134
A co-culture genome-wide RNAi screen with mammary epithelial cells reveals transmembrane signals required for growth and differentiation. PMID:25572802
Clinical and genetic investigation of a multi-generational Chinese family afflicted with Von Hippel-Lindau disease. PMID:25563310
A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. PMID:25559748
Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. PMID:25555398
Drosophila melanogaster show a threshold effect in response to radiation. PMID:25552957
Patterns of evolutionary conservation of ascorbic acid-related genes following whole-genome triplication in Brassica rapa. PMID:25552535
A novel dysregulated pathway-identification analysis based on global influence of within-pathway effects and crosstalk between pathways. PMID:25551156
Remodeling of intermediate metabolism in the diatom Phaeodactylum tricornutum under nitrogen stress. PMID:25548193
An integrated network visualization framework towards metabolic engineering applications. PMID:25547011
Convergent genetic and expression data implicate immunity in Alzheimer's disease. PMID:25533204
Computational methods and opportunities for phosphorylation network medicine. PMID:25530950
A substrate ambiguous enzyme facilitates genome reduction in an intracellular symbiont. PMID:25527092
TimeXNet: identifying active gene sub-networks using time-course gene expression profiles. PMID:25522063
Molecular profiling of thyroid cancer subtypes using large-scale text mining. PMID:25521965
Identification of differentially expressed genes regulated by transcription factors in glioblastomas by bioinformatics analysis. PMID:25514975
Subcellular metabolite and lipid analysis of Xenopus laevis eggs by LAESI mass spectrometry. PMID:25506922
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. PMID:25490956
Ancient and modern environmental DNA. PMID:25487334
Atom mapping with constraint programming. PMID:25484913
MicroRNA Dysregulation, Gene Networks, and Risk for Schizophrenia in 22q11.2 Deletion Syndrome. PMID:25484875
Development of Cymbidium ensifolium genic-SSR markers and their utility in genetic diversity and population structure analysis in cymbidiums. PMID:25481640
Graphical algorithm for integration of genetic and biological data: proof of principle using psoriasis as a model. PMID:25480373
BioAssay Research Database (BARD): chemical biology and probe-development enabled by structured metadata and result types. PMID:25477388
Identification of sumoylated proteins in the silkworm Bombyx mori. PMID:25470021
Profiling of concanavalin A-binding glycoproteins in human hepatic stellate cells activated with transforming growth factor-β1. PMID:25460309
Crosstalk between signaling pathways provided by single and multiple protein phosphorylation sites. PMID:25451034
Gene expression profiling studies in regenerating nerves in a mouse model for CMT1X: uninjured Cx32-knockout peripheral nerves display expression profile of injured wild type nerves. PMID:25447941
Early depletion of primordial germ cells in zebrafish promotes testis formation. PMID:25434820
The transcriptome of corona radiata cells from individual MІІ oocytes that after ICSI developed to embryos selected for transfer: PCOS women compared to healthy women. PMID:25432544
Using VisANT to Analyze Networks. PMID:25422679
Complete genome sequence and comparative genome analysis of Klebsiella oxytoca HKOPL1 isolated from giant panda feces. PMID:25417012
Predicting the functional repertoire of an organism from unassembled RNA-seq data. PMID:25409897
CMPD: cancer mutant proteome database. PMID:25398898
Comparative analysis of predicted plastid-targeted proteomes of sequenced higher plant genomes. PMID:25393533
Distinct strains of Toxoplasma gondii feature divergent transcriptomes regardless of developmental stage. PMID:25393307
Text mining in cancer gene and pathway prioritization. PMID:25392685
Whole-genome sequencing of the world's oldest people. PMID:25390934
GlycoRDF: an ontology to standardize glycomics data in RDF. PMID:25388145
Systems biology approaches for studying the pathogenesis of non-alcoholic fatty liver disease. PMID:25386055
Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and domestication. PMID:25385592
Pseudomonas aeruginosa LysR PA4203 regulator NmoR acts as a repressor of the PA4202 nmoA gene, encoding a nitronate monooxygenase. PMID:25384477
Systems level analysis and identification of pathways and networks associated with liver fibrosis. PMID:25380136
T3DB: the toxic exposome database. PMID:25378312
Antitumor activity of the MEK inhibitor TAK-733 against melanoma cell lines and patient-derived tumor explants. PMID:25376610
The role of cis regulatory evolution in maize domestication. PMID:25375861
Reconstruction of metabolic pathways by combining probabilistic graphical model-based and knowledge-based methods. PMID:25374614
From microbial gene essentiality to novel antimicrobial drug targets. PMID:25373505
Comparative analyses of nonpathogenic, opportunistic, and totally pathogenic mycobacteria reveal genomic and biochemical variabilities and highlight the survival attributes of Mycobacterium tuberculosis. PMID:25370496
Comparative genomics of pneumocystis species suggests the absence of genes for myo-inositol synthesis and reliance on inositol transport and metabolism. PMID:25370490
A phylogeny-based benchmarking test for orthology inference reveals the limitations of function-based validation. PMID:25369365
GeneFriends: a human RNA-seq-based gene and transcript co-expression database. PMID:25361971
Characterization of the rainbow trout spleen transcriptome and identification of immune-related genes. PMID:25352861
APC/C(Cdh1) controls CtIP stability during the cell cycle and in response to DNA damage. PMID:25349192
Comparative analysis and modeling of the severity of steatohepatitis in DDC-treated mouse strains. PMID:25347188
Understanding disease mechanisms with models of signaling pathway activities. PMID:25344409
Genome-scale transcriptome analysis of the alpine "glasshouse" plant Rheum nobile (Polygonaceae) with special translucent bracts. PMID:25343261
Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host. PMID:25339726
The Comparative Genomics and Phylogenomics of Leishmania amazonensis Parasite. PMID:25336895
Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities. PMID:25333462
Biogeochemical typing of paddy field by a data-driven approach revealing sub-systems within a complex environment--a pipeline to filtrate, organize and frame massive dataset from multi-omics analyses. PMID:25330259
Likelihood-based gene annotations for gap filling and quality assessment in genome-scale metabolic models. PMID:25329157
The Comparative Toxicogenomics Database's 10th year anniversary: update 2015. PMID:25326323
On dynamically generating relevant elementary flux modes in a metabolic network using optimization. PMID:25323319
Metastatic tumor evolution and organoid modeling implicate TGFBR2 as a cancer driver in diffuse gastric cancer. PMID:25315765
Computational approaches for microalgal biofuel optimization: a review. PMID:25309916
Systems level mapping of metabolic complexity in Mycobacterium tuberculosis to identify high-value drug targets. PMID:25304862
Comparative gene expression profiling of normal and human colorectal adenomatous tissues. PMID:25295094
Defining the role of common variation in the genomic and biological architecture of adult human height. PMID:25282103
A novel common variant in DCST2 is associated with length in early life and height in adulthood. PMID:25281659
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. PMID:25280501
Evolutionary strategies of viruses, bacteria and archaea in hydrothermal vent ecosystems revealed through metagenomics. PMID:25279954
Integration of heterogeneous molecular networks to unravel gene-regulation in Mycobacterium tuberculosis. PMID:25279447
Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides mccartyi Strain SG1, Which Carries a Circular Putative Plasmid. PMID:25278523
Structuring research methods and data with the research object model: genomics workflows as a case study. PMID:25276335
Predicting interactome network perturbations in human cancer: application to gene fusions in acute lymphoblastic leukemia. PMID:25273558
Tracking difference in gene expression in a time-course experiment using gene set enrichment analysis. PMID:25268590
Inferring novel indications of approved drugs via a learning method with local and global consistency. PMID:25268268
Disease pathways at the Rat Genome Database Pathway Portal: genes in context-a network approach to understanding the molecular mechanisms of disease. PMID:25265995
In-vivo fusion of human cancer and hamster stromal cells permanently transduces and transcribes human DNA. PMID:25259521
Large differences in global transcriptional regulatory programs of normal and tumor colon cells. PMID:25253512
Connecting prognostic ligand receptor signaling loops in advanced ovarian cancer. PMID:25244152
An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data. PMID:25244077
Genomic insights into processes driving the infection of Alexandrium tamarense by the Parasitoid Amoebophrya sp. PMID:25239978
Differential proteomic profiling unveils new molecular mechanisms associated with mitochondrial complex III deficiency. PMID:25239759
Are common fragile sites merely structural domains or highly organized "functional" units susceptible to oncogenic stress? PMID:25238782
Neurotoxin-induced pathway perturbation in human neuroblastoma SH-EP cells. PMID:25234470
A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD. PMID:25228925
Characterization of chemically induced liver injuries using gene co-expression modules. PMID:25226513
Full-length enriched cDNA libraries and ORFeome analysis of sugarcane hybrid and ancestor genotypes. PMID:25222706
Prioritizing genes for X-linked diseases using population exome data. PMID:25217573
Knowledge-driven genomic interactions: an application in ovarian cancer. PMID:25214892
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
Molecular network analysis suggests a logical hypothesis for the pathological role of c9orf72 in amyotrophic lateral sclerosis/frontotemporal dementia. PMID:25210488
Analysis of tumor suppressor genes based on gene ontology and the KEGG pathway. PMID:25207935
EC2KEGG: a command line tool for comparison of metabolic pathways. PMID:25202338
High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway. PMID:25197453
De novo transcriptome sequence assembly from coconut leaves and seeds with a focus on factors involved in RNA-directed DNA methylation. PMID:25193496
Deep proteomic evaluation of primary and cell line motoneuron disease models delineates major differences in neuronal characteristics. PMID:25193168
Profiles of the auditory epithelia related microRNA expression in neonatal and adult rats. PMID:25192719
MYCN repression of Lifeguard/FAIM2 enhances neuroblastoma aggressiveness. PMID:25188511
Systematic production of inactivating and non-inactivating suppressor mutations at the relA locus that compensate the detrimental effects of complete spot loss and affect glycogen content in Escherichia coli. PMID:25188023
Metabolomics in the fight against malaria. PMID:25185001
Microbiome analysis - from technical advances to biological relevance. PMID:25184041
BioModels linked dataset. PMID:25182954
DawnRank: discovering personalized driver genes in cancer. PMID:25177370
Mapping the inner workings of the microbiome: genomic- and metagenomic-based study of metabolism and metabolic interactions in the human microbiome. PMID:25176148
Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics. PMID:25173486
Identification of the ligand in the structure of the protein with unknown function STM4435 from Salmonella typhimurium. PMID:25172330
Gene co-expression network analysis in Rhodobacter capsulatus and application to comparative expression analysis of Rhodobacter sphaeroides. PMID:25164283
Whole genome sequencing and analysis of plant growth promoting bacteria isolated from the rhizosphere of plantation crops coconut, cocoa and arecanut. PMID:25162593
Comparative analysis of functional metagenomic annotation and the mappability of short reads. PMID:25148512
miRNA profiles in plasma from patients with sleep disorders reveal dysregulation of miRNAs in narcolepsy and other central hypersomnias. PMID:25142559
Contrasting metabolism in perenniating structures of upland and lowland switchgrass plants late in the growing season. PMID:25133804
A quest for miRNA bio-marker: a track back approach from gingivo buccal cancer to two different types of precancers. PMID:25126847
PlantCAZyme: a database for plant carbohydrate-active enzymes. PMID:25125445
Pathway analysis approaches for rare and common variants: insights from Genetic Analysis Workshop 18. PMID:25112195
Genome-wide association analyses identify variants in developmental genes associated with hypospadias. PMID:25108383
Genome-wide association study combined with biological context can reveal more disease-related SNPs altering microRNA target seed sites. PMID:25106527
Recently published Streptomyces genome sequences. PMID:25100265
GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. PMID:25099887
Novel entries in a fungal biofilm matrix encyclopedia. PMID:25096878
Bioinformatic approaches to augment study of epithelial-to-mesenchymal transition in lung cancer. PMID:25096367
Serum miRNA signature in Moyamoya disease. PMID:25093848
Interactive transcriptome analysis of malaria patients and infecting Plasmodium falciparum. PMID:25091627
De novo assembly and characterization of the transcriptome in the desiccation-tolerant moss Syntrichia caninervis. PMID:25086984
Gene set enrichment analysis for multiple continuous phenotypes. PMID:25086605
Phen-Gen: combining phenotype and genotype to analyze rare disorders. PMID:25086502
Concordance of deregulated mechanisms unveiled in underpowered experiments: PTBP1 knockdown case study. PMID:25079003
Furby: fuzzy force-directed bicluster visualization. PMID:25078951
Loss of nuclear PTEN in HCV-infected human hepatocytes. PMID:25075209
Network features suggest new hepatocellular carcinoma treatment strategies. PMID:25070212
Comparative metabolomics in primates reveals the effects of diet and gene regulatory variation on metabolic divergence. PMID:25069065
Comparison of the mammalian insulin signalling pathway to invertebrates in the context of FOXO-mediated ageing. PMID:25064569
UVB induces a genome-wide acting negative regulatory mechanism that operates at the level of transcription initiation in human cells. PMID:25058334
iRegulon: from a gene list to a gene regulatory network using large motif and track collections. PMID:25058159
Identification and Function Prediction of Novel MicroRNAs in Laoshan Dairy Goats. PMID:25049792
Complete genome of a nonphotosynthetic cyanobacterium in a diatom reveals recent adaptations to an intracellular lifestyle. PMID:25049384
Bayesian pathway analysis of cancer microarray data. PMID:25036210
Dermal wound transcriptomic responses to Infection with Pseudomonas aeruginosa versus Klebsiella pneumoniae in a rabbit ear wound model. PMID:25035691
Copy number variable microRNAs in schizophrenia and their neurodevelopmental gene targets. PMID:25034949
Bioinformatic analysis of proteomics data. PMID:25033288
Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data. PMID:25033193
DBSecSys: a database of Burkholderia mallei secretion systems. PMID:25030112
Top associated SNPs in prostate cancer are significantly enriched in cis-expression quantitative trait loci and at transcription factor binding sites. PMID:25026280
Functional genomics of Lactobacillus casei establishment in the gut. PMID:25024222
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. PMID:25003081
The combined structural and kinetic characterization of a bacterial nitronate monooxygenase from Pseudomonas aeruginosa PAO1 establishes NMO class I and II. PMID:25002579
RNA-Seq for gene identification and transcript profiling of three Stevia rebaudiana genotypes. PMID:25001368
Proteomic analysis of solid pseudopapillary tumor of the pancreas reveals dysfunction of the endoplasmic reticulum protein processing pathway. PMID:24997997
Expansion of biological pathways based on evolutionary inference. PMID:24995987
Proteogenomic convergence for understanding cancer pathways and networks. PMID:24994965
Complete genome assembly and characterization of an outbreak strain of the causative agent of swine erysipelas--Erysipelothrix rhusiopathiae SY1027. PMID:24993343
Emergent biosynthetic capacity in simple microbial communities. PMID:24992662
Homology modeling and protein engineering of alkane monooxygenase in Burkholderia thailandensis MSMB121: in silico insights. PMID:24990796
Gene response in rice plants treated with continuous fog influenced by pH, was similar to that treated with biotic stress. PMID:24987489
Minimal metabolic pathway structure is consistent with associated biomolecular interactions. PMID:24987116
Transcriptional targets of the schizophrenia risk gene MIR137. PMID:24984191
Elucidation of the evolutionary expansion of phosphorylation signaling networks using comparative phosphomotif analysis. PMID:24981518
Automated identification of stratifying signatures in cellular subpopulations. PMID:24979804
Identification of novel elements of the Drosophila blisterome sheds light on potential pathological mechanisms of several human diseases. PMID:24968325
Integrative identification of deregulated miRNA/TF-mediated gene regulatory loops and networks in prostate cancer. PMID:24968068
Comparative genomics and evolution of regulons of the LacI-family transcription factors. PMID:24966856
Gene Set Enrichment Analysis (GSEA) of Toxoplasma gondii expression datasets links cell cycle progression and the bradyzoite developmental program. PMID:24962434
Cytochrome P450 site of metabolism prediction from 2D topological fingerprints using GPU accelerated probabilistic classifiers. PMID:24959208
Limited influence of oxygen on the evolution of chemical diversity in metabolic networks. PMID:24958261
CASMI: And the Winner is . . PMID:24957999
CASMI-The Small Molecule Identification Process from a Birmingham Perspective. PMID:24957998
Current understanding of the formation and adaptation of metabolic systems based on network theory. PMID:24957641
Transcriptome profiling reveals higher vertebrate orthologous of intra-cytoplasmic pattern recognition receptors in grey bamboo shark. PMID:24956167
Biological overlap of attention-deficit/hyperactivity disorder and autism spectrum disorder: evidence from copy number variants. PMID:24954825
From prediction to function using evolutionary genomics: human-specific ecotypes of Lactobacillus reuteri have diverse probiotic functions. PMID:24951561
Breast cancer prognosis risk estimation using integrated gene expression and clinical data. PMID:24949450
Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data. PMID:24949426
PGS: a tool for association study of high-dimensional microRNA expression data with repeated measures. PMID:24947752
Salt-induced changes in cardiac phosphoproteome in a rat model of chronic renal failure. PMID:24945867
Proteomic analysis of embryogenesis and the acquisition of seed dormancy in Norway maple (Acer platanoides L.). PMID:24941250
Disrupting KATP channels diminishes the estrogen-mediated protection in female mutant mice during ischemia-reperfusion. PMID:24936167
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. PMID:24931980
Improving functional annotation for industrial microbes: a case study with Pichia pastoris. PMID:24929579
High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource. PMID:24927599
The multiple roles of hypothetical gene BPSS1356 in Burkholderia pseudomallei. PMID:24927285
Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. PMID:24921649
Population-specific common SNPs reflect demographic histories and highlight regions of genomic plasticity with functional relevance. PMID:24906912
Transcriptional consequences of 16p11.2 deletion and duplication in mouse cortex and multiplex autism families. PMID:24906019
Integrated pathway-based approach identifies association between genomic regions at CTCF and CACNB2 and schizophrenia. PMID:24901509
Molecular aspects of adipoepithelial transdifferentiation in mouse mammary gland. PMID:24898182
Protein-protein interactions and genetic diseases: The interactome. PMID:24892209
Exploring mechanisms of diet-colon cancer associations through candidate molecular interaction networks. PMID:24886433
Network topology-based detection of differential gene regulation and regulatory switches in cell metabolism and signaling. PMID:24886210
Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness. PMID:24885784
Toxoplasma gondii merozoite gene expression analysis with comparison to the life cycle discloses a unique expression state during enteric development. PMID:24885521
Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis. PMID:24885385
Inferring host gene subnetworks involved in viral replication. PMID:24874113
Chemotherapy-induced dynamic gene expression changes in vivo are prognostic in ovarian cancer. PMID:24867692
Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PMID:24866127
Carbohydrate catabolism in Phaeobacter inhibens DSM 17395, a member of the marine roseobacter clade. PMID:24858085
Signaling hypergraphs. PMID:24857424
Metagenomic analyses reveal the involvement of syntrophic consortia in methanol/electricity conversion in microbial fuel cells. PMID:24852573
The placenta harbors a unique microbiome. PMID:24848255
The ctenophore genome and the evolutionary origins of neural systems. PMID:24847885
Transcriptional response of virus-infected cassava and identification of putative sources of resistance for cassava brown streak disease. PMID:24846209
Relating the metatranscriptome and metagenome of the human gut. PMID:24843156
DINIES: drug-target interaction network inference engine based on supervised analysis. PMID:24838565
Handling temperature bursts reaching 464°C: different microbial strategies in the sisters peak hydrothermal chimney. PMID:24837379
Metabolomic Characterization of Knockout Mutants in Arabidopsis: Development of a Metabolite Profiling Database for Knockout Mutants in Arabidopsis. PMID:24828308
Genetic profiling of the isoprenoid and sterol biosynthesis pathway genes of Trypanosoma cruzi. PMID:24828104
Impact of adding the multikinase inhibitor sorafenib to endocrine therapy in metastatic estrogen receptor-positive breast cancer. PMID:24826798
Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. PMID:24816253
An atlas of genetic influences on human blood metabolites. PMID:24816252
A lack of parasitic reduction in the obligate parasitic green alga Helicosporidium. PMID:24809511
Prediction of substrates for glutathione transferases by covalent docking. PMID:24802635
Phosphokinase antibody arrays on dendron-coated surface. PMID:24802362
XTMS: pathway design in an eXTended metabolic space. PMID:24792156
A mutation in POLE predisposing to a multi-tumour phenotype. PMID:24788313
Pharmacomicrobiomics: the impact of human microbiome variations on systems pharmacology and personalized therapeutics. PMID:24785449
Developmental transcriptome analysis of human erythropoiesis. PMID:24781209
Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition. PMID:24779965
Applying genome-wide gene-based expression quantitative trait locus mapping to study population ancestry and pharmacogenetics. PMID:24779372
Copy number variation in schizophrenia in Sweden. PMID:24776740
Modeling disease progression using dynamics of pathway connectivity. PMID:24771518
Rac2 controls tumor growth, metastasis and M1-M2 macrophage differentiation in vivo. PMID:24770346
Genome-wide Mycobacterium tuberculosis variation (GMTV) database: a new tool for integrating sequence variations and epidemiology. PMID:24767249
EndoNet: an information resource about the intercellular signaling network. PMID:24758335
Gene expression signatures affected by alcohol-induced DNA methylomic deregulation in human embryonic stem cells. PMID:24751885
Microarray analysis of cell cycle gene expression in adult human corneal endothelial cells. PMID:24747418
Population genomic analyses based on 1 million SNPs in commercial egg layers. PMID:24739889
New insights into Dehalococcoides mccartyi metabolism from a reconstructed metabolic network-based systems-level analysis of D. mccartyi transcriptomes. PMID:24733489
Protein abundance changes and ubiquitylation targets identified after inhibition of the proteasome with syringolin A. PMID:24732913
Comparative genomics of flatworms (platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata. PMID:24732282
Characterization of biological pathways associated with a 1.37 Mbp genomic region protective of hypertension in Dahl S rats. PMID:24714719
Robustness and plasticity of metabolic pathway flux among uropathogenic isolates of Pseudomonas aeruginosa. PMID:24709961
Taxonomic and functional profiles of soil samples from Atlantic forest and Caatinga biomes in northeastern Brazil. PMID:24706600
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. PMID:24705354
SysPTM 2.0: an updated systematic resource for post-translational modification. PMID:24705204
The recA operon: A novel stress response gene cluster in Bacteroides fragilis. PMID:24703997
mtDNA haplogroup and single nucleotide polymorphisms structure human microbiome communities. PMID:24694284
Symbiotic adaptation drives genome streamlining of the cyanobacterial sponge symbiont "Candidatus Synechococcus spongiarum". PMID:24692632
Neanderthal ancestry drives evolution of lipid catabolism in contemporary Europeans. PMID:24690587
Integrative study of Arabidopsis thaliana metabolomic and transcriptomic data with the interactive MarVis-Graph software. PMID:24688832
Integrated LC-MS/MS system for plant metabolomics. PMID:24688692
Computational tools for the secondary analysis of metabolomics experiments. PMID:24688685
Global transcriptome analysis identifies regulated transcripts and pathways activated during oogenesis and early embryogenesis in Atlantic cod. PMID:24687555
Beyond genomic variation--comparison and functional annotation of three Brassica rapa genomes: a turnip, a rapid cycling and a Chinese cabbage. PMID:24684742
molBLOCKS: decomposing small molecule sets and uncovering enriched fragments. PMID:24681908
Biofragments: an approach towards predicting protein function using biologically related fragments and its application to Mycobacterium tuberculosis CYP126. PMID:24677424
Comparative proteomic analysis reveals that T3SS, Tfp, and xanthan gum are key factors in initial stages of Citrus sinensis infection by Xanthomonas citri subsp. citri. PMID:24676796
Identification and analysis of differential miRNAs in PK-15 cells after foot-and-mouth disease virus infection. PMID:24675746
Plant systems biology: insights, advances and challenges. PMID:24671625
Genome-wide association study for intramuscular fat deposition and composition in Nellore cattle. PMID:24666668
Comparative metagenomic analyses reveal viral-induced shifts of host metabolism towards nucleotide biosynthesis. PMID:24666644
Prediction of individualized therapeutic vulnerabilities in cancer from genomic profiles. PMID:24665131
A highly conserved family of domains related to the DNA-glycosylase fold helps predict multiple novel pathways for RNA modifications. PMID:24646681
Inferring gene dependency network specific to phenotypic alteration based on gene expression data and clinical information of breast cancer. PMID:24637666
Dysbiosis in the inflamed intestine: chance favors the prepared microbe. PMID:24637596
Investigation of key microRNAs associated with hepatocellular carcinoma using small RNA-seq data. PMID:24623406
Comparisons of Shewanella strains based on genome annotations, modeling, and experiments. PMID:24621294
The use of weighted graphs for large-scale genome analysis. PMID:24619061
Csnk1a1 inhibition has p53-dependent therapeutic efficacy in acute myeloid leukemia. PMID:24616378
Global analysis of Chlorella variabilis NC64A mRNA profiles during the early phase of Paramecium bursaria chlorella virus-1 infection. PMID:24608695
The yeast Sks1p kinase signaling network regulates pseudohyphal growth and glucose response. PMID:24603354
Interactive exploration of integrated biological datasets using context-sensitive workflows. PMID:24600467
From the environment to the host: re-wiring of the transcriptome of Pseudomonas aeruginosa from 22°C to 37°C. PMID:24587139
Meta-analysis of pathway enrichment: combining independent and dependent omics data sets. PMID:24586671
Effect of bodily fluids from honey bee (Apis mellifera) larvae on growth and genome-wide transcriptional response of the causal agent of American Foulbrood disease (Paenibacillus larvae). PMID:24586572
ENZYMAP: exploiting protein annotation for modeling and predicting EC number changes in UniProt/Swiss-Prot. PMID:24586563
Chemogenomics knowledgebased polypharmacology analyses of drug abuse related G-protein coupled receptors and their ligands. PMID:24567719
Molecular pathway identification using biological network-regularized logistic models. PMID:24564637
enRoute: dynamic path extraction from biological pathway maps for exploring heterogeneous experimental datasets. PMID:24564375
RRHGE: a novel approach to classify the estrogen receptor based breast cancer subtypes. PMID:24563630
Transcriptome profile of Trichoderma harzianum IOC-3844 induced by sugarcane bagasse. PMID:24558413
Exploiting cell metabolism for biocatalytic whole-cell transamination by recombinant Saccharomyces cerevisiae. PMID:24557569
PathNER: a tool for systematic identification of biological pathway mentions in the literature. PMID:24555844
LC-MS proteomics analysis of the insulin/IGF-1-deficient Caenorhabditis elegans daf-2(e1370) mutant reveals extensive restructuring of intermediary metabolism. PMID:24555535
Land use type significantly affects microbial gene transcription in soil. PMID:24553913
BiNA: a visual analytics tool for biological network data. PMID:24551056
Transcriptome sequencing of Atlantic salmon (Salmo salar L.) notochord prior to development of the vertebrae provides clues to regulation of positional fate, chordoblast lineage and mineralisation. PMID:24548379
Inferring metabolic networks using the Bayesian adaptive graphical lasso with informative priors. PMID:24533172
Interspecies systems biology uncovers metabolites affecting C. elegans gene expression and life history traits. PMID:24529378
Identification of core T cell network based on immunome interactome. PMID:24528953
VGX-1027 modulates genes involved in lipopolysaccharide-induced Toll-like receptor 4 activation and in a murine model of systemic lupus erythematosus. PMID:24527796
Radiation-induced gene signature predicts pathologic complete response to neoadjuvant chemotherapy in breast cancer patients. PMID:24527691
A Network Approach to Wound Healing. PMID:24527361
Genome-wide tissue-specific gene expression, co-expression and regulation of co-expressed genes in adult nematode Ascaris suum. PMID:24516681
Hyperexpression of α-hemolysin explains enhanced virulence of sequence type 93 community-associated methicillin-resistant Staphylococcus aureus. PMID:24512075
Identification of functional cooperative mutations of SETD2 in human acute leukemia. PMID:24509477
Identification and differential expression of microRNAs in ovaries of laying and Broody geese (Anser cygnoides) by Solexa sequencing. PMID:24505332
The pathway ontology - updates and applications. PMID:24499703
A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes. PMID:24498386
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
A network-assisted co-clustering algorithm to discover cancer subtypes based on gene expression. PMID:24491042
Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome. PMID:24489955
Loss of connectivity in cancer co-expression networks. PMID:24489837
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions. PMID:24478989
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. PMID:24478124
Pseudomonas putida CSV86: a candidate genome for genetic bioaugmentation. PMID:24475028
Elucidating the genetic basis of crystalline biofilm formation in Proteus mirabilis. PMID:24470471
Protein profiles associated with context fear conditioning and their modulation by memantine. PMID:24469516
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. PMID:24468196
Grimontia indica AK16(T), sp. nov., isolated from a seawater sample reports the presence of pathogenic genes similar to Vibrio genus. PMID:24465608
Genomic characterization of three urinary bladder cancer cell lines: understanding genomic types of urinary bladder cancer. PMID:24459064
NMDA receptor-dependent regulation of miRNA expression and association with Argonaute during LTP in vivo. PMID:24454279
A comprehensive tRNA deletion library unravels the genetic architecture of the tRNA pool. PMID:24453985
Innate immunity interactome dynamics. PMID:24453478
Genome resolved analysis of a premature infant gut microbial community reveals a Varibaculum cambriense genome and a shift towards fermentation-based metabolism during the third week of life. PMID:24451181
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. PMID:24450983
Early microbial and metabolomic signatures predict later onset of necrotizing enterocolitis in preterm infants. PMID:24450576
An evidence-based knowledgebase of pulmonary arterial hypertension to identify genes and pathways relevant to pathogenesis. PMID:24448676
Systems toxicology: from basic research to risk assessment. PMID:24446777
Genome of the human hookworm Necator americanus. PMID:24441737
Transcriptome analysis of psoriasis in a large case-control sample: RNA-seq provides insights into disease mechanisms. PMID:24441097
A systems toxicology approach identifies Lyn as a key signaling phosphoprotein modulated by mercury in a B lymphocyte cell model. PMID:24440445
DBM-DB: the diamondback moth genome database. PMID:24434032
Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures. PMID:24432194
Constraint-based models predict metabolic and associated cellular functions. PMID:24430943
A gene pathway analysis highlights the role of cellular adhesion molecules in multiple sclerosis susceptibility. PMID:24430173
Network understanding of herb medicine via rapid identification of ingredient-target interactions. PMID:24429698
Comparative genomics of cultured and uncultured strains suggests genes essential for free-living growth of Liberibacter. PMID:24416233
MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data. PMID:24413519
Arsenic exposure perturbs the gut microbiome and its metabolic profile in mice: an integrated metagenomics and metabolomics analysis. PMID:24413286
EC-BLAST: a tool to automatically search and compare enzyme reactions. PMID:24412978
Regulation of steatohepatitis and PPARγ signaling by distinct AP-1 dimers. PMID:24411941
Integrative radiation systems biology. PMID:24411063
Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. PMID:24402055
Polyploidy and the petal transcriptome of Gossypium. PMID:24393201
Automatic context-specific subnetwork discovery from large interaction networks. PMID:24392115
Deep sequencing-based analysis of the Cymbidium ensifolium floral transcriptome. PMID:24392013
Celiac anti-type 2 transglutaminase antibodies induce phosphoproteome modification in intestinal epithelial Caco-2 cells. PMID:24391952
Low frequency variants, collapsed based on biological knowledge, uncover complexity of population stratification in 1000 genomes project data. PMID:24385916
Galaxy tools to study genome diversity. PMID:24377391
Partitioning the human transcriptome using HKera, a novel classifier of housekeeping and tissue-specific genes. PMID:24376628
Rapid construction of metabolic models for a family of Cyanobacteria using a multiple source annotation workflow. PMID:24369854
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. PMID:24369052
The role of glutamine oxoglutarate aminotransferase and glutamate dehydrogenase in nitrogen metabolism in Mycobacterium bovis BCG. PMID:24367660
Valproic acid causes proteasomal degradation of DICER and influences miRNA expression. PMID:24358235
Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. PMID:24352427
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris). PMID:24352233
Metagenomic analysis reveals significant changes of microbial compositions and protective functions during drinking water treatment. PMID:24352003
CVDHD: a cardiovascular disease herbal database for drug discovery and network pharmacology. PMID:24344970
Semantic integration of gene expression analysis tools and data sources using software connectors. PMID:24341380
Systematically studying kinase inhibitor induced signaling network signatures by integrating both therapeutic and side effects. PMID:24339888
Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. PMID:24336318
Assessment of viral community functional potential from viral metagenomes may be hampered by contamination with cellular sequences. PMID:24335607
A genome-wide association study identifies major loci affecting the immune response against infectious bronchitis virus in chicken. PMID:24333371
INDIGO - INtegrated data warehouse of microbial genomes with examples from the red sea extremophiles. PMID:24324765
Causal inference of gene regulation with subnetwork assembly from genetical genomics data. PMID:24322297
Identification of 3-sulfinopropionyl coenzyme A (CoA) desulfinases within the Acyl-CoA dehydrogenase superfamily. PMID:24317404
Integrating gene and protein expression data with genome-scale metabolic networks to infer functional pathways. PMID:24314206
MycoCosm portal: gearing up for 1000 fungal genomes. PMID:24297253
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. PMID:24297251
The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). PMID:24293654
STITCH 4: integration of protein-chemical interactions with user data. PMID:24293645
Metabolic analysis of Chlorobium chlorochromatii CaD3 reveals clues of the symbiosis in 'Chlorochromatium aggregatum'. PMID:24285361
Pathways of lipid metabolism in marine algae, co-expression network, bottlenecks and candidate genes for enhanced production of EPA and DHA in species of Chromista. PMID:24284429
A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress. PMID:24280345
Identification of 50 class D β-lactamases and 65 Acinetobacter-derived cephalosporinases in Acinetobacter spp. PMID:24277043
Protein-driven inference of miRNA-disease associations. PMID:24273243
Glucose elevates NITRATE TRANSPORTER2.1 protein levels and nitrate transport activity independently of its HEXOKINASE1-mediated stimulation of NITRATE TRANSPORTER2.1 expression. PMID:24272701
The Structure-Function Linkage Database. PMID:24271399
Network portal: a database for storage, analysis and visualization of biological networks. PMID:24271392
De novo characterization of the Anthurium transcriptome and analysis of its digital gene expression under cold stress. PMID:24267953
MetaboLyzer: a novel statistical workflow for analyzing Postprocessed LC-MS metabolomics data. PMID:24266674
Widespread sex differences in gene expression and splicing in the adult human brain. PMID:24264146
Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response. PMID:24244133
Conserved changes in the dynamics of metabolic processes during fruit development and ripening across species. PMID:24243932
The Reactome pathway knowledgebase. PMID:24243840
Revealing the hidden functional diversity of an enzyme family. PMID:24240508
Integrating protein-protein interaction networks with phenotypes reveals signs of interactions. PMID:24240319
The IUPHAR/BPS Guide to PHARMACOLOGY: an expert-driven knowledgebase of drug targets and their ligands. PMID:24234439
Discovering disease-disease associations by fusing systems-level molecular data. PMID:24232732
PATRIC, the bacterial bioinformatics database and analysis resource. PMID:24225323
The Genome Database for Rosaceae (GDR): year 10 update. PMID:24225320
The transporter classification database. PMID:24225317
Comparative metagenomics of anode-associated microbiomes developed in rice paddy-field microbial fuel cells. PMID:24223712
A Drug-Target Network-Based Approach to Evaluate the Efficacy of Medicinal Plants for Type II Diabetes Mellitus. PMID:24223610
AVIA: an interactive web-server for annotation, visualization and impact analysis of genomic variations. PMID:24215028
Bayesian network prior: network analysis of biological data using external knowledge. PMID:24215027
DriverDB: an exome sequencing database for cancer driver gene identification. PMID:24214964
Data, information, knowledge and principle: back to metabolism in KEGG. PMID:24214961
Functional networking of human divergently paired genes (DPGs). PMID:24205343
Integrative pathway-based approach for genome-wide association studies: identification of new pathways for rheumatoid arthritis and type 1 diabetes. PMID:24205270
Prediction of oncogenic interactions and cancer-related signaling networks based on network topology. PMID:24204854
DrugBank 4.0: shedding new light on drug metabolism. PMID:24203711
SMPDB 2.0: big improvements to the Small Molecule Pathway Database. PMID:24203708
MetaRef: a pan-genomic database for comparative and community microbial genomics. PMID:24203705
CottonGen: a genomics, genetics and breeding database for cotton research. PMID:24203703
Distinct microRNA expression profile and targeted biological pathways in functional myeloid-derived suppressor cells induced by Δ9-tetrahydrocannabinol in vivo: regulation of CCAAT/enhancer-binding protein α by microRNA-690. PMID:24202177
Microgravity inhibition of lipopolysaccharide-induced tumor necrosis factor-α expression in macrophage cells. PMID:24196691
Transcription factors and genetic circuits orchestrating the complex, multilayered response of Clostridium acetobutylicum to butanol and butyrate stress. PMID:24196194
Qualitative modeling identifies IL-11 as a novel regulator in maintaining self-renewal in human pluripotent stem cells. PMID:24194720
Cell-specific gene expression in Anabaena variabilis grown phototrophically, mixotrophically, and heterotrophically. PMID:24191963
Metabolite and transcriptome analysis during fasting suggest a role for the p53-Ddit4 axis in major metabolic tissues. PMID:24191950
Expression levels of DNA replication and repair genes predict regional somatic repeat instability in the brain but are not altered by polyglutamine disease protein expression or age. PMID:24191263
FunCoup 3.0: database of genome-wide functional coupling networks. PMID:24185702
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
HypoxiaDB: a database of hypoxia-regulated proteins. PMID:24178989
MetaboNetworks, an interactive Matlab-based toolbox for creating, customizing and exploring sub-networks from KEGG. PMID:24177720
A stable-isotope mass spectrometry-based metabolic footprinting approach to analyze exudates from phytoplankton. PMID:24172212
The use of multidimensional data to identify the molecular biomarker for pancreatic ductal adenocarcinoma. PMID:24171174
High contents of very long-chain polyunsaturated fatty acids in different moss species. PMID:24170342
Genome-wide binding analysis of the transcription activator ideal plant architecture1 reveals a complex network regulating rice plant architecture. PMID:24170127
IMG 4 version of the integrated microbial genomes comparative analysis system. PMID:24165883
YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae. PMID:24165882
Virtual screening and pharmacophore design for a novel theoretical inhibitor of macrophage stimulating factor as a metastatic agent. PMID:24163807
PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. PMID:24163105
A potential source for cellulolytic enzyme discovery and environmental aspects revealed through metagenomics of Brazilian mangroves. PMID:24160319
Molecular pathways: sterols and receptor signaling in cancer. PMID:24158702
On Crowd-verification of Biological Networks. PMID:24151423
Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630. PMID:24150943
Metabolic adaptation and trophic strategies of soil bacteria-C1- metabolism and sulfur chemolithotrophy in Starkeya novella. PMID:24146664
Reconstructing the genomic content of microbiome taxa through shotgun metagenomic deconvolution. PMID:24146609
Riboswitches in eubacteria sense the second messenger c-di-AMP. PMID:24141192
De novo transcriptome profiling uncovers a drastic downregulation of photosynthesis upon nitrogen deprivation in the nonmodel green alga Botryosphaerella sudeticus. PMID:24138407
The human gut and groundwater harbor non-photosynthetic bacteria belonging to a new candidate phylum sibling to Cyanobacteria. PMID:24137540
IMG/M 4 version of the integrated metagenome comparative analysis system. PMID:24136997
Identification and validation of dysregulated metabolic pathways in metastatic renal cell carcinoma. PMID:24136743
Feature selection and survival modeling in The Cancer Genome Atlas. PMID:24098079
Review of mass spectrometry-based metabolomics in cancer research. PMID:24096148
afterParty: turning raw transcriptomes into permanent resources. PMID:24093729
Unsupervised automated high throughput phenotyping of RNAi time-lapse movies. PMID:24090185
Characterization of schizophrenia adverse drug interactions through a network approach and drug classification. PMID:24089679
A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities. PMID:24086414
A bacterial quercetin oxidoreductase QuoA-mediated perturbation in the phenylpropanoid metabolic network increases lignification with a concomitant decrease in phenolamides in Arabidopsis. PMID:24085580
Functional genomics of novel secondary metabolites from diverse cyanobacteria using untargeted metabolomics. PMID:24084783
Gene Expression Under the Influence: Transcriptional Profiling of Ethanol in the Brain. PMID:24078902
Multidrug resistance in chronic myeloid leukaemia: how much can we learn from MDR-CML cell lines? PMID:24070327
QSSPN: dynamic simulation of molecular interaction networks describing gene regulation, signalling and whole-cell metabolism in human cells. PMID:24064420
The mutational landscape of chromatin regulatory factors across 4,623 tumor samples. PMID:24063517
Pathway-based outlier method reveals heterogeneous genomic structure of autism in blood transcriptome. PMID:24063311
Mapping condition-dependent regulation of lipid metabolism in Saccharomyces cerevisiae. PMID:24062529
K-Map: connecting kinases with therapeutics for drug repurposing and development. PMID:24060470
Comparative genomics of metabolic capacities of regulons controlled by cis-regulatory RNA motifs in bacteria. PMID:24060102
In silico profiling of Escherichia coli and Saccharomyces cerevisiae as terpenoid factories. PMID:24059635
Doping control using high and ultra-high resolution mass spectrometry based non-targeted metabolomics-a case study of salbutamol and budesonide abuse. PMID:24058591
Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803. PMID:24056459
Polymorphisms in metabolism/antioxidant genes may mediate the effect of dietary intake on pancreatic cancer risk. PMID:24051964
Entourage: visualizing relationships between biological pathways using contextual subsets. PMID:24051820
Protooncogene TCL1b functions as an Akt kinase co-activator that exhibits oncogenic potency in vivo. PMID:24042734
Topology of molecular interaction networks. PMID:24041013
Genome wide transcriptome analysis of dendritic cells identifies genes with altered expression in psoriasis. PMID:24039940
Dissection of miRNA-miRNA interaction in esophageal squamous cell carcinoma. PMID:24039884
Control of RNA stability by NrrF, an iron-regulated small RNA in Neisseria gonorrhoeae. PMID:24039262
A high Notch pathway activation predicts response to γ secretase inhibitors in proneural subtype of glioma tumor-initiating cells. PMID:24038660
Stress-induced isoforms of MDM2 and MDM4 correlate with high-grade disease and an altered splicing network in pediatric rhabdomyosarcoma. PMID:24027430
Genetic interactions found between calcium channel genes modulate amyloid load measured by positron emission tomography. PMID:24026422
Complete genome analysis of a Haemophilus parasuis serovar 12 strain from China. PMID:24023711
Differential inhibition of ex-vivo tumor kinase activity by vemurafenib in BRAF(V600E) and BRAF wild-type metastatic malignant melanoma. PMID:24023633
Genomic investigation into strain heterogeneity and pathogenic potential of the emerging gastrointestinal pathogen Campylobacter ureolyticus. PMID:24023611
Expansion of ruminant-specific microRNAs shapes target gene expression divergence between ruminant and non-ruminant species. PMID:24020371
Microbial life in a fjord: metagenomic analysis of a microbial mat in Chilean patagonia. PMID:24015199
Regulation of constitutive and alternative splicing by PRMT5 reveals a role for Mdm4 pre-mRNA in sensing defects in the spliceosomal machinery. PMID:24013503
Whole transcriptome sequencing identifies tumor-specific mutations in human oral squamous cell carcinoma. PMID:24007313
Genome-wide signatures of convergent evolution in echolocating mammals. PMID:24005325
Topoisomerase IV is required for partitioning of circular chromosomes but not linear chromosomes in Streptomyces. PMID:23999094
Combining quantitative genetic footprinting and trait enrichment analysis to identify fitness determinants of a bacterial pathogen. PMID:23990803
Predicting disease risk using bootstrap ranking and classification algorithms. PMID:23990773
Richness of human gut microbiome correlates with metabolic markers. PMID:23985870
The genome and developmental transcriptome of the strongylid nematode Haemonchus contortus. PMID:23985341
Genome-wide modeling of complex phenotypes in Caenorhabditis elegans and Drosophila melanogaster. PMID:23984798
Understanding the interactions between bacteria in the human gut through metabolic modeling. PMID:23982459
S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA. PMID:23980204
SILAC-based proteomics of human primary endothelial cell morphogenesis unveils tumor angiogenic markers. PMID:23979707
GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data. PMID:23975765
A modular framework for gene set analysis integrating multilevel omics data. PMID:23975194
Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. PMID:23975157
Loss of phosphatase and tensin homolog (PTEN) induces leptin-mediated leptin gene expression: feed-forward loop operating in the lung. PMID:23963458
De novo transcriptome assembly of drought tolerant CAM plants, Agave deserti and Agave tequilana. PMID:23957668
Conversion of KEGG metabolic pathways to SBGN maps including automatic layout. PMID:23953132
Pathway analysis using genome-wide association study data for coronary restenosis--a potential role for the PARVB gene. PMID:23950981
Sociogenomics of cooperation and conflict during colony founding in the fire ant Solenopsis invicta. PMID:23950725
Extracting reaction networks from databases-opening Pandora's box. PMID:23946492
Genome annotation of Burkholderia sp. SJ98 with special focus on chemotaxis genes. PMID:23940608
Voting-based cancer module identification by combining topological and data-driven properties. PMID:23940583
Integrative modeling of eQTLs and cis-regulatory elements suggests mechanisms underlying cell type specificity of eQTLs. PMID:23935528
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research. PMID:23935057
A graphical model method for integrating multiple sources of genome-scale data. PMID:23934610
Vesicular trafficking and stress response coupled to PI3K inhibition by LY294002 as revealed by proteomic and cell biological analysis. PMID:23931732
Transcriptional network analysis for the regulation of left ventricular hypertrophy and microvascular remodeling. PMID:23929067
Expression of polycomb targets predicts breast cancer prognosis. PMID:23918806
RNA-Seq reveals early distinctions and late convergence of gene expression between diapause and quiescence in the Asian tiger mosquito, Aedes albopictus. PMID:23913949
in silico analyses of metabolic pathway and protein interaction network for identification of next gen therapeutic targets in Chlamydophila pneumoniae. PMID:23904736
Proteostasis in complex dendrites. PMID:23900412
Mining large-scale response networks reveals 'topmost activities' in Mycobacterium tuberculosis infection. PMID:23892477
The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases. PMID:23883183
TIMP1 overexpression mediates resistance of MCF-7 human breast cancer cells to fulvestrant and down-regulates progesterone receptor expression. PMID:23881388
MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways. PMID:23875173
Genes dysregulated to different extent or oppositely in estrogen receptor-positive and estrogen receptor-negative breast cancers. PMID:23875016
ERK positive feedback regulates a widespread network of tyrosine phosphorylation sites across canonical T cell signaling and actin cytoskeletal proteins in Jurkat T cells. PMID:23874979
NanoMiner - integrative human transcriptomics data resource for nanoparticle research. PMID:23874618
Transcriptome characterisation of the ant Formica exsecta with new insights into the evolution of desaturase genes in social hymenoptera. PMID:23874539
GEMINI: integrative exploration of genetic variation and genome annotations. PMID:23874191
A predicted functional gene network for the plant pathogen Phytophthora infestans as a framework for genomic biology. PMID:23865555
In silico synteny based comparative genomics approach for identification and characterization of novel therapeutic targets in Chlamydophila pneumoniae. PMID:23861566
Insights into TREM2 biology by network analysis of human brain gene expression data. PMID:23855984
Bioinformatics for spermatogenesis: annotation of male reproduction based on proteomics. PMID:23852026
JBioWH: an open-source Java framework for bioinformatics data integration. PMID:23846595
Community Structure Analysis of Gene Interaction Networks in Duchenne Muscular Dystrophy. PMID:23840633
Coregulation of Terpenoid Pathway Genes and Prediction of Isoprene Production in Bacillus subtilis Using Transcriptomics. PMID:23840410
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
Systems-level overview of host protein phosphorylation during Shigella flexneri infection revealed by phosphoproteomics. PMID:23828894
Flux balance impact degree: a new definition of impact degree to properly treat reversible reactions in metabolic networks. PMID:23828783
The Saccharomyces cerevisiae transcriptome as a mirror of phytochemical variation in complex extracts of Equisetum arvense from America, China, Europe and India. PMID:23826764
Comparative Genomics Reveal That Host-Innate Immune Responses Influence the Clinical Prevalence of Legionella pneumophila Serogroups. PMID:23826259
PUMA: a unified framework for penalized multiple regression analysis of GWAS data. PMID:23825936
Tracing evolutionary footprints to identify novel gene functional linkages. PMID:23825567
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PMID:23825549
Deciphering the response of Mycobacterium smegmatis to nitrogen stress using bipartite active modules. PMID:23819599
BioBin: a bioinformatics tool for automating the binning of rare variants using publicly available biological knowledge. PMID:23819467
Evolutionary rate heterogeneity of core and attachment proteins in yeast protein complexes. PMID:23814130
Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma. PMID:23814019
A nutrigenomic framework to identify time-resolving responses of hepatic genes in diet-induced obese mice. PMID:23813319
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways. PMID:23812978
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. PMID:23812977
Proteomic comparison of basal endosperm in maize miniature1 mutant and its wild-type Mn1. PMID:23805148
Consensus and conflict cards for metabolic pathway databases. PMID:23803311
Integrative relational machine-learning for understanding drug side-effect profiles. PMID:23802887
bioNerDS: exploring bioinformatics' database and software use through literature mining. PMID:23768135
Metingear: a development environment for annotating genome-scale metabolic models. PMID:23766418
PiHelper: an open source framework for drug-target and antibody-target data. PMID:23766416
Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot. PMID:23766402
Comparative genomics analysis in Prunoideae to identify biologically relevant polymorphisms. PMID:23763653
A Systems Biology Approach to Characterize Biomarkers for Blood Stasis Syndrome of Unstable Angina Patients by Integrating MicroRNA and Messenger RNA Expression Profiling. PMID:23762142
Silicon era of carbon-based life: application of genomics and bioinformatics in crop stress research. PMID:23759993
FIDEA: a server for the functional interpretation of differential expression analysis. PMID:23754850
Genomic association analysis of common variants influencing antihypertensive response to hydrochlorothiazide. PMID:23753411
An integrative approach for the large-scale identification of human genome kinases regulating cancer metastasis. PMID:23751374
Inferring the functional effect of gene expression changes in signaling pathways. PMID:23748960
Small-volume analysis of cell-cell signaling molecules in the brain. PMID:23748227
Genome-wide association study for backfat thickness in Canchim beef cattle using Random Forest approach. PMID:23738659
Transcriptome sequencing (RNA-seq) analysis of the effects of metal nanoparticle exposure on the transcriptome of Chlamydomonas reinhardtii. PMID:23728819
A new algorithm for integrated analysis of miRNA-mRNA interactions based on individual classification reveals insights into bladder cancer. PMID:23717626
Simultaneous identification of multiple driver pathways in cancer. PMID:23717195
VisANT 4.0: Integrative network platform to connect genes, drugs, diseases and therapies. PMID:23716640
β1- and αv-class integrins cooperate to regulate myosin II during rigidity sensing of fibronectin-based microenvironments. PMID:23708002
Pathway databases: making chemical and biological sense of the genomic data flood. PMID:23706629
Behavioral and neurogenomic transcriptome changes in wild-derived zebrafish with fluoxetine treatment. PMID:23706039
Metazoan innovation: from aromatic amino acids to extracellular signaling. PMID:23690137
The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification. PMID:23685612
JiffyNet: a web-based instant protein network modeler for newly sequenced species. PMID:23685435
DIANA-microT web server v5.0: service integration into miRNA functional analysis workflows. PMID:23680784
Integrating murine gene expression studies to understand obstructive lung disease due to chronic inhaled endotoxin. PMID:23675439
A semi-supervised method for drug-target interaction prediction with consistency in networks. PMID:23667553
LipidHome: a database of theoretical lipids optimized for high throughput mass spectrometry lipidomics. PMID:23667450
Interspecific bacterial sensing through airborne signals modulates locomotion and drug resistance. PMID:23651997
Genome-wide comparison of the transcriptomes of highly enriched normal and chronic myeloid leukemia stem and progenitor cell populations. PMID:23651669
Tumor suppressors status in cancer cell line Encyclopedia. PMID:23639312
A new 12-gene diagnostic biomarker signature of melanoma revealed by integrated microarray analysis. PMID:23638386
Transcriptome analysis of buds and leaves using 454 pyrosequencing to discover genes associated with the biosynthesis of active ingredients in Lonicera japonica Thunb. PMID:23638167
Components of the canonical and non-canonical Wnt pathways are not mis-expressed in pituitary tumors. PMID:23638078
Characterization of drug-induced transcriptional modules: towards drug repositioning and functional understanding. PMID:23632384
An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype. PMID:23631487
Novel insights into obesity and diabetes through genome-scale metabolic modeling. PMID:23630502
Peripheral blood gene expression signature differentiates children with autism from unaffected siblings. PMID:23625158
Punctuated evolution of prostate cancer genomes. PMID:23622249
Aneuploidy, oncogene amplification and epithelial to mesenchymal transition define spontaneous transformation of murine epithelial cells. PMID:23619298
Cytochrome P450 CYP78A9 is involved in Arabidopsis reproductive development. PMID:23610218
Transcriptional pathways associated with the slow growth phenotype of transformed Anaplasma marginale. PMID:23607288
Structural and functional characterization of solute binding proteins for aromatic compounds derived from lignin: p-coumaric acid and related aromatic acids. PMID:23606130
Disparate proteome responses of pathogenic and nonpathogenic aspergilli to human serum measured by activity-based protein profiling (ABPP). PMID:23599423
Draft Genome Sequence of Streptomyces gancidicus Strain BKS 13-15. PMID:23599292
Models incorporating chromatin modification data identify functionally important p53 binding sites. PMID:23599002
Does habitat variability really promote metabolic network modularity? PMID:23593470
Drug target prediction and repositioning using an integrated network-based approach. PMID:23593264
Pharmacometabolomic approach to predict QT prolongation in guinea pigs. PMID:23593245
Synthetic lethality between gene defects affecting a single non-essential molecular pathway with reversible steps. PMID:23592964
Protein-protein interactions: switch from classical methods to proteomics and bioinformatics-based approaches. PMID:23579629
Recent progress in the development of metabolome databases for plant systems biology. PMID:23577015
Bioanalysis of eukaryotic organelles. PMID:23570618
Exposure to airborne particulate matter is associated with methylation pattern in the asthma pathway. PMID:23566092
Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes. PMID:23559334
Tumour-suppressive microRNA-874 contributes to cell proliferation through targeting of histone deacetylase 1 in head and neck squamous cell carcinoma. PMID:23558898
Draft Genome Sequence of Amycolatopsis decaplanina Strain DSM 44594T. PMID:23558534
Gene regulation by CcpA and catabolite repression explored by RNA-Seq in Streptococcus mutans. PMID:23555977
Developmental profiles of the murine palatal methylome. PMID:23554260
Transcriptome Profiling Following Neuronal and Glial Expression of ALS-Linked SOD1 in Drosophila. PMID:23550139
Circulating miRNA profile in HCV infected serum: novel insight into pathogenesis. PMID:23549102
Pathway-based personalized analysis of cancer. PMID:23547110
Discovery-2: an interactive resource for the rational selection and comparison of putative drug target proteins in malaria. PMID:23537208
AMBIENT: Active Modules for Bipartite Networks--using high-throughput transcriptomic data to dissect metabolic response. PMID:23531303
Proteomic analysis of elite soybean Jidou17 and its parents using iTRAQ-based quantitative approaches. PMID:23531047
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
Network pharmacology strategies toward multi-target anticancer therapies: from computational models to experimental design principles. PMID:23530504
The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. PMID:23525042
Deep sequencing reveals complex mechanisms of diapause preparation in the invasive mosquito, Aedes albopictus. PMID:23516243
The human gene connectome as a map of short cuts for morbid allele discovery. PMID:23509278
Genomic reconstruction of the transcriptional regulatory network in Bacillus subtilis. PMID:23504016
Transcriptome exploration of the sex pheromone gland of Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae). PMID:23497448
A combined strategy involving Sanger and 454 pyrosequencing increases genomic resources to aid in the management of reproduction, disease control and genetic selection in the turbot (Scophthalmus maximus). PMID:23497389
Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection. PMID:23472090
Genome Sequence of the "Indian Bison Type" Biotype of Mycobacterium avium subsp. paratuberculosis Strain S5. PMID:23469332
Identification of shared genes and pathways: a comparative study of multiple sclerosis susceptibility, severity and response to interferon beta treatment. PMID:23469041
Preferential duplication of intermodular hub genes: an evolutionary signature in eukaryotes genome networks. PMID:23468868
Genes, environments, and developmental research: methods for a multi-site study of early substance abuse. PMID:23461817
Canonical correlation analysis for RNA-seq co-expression networks. PMID:23460206
Prenatal metformin exposure in mice programs the metabolic phenotype of the offspring during a high fat diet at adulthood. PMID:23457588
Non-homologous end-joining pathway associated with occurrence of myocardial infarction: gene set analysis of genome-wide association study data. PMID:23457540
Protein complex-based analysis framework for high-throughput data sets. PMID:23443684
Atypical glycolysis in Clostridium thermocellum. PMID:23435896
The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla). PMID:23435089
Transcriptome analysis of Inbred Long Sleep and Inbred Short Sleep mice. PMID:23433184
Genome-scale reconstruction and in silico analysis of Klebsiella oxytoca for 2,3-butanediol production. PMID:23432904
A de novo assembly of the newt transcriptome combined with proteomic validation identifies new protein families expressed during tissue regeneration. PMID:23425577
Improving microbial genome annotations in an integrated database context. PMID:23424620
Using BioBin to explore rare variant population stratification. PMID:23424138
A powerful Bayesian meta-analysis method to integrate multiple gene set enrichment studies. PMID:23418184
The Eimeria transcript DB: an integrated resource for annotated transcripts of protozoan parasites of the genus Eimeria. PMID:23411718
Genetic networks inducing invasive growth in Saccharomyces cerevisiae identified through systematic genome-wide overexpression. PMID:23410832
Interactome3D: adding structural details to protein networks. PMID:23399932
Computational model for pathway reconstruction to unravel the evolutionary significance of melanin synthesis. PMID:23390353
Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review. PMID:23384594
Modular architecture of metabolic pathways revealed by conserved sequences of reactions. PMID:23384306
Relevance of TNBS-colitis in rats: a methodological study with endoscopic, histologic and Transcriptomic [corrected] characterization and correlation to IBD. PMID:23382912
The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PMID:23382650
Deep proteome profiling of Trichoplax adhaerens reveals remarkable features at the origin of metazoan multicellularity. PMID:23360999
Estimation of data-specific constitutive exons with RNA-Seq data. PMID:23360225
The Epstein-Barr virus nuclear antigen-1 reprograms transcription by mimicry of high mobility group A proteins. PMID:23358825
MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks. PMID:23357920
De novo transcriptome sequencing and analysis for Venturia inaequalis, the devastating apple scab pathogen. PMID:23349770
APG: an Active Protein-Gene network model to quantify regulatory signals in complex biological systems. PMID:23346354
Subcellular compartmentation of sugar signaling: links among carbon cellular status, route of sucrolysis, sink-source allocation, and metabolic partitioning. PMID:23346090
Association analysis of reactive oxygen species-hypertension genes discovered by literature mining. PMID:23346037
Altered microRNA profiles in bronchoalveolar lavage fluid exosomes in asthmatic patients. PMID:23333113
Kerfuffle: a web tool for multi-species gene colocalization analysis. PMID:23327649
Coevolution trumps pleiotropy: carbon assimilation traits are independent of metabolic network structure in budding yeast. PMID:23326606
Host cell responses to persistent mycoplasmas--different stages in infection of HeLa cells with Mycoplasma hominis. PMID:23326599
Using databases and web resources for glycomics research. PMID:23325765
CRAVAT: cancer-related analysis of variants toolkit. PMID:23325621
Genetic variation and expression diversity between grain and sweet sorghum lines. PMID:23324212
Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies. PMID:23306528
Metabolism and the circadian clock converge. PMID:23303907
Transcriptome-wide expansion of non-coding regulatory switches: evidence from co-occurrence of Alu exonization, antisense and editing. PMID:23303787
Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. PMID:23302187
Exome capture sequencing of adenoma reveals genetic alterations in multiple cellular pathways at the early stage of colorectal tumorigenesis. PMID:23301059
Rice Annotation Project Database (RAP-DB): an integrative and interactive database for rice genomics. PMID:23299411
Complete genome sequences from three genetically distinct strains reveal high intraspecies genetic diversity in the microsporidian Encephalitozoon cuniculi. PMID:23291622
Global profiling of alternative splicing events and gene expression regulated by hnRNPH/F. PMID:23284676
Changes in eutopic endometrial gene expression during the progression of experimental endometriosis in the baboon, Papio anubis. PMID:23284138
An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. PMID:23282285
Cliques for the identification of gene signatures for colorectal cancer across population. PMID:23282040
Localization of Wolbachia-like gene transcripts and peptides in adult Onchocerca flexuosa worms indicates tissue specific expression. PMID:23281896
Genome-wide meta-analysis of genetic susceptible genes for Type 2 Diabetes. PMID:23281828
iLOCi: a SNP interaction prioritization technique for detecting epistasis in genome-wide association studies. PMID:23281813
Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. PMID:23281744
Subtypes of primary colorectal tumors correlate with response to targeted treatment in colorectal cell lines. PMID:23272949
Polypharmacology: drug discovery for the future. PMID:23272792
Systems biology, bioinformatics, and biomarkers in neuropsychiatry. PMID:23269912
TEAK: topology enrichment analysis framework for detecting activated biological subpathways. PMID:23268448
Using answer set programming to integrate RNA expression with signalling pathway information to infer how mutations affect ageing. PMID:23251396
TGF-β upregulates miR-181a expression to promote breast cancer metastasis. PMID:23241956
Discovering associations in biomedical datasets by link-based associative classifier (LAC). PMID:23227228
Inferring gene regulatory networks by singular value decomposition and gravitation field algorithm. PMID:23226565
A pathway-based analysis provides additional support for an immune-related genetic susceptibility to Parkinson's disease. PMID:23223016
Bioinformatics for the Human Microbiome Project. PMID:23209389
Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles. PMID:23209127
COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals. PMID:23203868
NetwoRx: connecting drugs to networks and phenotypes in Saccharomyces cerevisiae. PMID:23203867
The Disease and Gene Annotations (DGA): an annotation resource for human disease. PMID:23197658
H-InvDB in 2013: an omics study platform for human functional gene and transcript discovery. PMID:23197657
LUCApedia: a database for the study of ancient life. PMID:23193296
KIDFamMap: a database of kinase-inhibitor-disease family maps for kinase inhibitor selectivity and binding mechanisms. PMID:23193279
The Rice Genome Knowledgebase (RGKbase): an annotation database for rice comparative genomics and evolutionary biology. PMID:23193278
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. PMID:23193276
MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. PMID:23193269
HAMAP in 2013, new developments in the protein family classification and annotation system. PMID:23193261
Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. PMID:23193253
By their genes ye shall know them: genomic signatures of predatory bacteria. PMID:23190728
ChemProt-2.0: visual navigation in a disease chemical biology database. PMID:23185041
SomamiR: a database for somatic mutations impacting microRNA function in cancer. PMID:23180788
Proteomics: from single molecules to biological pathways. PMID:23180722
Bioinformatic approaches for functional annotation and pathway inference in metagenomics data. PMID:23175748
WholeCellKB: model organism databases for comprehensive whole-cell models. PMID:23175606
Bioinformatics Resource Manager v2.3: an integrated software environment for systems biology with microRNA and cross-species analysis tools. PMID:23174015
Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation. PMID:23166792
Identification of novel and differentially expressed MicroRNAs of dairy goat mammary gland tissues using solexa sequencing and bioinformatics. PMID:23166677
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PMID:23166598
Transcriptome sequencing and annotation for the Jamaican fruit bat (Artibeus jamaicensis). PMID:23166587
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
mzMatch-ISO: an R tool for the annotation and relative quantification of isotope-labelled mass spectrometry data. PMID:23162054
HMDB 3.0--The Human Metabolome Database in 2013. PMID:23161693
Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines. PMID:23158748
RNApathwaysDB--a database of RNA maturation and decay pathways. PMID:23155061
Genome sequences of wild and domestic bactrian camels. PMID:23149746
The ConsensusPathDB interaction database: 2013 update. PMID:23143270
SynSysNet: integration of experimental data on synaptic protein-protein interactions with drug-target relations. PMID:23143269
MonarchBase: the monarch butterfly genome database. PMID:23143105
VANTED v2: a framework for systems biology applications. PMID:23140568
Immunogenomics for identification of disease resistance genes in pigs: a review focusing on Gram-negative bacilli. PMID:23137309
Metagenomic analysis of the microbiota from the crop of an invasive snail reveals a rich reservoir of novel genes. PMID:23133637
Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. PMID:23132350
An integrated map of genetic variation from 1,092 human genomes. PMID:23128226
Evolution and diversity of periplasmic proteins involved in copper homeostasis in gamma proteobacteria. PMID:23122209
CellLineNavigator: a workbench for cancer cell line analysis. PMID:23118487
Enzyme informatics. PMID:23116471
Systems analysis of plant functional, transcriptional, physical interaction, and metabolic networks. PMID:23110892
ECMDB: the E. coli Metabolome Database. PMID:23109553
Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution. PMID:23095941
The Comparative Toxicogenomics Database: update 2013. PMID:23093600
BioLiP: a semi-manually curated database for biologically relevant ligand-protein interactions. PMID:23087378
IUPHAR-DB: updated database content and new features. PMID:23087376
Hybrid sequencing approach applied to human fecal metagenomic clone libraries revealed clones with potential biotechnological applications. PMID:23082187
Popular computational methods to assess multiprotein complexes derived from label-free affinity purification and mass spectrometry (AP-MS) experiments. PMID:23071097
TSGene: a web resource for tumor suppressor genes. PMID:23066107
Systematic analysis of microRNA targeting impacted by small insertions and deletions in human genome. PMID:23049969
Contribution of phage-derived genomic islands to the virulence of facultative bacterial pathogens. PMID:23035931
Genetic variation in metabolic phenotypes: study designs and applications. PMID:23032255
Profiling the anaerobic response of C. elegans using GC-MS. PMID:23029411
Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans. PMID:23028371
METscout: a pathfinder exploring the landscape of metabolites, enzymes and transporters. PMID:23019219
MetR-regulated Vibrio cholerae metabolism is required for virulence. PMID:23015737
Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease. PMID:23013645
Systematic deciphering of cancer genome networks. PMID:23012582
Genomic landscape of non-small cell lung cancer in smokers and never-smokers. PMID:22980976
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
Uncovering the co-evolutionary network among prokaryotic genes. PMID:22962457
A draft of the genome and four transcriptomes of a medicinal and pesticidal angiosperm Azadirachta indica. PMID:22958331
Evidence of abundant purifying selection in humans for recently acquired regulatory functions. PMID:22956687
Reconstructing differentially co-expressed gene modules and regulatory networks of soybean cells. PMID:22938179
Analysis of current antifungal agents and their targets within the Pneumocystis carinii genome. PMID:22934582
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment. PMID:22923307
Millimeter-scale patterns of phylogenetic and trait diversity in a salt marsh microbial mat. PMID:22908010
A map of human microRNA variation uncovers unexpectedly high levels of variability. PMID:22906193
Metagenomic annotation networks: construction and applications. PMID:22879885
Multiplexed activity-based protein profiling of the human pathogen Aspergillus fumigatus reveals large functional changes upon exposure to human serum. PMID:22865858
MicroRNA regulation of the synaptic plasticity-related gene Arc. PMID:22844515
Novel microRNAs differentially expressed during aging in the mouse brain. PMID:22844398
Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. PMID:22844098
Complete genome sequence of the opportunistic food-borne pathogen Cronobacter sakazakii ES15. PMID:22843579
Sequencing of the smallest Apicomplexan genome from the human pathogen Babesia microti. PMID:22833609
Remodeling of central metabolism in invasive breast cancer compared to normal breast tissue - a GC-TOFMS based metabolomics study. PMID:22823888
Transcriptome profiling of genes involved in neural tube closure during human embryonic development using long serial analysis of gene expression (long-SAGE). PMID:22806986
Endosomal crosstalk: meeting points for signaling pathways. PMID:22796207
Genetic architectures of psychiatric disorders: the emerging picture and its implications. PMID:22777127
Functional assignment of metagenomic data: challenges and applications. PMID:22772835
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Structure of the signal transduction protein TRAP (target of RNAIII-activating protein). PMID:22750855
Investigating metabolite-protein interactions: an overview of available techniques. PMID:22750303
The balance in the delivery of ER components and the vacuolar proton pump to the phagosome depends on myosin IK in Dictyostelium. PMID:22736568
Genome-wide profiling of peroxisome proliferator-activated receptor γ in primary epididymal, inguinal, and brown adipocytes reveals depot-selective binding correlated with gene expression. PMID:22733994
Engineering ecosystems and synthetic ecologies. PMID:22722235
Experimental evolution of Legionella pneumophila in mouse macrophages leads to strains with altered determinants of environmental survival. PMID:22693450
A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function. PMID:22651983
DIANA miRPath v.2.0: investigating the combinatorial effect of microRNAs in pathways. PMID:22649059
Evolution of lysine biosynthesis in the phylum deinococcus-thermus. PMID:22645699
Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. PMID:22636774
Translational research in infectious disease: current paradigms and challenges ahead. PMID:22633095
Personalized pathway enrichment map of putative cancer genes from next generation sequencing data. PMID:22624051
GENIES: gene network inference engine based on supervised analysis. PMID:22610856
GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics. PMID:22573175
Applications for next-generation sequencing in fish ecotoxicogenomics. PMID:22539934
OREMPdb: a semantic dictionary of computational pathway models. PMID:22536973
EnzML: multi-label prediction of enzyme classes using InterPro signatures. PMID:22533924
The Physalis peruviana leaf transcriptome: assembly, annotation and gene model prediction. PMID:22533342
Is EC class predictable from reaction mechanism? PMID:22530800
Computational analysis of cysteine and methionine metabolism and its regulation in dairy starter and related bacteria. PMID:22522891
Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function. PMID:22505803
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
Development of Ecom₅₀ and retention index models for nontargeted metabolomics: identification of 1,3-dicyclohexylurea in human serum by HPLC/mass spectrometry. PMID:22489687
Associations between HIV and human pathways revealed by protein-protein interactions and correlated gene expression profiles. PMID:22479575
Functional roles for redox genes in ethanol sensitivity in Drosophila. PMID:22430022
A genomewide survey of bHLH transcription factors in the coral Acropora digitifera identifies three novel orthologous families, pearl, amber, and peridot. PMID:22419240
Computational prediction of metabolism: sites, products, SAR, P450 enzyme dynamics, and mechanisms. PMID:22339582
microRNA-1/133a and microRNA-206/133b clusters: dysregulation and functional roles in human cancers. PMID:22308266
Inflammatory pathway genes belong to major targets of persistent organic pollutants in adipose cells. PMID:22262711
The 2012 Nucleic Acids Research Database Issue and the online Molecular Biology Database Collection. PMID:22144685
KEGG: Kyoto Encyclopedia of Genes and Genomes PubMed citations: 1947.

1947 articles citing: KEGG: Kyoto Encyclopedia of Genes and Genomes

Transcriptome analysis revealed gene expression feminization of testis after exogenous tetrodotoxin administration in pufferfish Takifugu flavidus. PMID:35922761
Metabolomic and proteomic profiling in bipolar disorder patients revealed potential molecular signatures related to hemostasis. PMID:35922643
Clarifying expression patterns by renal lesion using transcriptome analysis and vanin-1 as a potential novel biomarker for renal injury in chickens. PMID:35901645
Dynamic description of temporal changes of gut microbiota in broilers. PMID:35901643
Comprehensive Analysis of Immune-Related Metabolic Genes in Lung Adenocarcinoma. PMID:35898471
RNA-Seq Provides Insights into the Mechanisms Underlying Ilyonectria robusta Responding to Secondary Metabolites of Bacillus methylotrophicus NJ13. PMID:35893148
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
Chromatin Separation Regulators Predict the Prognosis and Immune Microenvironment Estimation in Lung Adenocarcinoma. PMID:35873497
Identification of BST2 Contributing to the Development of Glioblastoma Based on Bioinformatics Analysis. PMID:35865015
Cold exposure induces lipid dynamics and thermogenesis in brown adipose tissue of goats. PMID:35864448
A chromosome-level genome assembly of the jade perch (Scortum barcoo). PMID:35840598
Spatially resolved proteomic map shows that extracellular matrix regulates epidermal growth. PMID:35817779
Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing. PMID:35814706
A Novel Ferroptosis-Related Gene Signature to Predict Prognosis of Esophageal Carcinoma. PMID:35813863
Monocytic-Myeloid Derived Suppressor Cells Suppress T-Cell Responses in Recovered SARS CoV2-Infected Individuals. PMID:35812392
Systemic approaches using single cell transcriptome reveal that C/EBPγ regulates autophagy under amino acid starved condition. PMID:35801910
The role of toll-like receptors (TLRs) in pan-cancer. PMID:35801728
Biomimetic generation of the strongest known biomaterial found in limpet tooth. PMID:35798724
Identification of Immune-Related Gene Signature in Stanford Type A Aortic Dissection. PMID:35795203
Comprehensive Analysis of LINC01615 in Head and Neck Squamous Cell Carcinoma: A Hub Biomarker Identified by Machine Learning and Experimental Validation. PMID:35794984
Equus roundworms (Parascaris univalens) are undergoing rapid divergence while genes involved in metabolic as well as anthelminic resistance are under positive selection. PMID:35787772
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Boolean modelling as a logic-based dynamic approach in systems medicine. PMID:35782730
Transcriptomic analysis of starch accumulation patterns in different glutinous sorghum seeds. PMID:35778525
The close interaction between hypoxia-related proteins and metastasis in pancarcinomas. PMID:35773405
Icariside II Restores Vascular Smooth Muscle Cell Contractile Phenotype by Enhancing the Focal Adhesion Signaling Pathway in the Rat Vascular Remodeling Model. PMID:35770073
Pathway importance by graph convolutional network and Shapley additive explanations in gene expression phenotype of diffuse large B-cell lymphoma. PMID:35749395
Exosomal MicroRNA as Biomarkers for Diagnosing or Monitoring the Progression of Ovarian Clear Cell Carcinoma: A Pilot Study. PMID:35745075
Aphrodisiac Performance of Bioactive Compounds from Mimosa pudica Linn.: In Silico Molecular Docking and Dynamics Simulation Approach. PMID:35744923
Small-extracellular vesicles and their microRNA cargo from porcine follicular fluids: the potential association with oocyte quality. PMID:35725584
Evaluating hierarchical machine learning approaches to classify biological databases. PMID:35724625
Gut microbiome: Linking together obesity, bariatric surgery and associated clinical outcomes under a single focus. PMID:35720165
Integrating Network Pharmacology and Experimental Validation to Explore the Key Mechanism of Gubitong Recipe in the Treatment of Osteoarthritis. PMID:35720033
Transcriptome Analysis of Pennisetum glaucum (L.) R. Br. Provides Insight Into Heat Stress Responses. PMID:35719375
Genome-scale metabolic modelling enables deciphering ethanol metabolism via the acrylate pathway in the propionate-producer Anaerotignum neopropionicum. PMID:35710409
Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP. PMID:35688826
Ptpn1 deletion protects oval cells against lipoapoptosis by favoring lipid droplet formation and dynamics. PMID:35681014
Chromosome-Scale, Haplotype-Resolved Genome Assembly of Non-Sex-Reversal Females of Swamp Eel Using High-Fidelity Long Reads and Hi-C Data. PMID:35669182
Tyrosine catabolites influence SKN-1 signaling in a model of Type I Tyrosinemia. PMID:35668715
Identification of a TGF-β signaling-related gene signature for prediction of immunotherapy and targeted therapy for lung adenocarcinoma. PMID:35668494
miRNA-432 and SLC38A1 as Predictors of Hepatocellular Carcinoma Complicated with Alcoholic Steatohepatitis. PMID:35663198
Integrated proteogenomic characterization of urothelial carcinoma of the bladder. PMID:35659036
Artificial neural networks enable genome-scale simulations of intracellular signaling. PMID:35654811
Biocontrol Potential of Endophytic Streptomyces malaysiensis 8ZJF-21 From Medicinal Plant Against Banana Fusarium Wilt Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4. PMID:35646017
Short-chain fatty acids promote the effect of environmental signals on the gut microbiome and metabolome in mice. PMID:35641653
Intense Innate Immune Responses and Severe Metabolic Disorders in Chicken Embryonic Visceral Tissues Caused by Infection with Highly Virulent Newcastle Disease Virus Compared to the Avirulent Virus: A Bioinformatics Analysis. PMID:35632651
Leveraging Deep Learning Techniques and Integrated Omics Data for Tailored Treatment of Breast Cancer. PMID:35629097
Reprogramming of Plant Central Metabolism in Response to Abiotic Stresses: A Metabolomics View. PMID:35628526
Novel Role of AaMYBC1 in Regulating Actinidia arguta Vine Architecture by Elongating Internode Based on Multi-Omics Analysis of Transgenic Tobacco. PMID:35627204
Exploring the Effects of Six Weeks of Resistance Training on the Fecal Microbiome of Older Adult Males: Secondary Analysis of a Peanut Protein Supplemented Randomized Controlled Trial. PMID:35622473
Cytosolic aspartate aminotransferase moonlights as a ribosome-binding modulator of Gcn2 activity during oxidative stress. PMID:35621265
Association of a Novel DOCK2 Mutation-Related Gene Signature With Immune in Hepatocellular Carcinoma. PMID:35620462
Novel Bioinformatics Strategies Driving Dynamic Metaproteomic Studies. PMID:35612752
Chromosome-level genome assembly of the diploid blueberry Vaccinium darrowii provides insights into its subtropical adaptation and cuticle synthesis. PMID:35605198
A Four-Gene Prognostic Signature Based on the TEAD4 Differential Expression Predicts Overall Survival and Immune Microenvironment Estimation in Lung Adenocarcinoma. PMID:35600867
The Construction and Exploration of a Comprehensive MicroRNA Centered Regulatory Network in Foxtail Millet (Setaria italica L.). PMID:35599893
Immune-Related Biomarkers Associated with Lung Metastasis from the Colorectal Cancer Microenvironment. PMID:35576491
Transcriptome Analysis Reveals the Molecular Response to Salinity Challenge in Larvae of the Giant Freshwater Prawn Macrobrachium rosenbergii. PMID:35574435
Integrative clustering methods for multi-omics data. PMID:35573155
Effects of Different Formulations of Glyphosate on Rumen Microbial Metabolism and Bacterial Community Composition in the Rumen Simulation Technique System. PMID:35572709
Glomerular Expression of S100A8 in Lupus Nephritis: An Integrated Bioinformatics Analysis. PMID:35572531
Diagnosis of pulmonary tuberculosis via identification of core genes and pathways utilizing blood transcriptional signatures: a multicohort analysis. PMID:35568895
Enhanced Anti-Cancer Effects of Conditioned Medium from Hypoxic Human Adult Dermal Fibroblasts on Cervical Cancer Cells. PMID:35563525
Transcriptome and Metabolome Analyses Revealed the Response Mechanism of Quinoa Seedlings to Different Phosphorus Stresses. PMID:35563095
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Apex Predator Nematodes and Meso-Predator Bacteria Consume Their Basal Insect Prey through Discrete Stages of Chemical Transformations. PMID:35543104
Identification of key sex-specific pathways and genes in the subcutaneous adipose tissue from pigs using WGCNA method. PMID:35538407
Whole genome sequencing and analysis of fenvalerate degrading bacteria Citrobacter freundii CD-9. PMID:35523901
Construction and validation of a prognostic model of RNA binding proteins in clear cell renal carcinoma. PMID:35513791
Gaur genome reveals expansion of sperm odorant receptors in domesticated cattle. PMID:35508966
Identification of HMOX1 as a Critical Ferroptosis-Related Gene in Atherosclerosis. PMID:35498043
Comprehensive Characterization of the Function of Metabolic Genes and Establishment of a Prediction Model in Breast Cancer. PMID:35493305
GSEA-SDBE: A gene selection method for breast cancer classification based on GSEA and analyzing differences in performance metrics. PMID:35472078
Trans-cinnamaldehyde protects against phenylephrine-induced cardiomyocyte hypertrophy through the CaMKII/ERK pathway. PMID:35468773
Chromosome-level genome assembly and characterization of Sophora Japonica. PMID:35466378
Recognition of a Novel Gene Signature for Human Glioblastoma. PMID:35456975
Deciphering of Adult Glioma Vulnerabilities through Expression Pattern Analysis of GABA, Glutamate and Calcium Neurotransmitter Genes. PMID:35455749
Guide to Metabolomics Analysis: A Bioinformatics Workflow. PMID:35448542
The microbiome in reproductive health: protocol for a systems biology approach using a prospective, observational study design. PMID:35441092
The LINC00452/miR-204/CHST4 Axis Regulating Thymic Tregs Might Be Involved in the Progression of Thymoma-Associated Myasthenia Gravis. PMID:35432149
Pulmonary Inflammatory Response in Lethal COVID-19 Reveals Potential Therapeutic Targets and Drugs in Phases III/IV Clinical Trials. PMID:35422702
PTH2R is related to cell proliferation and migration in ovarian cancer: a multi-omics analysis of bioinformatics and experiments. PMID:35410353
Single-Cell RNA-Seq Analysis of Cells from Degenerating and Non-Degenerating Intervertebral Discs from the Same Individual Reveals New Biomarkers for Intervertebral Disc Degeneration. PMID:35409356
Transcriptome Analysis of Apples in High-Temperature Treatments Reveals a Role of MdLBD37 in the Inhibition of Anthocyanin Accumulation. PMID:35409122
Analysis of the Composition of Deinagkistrodon acutus Snake Venom Based on Proteomics, and Its Antithrombotic Activity and Toxicity Studies. PMID:35408629
An engineered nano-liposome-human ACE2 decoy neutralizes SARS-CoV-2 Spike protein-induced inflammation in both murine and human macrophages. PMID:35401811
Characteristics of the gut microbiota in pregnant women with fetal growth restriction. PMID:35392848
Chromosome-level genome assembly of grass carp (Ctenopharyngodon idella) provides insights into its genome evolution. PMID:35392810
MDN1 Mutation Is Associated With High Tumor Mutation Burden and Unfavorable Prognosis in Breast Cancer. PMID:35386280
The Microbiome Structure of a Rice-Crayfish Integrated Breeding Model and Its Association with Crayfish Growth and Water Quality. PMID:35384719
Genes Differentially Expressed by Haemophilus ducreyi during Anaerobic Growth Significantly Overlap Those Differentially Expressed during Experimental Infection of Human Volunteers. PMID:35377183
Identification of Prostate Cancer Risk Genetics Biomarkers Based on Intergraded Bioinformatics Analysis. PMID:35372462
Integrated LC-MS/MS and Transcriptome Sequencing Analysis Reveals the Mechanism of Color Formation During Prickly Ash Fruit Ripening. PMID:35369068
The D2R-DISC1 protein complex and associated proteins are altered in schizophrenia and normalized with antipsychotic treatment. PMID:35361701
Species Persistence with Hybridization in Toad-Headed Lizards Driven by Divergent Selection and Low Recombination. PMID:35356979
Elucidating the Synergistic Effect of Multiple Chinese Herbal Prescriptions in the Treatment of Post-stroke Neurological Damage. PMID:35355727
Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci. PMID:35347128
Integrative analysis of DNA methylation and gene expression reveals key molecular signatures in acute myocardial infarction. PMID:35346355
Transcriptome-wide N6-methyladenine methylation in granulosa cells of women with decreased ovarian reserve. PMID:35346019
The VarA-CsrA regulatory pathway influences cell shape in Vibrio cholerae. PMID:35344548
Whole-genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming. PMID:35333870
Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism. PMID:35330077
Comparative Analysis of Fruit Metabolome Using Widely Targeted Metabolomics Reveals Nutritional Characteristics of Different Rosa roxburghii Genotypes. PMID:35327272
Network Preservation Analysis Reveals Dysregulated Synaptic Modules and Regulatory Hubs Shared Between Alzheimer's Disease and Temporal Lobe Epilepsy. PMID:35309145
Establishment of a Combined Diagnostic Model of Abdominal Aortic Aneurysm with Random Forest and Artificial Neural Network. PMID:35299890
Triosephosphate isomerase of Streptococcus pneumoniae is released extracellularly by autolysis and binds to host plasminogen to promote its activation. PMID:35298875
Transcriptional Landscape of Cotton Fiber Development and Its Alliance With Fiber-Associated Traits. PMID:35283936
Cadmium Exposure Alters Rhizospheric Microbial Community and Transcriptional Expression of Vetiver Grass. PMID:35283903
Identification of Potential Key Biomarkers of Atrial Fibrillation and Their Correlation with Immune Infiltration in Atrial Tissue. PMID:35273648
Combined Transcriptomic and Proteomic Profiling of E. coli under Microaerobic versus Aerobic Conditions: The Multifaceted Roles of Noncoding Small RNAs and Oxygen-Dependent Sensing in Global Gene Expression Control. PMID:35269716
Transcriptomic Analysis of the Host Response to Mild and Severe CTV Strains in Naturally Infected Citrus sinensis Orchards. PMID:35269578
Yin Yang 1 regulates ITGAV and ITGB1, contributing to improved prognosis of colorectal cancer. PMID:35266011
iTRAQ Proteomic Analysis of Interactions Between 20E and Phospholipase C in Apolygus lucorum (Meyer-Dür). PMID:35250643
SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth. PMID:35223208
Computational Models for Clinical Applications in Personalized Medicine-Guidelines and Recommendations for Data Integration and Model Validation. PMID:35207655
Understanding of Waggle Dance in the Honey Bee (Apis mellifera) from the Perspective of Long Non-Coding RNA. PMID:35206685
miRNA-Mediated Priming of Macrophage M1 Differentiation Differs in Gram-Positive and Gram-Negative Settings. PMID:35205256
Weighted correlation network analysis revealed novel long non-coding RNAs for colorectal cancer. PMID:35194111
Chiral secondary amino acids, their importance, and methods of analysis. PMID:35192062
Metabolic Diversity and Aero-Tolerance in Anammox Bacteria from Geochemically Distinct Aquifers. PMID:35191775
Graph-guided Bayesian SVM with Adaptive Structured Shrinkage Prior for High-dimensional Data. PMID:35187547
A network pharmacology-based approach to explore mechanism of action of medicinal herbs for alopecia treatment. PMID:35181715
Comprehensive Detoxification Mechanism Assessment of Red Imported Fire Ant (Solenopsis invicta) against Indoxacarb. PMID:35164134
Insights into the Steps of Breast Cancer-Brain Metastases Development: Tumor Cell Interactions with the Blood-Brain Barrier. PMID:35163822
Transcriptome-wide changes in gene expression, splicing, and lncRNAs in response to a live attenuated dengue virus vaccine. PMID:35139383
Complete genome sequence of the kiwifruit bacterial canker pathogen Pseudomonas savastanoi strain MHT1. PMID:35120460
Identification of significant genes in non-small cell lung cancer by bioinformatics analyses. PMID:35117799
First genome-wide association study investigating blood pressure and renal traits in domestic cats. PMID:35115544
Impact of reduced uterine perfusion pressure model of preeclampsia on metabolism of placenta, maternal and fetal hearts. PMID:35064159
Quantitative Proteome and Transcriptome Dynamics Analysis Reveals Iron Deficiency Response Networks and Signature in Neuronal Cells. PMID:35056799
microRNA Profile Associated with Positive Lymph Node Metastasis in Early-Stage Cervical Cancer. PMID:35049697
Comprehensive characterization of 11 prognostic alternative splicing events in ovarian cancer interacted with the immune microenvironment. PMID:35046435
Adaptive Metabolism of Staphylococcus aureus Revealed by Untargeted Metabolomics. PMID:35043624
Assigning protein function from domain-function associations using DomFun. PMID:35033002
Insight into the symbiotic lifestyle of DPANN archaea revealed by cultivation and genome analyses. PMID:35022241
Evolutionary Ecology of Natural Comammox Nitrospira Populations. PMID:35014874
Transcriptome Analysis Reveals Candidate Genes Involved in Light-Induced Primordium Differentiation in Pleurotus eryngii. PMID:35008859
Local ancestry prediction with PyLAE. PMID:35003914
Comprehensive Annotation and Functional Exploration of MicroRNAs in Lettuce. PMID:35003165
Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism. PMID:34991725
The diagnostic and prognostic significance of small nuclear ribonucleoprotein Sm D1 aberrantly high expression in hepatocellular carcinoma. PMID:34976182
Crypt and Villus Transcriptomic Responses in Mouse Small Intestine Following Oral Exposure to Hexavalent Chromium. PMID:34935971
Identifying cancer pathway dysregulations using differential causal effects. PMID:34927666
Effects of Serum Metabolites on the Pancreatic Transcriptome in Acute Acalculous Cholecystitis. PMID:34925503
Time-Resolved Extracellular Matrix Atlas of the Developing Human Skin Dermis. PMID:34901026
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Identification of novel biomarkers in breast cancer via integrated bioinformatics analysis and experimental validation. PMID:34895070
Identification of an epithelial-mesenchymal transition-related lncRNA prognostic signature for patients with glioblastoma. PMID:34880375
Proteogenomics of non-small cell lung cancer reveals molecular subtypes associated with specific therapeutic targets and immune evasion mechanisms. PMID:34870237
Genome Sequence of Elaeagnus mollis, the First Chromosome-Level Genome of the Family Elaeagnaceae. PMID:34864990
The chromosome-level genome provides insight into the molecular mechanism underlying the tortuous-branch phenotype of Prunus mume. PMID:34861048
Transcriptomic Analysis Reveals the Positive Role of Abscisic Acid in Endodormancy Maintenance of Leaf Buds of Magnolia wufengensis. PMID:34858449
Identification of key pathways and RNAs associated with skeletal muscle atrophy after spinal cord injury. PMID:34854395
The Cymbidium genome reveals the evolution of unique morphological traits. PMID:34848682
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort. PMID:34839264
Chloranthus genome provides insights into the early diversification of angiosperms. PMID:34836973
How Microbial Food Web Interactions Shape the Arctic Ocean Bacterial Community Revealed by Size Fractionation Experiments. PMID:34835503
Accumulation Pattern of Flavonoids during Fruit Development of Lonicera maackii Determined by Metabolomics. PMID:34834005
Phosphoproteomic Comparison of Four Eimeria tenella Life Cycle Stages. PMID:34829991
Identification of Susceptibility Genes for Fusarium oxysporum in Cucumber via Comparative Proteomic Analysis. PMID:34828387
Overview of Metabolomic Analysis and the Integration with Multi-Omics for Economic Traits in Cattle. PMID:34822411
The Effects of Live Transport on Metabolism and Stress Responses of Abalone (Haliotis iris). PMID:34822406
Metabolomics Strategy Assisted by Transcriptomics Analysis to Identify Potential Biomarkers Associated with Tuberculosis. PMID:34815677
Bioinformatics analysis of high frequency mutations in myelodysplastic syndrome-related patients. PMID:34805353
DaiCee: A database for anti-cancer compounds with targets and side effect profiles. PMID:34803258
Transcriptome profiling based on Illumina- and SMRT-based RNA-seq reveals circadian regulation of key pathways in flower bud development in walnut. PMID:34793486
Transmission distortion and genetic incompatibilities between alleles in a multigenerational mouse advanced intercross line. PMID:34791189
MGEnrichment: A web application for microglia gene list enrichment analysis. PMID:34788279
Circular RNA screening identifies circMYLK4 as a regulator of fast/slow myofibers in porcine skeletal muscles. PMID:34786637
CyFi-MAP: an interactive pathway-based resource for cystic fibrosis. PMID:34782688
Discovery proteomics defines androgen-regulated glycoprotein networks in prostate cancer cells, as well as putative biomarkers of prostatic diseases. PMID:34782677
Identification of key genes involved in recovery from spinal cord injury in adult zebrafish. PMID:34782579
Trichoderma-Induced Ethylene Responsive Factor MsERF105 Mediates Defense Responses in Malus sieversii. PMID:34777407
Classification and Functional Analysis between Cancer and Normal Tissues Using Explainable Pathway Deep Learning through RNA-Sequencing Gene Expression. PMID:34768960
An RNA-Seq-Based Framework for Characterizing Canine Prostate Cancer and Prioritizing Clinically Relevant Biomarker Candidate Genes. PMID:34768937
Cuticle deposition duration in the uterus is correlated with eggshell cuticle quality in White Leghorn laying hens. PMID:34764400
Isolation and Evaluation of Rhizosphere Actinomycetes With Potential Application for Biocontrolling Fusarium Wilt of Banana Caused by Fusarium oxysporum f. sp. cubense Tropical Race 4. PMID:34759913
Circ-Usp10 promotes microglial activation and induces neuronal death by targeting miRNA-152-5p/CD84. PMID:34753388
Mining plant metabolomes: Methods, applications, and perspectives. PMID:34746766
International Prognostic Index-Based Immune Prognostic Model for Diffuse Large B-Cell Lymphoma. PMID:34745101
Integration Analysis of m6A Related Genes in Skin Cutaneous Melanoma and the Biological Function Research of the SPRR1B. PMID:34737950
Lymphocyte activation gene-3 is associated with programmed death-ligand 1 and programmed cell death protein 1 in small cell lung cancer. PMID:34734020
Organ-specific, integrated omics data-based study on the metabolic pathways of the medicinal plant Bletilla striata (Orchidaceae). PMID:34724893
Agent Repurposing for the Treatment of Advanced Stage Diffuse Large B-Cell Lymphoma Based on Gene Expression and Network Perturbation Analysis. PMID:34721544
Whole-Transcriptome Sequence of Degenerative Meniscus Cells Unveiling Diagnostic Markers and Therapeutic Targets for Osteoarthritis. PMID:34721542
The Codon Usage in the Minimal Natural Cell. PMID:34694559
Genomic insights into biocontrol potential of Bacillus stercoris LJBS06. PMID:34692367
Transcriptome changes in maternal peripheral blood during term parturition mimic perturbations preceding spontaneous preterm birth†. PMID:34686873
The fungal root endophyte Serendipita vermifera displays inter-kingdom synergistic beneficial effects with the microbiota in Arabidopsis thaliana and barley. PMID:34686763
Whole genome sequencing and comparative genomic analyses of Planococcus alpniumensis MSAK28401T, a new species isolated from Antarctic krill. PMID:34686131
Genomic Studies of White-Rot Fungus Cerrena unicolor SP02 Provide Insights into Food Safety Value-Added Utilization of Non-Food Lignocellulosic Biomass. PMID:34682256
Gene Network Analysis of Alzheimer's Disease Based on Network and Statistical Methods. PMID:34682089
Perspectives on the Role of Enzymatic Biocatalysis for the Degradation of Plastic PET. PMID:34681915
Structural Protein Analysis of Driver Gene Mutations in Conjunctival Melanoma. PMID:34681018
Mutational Characterization of Cutaneous Melanoma Supports Divergent Pathways Model for Melanoma Development. PMID:34680367
iMPT-FDNPL: Identification of Membrane Protein Types with Functional Domains and a Natural Language Processing Approach. PMID:34671418
Characterization and miRNA Profiling of Extracellular Vesicles from Human Osteoarthritic Subchondral Bone Multipotential Stromal Cells (MSCs). PMID:34667479
Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort. PMID:34658138
Genome features of common vetch (Vicia sativa) in natural habitats. PMID:34646975
Integrated analysis of dysregulated microRNA and mRNA expression in intestinal epithelial cells following ethanol intoxication and burn injury. PMID:34642361
Differences of Gut Microbiota in the Freshwater Blackworm (Lumbriculus variegatus: Oligochaeta) in Two Different Habitat Conditions. PMID:34639598
Comparison of Two Experimental Mouse Dry Eye Models through Inflammatory Gene Set Enrichment Analysis Based on a Multiplexed Transcriptomic Approach. PMID:34639111
Gut Microbiota in Lung Cancer: Where Do We Stand? PMID:34638770
Alterations in HLA Class I-Presented Immunopeptidome and Class I-Interactome upon Osimertinib Resistance in EGFR Mutant Lung Adenocarcinoma. PMID:34638461
POU class 2 homeobox associating factor 1 (POU2AF1) participates in abdominal aortic aneurysm enlargement based on integrated bioinformatics analysis. PMID:34637689
RNAseq and RNA molecular barcoding reveal differential gene expression in cortical bone following hindlimb unloading in female mice. PMID:34637435
Transcriptome Reprogramming of Tomato Orchestrate the Hormone Signaling Network of Systemic Resistance Induced by Chaetomium globosum. PMID:34630468
rPAC: Route based pathway analysis for cohorts of gene expression data sets. PMID:34628030
mRNA Network: Solution for Tracking Chemotherapy Insensitivity in Small-Cell Lung Cancer. PMID:34621500
Deep Investigating the Changes of Gut Microbiome and Its Correlation With the Shifts of Host Serum Metabolome Around Parturition in Sows. PMID:34603257
Comparative Immunogenomics of Canine Natural Killer Cells as Immunotherapy Target. PMID:34594320
VCAM1 expression in the myocardium is associated with the risk of heart failure and immune cell infiltration in myocardium. PMID:34593936
Ecogenomics Reveals Microbial Metabolic Networks in a Psychrophilic Methanogenic Bioreactor Treating Soy Sauce Production Wastewater. PMID:34588388
Modelling microbial communities: Harnessing consortia for biotechnological applications. PMID:34584635
Transcriptome Adaptation of the Ovine Mammary Gland to Dietary Supplementation of Extruded Linseed. PMID:34573673
Molecular Biology Networks and Key Gene Regulators for Inflammatory Biomarkers Shared by Breast Cancer Development: Multi-Omics Systems Analysis. PMID:34572592
Metabolic Reprogramming of Mammary Epithelial Cells during TGF-β-Induced Epithelial-to-Mesenchymal Transition. PMID:34564442
TCA cycle remodeling drives proinflammatory signaling in humans with pulmonary tuberculosis. PMID:34559866
Continental-Scale Paddy Soil Bacterial Community Structure, Function, and Biotic Interaction. PMID:34546068
Identification of BR biosynthesis genes in cotton reveals that GhCPD-3 restores BR biosynthesis and mediates plant growth and development. PMID:34533620
A combination approach of pseudotime analysis and mathematical modeling for understanding drug-resistant mechanisms. PMID:34531471
In silico predictions of protein interactions between Zika virus and human host. PMID:34513323
In Vitro and In Vivo Enhancement of Temozolomide Effect in Human Glioblastoma by Non-Invasive Application of Cold Atmospheric Plasma. PMID:34503293
Prediction of Drug-Target Interactions by Combining Dual-Tree Complex Wavelet Transform with Ensemble Learning Method. PMID:34500792
Weakly activated core inflammation pathways were identified as a central signaling mechanism contributing to the chronic neurodegeneration in Alzheimer's disease. PMID:34494019
Identification and Validation of a PPP1R12A-Related Five-Gene Signature Associated With Metabolism to Predict the Prognosis of Patients With Prostate Cancer. PMID:34484299
Meta-analysis of single-cell RNA-seq data reveals phenotypic switching of immune cells in severe COVID-19 patients. PMID:34478921
Changes in Nuclear Gene Expression Related to Mitochondrial Function Affect Extracellular Matrix, Collagens, and Focal Adhesion in Keratoconus. PMID:34478492
Stable-Isotope-Informed, Genome-Resolved Metagenomics Uncovers Potential Cross-Kingdom Interactions in Rhizosphere Soil. PMID:34468166
GSK2126458 has the potential to inhibit the proliferation of pancreatic cancer uncovered by bioinformatics analysis and pharmacological experiments. PMID:34461940
Gut Microbiome Changes Associated with Epithelial Barrier Damage and Systemic Inflammation during Antiretroviral Therapy of Chronic SIV Infection. PMID:34452432
The Role of Reduced Methionine in Mediating the Metabolic Responses to Protein Restriction Using Different Sources of Protein. PMID:34444768
A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. PMID:34442440
Plausibility of Early Life in a Relatively Wide Temperature Range: Clues from Simulated Metabolic Network Expansion. PMID:34440482
Identification of Key Volatiles Differentiating Aromatic Rice Cultivars Using an Untargeted Metabolomics Approach. PMID:34436469
Perturbed transcriptional profiles after chronic low dose rate radiation in mice. PMID:34428250
Utilization of Transcriptome, Small RNA, and Degradome Sequencing to Provide Insights Into Drought Stress and Rewatering Treatment in Medicago ruthenica. PMID:34413864
DiTing: A Pipeline to Infer and Compare Biogeochemical Pathways From Metagenomic and Metatranscriptomic Data. PMID:34408730
Lipidomic traits of plasma and cerebrospinal fluid in amyotrophic lateral sclerosis correlate with disease progression. PMID:34396104
Construction of a Potentially Functional circRNA-miRNA-mRNA Network in Intervertebral Disc Degeneration by Bioinformatics Analysis. PMID:34395625
Deciphering the Therapeutic Mechanisms of Wuzi Ershen Decoction in Treating Oligoasthenozoospermia through the Network Pharmacology Approach. PMID:34394386
Evaluation of Cocaine Effect on Endogenous Metabolites of HepG2 Cells Using Targeted Metabolomics. PMID:34361761
Chronic Kidney Disease Cohort Studies: A Guide to Metabolome Analyses. PMID:34357354
Computational Probing the Methylation Sites Related to EGFR Inhibitor-Responsive Genes. PMID:34356665
Analyzing Roles of NUSAP1 From Clinical, Molecular Mechanism and Immune Perspectives in Hepatocellular Carcinoma. PMID:34354737
Transcriptomic analyses of livers from mice exposed to 1,4-dioxane for up to 90 days to assess potential mode(s) of action underlying liver tumor development. PMID:34345848
Advances in the computational landscape for repurposed drugs against COVID-19. PMID:34339864
Comparative Transcriptome and Weighted Gene Co-expression Network Analysis Identify Key Transcription Factors of Rosa chinensis 'Old Blush' After Exposure to a Gradual Drought Stress Followed by Recovery. PMID:34335694
The characteristics of proteome and metabolome associated with contrasting sperm motility in goat seminal plasma. PMID:34330982
The transcriptome of rabbit conjunctiva in dry eye disease: Large-scale changes and similarity to the human dry eye. PMID:34324523
Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development. PMID:34315913
Study on potential differentially expressed genes in stroke by bioinformatics analysis. PMID:34313877
Drugs and Epigenetic Molecular Functions. A Pharmacological Data Scientometric Analysis. PMID:34298869
DysPIA: A Novel Dysregulated Pathway Identification Analysis Method. PMID:34290733
A novel ferroptosis-related 12-gene signature predicts clinical prognosis and reveals immune relevancy in clear cell renal cell carcinoma. PMID:34281531
Transcriptomic analyses of cacao flavonoids produced in photobioreactors. PMID:34281511
Development of a Novel Immune Infiltration-Related ceRNA Network and Prognostic Model for Sarcoma. PMID:34277600
Gene and protein expression profiles of olfactory ensheathing cells from olfactory bulb versus olfactory mucosa. PMID:34269221
Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs. PMID:34257377
Network and co-expression analysis of airway smooth muscle cell transcriptome delineates potential gene signatures in asthma. PMID:34257337
Application across species of a one health approach to liquid sample handling for respiratory based -omics analysis. PMID:34253818
DES-Tcell is a knowledgebase for exploring immunology-related literature. PMID:34253812
Loss of RND-Type Multidrug Efflux Pumps Triggers Iron Starvation and Lipid A Modifications in Pseudomonas aeruginosa. PMID:34252310
Microbiota Modulates Cardiac Transcriptional Responses to Intermittent Hypoxia and Hypercapnia. PMID:34248668
Dissecting immune cell stat regulation network reveals biomarkers to predict ICB therapy responders in melanoma. PMID:34238310
The association between serum microbial DNA composition and symptoms of depression and anxiety in mood disorders. PMID:34234173
Pharmacological mechanism of mylabris in the treatment of leukemia based on bioinformatics and systematic pharmacology. PMID:34224300
Review of Machine Learning Methods for the Prediction and Reconstruction of Metabolic Pathways. PMID:34222327
Comprehensive Analysis of Regulatory Network for LINC00472 in Clear Cell Renal Cell Carcinoma. PMID:34221297
Aberrantly methylated-differentially genes and pathways among Iranian patients with colorectal cancer. PMID:34217303
Is there a relationship between psoriasis and hepatitis C? A meta-analysis and bioinformatics investigation. PMID:34215260
Effects of the Developmental Regulator BOLITA on the Plant Metabolome. PMID:34209960
OmiEmbed: A Unified Multi-Task Deep Learning Framework for Multi-Omics Data. PMID:34207255
SurvCNN: A Discrete Time-to-Event Cancer Survival Estimation Framework Using Image Representations of Omics Data. PMID:34206288
Microbiota and Metabolite Modifications after Dietary Exclusion of Dairy Products and Reduced Consumption of Fermented Food in Young and Older Men. PMID:34205926
Association of Circadian Clock Gene Expression with Glioma Tumor Microenvironment and Patient Survival. PMID:34199348
Crowdsourcing assessment of maternal blood multi-omics for predicting gestational age and preterm birth. PMID:34195686
A systems pharmacology approach based on oncogenic signalling pathways to determine the mechanisms of action of natural products in breast cancer from transcriptome data. PMID:34193143
Expression Profiling and Functional Analysis of Circular RNAs in Inner Mongolian Cashmere Goat Hair Follicles. PMID:34178035
Identification of Key Genes and Pathways in Gefitinib-Resistant Lung Adenocarcinoma using Bioinformatics Analysis. PMID:34177255
Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems. PMID:34172070
A two-way rectification method for identifying differentially expressed genes by maximizing the co-function relationship. PMID:34171992
Chromosome-Scale Genome Assembly of the Resurrection Plant Acanthochlamys bracteata (Velloziaceae). PMID:34165527
Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease. PMID:34162989
Bioinformatics Analysis of Differentially Expressed Rhythm Genes in Liver Hepatocellular Carcinoma. PMID:34149816
Plasma metabolomic profiles as affected by diet and stress in Spanish goats. PMID:34131197
Transcriptional response to prolonged perchlorate exposure in the methanogen Methanosarcina barkeri and implications for Martian habitability. PMID:34117335
Implementation of dietary methionine restriction using casein after selective, oxidative deletion of methionine. PMID:34113817
Characterization of the chloroplast genome of Verbena officinalis Linn. (Verbenaceae) and its phylogenetic analysis. PMID:34104747
Characterization of terminal-ileal and colonic Crohn's disease in treatment-naïve paediatric patients based on transcriptomic profile using logistic regression. PMID:34098982
Integrated proteomics and metabolomics analysis of transgenic and gene-stacked maize line seeds. PMID:34097556
Development and Interpretation of a Genomic Instability Derived lncRNAs Based Risk Signature as a Predictor of Prognosis for Clear Cell Renal Cell Carcinoma Patients. PMID:34094983
PIGNON: a protein-protein interaction-guided functional enrichment analysis for quantitative proteomics. PMID:34088263
Wolfberry genomes and the evolution of Lycium (Solanaceae). PMID:34083720
Identification of biomarkers, pathways and potential therapeutic target for docetaxel resistant prostate cancer. PMID:34077304
Hepatic Nfe2l2 Is Not an Essential Mediator of the Metabolic Phenotype Produced by Dietary Methionine Restriction. PMID:34073838
Proteomic Analyses of Vitreous in Proliferative Diabetic Retinopathy: Prior Studies and Future Outlook. PMID:34070658
Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle. PMID:34068321
Effect of Graphene and Graphene Oxide on Airway Barrier and Differential Phosphorylation of Proteins in Tight and Adherens Junction Pathways. PMID:34068174
Comprehensive Transcriptome Analysis of Rare Carpinus putoensis Plants under NO2 stress. PMID:34067657
Vesicle transporter GOLT1B mediates the cell membrane localization of DVL2 and PD-L2 and promotes colorectal cancer metastasis. PMID:34059062
Aviator: a web service for monitoring the availability of web services. PMID:34038559
Mapping the transcriptomics landscape of post-traumatic stress disorder symptom dimensions in World Trade Center responders. PMID:34031375
Characterization and phylogenetic analysis of the complete chloroplast genome of Juncus effusus L. PMID:34027070
Transcriptome Analysis of Myzus persicae to UV-B Stress. PMID:34021758
Chromosome-scale assembly of the Sparassis latifolia genome obtained using long-read and Hi-C sequencing. PMID:34021320
Early-Life Immune System Maturation in Chickens Using a Synthetic Community of Cultured Gut Bacteria. PMID:34006629
Comparative Genome-Wide Alternative Splicing Analysis of Longissimus Dorsi Muscles Between Japanese Black (Wagyu) and Chinese Red Steppes Cattle. PMID:33996965
Gut microbiota profiles of young South Indian children: Child sex-specific relations with growth. PMID:33989353
Penalized estimation of the Gaussian graphical model from data with replicates. PMID:33987868
Mechanistic insight into the progressive retinal atrophy disease in dogs via pathway-based genome-wide association analysis. PMID:33987558
De novo transcriptome analysis for examination of the nutrition metabolic system related to the evolutionary process through which stick insects gain the ability of flight (Phasmatodea). PMID:33985569
Integrated Genomic and Functional Characterization of the Anti-diabetic Potential of Arthrobacter sp. SW1. PMID:33983483
Study on the Mechanism of Lianpu Drink for the Treatment of Chronic Gastritis Based on Network Pharmacology. PMID:33959188
Osteocyte transcriptome mapping identifies a molecular landscape controlling skeletal homeostasis and susceptibility to skeletal disease. PMID:33953184
Untargeted metabolomics for uncovering plasma biological markers of wet age-related macular degeneration. PMID:33946050
Predicting Tumor Cell Response to Synergistic Drug Combinations Using a Novel Simplified Deep Learning Model. PMID:33936513
Transcriptomic and microRNA Expression Profiles Identify Biomarkers for Predicting Neo-Chemoradiotherapy Response in Esophageal Squamous Cell Carcinomas (ESCC). PMID:33935718
The Ion-Translocating NrfD-Like Subunit of Energy-Transducing Membrane Complexes. PMID:33928068
Dynamic Changes in Fecal Microbial Communities of Neonatal Dairy Calves by Aging and Diarrhea. PMID:33924525
A First Insight into the Gonad Transcriptome of Hong Kong Catfish (Clarias fuscus). PMID:33920938
The Development of Bacteriophage Resistance in Vibrio alginolyticus Depends on a Complex Metabolic Adaptation Strategy. PMID:33920240
EGFR Activates a TAZ-Driven Oncogenic Program in Glioblastoma. PMID:33910930
Anaerobic gut fungi are an untapped reservoir of natural products. PMID:33906945
Drug repurposing for cancer treatment through global propagation with a greedy algorithm in a multilayer network. PMID:33893730
An Extracellular Matrix-Based Signature Associated With Immune Microenvironment Predicts the Prognosis and Therapeutic Responses of Patients With Oesophageal Squamous Cell Carcinoma. PMID:33869274
The Arachidonic Acid Metabolism Mechanism Based on UPLC-MS/MS Metabolomics in Recurrent Spontaneous Abortion Rats. PMID:33868179
Global coordination of metabolic pathways in Escherichia coli by active and passive regulation. PMID:33852189
An Ensemble Method to Predict Target Genes and Pathways in Uveal Melanoma. PMID:33817073
Transcriptomic and Metabolomic Basis of Short- and Long-Term Post-Harvest UV-C Application in Regulating Grape Berry Quality Development. PMID:33809507
Metabolite Analysis of Jerusalem Artichoke (Helianthus tuberosus L.) Seedlings in Response to Polyethylene Glycol-Simulated Drought Stress. PMID:33804948
A Comparison of the Transcriptomes of Cowpeas in Response to Two Different Ionizing Radiations. PMID:33802840
Multi-Omics Data Analysis Uncovers Molecular Networks and Gene Regulators for Metabolic Biomarkers. PMID:33801830
Transcriptome Analysis Reveals Genes Involved in Thermogenesis in Two Cold-Exposed Sheep Breeds. PMID:33800742
DEHP Down-Regulates Tshr Gene Expression in Rat Thyroid Tissues and FRTL-5 Rat Thyrocytes: A Potential Mechanism of Thyroid Disruption. PMID:33789034
Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study. PMID:33782480
Modulations of obesity-related microRNAs after exercise intervention: a systematic review and bioinformatics analysis. PMID:33772703
Discovery of New Protein Targets of BPA Analogs and Derivatives Associated with Noncommunicable Diseases: A Virtual High-Throughput Screening. PMID:33769846
Soil Metagenomics Reveals Effects of Continuous Sugarcane Cropping on the Structure and Functional Pathway of Rhizospheric Microbial Community. PMID:33746921
FunHoP: Enhanced Visualization and Analysis of Functionally Homologous Proteins in Complex Metabolic Networks. PMID:33741524
Identification of MEDAG as a Hub Candidate Gene in the Onset and Progression of Type 2 Diabetes Mellitus by Comprehensive Bioinformatics Analysis. PMID:33728329
PreDTIs: prediction of drug-target interactions based on multiple feature information using gradient boosting framework with data balancing and feature selection techniques. PMID:33709119
Uncovering Statistical Links Between Gene Expression and Structural Connectivity Patterns in the Mouse Brain. PMID:33704701
A nomogram combining PPARγ expression profiles and clinical factors predicts survival in patients with hepatocellular carcinoma. PMID:33692851
Combined Transcriptomic and Metabolomic Analysis Reveals the Role of Phenylpropanoid Biosynthesis Pathway in the Salt Tolerance Process of Sophora alopecuroides. PMID:33673678
Cytotoxic Fractions from Hechtia glomerata Extracts and p-Coumaric Acid as MAPK Inhibitors. PMID:33669666
Comparative Transcriptome Profiling of Human and Pig Intestinal Epithelial Cells after Porcine Deltacoronavirus Infection. PMID:33668405
Identify potential miRNA-mRNA regulatory networks contributing to high-risk neuroblastoma. PMID:33666785
Interactional mechanisms of Paenibacillus polymyxa SC2 and pepper (Capsicum annuum L.) suggested by transcriptomics. PMID:33663386
HoSeIn: A Workflow for Integrating Various Homology Search Results from Metagenomic and Metatranscriptomic Sequence Datasets. PMID:33659350
The Changes of Leukocytes in Brain and Blood After Intracerebral Hemorrhage. PMID:33659003
A novel DNA methylation-based model that effectively predicts prognosis in hepatocellular carcinoma. PMID:33634306
RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila. PMID:33617535
Identification of Primary and Metastatic Lung Cancer-Related lncRNAs and Potential Targeted Drugs Based on ceRNA Network. PMID:33614509
Identification of Protein Subcellular Localization With Network and Functional Embeddings. PMID:33584818
Alzheimer's Disease and Diabetes: Role of Diet, Microbiota and Inflammation in Preclinical Models. PMID:33578998
Guidelines for biomarker discovery in endometrium: correcting for menstrual cycle bias reveals new genes associated with uterine disorders. PMID:33576824
Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates. PMID:33565959
Microarray Data Mining and Preliminary Bioinformatics Analysis of Hepatitis D Virus-Associated Hepatocellular Carcinoma. PMID:33564675
Common differentially expressed genes and pathways correlating both coronary artery disease and atrial fibrillation. PMID:33564282
Gene networks and pathways for plasma lipid traits via multitissue multiomics systems analysis. PMID:33561811
A high-quality de novo genome assembly of one swamp eel (Monopterus albus) strain with PacBio and Hi-C sequencing data. PMID:33561235
A Novel 10-Gene Signature Predicts Poor Prognosis in Low Grade Glioma. PMID:33550903
Investigating the relevance of major signaling pathways in cancer survival using a biologically meaningful deep learning model. PMID:33546587
Genome-Wide Binding Analyses of HOXB1 Revealed a Novel DNA Binding Motif Associated with Gene Repression. PMID:33546292
Cycles, sources, and sinks: Conceptualizing how phosphate balance modulates carbon flux using yeast metabolic networks. PMID:33544078
A comprehensive evaluation of skin aging-related circular RNA expression profiles. PMID:33534927
Finding branched pathways in metabolic network via atom group tracking. PMID:33529200
Identification of key miRNA-gene pairs in gastric cancer through integrated analysis of mRNA and miRNA microarray. PMID:33527022
Glycolate combats massive oxidative stress by restoring redox potential in Caenorhabditis elegans. PMID:33526793
Effects of cannabis oil extract on immune response gene expression in human small airway epithelial cells (HSAEpC): implications for chronic obstructive pulmonary disease (COPD). PMID:33526116
Decreased p53 is associated with a decline in asymmetric stem cell self-renewal in aged human epidermis. PMID:33524216
Molecular subtyping of Alzheimer's disease using RNA sequencing data reveals novel mechanisms and targets. PMID:33523961
Multiple screening approaches reveal HDAC6 as a novel regulator of glycolytic metabolism in triple-negative breast cancer. PMID:33523897
Interspecific Variation in the Unsaturation Level of Seed Oils Were Associated With the Expression Pattern Shifts of Duplicated Desaturase Genes and the Potential Role of Other Regulatory Genes. PMID:33519875
A control theoretic three timescale model for analyzing energy management in mammalian cancer cells. PMID:33510857
Physiological Network From Anthropometric and Blood Test Biomarkers. PMID:33510648
Construction of a TF-miRNA-gene feed-forward loop network predicts biomarkers and potential drugs for myasthenia gravis. PMID:33510225
Identified GNGT1 and NMU as Combined Diagnosis Biomarker of Non-Small-Cell Lung Cancer Utilizing Bioinformatics and Logistic Regression. PMID:33505535
Inflammation and regulatory T cell genes are differentially expressed in peripheral blood mononuclear cells of Parkinson's disease patients. PMID:33504893
Metabotypes of Pseudomonas aeruginosa Correlate with Antibiotic Resistance, Virulence and Clinical Outcome in Cystic Fibrosis Chronic Infections. PMID:33494144
Genome-wide transcriptome profiling indicates the putative mechanism underlying enhanced grain size in a wheat mutant. PMID:33489673
Transcriptomic and Network Analysis of Minor Salivary Glands of Patients With Primary Sjögren's Syndrome. PMID:33488608
HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. PMID:33485349
Metabolomic and Transcriptomic Profiling Provide Novel Insights into Fruit Ripening and Ripening Disorder Caused by 1-MCP Treatments in Papaya. PMID:33477620
Metagenome Analysis of a Hydrocarbon-Degrading Bacterial Consortium Reveals the Specific Roles of BTEX Biodegraders. PMID:33466668
Human Plasma Metabolomics for Biomarker Discovery: Targeting the Molecular Subtypes in Breast Cancer. PMID:33466323
HIV Protein Tat Induces Macrophage Dysfunction and Atherosclerosis Development in Low-Density Lipoprotein Receptor-Deficient Mice. PMID:33459922
A chromosome-level genome assembly of the oriental river prawn, Macrobrachium nipponense. PMID:33459341
Vitamin B12-peptide nucleic acids use the BtuB receptor to pass through the Escherichia coli outer membrane. PMID:33453274
Transcriptomic biomarkers for predicting response to neoadjuvant treatment in oesophageal cancer. PMID:33442473
Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. PMID:33440171
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
BIRC5 is a prognostic biomarker associated with tumor immune cell infiltration. PMID:33431968
Induced organoids derived from patients with ulcerative colitis recapitulate colitic reactivity. PMID:33431859
Deregulation of extracellular matrix modeling with molecular prognostic markers revealed by transcriptome sequencing and validations in Oral Tongue squamous cell carcinoma. PMID:33420101
Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites. PMID:33413400
Computational analysis to repurpose drugs for COVID-19 based on transcriptional response of host cells to SARS-CoV-2. PMID:33413329
Transcriptome Analysis of the Cerebellum of Mice Fed a Manganese-Deficient Diet. PMID:33408735
Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis. PMID:33407096
Aedes aegypti post-emergence transcriptome: Unveiling the molecular basis for the hematophagic and gonotrophic capacitation. PMID:33406161
Dinoflagellates alter their carbon and nutrient metabolic strategies across environmental gradients in the central Pacific Ocean. PMID:33398100
Interdependence of metals and its binding proteins in Parkinson's disease for diagnosis. PMID:33398051
Pan-Cancer Molecular Patterns and Biological Implications Associated with a Tumor-Specific Molecular Signature. PMID:33396205
Immunological Role and Prognostic Value of APBB1IP in Pan-Cancer Analysis. PMID:33391455
Chromosomal-Level Genome Assembly of Silver Sillago (Sillago sihama). PMID:33367716
Transcriptome Profiling Provides Insights Into Potential Antagonistic Mechanisms Involved in Chaetomium globosum Against Bipolaris sorokiniana. PMID:33365017
Comparative genomic analysis of the principal Cryptosporidium species that infect humans. PMID:33344091
Compounds with Antiviral, Anti-Inflammatory and Anticancer Activity Identified in Wine from Hungary's Tokaj Region via High Resolution Mass Spectrometry and Bioinformatics Analyses. PMID:33334025
Marine Ultrasmall Prokaryotes Likely Affect the Cycling of Carbon, Methane, Nitrogen, and Sulfur. PMID:33325996
Loci Associated With Antibody Response in Feral Swine (Sus scrofa) Infected With Brucella suis. PMID:33324693
mTORC1 Transcriptional Regulation of Ribosome Subunits, Protein Synthesis, and Molecular Transport in Primary Human Trophoblast Cells. PMID:33324640
Identification of Metabolism-Associated Prostate Cancer Subtypes and Construction of a Prognostic Risk Model. PMID:33324566
A collection of bacterial isolates from the pig intestine reveals functional and taxonomic diversity. PMID:33319778
Olfactomedin 4 mediation of prostate stem/progenitor-like cell proliferation and differentiation via MYC. PMID:33318499
Identification of long non-coding RNA signatures for squamous cell carcinomas and adenocarcinomas. PMID:33318305
Chromosome-level genome assembly of the aphid parasitoid Aphidius gifuensis using Oxford Nanopore sequencing and Hi-C technology. PMID:33314728
Integrated Bioinformatics Analysis for the Screening of Associated Pathways and Therapeutic Drugs in Coronavirus Disease 2019. PMID:33309308
Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease. PMID:33297944
Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. PMID:33296723
Inhibition of miR-152 during In Vitro Maturation Enhances the Developmental Potential of Porcine Embryos. PMID:33291523
Comparative transcriptome analysis of three gonadal development stages reveals potential genes involved in gametogenesis of the fluted giant clam (Tridacna squamosa). PMID:33287701
multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data. PMID:33287694
Construction and Validation of Predictive Model to Identify Critical Genes Associated with Advanced Kidney Disease. PMID:33274190
Identification of Monotonically Differentially Expressed Genes across Pathologic Stages for Cancers. PMID:33273919
Pan-genome analysis and ancestral state reconstruction of class halobacteria: probability of a new super-order. PMID:33273480
Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. PMID:33271881
Gene Transfer Agents in Symbiotic Microbes. PMID:33263868
Chromosomal genome of Triplophysa bleekeri provides insights into its evolution and environmental adaptation. PMID:33231676
Spatial profiling of gastric cancer patient-matched primary and locoregional metastases reveals principles of tumour dissemination. PMID:33229445
Comprehensive proteomic atlas of skin biomatrix scaffolds reveals a supportive microenvironment for epidermal development. PMID:33224464
Localized effect of treated wastewater effluent on the resistome of an urban watershed. PMID:33215210
LINC01235-TWIST2 feedback loop facilitates epithelial-mesenchymal transition in gastric cancer by inhibiting THBS2. PMID:33206629
Tracing the footsteps of autophagy in computational biology. PMID:33201177
Divergent organ-specific isogenic metastatic cell lines identified using multi-omics exhibit differential drug sensitivity. PMID:33196681
Characterization of the transcriptional response of Candida parapsilosis to the antifungal peptide MAF-1A. PMID:33194346
Multi-Omics Analysis Detects Novel Prognostic Subgroups of Breast Cancer. PMID:33193681
Hub Genes Identification in a Murine Model of Allergic Rhinitis Based on Bioinformatics Analysis. PMID:33193578
Data mining combined with experiments to validate CEP55 as a prognostic biomarker in colorectal cancer. PMID:33190424
Anti‑inflammatory mechanism of berberine on lipopolysaccharide‑induced IEC‑18 models based on comparative transcriptomics. PMID:33174609
Plasma extracellular vesicle miRNAs as potential biomarkers of superstimulatory response in cattle. PMID:33154526
Age-related loss of gene-to-gene transcriptional coordination among single cells. PMID:33139959
Transcriptomic Analysis Reveals Important Roles of Lignin and Flavonoid Biosynthetic Pathways in Rice Thermotolerance During Reproductive Stage. PMID:33110421
Radiation of nitrogen-metabolizing enzymes across the tree of life tracks environmental transitions in Earth history. PMID:33108025
Computational Identification of Human Biological Processes and Protein Sequence Motifs Putatively Targeted by SARS-CoV-2 Proteins Using Protein-Protein Interaction Networks. PMID:33103435
Comprehensive Transcriptome Profiling of Dairy Goat Mammary Gland Identifies Genes and Networks Crucial for Lactation and Fatty Acid Metabolism. PMID:33101357
Cycloheximide-Producing Streptomyces Associated With Xyleborinus saxesenii and Xyleborus affinis Fungus-Farming Ambrosia Beetles. PMID:33101237
Prediction of severity and subtype of fibrosing disease using model informed by inflammation and extracellular matrix gene index. PMID:33095822
A genome-wide association study of severe asthma exacerbations in Latino children and adolescents. PMID:33093117
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network. PMID:33087039
Effects of miR-101-3p on goat granulosa cells in vitro and ovarian development in vivo via STC1. PMID:33072314
LRRK2 mediates microglial neurotoxicity via NFATc2 in rodent models of synucleinopathies. PMID:33055242
Virus database annotations assist in tracing information on patients infected with emerging pathogens. PMID:33052312
Identification of a Novel Immune-Related Prognostic Biomarker and Small-Molecule Drugs in Clear Cell Renal Cell Carcinoma (ccRCC) by a Merged Microarray-Acquired Dataset and TCGA Database. PMID:33014010
Comparative transcriptome analysis reveals heat stress-responsive genes and their signalling pathways in lilies (Lilium longiflorum vs. Lilium distichum). PMID:33006971
Selective Histone Deacetylase 6 Inhibitors Restore Cone Photoreceptor Vision or Outer Segment Morphology in Zebrafish and Mouse Models of Retinal Blindness. PMID:32984302
Matrix Metallopeptidase 14: A Candidate Prognostic Biomarker for Diffuse Large B-Cell Lymphoma. PMID:32974187
Identification of KIF18B as a Hub Candidate Gene in the Metastasis of Clear Cell Renal Cell Carcinoma by Weighted Gene Co-expression Network Analysis. PMID:32973873
CD73 contributes to anti-inflammatory properties of afferent lymphatic endothelial cells in humans and mice. PMID:32970335
Comprehensive Analysis of Differentially Expressed circRNAs Reveals a Colorectal Cancer-Related ceRNA Network. PMID:32952599
An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. PMID:32948837
Genome-Scale Metabolic Model of the Human Pathogen Candida albicans: A Promising Platform for Drug Target Prediction. PMID:32932905
A Genome-Scale Metabolic Model of Thalassiosira pseudonana CCMP 1335 for a Systems-Level Understanding of Its Metabolism and Biotechnological Potential. PMID:32932853
MasterPATH: network analysis of functional genomics screening data. PMID:32928103
Providing new insights on the biphasic lifestyle of the predatory bacterium Bdellovibrio bacteriovorus through genome-scale metabolic modeling. PMID:32925899
Identification of MTHFD2 as a novel prognosis biomarker in esophageal carcinoma patients based on transcriptomic data and methylation profiling. PMID:32925794
Exhaled volatile organic compounds analysis in clinical pediatrics: a systematic review. PMID:32919397
PI3K-Akt pathway mediated antiviral mechanism in silkworm Antheraea mylitta. PMID:32904810
Transcriptome Analysis of Solanum Tuberosum Genotype RH89-039-16 in Response to Chitosan. PMID:32903855
Identification of Immune-Related Prognostic Biomarkers Based on the Tumor Microenvironment in 20 Malignant Tumor Types With Poor Prognosis. PMID:32903590
Metabolic Responses to Arsenite Exposure Regulated through Histidine Kinases PhoR and AioS in Agrobacterium tumefaciens 5A. PMID:32887433
Effects of 9,10-phenanthrenequione on antioxidant indices and metabolite profiles in Takifugu obscurus plasma. PMID:32874598
Integrative genomics analysis of various omics data and networks identify risk genes and variants vulnerable to childhood-onset asthma. PMID:32867763
Genome-Wide Association Study and Pathway Analysis for Heterophil/Lymphocyte (H/L) Ratio in Chicken. PMID:32867375
Plasma metabolomic study in perinatally HIV-infected children using 1H NMR spectroscopy reveals perturbed metabolites that sustain during therapy. PMID:32866201
Intracellular sodium elevation reprograms cardiac metabolism. PMID:32859897
Prognostic model of patients with liver cancer based on tumor stem cell content and immune process. PMID:32852285
Comparative Analysis of the Development of Acquired Radioresistance in Canine and Human Mammary Cancer Cell Lines. PMID:32851022
Identification of MicroRNA-Related Tumorigenesis Variants and Genes in the Cancer Genome Atlas (TCGA) Data. PMID:32824926
Altered gut microbiota associated with symptom severity in schizophrenia. PMID:32821537
Risuteganib Protects against Hydroquinone-induced Injury in Human RPE Cells. PMID:32818234
The chromosome-level draft genome of Dalbergia odorifera. PMID:32808664
Transcriptome analysis of Aedes aegypti Aag2 cells in response to dengue virus-2 infection. PMID:32807211
Clinical, genomics and networking analyses of a high-altitude native American Ecuadorian patient with congenital insensitivity to pain with anhidrosis: a case report. PMID:32807182
Using Micro- and Macro-Level Network Metrics Unveils Top Communicative Gene Modules in Psoriasis. PMID:32785106
Network Medicine-Based Unbiased Disease Modules for Drug and Diagnostic Target Identification in ROSopathies. PMID:32780286
DHX36, BAX, and ARPC1B May Be Critical for the Diagnosis and Treatment of Tuberculosis. PMID:32774561
Role of CYP4F2 as a novel biomarker regulating malignant phenotypes of liver cancer cells via the Nrf2 signaling axis. PMID:32774486
Analysis and identification of novel biomarkers involved in neuroblastoma via integrated bioinformatics. PMID:32772341
Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. PMID:32769060
Atherosclerosis prediction by microarray-based DNA methylation analysis. PMID:32765783
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
Uncovering the Complexity Mechanism of Different Formulas Treatment for Rheumatoid Arthritis Based on a Novel Network Pharmacology Model. PMID:32754034
New Plant Growth-Promoting, Chromium-Detoxifying Microbacterium Species Isolated From a Tannery Wastewater: Performance and Genomic Insights. PMID:32719777
Multi-omic meta-analysis identifies functional signatures of airway microbiome in chronic obstructive pulmonary disease. PMID:32719402
Gene biomarker discovery at different stages of Alzheimer using gene co-expression network approach. PMID:32699331
The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. PMID:32684953
Identification of cell division cycle 20 as a candidate biomarker and potential therapeutic target in bladder cancer using bioinformatics analysis. PMID:32677673
Computational approaches in viral ecology. PMID:32670501
Shotgun Proteomics of Ascidians Tunic Gives New Insights on Host-Microbe Interactions by Revealing Diverse Antimicrobial Peptides. PMID:32668814
Leucine-Rich Diet Modulates the Metabolomic and Proteomic Profile of Skeletal Muscle during Cancer Cachexia. PMID:32668598
Genome-Scale Metabolic Model Driven Design of a Defined Medium for Campylobacter jejuni M1cam. PMID:32636809
Computational Identification of Kinases That Control Axon Growth in Mouse. PMID:32613890
Proteomic and Phosphoproteomic Maps of Lung Squamous Cell Carcinoma From Chinese Patients. PMID:32612956
Genome-wide high-throughput screening of interactive bacterial metabolite in the algal population using Escherichia coli K-12 Keio collection. PMID:32606320
Dynamical modeling of pro- and anti-inflammatory cytokines in the early stage of septic shock. PMID:32597796
Cell Cycle Genes Are Potential Diagnostic and Prognostic Biomarkers in Hepatocellular Carcinoma. PMID:32596342
Epigenome-450K-wide methylation signatures of active cigarette smoking: The Young Finns Study. PMID:32583859
Co-expression network analysis identifies a gene signature as a predictive biomarker for energy metabolism in osteosarcoma. PMID:32581649
Comprehensive characterization of driver genes in diffuse large B cell lymphoma. PMID:32565964
CRISPR/Cas9 knockout of human arylamine N-acetyltransferase 1 in MDA-MB-231 breast cancer cells suggests a role in cellular metabolism. PMID:32555504
Traditional rice beer depletes butyric acid-producing gut bacteria Faecalibacterium and Roseburia along with fecal butyrate levels in the ethnic groups of Northeast India. PMID:32550102
MicroRNA Signatures in Blood or Bone Marrow Distinguish Subtypes of Pediatric Acute Lymphoblastic Leukemia. PMID:32531485
The genome sequence of star fruit (Averrhoa carambola). PMID:32528707
Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.). PMID:32528697
Changes in the transcriptome, ploidy, and optimal light intensity of a cryptomonad upon integration into a kleptoplastic dinoflagellate. PMID:32514116
OsCpn60β1 is Essential for Chloroplast Development in Rice (Oryza sativa L.). PMID:32512821
IRESbase: A Comprehensive Database of Experimentally Validated Internal Ribosome Entry Sites. PMID:32512182
Characterization of imine reductases in reductive amination for the exploration of structure-activity relationships. PMID:32494734
Impact of Short-Term Isoflavone Intervention in Polycystic Ovary Syndrome (PCOS) Patients on Microbiota Composition and Metagenomics. PMID:32492805
Transcriptional profiling reveals a subset of human breast tumors that retain wt TP53 but display mutant p53-associated features. PMID:32484602
Sex-Specific Regulation of Inflammation and Metabolic Syndrome in Obesity. PMID:32460579
Metagenomics reveals impact of geography and acute diarrheal disease on the Central Indian human gut microbiome. PMID:32459982
A transcriptomic map of murine and human alopecia areata. PMID:32453712
Integrated analysis of lncRNA-associated ceRNA network identified potential regulatory interactions in osteosarcoma. PMID:32453338
GPS-PBS: A Deep Learning Framework to Predict Phosphorylation Sites that Specifically Interact with Phosphoprotein-Binding Domains. PMID:32443803
Genomic history of the Italian population recapitulates key evolutionary dynamics of both Continental and Southern Europeans. PMID:32438927
Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest. PMID:32438916
Robust Sampling of Defective Pathways in Alzheimer's Disease. Implications in Drug Repositioning. PMID:32438758
Construction and Validation of an Autophagy-Related Prognostic Risk Signature for Survival Predicting in Clear Cell Renal Cell Carcinoma Patients. PMID:32432045
Comprehensive transcriptomic analysis identifies novel regulators of lung adenocarcinoma. PMID:32415511
High confidence copy number variants identified in Holstein dairy cattle from whole genome sequence and genotype array data. PMID:32415111
Transcriptional Sequencing and Gene Expression Analysis of Various Genes in Fruit Development of Three Different Black Pepper (Piper nigrum L.) Varieties. PMID:32399475
Cell-specific metabolomic responses to injury: novel insights into blood-brain barrier modulation. PMID:32385409
Analysis of genes associated with prognosis of lung adenocarcinoma based on GEO and TCGA databases. PMID:32384511
Chromosome-scale assembly of the Kandelia obovata genome. PMID:32377365
A MicroRNA Signature Identifies Pancreatic Ductal Adenocarcinoma Patients at Risk for Lymph Node Metastases. PMID:32376411
A single-cell transcriptomic landscape of primate arterial aging. PMID:32371953
A Guide to Understanding "State-of-the-Art" Basic Research Techniques in Anesthesiology. PMID:32371742
Expression profiling and analysis of some miRNAs in subcutaneous white adipose tissue during development of obesity. PMID:32366215
The Role of lncRNAs TAPIR-1 and -2 as Diagnostic Markers and Potential Therapeutic Targets in Prostate Cancer. PMID:32365858
Intrinsic limitations in mainstream methods of identifying network motifs in biology. PMID:32349657
Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. PMID:32348760
ETS2 and microRNA-155 regulate the pathogenesis of heart failure through targeting and regulating GPR18 expression. PMID:32346408
Quantitative analysis of amino acid metabolism in liver cancer links glutamate excretion to nucleotide synthesis. PMID:32341162
Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:32340320
Traditional Chinese medicine Biqi capsule compared with leflunomide in combination with methotrexate in patients with rheumatoid arthritis: a randomized controlled trial. PMID:32336980
CRISPR/Cas9-deaminase enables robust base editing in Rhodobacter sphaeroides 2.4.1. PMID:32334589
Different "metabolomic niches" of the highly diverse tree species of the French Guiana rainforests. PMID:32332903
Transcriptional Dynamics and Candidate Genes Involved in Pod Maturation of Common Bean (Phaseolus vulgaris L.). PMID:32331491
Retinal astrocytes transcriptome reveals Cyp1b1 regulates the expression of genes involved in cell adhesion and migration. PMID:32330152
Identification of key miRNAs and genes for mouse retinal development using a linear model. PMID:32319662
High expression of CDCA7 predicts tumor progression and poor prognosis in human colorectal cancer. PMID:32319649
A 7-lncRNA signature associated with the prognosis of colon adenocarcinoma. PMID:32309045
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
A Five-Genes-Based Prognostic Signature for Cervical Cancer Overall Survival Prediction. PMID:32300605
Complete Genome Sequence of Athalassotoga saccharophila Strain NAS-01, a Deep-Branching Thermophilic Lineage in the Phylum Thermotogae. PMID:32299888
Integrated Analysis to Evaluate the Prognostic Value of Signature mRNAs in Glioblastoma Multiforme. PMID:32296458
Sepsis-associated pathways segregate cancer groups. PMID:32293345
Identifying nucleic acid-associated proteins in Mycobacterium smegmatis by mass spectrometry-based proteomics. PMID:32293251
First de novo whole genome sequencing and assembly of the bar-headed goose. PMID:32292659
Association Analysis of Driver Gene-Related Genetic Variants Identified Novel Lung Cancer Susceptibility Loci with 20,871 Lung Cancer Cases and 15,971 Controls. PMID:32277007
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
Gene expression profiling identifies pathways involved in seed maturation of Jatropha curcas. PMID:32272887
Systems Pharmacology-Based Strategy to Investigate Pharmacological Mechanisms of Radix Puerariae for Treatment of Hypertension. PMID:32265716
Draft genomes of two Atlantic bay scallop subspecies Argopecten irradians irradians and A. i. concentricus. PMID:32251283
Vertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth. PMID:32239170
Alterations in Immune-Related Genes as Potential Marker of Prognosis in Breast Cancer. PMID:32226776
OncoOmics approaches to reveal essential genes in breast cancer: a panoramic view from pathogenesis to precision medicine. PMID:32210335
Lipid analysis of CO2-rich subsurface aquifers suggests an autotrophy-based deep biosphere with lysolipids enriched in CPR bacteria. PMID:32203118
Gene signatures in peripheral blood immune cells related to insulin resistance and low tyrosine metabolism define a sub-type of depression with high CRP and anhedonia. PMID:32198016
Reconstruction and Validation of a Genome-Scale Metabolic Model of Streptococcus oralis (iCJ415), a Human Commensal and Opportunistic Pathogen. PMID:32194617
A Gene-Set Enrichment and Protein-Protein Interaction Network-Based GWAS with Regulatory SNPs Identifies Candidate Genes and Pathways Associated with Carcass Traits in Hanwoo Cattle. PMID:32188084
Transcriptome analysis of metabolic pathways associated with oil accumulation in developing seed kernels of Styrax tonkinensis, a woody biodiesel species. PMID:32183691
Methods detecting rhythmic gene expression are biologically relevant only for strong signal. PMID:32182235
DNA methylation QTL analysis identifies new regulators of human longevity. PMID:32160291
Carbon Assimilation Strategies in Ultrabasic Groundwater: Clues from the Integrated Study of a Serpentinization-Influenced Aquifer. PMID:32156795
DJ-1 is indispensable for the S-nitrosylation of Parkin, which maintains function of mitochondria. PMID:32152416
Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening. PMID:32152358
Comparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus. PMID:32150860
Identification of hub genes and pathways in adrenocortical carcinoma by integrated bioinformatic analysis. PMID:32147961
The genome evolution and domestication of tropical fruit mango. PMID:32143734
In silico Prediction of Protein-Protein Interaction Network Induced by Manganese II in Meyerozyma guilliermondii. PMID:32140149
A framework using topological pathways for deeper analysis of transcriptome data. PMID:32138666
Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks. PMID:32138627
Deregulation of miR-27a may contribute to canine fibroblast activation after coculture with a mast cell tumour cell line. PMID:32133790
LeukmiR: a database for miRNAs and their targets in acute lymphoblastic leukemia. PMID:32128558
Transcriptome Changes of Mycobacterium marinum in the Process of Resuscitation From Hypoxia-Induced Dormancy. PMID:32117415
The Integrated RNA Landscape of Renal Preconditioning against Ischemia-Reperfusion Injury. PMID:32111728
Proteogenomic analysis of pitaya reveals cold stress-related molecular signature. PMID:32095361
Controllability analysis of molecular pathways points to proteins that control the entire interaction network. PMID:32076007
Potential physiological roles of the 31/32-nucleotide Y4-RNA fragment in human plasma. PMID:32072081
Contents, Construction Methods, Data Resources, and Functions Comparative Analysis of Bacteria Databases. PMID:32071553
ASCL1- and DLX2-induced GABAergic neurons from hiPSC-derived NPCs. PMID:32065989
Associations between metabolites and pancreatic cancer risk in a large prospective epidemiological study. PMID:32060129
Transcriptome Profiling Analysis Reveals Co-regulation of Hormone Pathways in Foxtail Millet during Sclerospora graminicola Infection. PMID:32059399
Frequent mutation of hypoxia-related genes in persistent pulmonary hypertension of the newborn. PMID:32054482
TGF-ß1 Induces Changes in the Energy Metabolism of White Adipose Tissue-Derived Human Adult Mesenchymal Stem/Stromal Cells In Vitro. PMID:32046088
Comparative Transcriptome Analysis of the Heat Stress Response in Monochamus alternatus Hope (Coleoptera: Cerambycidae). PMID:32038275
Differential Gene Profiling of the Heartwood Formation Process in Taiwania cryptomerioides Hayata Xylem Tissues. PMID:32024007
Exploring Metabolic Consequences of CPS1 and CAD Dysregulation in Hepatocellular Carcinoma by Network Reconstruction. PMID:32021853
Comparison of Three Xylose Pathways in Pseudomonas putida KT2440 for the Synthesis of Valuable Products. PMID:32010683
Bioinformatics-based screening of key genes for transformation of liver cirrhosis to hepatocellular carcinoma. PMID:32000807
SPVec: A Word2vec-Inspired Feature Representation Method for Drug-Target Interaction Prediction. PMID:31998687
Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish. PMID:31998265
Integrated Bioinformatics Analysis for the Identification of Key Molecules and Pathways in the Hippocampus of Rats After Traumatic Brain Injury. PMID:31997105
Hepatic and intestinal biotransformation gene expression and drug disposition in a dextran sulfate sodium-induced colitis mouse model. PMID:31993311
Activation of Myd88-Dependent TLRs Mediates Local and Systemic Inflammation in a Mouse Model of Primary Sjögren's Syndrome. PMID:31993047
Utilization of GC-MS untargeted metabolomics to assess the delayed response of glufosinate treatment of transgenic herbicide resistant (HR) buffalo grasses (Stenotaphrum secundatum L.). PMID:31989303
Anaerobic methane oxidation coupled to manganese reduction by members of the Methanoperedenaceae. PMID:31988473
Metabonomic-Transcriptome Integration Analysis on Osteoarthritis and Rheumatoid Arthritis. PMID:31976312
Novel Approaches for Identifying the Molecular Background of Schizophrenia. PMID:31963710
Transcriptional analysis of THP-1 cells infected with Leishmania infantum indicates no activation of the inflammasome platform. PMID:31961876
Metabolomics Analysis of the Deterioration Mechanism and Storage Time Limit of Tender Coconut Water during Storage. PMID:31947875
Single-cell transcriptional profiles in human skeletal muscle. PMID:31937892
Maternal factor NELFA drives a 2C-like state in mouse embryonic stem cells. PMID:31932739
The Cellular Transcriptome in the Maternal Circulation During Normal Pregnancy: A Longitudinal Study. PMID:31921132
The Complete Genome of Emcibacter congregatus ZYLT, a Marine Bacterium Encoding a CRISPR-Cas 9 Immune System. PMID:31919672
Identification of Monotonically Differentially Expressed Genes for IFN-β-Treated Multiple Sclerosis Patients. PMID:31915697
LncRNA XIST serves as a ceRNA to regulate the expression of ASF1A, BRWD1M, and PFKFB2 in kidney transplant acute kidney injury via sponging hsa-miR-212-3p and hsa-miR-122-5p. PMID:31914881
Transcriptome analyses identify hub genes and potential mechanisms in adenoid cystic carcinoma. PMID:31914060
The Mouse Gut Microbial Biobank expands the coverage of cultured bacteria. PMID:31911589
Metabolite Profiling and Classification of Developing Styrax tonkinensis Kernels. PMID:31906354
Identification of key genes for predicting colorectal cancer prognosis by integrated bioinformatics analysis. PMID:31897151
HisCoM-PAGE: software for hierarchical structural component models for pathway analysis of gene expression data. PMID:31896245
A multiomics approach to heterogeneity in Alzheimer's disease: focused review and roadmap. PMID:31891371
Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities. PMID:31889100
Composite genome sequence of Bacillus clausii, a probiotic commercially available as Enterogermina®, and insights into its probiotic properties. PMID:31888501
Chromosome-Level Comprehensive Genome of Mangrove Sediment-Derived Fungus Penicillium variabile HXQ-H-1. PMID:31878043
Comparative Transcriptome Analysis of Thitarodes Armoricanus in Response to the Entomopathogenic Fungi Paecilomyces Hepiali and Ophiocordyceps Sinensis. PMID:31861642
Transcriptome landscape of Rafflesia cantleyi floral buds reveals insights into the roles of transcription factors and phytohormones in flower development. PMID:31851702
Transcriptome analysis reveals plasticity in gene regulation due to environmental cues in Primula sikkimensis, a high altitude plant species. PMID:31847812
BCL2 and hsa-miR-181a-5p are potential biomarkers associated with papillary thyroid cancer based on bioinformatics analysis. PMID:31842912
Battling Glioblastoma: A Novel Tyrosine Kinase Inhibitor with Multi-Dimensional Anti-Tumor Effect (Running Title: Cancer Cells Death Signalling Activation). PMID:31842391
Analysis of disease comorbidity patterns in a large-scale China population. PMID:31829182
Transcriptome analysis reveals an important candidate gene involved in both nodal metastasis and prognosis in lung adenocarcinoma. PMID:31827762
Exploring thematic structure and predicted functionality of 16S rRNA amplicon data. PMID:31825995
Assessing the performance of different approaches for functional and taxonomic annotation of metagenomes. PMID:31823721
Regulation underlying hierarchical and simultaneous utilization of carbon substrates by flux sensors in Escherichia coli. PMID:31819215
Genomic Survey, Transcriptome, and Metabolome Analysis of Apocynum venetum and Apocynum hendersonii to Reveal Major Flavonoid Biosynthesis Pathways. PMID:31817331
Transcriptome of Chicken Liver Tissues Reveals the Candidate Genes and Pathways Responsible for Adaptation into Two Different Climatic Conditions. PMID:31816986
Bioenergetics and translational metabolism: implications for genetics, physiology and precision medicine. PMID:31815377
Identification of potential pathogenic candidates or diagnostic biomarkers in papillary thyroid carcinoma using expression and methylation profiles. PMID:31814850
The Natural Products Atlas: An Open Access Knowledge Base for Microbial Natural Products Discovery. PMID:31807684
De Novo Genome Assembly of Populus simonii Further Supports That Populus simonii and Populus trichocarpa Belong to Different Sections. PMID:31806765
LncRNA PICSAR promotes cell proliferation, migration and invasion of fibroblast-like synoviocytes by sponging miRNA-4701-5p in rheumatoid arthritis. PMID:31791845
The core genes involved in the promotion of depression in patients with ovarian cancer. PMID:31788074
Carprofen-induced depletion of proton motive force reverses TetK-mediated doxycycline resistance in methicillin-resistant Staphylococcus pseudintermedius. PMID:31780689
Using Network Pharmacology to Explore Potential Treatment Mechanism for Coronary Heart Disease Using Chuanxiong and Jiangxiang Essential Oils in Jingzhi Guanxin Prescriptions. PMID:31772600
Competing endogenous network analysis identifies lncRNA Meg3 activates inflammatory damage in UVB induced murine skin lesion by sponging miR-93-5p/epiregulin axis. PMID:31761787
Transcriptome Analysis and Identification of Insecticide Tolerance-Related Genes after Exposure to Insecticide in Sitobion avenae. PMID:31757092
HisCoM-PAGE: Hierarchical Structural Component Models for Pathway Analysis of Gene Expression Data. PMID:31739607
Sequencing of the black rockfish chromosomal genome provides insight into sperm storage in the female ovary. PMID:31711192
Microbial metabolisms in an abyssal ferromanganese crust from the Takuyo-Daigo Seamount as revealed by metagenomics. PMID:31703093
The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae). PMID:31702783
Reconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model. PMID:31694544
Systematic identification of lncRNA-based prognostic biomarkers for glioblastoma. PMID:31692451
PRODIGY: personalized prioritization of driver genes. PMID:31681944
Cardiac and Skeletal Muscle Transcriptome Response to Heat Stress in Kenyan Chicken Ecotypes Adapted to Low and High Altitudes Reveal Differences in Thermal Tolerance and Stress Response. PMID:31681427
Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. PMID:31675502
Metabolic and gut microbiome changes following GLP-1 or dual GLP-1/GLP-2 receptor agonist treatment in diet-induced obese mice. PMID:31666597
Weighted single-step GWAS identified candidate genes associated with semen traits in a Duroc boar population. PMID:31666004
circ-016910 sponges miR-574-5p to regulate cell physiology and milk synthesis via MAPK and PI3K/AKT-mTOR pathways in GMECs. PMID:31663119
A survey of Fusobacterium nucleatum genes modulated by host cell infection. PMID:31661053
The miR-15a-5p-XIST-CUL3 regulatory axis is important for sepsis-induced acute kidney injury. PMID:31658856
Aconitine induces cardiomyocyte damage by mitigating BNIP3-dependent mitophagy and the TNFα-NLRP3 signalling axis. PMID:31657084
Kinome Profiling Reveals Abnormal Activity of Kinases in Skeletal Muscle From Adults With Obesity and Insulin Resistance. PMID:31652310
Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress. PMID:31623206
High-resolution transcriptional profiling of Anopheles gambiae spermatogenesis reveals mechanisms of sex chromosome regulation. PMID:31619757
Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case. PMID:31612015
sRNA OsiA Stabilizes Catalase mRNA during Oxidative Stress Response of Deincoccus radiodurans R1. PMID:31597319
iPSC-Derived Embryoid Bodies as Models of c-Met-Mutated Hereditary Papillary Renal Cell Carcinoma. PMID:31575031
Comparison of Gene Expression Responses in the Small Intestine of Mice Following Exposure to 3 Carcinogens Using the S1500+ Gene Set Informs a Potential Common Adverse Outcome Pathway. PMID:31558096
Functional metagenomic analysis of dust-associated microbiomes above the Red Sea. PMID:31551441
Discovering genetic interactions bridging pathways in genome-wide association studies. PMID:31537791
Bioinformatic identification of key candidate genes and pathways in axon regeneration after spinal cord injury in zebrafish. PMID:31535658
Whole-Genome Sequence of Enterobacter sp. Strain MF024, Isolated from Soil in Shanghai, China. PMID:31515338
Estrogen receptors promote NSCLC progression by modulating the membrane receptor signaling network: a systems biology perspective. PMID:31511014
pathCHEMO, a generalizable computational framework uncovers molecular pathways of chemoresistance in lung adenocarcinoma. PMID:31508508
Metabolomic analysis of date palm seedlings exposed to salinity and silicon treatments. PMID:31505987
Circulating microRNA trafficking and regulation: computational principles and practice. PMID:31504144
Analysis of chickpea gene co-expression networks and pathways during heavy metal stress. PMID:31502577
Gene set enrichment analysis to create polygenic scores: a developmental examination of aggression. PMID:31477688
Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic. PMID:31471308
HTR1D, TIMP1, SERPINE1, MMP3 and CNR2 affect the survival of patients with colon adenocarcinoma. PMID:31452735
High expression of EZR (ezrin) gene is correlated with the poor overall survival of breast cancer patients. PMID:31452341
ComplexBrowser: A Tool for Identification and Quantification of Protein Complexes in Large-scale Proteomics Datasets. PMID:31447428
A Tripartite Microbial-Environment Network Indicates How Crucial Microbes Influence the Microbial Community Ecology. PMID:31428833
LAMTOR/Ragulator regulates lipid metabolism in macrophages and foam cell differentiation. PMID:31423582
A five-gene signature to predict the overall survival time of patients with esophageal squamous cell carcinoma. PMID:31423201
Stoichiometric gene-to-reaction associations enhance model-driven analysis performance: Metabolic response to chronic exposure to Aldrin in prostate cancer. PMID:31416420
The Methodological Trends of Traditional Herbal Medicine Employing Network Pharmacology. PMID:31412658
Brain Gene Expression in a Novel Mouse Model of Postpartum Mood Disorder. PMID:31410299
Construction of subtype-specific prognostic gene signatures for early-stage non-small cell lung cancer using meta feature selection methods. PMID:31402939
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Direct and Specific Functional Evaluation of the Nrf2 and MafG Heterodimer by Introducing a Tethered Dimer into Small Maf-Deficient Cells. PMID:31383749
Phosphoproteomics reveals conserved exercise-stimulated signaling and AMPK regulation of store-operated calcium entry. PMID:31381180
Metabolic Potential of As-yet-uncultured Archaeal Lineages of Candidatus Hydrothermarchaeota Thriving in Deep-sea Metal Sulfide Deposits. PMID:31378759
An integrative bioinformatics analysis identified miR-375 as a candidate key regulator of malignant breast cancer. PMID:31372832
Whole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23. PMID:31371382
The prognostic value of JUNB-positive CTCs in metastatic breast cancer: from bioinformatics to phenotypic characterization. PMID:31370904
Transcriptome analysis of acerola fruit ripening: insights into ascorbate, ethylene, respiration, and softening metabolisms. PMID:31338671
FindTargetsWEB: A User-Friendly Tool for Identification of Potential Therapeutic Targets in Metabolic Networks of Bacteria. PMID:31333719
Insights about multi-targeting and synergistic neuromodulators in Ayurvedic herbs against epilepsy: integrated computational studies on drug-target and protein-protein interaction networks. PMID:31332210
Genome Sequencing of the Japanese Eel (Anguilla japonica) for Comparative Genomic Studies on tbx4 and a tbx4 Gene Cluster in Teleost Fishes. PMID:31330852
Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome. PMID:31321198
Shiny-Seq: advanced guided transcriptome analysis. PMID:31319888
Musa balbisiana genome reveals subgenome evolution and functional divergence. PMID:31308504
Identification of potential diagnostic and therapeutic target genes for lung squamous cell carcinoma. PMID:31289486
TNF-α Differentially Regulates Cell Cycle Genes in Promyelocytic and Granulocytic HL-60/S4 Cells. PMID:31263060
Oxidative stress under low oxygen conditions triggers hyperflagellation and motility in the Antarctic bacterium Pseudomonas extremaustralis. PMID:31250111
Integrative analysis of genomic and transcriptomic characteristics associated with progression of aggressive thyroid cancer. PMID:31235699
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. PMID:31216234
miR-142-3p suppresses uveal melanoma by targeting CDC25C, TGFβR1, GNAQ, WASL, and RAC1. PMID:31213897
Genetic Diversity of Indigenous Pigs from South China Area Revealed by SNP Array. PMID:31208134
Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution. PMID:31206013
Deciphering the metabolic perturbation in hepatic alveolar echinococcosis: a 1H NMR-based metabolomics study. PMID:31196218
High Quality Draft Genome of Arogyapacha (Trichopus zeylanicus), an Important Medicinal Plant Endemic to Western Ghats of India. PMID:31189529
Identification of co-evolving temporal networks. PMID:31189471
Gene set enrichment analysis and meta-analysis identified 12 key genes regulating and controlling the prognosis of lung adenocarcinoma. PMID:31186783
Dynamic genome-scale cell-specific metabolic models reveal novel inter-cellular and intra-cellular metabolic communications during ovarian follicle development. PMID:31182013
Differentially Expressed Gene Screening, Biological Function Enrichment, and Correlation with Prognosis in Non-Small Cell Lung Cancer. PMID:31181055
Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring. PMID:31171857
Collateral Sensitivity of Parthenolide via NF-κB and HIF-α Inhibition and Epigenetic Changes in Drug-Resistant Cancer Cell Lines. PMID:31164821
The prediction of early preeclampsia: Results from a longitudinal proteomics study. PMID:31163045
The genomes of polyextremophilic cyanidiales contain 1% horizontally transferred genes with diverse adaptive functions. PMID:31149898
Network pharmacology-based identifcation of potential targets of the flower of Trollius chinensis Bunge acting on anti-inflammatory effectss. PMID:31147584
Comparative transcriptomic analysis reveals genetic divergence and domestication genes in Diospyros. PMID:31146695
Back to the Salt Mines: Genome and Transcriptome Comparisons of the Halophilic Fungus Aspergillus salisburgensis and Its Halotolerant Relative Aspergillus sclerotialis. PMID:31137536
Expression Profile Analysis Identifies a Novel Five-Gene Signature to Improve Prognosis Prediction of Glioblastoma. PMID:31130992
Systematic Analysis of Non-coding RNAs Involved in the Angora Rabbit (Oryctolagus cuniculus) Hair Follicle Cycle by RNA Sequencing. PMID:31130985
Transcriptome Analysis Provides Novel Insights into the Capacity of the Ectomycorrhizal Fungus Amanita pantherina To Weather K-Containing Feldspar and Apatite. PMID:31126945
KEGG-expressed genes and pathways in intervertebral disc degeneration: Protocol for a systematic review and data mining. PMID:31124977
Overlapping and unique roles played by ROCK1 and 2 in the modulation of coding and long noncoding RNA expression. PMID:31117934
Metagenomic recovery of two distinct comammox Nitrospira from the terrestrial subsurface. PMID:31107587
Macrophage centripetal migration drives spontaneous healing process after spinal cord injury. PMID:31106270
Extensive metabolic remodeling after limiting mitochondrial lipid burden is consistent with an improved metabolic health profile. PMID:31097541
Co-cultivation of the anaerobic fungus Anaeromyces robustus with Methanobacterium bryantii enhances transcription of carbohydrate active enzymes. PMID:31089985
GPCRomics: An Approach to Discover GPCR Drug Targets. PMID:31078319
Incorporating Pathway Information into Feature Selection towards Better Performed Gene Signatures. PMID:31073522
Genome-Wide Signatures of Selection Detection in Three South China Indigenous Pigs. PMID:31067806
MicroRNAs as possible indicators of drug sensitivity in breast cancer cell lines. PMID:31063487
A metabolomic approach to understand the solid-state fermentation of okara using Bacillus subtilis WX-17 for enhanced nutritional profile. PMID:31055712
Developmental transcriptomics of Chinese cordyceps reveals gene regulatory network and expression profiles of sexual development-related genes. PMID:31054562
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks. PMID:31053864
Muscle Gene Sets: a versatile methodological aid to functional genomics in the neuromuscular field. PMID:31053169
Linkage-based genome assembly improvement of oil palm (Elaeis guineensis). PMID:31036825
A systematic approach re-analyzing the effects of temperature disturbance on the microbial community of mesophilic anaerobic digestion. PMID:31024021
Pathway-Based Analysis of the Liver Response to Intravenous Methylprednisolone Administration in Rats: Acute Versus Chronic Dosing. PMID:31019365
Transcriptional Regulation of Early Growth Response Gene-1 (EGR1) is Associated with Progression of Nonalcoholic Fatty Liver Disease (NAFLD) in Patients with Insulin Resistance. PMID:31013265
[Role of miR-106b-5p in the regulation of gene profiles in endothelial cells]. PMID:30996357
Systematic analysis of the effects of different nitrogen source and ICDH knockout on glycolate synthesis in Escherichia coli. PMID:30988698
Development and characterisation of acquired radioresistant breast cancer cell lines. PMID:30987655
The histone deacetylase NlHDAC1 regulates both female and male fertility in the brown planthopper, Nilaparvata lugens. PMID:30977704
Comparative RNA sequencing reveals that HPV16 E6 abrogates the effect of E6*I on ROS metabolism. PMID:30976051
omu, a Metabolomics Count Data Analysis Tool for Intuitive Figures and Convenient Metadata Collection. PMID:30975806
The Distribution of Tryptophan-Dependent Indole-3-Acetic Acid Synthesis Pathways in Bacteria Unraveled by Large-Scale Genomic Analysis. PMID:30974826
Hypocrellin A-based photodynamic action induces apoptosis in A549 cells through ROS-mediated mitochondrial signaling pathway. PMID:30972277
Impact of antibiotic treatment and host innate immune pressure on enterococcal adaptation in the human bloodstream. PMID:30971455
Association Analysis of Deep Genomic Features Extracted by Denoising Autoencoders in Breast Cancer. PMID:30959966
Sequencing the Obligate Intracellular Rhabdochlamydia helvetica within Its Tick Host Ixodes ricinus to Investigate Their Symbiotic Relationship. PMID:30949677
A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures. PMID:30941158
Comparative Analysis of the Liver Transcriptome among Cattle Breeds Using RNA-seq. PMID:30934933
Integrative Genomics Analysis Unravels Tissue-Specific Pathways, Networks, and Key Regulators of Blood Pressure Regulation. PMID:30931314
A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis. PMID:30923439
Transcriptome Analysis Reveals Cotton (Gossypium hirsutum) Genes That Are Differentially Expressed in Cadmium Stress Tolerance. PMID:30909634
Identification of hub genes associated with postmenopausal osteoporosis by Gibbs sampling method. PMID:30906457
Carbon Fixation by Marine Ultrasmall Prokaryotes. PMID:30903144
Common miRNA Patterns of Alzheimer's Disease and Parkinson's Disease and Their Putative Impact on Commensal Gut Microbiota. PMID:30890906
Strain-Level Differentiation of Bacteria by Paper Spray Ionization Mass Spectrometry. PMID:30888152
Frequency of Tongue Cleaning Impacts the Human Tongue Microbiome Composition and Enterosalivary Circulation of Nitrate. PMID:30881924
KIF15 promotes bladder cancer proliferation via the MEK-ERK signaling pathway. PMID:30881113
Identification of aberrantly methylated differentially expressed genes in prostate carcinoma using integrated bioinformatics. PMID:30872976
Global Ubiquitome Profiling Revealed the Roles of Ubiquitinated Proteins in Metabolic Pathways of Tea Leaves in Responding to Drought Stress. PMID:30862833
Metabolite-based mutualism enhances hydrogen production in a two-species microbial consortium. PMID:30854474
Identification of co-expression modules and pathways correlated with osteosarcoma and its metastasis. PMID:30849987
Glycine promotes longevity in Caenorhabditis elegans in a methionine cycle-dependent fashion. PMID:30845140
New molecular insights on the response of the green alga Tetraselmis suecica to nitrogen starvation. PMID:30833632
Metabolite and gene expression profiles suggest a putative mechanism through which high dietary carbohydrates reduce the content of hepatic betaine in Megalobrama amblycephala. PMID:30830423
Metabolic fingerprinting analysis of oil palm reveals a set of differentially expressed metabolites in fatal yellowing symptomatic and non-symptomatic plants. PMID:30830392
Genetic meta-analysis of diagnosed Alzheimer's disease identifies new risk loci and implicates Aβ, tau, immunity and lipid processing. PMID:30820047
A novel approach to modelling transcriptional heterogeneity identifies the oncogene candidate CBX2 in invasive breast carcinoma. PMID:30820027
FAIRness and Usability for Open-access Omics Data Systems. PMID:30815061
Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains. PMID:30814998
Transcriptional Dynamics of Grain Development in Barley (Hordeum vulgare L.). PMID:30813307
Comprehensive characterization of the mutational landscape in multiple myeloma cell lines reveals potential drivers and pathways associated with tumor progression and drug resistance. PMID:30809292
Comparative Study of Immune Reaction Against Bacterial Infection From Transcriptome Analysis. PMID:30804945
New Insights for RANKL as a Proinflammatory Modulator in Modeled Inflammatory Arthritis. PMID:30804932
Comparative analysis of the transcriptome of the Amazonian fish species Colossoma macropomum (tambaqui) and hybrid tambacu by next generation sequencing. PMID:30802266
Predicted secreted protein analysis reveals synaptogenic function of Clstn3 during WAT browning and BAT activation in mice. PMID:30796355
Comparative Analysis of Brain and Fat Body Gene Splicing Patterns in the Honey Bee, Apis mellifera. PMID:30792192
Identification of Potential Key Genes and Pathways in Early-Onset Colorectal Cancer Through Bioinformatics Analysis. PMID:30786729
Genome-wide miRNA profiling reinforces the importance of miR-9 in human papillomavirus associated oral and oropharyngeal head and neck cancer. PMID:30783190
Shift in Bacterial Community Structure Drives Different Atrazine-Degrading Efficiencies. PMID:30761118
Disease Pathway Cut for Multi-Target drugs. PMID:30760209
The identification of gene signature and critical pathway associated with childhood-onset type 2 diabetes. PMID:30755828
Data mining for mutation-specific targets in acute myeloid leukemia. PMID:30728456
Machine Learning of Stem Cell Identities From Single-Cell Expression Data via Regulatory Network Archetypes. PMID:30723489
Genome sequence of the barred knifejaw Oplegnathus fasciatus (Temminck & Schlegel, 1844): the first chromosome-level draft genome in the family Oplegnathidae. PMID:30715332
RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. PMID:30707687
Megaphages infect Prevotella and variants are widespread in gut microbiomes. PMID:30692672
Hydrogen-based metabolism as an ancestral trait in lineages sibling to the Cyanobacteria. PMID:30692531
A selective genome-guided method for environmental Burkholderia isolation. PMID:30680473
Integrative analysis of gene expression profiles reveals distinct molecular characteristics in oral tongue squamous cell carcinoma. PMID:30675303
Unveiling Active Constituents and Potential Targets Related to the Hematinic Effect of Steamed Panax notoginseng Using Network Pharmacology Coupled With Multivariate Data Analyses. PMID:30670967
Circ-ZNF609 regulates G1-S progression in rhabdomyosarcoma. PMID:30670781
Mechanistic Target of Rapamycin Complex 1 Promotes the Expression of Genes Encoding Electron Transport Chain Proteins and Stimulates Oxidative Phosphorylation in Primary Human Trophoblast Cells by Regulating Mitochondrial Biogenesis. PMID:30670706
Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes. PMID:30670614
De Novo Sequencing and Hybrid Assembly of the Biofuel Crop Jatropha curcas L.: Identification of Quantitative Trait Loci for Geminivirus Resistance. PMID:30669588
GC-MS Metabolomics Reveals Distinct Profiles of Low- and High-Grade Bladder Cancer Cultured Cells. PMID:30669322
Contrasting Patterns of Rapid Molecular Evolution within the p53 Network across Mammal and Sauropsid Lineages. PMID:30668691
Memory CD4+ T cells are generated in the human fetal intestine. PMID:30664737
The Genetic Structures of an Extensively Drug Resistant (XDR) Klebsiella pneumoniae and Its Plasmids. PMID:30662878
Comparative analysis reveals the Genomic Islands in Pasteurella multocida population genetics: on Symbiosis and adaptability. PMID:30658579
Multi-omics integration reveals molecular networks and regulators of psoriasis. PMID:30642337
Analysis of the complete genome sequence of a marine-derived strain Streptomyces sp. S063 CGMCC 14582 reveals its biosynthetic potential to produce novel anti-complement agents and peptides. PMID:30627488
Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. PMID:30622520
The Change of Teleost Skin Commensal Microbiota Is Associated With Skin Mucosal Transcriptomic Responses During Parasitic Infection by Ichthyophthirius multifillis. PMID:30619329
Palbociclib and Fulvestrant Act in Synergy to Modulate Central Carbon Metabolism in Breast Cancer Cells. PMID:30609717
Optimizing gene set annotations combining GO structure and gene expression data. PMID:30598093
Analysis of Dendrobium huoshanense transcriptome unveils putative genes associated with active ingredients synthesis. PMID:30594136
Gut colonization by a novel Clostridium species is associated with the onset of epizootic rabbit enteropathy. PMID:30572930
Plasma miR-21, miR-155, miR-10b, and Let-7a as the potential biomarkers for the monitoring of breast cancer patients. PMID:30568292
An integrative approach for building personalized gene regulatory networks for precision medicine. PMID:30567569
A Cellular Anatomy of the Normal Adult Human Prostate and Prostatic Urethra. PMID:30566875
Up-Regulation of hsa-miR-210 Promotes Venous Metastasis and Predicts Poor Prognosis in Hepatocellular Carcinoma. PMID:30560088
Transcriptome Analysis of Phycocyanin-Mediated Inhibitory Functions on Non-Small Cell Lung Cancer A549 Cell Growth. PMID:30558318
Proteome Map of Pea (Pisum sativum L.) Embryos Containing Different Amounts of Residual Chlorophylls. PMID:30558315
Transcriptional Approach for Decoding the Mechanism of rpoC Compensatory Mutations for the Fitness Cost in Rifampicin-Resistant Mycobacterium tuberculosis. PMID:30555440
Identifying the key genes and microRNAs in colorectal cancer liver metastasis by bioinformatics analysis and in vitro experiments. PMID:30542696
Effects of short-term endurance exercise on gut microbiota in elderly men. PMID:30536648
Comparative Analysis of Oomycete Genome Evolution Using the Oomycete Gene Order Browser (OGOB). PMID:30535146
Artificial Activation of Escherichia coli mazEF and hipBA Toxin-Antitoxin Systems by Antisense Peptide Nucleic Acids as an Antibacterial Strategy. PMID:30534121
A longitudinal feature selection method identifies relevant genes to distinguish complicated injury and uncomplicated injury over time. PMID:30526581
PaDuA: A Python Library for High-Throughput (Phospho)proteomics Data Analysis. PMID:30525654
Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity. PMID:30518766
Pathways and Network Based Analysis of Candidate Genes to Reveal Cross-Talk and Specificity in the Sorghum (Sorghum bicolor (L.) Moench) Responses to Drought and It's Co-occurring Stresses. PMID:30515190
Genome-wide identification of lncRNAs and mRNAs differentially expressed in non-functioning pituitary adenoma and construction of an lncRNA-mRNA co-expression network. PMID:30504132
Genome and Transcriptome Sequencing of the Astaxanthin-Producing Green Microalga, Haematococcus pluvialis. PMID:30496415
Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma. PMID:30486822
Microarray analysis of the molecular mechanisms associated with age and body mass index in human meniscal injury. PMID:30483788
Chi-miR-3031 regulates beta-casein via the PI3K/AKT-mTOR signaling pathway in goat mammary epithelial cells (GMECs). PMID:30482199
Whole-Genome Sequencing of Chinese Yellow Catfish Provides a Valuable Genetic Resource for High-Throughput Identification of Toxin Genes. PMID:30477130
CMTCN: a web tool for investigating cancer-specific microRNA and transcription factor co-regulatory networks. PMID:30473937
CCNA2 acts as a novel biomarker in regulating the growth and apoptosis of colorectal cancer. PMID:30464611
Drug repositioning using drug-disease vectors based on an integrated network. PMID:30463505
Elevation in Cell Cycle and Protein Metabolism Gene Transcription in Inactive Colonic Tissue From Icelandic Patients With Ulcerative Colitis. PMID:30452647
Integrated PTR-ToF-MS, GWAS and biological pathway analyses reveal the contribution of cow's genome to cheese volatilome. PMID:30451907
Single-molecule long-read sequencing facilitates shrimp transcriptome research. PMID:30446694
Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism. PMID:30445460
Selective colonization ability of human fecal microbes in different mouse gut environments. PMID:30442907
Dynamics of the Phanerochaete carnosa transcriptome during growth on aspen and spruce. PMID:30424733
PSMD12 haploinsufficiency in a neurodevelopmental disorder with autistic features. PMID:30421579
Gene prioritization, communality analysis, networking and metabolic integrated pathway to better understand breast cancer pathogenesis. PMID:30420728
SynerClust: a highly scalable, synteny-aware orthologue clustering tool. PMID:30418868
Machine Learning Reveals Missing Edges and Putative Interaction Mechanisms in Microbial Ecosystem Networks. PMID:30417106
A Mobile-Based Diet Monitoring System for Obesity Management. PMID:30416865
Screening of key candidate genes and pathways for osteocytes involved in the differential response to different types of mechanical stimulation using a bioinformatics analysis. PMID:30413886
Study of the Treatment Effects of Compound Tufuling Granules in Hyperuricemic Rats Using Serum Metabolomics. PMID:30410553
Vitamin D and its receptor polymorphisms: New possible prognostic biomarkers in leukemias. PMID:30405894
Identification of Core Biomarkers Associated with Outcome in Glioma: Evidence from Bioinformatics Analysis. PMID:30405856
Correlating enzyme annotations with a large set of microbial growth temperatures reveals metabolic adaptations to growth at diverse temperatures. PMID:30400856
Comparative transcriptomics identifies genes differentially expressed in the intestine of a new fast-growing strain of common carp with higher unsaturated fatty acid content in muscle. PMID:30395585
A Systems-Level Analysis of Mechanisms of Platycodon grandiflorum Based on A Network Pharmacological Approach. PMID:30388815
Network pharmacology-based strategy to investigate pharmacological mechanisms of Zuojinwan for treatment of gastritis. PMID:30382864
Application of Proteomics Technologies in Oil Palm Research. PMID:30367348
Genomic and Transcriptomic Basis of Hanseniaspora vineae's Impact on Flavor Diversity and Wine Quality. PMID:30366992
Downregulation of miR-145-5p in cancer cells and their derived exosomes may contribute to the development of ovarian cancer by targeting CT. PMID:30365097
Cross-cancer Prediction: A Novel Machine Learning Approach to Discover Molecular Targets for Development of Treatments for Multiple Cancers. PMID:30364884
Root Microbiota in Primary and Secondary Apical Periodontitis. PMID:30356779
Temporal development of the gut microbiome in early childhood from the TEDDY study. PMID:30356187
Genomic comparison of Trypanosoma conorhini and Trypanosoma rangeli to Trypanosoma cruzi strains of high and low virulence. PMID:30355302
The chemodiversity of paddy soil dissolved organic matter correlates with microbial community at continental scales. PMID:30340631
A novel pathway analysis approach based on the unexplained disregulation of genes. PMID:30337764
Programmed DNA destruction by miniature CRISPR-Cas14 enzymes. PMID:30337455
Distinct co-expression networks using multi-omic data reveal novel interventional targets in HPV-positive and negative head-and-neck squamous cell cancer. PMID:30323202
EWASdb: epigenome-wide association study database. PMID:30321400
Mining the potential therapeutic targets for coronary artery disease by bioinformatics analysis. PMID:30320387
Systems vaccinology and big data in the vaccine development chain. PMID:30317555
p53 modeling as a route to mesothelioma patients stratification and novel therapeutic identification. PMID:30316293
A miRNA Combination as Promising Biomarker for Hepatocellular Carcinoma Diagnosis: A Study Based on Bioinformatics Analysis. PMID:30310500
High-resolution plasma metabolomics analysis to detect Mycobacterium tuberculosis-associated metabolites that distinguish active pulmonary tuberculosis in humans. PMID:30308073
Genome-wide association study identifies glutamate ionotropic receptor GRIA4 as a risk gene for comorbid nicotine dependence and major depression. PMID:30287806
Mangrove Sediment Microbiome: Adaptive Microbial Assemblages and Their Routed Biogeochemical Processes in Yunxiao Mangrove National Nature Reserve, China. PMID:30284602
Genome-wide profiling of histone H3K27 acetylation featured fatty acid signalling in pancreatic beta cells in diet-induced obesity in mice. PMID:30284014
De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. PMID:30271965
To select relevant features for longitudinal gene expression data by extending a pathway analysis method. PMID:30271585
Genomic islands of divergence in the Yellow Tang and the Brushtail Tang Surgeonfishes. PMID:30271536
Identification by Tn-seq of Dickeya dadantii genes required for survival in chicory plants. PMID:30267562
The identification of induction chemo-sensitivity genes of laryngeal squamous cell carcinoma and their clinical utilization. PMID:30267217
Cooperation of loss of NKX3.1 and inflammation in prostate cancer initiation. PMID:30266798
Chromosomal-level assembly of yellow catfish genome using third-generation DNA sequencing and Hi-C analysis. PMID:30256939
Identification of key pathways and genes in lung carcinogenesis. PMID:30250533
Computer-aided identification of protein targets of four polyphenols in Alzheimer's disease (AD) and validation in a mouse AD model. PMID:30249814
PGD: Pineapple Genomics Database. PMID:30245835
A reverse metabolic approach to weaning: in silico identification of immune-beneficial infant gut bacteria, mining their metabolism for prebiotic feeds and sourcing these feeds in the natural product space. PMID:30241567
Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci. PMID:30227868
Suppression of GPR56 expression by pyrrole-imidazole polyamide represents a novel therapeutic drug for AML with high EVI1 expression. PMID:30214063
Gene co-expression network analysis identifies the hub genes associated with immune functions for nocturnal hemodialysis in patients with end-stage renal disease. PMID:30212930
A draft genome assembly of the Chinese sillago (Sillago sinica), the first reference genome for Sillaginidae fishes. PMID:30202912
Mitochondrial ubiquinone-mediated longevity is marked by reduced cytoplasmic mRNA translation. PMID:30198021
Resistance training in young men induces muscle transcriptome-wide changes associated with muscle structure and metabolism refining the response to exercise-induced stress. PMID:30196447
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
Identification of key pathways and genes in response to trastuzumab treatment in breast cancer using bioinformatics analysis. PMID:30181805
A network pharmacology approach to explore the mechanisms of Erxian decoction in polycystic ovary syndrome. PMID:30181771
The protective effect of Er-Xian decoction against myocardial injury in menopausal rat model. PMID:30176849
The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli. PMID:30158905
Comprehensive innate immune profiling of chikungunya virus infection in pediatric cases. PMID:30150281
Identification of key genes and pathways using bioinformatics analysis in septic shock children. PMID:30147344
Epigenetic regulation of the circadian gene Per1 contributes to age-related changes in hippocampal memory. PMID:30127461
Functional interplay between c-Myc and Max in B lymphocyte differentiation. PMID:30126925
Bioinformatics Analysis of Transcriptomic Data Reveals Refined Functional Networks for the Self-Renewal of Mouse Spermatogonial Stem Cells. PMID:30123288
Review of Drug Repositioning Approaches and Resources. PMID:30123072
Genetic dissection of bull fertility in US Jersey dairy cattle. PMID:30109710
Identification of susceptibility pathways for the role of chromosome 15q25.1 in modifying lung cancer risk. PMID:30104567
CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type. PMID:30102368
Genome Variation in the Model Halophilic Bacterium Salinibacter ruber. PMID:30072959
Identification and expression analysis of a microRNA cluster derived from pre-ribosomal RNA in Papaver somniferum L. and Papaver bracteatum L. PMID:30067748
Inflammation and Immunity Pathways Regulate Genetic Susceptibility to Diabetic Nephropathy. PMID:30065034
Systems Pharmacological Approach to Investigate the Mechanism of Acori Tatarinowii Rhizoma for Alzheimer's Disease. PMID:30050590
A Genome-Scale Metabolic Reconstruction of Phytophthora infestans With the Integration of Transcriptional Data Reveals the Key Metabolic Patterns Involved in the Interaction of Its Host. PMID:30042788
Identification and Characterization of Long Noncoding RNAs in Ovine Skeletal Muscle. PMID:30041440
Lateral Gene Transfer Between Protozoa-Related Giant Viruses of Family Mimiviridae and Chlamydiae. PMID:30038484
Genome-Scale Metabolic Model of Actinosynnema pretiosum ATCC 31280 and Its Application for Ansamitocin P-3 Production Improvement. PMID:30036981
Candidate genes and microRNAs for glioma pathogenesis and prognosis based on gene expression profiles. PMID:30015885
RabGTD: a comprehensive database of rabbit genome and transcriptome. PMID:30010730
The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut. PMID:30008292
Evaluation of dairy processing wastewater biotreatment in an IASBR system: Aeration rate impacts on performance and microbial ecology. PMID:29992097
Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges. PMID:29989102
The prognostic value of differentially expressed CYP3A subfamily members for hepatocellular carcinoma. PMID:29983591
Genome Mining of the Marine Actinomycete Streptomyces sp. DUT11 and Discovery of Tunicamycins as Anti-complement Agents. PMID:29973921
Stable isotope informed genome-resolved metagenomics reveals that Saccharibacteria utilize microbially-processed plant-derived carbon. PMID:29970182
Clostridium difficile Alters the Structure and Metabolism of Distinct Cecal Microbiomes during Initial Infection To Promote Sustained Colonization. PMID:29950381
Comparative Evaluation of MS-based Metabolomics Software and Its Application to Preclinical Alzheimer's Disease. PMID:29915347
Computational study on a puzzle in the biosynthetic pathway of anthocyanin: Why is an enzymatic oxidation/ reduction process required for a simple tautomerization? PMID:29897974
Gene datasets associated with mouse cleft palate. PMID:29896534
The Presence or Absence of Intestinal Microbiota Affects Lipid Deposition and Related Genes Expression in Zebrafish (Danio rerio). PMID:29896183
Transcriptome analysis of the threatened snail Ellobium chinense reveals candidate genes for adaptation and identifies SSRs for conservation genetics. PMID:29892840
Changing Trends in Computational Drug Repositioning. PMID:29874824
Molecular and clinical characterization of IDH associated immune signature in lower-grade gliomas. PMID:29872572
Spatial transcriptomic survey of human embryonic cerebral cortex by single-cell RNA-seq analysis. PMID:29867213
Comparative transcriptomics reveals shared gene expression changes during independent evolutionary origins of stem and hypocotyl/root tubers in Brassica (Brassicaceae). PMID:29856865
Comparative transcriptome analysis of silkworm, Bombyx mori colleterial gland suggests their functional role in mucous secretion. PMID:29852007
Genes associated with inflammation and the cell cycle may serve as biomarkers for the diagnosis and prognosis of acute myocardial infarction in a Chinese population. PMID:29845217
Comparative expression analysis identifies the respiratory transition-related miRNAs and their target genes in tissues of metamorphosing Chinese giant salamander (Andrias davidianus). PMID:29843595
Identification of key genes and pathways in meningioma by bioinformatics analysis. PMID:29805558
Sorting Five Human Tumor Types Reveals Specific Biomarkers and Background Classification Genes. PMID:29802335
Beyond degree and betweenness centrality: Alternative topological measures to predict viral targets. PMID:29795705
Traceability, reproducibility and wiki-exploration for "à-la-carte" reconstructions of genome-scale metabolic models. PMID:29791443
Isolation and characterization of Bacillus sp. GFP-2, a novel Bacillus strain with antimicrobial activities, from Whitespotted bamboo shark intestine. PMID:29785529
GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma. PMID:29760045
Potential molecular mechanisms of overgrazing-induced dwarfism in sheepgrass (Leymus chinensis) analyzed using proteomic data. PMID:29739327
Streamlined Tandem Mass Tag (SL-TMT) Protocol: An Efficient Strategy for Quantitative (Phospho)proteome Profiling Using Tandem Mass Tag-Synchronous Precursor Selection-MS3. PMID:29734811
Genetic rearrangements, hotspot mutations, and microRNA expression in the progression of metastatic adenoid cystic carcinoma of the salivary gland. PMID:29731974
Data Mining Mycobacterium tuberculosis Pathogenic Gene Transcription Factors and Their Regulatory Network Nodes. PMID:29725597
A Strategy for Discovery of Endocrine Interactions with Application to Whole-Body Metabolism. PMID:29719227
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis. PMID:29706661
Molecular mechanisms of an antimicrobial peptide piscidin (Lc-pis) in a parasitic protozoan, Cryptocaryon irritans. PMID:29703140
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
Integrated bioinformatics analysis reveals key candidate genes and pathways in breast cancer. PMID:29693125
GAN: a platform of genomics and genetics analysis and application in Nicotiana. PMID:29688356
A window into extreme longevity; the circulating metabolomic signature of the naked mole-rat, a mammal that shows negligible senescence. PMID:29679203
Propagating annotations of molecular networks using in silico fragmentation. PMID:29668671
Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis. PMID:29666288
Draft genome of the protandrous Chinese black porgy, Acanthopagrus schlegelii. PMID:29659813
Effects of nicotine on the metabolism and gene expression profile of Sprague‑Dawley rat primary osteoblasts. PMID:29658611
A genetically and functionally diverse group of non-diazotrophic Bradyrhizobium spp. colonizes the root endophytic compartment of Arabidopsis thaliana. PMID:29642886
A Retrospective Review of Microbiological Methods Applied in Studies Following the Deepwater Horizon Oil Spill. PMID:29628913
Draft genome of the Peruvian scallop Argopecten purpuratus. PMID:29617765
Radiation-Induced Gene Expression Changes in High and Low Grade Breast Cancer Cell Types. PMID:29617354
Analyzing AbrB-Knockout Effects through Genome and Transcriptome Sequencing of Bacillus licheniformis DW2. PMID:29599755
Yeast culture dietary supplementation modulates gut microbiota, growth and biochemical parameters of grass carp. PMID:29578305
Co-administration of resveratrol with doxorubicin in young mice attenuates detrimental late-occurring cardiovascular changes. PMID:29566148
Transcriptome analysis reveals in vitro-cultured regeneration bulbs as a promising source for targeted Fritillaria cirrhosa steroidal alkaloid biosynthesis. PMID:29564202
Glucose Levels Alter the Mga Virulence Regulon in the Group A Streptococcus. PMID:29563558
Genomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39. PMID:29556852
Species translatable blood gene signature as a marker of exposure to smoking: computational approaches of the top ranked teams in the sbv IMPROVER Systems Toxicology challenge. PMID:29556587
Analysis of microRNA and Gene Expression Profiles in Alzheimer's Disease: A Meta-Analysis Approach. PMID:29555910
BIOPYDB: A Dynamic Human Cell Specific Biochemical Pathway Database with Advanced Computational Analyses Platform. PMID:29547394
A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex. PMID:29539641
Identification of potential genes and miRNAs associated with sepsis based on microarray analysis. PMID:29512785
STRENDA DB: enabling the validation and sharing of enzyme kinetics data. PMID:29498804
From gene networks to drugs: systems pharmacology approaches for AUD. PMID:29497781
Identification of transcripts potentially involved in neural tube closure using RNA sequencing. PMID:29488319
Intravenous morphine self-administration alters accumbal microRNA profiles in the mouse brain. PMID:29451210
Identification of a single nucleotide polymorphism indicative of high risk in acute myocardial infarction. PMID:29434065
NAD+ supplementation normalizes key Alzheimer's features and DNA damage responses in a new AD mouse model with introduced DNA repair deficiency. PMID:29432159
Differences in MWCNT- and SWCNT-induced DNA methylation alterations in association with the nuclear deposition. PMID:29426343
Diversity and metabolic potential of the microbiota associated with a soil arthropod. PMID:29410494
Interaction of genotype and diet on small intestine microbiota of Japanese quail fed a cholesterol enriched diet. PMID:29402949
Identification of microRNAs as potential markers of ovarian toxicity. PMID:29377183
Parallel derivation of isogenic human primed and naive induced pluripotent stem cells. PMID:29367672
Skin transcriptome reveals the dynamic changes in the Wnt pathway during integument morphogenesis of chick embryos. PMID:29351308
Molecular Network-Based Identification of Competing Endogenous RNAs in Thyroid Carcinoma. PMID:29351231
Expansion of cytochrome P450 and cathepsin genes in the generalist herbivore brown marmorated stink bug. PMID:29347977
Deeply-sourced formate fuels sulfate reducers but not methanogens at Lost City hydrothermal field. PMID:29335466
Differential requirements of androgen receptor in luminal progenitors during prostate regeneration and tumor initiation. PMID:29334357
Integration of GWAS, pathway and network analyses reveals novel mechanistic insights into the synthesis of milk proteins in dairy cows. PMID:29330500
Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel. PMID:29330494
Pathway design using de novo steps through uncharted biochemical spaces. PMID:29330441
Listeria monocytogenes Induces a Virulence-Dependent microRNA Signature That Regulates the Immune Response in Galleria mellonella. PMID:29312175
Metabolic capability and in situ activity of microorganisms in an oil reservoir. PMID:29304850
Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. PMID:29298729
Mutation status coupled with RNA-sequencing data can efficiently identify important non-significantly mutated genes serving as diagnostic biomarkers of endometrial cancer. PMID:29297280
Integrated analysis of transcriptomic and metabolomic data reveals critical metabolic pathways involved in rotenoid biosynthesis in the medicinal plant Mirabilis himalaica. PMID:29285563
Metabolomics and Precision Medicine in Trauma: The State of the Field. PMID:29280924
Comparative transcriptome analysis of Glyphodes pyloalis Walker (Lepidoptera: Pyralidae) reveals novel insights into heat stress tolerance in insects. PMID:29258441
The transcriptome of Mycobacterium tuberculosis in a lipid-rich dormancy model through RNAseq analysis. PMID:29247215
SNP co-association and network analyses identify E2F3, KDM5A and BACH2 as key regulators of the bovine milk fatty acid profile. PMID:29230020
Identification of differentially expressed genes, lncRNAs and miRNAs which are associated with tumor malignant phenotypes in hepatoblastoma patients. PMID:29228631
Loci and pathways associated with uterine capacity for pregnancy and fertility in beef cattle. PMID:29228019
Functional network community detection can disaggregate and filter multiple underlying pathways in enrichment analyses. PMID:29218878
Ultra-low input transcriptomics reveal the spore functional content and phylogenetic affiliations of poorly studied arbuscular mycorrhizal fungi. PMID:29211832
De Novo RNA Sequencing and Expression Analysis of Aconitum carmichaelii to Analyze Key Genes Involved in the Biosynthesis of Diterpene Alkaloids. PMID:29206203
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE). PMID:29186820
Computational systems biology approaches for Parkinson's disease. PMID:29185073
Uncovering the relationship and mechanisms of Tartary buckwheat (Fagopyrum tataricum) and Type II diabetes, hypertension, and hyperlipidemia using a network pharmacology approach. PMID:29177114
Driver pattern identification over the gene co-expression of drug response in ovarian cancer by integrating high throughput genomics data. PMID:29170526
A 16-gene signature predicting prognosis of patients with oral tongue squamous cell carcinoma. PMID:29158988
A transcriptomic insight into the impacts of mast cells in lung, breast, and colon cancers. PMID:29147625
Genome-scale modeling and transcriptome analysis of Leuconostoc mesenteroides unravel the redox governed metabolic states in obligate heterofermentative lactic acid bacteria. PMID:29147021
Using an NMR metabolomics approach to investigate the pathogenicity of amyloid-beta and alpha-synuclein. PMID:29142509
Investigation of candidate genes and mechanisms underlying postmenopausal osteoporosis using bioinformatics analysis. PMID:29138843
PAGER 2.0: an update to the pathway, annotated-list and gene-signature electronic repository for Human Network Biology. PMID:29126216
Transcriptomics, metabolomics and histology indicate that high-carbohydrate diet negatively affects the liver health of blunt snout bream (Megalobrama amblycephala). PMID:29121861
Identification of potential therapeutic targets for gliomas by bioinformatics analysis. PMID:29113156
Mammalian γ2 AMPK regulates intrinsic heart rate. PMID:29097735
Quantitative proteomic Analysis Reveals up-regulation of caveolin-1 in FOXP3-overexpressed human gastric cancer cells. PMID:29089565
Whole exome sequencing in 342 congenital cardiac left sided lesion cases reveals extensive genetic heterogeneity and complex inheritance patterns. PMID:29089047
Activation of Wnt signaling reduces high-glucose mediated damages on skin fibroblast cells. PMID:29085587
PLATO software provides analytic framework for investigating complexity beyond genome-wide association studies. PMID:29079728
Identification of miR-24 and miR-137 as novel candidate multiple sclerosis miRNA biomarkers using multi-staged data analysis protocol. PMID:29071282
A systematic study of the whole genome sequence of Amycolatopsis methanolica strain 239T provides an insight into its physiological and taxonomic properties which correlate with its position in the genus. PMID:29062941
Integrated analysis of mRNA and viral miRNAs in the kidney of Carassius auratus gibelio response to cyprinid herpesvirus 2. PMID:29062054
Diatom flagellar genes and their expression during sexual reproduction in Leptocylindrus danicus. PMID:29061117
Identification of core genes and outcome in gastric cancer using bioinformatics analysis. PMID:29050278
The genome draft of coconut (Cocos nucifera). PMID:29048487
Phylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal. PMID:29026656
RNA-Seq Analysis of Differentiated Keratinocytes Reveals a Massive Response to Late Events during Human Papillomavirus 16 Infection, Including Loss of Epithelial Barrier Function. PMID:29021401
The draft genome assembly of Rhododendron delavayi Franch. var. delavayi. PMID:29020749
Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus). PMID:28980357
Drug repurposing in idiopathic pulmonary fibrosis filtered by a bioinformatics-derived composite score. PMID:28974751
BPTF inhibits NK cell activity and the abundance of natural cytotoxicity receptor co-ligands. PMID:28969075
Identification of long non-coding RNA signature for paclitaxel-resistant patients with advanced ovarian cancer. PMID:28969062
Pathway-based discovery of genetic interactions in breast cancer. PMID:28957314
iTRAQ protein profile analysis of developmental dynamics in soybean [Glycine max (L.) Merr.] leaves. PMID:28953898
Denitrification potential of the eastern oyster microbiome using a 16S rRNA gene based metabolic inference approach. PMID:28934286
De novo transcriptome of the cosmopolitan dinoflagellate Amphidinium carterae to identify enzymes with biotechnological potential. PMID:28916825
Genome sequence of the ectophytic fungus Ramichloridium luteum reveals unique evolutionary adaptations to plant surface niche. PMID:28915794
The Apostasia genome and the evolution of orchids. PMID:28902843
Genome-wide DNA methylation patterns in coronary heart disease. PMID:28884387
RNA Sequencing and Co-expressed Long Non-coding RNA in Modern and Wild Wheats. PMID:28878329
Effects of dietary sodium on metabolites: the Dietary Approaches to Stop Hypertension (DASH)-Sodium Feeding Study. PMID:28855223
Mitochondrial Genome Assemblies of Elysia timida and Elysia cornigera and the Response of Mitochondrion-Associated Metabolism during Starvation. PMID:28854599
A computational method for the identification of candidate drugs for non-small cell lung cancer. PMID:28820893
Discovering Condition-Specific Gene Co-Expression Patterns Using Gaussian Mixture Models: A Cancer Case Study. PMID:28819158
Draft de novo transcriptome assembly and proteome characterization of the electric lobe of Tetronarce californica: a molecular tool for the study of cholinergic neurotransmission in the electric organ. PMID:28806931
Nitrate Sensing and Metabolism Inhibit Biofilm Formation in the Opportunistic Pathogen Burkholderia pseudomallei by Reducing the Intracellular Concentration of c-di-GMP. PMID:28790983
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
Compartmentalized metabolic network reconstruction of microbial communities to determine the effect of agricultural intervention on soils. PMID:28767679
Large-scale identification of Gossypium hirsutum genes associated with Verticillium dahliae by comparative transcriptomic and reverse genetics analysis. PMID:28767675
Clostridium difficile Colonizes Alternative Nutrient Niches during Infection across Distinct Murine Gut Microbiomes. PMID:28761936
Ras/MAPK Modifier Loci Revealed by eQTL in Caenorhabditis elegans. PMID:28751501
lumpGEM: Systematic generation of subnetworks and elementally balanced lumped reactions for the biosynthesis of target metabolites. PMID:28727789
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium incisum and Notopterygium franchetii, Two High-Alpine Herbal Species Endemic to China. PMID:28696392
Proteomics-based identification of differentially abundant proteins reveals adaptation mechanisms of Xanthomonas citri subsp. citri during Citrus sinensis infection. PMID:28693412
Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. PMID:28672765
Characterization of the emerging zoonotic pathogen Arcobacter thereius by whole genome sequencing and comparative genomics. PMID:28671965
Contribution of trans regulatory eQTL to cryptic genetic variation in C. elegans. PMID:28662696
Simulation of Deepwater Horizon oil plume reveals substrate specialization within a complex community of hydrocarbon degraders. PMID:28652349
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression. PMID:28606108
Ell3 stimulates 5-FU resistance in a breast cancer cell line. PMID:28588704
Methane Dynamics in a Tropical Serpentinizing Environment: The Santa Elena Ophiolite, Costa Rica. PMID:28588569
Characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling by integrative analysis of transcriptomic and proteomic data. PMID:28588230
Loss of transcriptional activation of the potassium channel Kir5.1 by HNF1β drives autosomal dominant tubulointerstitial kidney disease. PMID:28577853
Complete Genome Sequence of Veillonella atypica OK5, the First Transformable Strain in the Species. PMID:28572307
The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding. PMID:28541388
Insights from the complete genome sequence of Clostridium tyrobutyricum provide a platform for biotechnological and industrial applications. PMID:28536840
An integrative analysis of tissue-specific transcriptomic and metabolomic responses to short-term dietary methionine restriction in mice. PMID:28520765
Establishment of a Strong Link Between Smoking and Cancer Pathogenesis through DNA Methylation Analysis. PMID:28500316
Identification and Differential Expression of Biomineralization Genes in the Mantle of Pearl Oyster Pinctada fucata. PMID:28493049
CSTEA: a webserver for the Cell State Transition Expression Atlas. PMID:28486666
Identifying biologically relevant putative mechanisms in a given phenotype comparison. PMID:28486531
Pathview Web: user friendly pathway visualization and data integration. PMID:28482075
WebGIVI: a web-based gene enrichment analysis and visualization tool. PMID:28472919
Comparative Genomics and Transcriptional Analysis of Flavobacterium columnare Strain ATCC 49512. PMID:28469601
Lipidomics and RNA-Seq Study of Lipid Regulation in Aphis gossypii parasitized by Lysiphlebia japonica. PMID:28465512
A comprehensive analysis of cancer-driving mutations and genes in kidney cancer. PMID:28454375
Polyphenolic extract of InsP 5-ptase expressing tomato plants reduce the proliferation of MCF-7 breast cancer cells. PMID:28448505
Transcriptome analysis of creeping bentgrass exposed to drought stress and polyamine treatment. PMID:28445484
Delineating the Common Biological Pathways Perturbed by ASD's Genetic Etiology: Lessons from Network-Based Studies. PMID:28420080
Genetic variant of miR-4293 rs12220909 is associated with susceptibility to non-small cell lung cancer in a Chinese Han population. PMID:28410417
Genomics and Comparative Genomic Analyses Provide Insight into the Taxonomy and Pathogenic Potential of Novel Emmonsia Pathogens. PMID:28409126
The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PMID:28394946
Three serum metabolite signatures for diagnosing low-grade and high-grade bladder cancer. PMID:28382976
Integrated omics analyses of retrograde signaling mutant delineate interrelated stress-response strata. PMID:28370892
Bioinformatic identification of candidate genes induced by trichostatin A in BGC-823 gastric cancer cells. PMID:28356958
Bacterial virulence phenotypes of Escherichia coli and host susceptibility determine risk for urinary tract infections. PMID:28330863
De novo transcriptome sequencing in Monsonia burkeana revealed putative genes for key metabolic pathways involved in tea quality and medicinal value. PMID:28330322
Whole genome sequencing of Chinese clearhead icefish, Protosalanx hyalocranius. PMID:28327943
Disease Risk Assessment Using a Voronoi-Based Network Analysis of Genes and Variants Scores. PMID:28326099
Joint Estimation of Multiple High-dimensional Precision Matrices. PMID:28316451
Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH. PMID:28298908
Pathway Cross-Talk Analysis in Detecting Significant Pathways in Barrett's Esophagus Patients. PMID:28263955
The Histidine Decarboxylase Gene Cluster of Lactobacillus parabuchneri Was Gained by Horizontal Gene Transfer and Is Mobile within the Species. PMID:28261177
Id2 Collaborates with Id3 To Suppress Invariant NKT and Innate-like Tumors. PMID:28258199
Decreased Tissue COX5B Expression and Mitochondrial Dysfunction during Sepsis-Induced Kidney Injury in Rats. PMID:28246552
A global characterization of the translational and transcriptional programs induced by methionine restriction through ribosome profiling and RNA-seq. PMID:28212626
Transcriptomic meta-analysis reveals up-regulation of gene expression functional in osteoclast differentiation in human septic shock. PMID:28199355
Metabolite profiling of infection-associated metabolic markers of onchocerciasis. PMID:28188804
Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. PMID:28168224
In silico analyses and global transcriptional profiling reveal novel putative targets for Pea3 transcription factor related to its function in neurons. PMID:28158215
Aspirin-Induced Chemoprevention and Response Kinetics Are Enhanced by PIK3CA Mutations in Colorectal Cancer Cells. PMID:28154202
Metagenomic identification of active methanogens and methanotrophs in serpentinite springs of the Voltri Massif, Italy. PMID:28149702
Identification of Submergence-Responsive MicroRNAs and Their Targets Reveals Complex MiRNA-Mediated Regulatory Networks in Lotus (Nelumbo nucifera Gaertn). PMID:28149304
Identification of the Relationship between Oil Body Morphology and Oil Content by Microstructure Comparison Combining with QTL Analysis in Brassica napus. PMID:28111582
Integrating gene set analysis and nonlinear predictive modeling of disease phenotypes using a Bayesian multitask formulation. PMID:28105911
Hydrogel scaffolds promote neural gene expression and structural reorganization in human astrocyte cultures. PMID:28097054
Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability. PMID:28078297
Faba bean drought responsive gene identification and validation. PMID:28053575
Overexpression of AmRosea1 Gene Confers Drought and Salt Tolerance in Rice. PMID:28025485
Host-Microbiome Interaction and Cancer: Potential Application in Precision Medicine. PMID:28018236
Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy. PMID:27997585
The Transcriptional Regulator CpsY Is Important for Innate Immune Evasion in Streptococcus pyogenes. PMID:27993974
Acanthamoeba containing endosymbiotic chlamydia isolated from hospital environments and its potential role in inflammatory exacerbation. PMID:27978822
CanProVar 2.0: An Updated Database of Human Cancer Proteome Variation. PMID:27977206
Genome Sequencing of Sulfolobus sp. A20 from Costa Rica and Comparative Analyses of the Putative Pathways of Carbon, Nitrogen, and Sulfur Metabolism in Various Sulfolobus Strains. PMID:27965637
Analysis of Important Gene Ontology Terms and Biological Pathways Related to Pancreatic Cancer. PMID:27957501
Transcriptomic Changes in Liver of Young Bulls Caused by Diets Low in Mineral and Protein Contents and Supplemented with n-3 Fatty Acids and Conjugated Linoleic Acid. PMID:27930681
Comparative Functional Genomic Analysis of Two Vibrio Phages Reveals Complex Metabolic Interactions with the Host Cell. PMID:27895630
Mitochondrial fat oxidation is essential for lipid-induced inflammation in skeletal muscle in mice. PMID:27892502
Identification of Genes Discriminating Multiple Sclerosis Patients from Controls by Adapting a Pathway Analysis Method. PMID:27846233
Proteogenomic analyses indicate bacterial methylotrophy and archaeal heterotrophy are prevalent below the grass root zone. PMID:27843720
libFLASM: a software library for fixed-length approximate string matching. PMID:27832739
Discovery of the molecular mechanisms of the novel chalcone-based Magnaporthe oryzae inhibitor C1 using transcriptomic profiling and co-expression network analysis. PMID:27818889
The Genome of the Toluene-Degrading Pseudomonas veronii Strain 1YdBTEX2 and Its Differential Gene Expression in Contaminated Sand. PMID:27812150
Impact of neonatal iron deficiency on hippocampal DNA methylation and gene transcription in a porcine biomedical model of cognitive development. PMID:27809765
Microbial community analysis of pH 4 thermal springs in Yellowstone National Park. PMID:27807621
Prediction, Detection, and Validation of Isotope Clusters in Mass Spectrometry Data. PMID:27775610
Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency. PMID:27723758
Transcriptomic characterization of differential gene expression in oral squamous cell carcinoma: a meta-analysis of publicly available microarray data sets. PMID:27704359
The Thiamine Biosynthesis Gene THI1 Promotes Nodule Growth and Seed Maturation. PMID:27702844
VEGF-A/VEGFR2 signaling network in endothelial cells relevant to angiogenesis. PMID:27619687
Comprehensive evaluation of serum microRNAs as biomarkers in multiple sclerosis. PMID:27606352
A Flux Balance of Glucose Metabolism Clarifies the Requirements of the Warburg Effect. PMID:27602736
Reconstruction of the Fatty Acid Biosynthetic Pathway of Exiguobacterium antarcticum B7 Based on Genomic and Bibliomic Data. PMID:27595107
Oncometabolite d-2-hydroxyglutarate impairs α-ketoglutarate dehydrogenase and contractile function in rodent heart. PMID:27582470
DRUG-DRUG INTERACTION PROFILES OF MEDICATION REGIMENS EXTRACTED FROM A DE-IDENTIFIED ELECTRONIC MEDICAL RECORDS SYSTEM. PMID:27570646
A Cell-type-resolved Liver Proteome. PMID:27562671
The physiology and habitat of the last universal common ancestor. PMID:27562259
Genomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments. PMID:27552639
High-quality genome assembly of channel catfish, Ictalurus punctatus. PMID:27549802
Draft genome sequence of subterranean clover, a reference for genus Trifolium. PMID:27545089
STAMS: STRING-assisted module search for genome wide association studies and application to autism. PMID:27542772
MetaboTools: A Comprehensive Toolbox for Analysis of Genome-Scale Metabolic Models. PMID:27536246
Human INO80/YY1 chromatin remodeling complex transcriptionally regulates the BRCA2- and CDKN1A-interacting protein (BCCIP) in cells. PMID:27535137
MALDI imaging reveals NCOA7 as a potential biomarker in oral squamous cell carcinoma arising from oral submucous fibrosis. PMID:27509054
High resolution metabolomics to discriminate compounds in serum of male lung cancer patients in South Korea. PMID:27506545
In-Depth Characterization and Validation of Human Urine Metabolomes Reveal Novel Metabolic Signatures of Lower Urinary Tract Symptoms. PMID:27502322
Comprehensive Analysis of the Transcriptional and Mutational Landscape of Follicular and Papillary Thyroid Cancers. PMID:27494611
A genome-wide IR-induced RAD51 foci RNAi screen identifies CDC73 involved in chromatin remodeling for DNA repair. PMID:27462432
Transcriptomic Analysis of the Endangered Neritid Species Clithon retropictus: De Novo Assembly, Functional Annotation, and Marker Discovery. PMID:27455329
Excessive Reversal of Epidermal Growth Factor Receptor and Ephrin Signaling Following Tracheal Occlusion in Rabbit Model of Congenital Diaphragmatic Hernia. PMID:27452320
Classification of Non-Small Cell Lung Cancer Using Significance Analysis of Microarray-Gene Set Reduction Algorithm. PMID:27446945
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Evolution of the Calcium-Based Intracellular Signaling System. PMID:27358427
Convergent evidence from systematic analysis of GWAS revealed genetic basis of esophageal cancer. PMID:27331408
Critical Role of COI1-Dependent Jasmonate Pathway in AAL toxin induced PCD in Tomato Revealed by Comparative Proteomics. PMID:27324416
Inferring active regulatory networks from gene expression data using a combination of prior knowledge and enrichment analysis. PMID:27295045
Virus-induced gene silencing of the RPC5-like subunit of RNA polymerase III caused pleiotropic effects in Nicotiana benthamiana. PMID:27282827
Comparative genomic and transcriptomic analyses of the Fuzhuan brick tea-fermentation fungus Aspergillus cristatus. PMID:27267057
First Complete Genome Sequence of a Subdivision 6 Acidobacterium Strain. PMID:27231379
Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases. PMID:27200087
Carbon and Sulfur Cycling below the Chemocline in a Meromictic Lake and the Identification of a Novel Taxonomic Lineage in the FCB Superphylum, Candidatus Aegiribacteria. PMID:27199928
SPATIAL: A System-level PAThway Impact AnaLysis approach. PMID:27193997
Practical aspects of NGS-based pathways analysis for personalized cancer science and medicine. PMID:27191992
Effects of ADMA on gene expression and metabolism in serum-starved LoVo cells. PMID:27180883
MetaNetVar: Pipeline for applying network analysis tools for genomic variants analysis. PMID:27158457
An algorithm for designing minimal microbial communities with desired metabolic capacities. PMID:27153571
The omic approach to parasitic trematode research-a review of techniques and developments within the past 5 years. PMID:27126082
De Novo Adult Transcriptomes of Two European Brittle Stars: Spotlight on Opsin-Based Photoreception. PMID:27119739
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Integrative Genomics and Transcriptomics Analysis Reveals Potential Mechanisms for Favorable Prognosis of Patients with HPV-Positive Head and Neck Carcinomas. PMID:27108969
Draft genome sequencing and secretome analysis of fungal phytopathogen Ascochyta rabiei provides insight into the necrotrophic effector repertoire. PMID:27091329
A genetic network that suppresses genome rearrangements in Saccharomyces cerevisiae and contains defects in cancers. PMID:27071721
Metabolic Engineering of Microalgal Based Biofuel Production: Prospects and Challenges. PMID:27065986
Deletion and low expression of NFKBIA are associated with poor prognosis in lower-grade glioma patients. PMID:27052952
iTRAQ-based analysis of developmental dynamics in the soybean leaf proteome reveals pathways associated with leaf photosynthetic rate. PMID:27048574
Transcriptome Analysis of an Insecticide Resistant Housefly Strain: Insights about SNPs and Regulatory Elements in Cytochrome P450 Genes. PMID:27019205
Response and resilience of soil microbial communities inhabiting in edible oil stress/contamination from industrial estates. PMID:27001503
Urinary proteomics and metabolomics studies to monitor bladder health and urological diseases. PMID:27000794
Glutathione biosynthesis is upregulated at the initiation of MYCN-driven neuroblastoma tumorigenesis. PMID:26996379
Metabolomics: beyond biomarkers and towards mechanisms. PMID:26979502
Sequencing and comparative analyses of the genomes of zoysiagrasses. PMID:26975196
Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers. PMID:26972162
Isolation and Complete Genome Sequence of Algibacter alginolytica sp. nov., a Novel Seaweed-Degrading Bacteroidetes Bacterium with Diverse Putative Polysaccharide Utilization Loci. PMID:26969704
Integrated metabolomics and metagenomics analysis of plasma and urine identified microbial metabolites associated with coronary heart disease. PMID:26932197
Metabolic Trade-offs in Yeast are Caused by F1F0-ATP synthase. PMID:26928598
Unravelling potential virulence factor candidates in Xanthomonas citri. subsp. citri by secretome analysis. PMID:26925342
ROMA: Representation and Quantification of Module Activity from Target Expression Data. PMID:26925094
Global Metabolic Profiling of Arabidopsis Polyamine Oxidase 4 (AtPAO4) Loss-of-Function Mutants Exhibiting Delayed Dark-Induced Senescence. PMID:26925084
High frequency of +1 programmed ribosomal frameshifting in Euplotes octocarinatus. PMID:26891713
Genome wide transcriptome profiling reveals differential gene expression in secondary metabolite pathway of Cymbopogon winterianus. PMID:26877149
Identification of potential therapeutic targets for papillary thyroid carcinoma by bioinformatics analysis. PMID:26870166
Complete Genome Sequence of Streptococcus salivarius HSISS4, a Human Commensal Bacterium Highly Prevalent in the Digestive Tract. PMID:26847886
Multi-Omics Approach Identifies Molecular Mechanisms of Plant-Fungus Mycorrhizal Interaction. PMID:26834754
A network based covariance test for detecting multivariate eQTL in saccharomyces cerevisiae. PMID:26818242
A new scheme to discover functional associations and regulatory networks of E3 ubiquitin ligases. PMID:26818115
Gene expression profiling and mechanism study of neural stem cells response to surface chemistry. PMID:26816623
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PMID:26808494
Novel Approaches in Astrocyte Protection: from Experimental Methods to Computational Approaches. PMID:26803310
Genome-Resolved Metagenomic Analysis Reveals Roles for Candidate Phyla and Other Microbial Community Members in Biogeochemical Transformations in Oil Reservoirs. PMID:26787827
The fruRBA Operon Is Necessary for Group A Streptococcal Growth in Fructose and for Resistance to Neutrophil Killing during Growth in Whole Human Blood. PMID:26787724
Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis. PMID:26784944
Extensive Transcriptome Changes Underlying the Flower Color Intensity Variation in Paeonia ostii. PMID:26779235
Assessing methanotrophy and carbon fixation for biofuel production by Methanosarcina acetivorans. PMID:26776497
Early Regulation of Profibrotic Genes in Primary Human Cardiac Myocytes by Trypanosoma cruzi. PMID:26771187
The Dendrobium catenatum Lindl. genome sequence provides insights into polysaccharide synthase, floral development and adaptive evolution. PMID:26754549
Whole Genome Sequencing of Mycobacterium africanum Strains from Mali Provides Insights into the Mechanisms of Geographic Restriction. PMID:26751217
Identification of potential therapeutic targets for lung cancer by bioinformatics analysis. PMID:26739332
The complete genome sequence and analysis of a plasmid-bearing myxobacterial strain Myxococcus fulvus 124B02 (M 206081). PMID:26734118
The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics. PMID:26734060
Cigarette smoking behaviour and blood metabolomics. PMID:26721601
Bidirectional interactions between indomethacin and the murine intestinal microbiota. PMID:26701907
Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium. PMID:26692227
Comparative Proteomic Profiling of Ehrlichia ruminantium Pathogenic Strain and Its High-Passaged Attenuated Strain Reveals Virulence and Attenuation-Associated Proteins. PMID:26691135
Cofunctional Subpathways Were Regulated by Transcription Factor with Common Motif, Common Family, or Common Tissue. PMID:26688819
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792. PMID:26664654
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics. PMID:26656885
Reproducibility of Differential Proteomic Technologies in CPTAC Fractionated Xenografts. PMID:26653538
De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite. PMID:26645667
Privatization of cooperative benefits stabilizes mutualistic cross-feeding interactions in spatially structured environments. PMID:26623546
Gene Expression Reaction Norms Unravel the Molecular and Cellular Processes Underpinning the Plastic Phenotypes of Alternanthera Philoxeroides in Contrasting Hydrological Conditions. PMID:26617628
Comparative Genomic Insights into Ecophysiology of Neutrophilic, Microaerophilic Iron Oxidizing Bacteria. PMID:26617599
Metagenome and Metatranscriptome Revealed a Highly Active and Intensive Sulfur Cycle in an Oil-Immersed Hydrothermal Chimney in Guaymas Basin. PMID:26617579
Metformin suppressed the proliferation of LoVo cells and induced a time-dependent metabolic and transcriptional alteration. PMID:26616174
Comparative Transcriptome Analysis between the Fungal Plant Pathogens Sclerotinia sclerotiorum and S. trifoliorum Using RNA Sequencing. PMID:26615185
Dealing with the Data Deluge: Handling the Multitude Of Chemical Biology Data Sources. PMID:26609498
Advanced Applications of RNA Sequencing and Challenges. PMID:26609224
NDEx, the Network Data Exchange. PMID:26594663
Precision Subtypes of T Cell-Mediated Rejection Identified by Molecular Profiles. PMID:26594210
A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels. PMID:26589719
Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. PMID:26573226
Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples. PMID:26556243
Transcriptomic analysis of cobalt stress in the marine yeast Debaryomyces hansenii. PMID:26546454
Complete genome sequences and analysis of the Fusobacterium nucleatum subspecies animalis 7-1 bacteriophage ɸFunu1 and ɸFunu2. PMID:26545740
Understanding drugs in breast cancer through drug sensitivity screening. PMID:26543746
Pancreatic β cell enhancers regulate rhythmic transcription of genes controlling insulin secretion. PMID:26542580
SynRio: R and Shiny based application platform for cyanobacterial genome analysis. PMID:26527850
Resource base influences genome-wide DNA methylation levels in wild baboons (Papio cynocephalus). PMID:26508127
Draft Genome Sequence of Chlamydia trachomatis Strain 54, Isolated from the Urogenital Tract of a Male in Japan. PMID:26494683
Six-month Calorie Restriction in Overweight Individuals Elicits Transcriptomic Response in Subcutaneous Adipose Tissue That is Distinct From Effects of Energy Deficit. PMID:26486851
Systems Biology for Smart Crops and Agricultural Innovation: Filling the Gaps between Genotype and Phenotype for Complex Traits Linked with Robust Agricultural Productivity and Sustainability. PMID:26484978
WikiPathways: capturing the full diversity of pathway knowledge. PMID:26481357
A novel bi-level meta-analysis approach: applied to biological pathway analysis. PMID:26471455
Estimating cumulative pathway effects on risk for age-related macular degeneration using mixed linear models. PMID:26467978
The bacterial pangenome as a new tool for analysing pathogenic bacteria. PMID:26442149
Precritical State Transition Dynamics in the Attractor Landscape of a Molecular Interaction Network Underlying Colorectal Tumorigenesis. PMID:26439385
Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing. PMID:26431969
Polymorphisms in genes in the androgen pathway and risk of Barrett's esophagus and esophageal adenocarcinoma. PMID:26414697
A catalog of the mouse gut metagenome. PMID:26414350
Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. PMID:26413196
Genome analysis and in vivo virulence of porcine extraintestinal pathogenic Escherichia coli strain PCN033. PMID:26391348
Transcriptomic Heterogeneity in Cancer as a Consequence of Dysregulation of the Gene-Gene Interaction Network. PMID:26376888
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
Metabolomics reveals differences of metal toxicity in cultures of Pseudomonas pseudoalcaligenes KF707 grown on different carbon sources. PMID:26347721
The genetics of human autoimmune disease: A perspective on progress in the field and future directions. PMID:26343334
Negative Regulation of p21Waf1/Cip1 by Human INO80 Chromatin Remodeling Complex Is Implicated in Cell Cycle Phase G2/M Arrest and Abnormal Chromosome Stability. PMID:26340092
Genetic Analysis of Association Between Calcium Signaling and Hippocampal Activation, Memory Performance in the Young and Old, and Risk for Sporadic Alzheimer Disease. PMID:26332608
Predicting Ecological Roles in the Rhizosphere Using Metabolome and Transportome Modeling. PMID:26332409
Novel Application of Junction Trees to the Interpretation of Epigenetic Differences among Lung Cancer Subtypes. PMID:26306226
Which Way In? The RalF Arf-GEF Orchestrates Rickettsia Host Cell Invasion. PMID:26291822
MUCOSAL IMMUNOLOGY. Individual intestinal symbionts induce a distinct population of RORγ⁺ regulatory T cells. PMID:26272906
Genome Sequence of Schizochytrium sp. CCTCC M209059, an Effective Producer of Docosahexaenoic Acid-Rich Lipids. PMID:26251485
Endogenous DUX4 expression in FSHD myotubes is sufficient to cause cell death and disrupts RNA splicing and cell migration pathways. PMID:26246499
Evidence of perturbations of the cytokine network in preterm labor. PMID:26232508
Effects of β-catenin on differentially expressed genes in multiple myeloma. PMID:26223925
Gene regulation by dietary microRNAs. PMID:26222444
Genes Caught In Flagranti: Integrating Renal Transcriptional Profiles With Genotypes and Phenotypes. PMID:26215861
Abraxane, the Nanoparticle Formulation of Paclitaxel Can Induce Drug Resistance by Up-Regulation of P-gp. PMID:26182353
A novel intracellular mutualistic bacterium in the invasive ant Cardiocondyla obscurior. PMID:26172209
Search for common targets of lithium and valproic acid identifies novel epigenetic effects of lithium on the rat leptin receptor gene. PMID:26171981
RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway. PMID:26170170
Digital gene expression analysis of male and female bud transition in Metasequoia reveals high activity of MADS-box transcription factors and hormone-mediated sugar pathways. PMID:26157452
Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders. PMID:26149713
Using prior knowledge from cellular pathways and molecular networks for diagnostic specimen classification. PMID:26141830
Drug-Path: a database for drug-induced pathways. PMID:26130661
Genes associated with the progression of neurofibrillary tangles in Alzheimer's disease. PMID:26126179
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway. PMID:26075876
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
Lhx6 and Lhx8 promote palate development through negative regulation of a cell cycle inhibitor gene, p57Kip2. PMID:26071365
Gene expression changes reflect clinical response in a placebo-controlled randomized trial of abatacept in patients with diffuse cutaneous systemic sclerosis. PMID:26071192
From Glacier to Sauna: RNA-Seq of the Human Pathogen Black Fungus Exophiala dermatitidis under Varying Temperature Conditions Exhibits Common and Novel Fungal Response. PMID:26061625
An Ebola virus-centered knowledge base. PMID:26055098
DECODE: an integrated differential co-expression and differential expression analysis of gene expression data. PMID:26026612
Direct estimation of differential networks. PMID:26023240
Temporal gene expression profiling of the rat knee joint capsule during immobilization-induced joint contractures. PMID:26006773
High throughput profiling of the cotton bollworm Helicoverpa armigera immunotranscriptome during the fungal and bacterial infections. PMID:26001831
Metabolic Needs and Capabilities of Toxoplasma gondii through Combined Computational and Experimental Analysis. PMID:26001086
Defining the metabolome: size, flux, and regulation. PMID:26000853
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. PMID:25999509
MicroRNA Expression Profile in Bovine Granulosa Cells of Preovulatory Dominant and Subordinate Follicles during the Late Follicular Phase of the Estrous Cycle. PMID:25993098
Metagenomics: tools and insights for analyzing next-generation sequencing data derived from biodiversity studies. PMID:25983555
Biology-Driven Gene-Gene Interaction Analysis of Age-Related Cataract in the eMERGE Network. PMID:25982363
FuncTree: Functional Analysis and Visualization for Large-Scale Omics Data. PMID:25974630
Multiscale Modeling of Drug-induced Effects of ReDuNing Injection on Human Disease: From Drug Molecules to Clinical Symptoms of Disease. PMID:25973739
Candidate pathways and genes for nasopharyngeal carcinoma based on bioinformatics study. PMID:25973099
Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach. PMID:25972988
Different Temporal Effects of Ebola Virus VP35 and VP24 Proteins on Global Gene Expression in Human Dendritic Cells. PMID:25972536
Solexa-Sequencing Based Transcriptome Study of Plaice Skin Phenotype in Rex Rabbits (Oryctolagus cuniculus). PMID:25955442
Characterization and Genomic Analysis of Quinolone-Resistant Delftia sp. 670 Isolated from a Patient Who Died from Severe Pneumonia. PMID:25935202
The histone methyltransferase SDG8 mediates the epigenetic modification of light and carbon responsive genes in plants. PMID:25928034
Small mosquitoes, large implications: crowding and starvation affects gene expression and nutrient accumulation in Aedes aegypti. PMID:25924822
Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis. PMID:25888205
Transcriptome analysis of leaves, roots and flowers of Panax notoginseng identifies genes involved in ginsenoside and alkaloid biosynthesis. PMID:25886736
Metatranscriptomes reveal functional variation in diatom communities from the Antarctic Peninsula. PMID:25871931
Abundant genetic overlap between blood lipids and immune-mediated diseases indicates shared molecular genetic mechanisms. PMID:25853426
Reconstructing genome-scale metabolic models with merlin. PMID:25845595
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer. PMID:25824651
Isoflavones in soy flour diet have different effects on whole-genome expression patterns than purified isoflavone mix in human MCF-7 breast tumors in ovariectomized athymic nude mice. PMID:25820259
Ligand-target prediction by structural network biology using nAnnoLyze. PMID:25816344
Survey of genome sequences in a wild sweet potato, Ipomoea trifida (H. B. K.) G. Don. PMID:25805887
Temperature and oxygen dependent metabolite utilization by Salmonella enterica serovars Derby and Mbandaka. PMID:25798944
Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PMID:25790137
Transcriptome analysis of maize leaf systemic symptom infected by Bipolaris zeicola. PMID:25781606
Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST. PMID:25754993
Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights. PMID:25745418
Mining host-pathogen protein interactions to characterize Burkholderia mallei infectivity mechanisms. PMID:25738731
Metabolic variation in natural populations of wild yeast. PMID:25691993
Draft genome sequence of Bacillus azotoformans MEV2011, a (Co-) denitrifying strain unable to grow with oxygen. PMID:25685261
Identification of a new Alcaligenes faecalis strain MOR02 and assessment of its toxicity and pathogenicity to insects. PMID:25667924
Biological mechanism analysis of acute renal allograft rejection: integrated of mRNA and microRNA expression profiles. PMID:25664019
Draft Genome Sequence of High-Temperature-Adapted Protochlamydia sp. HS-T3, an Amoebal Endosymbiotic Bacterium Found in Acanthamoeba Isolated from a Hot Spring in Japan. PMID:25657277
Comparison of sister species identifies factors underpinning plastid compatibility in green sea slugs. PMID:25652835
Aquifer environment selects for microbial species cohorts in sediment and groundwater. PMID:25647349
Experimental resistance to drug combinations in Leishmania donovani: metabolic and phenotypic adaptations. PMID:25645828
Comparison of human cell signaling pathway databases--evolution, drawbacks and challenges. PMID:25632107
Genomic and transcriptomic analysis of the endophytic fungus Pestalotiopsis fici reveals its lifestyle and high potential for synthesis of natural products. PMID:25623211
Identification of key genes associated with colorectal cancer based on the transcriptional network. PMID:25613817
Comparative computational analysis of pluripotency in human and mouse stem cells. PMID:25604210
Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. PMID:25577200
Genomic analysis of three African strains of Bacillus anthracis demonstrates that they are part of the clonal expansion of an exclusively pathogenic bacterium. PMID:25566394
A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. PMID:25523208
Pedigree-based random effect tests to screen gene pathways. PMID:25519354
RNA-seq analysis of equine conceptus transcripts during embryo fixation and capsule disappearance. PMID:25514169
Comparison of environmental and isolate Sulfobacillus genomes reveals diverse carbon, sulfur, nitrogen, and hydrogen metabolisms. PMID:25511286
MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule. PMID:25500075
The Triple-Negative Breast Cancer Database: an omics platform for reference, integration and analysis of triple-negative breast cancer data. PMID:25472854
Structure-guided functional characterization of DUF1460 reveals a highly specific NlpC/P60 amidase family. PMID:25465128
Genes regulating lipid and protein metabolism are highly expressed in mammary gland of lactating dairy goats. PMID:25433708
The InterPro protein families database: the classification resource after 15 years. PMID:25428371
ALLocator: an interactive web platform for the analysis of metabolomic LC-ESI-MS datasets, enabling semi-automated, user-revised compound annotation and mass isotopomer ratio analysis. PMID:25426929
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. PMID:25399423
RNA-Seq reveals a xenobiotic stress response in the soybean aphid, Aphis glycines, when fed aphid-resistant soybean. PMID:25399334
Bioinformatics: the next frontier of metabolomics. PMID:25389922
The genome of a Mongolian individual reveals the genetic imprints of Mongolians on modern human populations. PMID:25377941
Profiling status epilepticus-induced changes in hippocampal RNA expression using high-throughput RNA sequencing. PMID:25373493
Systematic analysis of time-series gene expression data on tumor cell-selective apoptotic responses to HDAC inhibitors. PMID:25371703
Evolution of invasion in a diverse set of Fusobacterium species. PMID:25370491
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Protein-protein interaction network and mechanism analysis in ischemic stroke. PMID:25333814
Plasma metabolomics in human pulmonary tuberculosis disease: a pilot study. PMID:25329995
De novo transcriptome sequencing analysis and comparison of differentially expressed genes (DEGs) in Macrobrachium rosenbergii in China. PMID:25329319
DEOP: a database on osmoprotectants and associated pathways. PMID:25326239
Transcriptome sequencing of rhizome tissue of Sinopodophyllum hexandrum at two temperatures. PMID:25287271
Curation, integration and visualization of bacterial virulence factors in PATRIC. PMID:25273106
Human metabolic correlates of body mass index. PMID:25254000
Epigenomic profiling of men exposed to early-life stress reveals DNA methylation differences in association with current mental state. PMID:25247593
Leaf-, panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: the development of gene-targeted functional markers for stress response. PMID:25242886
Genome sequence and genetic diversity of the common carp, Cyprinus carpio. PMID:25240282
Draft genome sequence of eggplant (Solanum melongena L.): the representative solanum species indigenous to the old world. PMID:25233906
A systems biology approach reveals a link between systemic cytokines and skeletal muscle energy metabolism in a rodent smoking model and human COPD. PMID:25228925
The influence of mtDNA deletion on lung cancer cells under the conditions of hypoxia and irradiation. PMID:25218334
Annotation and re-sequencing of genes from de novo transcriptome assembly of Abies alba (Pinaceae). PMID:25202477
Genes contributing to Staphylococcus aureus fitness in abscess- and infection-related ecologies. PMID:25182329
Gene ontology and KEGG enrichment analyses of genes related to age-related macular degeneration. PMID:25165703
A bayesian framework that integrates heterogeneous data for inferring gene regulatory networks. PMID:25152886
Inter-species pathway perturbation prediction via data-driven detection of functional homology. PMID:25150249
Depletion of STAT5 blocks TEL-SYK-induced APMF-type leukemia with myelofibrosis and myelodysplasia in mice. PMID:25148222
Transcriptome sequencing of a chimaera reveals coordinated expression of anthocyanin biosynthetic genes mediating yellow formation in herbaceous peony (Paeonia lactiflora Pall.). PMID:25134523
Identification of a human neonatal immune-metabolic network associated with bacterial infection. PMID:25120092
Transcriptome analysis of red swamp crawfish Procambarus clarkii reveals genes involved in gonadal development. PMID:25118947
Glycan degradation (GlyDeR) analysis predicts mammalian gut microbiota abundance and host diet-specific adaptations. PMID:25118239
The conserved PFT1 tandem repeat is crucial for proper flowering in Arabidopsis thaliana. PMID:25116137
Microscopy and genomic analysis of Mycoplasma parvum strain Indiana. PMID:25113534
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Target network differences between western drugs and Chinese herbal ingredients in treating cardiovascular disease. PMID:25104437
MediaDB: a database of microbial growth conditions in defined media. PMID:25098325
Transcriptomic profiling revealed an important role of cell wall remodeling and ethylene signaling pathway during salt acclimation in Arabidopsis. PMID:25092201
Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells. PMID:25080971
Predicting protein phosphorylation from gene expression: top methods from the IMPROVER Species Translation Challenge. PMID:25061067
Proteome-wide analysis of human disease mutations in short linear motifs: neglected players in cancer? PMID:25057855
A dedicated database system for handling multi-level data in systems biology. PMID:25053973
Integrative genomics reveals novel molecular pathways and gene networks for coronary artery disease. PMID:25033284
Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin. PMID:25028574
Network-based analysis identifies epigenetic biomarkers of esophageal squamous cell carcinoma progression. PMID:25015989
Two-layer modular analysis of gene and protein networks in breast cancer. PMID:24997799
Analysis of gene expression changes in peach leaves in response to Plum pox virus infection using RNA-Seq. PMID:24989162
Pathway analysis with next-generation sequencing data. PMID:24986826
An orthology-based analysis of pathogenic protozoa impacting global health: an improved comparative genomics approach with prokaryotes and model eukaryote orthologs. PMID:24960463
Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis. PMID:24959711
Integrative analysis of longitudinal metabolomics data from a personal multi-omics profile. PMID:24958148
Tackling CASMI 2012: Solutions from MetFrag and MetFusion. PMID:24958142
Amino Acid biosynthesis pathways in diatoms. PMID:24957993
Construction and analysis of regulatory genetic networks in cervical cancer based on involved microRNAs, target genes, transcription factors and host genes. PMID:24944708
Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST. PMID:24940621
dbCerEx: a web-based database for the analysis of cervical cancer transcriptomes. PMID:24918550
Dietary history contributes to enterotype-like clustering and functional metagenomic content in the intestinal microbiome of wild mice. PMID:24912178
Chronic alcohol consumption from adolescence-to-adulthood in mice--hypothalamic gene expression changes in the dilated cardiomyopathy signaling pathway. PMID:24884436
Genome Sequence of the Native Apiculate Wine Yeast Hanseniaspora vineae T02/19AF. PMID:24874663
Dietary switch reveals fast coordinated gene expression changes in Drosophila melanogaster. PMID:24864304
Phenotypic mapping of metabolic profiles using self-organizing maps of high-dimensional mass spectrometry data. PMID:24856386
Draft Genome Sequence of Pseudomonas aeruginosa Strain RB, a Bacterium Capable of Synthesizing Cadmium Selenide Nanoparticles. PMID:24831140
Elementary Flux Mode Analysis of Acetyl-CoA Pathway in Carboxydothermus hydrogenoformans Z-2901. PMID:24822064
Transcriptional response to dietary restriction in Drosophila melanogaster. PMID:24819200
Identification and profiling of microRNAs and their target genes from developing caprine skeletal Muscle. PMID:24818606
Variant association tools for quality control and analysis of large-scale sequence and genotyping array data. PMID:24791902
Genetic variants in mammary development, prolactin signalling and involution pathways explain considerable variation in bovine milk production and milk composition. PMID:24779965
Whole-exome sequencing for the identification of susceptibility genes of Kashin-Beck disease. PMID:24776925
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. PMID:24771658
β1-integrin-dependent migration of microglia in response to neuron-released α-synuclein. PMID:24743837
An extensive analysis of disease-gene associations using network integration and fast kernel-based gene prioritization methods. PMID:24726035
The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments. PMID:24723913
Transcriptome analysis of the Portunus trituberculatus: de novo assembly, growth-related gene identification and marker discovery. PMID:24722690
The immune strategy and stress response of the Mediterranean species of the Bemisia tabaci complex to an orally delivered bacterial pathogen. PMID:24722540
Stringent homology-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions. PMID:24708540
Gene-expression analysis of hair cell regeneration in the zebrafish lateral line. PMID:24706903
Uncoupling reproduction from metabolism extends chronological lifespan in yeast. PMID:24706810
Metatranscriptomics of the human oral microbiome during health and disease. PMID:24692635
A rough guide to metabolite identification using high resolution liquid chromatography mass spectrometry in metabolomic profiling in metazoans. PMID:24688687
DNA methylation subgroups and the CpG island methylator phenotype in gastric cancer: a comprehensive profiling approach. PMID:24674026
Resources for functional genomics studies in Drosophila melanogaster. PMID:24653003
Comparative genomics and phylogenomics of hemotrophic mycoplasmas. PMID:24642917
Hantavirus immunology of rodent reservoirs: current status and future directions. PMID:24638205
Streptococcus iniae SF1: complete genome sequence, proteomic profile, and immunoprotective antigens. PMID:24621602
Identification of candidate miRNA biomarkers from miRNA regulatory network with application to prostate cancer. PMID:24618011
A conceptual review on systems biology in health and diseases: from biological networks to modern therapeutics. PMID:24592295
Weighting schemes in metabolic graphs for identifying biochemical routes. PMID:24592291
New hydrocarbon degradation pathways in the microbial metagenome from Brazilian petroleum reservoirs. PMID:24587220
A systems biology analysis of the unique and overlapping transcriptional responses to caloric restriction and dietary methionine restriction in rats. PMID:24571921
Comparative genomics analysis of Lactobacillus species associated with weight gain or weight protection. PMID:24567124
Corbi: a new R package for biological network alignment and querying. PMID:24565104
Optimal experiment design for model selection in biochemical networks. PMID:24555498
Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PMID:24550716
Converging genetic and functional brain imaging evidence links neuronal excitability to working memory, psychiatric disease, and brain activity. PMID:24529980
Evolutionary insights about bacterial GlxRS from whole genome analyses: is GluRS2 a chimera? PMID:24521160
Ubiquinone accumulation improves osmotic-stress tolerance in Escherichia coli. PMID:24509820
Meta-analysis and gene set analysis of archived microarrays suggest implication of the spliceosome in metastatic and hypoxic phenotypes. PMID:24497970
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. PMID:24475928
The role of viral and host microRNAs in the Aujeszky's disease virus during the infection process. PMID:24475202
Production of a reference transcriptome and transcriptomic database (EdwardsiellaBase) for the lined sea anemone, Edwardsiella lineata, a parasitic cnidarian. PMID:24467778
Pathway-based analysis of the hidden genetic heterogeneities in cancers. PMID:24462714
BurrH: a new modular DNA binding protein for genome engineering. PMID:24452192
Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill. PMID:24451203
Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling. PMID:24450983
A network-based kernel machine test for the identification of risk pathways in genome-wide association studies. PMID:24434848
ISAAC - InterSpecies Analysing Application using Containers. PMID:24428905
Construction of a public CHO cell line transcript database using versatile bioinformatics analysis pipelines. PMID:24427317
Genome expression profile analysis of the maize sheath in response to inoculation to R. solani. PMID:24420865
Clustering gene expression regulators: new approach to disease subtyping. PMID:24416320
Phenylalanine metabolism regulates reproduction and parasite melanization in the malaria mosquito. PMID:24409310
Genome degeneration and adaptation in a nascent stage of symbiosis. PMID:24407854
Genome-wide transcriptional response of silkworm (Bombyx mori) to infection by the microsporidian Nosema bombycis. PMID:24386341
Candida utilis and Chlorella vulgaris counteract intestinal inflammation in Atlantic salmon (Salmo salar L.). PMID:24386162
Vitamin D receptor, an important transcription factor associated with aldosterone-producing adenoma. PMID:24376526
High-Quality Draft Genome Sequence of Vagococcus lutrae Strain LBD1, Isolated from the Largemouth Bass Micropterus salmoides. PMID:24371201
A systematic exploration of high-temperature stress-responsive genes in potato using large-scale yeast functional screening. PMID:24357347
MOPED enables discoveries through consistently processed proteomics data. PMID:24350770
Prediction of drugs target groups based on ChEBI ontology. PMID:24350241
Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation. PMID:24341328
Methanotrophic archaea possessing diverging methane-oxidizing and electron-transporting pathways. PMID:24335827
Exploring the "dark matter" of a mammalian proteome by protein structure and function modeling. PMID:24321360
Comparative transcriptional profiling analysis of olive ripe-fruit pericarp and abscission zone tissues shows expression differences and distinct patterns of transcriptional regulation. PMID:24320622
Transcriptional regulatory network and protein-protein interaction to reveal the mechanism of pancreatic cancer. PMID:24307251
Grouped False-Discovery Rate for Removing the Gene-Set-Level Bias of RNA-seq. PMID:24277981
Databases and Software for NMR-Based Metabolomics. PMID:24260723
Biosynthesis of vitamins and cofactors in bacterium-harbouring trypanosomatids depends on the symbiotic association as revealed by genomic analyses. PMID:24260300
A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity. PMID:24260172
Discovering transcription and splicing networks in myelodysplastic syndromes. PMID:24244432
Proteomic changes during B cell maturation: 2D-DIGE approach. PMID:24205016
Metabolic proximity in the order of colonization of a microbial community. PMID:24204896
Relative amino acid composition signatures of organisms and environments. PMID:24204807
Identification of direction in gene networks from expression and methylation. PMID:24182195
Targeting lipid biosynthesis and salvage in apicomplexan parasites for improved chemotherapies. PMID:24162026
Effect of curcumin on aged Drosophila melanogaster: a pathway prediction analysis. PMID:24155070
Comprehensive gene expression analysis reveals multiple signal pathways associated with prostate cancer. PMID:24154878
A scalable, knowledge-based analysis framework for genetic association studies. PMID:24152222
LIN28B promotes growth and tumorigenesis of the intestinal epithelium via Let-7. PMID:24142874
Methods and approaches in the topology-based analysis of biological pathways. PMID:24133454
Genome analysis of Pseudoalteromonas flavipulchra JG1 reveals various survival advantages in marine environment. PMID:24131871
The genome of Mesobuthus martensii reveals a unique adaptation model of arthropods. PMID:24129506
Using random walks to identify cancer-associated modules in expression data. PMID:24128261
Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PMID:24098102
Peripheral blood mononuclear cell gene expression profiles predict poor outcome in idiopathic pulmonary fibrosis. PMID:24089408
Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling. PMID:24084807
Network-based inference framework for identifying cancer genes from gene expression data. PMID:24073403
Drug synergy screen and network modeling in dedifferentiated liposarcoma identifies CDK4 and IGF1R as synergistic drug targets. PMID:24065146
A network study of chinese medicine xuesaitong injection to elucidate a complex mode of action with multicompound, multitarget, and multipathway. PMID:24058375
Colorectal cancer through simulation and experiment. PMID:24046975
Genome wide transcriptome analysis of dendritic cells identifies genes with altered expression in psoriasis. PMID:24039940
Genomic properties of Marine Group A bacteria indicate a role in the marine sulfur cycle. PMID:24030600
Endosymbiosis in trypanosomatids: the genomic cooperation between bacterium and host in the synthesis of essential amino acids is heavily influenced by multiple horizontal gene transfers. PMID:24015778
The genome of the alga-associated marine flavobacterium Formosa agariphila KMM 3901T reveals a broad potential for degradation of algal polysaccharides. PMID:23995932
Genome-wide gene expression profiling of stress response in a spinal cord clip compression injury model. PMID:23984903
Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment. PMID:23979677
SHARP: genome-scale identification of gene-protein-reaction associations in cyanobacteria. PMID:23975204
ESTs analysis reveals putative genes involved in symbiotic seed germination in Dendrobium officinale. PMID:23967335
The root transcriptome for North American ginseng assembled and profiled across seasonal development. PMID:23957709
Application of Cydia pomonella expressed sequence tags: Identification and expression of three general odorant binding proteins in codling moth. PMID:23956229
PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes. PMID:23951317
Key pathways and genes controlling the development and progression of clear cell renal cell carcinoma (ccRCC) based on gene set enrichment analysis. PMID:23943374
Starch biosynthesis in cassava: a genome-based pathway reconstruction and its exploitation in data integration. PMID:23938102
Transcriptomic analysis of insulin-sensitive tissues from anti-diabetic drug treated ZDF rats, a T2DM animal model. PMID:23922760
ETV4 promotes metastasis in response to activation of PI3-kinase and Ras signaling in a mouse model of advanced prostate cancer. PMID:23918374
Reannotation and extended community resources for the genome of the non-seed plant Physcomitrella patens provide insights into the evolution of plant gene structures and functions. PMID:23879659
Genome-scale co-evolutionary inference identifies functions and clients of bacterial Hsp90. PMID:23874229
Mining differential top-k co-expression patterns from time course comparative gene expression datasets. PMID:23870110
Populus euphratica: the transcriptomic response to drought stress. PMID:23857471
PPARβ/δ modulates ethanol-induced hepatic effects by decreasing pyridoxal kinase activity. PMID:23851158
Predicting and analyzing interactions between Mycobacterium tuberculosis and its human host. PMID:23844013
Integrated phosphoproteomic and metabolomic profiling reveals NPM-ALK-mediated phosphorylation of PKM2 and metabolic reprogramming in anaplastic large cell lymphoma. PMID:23814019
Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. PMID:23803171
Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. PMID:23793264
Metagenome reveals potential microbial degradation of hydrocarbon coupled with sulfate reduction in an oil-immersed chimney from Guaymas Basin. PMID:23785357
Integrative analysis of cancer-related signaling pathways. PMID:23760067
Skin transcriptome profiles associated with coat color in sheep. PMID:23758853
Redundancy control in pathway databases (ReCiPa): an application for improving gene-set enrichment analysis in Omics studies and "Big data" biology. PMID:23758478
Elucidating rice cell metabolism under flooding and drought stresses using flux-based modeling and analysis. PMID:23753178
Network2Canvas: network visualization on a canvas with enrichment analysis. PMID:23749960
Characterizing protein domain associations by Small-molecule ligand binding. PMID:23745168
De novo characterization of Japanese scallop Mizuhopecten yessoensis transcriptome and analysis of its gene expression following cadmium exposure. PMID:23741332
Pathview: an R/Bioconductor package for pathway-based data integration and visualization. PMID:23740750
A network pharmacology approach to evaluating the efficacy of chinese medicine using genome-wide transcriptional expression data. PMID:23737854
Transcriptomic analysis of Ustilago maydis infecting Arabidopsis reveals important aspects of the fungus pathogenic mechanisms. PMID:23733054
Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges. PMID:23728164
Comparative genomics of Salmonella enterica serovars Derby and Mbandaka, two prevalent serovars associated with different livestock species in the UK. PMID:23725633
HGPGD: the human gene population genetic difference database. PMID:23717556
Combined sequence-based and genetic mapping analysis of complex traits in outbred rats. PMID:23708188
Transcriptome analysis of Thapsia laciniata Rouy provides insights into terpenoid biosynthesis and diversity in Apiaceae. PMID:23698765
ExtremeDB: a unified web repository of extremophilic archaea and bacteria. PMID:23696792
Semi-supervised prediction of SH2-peptide interactions from imbalanced high-throughput data. PMID:23690949
Rapid catalytic template searching as an enzyme function prediction procedure. PMID:23675414
Research resource: small RNA-seq of human granulosa cells reveals miRNAs in FSHR and aromatase genes. PMID:23660593
DNA marker applications to molecular genetics and genomics in tomato. PMID:23641178
Transcriptome analysis of buds and leaves using 454 pyrosequencing to discover genes associated with the biosynthesis of active ingredients in Lonicera japonica Thunb. PMID:23638167
Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis. PMID:23627640
Genomes of the class Erysipelotrichia clarify the firmicute origin of the class Mollicutes. PMID:23606477
Biographer: web-based editing and rendering of SBGN compliant biochemical networks. PMID:23574737
Metabolite profiling to characterize disease-related bacteria: gluconate excretion by Pseudomonas aeruginosa mutants and clinical isolates from cystic fibrosis patients. PMID:23572517
Exposure to airborne particulate matter is associated with methylation pattern in the asthma pathway. PMID:23566092
Natural variation in Fc glycosylation of HIV-specific antibodies impacts antiviral activity. PMID:23563315
Defining the transcriptional and cellular landscape of type 1 diabetes in the NOD mouse. PMID:23555752
Transcriptional responses of in vivo praziquantel exposure in schistosomes identifies a functional role for calcium signalling pathway member CamKII. PMID:23555262
The RAVEN toolbox and its use for generating a genome-scale metabolic model for Penicillium chrysogenum. PMID:23555215
Genomic analysis by deep sequencing of the probiotic Lactobacillus brevis KB290 harboring nine plasmids reveals genomic stability. PMID:23544154
Pharmacometabolomics reveals racial differences in response to atenolol treatment. PMID:23536766
Replacements of rare herbs and simplifications of traditional chinese medicine formulae based on attribute similarities and pathway enrichment analysis. PMID:23533462
From ontology to semantic similarity: calculation of ontology-based semantic similarity. PMID:23533360
A systematic comparison of the MetaCyc and KEGG pathway databases. PMID:23530693
Seasonal and regional differences in gene expression in the brain of a hibernating mammal. PMID:23526982
The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. PMID:23525042
Identifying gene set association enrichment using the coefficient of intrinsic dependence. PMID:23516564
Differential expression analysis for pathways. PMID:23516350
Proteomic analysis indicates massive changes in metabolism prior to the inhibition of growth and photosynthesis of grapevine (Vitis vinifera L.) in response to water deficit. PMID:23514573
Whole transcriptome analysis using next-generation sequencing of model species Setaria viridis to support C4 photosynthesis research. PMID:23512102
Interpretation of genomic variants using a unified biological network approach. PMID:23505346
Screening key genes and pathways in glioma based on gene set enrichment analysis and meta-analysis. PMID:23494636
Genome-wide SNP genotyping to infer the effects on gene functions in tomato. PMID:23482505
Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition. PMID:23481595
Regulation of SIRT1 by oxidative stress-responsive miRNAs and a systematic approach to identify its role in the endothelium. PMID:23477488
A novel kernel for correcting size bias in the logistic kernel machine test with an application to rheumatoid arthritis. PMID:23466369
Metagenomic analysis of the pygmy loris fecal microbiome reveals unique functional capacity related to metabolism of aromatic compounds. PMID:23457582
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats. PMID:23453054
Lineage analysis of basal epithelial cells reveals their unexpected plasticity and supports a cell-of-origin model for prostate cancer heterogeneity. PMID:23434823
Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data. PMID:23424121
Next-generation analysis of cataracts: determining knowledge driven gene-gene interactions using Biofilter, and gene-environment interactions using the PhenX Toolkit. PMID:23424120
Functional-network-based gene set analysis using gene-ontology. PMID:23418449
Increased expression of endoplasmic reticulum stress and unfolded protein response genes in peripheral blood mononuclear cells from patients with limited cutaneous systemic sclerosis and pulmonary arterial hypertension. PMID:23400395
Equal opportunity for low-degree network nodes: a PageRank-based method for protein target identification in metabolic graphs. PMID:23382878
Drug repurposing screen reveals FDA-approved inhibitors of human HMG-CoA reductase and isoprenoid synthesis that block Cryptosporidium parvum growth. PMID:23380723
miRNA expression profile analysis in kidney of different porcine breeds. PMID:23372853
Genome-wide assessment of the association of rare and common copy number variations to testicular germ cell cancer. PMID:23372565
Exploring the pathogenetic association between schizophrenia and type 2 diabetes mellitus diseases based on pathway analysis. PMID:23369358
Molecular tools for the detection of nitrogen cycling Archaea. PMID:23365509
Visualizing multidimensional cancer genomics data. PMID:23363777
Network models of genome-wide association studies uncover the topological centrality of protein interactions in complex diseases. PMID:23355459
'Omics' approaches to understanding interstitial cystitis/painful bladder syndrome/bladder pain syndrome. PMID:23346481
Genome evolution and phylogenomic analysis of Candidatus Kinetoplastibacterium, the betaproteobacterial endosymbionts of Strigomonas and Angomonas. PMID:23345457
Altered microRNA profiles in bronchoalveolar lavage fluid exosomes in asthmatic patients. PMID:23333113
SignaLink 2 - a signaling pathway resource with multi-layered regulatory networks. PMID:23331499
On the geometric modeling approach to empirical null distribution estimation for empirical Bayes modeling of multiple hypothesis testing. PMID:23314152
A heterozygous moth genome provides insights into herbivory and detoxification. PMID:23313953
Prediction of breast cancer metastasis by gene expression profiles: a comparison of metagenes and single genes. PMID:23304070
Systematic analysis of the gene expression in the livers of nonalcoholic steatohepatitis: implications on potential biomarkers and molecular pathological mechanism. PMID:23300535
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. PMID:23282057
Docking studies and network analyses reveal capacity of compounds from Kandelia rheedii to strengthen cellular immunity by interacting with host proteins during tuberculosis infection. PMID:23275699
A genomic scale map of genetic diversity in Trypanosoma cruzi. PMID:23270511
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). PMID:23263233
A systems approach to rheumatoid arthritis. PMID:23240033
Metabolomic analysis of dynamic response and drug resistance of gastric cancer cells to 5-fluorouracil. PMID:23232983
Comparative approaches to the study of physiology: Drosophila as a physiological tool. PMID:23220476
Suppression subtractive hybridization reveals transcript profiling of Chlorella under heterotrophy to photoautotrophy transition. PMID:23209737
Genome sequence of the protease-producing bacterium Rheinheimera nanhaiensis E407-8T, isolated from deep-sea sediment of the South China Sea. PMID:23209246
A novel in silico approach to identify potential therapeutic targets in human bacterial pathogens. PMID:23205162
Anoxic carbon flux in photosynthetic microbial mats as revealed by metatranscriptomics. PMID:23190731
GraphAlignment: Bayesian pairwise alignment of biological networks. PMID:23171476
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
PMRD: a curated database for genes and mutants involved in plant male reproduction. PMID:23153247
Genome sequence of the biocontrol agent Microbacterium barkeri strain 2011-R4. PMID:23144410
Draft genome sequence of strain P7-3-5, a new Flavobacteriaceae bacterium isolated from intertidal sand. PMID:23144387
Draft genome sequence of Actinobacillus pleuropneumoniae serotype 7 strain S-8. PMID:23144372
Combining next-generation sequencing and microarray technology into a transcriptomics approach for the non-model organism Chironomus riparius. PMID:23133553
The genome of the obligate intracellular parasite Trachipleistophora hominis: new insights into microsporidian genome dynamics and reductive evolution. PMID:23133373
A combined histology and transcriptome analysis unravels novel questions on Medicago truncatula seed coat. PMID:23125357
The effect of environmental enrichment on substantia nigra gene expression after traumatic brain injury in rats. PMID:23094804
Strand-biased gene distribution in bacteria is related to both horizontal gene transfer and strand-biased nucleotide composition. PMID:23084774
The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential. PMID:23083487
Analysis of Litopenaeus vannamei transcriptome using the next-generation DNA sequencing technique. PMID:23071809
SALMONELLABASE - An online database of druggable targets of Salmonella species. PMID:23055621
The relationship between the hierarchical position of proteins in the human signal transduction network and their rate of evolution. PMID:23020283
Mycoplasma haemocanis--the canine hemoplasma and its feline counterpart in the genomic era. PMID:23020168
HIDEN: Hierarchical decomposition of regulatory networks. PMID:23016513
Transcriptomic analysis of the oleaginous microalga Neochloris oleoabundans reveals metabolic insights into triacylglyceride accumulation. PMID:23006831
Along signal paths: an empirical gene set approach exploiting pathway topology. PMID:23002139
In silico evolutionary analysis of Helicobacter pylori outer membrane phospholipase A (OMPLA). PMID:22974200
Uncovering networks from genome-wide association studies via circular genomic permutation. PMID:22973544
A small predatory core genome in the divergent marine Bacteriovorax marinus SJ and the terrestrial Bdellovibrio bacteriovorus. PMID:22955231
Phylogenetic and functional metagenomic profiling for assessing microbial biodiversity in environmental monitoring. PMID:22952724
Recombinant E. coli expressing Vitreoscilla haemoglobin prefers aerobic metabolism under microaerobic conditions: a proteome-level study. PMID:22922188
The identification of candidate genes and SNP markers for classical bovine spongiform encephalopathy susceptibility. PMID:22918267
Prioritizing cancer therapeutic small molecules by integrating multiple OMICS datasets. PMID:22917481
The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. PMID:22889830
Genome-wide association study identifies eight new risk loci for polycystic ovary syndrome. PMID:22885925
Integrating genetic association, genetics of gene expression, and single nucleotide polymorphism set analysis to identify susceptibility Loci for type 2 diabetes mellitus. PMID:22865700
Novel microRNAs differentially expressed during aging in the mouse brain. PMID:22844398
State of the art in silico tools for the study of signaling pathways in cancer. PMID:22837650
B-Raf activation cooperates with PTEN loss to drive c-Myc expression in advanced prostate cancer. PMID:22836754
Leveraging models of cell regulation and GWAS data in integrative network-based association studies. PMID:22836096
A smoking-associated 7-gene signature for lung cancer diagnosis and prognosis. PMID:22825454
Dual targeting of the Akt/mTOR signaling pathway inhibits castration-resistant prostate cancer in a genetically engineered mouse model. PMID:22815528
Crowd sourcing a new paradigm for interactome driven drug target identification in Mycobacterium tuberculosis. PMID:22808064
Cancer develops, progresses and responds to therapies through restricted perturbation of the protein-protein interaction network. PMID:22806580
Ultrafast clustering algorithms for metagenomic sequence analysis. PMID:22772836
Pathway-based classification of cancer subtypes. PMID:22759382
Mathematical and statistical modeling in cancer systems biology. PMID:22754537
Epimerase (Msed_0639) and mutase (Msed_0638 and Msed_2055) convert (S)-methylmalonyl-coenzyme A (CoA) to succinyl-CoA in the Metallosphaera sedula 3-hydroxypropionate/4-hydroxybutyrate cycle. PMID:22752162
Transcriptional profiling of serogroup B Neisseria meningitidis growing in human blood: an approach to vaccine antigen discovery. PMID:22745818
The balance in the delivery of ER components and the vacuolar proton pump to the phagosome depends on myosin IK in Dictyostelium. PMID:22736568
Integrating literature-constrained and data-driven inference of signalling networks. PMID:22734019
Genome-wide mapping of cystitis due to Streptococcus agalactiae and Escherichia coli in mice identifies a unique bladder transcriptome that signifies pathogen-specific antimicrobial defense against urinary tract infection. PMID:22733575
Public domain databases for medicinal chemistry. PMID:22731701
Down-weighting overlapping genes improves gene set analysis. PMID:22713124
Genome sequencing and mapping reveal loss of heterozygosity as a mechanism for rapid adaptation in the vegetable pathogen Phytophthora capsici. PMID:22712506
Global Gene Expression Profiling in PPAR-γ Agonist-Treated Kidneys in an Orthologous Rat Model of Human Autosomal Recessive Polycystic Kidney Disease. PMID:22666229
Temporal analysis of xylose fermentation by Scheffersomyces stipitis using shotgun proteomics. PMID:22638791
Engineering of a xylose metabolic pathway in Rhodococcus strains. PMID:22636009
Identifying gnostic predictors of the vaccine response. PMID:22633886
The genome of the polar eukaryotic microalga Coccomyxa subellipsoidea reveals traits of cold adaptation. PMID:22630137
Computational tools for metabolic engineering. PMID:22629572
Genome sequence of proteorhodopsin-containing sea ice bacterium Glaciecola punicea ACAM 611T. PMID:22628500
Multi-copy genes that enhance the yield of mammalian G protein-coupled receptors in Escherichia coli. PMID:22609824
De novo transcriptome sequencing of Momordica cochinchinensis to identify genes involved in the carotenoid biosynthesis. PMID:22580955
Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance. PMID:22558125
Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE). PMID:22558086
Possible connection between imidacloprid-induced changes in rice gene transcription profiles and susceptibility to the brown plant hopper Nilaparvatalugens Stål (Hemiptera: Delphacidae). PMID:22544984
BEAT: Bioinformatics Exon Array Tool to store, analyze and visualize Affymetrix GeneChip Human Exon Array data from disease experiments. PMID:22536968
Metabolic network alignment in large scale by network compression. PMID:22536900
Genome sequences of type strains of seven species of the marine bacterium Pseudoalteromonas. PMID:22535931
Generation, functional analysis and utility of Citrus grandis EST from a flower-derived cDNA library. PMID:22477149
Differential gene expression profile in PBMCs from subjects with AERD and ATA: a gene marker for AERD. PMID:22457146
SpiroESTdb: a transcriptome database and online tool for sparganum expressed sequences tags. PMID:22397686
Identification of candidate susceptibility and resistance genes of mice infected with Streptococcus suis type 2. PMID:22384161
Genome sequence of the cycloprodigiosin-producing bacterial strain Pseudoalteromonas rubra ATCC 29570(T). PMID:22374963
Putative essential and core-essential genes in Mycoplasma genomes. PMID:22355572
Draft genome sequence of Mesorhizobium alhagi CCNWXJ12-2T, a novel salt-resistant species isolated from the desert of northwestern China. PMID:22328758
Systems Biology Reveals MicroRNA-Mediated Gene Regulation. PMID:22303325
The diversity of cyanobacterial metabolism: genome analysis of multiple phototrophic microorganisms. PMID:22300633
Analysis of 2,297 expressed sequence tags (ESTs) from a cDNA library of flax (Linum ustitatissimum L.) bark tissue. PMID:22294104
graphite - a Bioconductor package to convert pathway topology to gene network. PMID:22292714
Single sample expression-anchored mechanisms predict survival in head and neck cancer. PMID:22291585
Genome sequences of six Pseudoalteromonas strains isolated from Arctic sea ice. PMID:22275105
Accurate evaluation and analysis of functional genomics data and methods. PMID:22268703
Proteomic analysis (GeLC-MS/MS) of ePFT-collected pancreatic fluid in chronic pancreatitis. PMID:22243521
Eight paths of ERK1/2 signalling pathway regulating hepatocyte proliferation in rat liver regeneration. PMID:22227930
RNA-Seq and molecular docking reveal multi-level pesticide resistance in the bed bug. PMID:22226239
Global analysis of DNA methylation by Methyl-Capture sequencing reveals epigenetic control of cisplatin resistance in ovarian cancer cell. PMID:22216282
An approach for searching insertions in bacterial genes leading to the phase shift of triplet periodicity. PMID:22196359
Generation and Analysis of Large-Scale Data-Driven Mycobacterium tuberculosis Functional Networks for Drug Target Identification. PMID:22190924
Elucidating the identity of resistance mechanisms to prednisolone exposure in acute lymphoblastic leukemia cells through transcriptomic analysis: A computational approach. PMID:22185641
Identification of cis-acting promoter elements in cold- and dehydration-induced transcriptional pathways in Arabidopsis, rice, and soybean. PMID:22184637
A HNMR-based metabonomics study of postmenopausal osteoporosis and intervention effects of Er-Xian Decoction in ovariectomized rats. PMID:22174622
Competitive and cooperative metabolic interactions in bacterial communities. PMID:22158444
Identifying highly conserved and highly differentiated gene ontology categories in human populations. PMID:22140477
Analyses of Expressed Sequence Tags from Chironomus riparius Using Pyrosequencing : Molecular Ecotoxicology Perspective. PMID:22125771
Complete genome sequence of seawater bacterium Glaciecola nitratireducens FR1064(T). PMID:22123761
Computational toxicology using the OpenTox application programming interface and Bioclipse. PMID:22075173
A point mutation in translation initiation factor eIF2B leads to function--and time-specific changes in brain gene expression. PMID:22073122
Comparative genomics study of polyhydroxyalkanoates (PHA) and ectoine relevant genes from Halomonas sp. TD01 revealed extensive horizontal gene transfer events and co-evolutionary relationships. PMID:22040376
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
Proteomic analysis of formalin-fixed paraffin-embedded pancreatic tissue using liquid chromatography tandem mass spectrometry. PMID:22015969
Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property. PMID:21980418
Proteomic analysis of a rat pancreatic stellate cell line using liquid chromatography tandem mass spectrometry (LC-MS/MS). PMID:21968429
The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions. PMID:21962087
Genome of Mycoplasma haemofelis, unraveling its strategies for survival and persistence. PMID:21936946
Complete genome sequence of the ureolytic Streptococcus salivarius strain 57.I. PMID:21914897
CastorDB: a comprehensive knowledge base for Ricinus communis. PMID:21914200
A computational method based on the integration of heterogeneous networks for predicting disease-gene associations. PMID:21912671
PATRIC: the comprehensive bacterial bioinformatics resource with a focus on human pathogenic species. PMID:21896772
Bioinformatic-driven search for metabolic biomarkers in disease. PMID:21884622
A face in the crowd: recognizing peptides through database search. PMID:21876205
Identification and phylogenetic analysis of heme synthesis genes in trypanosomatids and their bacterial endosymbionts. PMID:21853145
Proteomic analysis of an immortalized mouse pancreatic stellate cell line identifies differentially-expressed proteins in activated vs nonproliferating cell states. PMID:21838295
Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PMID:21829504
Differential protein expression profiles in estrogen receptor-positive and -negative breast cancer tissues using label-free quantitative proteomics. PMID:21779449
A cross-species analysis of a mouse model of breast cancer-specific osteolysis and human bone metastases using gene expression profiling. PMID:21774828
From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems. PMID:21685094
RINQ: Reference-based Indexing for Network Queries. PMID:21685064
Generation and analysis of expressed sequence tags from the bone marrow of Chinese Sika deer. PMID:21681423
Comparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential. PMID:21631945
AtIPD: a curated database of Arabidopsis isoprenoid pathway models and genes for isoprenoid network analysis. PMID:21617028
Multiple testing for gene sets from microarray experiments. PMID:21615889
BioProfiling.de: analytical web portal for high-throughput cell biology. PMID:21609949
Evolutionary plasticity determination by orthologous groups distribution. PMID:21586164
Computational integration of homolog and pathway gene module expression reveals general stemness signatures. PMID:21559491
Signalogs: orthology-based identification of novel signaling pathway components in three metazoans. PMID:21559328
Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. PMID:21493686
The Rat Genome Database pathway portal. PMID:21478484
Untargeted metabolomics identifies enterobiome metabolites and putative uremic toxins as substrates of organic anion transporter 1 (Oat1). PMID:21476605
Transcriptional regulation via TF-modifying enzymes: an integrative model-based analysis. PMID:21470963
Appearance frequency modulated gene set enrichment testing. PMID:21418606
Transcriptome sequencing and annotation of the microalgae Dunaliella tertiolecta: pathway description and gene discovery for production of next-generation biofuels. PMID:21401935
Phospho-proteomic analysis of mantle cell lymphoma cells suggests a pro-survival role of B-cell receptor signaling. PMID:21394647
SubMAP: aligning metabolic pathways with subnetwork mappings. PMID:21385030
Visualize: a free and open source multifunction tool for proteomics data analysis. PMID:21365761
Mass spectrometry-based proteomics of endoscopically collected pancreatic fluid in chronic pancreatitis research. PMID:21360826
FNV: light-weight flash-based network and pathway viewer. PMID:21349871
Reconstructing phylogeny from metabolic substrate-product relationships. PMID:21342557
Mass conservation and inference of metabolic networks from high-throughput mass spectrometry data. PMID:21314454
Landscape mapping of functional proteins in insulin signal transduction and insulin resistance: a network-based protein-protein interaction analysis. PMID:21305025
Systems biology of the autophagy-lysosomal pathway. PMID:21293178
Genome-wide polymorphism and comparative analyses in the white-tailed deer (Odocoileus virginianus): a model for conservation genomics. PMID:21283515
Transcriptome atlas of eight liver cell types uncovers effects of histidine catabolites on rat liver regeneration. PMID:21273693
An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. PMID:21266443
Role of the autonomic nervous system in rat liver regeneration. PMID:21264506
Circadian rhythm and cartilage extracellular matrix genes in osseointegration: a genome-wide screening of implant failure by vitamin D deficiency. PMID:21264318
BiologicalNetworks 2.0--an integrative view of genome biology data. PMID:21190573
Metabolomics to unveil and understand phenotypic diversity between pathogen populations. PMID:21152055
Sequence analysis of the genome of an oil-bearing tree, Jatropha curcas L. PMID:21149391
Gene expression profiling in whole blood identifies distinct biological pathways associated with obesity. PMID:21122113
Entrez Gene: gene-centered information at NCBI. PMID:21115458
Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak. PMID:21092232
Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PMID:21085593
Changes in hepatic gene expression upon oral administration of taurine-conjugated ursodeoxycholic acid in ob/ob mice. PMID:21079772
Analysis of protein pathway networks using hybrid properties. PMID:21076385
EMA - A R package for Easy Microarray data analysis. PMID:21047405
Identification and modeling of a drug target for Clostridium perfringens SM101. PMID:20978600
Genomic survey of the ectoparasitic mite Varroa destructor, a major pest of the honey bee Apis mellifera. PMID:20973996
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
Heading down the wrong pathway: on the influence of correlation within gene sets. PMID:20955544
A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. PMID:20946988
TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures. PMID:20944203
Essential role of glutathione in acclimation to environmental and redox perturbations in the cyanobacterium Synechocystis sp. PCC 6803. PMID:20935175
Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase. PMID:20929569
Systems analysis of salivary gland development and disease. PMID:20890964
Domain altering SNPs in the human proteome and their impact on signaling pathways. PMID:20886114
A novel statistic for genome-wide interaction analysis. PMID:20885795
Endocrine profiling and prioritization of environmental chemicals using ToxCast data. PMID:20826373
Consistency, comprehensiveness, and compatibility of pathway databases. PMID:20819233
Gene set analysis exploiting the topology of a pathway. PMID:20809931
Ranked retrieval of Computational Biology models. PMID:20701772
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. PMID:20663121
Tourette syndrome: gene expression as a tool to discover drug targets. PMID:20643383
The role of nucleosome positioning in the evolution of gene regulation. PMID:20625544
Optimal selection of epitopes for TXP-immunoaffinity mass spectrometry. PMID:20579369
Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. PMID:20529912
Ontologies in quantitative biology: a basis for comparison, integration, and discovery. PMID:20520843
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases. PMID:20519200
Searching for signaling balance through the identification of genetic interactors of the Rab guanine-nucleotide dissociation inhibitor gdi-1. PMID:20498707
Dynamic cross-talk analysis among TNF-R, TLR-4 and IL-1R signalings in TNFalpha-induced inflammatory responses. PMID:20497537
Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. PMID:20459735
Genome-wide gene and pathway analysis. PMID:20442747
Identifying essential genes in bacterial metabolic networks with machine learning methods. PMID:20438628
i-GSEA4GWAS: a web server for identification of pathways/gene sets associated with traits by applying an improved gene set enrichment analysis to genome-wide association study. PMID:20435672
Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells. PMID:20433688
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
Prediction of novel synthetic pathways for the production of desired chemicals. PMID:20346180
Bioinformatic tools for identifying disease gene and SNP candidates. PMID:20238089
Distinct hematopoietic stem cell subtypes are differentially regulated by TGF-beta1. PMID:20207229
Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis. PMID:20192823
Transcriptional profiling of luteinizing hormone receptor-deficient mice before and after testosterone treatment provides insight into the hormonal control of postnatal testicular development and Leydig cell differentiation. PMID:20164437
Lists2Networks: integrated analysis of gene/protein lists. PMID:20152038
Characterization of expressed sequence tags (ESTs) of pigeonpea (Cajanus cajan L.) and functional validation of selected genes for abiotic stress tolerance in Arabidopsis thaliana. PMID:20131066
FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology. PMID:20122162
LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. PMID:20122157
Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. PMID:20118918
Transcriptome analysis of the Cryptocaryon irritans tomont stage identifies potential genes for the detection and control of cryptocaryonosis. PMID:20113487
Relationship between operon preference and functional properties of persistent genes in bacterial genomes. PMID:20109203
Biana: a software framework for compiling biological interactions and analyzing networks. PMID:20105306
Unbiased transcriptional comparisons of generalist and specialist herbivores feeding on progressively defenseless Nicotiana attenuata plants. PMID:20090945
The Medicago truncatula gene expression atlas web server. PMID:20028527
Aging mice show a decreasing correlation of gene expression within genetic modules. PMID:20019809
Genomic Target Database (GTD): a database of potential targets in human pathogenic bacteria. PMID:20011153
Metastasis-Associated Gene Expression Changes Predict Poor Outcomes in Patients with Dukes Stage B and C Colorectal Cancer. PMID:19996206
MitoInteractome: mitochondrial protein interactome database, and its application in 'aging network' analysis. PMID:19958484
Scalable steady state analysis of Boolean biological regulatory networks. PMID:19956604
Genome sequence of the versatile fish pathogen Edwardsiella tarda provides insights into its adaptation to broad host ranges and intracellular niches. PMID:19865481
Towards a systems biology approach to mammalian cell cycle: modeling the entrance into S phase of quiescent fibroblasts after serum stimulation. PMID:19828076
Plant MetGenMAP: an integrative analysis system for plant systems biology. PMID:19819981
Draft genome sequence of the Daphnia pathogen Octosporea bayeri: insights into the gene content of a large microsporidian genome and a model for host-parasite interactions. PMID:19807911
The Modular Organization of Protein Interactions in Escherichia coli. PMID:19798435
Improved mutation tagging with gene identifiers applied to membrane protein stability prediction. PMID:19758467
Automated seeding of specialised wiki knowledgebases with BioKb. PMID:19758431
Evolutionary constraints permeate large metabolic networks. PMID:19747381
The complete genome of Comamonas testosteroni reveals its genetic adaptations to changing environments. PMID:19734336
Integrating multiple microarray data for cancer pathway analysis using bootstrapping K-S test. PMID:19704919
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example. PMID:19698148
Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology. PMID:19653916
Mining gene functional networks to improve mass-spectrometry-based protein identification. PMID:19633097
mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics. PMID:19624850
Genomic resources of Magnaporthe oryzae (GROMO): a comprehensive and integrated database on rice blast fungus. PMID:19604367
Gene and pathway-based second-wave analysis of genome-wide association studies. PMID:19584899
Gene expression profiling within the spleen of Clostridium perfringens-challenged broilers fed antibiotic-medicated and non-medicated diets. PMID:19500416
Semantic Web-based integration of cancer pathways and allele frequency data. PMID:19458791
Similar gene expression profiles of sporadic, PGL2-, and SDHD-linked paragangliomas suggest a common pathway to tumorigenesis. PMID:19432956
The Pathway Less Traveled: Moving from Candidate Genes to Candidate Pathways in the Analysis of Genome-Wide Data from Large Scale Pharmacogenetic Association Studies. PMID:19421424
GeneSet2miRNA: finding the signature of cooperative miRNA activities in the gene lists. PMID:19420064
Computational and functional analysis of growth hormone (GH)-regulated genes identifies the transcriptional repressor B-cell lymphoma 6 (Bc16) as a participant in GH-regulated transcription. PMID:19406940
Mouse models of human AML accurately predict chemotherapy response. PMID:19339691
Using triplet periodicity of nucleotide sequences for finding potential reading frame shifts in genes. PMID:19261626
A factor graph nested effects model to identify networks from genetic perturbations. PMID:19180177
An innovative approach for testing bioinformatics programs using metamorphic testing. PMID:19152705
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. PMID:19144170
Genetic effects in the leukotriene biosynthesis pathway and association with atherosclerosis. PMID:19130089
Flux balance analysis of primary metabolism in Chlamydomonas reinhardtii. PMID:19128495
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy. PMID:19098030
POLAR MAPPER: a computational tool for integrated visualization of protein interaction networks and mRNA expression data. PMID:19091689
Towards high-throughput metabolomics using ultrahigh-field Fourier transform ion cyclotron resonance mass spectrometry. PMID:19081807
A Neisseria meningitidis NMB1966 mutant is impaired for invasion of respiratory epithelial cells, survival in human blood and for virulence in vivo. PMID:19050914
Network integration and graph analysis in mammalian molecular systems biology. PMID:19045817
A survey of visualization tools for biological network analysis. PMID:19040716
The role of bioinformatics in pathway curation. PMID:19034548
A novel signaling pathway impact analysis. PMID:18990722
Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray. PMID:18990222
Gene expression profiling analysis reveals arsenic-induced cell cycle arrest and apoptosis in p53-proficient and p53-deficient cells through differential gene pathways. PMID:18929588
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. PMID:18925949
TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. PMID:18854039
Proteome-based comparative analyses of growth stages reveal new cell cycle-dependent functions in the predatory bacterium Bdellovibrio bacteriovorus. PMID:18836011
Testing gene set enrichment for subset of genes: Sub-GSE. PMID:18764941
Identification of intra-group, inter-individual, and gene-specific variances in mRNA expression profiles in the rheumatoid arthritis synovial membrane. PMID:18721452
The cis-regulatory map of Shewanella genomes. PMID:18701645
Group contribution method for thermodynamic analysis of complex metabolic networks. PMID:18645197
Combining genomics, metabolome analysis, and biochemical modelling to understand metabolic networks. PMID:18628911
MicroRNA miR-124 regulates neurite outgrowth during neuronal differentiation. PMID:18619591
MAID : an effect size based model for microarray data integration across laboratories and platforms. PMID:18616827
Computational systems analysis of dopamine metabolism. PMID:18568086
Gene-expression of metastasized versus non-metastasized primary head and neck squamous cell carcinomas: a pathway-based analysis. PMID:18544165
Targeting the human cancer pathway protein interaction network by structural genomics. PMID:18487680
Blast2GO: A comprehensive suite for functional analysis in plant genomics. PMID:18483572
Microbial genotype-phenotype mapping by class association rule mining. PMID:18467347
Exploration of non-hierarchical classification methods combined with linkage analysis to identify loci influencing clusters of co-regulated transcripts. PMID:18466547
Analysis of gene expression in Parkinson's disease: possible involvement of neurotrophic support and axon guidance in dopaminergic cell death. PMID:18462474
Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. PMID:18434084
Hematopoietic fingerprints: an expression database of stem cells and their progeny. PMID:18371395
Can subtle changes in gene expression be consistently detected with different microarray platforms? PMID:18331641
Complete genome sequence of the mosquitocidal bacterium Bacillus sphaericus C3-41 and comparison with those of closely related Bacillus species. PMID:18296527
Protein databases on the internet. PMID:18265344
Characterization of a newly developed chicken 44K Agilent microarray. PMID:18237426
The Caenorhabditis elegans K10C2.4 gene encodes a member of the fumarylacetoacetate hydrolase family: a Caenorhabditis elegans model of type I tyrosinemia. PMID:18227072
MeInfoText: associated gene methylation and cancer information from text mining. PMID:18194557
The cell cycle DB: a systems biology approach to cell cycle analysis. PMID:18160409
Cloning, analysis and functional annotation of expressed sequence tags from the Earthworm Eisenia fetida. PMID:18047730
A bifunctional locus (BIO3-BIO1) required for biotin biosynthesis in Arabidopsis. PMID:17993549
Discovery of protein interaction networks shared by diseases. PMID:17992746
Genes involved in TGF beta1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map. PMID:17953753
Modularized study of human calcium signalling pathway. PMID:17914243
Linking microarray reporters with protein functions. PMID:17897448
Consistency analysis of metabolic correlation networks. PMID:17892579
A systems biology approach for pathway level analysis. PMID:17785539
PROCOGNATE: a cognate ligand domain mapping for enzymes. PMID:17720712
A multidimensional analysis of genes mutated in breast and colorectal cancers. PMID:17693572
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
EGFR associated expression profiles vary with breast tumor subtype. PMID:17663798
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. PMID:17651921
DrugMetZ DB: an anthology of human drug metabolizing Chytochrome P450 enzymes. PMID:17597900
Onto-Tools: new additions and improvements in 2006. PMID:17584796
Detecting multivariate differentially expressed genes. PMID:17490475
A search engine to identify pathway genes from expression data on multiple organisms. PMID:17477880
Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis. PMID:17437024
Formal TCA cycle description based on elementary actions. PMID:17426387
Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PMID:17373854
Lipidomics reveals control of Mycobacterium tuberculosis virulence lipids via metabolic coupling. PMID:17360366
An integrative genomic approach to uncover molecular mechanisms of prokaryotic traits. PMID:17112314
cPath: open source software for collecting, storing, and querying biological pathways. PMID:17101041
Analysis and functional annotation of expressed sequence tags from the fall armyworm Spodoptera frugiperda. PMID:17052344
Topological properties of protein-protein and metabolic interaction networks of Drosophila melanogaster. PMID:16970548
Exopolysaccharide-associated protein sorting in environmental organisms: the PEP-CTERM/EpsH system. Application of a novel phylogenetic profiling heuristic. PMID:16930487
BiologicalNetworks: visualization and analysis tool for systems biology. PMID:16845051
BBP: Brucella genome annotation with literature mining and curation. PMID:16842628
Array2BIO: from microarray expression data to functional annotation of co-regulated genes. PMID:16780584
Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks. PMID:16753070
Toward understanding the genetics of alcohol drinking through transcriptome meta-analysis. PMID:16618939
EST2Prot: mapping EST sequences to proteins. PMID:16515706
Gene connectivity, function, and sequence conservation: predictions from modular yeast co-expression networks. PMID:16515682
A flexible representation of omic knowledge for thorough analysis of microarray data. PMID:16509996
BIOZON: a system for unification, management and analysis of heterogeneous biological data. PMID:16480510
Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities. PMID:16480496
Asymmetrical evolution of cytochrome bd subunits. PMID:16474982
PathSys: integrating molecular interaction graphs for systems biology. PMID:16464251
13C isotopologue perturbation studies of Listeria monocytogenes carbon metabolism and its modulation by the virulence regulator PrfA. PMID:16461909
MODBASE: a database of annotated comparative protein structure models and associated resources. PMID:16381869
BIOZON: a hub of heterogeneous biological data. PMID:16381854
GNARE: automated system for high-throughput genome analysis with grid computational backend. PMID:16328950
Genome-scale thermodynamic analysis of Escherichia coli metabolism. PMID:16299075
Gene expression evidence for remodeling of lateral hypothalamic circuitry in cocaine addiction. PMID:16076954
GBA server: EST-based digital gene expression profiling. PMID:15980560
Metabolic PathFinding: inferring relevant pathways in biochemical networks. PMID:15980483
Nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. PMID:15867197
Molecular models of protein targets from Mycobacterium tuberculosis. PMID:15759144
The genome sequence of Xanthomonas oryzae pathovar oryzae KACC10331, the bacterial blight pathogen of rice. PMID:15673718
The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number. PMID:15637156
Higher gene duplicabilities for metabolic proteins than for nonmetabolic proteins in yeast and E. coli. PMID:15599512
Mycobacterium tuberculosis functional network analysis by global subcellular protein profiling. PMID:15525680
Gene co-regulation is highly conserved in the evolution of eukaryotes and prokaryotes. PMID:15353560
The complete genome and proteome of Mycoplasma mobile. PMID:15289470
Onto-Tools: an ensemble of web-accessible, ontology-based tools for the functional design and interpretation of high-throughput gene expression experiments. PMID:15215428
Quantifying modularity in the evolution of biomolecular systems. PMID:14993205
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets. PMID:14563874
The genome sequence of Blochmannia floridanus: comparative analysis of reduced genomes. PMID:12886019
Network genomics--a novel approach for the analysis of biological systems in the post-genomic era. PMID:12463419
Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. PMID:11904428
Metabolomics--the link between genotypes and phenotypes. PMID:11860207
Comparative analysis of FUR regulons in gamma-proteobacteria. PMID:11812853
DIAN: a novel algorithm for genome ontological classification. PMID:11591654
Identification and characterization of mycobacterial proteins differentially expressed under standing and shaking culture conditions, including Rv2623 from a novel class of putative ATP-binding proteins. PMID:11500455
Transcript analysis of 1003 novel yeast genes using high-throughput northern hybridizations. PMID:11406594
A phylogenomic approach to microbial evolution. PMID:11139625
Predicting regulons and their cis-regulatory motifs by comparative genomics. PMID:11071941
Automatic detection of conserved gene clusters in multiple genomes by graph comparison and P-quasi grouping. PMID:11024184
Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. PMID:10958638
DIP: the database of interacting proteins. PMID:10592249
MAGEST: MAboya gene expression patterns and sequence tags. PMID:10592202
WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction. PMID:10592199
KEGG: kyoto encyclopedia of genes and genomes. PMID:10592173
Data, information, knowledge and principle: back to metabolism in KEGG PubMed citations: 1473.

1473 articles citing: Data, information, knowledge and principle: back to metabolism in KEGG

A balanced gut microbiota is essential to maintain health in captive sika deer. PMID:35922588
Chromosome-level assembly of Gymnocypris eckloni genome. PMID:35918339
A diagnostic model for overweight and obesity from untargeted urine metabolomics of soldiers. PMID:35898940
Phylotypic Diversity of Bacteria Associated with Speleothems of a Silicate Cave in a Guiana Shield Tepui. PMID:35889113
Effects of lactoferrin on intestinal flora of metabolic disorder mice. PMID:35869430
Impact of Geographical Location on the Gut Microbiota Profile in Egyptian Children with Type 1 Diabetes Mellitus: A Pilot Study. PMID:35864993
Gut Microbiome Differences in Rescued Common Kestrels (Falco tinnunculus) Before and After Captivity. PMID:35794924
Computational design and engineering of an Escherichia coli strain producing the nonstandard amino acid para-aminophenylalanine. PMID:35789833
Genome-Resolved Characterization of Structure and Potential Functions of the Zebrafish Stool Microbiome. PMID:35782152
Orrella daihaiensis sp. nov., a bacterium isolated from Daihai Lake in Inner Mongolia. PMID:35751751
Transcriptome Analysis Reveals the Regulatory Networks of Cytokinin in Promoting Floral Feminization in Castanea henryi. PMID:35742833
NMR-Based Metabolomics Identify Metabolic Change in Spleen of Idiopathic Thrombocytopenic Purpura Patients. PMID:35736497
Lessons From Insect Fungiculture: From Microbial Ecology to Plastics Degradation. PMID:35685924
Identification of Prognostic Biomarkers of Glioblastoma Based on Multidatabase Integration and Its Correlation with Immune-Infiltration Cells. PMID:35685428
Comparative genomics reveals low levels of inter- and intraspecies diversity in the causal agents of dwarf and common bunt of wheat and hint at conspecificity of Tilletia caries and T. laevis. PMID:35672841
Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review. PMID:35655999
Breast milk-derived extracellular vesicle miRNAs are associated with maternal asthma and atopy. PMID:35638388
Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities. PMID:35627157
Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes. PMID:35620097
Disruption of β-catenin-mediated negative feedback reinforces cAMP-induced neuronal differentiation in glioma stem cells. PMID:35610201
In-depth proteomics characterization of ∆Np73 effectors identifies key proteins with diagnostic potential implicated in lymphangiogenesis, vasculogenesis and metastasis in colorectal cancer. PMID:35586989
Studying Metabolism by NMR-Based Metabolomics. PMID:35573745
Deciphering the Underlying Mechanisms of Formula Le-Cao-Shi Against Liver Injuries by Integrating Network Pharmacology, Metabonomics, and Experimental Validation. PMID:35548342
Survival Characteristics and Transcriptomic Analyses Reveal the Adaptive Response of the Aquatic Pathogen Non-O1/O139 Vibrio cholerae to Starvation Stress. PMID:35532354
A Chromosome-Level Reference Genome of Chinese Balloon Flower (Platycodon grandiflorus). PMID:35464833
Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome. PMID:35456791
KEMET - A python tool for KEGG Module evaluation and microbial genome annotation expansion. PMID:35422973
Biosynthesis of exopolysaccharide and structural characterization by Lacticaseibacillus paracasei ZY-1 isolated from Tibetan kefir. PMID:35415646
PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search. PMID:35404943
Effects of Short-Chain Fatty Acid Modulation on Potentially Diarrhea-Causing Pathogens in Yaks Through Metagenomic Sequencing. PMID:35402298
Comparative Analysis of the Gut Microbiota of Mongolian Gazelle (Procapra gutturosa) Under Fragmented Habitats. PMID:35369477
Bladder cancer cells shift rapidly and spontaneously to cisplatin-resistant oxidative phosphorylation that is trackable in real time. PMID:35365706
Genome Sequence and Description of Paracoccus denitrificans Strain R-1, Isolated from Activated Sludge. PMID:35343764
Tumor Heterogeneity and Molecular Characteristics of Glioblastoma Revealed by Single-Cell RNA-Seq Data Analysis. PMID:35327982
Identification and Characterization of Bacillus tequilensis GYUN-300: An Antagonistic Bacterium Against Red Pepper Anthracnose Caused by Colletotrichum acutatum in Korea. PMID:35308370
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:35300459
Impact of 6 month conjugated equine estrogen versus estradiol-treatment on biomarkers and enriched gene sets in healthy mammary tissue of non-human primates. PMID:35298474
Decoding the Role of Astrocytes in the Entorhinal Cortex in Alzheimer's Disease Using High-Dimensional Single-Nucleus RNA Sequencing Data and Next-Generation Knowledge Discovery Methodologies: Focus on Drugs and Natural Product Remedies for Dementia. PMID:35295737
Predictive metabolomics of multiple Atacama plant species unveils a core set of generic metabolites for extreme climate resilience. PMID:35288949
Draft genome sequence of myo-inositol utilizing Aeromonas dhakensis 1P11S3 isolated from striped catfish (Pangasianodon hypopthalmus) in a local fish farm in Malaysia. PMID:35252492
Preterm birth buccal cell epigenetic biomarkers to facilitate preventative medicine. PMID:35232984
Comparative systeomics to elucidate physiological differences between CHO and SP2/0 cell lines. PMID:35228567
The Anticancer Ruthenium Compound BOLD-100 Targets Glycolysis and Generates a Metabolic Vulnerability towards Glucose Deprivation. PMID:35213972
Solea senegalensis Bacterial Intestinal Microbiota Is Affected by Low Dietary Inclusion of Ulva ohnoi. PMID:35211100
Chromosome-scale assembly and population diversity analyses provide insights into the evolution of Sapindus mukorossi. PMID:35178562
Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. PMID:35174104
Metagenomics of the midgut microbiome of Rhipicephalus microplus from China. PMID:35135613
Transcriptome analysis of the effect of a novel human serine protease inhibitor SPINK13 on gene expression in MHCC97-H cells. PMID:35116303
UCP1 Knockin Induces Lipid Dynamics and Transcriptional Programs in the Skeletal Muscles of Pigs. PMID:35096834
Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota. PMID:35058457
Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome. PMID:35014869
Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer. PMID:35013454
Bacteriome of Moist Smokeless Tobacco Products Consumed in India With Emphasis on the Predictive Functional Potential. PMID:35003015
Different dietary protein sources influence growth performance, antioxidant capacity, immunity, fecal microbiota and metabolites in weaned piglets. PMID:34977377
Computational Prediction of Biomarkers, Pathways, and New Target Drugs in the Pathogenesis of Immune-Based Diseases Regarding Kidney Transplantation Rejection. PMID:34975915
Mongoliitalea daihaiensis sp. nov., isolated from Daihai Lake in Inner Mongolia. PMID:34962584
Suitability of GWAS as a Tool to Discover SNPs Associated with Tick Resistance in Cattle: A Review. PMID:34959558
Comparative Analysis of Sugar Metabolites and Their Transporters in Sugarcane Following Sugarcane mosaic virus (SCMV) Infection. PMID:34948367
Predictive Biomarkers of Age-Related Macular Degeneration Response to Anti-VEGF Treatment. PMID:34945801
Loss of microRNA-135b Enhances Bone Metastasis in Prostate Cancer and Predicts Aggressiveness in Human Prostate Samples. PMID:34944822
Thalidomide Exerts Anti-Inflammatory Effects in Cutaneous Lupus by Inhibiting the IRF4/NF-ҡB and AMPK1/mTOR Pathways. PMID:34944673
Development and Validation of a Prognostic N6-Methyladenosine-Related Immune Gene Signature for Lung Adenocarcinoma. PMID:34876833
reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization. PMID:34873191
Lactiplantibacillus plantarum LRCC5314 includes a gene for serotonin biosynthesis via the tryptophan metabolic pathway. PMID:34865198
Macrophage Selenoproteins Restrict Intracellular Replication of Francisella tularensis and Are Essential for Host Immunity. PMID:34777335
Expression Profile and Potential Function of Circular RNAs in Peripheral Blood Mononuclear Cells in Male Patients With Primary Gout. PMID:34764979
The origin and impeded dissemination of the DNA phosphorothioation system in prokaryotes. PMID:34737280
Chromosome-Level Genome Assembly of the Asian Red-Tail Catfish (Hemibagrus wyckioides). PMID:34712270
Current State of Metabolomics Research in Meat Quality Analysis and Authentication. PMID:34681437
A Systems Approach to Interrogate Gene Expression Patterns in African American Men Presenting with Clinically Localized Prostate Cancer. PMID:34680291
Metabolomics and Inflammatory Mediator Profiling for the Differentiation of Life-Threatening and Non-Severe Appendicitis in the Pediatric Population. PMID:34677379
Circular RNAs in peripheral blood mononuclear cells from ankylosing spondylitis. PMID:34670246
Characterization of the First Cultured Psychrotolerant Representative of Legionella from Antarctica Reveals Its Unique Genome Structure. PMID:34668737
Metagenomic Analysis Identifies Sex-Related Cecal Microbial Gene Functions and Bacterial Taxa in the Quail. PMID:34660751
Microbiome Compositions From Infertile Couples Seeking In Vitro Fertilization, Using 16S rRNA Gene Sequencing Methods: Any Correlation to Clinical Outcomes? PMID:34660337
High-Quality Genome of the Medicinal Plant Strobilanthes cusia Provides Insights Into the Biosynthesis of Indole Alkaloids. PMID:34659312
A Method to Monitor the NAD+ Metabolome-From Mechanistic to Clinical Applications. PMID:34638936
The metabolomic landscape of rice heterosis highlights pathway biomarkers for predicting complex phenotypes. PMID:34608951
Microcoleus (Cyanobacteria) form watershed-wide populations without strong gradients in population structure. PMID:34608694
A Catalog of Natural Products Occurring in Watermelon-Citrullus lanatus. PMID:34595201
Improved Large-Scale Homology Search by Two-Step Seed Search Using Multiple Reduced Amino Acid Alphabets. PMID:34573438
Structural changes in the gut microbiota community of the black-necked crane (Grus nigricollis) in the wintering period. PMID:34561717
Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with ramie (Boehmeria nivea (L.) Gaud.) leaf color formation. PMID:34548018
Identifying the dynamic gene regulatory network during latent HIV-1 reactivation using high-dimensional ordinary differential equations. PMID:34531927
Identification of Novel Gene Signatures using Next-Generation Sequencing Data from COVID-19 Infection Models: Focus on Neuro-COVID and Potential Therapeutics. PMID:34531741
Temporal Transcriptomics of Gut Escherichia coli in Caenorhabditis elegans Models of Aging. PMID:34523995
RhoC Modulates Cell Junctions and Type I Interferon Response in Aggressive Breast Cancers. PMID:34513691
Bioaccumulation of therapeutic drugs by human gut bacteria. PMID:34497420
A machine learning framework for predicting drug-drug interactions. PMID:34475500
ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research. PMID:34471489
Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. PMID:34445339
Characterization of Martelella soudanensis sp. nov., Isolated from a Mine Sediment. PMID:34442814
Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle. PMID:34440337
H2O2 Induces Major Phosphorylation Changes in Critical Regulators of Signal Transduction, Gene Expression, Metabolism and Developmental Networks in Aspergillus nidulans. PMID:34436163
Metabolism of Poly-β1,4-N-Acetylglucosamine Substrates and Importation of N-Acetylglucosamine and Glucosamine by Enterococcus faecalis. PMID:34424034
Gene expression profile analysis of gallic acid-induced cell death process. PMID:34408198
The Application of High-Throughput Technologies for the Study of Microbiome and Cancer. PMID:34394190
High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement. PMID:34373642
Circulating Levels of the Short-Chain Fatty Acid Acetate Mediate the Effect of the Gut Microbiome on Visceral Fat. PMID:34335546
Morpho-metabotyping the oxidative stress response. PMID:34326354
Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. PMID:34316686
Insulin signaling regulates longevity through protein phosphorylation in Caenorhabditis elegans. PMID:34315882
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. PMID:34312531
The change of gut microbiota in MDD patients under SSRIs treatment. PMID:34290352
Diversity and function of culturable actinobacteria in the root-associated of Salvia miltiorrhiza Bunge. PMID:34285837
High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui. PMID:34282459
Functional annotation of noncoding mutations in cancer. PMID:34282050
Diet-induced microbiome shifts of sympatric overwintering birds. PMID:34272578
DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data. PMID:34241589
Genome-Wide Associations for Microscopic Differential Somatic Cell Count and Specific Mastitis Pathogens in Holstein Cows in Compost-Bedded Pack and Cubicle Farming Systems. PMID:34205623
Epigenetic inheritance of DNA methylation changes in fish living in hydrogen sulfide-rich springs. PMID:34185679
CROssBAR: comprehensive resource of biomedical relations with knowledge graph representations. PMID:34181736
Gut microbiome and its meta-omics perspectives: profound implications for cardiovascular diseases. PMID:34170211
Tailoring strain construction strategies for muconic acid production in S. cerevisiae and E. coli. PMID:34150501
Assessment of Oral Vancomycin-Induced Alterations in Gut Bacterial Microbiota and Metabolome of Healthy Men. PMID:34123865
Comprehensive Plasma Metabolomic Profile of Patients with Advanced Neuroendocrine Tumors (NETs). Diagnostic and Biological Relevance. PMID:34072010
Metatranscriptomic Analysis Reveals an Imbalance of Hepatopancreatic Flora of Chinese Mitten Crab Eriocheir sinensis with Hepatopancreatic Necrosis Disease. PMID:34071147
IDARE2-Simultaneous Visualisation of Multiomics Data in Cytoscape. PMID:34066448
Pharmacological targeting of TNS3 with histone deacetylase inhibitor as a therapeutic strategy in esophageal squamous cell carcinoma. PMID:34047714
Predicting Drug-Disease Association Based on Ensemble Strategy. PMID:34012464
Gut microbiome diversity and composition is associated with hypertension in women. PMID:33973959
hu.MAP 2.0: integration of over 15,000 proteomic experiments builds a global compendium of human multiprotein assemblies. PMID:33973408
Diversity and distribution of viruses inhabiting the deepest ocean on Earth. PMID:33972725
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes. PMID:33961223
Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study. PMID:33961220
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
From Proteomic Mapping to Invasion-Metastasis-Cascade Systemic Biomarkering and Targeted Drugging of Mutant BRAF-Dependent Human Cutaneous Melanomagenesis. PMID:33922182
Improvement of Torulaspora delbrueckii Genome Annotation: Towards the Exploitation of Genomic Features of a Biotechnologically Relevant Yeast. PMID:33920164
A computational method for drug sensitivity prediction of cancer cell lines based on various molecular information. PMID:33914775
A Bayesian Approach for Learning Gene Networks Underlying Disease Severity in COPD. PMID:33912251
Quantitative proteomics reveals the antifungal effect of canthin-6-one isolated from Ailanthus altissima against Fusarium oxysporum f. sp. cucumerinum in vitro. PMID:33891670
Gut microbiota of endangered crested ibis: Establishment, diversity, and association with reproductive output. PMID:33891612
Isolation and genomic characterization of five novel strains of Erysipelotrichaceae from commercial pigs. PMID:33888068
The BioCyc Metabolic Network Explorer. PMID:33882841
Mucosa-associated gut microbiome in Japanese patients with functional constipation. PMID:33879972
Pikeienuella piscinae gen. nov., sp. nov., a novel genus in the family Rhodobacteraceae. PMID:33877579
The landscape of metabolic pathway dependencies in cancer cell lines. PMID:33872312
Mahuang Decoction Antagonizes Acute Liver Failure via Modulating Tricarboxylic Acid Cycle and Amino Acids Metabolism. PMID:33859560
Tumor Microenvironment Proteomics: Lessons From Multiple Myeloma. PMID:33833982
Effects of Exercise on the Oral Microbiota and Saliva of Patients with Non-Alcoholic Fatty Liver Disease. PMID:33810609
Protection against Glucolipotoxicity by High Density Lipoprotein in Human PANC-1 Hybrid 1.1B4 Pancreatic Beta Cells: The Role of microRNA. PMID:33805674
Microbial Metabolomics: From Methods to Translational Applications. PMID:33791977
Longitudinal study of the scalp microbiome suggests coconut oil to enrich healthy scalp commensals. PMID:33790324
Nitidine chloride suppresses epithelial-mesenchymal transition and stem cell-like properties in glioblastoma by regulating JAK2/STAT3 signaling. PMID:33788424
Gene Expression Analysis Suggests Immunological Changes of Peripheral Blood Monocytes in the Progression of Patients With Coronary Artery Disease. PMID:33777109
SOFAR: Large-Scale Association Network Learning. PMID:33746241
NOGEA: A Network-oriented Gene Entropy Approach for Dissecting Disease Comorbidity and Drug Repositioning. PMID:33744433
Pre-Cambrian roots of novel Antarctic cryptoendolithic bacterial lineages. PMID:33741058
Differential microRNAs expression profiles in liver from three different lifestyle modification mice models. PMID:33740891
Alterations in skin microbiome mediated by radiotherapy and their potential roles in the prognosis of radiotherapy-induced dermatitis: a pilot study. PMID:33664352
Evaluation of an O2-Substituted (1-3)-β-D-Glucan, Produced by Pediococcus parvulus 2.6, in ex vivo Models of Crohn's Disease. PMID:33613490
LncRNAs Landscape in the patients of primary gout by microarray analysis. PMID:33600466
MetNet: A two-level approach to reconstructing and comparing metabolic networks. PMID:33577575
Microbiota alteration at different stages in gastric lesion progression: a population-based study in Linqu, China. PMID:33575087
Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis. PMID:33574331
A genome-wide association study for gut metagenome in Chinese adults illuminates complex diseases. PMID:33563976
Myeloid-derived suppressor cell (MDSC) key genes analysis in rat anti-CD28-induced immune tolerance kidney transplantation. PMID:33532310
Finding branched pathways in metabolic network via atom group tracking. PMID:33529200
Higher genome variability within metabolism genes associates with recurrent Clostridium difficile infection. PMID:33509087
Design and evaluation of synthetic bacterial consortia for optimized phenanthrene degradation through the integration of genomics and shotgun proteomics. PMID:33489789
An Ion Chromatography-Ultrahigh-Resolution-MS1/Data-Independent High-Resolution MS2 Method for Stable Isotope-Resolved Metabolomics Reconstruction of Central Metabolic Networks. PMID:33482055
The role of host promiscuity in the invasion process of a seaweed holobiont. PMID:33479490
Genome-scale revealing the central metabolic network of the fast growing methanotroph Methylomonas sp. ZR1. PMID:33452942
Spatiotemporal Analysis of the Water and Sediment Nile Microbial Community Along an Urban Metropolis. PMID:33420624
Intestinal Microbiome in Preterm Infants Influenced by Enteral Iron Dosing. PMID:33394885
Effects of Co-culture on Improved Productivity and Bioresource for Microalgal Biomass Using the Floc-Forming Bacteria Melaminivora Jejuensis. PMID:33392165
Epigenome-wide association study (EWAS) for potential transgenerational disease epigenetic biomarkers in sperm following ancestral exposure to the pesticide methoxychlor. PMID:33391823
The Large Scale Structure of Human Metabolism Reveals Resilience via Extensive Signaling Crosstalk. PMID:33391012
E. coli NF73-1 Isolated From NASH Patients Aggravates NAFLD in Mice by Translocating Into the Liver and Stimulating M1 Polarization. PMID:33363046
Arsenate-Induced Changes in Bacterial Metabolite and Lipid Pools during Phosphate Stress. PMID:33361371
Gut Microbiota in Dholes During Estrus. PMID:33329438
Epigenome-wide association study for atrazine induced transgenerational DNA methylation and histone retention sperm epigenetic biomarkers for disease. PMID:33326428
Deciphering rice metabolic flux reprograming under salinity stress via in silico metabolic modeling. PMID:33304454
Proteome size reduction in Apicomplexans is linked with loss of DNA repair and host redundant pathways. PMID:33296723
LKB1 Differently Regulates Adipogenesis in Intramuscular and Subcutaneous Adipocytes through Metabolic and Cytokine-Related Signaling Pathways. PMID:33291665
Bringing New Methods to the Seed Proteomics Platform: Challenges and Perspectives. PMID:33271881
Rumen and Serum Metabolomes in Response to Endophyte-Infected Tall Fescue Seed and Isoflavone Supplementation in Beef Steers. PMID:33256042
Mobilization of Iron Stored in Bacterioferritin Is Required for Metabolic Homeostasis in Pseudomonas aeruginosa. PMID:33255203
Zygosaccharomyces rouxii, an Aromatic Yeast Isolated From Chili Sauce, Is Able to Biosynthesize 2-Phenylethanol via the Shikimate or Ehrlich Pathways. PMID:33250885
Single-cell RNA sequencing and lipidomics reveal cell and lipid dynamics of fat infiltration in skeletal muscle. PMID:33244879
Comprehensive Multi-omics Analysis Reveals Mitochondrial Stress as a Central Biological Hub for Spaceflight Impact. PMID:33242417
Chemotherapeutic efficacy of cucurmosin for pancreatic cancer as an alternative of gemcitabine: a comparative metabolomic study. PMID:33224818
Identification and quantification of target metabolites combined with transcriptome of two rheum species focused on anthraquinone and flavonoids biosynthesis. PMID:33219248
Analysis of the vaginal microbiome of giant pandas using metagenomics sequencing. PMID:33205903
Targeted Metagenomics of Retting in Flax: The Beginning of the Quest to Harness the Secret Powers of the Microbiota. PMID:33193706
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research. PMID:33173863
Quorum Sensing System in Bacteroides thetaiotaomicron Strain Identified by Genome Sequence Analysis. PMID:33134713
KEGG: integrating viruses and cellular organisms. PMID:33125081
Cp1/cathepsin L is required for autolysosomal clearance in Drosophila. PMID:33112206
Effects of Selenium- and Zinc-Enriched Lactobacillus plantarum SeZi on Antioxidant Capacities and Gut Microbiome in an ICR Mouse Model. PMID:33096847
Microbial community successions and their dynamic functions during harmful cyanobacterial blooms in a freshwater lake. PMID:33086464
Metagenomics Reveals Diet-Specific Specialization of Bacterial Communities in Fungus Gardens of Grass- and Dicot-Cutter Ants. PMID:33072030
Genome-wide analysis of PRR gene family uncovers their roles in circadian rhythmic changes and response to drought stress in Gossypium hirsutum L. PMID:33033660
A high-quality chromosome-level genome assembly reveals genetics for important traits in eggplant. PMID:33024567
Complete Genome Sequencing and Transcriptome Analysis of Nitrogen Metabolism of Succinivibrio dextrinosolvens Strain Z6 Isolated From Dairy Cow Rumen. PMID:33013723
Changes in the Gut Microbiota are Associated with Hypertension, Hyperlipidemia, and Type 2 Diabetes Mellitus in Japanese Subjects. PMID:33007825
Dynamic distribution of gut microbiota during embryonic development in chicken. PMID:32988546
The ModelSEED Biochemistry Database for the integration of metabolic annotations and the reconstruction, comparison and analysis of metabolic models for plants, fungi and microbes. PMID:32986834
Metagenomic Functional Profiling Reveals Differences in Bacterial Composition and Function During Bioaugmentation of Aged Petroleum-Contaminated Soil. PMID:32983067
Metabolomic Approaches to Study Chemical Exposure-Related Metabolism Alterations in Mammalian Cell Cultures. PMID:32961865
The intestinal microbiome is a co-determinant of the postprandial plasma glucose response. PMID:32947608
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. PMID:32941628
Cell Plasticity and Genomic Structure of a Novel Filterable Rhizobiales Bacterium that Belongs to a Widely Distributed Lineage. PMID:32906802
Modeling Novel Putative Drugs and Vaccine Candidates against Tick-Borne Pathogens: A Subtractive Proteomics Approach. PMID:32906620
The Gut Microbiota of Pheasant Lineages Reflects Their Host Genetic Variation. PMID:32903781
Comparative iTRAQ proteomic profiling of proteins associated with the adaptation of brown planthopper to moderately resistant vs. susceptible rice varieties. PMID:32903256
The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16. PMID:32901024
Metabolic Responses to Arsenite Exposure Regulated through Histidine Kinases PhoR and AioS in Agrobacterium tumefaciens 5A. PMID:32887433
Transcriptomic analysis reveals ethylene signal transduction genes involved in pistil development of pumpkin. PMID:32879792
The relationship between the rumen microbiome and carcass merit in Angus steers. PMID:32877916
Ion mobility collision cross-section atlas for known and unknown metabolite annotation in untargeted metabolomics. PMID:32859911
Chromosome-level genome assembly of the female western mosquitofish (Gambusia affinis). PMID:32852039
Aphid-Responsive Defense Networks in Hybrid Switchgrass. PMID:32849703
Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C sequencing. PMID:32821405
Comparative gut microbiome analysis of the Prakriti and Sasang systems reveals functional level similarities in constitutionally similar classes. PMID:32802721
Alterations of Gut Microbiome in Tibetan Patients With Coronary Heart Disease. PMID:32793515
Biliary Tract Carcinogenesis Model Based on Bile Metaproteomics. PMID:32793466
Associations between maternal lifetime stressors and negative events in pregnancy and breast milk-derived extracellular vesicle microRNAs in the programming of intergenerational stress mechanisms (PRISM) pregnancy cohort. PMID:32777999
Danon Disease-Associated LAMP-2 Deficiency Drives Metabolic Signature Indicative of Mitochondrial Aging and Fibrosis in Cardiac Tissue and hiPSC-Derived Cardiomyocytes. PMID:32751926
Genome-scale reconstruction of Paenarthrobacter aurescens TC1 metabolic model towards the study of atrazine bioremediation. PMID:32747737
The alteration of gut microbiome and metabolism in amyotrophic lateral sclerosis patients. PMID:32747678
Sequencing effort dictates gene discovery in marine microbial metagenomes. PMID:32743860
Structural Variability and Functional Prediction in the Epiphytic Bacteria Assemblies of Myriophyllum spicatum. PMID:32740714
Expression profiling of circular RNAs and their potential role in early‑stage diabetic cardiomyopathy. PMID:32705182
Genomics of Heat Tolerance in Reproductive Performance Investigated in Four Independent Maternal Lines of Pigs. PMID:32695139
Differential Gene Set Enrichment Analysis: a statistical approach to quantify the relative enrichment of two gene sets. PMID:32692836
Enterotoxigenic Bacteroides fragilis induces the stemness in colorectal cancer via upregulating histone demethylase JMJD2B. PMID:32684087
Impact of processing method on donated human breast milk microRNA content. PMID:32667939
The duodenal microbiome is altered in small intestinal bacterial overgrowth. PMID:32645011
Developmental origins of transgenerational sperm histone retention following ancestral exposures. PMID:32628935
Directed evolution approach to enhance efficiency and speed of outgrowth during single cell subcloning of Chinese Hamster Ovary cells. PMID:32612755
The effect of a diet based on rice straw co-fermented with probiotics and enzymes versus a fresh corn Stover-based diet on the rumen bacterial community and metabolites of beef cattle. PMID:32612135
Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. PMID:32610626
Effects of diet, habitat, and phylogeny on the fecal microbiome of wild African savanna (Loxodonta africana) and forest elephants (L. cyclotis). PMID:32607180
The Trait Repertoire Enabling Cyanobacteria to Bloom Assessed through Comparative Genomic Complexity and Metatranscriptomics. PMID:32605986
Genome-Wide Analysis Reveals Genetic Potential for Aromatic Compounds Biodegradation of Sphingopyxis. PMID:32596333
Bioprospecting Microbial Diversity for Lignin Valorization: Dry and Wet Screening Methods. PMID:32582068
Expression regulation of MALATE SYNTHASE involved in glyoxylate cycle during protocorm development in Phalaenopsis aphrodite (Orchidaceae). PMID:32572104
A de novo assembly of the sweet cherry (Prunus avium cv. Tieton) genome using linked-read sequencing technology. PMID:32547856
Enhanced Hyaluronan Signaling and Autophagy Dysfunction by VPS35 D620N. PMID:32540366
Bacterial community composition and potential pathogens along the Pinheiros River in the southeast of Brazil. PMID:32518363
Transcriptome Analysis of Maternal Gene Transcripts in Unfertilized Eggs of Misgurnus anguillicaudatus and Identification of Immune-Related Maternal Genes. PMID:32485896
Applications of Chromatography-Ultra High-Resolution MS for Stable Isotope-Resolved Metabolomics (SIRM) Reconstruction of Metabolic Networks. PMID:32483395
Characterization of a potential probiotic bacterium Lactococcus raffinolactis WiKim0068 isolated from fermented vegetable using genomic and in vitro analyses. PMID:32460704
De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells. PMID:32453724
Adaptive matching between phyllosphere bacteria and their tree hosts in a neotropical forest. PMID:32438916
β-Oxidation and autophagy are critical energy providers during acute glucose depletion in Saccharomyces cerevisiae. PMID:32430326
Serum metabolic signatures of high myopia among older Chinese adults. PMID:32424328
Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. PMID:32414048
Genome-Wide Transcriptomic Analysis Identifies Pathways Regulated by Sterculic Acid in Retinal Pigmented Epithelium Cells. PMID:32403229
An integrative multi-omics approach uncovers the regulatory role of CDK7 and CDK4 in autophagy activation induced by silica nanoparticles. PMID:32397800
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
Effect of 3,3'-Diindolylmethane on Pulmonary Injury Following Thoracic Irradiation in CBA Mice. PMID:32384373
Differential metabolic markers associated with primary open-angle glaucoma and cataract in human aqueous humor. PMID:32375707
Genome and Transcriptome Analyses Provide Insight Into the Omega-3 Long-Chain Polyunsaturated Fatty Acids Biosynthesis of Schizochytrium limacinum SR21. PMID:32373097
Ancient genes can be served as pan-cancer diagnostic and prognostic biomarkers. PMID:32368859
Divergent Co-occurrence Patterns and Assembly Processes Structure the Abundant and Rare Bacterial Communities in a Salt Marsh Ecosystem. PMID:32358000
Maternal H. pylori is associated with differential fecal microbiota in infants born by vaginal delivery. PMID:32350392
Incomplete Freund's adjuvant reduces arginase and enhances Th1 dominance, TLR signaling and CD40 ligand expression in the vaccine site microenvironment. PMID:32350119
Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis. PMID:32325894
A Brain Signaling Framework for Stress-Induced Depression and Ketamine Treatment Elucidated by Phosphoproteomics. PMID:32317933
Succession of physiological stages hallmarks the transcriptomic response of the fungus Aspergillus niger to lignocellulose. PMID:32313551
Metagenome-assembled genome distribution and key functionality highlight importance of aerobic metabolism in Svalbard permafrost. PMID:32301987
Transcriptomic Changes in the Rumen Epithelium of Cattle after the Induction of Acidosis. PMID:32292009
Insights into the origin of metazoan multicellularity from predatory unicellular relatives of animals. PMID:32272915
A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae). PMID:32257232
Structure of the Mucosal and Stool Microbiome in Lynch Syndrome. PMID:32240601
Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans Model. PMID:32231124
Applying the exposome concept in birth cohort research: a review of statistical approaches. PMID:32221742
WeiBI (web-based platform): Enriching integrated interaction network with increased coverage and functional proteins from genome-wide experimental OMICS data. PMID:32221380
Improving lipid mapping in Genome Scale Metabolic Networks using ontologies. PMID:32215752
Exploring metabolic adaptation of Streptococcus pneumoniae to antibiotics. PMID:32210362
Environmental remodeling of human gut microbiota and antibiotic resistome in livestock farms. PMID:32188862
Complete Genome Insights into Lactococcus petauri CF11 Isolated from a Healthy Human Gut Using Second- and Third-Generation Sequencing. PMID:32174973
What's Genetic Variation Got to Do with It? Starvation-Induced Self-Fertilization Enhances Survival in Paramecium. PMID:32163147
Metagenomic analysis reveals the microbiome and resistome in migratory birds. PMID:32122398
Risk of epilepsy in rheumatoid arthritis: a meta-analysis of population based studies and bioinformatics analysis. PMID:32095225
Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis. PMID:32094181
Untargeted metabolomics links glutathione to bacterial cell cycle progression. PMID:32090198
Systems biology approach identifies functional modules and regulatory hubs related to secondary metabolites accumulation after transition from autotrophic to heterotrophic growth condition in microalgae. PMID:32084664
Multiple Pathways Involved in Palmitic Acid-Induced Toxicity: A System Biology Approach. PMID:32076395
Systematic genetics and single-cell imaging reveal widespread morphological pleiotropy and cell-to-cell variability. PMID:32064787
"Candidatus Galacturonibacter soehngenii" Shows Acetogenic Catabolism of Galacturonic Acid but Lacks a Canonical Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase Complex. PMID:32063897
High Throughput Sediment DNA Sequencing Reveals Azo Dye Degrading Bacteria Inhabit Nearshore Sediments. PMID:32050437
Comprehensive Analysis of the mRNA-lncRNA Co-expression Profile and ceRNA Networks Patterns in Chronic Hepatitis B. PMID:32030083
Toward a gold standard for benchmarking gene set enrichment analysis. PMID:32026945
A Novel D-Galacturonate Fermentation Pathway in Lactobacillus suebicus Links Initial Reactions of the Galacturonate-Isomerase Route With the Phosphoketolase Pathway. PMID:32010092
LC-MS metabolomics comparisons of cancer cell and macrophage responses to methotrexate and polymer-encapsulated methotrexate. PMID:31993584
Rumen fluid metabolomics of beef steers differing in feed efficiency. PMID:31989305
Integrative Metabolic Pathway Analysis Reveals Novel Therapeutic Targets in Osteoarthritis. PMID:31980557
Domain-mediated interactions for protein subfamily identification. PMID:31937869
Effects of spaceflight on the composition and function of the human gut microbiota. PMID:31924114
Photosynthetic characterization and expression profiles of sugarcane infected by Sugarcane mosaic virus (SCMV). PMID:31900791
Leveraging complementary computational models for prioritizing chemicals of developmental and reproductive toxicity concern: an example of food contact materials. PMID:31897520
Novel syntrophic bacteria in full-scale anaerobic digesters revealed by genome-centric metatranscriptomics. PMID:31896784
Overlap matrix completion for predicting drug-associated indications. PMID:31869322
Complete Genome Sequence of Acidithiobacillus Ferrooxidans YNTRS-40, a Strain of the Ferrous Iron- and Sulfur-Oxidizing Acidophile. PMID:31861345
Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer. PMID:31857433
Extracellular Vesicles From Auditory Cells as Nanocarriers for Anti-inflammatory Drugs and Pro-resolving Mediators. PMID:31849615
Thriving in Wetlands: Ecophysiology of the Spiral-Shaped Methanotroph Methylospira mobilis as Revealed by the Complete Genome Sequence. PMID:31835835
Metabolomics of Small Intestine Neuroendocrine Tumors and Related Hepatic Metastases. PMID:31835679
Metagenomics of Atacama Lithobiontic Extremophile Life Unveils Highlights on Fungal Communities, Biogeochemical Cycles and Carbohydrate-Active Enzymes. PMID:31783517
A comparative analysis of gene expression induced by the embryo in the caprine endometrium. PMID:31782264
The State-of-the Art of Environmental Toxicogenomics: Challenges and Perspectives of "Omics" Approaches Directed to Toxicant Mixtures. PMID:31779274
Hypoxic Environment and Paired Hierarchical 3D and 2D Models of Pediatric H3.3-Mutated Gliomas Recreate the Patient Tumor Complexity. PMID:31779235
Adipocyte epigenetic alterations and potential therapeutic targets in transgenerationally inherited lean and obese phenotypes following ancestral exposures. PMID:31755359
Enhanced Microbial Interactions and Deterministic Successions During Anoxic Decomposition of Microcystis Biomass in Lake Sediment. PMID:31736913
A therapeutic antibody targeting osteoprotegerin attenuates severe experimental pulmonary arterial hypertension. PMID:31729368
Sperm DNA Methylation Epimutation Biomarkers for Male Infertility and FSH Therapeutic Responsiveness. PMID:31727924
A Bioinformatics Guide to Plant Microbiome Analysis. PMID:31708944
Metabolomic Analysis of Radiation-Induced Lung Injury in Rats: The Potential Radioprotective Role of Taurine. PMID:31700502
Comprehensive Stress-Based De Novo Transcriptome Assembly and Annotation of Guar (Cyamopsis tetragonoloba (L.) Taub.): An Important Industrial and Forage Crop. PMID:31687376
Metabolomic Analysis of Influenza A Virus A/WSN/1933 (H1N1) Infected A549 Cells during First Cycle of Viral Replication. PMID:31683654
Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations. PMID:31682807
circ-016910 sponges miR-574-5p to regulate cell physiology and milk synthesis via MAPK and PI3K/AKT-mTOR pathways in GMECs. PMID:31663119
Draft genome sequence of cauliflower (Brassica oleracea L. var. botrytis) provides new insights into the C genome in Brassica species. PMID:31645943
Draft genome sequences of two oriental melons, Cucumis melo L. var. makuwa. PMID:31641135
Herbal Formula-3 ameliorates OVA-induced food allergy in mice may via modulating the gut microbiota. PMID:31632550
Influence of Maternal Inulin-Type Prebiotic Intervention on Glucose Metabolism and Gut Microbiota in the Offspring of C57BL Mice. PMID:31632351
Small RNA and degradome deep sequencing reveal respective roles of cold-related microRNAs across Chinese wild grapevine and cultivated grapevine. PMID:31615400
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Gut microbiota differences in elderly subjects between rural city Kyotango and urban city Kyoto: an age-gender-matched study. PMID:31592207
Elemental diet induces alterations of the gut microbial community in mice. PMID:31592206
Glutarate L-2-hydroxylase (CsiD/GlaH) is an archetype Fe(II)/2-oxoglutarate-dependent dioxygenase. PMID:31564307
Metabolic profiles of serum samples from ground glass opacity represent potential diagnostic biomarkers for lung cancer. PMID:31555521
Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment. PMID:31549347
Effects of a vinegar-based multi-micronutrient supplement in rats: a multi-pronged assessment of dietary impact. PMID:31531127
Cold-induced lipid dynamics and transcriptional programs in white adipose tissue. PMID:31530289
Epigenetic transgenerational inheritance of testis pathology and Sertoli cell epimutations: generational origins of male infertility. PMID:31528361
Transcriptome divergence during leaf development in two contrasting switchgrass (Panicum virgatum L.) cultivars. PMID:31513611
Drug repositioning based on bounded nuclear norm regularization. PMID:31510658
ePath: an online database towards comprehensive essential gene annotation for prokaryotes. PMID:31506471
Longitudinal development of the gut microbiota in healthy and diarrheic piglets induced by age-related dietary changes. PMID:31496126
Bromodomain inhibitor jq1 induces cell cycle arrest and apoptosis of glioma stem cells through the VEGF/PI3K/AKT signaling pathway. PMID:31485609
The improved assembly of 7DL chromosome provides insight into the structure and evolution of bread wheat. PMID:31471988
Metabolome-based discrimination of chrysanthemum cultivars for the efficient generation of flower color variations in mutation breeding. PMID:31451959
Decreased FBP1 expression rewires metabolic processes affecting aggressiveness of glioblastoma. PMID:31444412
Toward understanding the origin and evolution of cellular organisms. PMID:31441146
Antibiotic resistance and metabolic profiles as functional biomarkers that accurately predict the geographic origin of city metagenomics samples. PMID:31429791
Pretreatment With Bacillus cereus Preserves Against D-Galactosamine-Induced Liver Injury in a Rat Model. PMID:31417535
The liver proteome in a mouse model for Ascaris suum resistance and susceptibility: evidence for an altered innate immune response. PMID:31412915
Obese Individuals with and without Type 2 Diabetes Show Different Gut Microbial Functional Capacity and Composition. PMID:31399369
The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. PMID:31387118
Microbiomes of Velloziaceae from phosphorus-impoverished soils of the campos rupestres, a biodiversity hotspot. PMID:31366912
Metabolic diversification of nitrogen-containing metabolites by the expression of a heterologous lysine decarboxylase gene in Arabidopsis. PMID:31364191
Mitochondrial oxidative stress-induced transcript variants of ATF3 mediate lipotoxic brain microvascular injury. PMID:31356870
Salivary Metabolomics of Total Body Irradiated Nonhuman Primates Reveals Long-Term Normal Tissue Responses to Radiation. PMID:31352081
Gains and losses of metabolic function inferred from a phylotranscriptomic analysis of algae. PMID:31324835
Finding Functional Differences Between Species in a Microbial Community: Case Studies in Wine Fermentation and Kefir Culture. PMID:31293529
RNA-Sequencing Analysis of Paternal Low-Protein Diet-Induced Gene Expression Change in Mouse Offspring Adipocytes. PMID:31289120
Classification of alkaloids according to the starting substances of their biosynthetic pathways using graph convolutional neural networks. PMID:31288752
Micronutrient Requirements and Sharing Capabilities of the Human Gut Microbiome. PMID:31275260
Chitosan Oligosaccharide Ameliorates Nonalcoholic Fatty Liver Disease (NAFLD) in Diet-Induced Obese Mice. PMID:31269758
Identifying miRNA-mRNA Pairs and Novel miRNAs from Hepatocelluar Carcinoma miRNomes and TCGA Database. PMID:31258761
Site-specific cleavage of bacterial MucD by secreted proteases mediates antibacterial resistance in Arabidopsis. PMID:31253808
Dual pathways of tRNA hydroxylation ensure efficient translation by expanding decoding capability. PMID:31253794
Combined network analysis and machine learning allows the prediction of metabolic pathways from tomato metabolomics data. PMID:31240252
Metabolic Effect of Dietary Taurine Supplementation on Grouper (Epinephelus coioides): A 1H-NMR-Based Metabolomics Study. PMID:31212947
High-Fat Diet Alters the Intestinal Microbiota in Streptozotocin-Induced Type 2 Diabetic Mice. PMID:31208113
Sperm epimutation biomarkers of obesity and pathologies following DDT induced epigenetic transgenerational inheritance of disease. PMID:31186947
Geochemical-Compositional-Functional Changes in Arctic Soil Microbiomes Post Land Submergence Revealed by Metagenomics. PMID:31178526
The diversity, evolution and ecology of Salmonella in venomous snakes. PMID:31163033
Negative regulation of miR-1275 by H3K27me3 is critical for glial induction of glioblastoma cells. PMID:31162799
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language. PMID:31159881
LnCompare: gene set feature analysis for human long non-coding RNAs. PMID:31147707
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. PMID:31142855
Absolute Measurements of mRNA Translation in Caulobacter crescentus Reveal Important Fitness Costs of Vitamin B12 Scavenging. PMID:31138672
Inhibition of nucleotide synthesis promotes replicative senescence of human mammary epithelial cells. PMID:31138644
Drug repositioning of herbal compounds via a machine-learning approach. PMID:31138103
An integrated insight into the response of bacterial communities to anthropogenic contaminants in a river: A case study of the Wonderfonteinspruit catchment area, South Africa. PMID:31112559
Jackknife Model Averaging Prediction Methods for Complex Phenotypes with Gene Expression Levels by Integrating External Pathway Information. PMID:31089389
Carbohydrate metabolism genes dominant in a subtropical marine mangrove ecosystem revealed by metagenomics analysis. PMID:31073898
Horizontal acquisition of hydrogen conversion ability and other habitat adaptations in the Hydrogenovibrio strains SP-41 and XCL-2. PMID:31060509
Superantigen SpeA attenuates the biofilm forming capacity of Streptococcus pyogenes. PMID:31054134
Disruption of the pleiotropic gene scoC causes transcriptomic and phenotypical changes in Bacillus pumilus BA06. PMID:31039790
An integrated genomic and metabolomic approach for defining survival time in adult oligodendrogliomas patients. PMID:31037432
Identification and functional prediction of cold-related long non-coding RNA (lncRNA) in grapevine. PMID:31036931
Parallel repulsive logic regression with biological adjacency. PMID:31030217
A signature of circulating inflammatory proteins and development of end-stage renal disease in diabetes. PMID:31011203
Assessment of Glyphosate Induced Epigenetic Transgenerational Inheritance of Pathologies and Sperm Epimutations: Generational Toxicology. PMID:31011160
FuncTree2: an interactive radial tree for functional hierarchies and omics data visualization. PMID:31004476
Immunometabolic Signatures Predict Risk of Progression to Active Tuberculosis and Disease Outcome. PMID:30967866
Novel insights into gene expression regulation during meiosis revealed by translation elongation dynamics. PMID:30962948
Genome-wide associations and functional gene analyses for endoparasite resistance in an endangered population of native German Black Pied cattle. PMID:30961534
Genome-wide identification and co-expression network analysis of nuclear factor-Y in barley revealed potential functions in salt stress. PMID:30956430
Metabolic reaction network-based recursive metabolite annotation for untargeted metabolomics. PMID:30944337
Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer. PMID:30936547
Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. PMID:30886425
High-throughput sequence analysis of bacterial communities in commercial biofertiliser products marketed in South Africa: an independent snapshot quality assessment. PMID:30863692
Genome-Wide Association Study for Milk Protein Composition Traits in a Chinese Holstein Population Using a Single-Step Approach. PMID:30838020
Evolutionary design principles in metabolism. PMID:30836874
A metabolomics-based approach for non-invasive screening of fetal central nervous system anomalies. PMID:30830338
Impacts of microbial assemblage and environmental conditions on the distribution of anatoxin-a producing cyanobacteria within a river network. PMID:30809011
Central systolic pressure and a nonessential amino acid metabolomics profile: the African Prospective study on the Early Detection and Identification of Cardiovascular disease and Hypertension. PMID:30801385
Environmental Toxicant Induced Epigenetic Transgenerational Inheritance of Prostate Pathology and Stromal-Epithelial Cell Epigenome and Transcriptome Alterations: Ancestral Origins of Prostate Disease. PMID:30778168
The sequence and de novo assembly of Oxygymnocypris stewartii genome. PMID:30720802
The neuroactive potential of the human gut microbiota in quality of life and depression. PMID:30718848
Transcriptome Analysis of Mesenchymal Stem Cells from Multiple Myeloma Patients Reveals Downregulation of Genes Involved in Cell Cycle Progression, Immune Response, and Bone Metabolism. PMID:30705326
Identification of Early Salinity Stress-Responsive Proteins in Dunaliella salina by isobaric tags for relative and absolute quantitation (iTRAQ)-Based Quantitative Proteomic Analysis. PMID:30704074
Metabolic Modeling of Human Gut Microbiota on a Genome Scale: An Overview. PMID:30695998
Complete Genome Sequence Analysis and Characterization of Selected Iron Regulation Genes of Pasteurella Multocida Serotype A Strain PMTB2.1. PMID:30691021
Vertical Stratification of Sediment Microbial Communities Along Geochemical Gradients of a Subterranean Estuary Located at the Gloucester Beach of Virginia, United States. PMID:30687299
Synthetic lethality guiding selection of drug combinations in ovarian cancer. PMID:30682083
Dose-dependent impact of oxytetracycline on the veal calf microbiome and resistome. PMID:30660184
Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. PMID:30647083
Robust analysis of novel mRNA-lncRNA cross talk based on ceRNA hypothesis uncovers carcinogenic mechanism and promotes diagnostic accuracy in esophageal cancer. PMID:30643460
Determination of host proteins composing the microenvironment of coronavirus replicase complexes by proximity-labeling. PMID:30632963
The RNA degradosome promotes tRNA quality control through clearance of hypomodified tRNA. PMID:30622183
The Relationship Between Microbial Community Structures and Environmental Parameters Revealed by Metagenomic Analysis of Hot Spring Water in the Kirishima Area, Japan. PMID:30619848
Methanogenesis on Early Stages of Life: Ancient but Not Primordial. PMID:30612264
Gene Expression Profiles of Two Coral Species with Varied Resistance to Ocean Acidification. PMID:30612219
Time-lagged Ordered Lasso for network inference. PMID:30594121
Bayesian inference of networks across multiple sample groups and data types. PMID:30590505
Transcriptomic profiles of muscle, heart, and spleen in reaction to circadian heat stress in Ethiopian highland and lowland male chicken. PMID:30565091
Spatially resolved metabolomics to discover tumor-associated metabolic alterations. PMID:30559182
Integrating tumor genomics into studies of the microbiome in colorectal cancer. PMID:30556775
Synthetic lethal combinations of low-toxicity drugs for breast cancer identified in silico by genetic screens in yeast. PMID:30555636
RNA Sequencing Provides Insights into the Regulation of Solanesol Biosynthesis in Nicotiana tabacum Induced by Moderately High Temperature. PMID:30544626
Survival, Virulent Characteristics, and Transcriptomic Analyses of the Pathogenic Vibrio anguillarum Under Starvation Stress. PMID:30505805
Developmental origins of transgenerational sperm DNA methylation epimutations following ancestral DDT exposure. PMID:30500333
Intestinal in vitro and ex vivo Models to Study Host-Microbiome Interactions and Acute Stressors. PMID:30483150
funcExplorer: a tool for fast data-driven functional characterisation of high-throughput expression data. PMID:30428831
Qi-Deficiency Related Increases in Disease Susceptibility Are Potentially Mediated by the Intestinal Microbiota. PMID:30425748
A low-gluten diet induces changes in the intestinal microbiome of healthy Danish adults. PMID:30425247
Spatial Variability and Co-acclimation of Phytoplankton and Bacterioplankton Communities in the Pearl River Estuary, China. PMID:30405565
Metabolomic insights of macrophage responses to graphene nanoplatelets: Role of scavenger receptor CD36. PMID:30403754
Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction. PMID:30393775
The Crabtree Effect Shapes the Saccharomyces cerevisiae Lag Phase during the Switch between Different Carbon Sources. PMID:30377274
Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding. PMID:30353370
3D Network exploration and visualisation for lifespan data. PMID:30352578
Somatic mutations in renal cell carcinomas from Chinese patients revealed by whole exome sequencing. PMID:30349421
Comparative Genomics of Lactobacillus brevis Reveals a Significant Plasmidome Overlap of Brewery and Insect Isolates. PMID:30341451
Comparison of Healthy and Dandruff Scalp Microbiome Reveals the Role of Commensals in Scalp Health. PMID:30338244
Comparative Genomics of Degradative Novosphingobium Strains With Special Reference to Microcystin-Degrading Novosphingobium sp. THN1. PMID:30319567
Re-thinking Alzheimer's disease therapeutic targets using gene-based tests. PMID:30314892
Comparative metagenomics of the gut microbiota in wild greylag geese (Anser anser) and ruddy shelducks (Tadorna ferruginea). PMID:30296008
Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions. PMID:30291327
First insight into microbiome profile of fungivorous thrips Hoplothrips carpathicus (Insecta: Thysanoptera) at different developmental stages: molecular evidence of Wolbachia endosymbiosis. PMID:30258200
C.el Phosphatome: A Catalogue of Actual and Pseudo Phosphatases Based on In-Silico Studies in Caenorhabditis elegans. PMID:30242660
Genomic responses to selection for tame/aggressive behaviors in the silver fox (Vulpes vulpes). PMID:30228118
Environmental toxicant induced epigenetic transgenerational inheritance of ovarian pathology and granulosa cell epigenome and transcriptome alterations: ancestral origins of polycystic ovarian syndrome and primary ovarian insufiency. PMID:30207508
An exploration of microbial and associated functional diversity in the OMZ and non-OMZ areas in the Bay of Bengal. PMID:30207310
Proteomic Analysis of Rapeseed Root Response to Waterlogging Stress. PMID:30205432
Genome sequence analysis of Zooshikella ganghwensis strain VG4 and its potential for the synthesis of antimicrobial metabolites. PMID:30197874
Adaptive Evolution of Animal Proteins over Development: Support for the Darwin Selection Opportunity Hypothesis of Evo-Devo. PMID:30184095
Vinclozolin induced epigenetic transgenerational inheritance of pathologies and sperm epimutation biomarkers for specific diseases. PMID:30157260
Transcriptomic Analysis of Oryza sativa Leaves Reveals Key Changes in Response to Magnaporthe oryzae MSP1. PMID:30140180
Models of cell signaling uncover molecular mechanisms of high-risk neuroblastoma and predict disease outcome. PMID:30134948
Trans-heterozygosity for mutations enhances the risk of recurrent/chronic pancreatitis in patients with Cystic Fibrosis. PMID:30134826
Draft genome of Glyptosternon maculatum, an endemic fish from Tibet Plateau. PMID:30124856
Comparative Metagenomic Analysis of Rhizosphere Microbial Community Composition and Functional Potentials under Rehmannia glutinosa Consecutive Monoculture. PMID:30110928
Global metabolomic responses in urine from atm deficient mice in response to LD50/30 gamma irradiation doses. PMID:30095186
Systems toxicology meta-analysis of in vitro assessment studies: biological impact of a candidate modified-risk tobacco product aerosol compared with cigarette smoke on human organotypic cultures of the aerodigestive tract. PMID:30090531
Quorum-Quenching Bacteria Isolated From Red Sea Sediments Reduce Biofilm Formation by Pseudomonas aeruginosa. PMID:30065702
Metagenomic analysis of gut microbial communities from a Central Asian population. PMID:30056386
ChemDIS 2: an update of chemical-disease inference system. PMID:30053236
Microbial Community Structure and Functional Potential Along a Hypersaline Gradient. PMID:30042744
Potential biomarkers and therapeutic targets in cervical cancer: Insights from the meta-analysis of transcriptomics data within network biomedicine perspective. PMID:30020984
Defining the Species Micromonospora saelicesensis and Micromonospora noduli Under the Framework of Genomics. PMID:29988535
MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. PMID:29982278
NADH-Mediated Gene Expression in Streptococcus pneumoniae and Role of Rex as a Transcriptional Repressor of the Rex-Regulon. PMID:29971050
Expression profiling of Trypanosoma congolense genes during development in the tsetse fly vector Glossina morsitans morsitans. PMID:29970164
ChemDIS-Mixture: an online tool for analyzing potential interaction effects of chemical mixtures. PMID:29968796
Autophagic reliance promotes metabolic reprogramming in oncogenic KRAS-driven tumorigenesis. PMID:29956571
Colorectal cancer mutational profiles correlate with defined microbial communities in the tumor microenvironment. PMID:29924794
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Comprehensive analysis of Verticillium nonalfalfae in silico secretome uncovers putative effector proteins expressed during hop invasion. PMID:29894496
Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics. PMID:29892275
Gene set analysis methods: a systematic comparison. PMID:29881462
Differential Connectivity in Colorectal Cancer Gene Expression Network. PMID:29843204
Taxon Richness of "Megaviridae" Exceeds those of Bacteria and Archaea in the Ocean. PMID:29806626
Towards a complete map of the human long non-coding RNA transcriptome. PMID:29795125
Identification and analysis of key genes associated with ulcerative colitis based on DNA microarray data. PMID:29794741
SAMSA2: a standalone metatranscriptome analysis pipeline. PMID:29783945
Comparative Metatranscriptomics of Wheat Rhizosphere Microbiomes in Disease Suppressive and Non-suppressive Soils for Rhizoctonia solani AG8. PMID:29780371
RNA-Seq and UHPLC-Q-TOF/MS Based Lipidomics Study in Lysiphlebia japonica. PMID:29773840
A Multi-Omics Database for Parasitic Nematodes and Trematodes. PMID:29761465
Anti-tumoral effects of exercise on hepatocellular carcinoma growth. PMID:29761175
Patterns of chemical diversity in the marine ascidian Phallusia spp.: anti-tumor activity and metabolic pathway inhibiting steroid biosynthesis. PMID:29755920
Metallopeptidases of Toxoplasma gondii: in silico identification and gene expression. PMID:29737275
Comparative transcriptome analyses of three medicinal Forsythia species and prediction of candidate genes involved in secondary metabolisms. PMID:29736697
Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes. PMID:29734356
Alterations in sperm DNA methylation, non-coding RNA expression, and histone retention mediate vinclozolin-induced epigenetic transgenerational inheritance of disease. PMID:29732173
iPath3.0: interactive pathways explorer v3. PMID:29718427
Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion. PMID:29713376
An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance. PMID:29677511
The role of the Human Metabolome Database in inborn errors of metabolism. PMID:29663269
Substrate Specificities and Efflux Efficiencies of RND Efflux Pumps of Acinetobacter baumannii. PMID:29661860
Dual Role of Humic Substances As Electron Donor and Shuttle for Dissimilatory Iron Reduction. PMID:29658273
Metabolomic study of human tissue and urine in clear cell renal carcinoma by LC-HRMS and PLS-DA. PMID:29658093
Functional Precision Medicine Identifies Novel Druggable Targets and Therapeutic Options in Head and Neck Cancer. PMID:29599409
Epigenetic Transgenerational Inheritance of Altered Sperm Histone Retention Sites. PMID:29593303
Screening of medium constituents for clavulanic acid production by Streptomyces clavuligerus. PMID:29588197
Genome-Scale, Constraint-Based Modeling of Nitrogen Oxide Fluxes during Coculture of Nitrosomonas europaea and Nitrobacter winogradskyi. PMID:29577088
Uncovering the regeneration strategies of zebrafish organs: a comprehensive systems biology study on heart, cerebellum, fin, and retina regeneration. PMID:29560825
Exploration of the Anti-Inflammatory Drug Space Through Network Pharmacology: Applications for Drug Repurposing. PMID:29545755
Metabolomic and inflammatory mediator based biomarker profiling as a potential novel method to aid pediatric appendicitis identification. PMID:29529041
Inter-niche and inter-individual variation in gut microbial community assessment using stool, rectal swab, and mucosal samples. PMID:29515151
The Use of Metabolomics and Inflammatory Mediator Profiling Provides a Novel Approach to Identifying Pediatric Appendicitis in the Emergency Department. PMID:29511263
Plasma miR-199a-5p is increased in neutrophilic phenotype asthma patients and negatively correlated with pulmonary function. PMID:29505605
Improving eukaryotic genome annotation using single molecule mRNA sequencing. PMID:29495964
Structure Based Virtual Screening Studies to Identify Novel Potential Compounds for GPR142 and Their Relative Dynamic Analysis for Study of Type 2 Diabetes. PMID:29492402
Comparative and integrative metabolomics reveal that S-nitrosation inhibits physiologically relevant metabolic enzymes. PMID:29483187
Alterations in sperm DNA methylation, non-coding RNA and histone retention associate with DDT-induced epigenetic transgenerational inheritance of disease. PMID:29482626
Reconstructing Phylogeny by Aligning Multiple Metabolic Pathways Using Functional Module Mapping. PMID:29473850
Draft Genome Sequence of Micromonospora sp. Strain WMMA1996, a Marine Sponge-Associated Bacterium. PMID:29472337
Selection Finder (SelFi): A computational metabolic engineering tool to enable directed evolution of enzymes. PMID:29468131
Promiscuous plasmid replication in thermophiles: Use of a novel hyperthermophilic replicon for genetic manipulation of Clostridium thermocellum at its optimum growth temperature. PMID:29468112
Draft genomes of two blister beetles Hycleus cichorii and Hycleus phaleratus. PMID:29444297
Influence of Different Sugars and Initial pH on β-Glucan Formation by Lactobacillus brevis TMW 1.2112. PMID:29442149
Ribonuclease inhibitor 1 regulates erythropoiesis by controlling GATA1 translation. PMID:29408805
Disconnect Between Genes Associated With Ischemic Heart Disease and Targets of Ischemic Heart Disease Treatments. PMID:29396305
Loss of CNFY toxin-induced inflammation drives Yersinia pseudotuberculosis into persistency. PMID:29390040
Transcriptomic alterations during ageing reflect the shift from cancer to degenerative diseases in the elderly. PMID:29382830
Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment. PMID:29372281
The influence of long-term use of proton pump inhibitors on the gut microbiota: an age-sex-matched case-control study. PMID:29371761
Pathway design using de novo steps through uncharted biochemical spaces. PMID:29330441
Untargeted Metabolomics Approach in Halophiles: Understanding the Biodeterioration Process of Building Materials. PMID:29321766
Muscle molecular adaptations to endurance exercise training are conditioned by glycogen availability: a proteomics-based analysis in the McArdle mouse model. PMID:29315579
A High-Resolution Proteomic Landscaping of Primary Human Dental Stem Cells: Identification of SHED- and PDLSC-Specific Biomarkers. PMID:29304003
Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. PMID:29298729
Genome-Wide Analysis of Long Non-Coding RNAs in Potato and Their Potential Role in Tuber Sprouting Process. PMID:29286332
Multiple functions of CREB-binding protein during postembryonic development: identification of target genes. PMID:29284404
Genome variation and conserved regulation identify genomic regions responsible for strain specific phenotypes in rat. PMID:29272997
Analysis of Draft Genome Sequence of Pseudomonas sp. QTF5 Reveals Its Benzoic Acid Degradation Ability and Heavy Metal Tolerance. PMID:29270429
Identification of SPOP related metabolic pathways in prostate cancer. PMID:29262542
Gene Network Analysis of Interstitial Macrophages After Treatment with Induced Pluripotent Stem Cells Secretome (iPSC-cm) in the Bleomycin Injured Rat Lung. PMID:29256173
Evolutionary transition from blood feeding to obligate nonbiting in a mosquito. PMID:29255013
Alterations in oral bacterial communities are associated with risk factors for oral and oropharyngeal cancer. PMID:29247187
Systematic analysis of the expression profile of non-coding RNAs involved in ischemia/reperfusion-induced acute kidney injury in mice using RNA sequencing. PMID:29245971
Identification and validation of FaP1D7, a putative marker associated with the biosynthesis of methyl butanoate in cultivated strawberry (Fragaria x ananassa). PMID:29234071
EGR1 regulates cellular metabolism and survival in endocrine resistant breast cancer. PMID:29228577
Comparative transcriptomic analysis of human placentae at term and preterm delivery. PMID:29228154
Yale school of public health symposium on lifetime exposures and human health: the exposome; summary and future reflections. PMID:29221465
Delivery Mode and the Transition of Pioneering Gut-Microbiota Structure, Composition and Predicted Metabolic Function. PMID:29207565
OCDD: an obesity and co-morbid disease database. PMID:29201145
Shotgun Metagenomics and Volatilome Profile of the Microbiota of Fermented Sausages. PMID:29196291
On the Early Evolution of Catabolic Pathways: A Comparative Genomics Approach. I. The Cases of Glucose, Ribose, and the Nucleobases Catabolic Routes. PMID:29189888
Reactome diagram viewer: data structures and strategies to boost performance. PMID:29186351
Semi-supervised network inference using simulated gene expression dynamics. PMID:29186340
Molecular Basis of Bacterial Longevity. PMID:29184015
Analysis of MicroRNA Expression in Newborns with Differential Birth Weight Using Newborn Screening Cards. PMID:29182561
Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome. PMID:29180750
Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem. PMID:29177104
The genome of an intranuclear parasite, Paramicrosporidium saccamoebae, reveals alternative adaptations to obligate intracellular parasitism. PMID:29171834
Nonmonotonic Pathway Gene Expression Analysis Reveals Oncogenic Role of p27/Kip1 at Intermediate Dose. PMID:29162974
Investigation of common, low-frequency and rare genome-wide variation in anorexia nervosa. PMID:29155802
Generational comparisons (F1 versus F3) of vinclozolin induced epigenetic transgenerational inheritance of sperm differential DNA methylation regions (epimutations) using MeDIP-Seq. PMID:29147574
Characterizing steady states of genome-scale metabolic networks in continuous cell cultures. PMID:29131817
miRNA profiling identifies deregulated miRNAs associated with osteosarcoma development and time to metastasis in two large cohorts. PMID:29120535
Wild Silkworm Cocoon Contains More Metabolites Than Domestic Silkworm Cocoon to Improve Its Protection. PMID:29117380
Metabolic profiles of adipose-derived and bone marrow-derived stromal cells from elderly coronary heart disease patients by capillary liquid chromatography quadrupole time-of-flight mass spectrometry. PMID:29115374
Penicillin induces alterations in glutamine metabolism in Streptococcus pneumoniae. PMID:29109543
Granzyme B Disrupts Central Metabolism and Protein Synthesis in Bacteria to Promote an Immune Cell Death Program. PMID:29107333
Non-invasively predicting differentiation of pancreatic cancer through comparative serum metabonomic profiling. PMID:29096620
Acetylome Profiling Reveals Extensive Lysine Acetylation of the Fatty Acid Metabolism Pathway in the Diatom Phaeodactylum tricornutum. PMID:29093020
Dorsal and Ventral Hippocampus Differentiate in Functional Pathways and Differentially Associate with Neurological Disease-Related Genes during Postnatal Development. PMID:29085281
Reactome enhanced pathway visualization. PMID:29077811
Epigenetics and adaptive phenotypic variation between habitats in an asexual snail. PMID:29074962
Complete Genome Sequence of Mesorhizobium sophorae ICMP 19535T, a Highly Specific, Nitrogen-Fixing Symbiont of New Zealand Endemic Sophora spp. PMID:29074646
SaVanT: a web-based tool for the sample-level visualization of molecular signatures in gene expression profiles. PMID:29070035
Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1α axis inhibition. PMID:29069732
Biogenesis and iron-dependency of ribosomal RNA hydroxylation. PMID:29069499
Inheritance and Establishment of Gut Microbiota in Chickens. PMID:29067020
SalmoNet, an integrated network of ten Salmonella enterica strains reveals common and distinct pathways to host adaptation. PMID:29057095
Draft genome of the gayal, Bos frontalis. PMID:29048483
Genome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas. PMID:29047329
Identification of genes and pathways potentially related to PHF20 by gene expression profile analysis of glioblastoma U87 cell line. PMID:29033691
Predicting novel substrates for enzymes with minimal experimental effort with active learning. PMID:29030274
MG-RAST version 4-lessons learned from a decade of low-budget ultra-high-throughput metagenome analysis. PMID:29028869
High-Quality Draft Genome Sequence of Burkholderia contaminans CH-1, a Gram-Negative Bacterium That Metabolizes 2-Azahypoxanthine, a Plant Growth-Regulating Compound. PMID:29025950
A Community Challenge for Inferring Genetic Predictors of Gene Essentialities through Analysis of a Functional Screen of Cancer Cell Lines. PMID:28988802
Signatures of positive selection and local adaptation to urbanization in white-footed mice (Peromyscus leucopus). PMID:28980357
The transcription factor ATF7 mediates in vitro fertilization-induced gene expression changes in mouse liver. PMID:28979846
Identification and causes of metabonomic difference between orthotopic and subcutaneous xenograft of pancreatic cancer. PMID:28977862
The ESRP1-GPR137 axis contributes to intestinal pathogenesis. PMID:28975893
A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis. PMID:28970579
Omega-6 and omega-3 oxylipins are implicated in soybean oil-induced obesity in mice. PMID:28970503
MetExploreViz: web component for interactive metabolic network visualization. PMID:28968733
PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data. PMID:28961954
Network-Based Identification of Adaptive Pathways in Evolved Ethanol-Tolerant Bacterial Populations. PMID:28961727
Identification of drought-responsive microRNAs in tomato using high-throughput sequencing. PMID:28956210
Comparative Genomics of Ralstonia solanacearum Identifies Candidate Genes Associated with Cool Virulence. PMID:28955357
Short overview on metabolomic approach and redox changes in psychiatric disorders. PMID:28942195
Atrazine induced epigenetic transgenerational inheritance of disease, lean phenotype and sperm epimutation pathology biomarkers. PMID:28931070
Elucidation of complexity and prediction of interactions in microbial communities. PMID:28925555
Understanding mutational effects in digenic diseases. PMID:28911095
Is systems pharmacology ready to impact upon therapy development? A study on the cholesterol biosynthesis pathway. PMID:28910500
Identification of key metabolic changes during liver fibrosis progression in rats using a urine and serum metabolomics approach. PMID:28900168
Shotgun metagenomics, from sampling to analysis. PMID:28898207
Genomic insights into temperature-dependent transcriptional responses of Kosmotoga olearia, a deep-biosphere bacterium that can grow from 20 to 79 °C. PMID:28894932
Alterations of the Gut Microbiome in Hypertension. PMID:28884091
MicroRNA Profiling in Aging Brain of PSEN1/PSEN2 Double Knockout Mice. PMID:28879407
Assessment of Whole-Exome Sequence Data in Attempted Suicide within a Bipolar Disorder Cohort. PMID:28879196
Analysis of Microbial Functions in the Rhizosphere Using a Metabolic-Network Based Framework for Metagenomics Interpretation. PMID:28878756
BioFuelDB: a database and prediction server of enzymes involved in biofuels production. PMID:28875065
Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease. PMID:28852861
Intermolecular base stacking mediates RNA-RNA interaction in a crystal structure of the RNA chaperone Hfq. PMID:28852099
The Essential Genome of Burkholderia cenocepacia H111. PMID:28847919
Epigenetic variation between urban and rural populations of Darwin's finches. PMID:28835203
A large scale Plasmodium vivax- Saimiri boliviensis trophozoite-schizont transition proteome. PMID:28829774
A Serum Small Molecule Biosignature of Radiation Exposure from Total Body Irradiated Patients. PMID:28825479
Microbial Communities and Their Predicted Metabolic Functions in Growth Laminae of a Unique Large Conical Mat from Lake Untersee, East Antarctica. PMID:28824553
2-Deoxy-D-glucose Restore Glucocorticoid Sensitivity in Acute Lymphoblastic Leukemia via Modification of N-Linked Glycosylation in an Oxygen Tension-Independent Manner. PMID:28814986
Fluoride Depletes Acidogenic Taxa in Oral but Not Gut Microbial Communities in Mice. PMID:28808691
Pathway-Based Kernel Boosting for the Analysis of Genome-Wide Association Studies. PMID:28785300
New frontiers in metabolomics: from measurement to insight. PMID:28781759
Aspergillus Secondary Metabolite Database, a resource to understand the Secondary metabolome of Aspergillus genus. PMID:28779078
Identification of an early transcriptomic signature of insulin resistance and related diseases in lymphomonocytes of healthy subjects. PMID:28777829
OsbZIP48, a HY5 Transcription Factor Ortholog, Exerts Pleiotropic Effects in Light-Regulated Development. PMID:28775143
PiiL: visualization of DNA methylation and gene expression data in gene pathways. PMID:28768481
Molecular Characterization of the Human Stomach Microbiota in Gastric Cancer Patients. PMID:28730144
Assessment of genome annotation using gene function similarity within the gene neighborhood. PMID:28724412
Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. PMID:28721231
Mutation intolerant genes and targets of FMRP are enriched for nonsynonymous alleles in schizophrenia. PMID:28719003
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes. PMID:28705224
Phenotypic and genomic comparison of Mycobacterium aurum and surrogate model species to Mycobacterium tuberculosis: implications for drug discovery. PMID:28705154
Genome-wide meta-analysis of copy number variations with alcohol dependence. PMID:28696413
Differential co-expression analysis reveals a novel prognostic gene module in ovarian cancer. PMID:28694494
Culture-Independent Analyses Reveal Novel Anaerolineaceae as Abundant Primary Fermenters in Anaerobic Digesters Treating Waste Activated Sludge. PMID:28690595
Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. PMID:28685384
Comparison of two bioinformatics tools used to characterize the microbial diversity and predictive functional attributes of microbial mats from Lake Obersee, Antarctica. PMID:28655556
Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. PMID:28651543
Genetic Indicators of Drug Resistance in the Highly Repetitive Genome of Trichomonas vaginalis. PMID:28633446
Construction of a synthetic metabolic pathway for biosynthesis of the non-natural methionine precursor 2,4-dihydroxybutyric acid. PMID:28631755
Clinical Applicability of Whole-Exome Sequencing Exemplified by a Study in Young Adults with the Advanced Cryptogenic Cholestatic Liver Diseases. PMID:28626473
De novo assembly and annotation of the Zhe-Maidong (Ophiopogon japonicus (L.f.) Ker-Gawl) transcriptome in different growth stages. PMID:28620183
Omics Data Complementarity Underlines Functional Cross-Communication in Yeast. PMID:28600905
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. PMID:28596423
The genomic road to invasion-examining the similarities and differences in the genomes of associated oral pre-cancer and cancer samples. PMID:28592326
Lateral Gene Transfer Dynamics in the Ancient Bacterial Genus Streptomyces. PMID:28588130
Liquid Chromatography Mass Spectrometry-Based Metabolite Pathway Analyses of Myeloma and Non-Hodgkin's Lymphoma Patients. PMID:28580307
RNA-sequencing Identifies Novel Pathways in Sarcoidosis Monocytes. PMID:28577019
The replicative lifespan-extending deletion of SGF73 results in altered ribosomal gene expression in yeast. PMID:28568901
Lysine Acetylome Analysis Reveals Photosystem II Manganese-stabilizing Protein Acetylation is Involved in Negative Regulation of Oxygen Evolution in Model Cyanobacterium Synechococcus sp. PCC 7002. PMID:28550166
Genomic adaptation to agricultural environments: cabbage white butterflies (Pieris rapae) as a case study. PMID:28549454
Identification of breast cancer prognostic modules based on weighted protein-protein interaction networks. PMID:28529601
Gene expression of Vibrio parahaemolyticus growing in laboratory isolation conditions compared to those common in its natural ocean environment. PMID:28525966
GeMSTONE: orchestrated prioritization of human germline mutations in the cloud. PMID:28521008
Decoding the complex genetic causes of heart diseases using systems biology. PMID:28509974
Quantitative Succinyl-Proteome Profiling of Camellia sinensis cv. 'Anji Baicha' During Periodic Albinism. PMID:28500349
Investigating the neuroimmunogenic architecture of schizophrenia. PMID:28485405
Identification of potential new treatment response markers and therapeutic targets using a Gaussian process-based method in lapatinib insensitive breast cancer models. PMID:28481952
Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. PMID:28478508
Draft genome sequence of the Tibetan medicinal herb Rhodiola crenulata. PMID:28475810
Metabolic Dysregulation after Neutron Exposures Expected from an Improvised Nuclear Device. PMID:28475424
Organ-specific transcriptome profiling of metabolic and pigment biosynthesis pathways in the floral ornamental progenitor species Anthurium amnicola Dressler. PMID:28473720
Parameter identifiability-based optimal observation remedy for biological networks. PMID:28472965
Lipidomics and RNA-Seq Study of Lipid Regulation in Aphis gossypii parasitized by Lysiphlebia japonica. PMID:28465512
Mercury-induced epigenetic transgenerational inheritance of abnormal neurobehavior is correlated with sperm epimutations in zebrafish. PMID:28464002
Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper. PMID:28460117
Pioneering topological methods for network-based drug-target prediction by exploiting a brain-network self-organization theory. PMID:28453640
Transcriptome analysis of creeping bentgrass exposed to drought stress and polyamine treatment. PMID:28445484
Identification of MicroRNA Targets of Capsicum spp. Using MiRTrans-a Trans-Omics Approach. PMID:28443105
Proteomic profiling of HBV infected liver biopsies with different fibrotic stages. PMID:28439208
MicroRNA-145 exerts tumor-suppressive and chemo-resistance lowering effects by targeting CD44 in gastric cancer. PMID:28428713
PIF* promotes brain re-myelination locally while regulating systemic inflammation- clinically relevant multiple sclerosis M.smegmatis model. PMID:28423529
Comparison of different cell type correction methods for genome-scale epigenetics studies. PMID:28410574
High prevalence of TP53 mutations is associated with poor survival and an EMT signature in gliosarcoma patients. PMID:28408749
A geographically-diverse collection of 418 human gut microbiome pathway genome databases. PMID:28398290
Profiling transcriptomes of human SH-SY5Y neuroblastoma cells exposed to maleic acid. PMID:28392987
Exploring the differences in metabolic behavior of astrocyte and glioblastoma: a flux balance analysis approach. PMID:28392849
Structure and Function of the Fecal Microbiota in Diarrheic Neonatal Piglets. PMID:28392784
Assessing biosynthetic potential of agricultural groundwater through metagenomic sequencing: A diverse anammox community dominates nitrate-rich groundwater. PMID:28384184
Brain Transcriptome Sequencing of a Natural Model of Alzheimer's Disease. PMID:28373841
RNA-sequence analysis of gene expression from honeybees (Apis mellifera) infected with Nosema ceranae. PMID:28350872
Methionine-mediated gene expression and characterization of the CmhR regulon in Streptococcus pneumoniae. PMID:28348831
The autophagy interaction network of the aging model Podospora anserina. PMID:28347269
In silico functional elucidation of uncharacterized proteins of Chlamydia abortus strain LLG. PMID:28344832
Niacin-mediated Gene Expression and Role of NiaR as a Transcriptional Repressor of niaX, nadC, and pnuC in Streptococcus pneumoniae. PMID:28337428
Comparative Genomic Analysis Reveals Ecological Differentiation in the Genus Carnobacterium. PMID:28337181
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. PMID:28333345
The nasopharyngeal microbiota of beef cattle before and after transport to a feedlot. PMID:28330466
Developing Human Radiation Biodosimetry Models: Testing Cross-Species Conversion Approaches Using an Ex Vivo Model System. PMID:28328310
On DNA numerical representations for genomic similarity computation. PMID:28323839
Gastric microbiota features associated with cancer risk factors and clinical outcomes: A pilot study in gastric cardia cancer patients from Shanxi, China. PMID:28319273
Metabolomics approaches in pancreatic adenocarcinoma: tumor metabolism profiling predicts clinical outcome of patients. PMID:28298227
Seasonal patterns in Arctic prasinophytes and inferred ecology of Bathycoccus unveiled in an Arctic winter metagenome. PMID:28267153
Avoiding the pitfalls of gene set enrichment analysis with SetRank. PMID:28259142
Three Unique Interstitial Macrophages in the Murine Lung at Steady State. PMID:28257233
Identification of somatic mutations using whole-exome sequencing in Korean patients with acute myeloid leukemia. PMID:28249600
Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network. PMID:28243200
Cyclin Y-mediated transcript profiling reveals several important functional pathways regulated by Cyclin Y in hippocampal neurons. PMID:28241067
Effects upon metabolic pathways and energy production by Sb(III) and As(III)/Sb(III)-oxidase gene aioA in Agrobacterium tumefaciens GW4. PMID:28241045
Genome-Wide Prediction of Metabolic Enzymes, Pathways, and Gene Clusters in Plants. PMID:28228535
The Source and Evolutionary History of a Microbial Contaminant Identified Through Soil Metagenomic Analysis. PMID:28223457
Identification of miRNA-mRNA Modules in Colorectal Cancer Using Rough Hypercuboid Based Supervised Clustering. PMID:28220871
Transcriptomic dynamics of breast cancer progression in the MMTV-PyMT mouse model. PMID:28212608
Pathway deviation-based biomarker and multi-effect target identification in asbestos-related squamous cell carcinoma of the lung. PMID:28204826
Recurrent patterns of DNA copy number alterations in tumors reflect metabolic selection pressures. PMID:28202506
Metabolomic and Metagenomic Analysis of Two Crude Oil Production Pipelines Experiencing Differential Rates of Corrosion. PMID:28197141
Metabolomics: A Primer. PMID:28196646
The post-genomic era of biological network alignment. PMID:28194172
Construction and Analysis of Two Genome-Scale Deletion Libraries for Bacillus subtilis. PMID:28189581
Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions. PMID:28176778
Metagenomics approach to the study of the gut microbiome structure and function in zebrafish Danio rerio fed with gluten formulated diet. PMID:28167213
Deep-proteome mapping of WM-266-4 human metastatic melanoma cells: From oncogenic addiction to druggable targets. PMID:28158294
TrypsNetDB: An integrated framework for the functional characterization of trypanosomatid proteins. PMID:28158179
Genomic variants in mouse model induced by azoxymethane and dextran sodium sulfate improperly mimic human colorectal cancer. PMID:28154415
Differential DNA Methylation Regions in Adult Human Sperm following Adolescent Chemotherapy: Potential for Epigenetic Inheritance. PMID:28146567
Skewing in Arabidopsis roots involves disparate environmental signaling pathways. PMID:28143395
Proteomic and transcriptomic study of brain microvessels in neonatal and adult mice. PMID:28141873
Protein biomarker druggability profiling. PMID:28131723
Assessing in silico the recruitment and functional spectrum of bacterial enzymes from secondary metabolism. PMID:28125959
Epigenetic profiling of human brain differential DNA methylation networks in schizophrenia. PMID:28117656
An inhaled dose of budesonide induces genes involved in transcription and signaling in the human airways: enhancement of anti- and proinflammatory effector genes. PMID:28116096
High quality draft genome sequence of Janthinobacterium psychrotolerans sp. nov., isolated from a frozen freshwater pond. PMID:28116042
SecretEPDB: a comprehensive web-based resource for secreted effector proteins of the bacterial types III, IV and VI secretion systems. PMID:28112271
Comparative interactomics for virus-human protein-protein interactions: DNA viruses versus RNA viruses. PMID:28097092
The Gut Microbiome of the Vector Lutzomyia longipalpis Is Essential for Survival of Leishmania infantum. PMID:28096483
Poly(ADP-ribose) polymerase inhibitors activate the p53 signaling pathway in neural stem/progenitor cells. PMID:28095779
Expression of specific inflammasome gene modules stratifies older individuals into two extreme clinical and immunological states. PMID:28092664
microRNAs and DICER1 are regulated by 1,25-dihydroxyvitamin D in prostate stroma. PMID:28089917
Genomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts. PMID:28088165
Draft Genome Sequence of Micromonospora sp. Strain WMMB235, a Marine Ascidian-Associated Bacterium. PMID:28082484
Modeling gene-wise dependencies improves the identification of drug response biomarkers in cancer studies. PMID:28082455
The Anti-Warburg Effect Elicited by the cAMP-PGC1α Pathway Drives Differentiation of Glioblastoma Cells into Astrocytes. PMID:28076790
Identical bacterial populations colonize premature infant gut, skin, and oral microbiomes and exhibit different in situ growth rates. PMID:28073918
A Method for Finding Metabolic Pathways Using Atomic Group Tracking. PMID:28068354
Comparative Characterization of the Leaf Tissue of Physalis alkekengi and Physalis peruviana Using RNA-seq and Metabolite Profiling. PMID:28066454
PaPrBaG: A machine learning approach for the detection of novel pathogens from NGS data. PMID:28051068
High throughput estimation of functional cell activities reveals disease mechanisms and predicts relevant clinical outcomes. PMID:28042959
Metabolic model of central carbon and energy metabolisms of growing Arabidopsis thaliana in relation to sucrose translocation. PMID:28031032
Considerations when choosing a genetic model organism for metabolomics studies. PMID:28025166
Molecular and Proteomic Analysis of Levofloxacin and Metronidazole Resistant Helicobacter pylori. PMID:28018334
Transcriptomic analysis displays the effect of (-)-roemerine on the motility and nutrient uptake in Escherichia coli. PMID:28013396
Cysteine-Mediated Gene Expression and Characterization of the CmbR Regulon in Streptococcus pneumoniae. PMID:27990139
Inferring Aggregated Functional Traits from Metagenomic Data Using Constrained Non-negative Matrix Factorization: Application to Fiber Degradation in the Human Gut Microbiota. PMID:27984592
Complete Genome Sequence of Rhodococcus sp. Strain WMMA185, a Marine Sponge-Associated Bacterium. PMID:27979952
Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil. PMID:27977803
A pathway-centric view of spatial proximity in the 3D nucleome across cell lines. PMID:27976707
Microbial Community Composition Impacts Pathogen Iron Availability during Polymicrobial Infection. PMID:27973608
Microarray analysis of long noncoding RNA and mRNA expression profiles in human macrophages infected with Mycobacterium tuberculosis. PMID:27966580
Identification of Risk Pathways and Functional Modules for Coronary Artery Disease Based on Genome-wide SNP Data. PMID:27965104
Pathway collages: personalized multi-pathway diagrams. PMID:27964719
Mobile-phone radiation-induced perturbation of gene-expression profiling, redox equilibrium and sporadic-apoptosis control in the ovary of Drosophila melanogaster. PMID:27960592
RBM5 reduces small cell lung cancer growth, increases cisplatin sensitivity and regulates key transformation-associated pathways. PMID:27957556
Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. PMID:27941785
Impaired liver regeneration in aged mice can be rescued by silencing Hippo core kinases MST1 and MST2. PMID:27940445
Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes. PMID:27939572
Aligning Metabolic Pathways Exploiting Binary Relation of Reactions. PMID:27936108
Finding Potential Therapeutic Targets against Shigella flexneri through Proteome Exploration. PMID:27920755
N-acetylglucosamine-Mediated Expression of nagA and nagB in Streptococcus pneumoniae. PMID:27900287
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:27899636
The KDM5 family is required for activation of pro-proliferative cell cycle genes during adipocyte differentiation. PMID:27899593
Divergent selection-induced obesity alters the composition and functional pathways of chicken gut microbiota. PMID:27894254
Computational Discovery of Putative Leads for Drug Repositioning through Drug-Target Interaction Prediction. PMID:27893735
Systems Biomedicine of Rabies Delineates the Affected Signaling Pathways. PMID:27872612
Transcriptome analysis reveals manifold mechanisms of cyst development in ADPKD. PMID:27871310
Genome and transcriptome sequencing characterises the gene space of Macadamia integrifolia (Proteaceae). PMID:27855648
A core phylogeny of Dictyostelia inferred from genomes representative of the eight major and minor taxonomic divisions of the group. PMID:27855631
Immunosenescence-Related Transcriptomic and Immunologic Changes in Older Individuals Following Influenza Vaccination. PMID:27853459
DGCA: A comprehensive R package for Differential Gene Correlation Analysis. PMID:27846853
Untargeted metabolomics unravels functionalities of phosphorylation sites in Saccharomyces cerevisiae. PMID:27846849
Alteration of Fecal Microbiota Profiles in Juvenile Idiopathic Arthritis. Associations with HLA-B27 Allele and Disease Status. PMID:27833598
Draft Genome Sequence of Enterococcus mundtii SL 16, an Indigenous Gut Bacterium of the Polyphagous Pest Spodoptera littoralis. PMID:27826292
Thermus and the Pink Discoloration Defect in Cheese. PMID:27822529
Urban Transit System Microbial Communities Differ by Surface Type and Interaction with Humans and the Environment. PMID:27822528
HIPPIE v2.0: enhancing meaningfulness and reliability of protein-protein interaction networks. PMID:27794551
Draft genome of the leopard gecko, Eublepharis macularius. PMID:27784328
Birth of Archaeal Cells: Molecular Phylogenetic Analyses of G1P Dehydrogenase, G3P Dehydrogenases, and Glycerol Kinase Suggest Derived Features of Archaeal Membranes Having G1P Polar Lipids. PMID:27774041
Genome evolution in the allotetraploid frog Xenopus laevis. PMID:27762356
Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria. PMID:27762279
Identification of a regulation network in response to cadmium toxicity using blood clam Tegillarca granosa as model. PMID:27760991
Deciphering Transcriptional Programming during Pod and Seed Development Using RNA-Seq in Pigeonpea (Cajanus cajan). PMID:27760186
Gold Nanoparticle Reprograms Pancreatic Tumor Microenvironment and Inhibits Tumor Growth. PMID:27758098
Characterization of the Neisseria meningitidis Helicase RecG. PMID:27736945
Enterococcal Metabolite Cues Facilitate Interspecies Niche Modulation and Polymicrobial Infection. PMID:27736645
A global genetic interaction network maps a wiring diagram of cellular function. PMID:27708008
Divergent Isoprenoid Biosynthesis Pathways in Staphylococcus Species Constitute a Drug Target for Treating Infections in Companion Animals. PMID:27704053
Importance of metabolic rate to the relationship between the number of genes in a functional category and body size in Peto's paradox for cancer. PMID:27703689
Atlas of human diseases influenced by genetic variants with extreme allele frequency differences. PMID:27699474
Elimination of p19ARF-expressing cells enhances pulmonary function in mice. PMID:27699227
Metabolic flexibility of mitochondrial respiratory chain disorders predicted by computer modelling. PMID:27697518
A capillary electrophoresis coupled to mass spectrometry pipeline for long term comparable assessment of the urinary metabolome. PMID:27694997
Transcriptional Fingerprint of Hypomyelination in Zfp191null and Shiverer (Mbpshi) Mice. PMID:27683878
N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae. PMID:27672623
A systems biology approach to defining regulatory mechanisms for cartilage and tendon cell phenotypes. PMID:27670352
Urinary microbiome of kidney transplant patients reveals dysbiosis with potential for antibiotic resistance. PMID:27669488
Functional Metagenomics of Spacecraft Assembly Cleanrooms: Presence of Virulence Factors Associated with Human Pathogens. PMID:27667984
Metabolomic profiling predicts outcome of rituximab therapy in rheumatoid arthritis. PMID:27651926
Quantitative metabolomics of photoreceptor degeneration and the effects of stem cell-derived retinal pigment epithelium transplantation. PMID:27644974
Networks Models of Actin Dynamics during Spermatozoa Postejaculatory Life: A Comparison among Human-Made and Text Mining-Based Models. PMID:27642606
Characterization of the mechanism of prolonged adaptation to osmotic stress of Jeotgalibacillus malaysiensis via genome and transcriptome sequencing analyses. PMID:27641516
A Network-Based Data Integration Approach to Support Drug Repurposing and Multi-Target Therapies in Triple Negative Breast Cancer. PMID:27632168
Computational Metabolomics: A Framework for the Million Metabolome. PMID:27629808
De novo transcriptome assembly and characterization of nine tissues of Lonicera japonica to identify potential candidate genes involved in chlorogenic acid, luteolosides, and secoiridoid biosynthesis pathways. PMID:27629269
The Multivesicular Bodies (MVBs)-Localized AAA ATPase LRD6-6 Inhibits Immunity and Cell Death Likely through Regulating MVBs-Mediated Vesicular Trafficking in Rice. PMID:27618555
Exploiting rRNA operon copy number to investigate bacterial reproductive strategies. PMID:27617693
Nitrogen Fixation and Molecular Oxygen: Comparative Genomic Reconstruction of Transcription Regulation in Alphaproteobacteria. PMID:27617010
Excess Polθ functions in response to replicative stress in homologous recombination-proficient cancer cells. PMID:27612511
GenToS: Use of Orthologous Gene Information to Prioritize Signals from Human GWAS. PMID:27612175
Analyzing and interpreting genome data at the network level with ConsensusPathDB. PMID:27606777
De Novo Transcriptome Assembly and Sex-Biased Gene Expression in the Cyclical Parthenogenetic Daphnia galeata. PMID:27604882
Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions. PMID:27597445
Self-regulation of functional pathways by motifs inside the disordered tails of beta-catenin. PMID:27585692
An Untargeted Metabolomics Approach to Characterize Short-Term and Long-Term Metabolic Changes after Bariatric Surgery. PMID:27584017
Species-function relationships shape ecological properties of the human gut microbiome. PMID:27573110
Transcriptome Characterization of Dendrolimus punctatus and Expression Profiles at Different Developmental Stages. PMID:27560151
Systems-level effects of ectopic galectin-7 reconstitution in cervical cancer and its microenvironment. PMID:27558259
A system biology approach to understanding the molecular mechanisms of Gubentongluo decoction acting on IgA Nephropathy. PMID:27558012
EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks. PMID:27556637
High quality draft genome sequence of the type strain of Pseudomonas lutea OK2(T), a phosphate-solubilizing rhizospheric bacterium. PMID:27555890
FastProject: a tool for low-dimensional analysis of single-cell RNA-Seq data. PMID:27553427
mTORC2 controls cancer cell survival by modulating gluconeogenesis. PMID:27551450
Circulating microRNAs are deregulated in overweight/obese children: preliminary results of the I.Family study. PMID:27551310
Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding. PMID:27549116
A protein network descriptor server and its use in studying protein, disease, metabolic and drug targeted networks. PMID:27542402
Gut Microbial Diversity Is Reduced in Smokers with Crohn's Disease. PMID:27542127
Shifting patterns of genomic variation in the somatic evolution of papillary thyroid carcinoma. PMID:27538953
Draft genome sequences of three Xanthomonas translucens pathovar reference strains (pv. arrhenatheri, pv. poae and pv. phlei) with different specificities for forage grasses. PMID:27536340
Mucosal Interactions between Genetics, Diet, and Microbiome in Inflammatory Bowel Disease. PMID:27531998
Whole Transcriptome Profiling Identifies CD93 and Other Plasma Cell Survival Factor Genes Associated with Measles-Specific Antibody Response after Vaccination. PMID:27529750
PoplarGene: poplar gene network and resource for mining functional information for genes from woody plants. PMID:27515999
Late-Exponential Gene Expression in codY-Deficient Bacillus anthracis in a Host-Like Environment. PMID:27515669
Evaluation of artificial selection in Standard Poodles using whole-genome sequencing. PMID:27510710
Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake. PMID:27506548
Multivariate Imaging Genetics Study of MRI Gray Matter Volume and SNPs Reveals Biological Pathways Correlated with Brain Structural Differences in Attention Deficit Hyperactivity Disorder. PMID:27504100
MicroRNAs as Novel Biomarkers of Deployment Status and Exposure to Polychlorinated Dibenzo-p-Dioxins/Dibenzofurans. PMID:27501109
Detection of Serum microRNAs From Department of Defense Serum Repository: Correlation With Cotinine, Cytokine, and Polycyclic Aromatic Hydrocarbon Levels. PMID:27501106
High-Resolution Metabolomics Assessment of Military Personnel: Evaluating Analytical Strategies for Chemical Detection. PMID:27501105
A transcriptional blueprint for a spiral-cleaving embryo. PMID:27496340
A Proteomic Investigation of Hepatic Resistance to Ascaris in a Murine Model. PMID:27490109
Normalized lmQCM: An Algorithm for Detecting Weak Quasi-Cliques in Weighted Graph with Applications in Gene Co-Expression Module Discovery in Cancers. PMID:27486298
Effect of a diet enriched with omega-6 and omega-3 fatty acids on the pig liver transcriptome. PMID:27482299
A Catalogue of Altered Salivary Proteins Secondary to Invasive Ductal Carcinoma: A Novel In Vivo Paradigm to Assess Breast Cancer Progression. PMID:27477923
Characterizing human lung tissue microbiota and its relationship to epidemiological and clinical features. PMID:27468850
NCMine: Core-peripheral based functional module detection using near-clique mining. PMID:27466623
Correlation-Based Network Analysis of Metabolite and Enzyme Profiles Reveals a Role of Citrate Biosynthesis in Modulating N and C Metabolism in Zea mays. PMID:27462343
"Candidatus Propionivibrio aalborgensis": A Novel Glycogen Accumulating Organism Abundant in Full-Scale Enhanced Biological Phosphorus Removal Plants. PMID:27458436
Deep Proteome Analysis Identifies Age-Related Processes in C. elegans. PMID:27453442
PreImplantation factor (PIF) therapy provides comprehensive protection against radiation induced pathologies. PMID:27449294
Immune Response and Mortality Risk Relate to Distinct Lung Microbiomes in Patients with HIV and Pneumonia. PMID:27447987
Seven protective miRNA signatures for prognosis of cervical cancer. PMID:27447860
Identification of Key Proteins and Networks Related to Grain Development in Wheat (Triticum aestivum L.) by Comparative Transcription and Proteomic Analysis of Allelic Variants in TaGW2-6A. PMID:27446152
Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach. PMID:27446133
Interpretable per case weighted ensemble method for cancer associations. PMID:27435615
Coordinate Regulation of Metabolite Glycosylation and Stress Hormone Biosynthesis by TT8 in Arabidopsis. PMID:27432888
Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications. PMID:27429547
Mobile genes in the human microbiome are structured from global to individual scales. PMID:27409808
Integrating Transcriptomic and Proteomic Data Using Predictive Regulatory Network Models of Host Response to Pathogens. PMID:27403523
Identification, Functional Characterization and Regulon Prediction of a Novel Two Component System Comprising BAS0540-BAS0541 of Bacillus anthracis. PMID:27392063
A perspective on interaction effects in genetic association studies. PMID:27390122
Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. PMID:27379244
High-throughput sequencing and de novo transcriptome assembly of Swertia japonica to identify genes involved in the biosynthesis of therapeutic metabolites. PMID:27378356
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Genome-Scale Metabolic Model for the Green Alga Chlorella vulgaris UTEX 395 Accurately Predicts Phenotypes under Autotrophic, Heterotrophic, and Mixotrophic Growth Conditions. PMID:27372244
The gut microbiome of the sea urchin, Lytechinus variegatus, from its natural habitat demonstrates selective attributes of microbial taxa and predictive metabolic profiles. PMID:27368709
Data set for diet specific differential gene expression analysis in three Spodoptera moths. PMID:27366783
Genomic alterations underlie a pan-cancer metabolic shift associated with tumour hypoxia. PMID:27358048
Genome wide analysis of protein production load in Trichoderma reesei. PMID:27354857
Use of RNA-seq to identify cardiac genes and gene pathways differentially expressed between dogs with and without dilated cardiomyopathy. PMID:27347821
A key genetic factor for fucosyllactose utilization affects infant gut microbiota development. PMID:27340092
Assessment of Saliva as a Potential Biofluid for Biodosimetry: A Pilot Metabolomics Study in Mice. PMID:27332953
Targeting MTHFD2 in acute myeloid leukemia. PMID:27325891
Human Milk Cells Contain Numerous miRNAs that May Change with Milk Removal and Regulate Multiple Physiological Processes. PMID:27322254
Transcriptional signatures of influenza A/H1N1-specific IgG memory-like B cell response in older individuals. PMID:27317456
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. PMID:27307627
Roux-en-Y gastric bypass surgery of morbidly obese patients induces swift and persistent changes of the individual gut microbiota. PMID:27306058
Gene Loss and Horizontal Gene Transfer Contributed to the Genome Evolution of the Extreme Acidophile "Ferrovum". PMID:27303384
Antimicrobial Resistance Prediction in PATRIC and RAST. PMID:27297683
Structural identifiability of cyclic graphical models of biological networks with latent variables. PMID:27296452
Differential proteomics profiling of the ova between healthy and Rice stripe virus-infected female insects of Laodelphax striatellus. PMID:27277140
Presence of TMPRSS2-ERG is associated with alterations of the metabolic profile in human prostate cancer. PMID:27276682
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. PMID:27275538
Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters in Aspergillus oryzae: A Representative Case Study. PMID:27274991
Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches. PMID:27273017
Extensive molecular analysis suggested the strong genetic heterogeneity of idiopathic chronic pancreatitis. PMID:27264265
Evidence for persistent and shared bacterial strains against a background of largely unique gut colonization in hospitalized premature infants. PMID:27258951
Computational recognition and analysis of hitherto uncharacterized nucleotide cyclase-like proteins in bacteria. PMID:27246835
Differentially expressed genes in preimplantation human embryos: potential candidate genes for blastocyst formation and implantation. PMID:27241529
Yin Yang 1 is associated with cancer stem cell transcription factors (SOX2, OCT4, BMI1) and clinical implication. PMID:27225481
Composition and function of the pediatric colonic mucosal microbiome in untreated patients with ulcerative colitis. PMID:27217061
Research Resources for Nuclear Receptor Signaling Pathways. PMID:27216565
Nrf2 suppresses macrophage inflammatory response by blocking proinflammatory cytokine transcription. PMID:27211851
Reprogramming human A375 amelanotic melanoma cells by catalase overexpression: Upregulation of antioxidant genes correlates with regression of melanoma malignancy and with malignant progression when downregulated. PMID:27206673
A flexible method for estimating the fraction of fitness influencing mutations from large sequencing data sets. PMID:27197222
Control of fluxes in metabolic networks. PMID:27197218
Network-assisted investigation of virulence and antibiotic-resistance systems in Pseudomonas aeruginosa. PMID:27194047
LDSS-P: an advanced algorithm to extract functional short motifs associated with coordinated gene expression. PMID:27190233
Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases. PMID:27189340
KdgF, the missing link in the microbial metabolism of uronate sugars from pectin and alginate. PMID:27185956
Complete genome sequence of 'Halanaeroarchaeum sulfurireducens' M27-SA2, a sulfur-reducing and acetate-oxidizing haloarchaeon from the deep-sea hypersaline anoxic lake Medee. PMID:27182430
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. PMID:27173523
A single gene of a commensal microbe affects host susceptibility to enteric infection. PMID:27173141
An Improved Genome Assembly of Azadirachta indica A. Juss. PMID:27172223
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage. PMID:27159581
Reaction Decoder Tool (RDT): extracting features from chemical reactions. PMID:27153692
MOCAT2: a metagenomic assembly, annotation and profiling framework. PMID:27153620
An algorithm for designing minimal microbial communities with desired metabolic capacities. PMID:27153571
Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom. PMID:27152931
DrugGenEx-Net: a novel computational platform for systems pharmacology and gene expression-based drug repurposing. PMID:27151405
KeyPathwayMinerWeb: online multi-omics network enrichment. PMID:27150809
Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma. PMID:27149842
SpinachDB: A Well-Characterized Genomic Database for Gene Family Classification and SNP Information of Spinach. PMID:27148975
RNA-seq Transcriptome Analysis of Panax japonicus, and Its Comparison with Other Panax Species to Identify Potential Genes Involved in the Saponins Biosynthesis. PMID:27148308
Characterization of the Gut Microbiome Using 16S or Shotgun Metagenomics. PMID:27148170
Actionable pathways: interactive discovery of therapeutic targets using signaling pathway models. PMID:27137885
Composition and Predicted Metabolic Capacity of Upper and Lower Airway Microbiota of Healthy Dogs in Relation to the Fecal Microbiota. PMID:27136381
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind. PMID:27131375
Ancestral genome reconstruction identifies the evolutionary basis for trait acquisition in polyphosphate accumulating bacteria. PMID:27128993
Metabolomics in epidemiology: from metabolite concentrations to integrative reaction networks. PMID:27118561
Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system. PMID:27118214
A spectrum of CodY activities drives metabolic reorganization and virulence gene expression in Staphylococcus aureus. PMID:27116338
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. PMID:27114492
Towards a functional hypothesis relating anti-islet cell autoimmunity to the dietary impact on microbial communities and butyrate production. PMID:27114075
Hipposeq: a comprehensive RNA-seq database of gene expression in hippocampal principal neurons. PMID:27113915
Gene Expression Profiling Identifies Cell Proliferation and Inflammation as the Predominant Pathways Regulated by Aryl Hydrocarbon Receptor in Primary Human Fetal Lung Cells Exposed to Hyperoxia. PMID:27103661
Analysis of proteome dynamics inside the silk gland lumen of Bombyx mori. PMID:27102218
The adaptive potential of subtropical rainbowfish in the face of climate change: heritability and heritable plasticity for the expression of candidate genes. PMID:27099620
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Ultrastructure of the liver microcirculation influences hepatic and systemic insulin activity and provides a mechanism for age-related insulin resistance. PMID:27095270
ChemiRs: a web application for microRNAs and chemicals. PMID:27091357
Gene-set Analysis with CGI Information for Differential DNA Methylation Profiling. PMID:27090937
MBROLE 2.0-functional enrichment of chemical compounds. PMID:27084944
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PMID:27081850
An NGS Workflow Blueprint for DNA Sequencing Data and Its Application in Individualized Molecular Oncology. PMID:27081306
Selective enrichment of microRNAs in extracellular matrix vesicles produced by growth plate chondrocytes. PMID:27080510
Novel Biomarker Proteins in Chronic Lymphocytic Leukemia: Impact on Diagnosis, Prognosis and Treatment. PMID:27078856
Computational Reconstruction of NFκB Pathway Interaction Mechanisms during Prostate Cancer. PMID:27078000
Human Milk Cells and Lipids Conserve Numerous Known and Novel miRNAs, Some of Which Are Differentially Expressed during Lactation. PMID:27074017
Gut microbiome remodeling induces depressive-like behaviors through a pathway mediated by the host's metabolism. PMID:27067014
Genomic insights into members of the candidate phylum Hyd24-12 common in mesophilic anaerobic digesters. PMID:27058503
A Novel Prioritization Method in Identifying Recurrent Venous Thromboembolism-Related Genes. PMID:27050193
SoftPanel: a website for grouping diseases and related disorders for generation of customized panels. PMID:27044653
Implications of genotypic differences in the generation of a urinary metabolomics radiation signature. PMID:27040378
Birth mode-dependent association between pre-pregnancy maternal weight status and the neonatal intestinal microbiome. PMID:27033998
Involvement of Alternative Splicing in Barley Seed Germination. PMID:27031341
Mycobacterium bovis BCG Interferes with miR-3619-5p Control of Cathepsin S in the Process of Autophagy. PMID:27014637
Role of MicroRNAs in carcinogenesis that potential for biomarker of endometrial cancer. PMID:27006767
Changes in the Eye Microbiota Associated with Contact Lens Wearing. PMID:27006462
Metagenomic Sequencing with Strain-Level Resolution Implicates Uropathogenic E. coli in Necrotizing Enterocolitis and Mortality in Preterm Infants. PMID:26997279
Two Bacterial Genera, Sodalis and Rickettsia, Associated with the Seal Louse Proechinophthirus fluctus (Phthiraptera: Anoplura). PMID:26994086
Wolbachia Modulates Lipid Metabolism in Aedes albopictus Mosquito Cells. PMID:26994075
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PMID:26992093
A Protein Complex Map of Trypanosoma brucei. PMID:26991453
Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves. PMID:26990967
Global Mapping of Traditional Chinese Medicine into Bioactivity Space and Pathways Annotation Improves Mechanistic Understanding and Discovers Relationships between Therapeutic Action (Sub)classes. PMID:26989424
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. PMID:26989151
Pipeline for the identification and classification of ion channels in parasitic flatworms. PMID:26983991
Microarray expression analysis of genes involved in innate immune memory in peritoneal macrophages. PMID:26981372
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. PMID:26980520
Prioritizing Environmental Chemicals for Obesity and Diabetes Outcomes Research: A Screening Approach Using ToxCast™ High-Throughput Data. PMID:26978842
Challenges in horizontal model integration. PMID:26968798
Genetic Passive Immunization with Adenoviral Vector Expressing Chimeric Nanobody-Fc Molecules as Therapy for Genital Infection Caused by Mycoplasma hominis. PMID:26962869
Translational Meta-analytical Methods to Localize the Regulatory Patterns of Neurological Disorders in the Human Brain. PMID:26958307
Discovery and dissection of metabolic oscillations in the microaerobic nitric oxide response network of Escherichia coli. PMID:26951670
Cancer Metabolomics and the Human Metabolome Database. PMID:26950159
Melatonin Pathway and Atenolol-Related Glucose Dysregulation: Is There a Correlation? PMID:26946962
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. PMID:26939900
Genome dynamics of multidrug-resistant Acinetobacter baumannii during infection and treatment. PMID:26939581
Linking Virus Genomes with Host Taxonomy. PMID:26938550
Multidimensional Screening Platform for Simultaneously Targeting Oncogenic KRAS and Hypoxia-Inducible Factors Pathways in Colorectal Cancer. PMID:26938486
Network Analysis of Metabolite GWAS Hits: Implication of CPS1 and the Urea Cycle in Weight Maintenance. PMID:26938218
Metabolic profiling during ex vivo machine perfusion of the human liver. PMID:26935866
Deciphering the Potential Pharmaceutical Mechanism of Chinese Traditional Medicine (Gui-Zhi-Shao-Yao-Zhi-Mu) on Rheumatoid Arthritis. PMID:26935797
Gene dysregulation is restored in the Parkinson's disease MPTP neurotoxic mice model upon treatment of the therapeutic drug Cu(II)(atsm). PMID:26928495
A Multi-Method Approach for Proteomic Network Inference in 11 Human Cancers. PMID:26928298
Global Metabolic Profiling of Arabidopsis Polyamine Oxidase 4 (AtPAO4) Loss-of-Function Mutants Exhibiting Delayed Dark-Induced Senescence. PMID:26925084
Exercise-driven metabolic pathways in healthy cartilage. PMID:26924420
Cognitive impairment by antibiotic-induced gut dysbiosis: Analysis of gut microbiota-brain communication. PMID:26923630
Establishing gene models from the Pinus pinaster genome using gene capture and BAC sequencing. PMID:26922242
Mutations in Novel Lipopolysaccharide Biogenesis Genes Confer Resistance to Amoebal Grazing in Synechococcus elongatus. PMID:26921432
PKCδ regulates integrin αVβ3 expression and transformed growth of K-ras dependent lung cancer cells. PMID:26918447
The standard operating procedure of the DOE-JGI Metagenome Annotation Pipeline (MAP v.4). PMID:26918089
Skeletal muscle and plasma lipidomic signatures of insulin resistance and overweight/obesity in humans. PMID:26916476
Venom gland transcriptome analyses of two freshwater stingrays (Myliobatiformes: Potamotrygonidae) from Brazil. PMID:26916342
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. PMID:26912667
New strategy for drug discovery by large-scale association analysis of molecular networks of different species. PMID:26912056
Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate. PMID:26911915
Multi-omics analysis reveals regulators of the response to nitrogen limitation in Yarrowia lipolytica. PMID:26911370
A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks. PMID:26909353
Inhibitory effect of traditional oriental medicine-derived monoamine oxidase B inhibitor on radioresistance of non-small cell lung cancer. PMID:26906215
Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. PMID:26905629
Antipsychotic pharmacogenomics in first episode psychosis: a role for glutamate genes. PMID:26905411
Functional Evaluations of Genes Disrupted in Patients with Tourette's Disorder. PMID:26903887
Pooled screening for antiproliferative inhibitors of protein-protein interactions. PMID:26900867
Individual Differences in Scotopic Visual Acuity and Contrast Sensitivity: Genetic and Non-Genetic Influences. PMID:26886100
MCT1 Modulates Cancer Cell Pyruvate Export and Growth of Tumors that Co-express MCT1 and MCT4. PMID:26876179
Major remodeling of brain microvessels during neonatal period in the mouse: A proteomic and transcriptomic study. PMID:26873886
Integration of lipidomics and transcriptomics unravels aberrant lipid metabolism and defines cholesteryl oleate as potential biomarker of prostate cancer. PMID:26865432
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. PMID:26860319
Sequencing, De novo Assembly, Functional Annotation and Analysis of Phyllanthus amarus Leaf Transcriptome Using the Illumina Platform. PMID:26858723
Small RNA and degradome deep sequencing reveals drought-and tissue-specific micrornas and their important roles in drought-sensitive and drought-tolerant tomato genotypes. PMID:26857916
Human milk miRNAs primarily originate from the mammary gland resulting in unique miRNA profiles of fractionated milk. PMID:26854194
Downregulation of histone H2A and H2B pathways is associated with anthracycline sensitivity in breast cancer. PMID:26852132
Proteomics reveals major components of oogenesis in the reproductive tract of sugar-fed Anopheles aquasalis. PMID:26850722
Transcriptome Analysis of an Anthracnose-Resistant Tea Plant Cultivar Reveals Genes Associated with Resistance to Colletotrichum camelliae. PMID:26849553
Global Metabolic Responses to Salt Stress in Fifteen Species. PMID:26848578
Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy. PMID:26839589
Ecological Genomics of the Uncultivated Marine Roseobacter Lineage CHAB-I-5. PMID:26826224
Detailed Mechanistic Study of the Non-enzymatic Formation of the Discoipyrrole Family of Natural Products. PMID:26824832
High yield 1,3-propanediol production by rational engineering of the 3-hydroxypropionaldehyde bottleneck in Citrobacter werkmanii. PMID:26822953
MTD: a mammalian transcriptomic database to explore gene expression and regulation. PMID:26822098
Winners of CASMI2013: Automated Tools and Challenge Data. PMID:26819882
Rethinking Mass Spectrometry-Based Small Molecule Identification Strategies in Metabolomics. PMID:26819881
Solving CASMI 2013 with MetFrag, MetFusion and MOLGEN-MS/MS. PMID:26819879
Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism. PMID:26812499
Integrating mutation and gene expression cross-sectional data to infer cancer progression. PMID:26810975
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Fast and Rigorous Computation of Gene and Pathway Scores from SNP-Based Summary Statistics. PMID:26808494
Genome Analysis of the Biotechnologically Relevant Acidophilic Iron Oxidising Strain JA12 Indicates Phylogenetic and Metabolic Diversity within the Novel Genus "Ferrovum". PMID:26808278
Induction of Viable but Nonculturable State in Rhodococcus and Transcriptome Analysis Using RNA-seq. PMID:26808070
Network-Based Analysis of eQTL Data to Prioritize Driver Mutations. PMID:26802430
Multi-task consensus clustering of genome-wide transcriptomes from related biological conditions. PMID:26801959
Ascochyta blight disease of pea (Pisum sativum L.): defence-related candidate genes associated with QTL regions and identification of epistatic QTL. PMID:26801334
RNA-seq transcriptional profiling of Herbaspirillum seropedicae colonizing wheat (Triticum aestivum) roots. PMID:26801330
Core Proteomic Analysis of Unique Metabolic Pathways of Salmonella enterica for the Identification of Potential Drug Targets. PMID:26799565
Deciphering the Substrate Specificity of SbnA, the Enzyme Catalyzing the First Step in Staphyloferrin B Biosynthesis. PMID:26794841
Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations. PMID:26792120
Gene Expressing and sRNA Sequencing Show That Gene Differentiation Associates with a Yellow Acer palmatum Mutant Leaf in Different Light Conditions. PMID:26788511
Parkin-mediated mitophagy directs perinatal cardiac metabolic maturation in mice. PMID:26785495
Characterization of Bacterial Communities in Selected Smokeless Tobacco Products Using 16S rDNA Analysis. PMID:26784944
Serum Metabolite Profiles Are Altered by Erlotinib Treatment and the Integrin α1-Null Genotype but Not by Post-Traumatic Osteoarthritis. PMID:26784366
Correlative Gene Expression to Protective Seroconversion in Rift Valley Fever Vaccinates. PMID:26783758
Decoding Cellular Dynamics in Epidermal Growth Factor Signaling Using a New Pathway-Based Integration Approach for Proteomics and Transcriptomics Data. PMID:26779252
COMPUTING THERAPY FOR PRECISION MEDICINE: COLLABORATIVE FILTERING INTEGRATES AND PREDICTS MULTI-ENTITY INTERACTIONS. PMID:26776170
COPD subtypes identified by network-based clustering of blood gene expression. PMID:26773458
Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing. PMID:26763747
A draft map of the mouse pluripotent stem cell spatial proteome. PMID:26754106
Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus. PMID:26747700
Exome arrays capture polygenic rare variant contributions to schizophrenia. PMID:26740555
Effect of chronic uremia on the transcriptional profile of the calcified aorta analyzed by RNA sequencing. PMID:26739890
Path2PPI: an R package to predict protein-protein interaction networks for a set of proteins. PMID:26733452
Sequencing the exposome: A call to action. PMID:26722641
The transcriptome of nitrofen-induced pulmonary hypoplasia in the rat model of congenital diaphragmatic hernia. PMID:26720608
Brain Transcriptomic Response to Social Eavesdropping in Zebrafish (Danio rerio). PMID:26713440
Essential Genome of the Metabolically Versatile Alphaproteobacterium Rhodopseudomonas palustris. PMID:26712940
New Coffee Plant-Infecting Xylella fastidiosa Variants Derived via Homologous Recombination. PMID:26712553
Selective Spectrum Antibiotic Modulation of the Gut Microbiome in Obesity and Diabetes Rodent Models. PMID:26709835
Mathematical models of cancer metabolism. PMID:26702357
Blood transcriptomics and metabolomics for personalized medicine. PMID:26702339
Profiling of Sox4-dependent transcriptome in skin links tumour suppression and adult stem cell activation. PMID:26697322
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. PMID:26695483
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. PMID:26693857
Predictive Modeling of Drug Treatment in the Area of Personalized Medicine. PMID:26692759
Microarray analysis of Long non-coding RNA expression profiles in human gastric cells and tissues with Helicobacter pylori Infection. PMID:26690385
High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED. PMID:26682918
Obtaining long 16S rDNA sequences using multiple primers and its application on dioxin-containing samples. PMID:26681335
Multiple target drug cocktail design for attacking the core network markers of four cancers using ligand-based and structure-based virtual screening methods. PMID:26680552
Genome-wide transcriptomic analyses provide insights into the lifestyle transition and effector repertoire of Leptosphaeria maculans during the colonization of Brassica napus seedlings. PMID:26679637
Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out. PMID:26678747
Using activation status of signaling pathways as mechanism-based biomarkers to predict drug sensitivity. PMID:26678097
Taking Bioinformatics to Systems Medicine. PMID:26677177
Genomic Targets and Features of BarA-UvrY (-SirA) Signal Transduction Systems. PMID:26673755
Mutation Screening of 1,237 Cancer Genes across Six Model Cell Lines of Basal-Like Breast Cancer. PMID:26670335
Application of Gene Expression Trajectories Initiated from ErbB Receptor Activation Highlights the Dynamics of Divergent Promoter Usage. PMID:26658111
HRGRN: A Graph Search-Empowered Integrative Database of Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks. PMID:26657893
The MG-RAST metagenomics database and portal in 2015. PMID:26656948
Deletion of GSTA4-4 results in increased mitochondrial post-translational modification of proteins by reactive aldehydes following chronic ethanol consumption in mice. PMID:26654979
De novo dominant ASXL3 mutations alter H2A deubiquitination and transcription in Bainbridge-Ropers syndrome. PMID:26647312
TAF1 Variants Are Associated with Dysmorphic Features, Intellectual Disability, and Neurological Manifestations. PMID:26637982
Challenges of Inversely Estimating Jacobian from Metabolomics Data. PMID:26636075
Functional overlap of the Arabidopsis leaf and root microbiota. PMID:26633631
Messenger RNA profile analysis deciphers new Esrrb responsive genes in prostate cancer cells. PMID:26627478
Genomic insights into the evolutionary origin of Myxozoa within Cnidaria. PMID:26627241
The role of gut microbiota in fetal methylmercury exposure: Insights from a pilot study. PMID:26626101
Towards biome-specific analysis of meta-omics data. PMID:26623543
Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage. PMID:26615204
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
SVD-phy: improved prediction of protein functional associations through singular value decomposition of phylogenetic profiles. PMID:26614125
In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories. PMID:26609052
Analysis of volatile organic compounds in exhaled breath to diagnose ventilator-associated pneumonia. PMID:26608483
SymbioGenomesDB: a database for the integration and access to knowledge on host-symbiont relationships. PMID:26607947
Functional Cross-Talking between Differentially Expressed and Alternatively Spliced Genes in Human Liver Cancer Cells Treated with Berberine. PMID:26606055
Systematic identification and correction of annotation errors in the genetic interaction map of Saccharomyces cerevisiae. PMID:26602688
Identification of Putative Nuclear Receptors and Steroidogenic Enzymes in Murray-Darling Rainbowfish (Melanotaenia fluviatilis) Using RNA-Seq and De Novo Transcriptome Assembly. PMID:26599404
CancerResource--updated database of cancer-relevant proteins, mutations and interacting drugs. PMID:26590406
The UCSC Genome Browser database: 2016 update. PMID:26590259
STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data. PMID:26590256
Transcriptomic profiling of host-parasite interactions in the microsporidian Trachipleistophora hominis. PMID:26589282
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. PMID:26582926
enviPath--The environmental contaminant biotransformation pathway resource. PMID:26582924
Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad. PMID:26581338
Plasma Metabolic Profiles in Women are Menopause Dependent. PMID:26580805
Changes in the nuclear proteome of developing wheat (Triticum aestivum L.) grain. PMID:26579155
Dual RNA-seq of Nontypeable Haemophilus influenzae and Host Cell Transcriptomes Reveals Novel Insights into Host-Pathogen Cross Talk. PMID:26578681
Therapeutic target database update 2016: enriched resource for bench to clinical drug target and targeted pathway information. PMID:26578601
SomamiR 2.0: a database of cancer somatic mutations altering microRNA-ceRNA interactions. PMID:26578591
Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database. PMID:26578582
Assembly: a resource for assembled genomes at NCBI. PMID:26578580
dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins. PMID:26578568
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
Mining for novel candidate clock genes in the circadian regulatory network. PMID:26576534
A new network representation of the metabolism to detect chemical transformation modules. PMID:26573681
Molecular tools for studying the major malaria vector Anopheles funestus: improving the utility of the genome using a comparative poly(A) and Ribo-Zero RNAseq analysis. PMID:26573092
A Comprehensive MicroRNA Expression Profile Related to Hypoxia Adaptation in the Tibetan Pig. PMID:26571238
Bringing Down Cancer Aircraft: Searching for Essential Hypomutated Proteins in Skin Melanoma. PMID:26565620
Phylogeny of metabolic networks: a spectral graph theoretical approach. PMID:26564980
High quality draft genomic sequence of Flavobacterium enshiense DK69(T) and comparison among Flavobacterium genomes. PMID:26561515
COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets. PMID:26561344
A Systems Biology-Based Investigation into the Pharmacological Mechanisms of Sheng-ma-bie-jia-tang Acting on Systemic Lupus Erythematosus by Multi-Level Data Integration. PMID:26560501
Genetic Adaptation to Climate in White Spruce Involves Small to Moderate Allele Frequency Shifts in Functionally Diverse Genes. PMID:26560341
Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma. PMID:26558755
Metabolomics, Standards, and Metabolic Modeling for Synthetic Biology in Plants. PMID:26557642
Methanosarcina Play an Important Role in Anaerobic Co-Digestion of the Seaweed Ulva lactuca: Taxonomy and Predicted Metabolism of Functional Microbial Communities. PMID:26555136
WITHDRAWN--a resource for withdrawn and discontinued drugs. PMID:26553801
Molecular systems evaluation of oligomerogenic APP(E693Q) and fibrillogenic APP(KM670/671NL)/PSEN1(Δexon9) mouse models identifies shared features with human Alzheimer's brain molecular pathology. PMID:26552589
Untargeted metabolite profiling reveals that nitric oxide bioynthesis is an endogenous modulator of carotenoid biosynthesis in Deinococcus radiodurans and is required for extreme ionizing radiation resistance. PMID:26550929
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
Transcriptomic analysis of cobalt stress in the marine yeast Debaryomyces hansenii. PMID:26546454
Functional and expression analyses of transcripts based on full-length cDNAs of Sorghum bicolor. PMID:26546227
Pancreatic β cell enhancers regulate rhythmic transcription of genes controlling insulin secretion. PMID:26542580
Structural Characterisation of FabG from Yersinia pestis, a Key Component of Bacterial Fatty Acid Synthesis. PMID:26539719
SR4 Uncouples Mitochondrial Oxidative Phosphorylation, Modulates AMP-dependent Kinase (AMPK)-Mammalian Target of Rapamycin (mTOR) Signaling, and Inhibits Proliferation of HepG2 Hepatocarcinoma Cells. PMID:26534958
Designing overall stoichiometric conversions and intervening metabolic reactions. PMID:26530953
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. PMID:26527732
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. PMID:26527726
MetaNetX/MNXref--reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. PMID:26527720
ccmGDB: a database for cancer cell metabolism genes. PMID:26519468
Increased hepatocellular protein carbonylation in human end-stage alcoholic cirrhosis. PMID:26518673
Genomic information of the arsenic-resistant bacterium Lysobacter arseniciresistens type strain ZS79(T) and comparison of Lysobacter draft genomes. PMID:26516404
Mutations in the TLR3 signaling pathway and beyond in adult patients with herpes simplex encephalitis. PMID:26513235
The standard operating procedure of the DOE-JGI Microbial Genome Annotation Pipeline (MGAP v.4). PMID:26512311
A constraint-based modelling approach to metabolic dysfunction in Parkinson's disease. PMID:26504511
Colorectal cancer atlas: An integrative resource for genomic and proteomic annotations from colorectal cancer cell lines and tissues. PMID:26496946
A dual control mechanism synchronizes riboflavin and sulphur metabolism in Bacillus subtilis. PMID:26494285
The first whole genome and transcriptome of the cinereous vulture reveals adaptation in the gastric and immune defense systems and possible convergent evolution between the Old and New World vultures. PMID:26486310
A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses. PMID:26485611
Metabolomic and high-throughput sequencing analysis-modern approach for the assessment of biodeterioration of materials from historic buildings. PMID:26483760
Protein Analysis of Sapienic Acid-Treated Porphyromonas gingivalis Suggests Differential Regulation of Multiple Metabolic Pathways. PMID:26483519
Defining the nitrogen regulated transcriptome of Mycobacterium smegmatis using continuous culture. PMID:26482235
Weevil endosymbiont dynamics is associated with a clamping of immunity. PMID:26482132
ECMDB 2.0: A richer resource for understanding the biochemistry of E. coli. PMID:26481353
DIDA: A curated and annotated digenic diseases database. PMID:26481352
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
KEGG as a reference resource for gene and protein annotation. PMID:26476454
CauloBrowser: A systems biology resource for Caulobacter crescentus. PMID:26476443
An overview of bioinformatics methods for modeling biological pathways in yeast. PMID:26476430
Draft Genome Sequence of Lactobacillus gorillae Strain KZ01T, Isolated from a Western Lowland Gorilla. PMID:26472838
Single-Cell Expression Profiling Reveals a Dynamic State of Cardiac Precursor Cells in the Early Mouse Embryo. PMID:26469858
SIGNOR: a database of causal relationships between biological entities. PMID:26467481
Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools. PMID:26467476
Gene Prioritization by Compressive Data Fusion and Chaining. PMID:26465776
Encyclopedia of bacterial gene circuits whose presence or absence correlate with pathogenicity--a large-scale system analysis of decoded bacterial genomes. PMID:26459834
Genome-wide analysis of differentially expressed miRNA in PLX4720-resistant and parental human thyroid cancer cell lines. PMID:26456124
Functional and Structural Consequence of Rare Exonic Single Nucleotide Polymorphisms: One Story, Two Tales. PMID:26454016
Prediction of microbial phenotypes based on comparative genomics. PMID:26451672
Habitat fragmentation is associated to gut microbiota diversity of an endangered primate: implications for conservation. PMID:26445280
Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening. PMID:26444490
Cheminformatics Research at the Unilever Centre for Molecular Science Informatics Cambridge. PMID:26435758
SubtiWiki 2.0--an integrated database for the model organism Bacillus subtilis. PMID:26433225
MitoMiner v3.1, an update on the mitochondrial proteomics database. PMID:26432830
Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis. PMID:26430493
PyMine: a PyMOL plugin to integrate and visualize data for drug discovery. PMID:26429562
PatchSurfers: Two methods for local molecular property-based binding ligand prediction. PMID:26427548
Genome and Phenotype Microarray Analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic Determinants and Metabolic Abilities with Environmental Relevance. PMID:26426997
Analysis of Proteins That Rapidly Change Upon Mechanistic/Mammalian Target of Rapamycin Complex 1 (mTORC1) Repression Identifies Parkinson Protein 7 (PARK7) as a Novel Protein Aberrantly Expressed in Tuberous Sclerosis Complex (TSC). PMID:26419955
Elucidation of the CHO Super-Ome (CHO-SO) by Proteoinformatics. PMID:26418914
Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera. PMID:26415554
Genome sequence of Anoxybacillus ayderensis AB04(T) isolated from the Ayder hot spring in Turkey. PMID:26413199
Reporter pathway analysis from transcriptome data: Metabolite-centric versus Reaction-centric approach. PMID:26411587
Genome-Wide Assessment of Outer Membrane Vesicle Production in Escherichia coli. PMID:26406465
Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel. PMID:26406373
DAPPER: a data-mining resource for protein-protein interactions. PMID:26405458
Genomic alterations in BCL2L1 and DLC1 contribute to drug sensitivity in gastric cancer. PMID:26401016
High-Throughput Identification of Cis-Regulatory Rewiring Events in Yeast. PMID:26399482
Cis-eQTL analysis and functional validation of candidate susceptibility genes for high-grade serous ovarian cancer. PMID:26391404
In Silico Analysis and Experimental Validation of Active Compounds from Cichorium intybus L. Ameliorating Liver Injury. PMID:26389883
FOXC2 and fluid shear stress stabilize postnatal lymphatic vasculature. PMID:26389677
High quality draft genomic sequence of Flavihumibacter solisilvae 3-3(T). PMID:26388970
High quality draft genomic sequence of Arenimonas donghaensis DSM 18148(T). PMID:26380644
Physiological roles of pyruvate ferredoxin oxidoreductase and pyruvate formate-lyase in Thermoanaerobacterium saccharolyticum JW/SL-YS485. PMID:26379770
Characterization of the Transcriptional Complexity of the Receptive and Pre-receptive Endometria of Dairy Goats. PMID:26373443
Different combinations of atomic interactions predict protein-small molecule and protein-DNA/RNA affinities with similar accuracy. PMID:26370248
Embryonic Lethality Due to Arrested Cardiac Development in Psip1/Hdgfrp2 Double-Deficient Mice. PMID:26367869
Dissecting Leishmania infantum Energy Metabolism - A Systems Perspective. PMID:26367006
ASD v3.0: unraveling allosteric regulation with structural mechanisms and biological networks. PMID:26365237
Expansion of the tetracycline-dependent regulation toolbox for Helicobacter pylori. PMID:26362986
A new approach for investigating venom function applied to venom calreticulin in a parasitoid wasp. PMID:26359852
ConTour: Data-Driven Exploration of Multi-Relational Datasets for Drug Discovery. PMID:26356902
Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens. PMID:26350629
Discovery of Intermediary Genes between Pathways Using Sparse Regression. PMID:26348038
Draft genome of a commonly misdiagnosed multidrug resistant pathogen Candida auris. PMID:26346253
Pervasive pleiotropy between psychiatric disorders and immune disorders revealed by integrative analysis of multiple GWAS. PMID:26340901
Deregulation of SYCP2 predicts early stage human papillomavirus-positive oropharyngeal carcinoma: A prospective whole transcriptome analysis. PMID:26334652
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics. PMID:26322134
Mutual Cross-Feeding Interactions between Bifidobacterium longum subsp. longum NCC2705 and Eubacterium rectale ATCC 33656 Explain the Bifidogenic and Butyrogenic Effects of Arabinoxylan Oligosaccharides. PMID:26319874
SNP-SNP interaction analysis of NF-κB signaling pathway on breast cancer survival. PMID:26317411
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
Transcriptional dysregulation of inflammatory/immune pathways after active vaccination against Huntington's disease. PMID:26307082
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. PMID:26307061
Composition and Diversity of the Fecal Microbiome and Inferred Fecal Metagenome Does Not Predict Subsequent Pneumonia Caused by Rhodococcus equi in Foals. PMID:26305682
Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. PMID:26298294
Large-scale RNA-Seq Transcriptome Analysis of 4043 Cancers and 548 Normal Tissue Controls across 12 TCGA Cancer Types. PMID:26292924
Moyamoya disease susceptibility gene RNF213 links inflammatory and angiogenic signals in endothelial cells. PMID:26278786
Directional migration and transcriptional analysis of oligodendrocyte precursors subjected to stimulation of electrical signal. PMID:26269459
Identifying miRNA/mRNA negative regulation pairs in colorectal cancer. PMID:26269151
Integrated miRNA-mRNA analysis in the habenula nuclei of mice intravenously self-administering nicotine. PMID:26260614
Prediction of human population responses to toxic compounds by a collaborative competition. PMID:26258538
An Integrated Transcriptome Atlas of Embryonic Hair Follicle Progenitors, Their Niche, and the Developing Skin. PMID:26256211
Genetic underpinnings of left superior temporal gyrus thickness in patients with schizophrenia. PMID:26249676
Thalamic WNT3 Secretion Spatiotemporally Regulates the Neocortical Ribosome Signature and mRNA Translation to Specify Neocortical Cell Subtypes. PMID:26245956
Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant. PMID:26229594
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder. PMID:26228432
Gene expression profiling of ovarian carcinomas and prognostic analysis of outcome. PMID:26228058
Distinct Responses of Mycobacterium smegmatis to Exposure to Low and High Levels of Hydrogen Peroxide. PMID:26225431
ExAtlas: An interactive online tool for meta-analysis of gene expression data. PMID:26223199
Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans. PMID:26221956
SpirPro: A Spirulina proteome database and web-based tools for the analysis of protein-protein interactions at the metabolic level in Spirulina (Arthrospira) platensis C1. PMID:26220682
Data for iTRAQ-based quantitative proteomics analysis of Brassica napus leaves in response to chlorophyll deficiency. PMID:26217696
A novel, dynamic pattern-based analysis of NF-κB binding during the priming phase of liver regeneration reveals switch-like functional regulation of target genes. PMID:26217230
Functional IRF3 deficiency in a patient with herpes simplex encephalitis. PMID:26216125
Macroscopic modeling of mammalian cell growth and metabolism. PMID:26198881
Strain-resolved microbial community proteomics reveals simultaneous aerobic and anaerobic function during gastrointestinal tract colonization of a preterm infant. PMID:26191049
Combined Analysis of SNP Array Data Identifies Novel CNV Candidates and Pathways in Ependymoma and Mesothelioma. PMID:26185765
Interaction networks for identifying coupled molecular processes in microbial communities. PMID:26180552
Chromerid genomes reveal the evolutionary path from photosynthetic algae to obligate intracellular parasites. PMID:26175406
Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment. PMID:26170900
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PMID:26157614
Electron transport phosphorylation in rumen butyrivibrios: unprecedented ATP yield for glucose fermentation to butyrate. PMID:26157432
RNA-seq Reveals Complicated Transcriptomic Responses to Drought Stress in a Nonmodel Tropic Plant, Bombax ceiba L. PMID:26157330
Novel drug target identification for the treatment of dementia using multi-relational association mining. PMID:26154857
In Silico Identification and In Vitro and In Vivo Validation of Anti-Psychotic Drug Fluspirilene as a Potential CDK2 Inhibitor and a Candidate Anti-Cancer Drug. PMID:26147897
iCOSSY: An Online Tool for Context-Specific Subnetwork Discovery from Gene Expression Data. PMID:26147457
The Convergence of Systems and Reductionist Approaches in Complex Trait Analysis. PMID:26140590
Integrative network analysis for survival-associated gene-gene interactions across multiple genomic profiles in ovarian cancer. PMID:26138921
Detoxification mechanisms of honey bees (Apis mellifera) resulting in tolerance of dietary nicotine. PMID:26134631
Identification of Candidate Adherent-Invasive E. coli Signature Transcripts by Genomic/Transcriptomic Analysis. PMID:26125937
Independent Effects of γ-Aminobutyric Acid Transaminase (GABAT) on Metabolic and Sleep Homeostasis. PMID:26124278
Application of whole genome and RNA sequencing to investigate the genomic landscape of common variable immunodeficiency disorders. PMID:26122175
iTRAQ-based quantitative proteomics analysis of rice leaves infected by Rice stripe virus reveals several proteins involved in symptom formation. PMID:26113023
Computational methods and resources for the interpretation of genomic variants in cancer. PMID:26111056
DNA microarray integromics analysis platform. PMID:26110022
A New Combinatorial Optimization Approach for Integrated Feature Selection Using Different Datasets: A Prostate Cancer Transcriptomic Study. PMID:26106884
Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. PMID:26106450
Inference of Network Dynamics and Metabolic Interactions in the Gut Microbiome. PMID:26102287
Publisher’s Note:Abstraction for data integration:Fusing mammalian molecular, cellular and phenotype big datasets for better knowledge extraction. PMID:26101093
Dysregulated transcription across diverse cancer types reveals the importance of RNA-binding protein in carcinogenesis. PMID:26100984
Metabolomic profiling of Burkholderia pseudomallei using UHPLC-ESI-Q-TOF-MS reveals specific biomarkers including 4-methyl-5-thiazoleethanol and unique thiamine degradation pathway. PMID:26097677
Proteins interaction network and modeling of IGVH mutational status in chronic lymphocytic leukemia. PMID:26088082
Measuring information flow in cellular networks by the systems biology method through microarray data. PMID:26082788
ChemDIS: a chemical-disease inference system based on chemical-protein interactions. PMID:26078786
Suppression of cell division-associated genes by Helicobacter pylori attenuates proliferation of RAW264.7 monocytic macrophage cells. PMID:26078204
Metabolic fingerprinting of Arabidopsis thaliana accessions. PMID:26074932
Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. PMID:26072478
High-Throughput Sequencing and De Novo Assembly of Red and Green Forms of the Perilla frutescens var. crispa Transcriptome. PMID:26070213
Cyclic Rhamnosylated Elongation Factor P Establishes Antibiotic Resistance in Pseudomonas aeruginosa. PMID:26060278
Gene set analysis: A step-by-step guide. PMID:26059482
High-throughput sequencing of small RNAs and anatomical characteristics associated with leaf development in celery. PMID:26057455
kpath: integration of metabolic pathway linked data. PMID:26055101
Detection of miRNA regulatory effect on triple negative breast cancer transcriptome. PMID:26046581
Impact of microfluidic processing on bacterial ribonucleic acid expression. PMID:26045727
A manual curation strategy to improve genome annotation: application to a set of haloarchael genomes. PMID:26042526
Sequence-based Network Completion Reveals the Integrality of Missing Reactions in Metabolic Networks. PMID:26041773
Quantification of circulating steroids in individual zebrafish using stacking to achieve nanomolar detection limits with capillary electrophoresis and UV-visible absorbance detection. PMID:26041454
In Silico Analysis of the Metabolic Potential and Niche Specialization of Candidate Phylum "Latescibacteria" (WS3). PMID:26039074
Screening currency notes for microbial pathogens and antibiotic resistance genes using a shotgun metagenomic approach. PMID:26035208
Defining bacterial regulons using ChIP-seq. PMID:26032817
BOWS (bioinformatics open web services) to centralize bioinformatics tools in web services. PMID:26032494
Maltose-Dependent Transcriptional Regulation of the mal Regulon by MalR in Streptococcus pneumoniae. PMID:26030923
Activation of the Nrf2 response by intrinsic hepatotoxic drugs correlates with suppression of NF-κB activation and sensitizes toward TNFα-induced cytotoxicity. PMID:26026609
Neural transcriptome reveals molecular mechanisms for temporal control of vocalization across multiple timescales. PMID:26014649
Databases for Microbiologists. PMID:26013493
Using Genome-scale Models to Predict Biological Capabilities. PMID:26000478
Noteworthy Facts about a Methane-Producing Microbial Community Processing Acidic Effluent from Sugar Beet Molasses Fermentation. PMID:26000448
Autocatalytic sets in E. coli metabolism. PMID:25995773
Multi-omic profiling -of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production. PMID:25995028
Draft Genome Sequence of Oleiagrimonas soli 3.5XT, a Type Species in a Newly Identified Genus, Isolated from an Oil Field in China. PMID:25977438
DIANA-miRPath v3.0: deciphering microRNA function with experimental support. PMID:25977294
Combination of inflammation-related cytokines promotes long-term muscle stem cell expansion. PMID:25976405
Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach. PMID:25972988
Inference of Evolutionary Forces Acting on Human Biological Pathways. PMID:25971280
Peripheral blood mononuclear cell proteome changes in patients with myelodysplastic syndrome. PMID:25969835
Function of cancer associated genes revealed by modern univariate and multivariate association tests. PMID:25965968
Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data. PMID:25957349
Comprehensive analysis of transcriptome response to salinity stress in the halophytic turf grass Sporobolus virginicus. PMID:25954282
Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests. PMID:25954263
Efficient exploration of pan-cancer networks by generalized covariance selection and interactive web content. PMID:25953855
Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing. PMID:25953818
The proportion of genes in a functional category is linked to mass-specific metabolic rate and lifespan. PMID:25943793
FlyNet: a versatile network prioritization server for the Drosophila community. PMID:25943544
The SwissLipids knowledgebase for lipid biology. PMID:25943471
Anti-obese effect of glucosamine and chitosan oligosaccharide in high-fat diet-induced obese rats. PMID:25942093
Single-cell mass spectrometry reveals small molecules that affect cell fates in the 16-cell embryo. PMID:25941375
Pathways with PathWhiz. PMID:25934797
novPTMenzy: a database for enzymes involved in novel post-translational modifications. PMID:25931459
A comparison of aggregate p-value methods and multivariate statistics for self-contained tests of metabolic pathway analysis. PMID:25927705
Temperament type specific metabolite profiles of the prefrontal cortex and serum in cattle. PMID:25927228
Principal component analysis-based unsupervised feature extraction applied to in silico drug discovery for posttraumatic stress disorder-mediated heart disease. PMID:25925353
Toward a complete dataset of drug-drug interaction information from publicly available sources. PMID:25917055
Protein expression profiles characterize distinct features of mouse cerebral cortices at different developmental stages. PMID:25915664
Sequencing and beyond: integrating molecular 'omics' for microbial community profiling. PMID:25915636
Mapping and analysis of Caenorhabditis elegans transcription factor sequence specificities. PMID:25905672
Linking gene expression to phenotypes via pathway information. PMID:25901272
Redox-Mediated Suberoylanilide Hydroxamic Acid Sensitivity in Breast Cancer. PMID:25897982
Creation of a free, Internet-accessible database: the Multiple Target Ligand Database. PMID:25897329
MetaboAnalyst 3.0--making metabolomics more meaningful. PMID:25897128
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. PMID:25893781
Plasmodium vivax inhibits erythroid cell growth through altered phosphorylation of the cytoskeletal protein ezrin. PMID:25889165
A RNA-seq approach to identify putative toxins from acrorhagi in aggressive and non-aggressive Anthopleura elegantissima polyps. PMID:25886045
Assessing the impact of mutations found in next generation sequencing data over human signaling pathways. PMID:25883139
Nourishment level affects caste-related gene expression in Polistes wasps. PMID:25880983
The central nervous system transcriptome of the weakly electric brown ghost knifefish (Apteronotus leptorhynchus): de novo assembly, annotation, and proteomics validation. PMID:25879418
Pan-cancer transcriptome analysis reveals long noncoding RNAs with conserved function. PMID:25864709
Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome. PMID:25853934
Transcript and protein expression decoupling reveals RNA binding proteins and miRNAs as potential modulators of human aging. PMID:25853883
Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution. PMID:25848874
MetaMapR: pathway independent metabolomic network analysis incorporating unknowns. PMID:25847005
Multivariate analysis of subjective responses to d-amphetamine in healthy volunteers finds novel genetic pathway associations. PMID:25843748
Complete genome-wide screening and subtractive genomic approach revealed new virulence factors, potential drug targets against bio-war pathogen Brucella melitensis 16M. PMID:25834405
The promise of multi-omics and clinical data integration to identify and target personalized healthcare approaches in autism spectrum disorders. PMID:25831060
A comparative study of improvements Pre-filter methods bring on feature selection using microarray data. PMID:25825671
Properties of protein drug target classes. PMID:25822509
Key challenges for the creation and maintenance of specialist protein resources. PMID:25820941
The Listeria monocytogenes strain 10403S BioCyc database. PMID:25819074
RiceNet v2: an improved network prioritization server for rice genes. PMID:25813048
The cost of phage resistance in a plant pathogenic bacterium is context-dependent. PMID:25809535
Environmentally induced changes in correlated responses to selection reveal variable pleiotropy across a complex genetic network. PMID:25809411
Subsistence strategies in traditional societies distinguish gut microbiomes. PMID:25807110
An epigenetic map of age-associated autosomal loci in northern European families at high risk for the metabolic syndrome. PMID:25806089
Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm. PMID:25806041
Genome-wide scan of gastrointestinal nematode resistance in closed Angus population selected for minimized influence of MHC. PMID:25803687
Pathway analysis from lists of microRNAs: common pitfalls and alternative strategy. PMID:25800743
Developmental exposure to estrogen alters differentiation and epigenetic programming in a human fetal prostate xenograft model. PMID:25799167
Towards a PBMC "virogram assay" for precision medicine: Concordance between ex vivo and in vivo viral infection transcriptomes. PMID:25797143
Open-access metabolomics databases for natural product research: present capabilities and future potential. PMID:25789275
The beta-3 adrenergic agonist (CL-316,243) restores the expression of down-regulated fatty acid oxidation genes in type 2 diabetic mice. PMID:25784953
Performance of case-control rare copy number variation annotation in classification of autism. PMID:25783485
Analysis of expressed sequence tags from cDNA library of Fusarium culmorum infected barley (Hordeum vulgare L.) roots. PMID:25780278
Social networks predict gut microbiome composition in wild baboons. PMID:25774601
Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PMID:25774498
Phylogenetic and functional alterations in bacterial community compositions in broiler ceca as a result of mannan oligosaccharide supplementation. PMID:25769823
Serum biomarkers of habitual coffee consumption may provide insight into the mechanism underlying the association between coffee consumption and colorectal cancer. PMID:25762808
A 'rule of 0.5' for the metabolite-likeness of approved pharmaceutical drugs. PMID:25750602
New compound sets identified from high throughput phenotypic screening against three kinetoplastid parasites: an open resource. PMID:25740547
Gut bacteria are rarely shared by co-hospitalized premature infants, regardless of necrotizing enterocolitis development. PMID:25735037
MicroRNA-30c-2-3p negatively regulates NF-κB signaling and cell cycle progression through downregulation of TRADD and CCNE1 in breast cancer. PMID:25732226
Randomized trial of glucosamine and chondroitin supplementation on inflammation and oxidative stress biomarkers and plasma proteomics profiles in healthy humans. PMID:25719429
The gut bacterium Bacteroides thetaiotaomicron influences the virulence potential of the enterohemorrhagic Escherichia coli O103:H25. PMID:25719195
Integrative analysis of circadian transcriptome and metabolic network reveals the role of de novo purine synthesis in circadian control of cell cycle. PMID:25714999
High-throughput analysis of gene essentiality and sporulation in Clostridium difficile. PMID:25714712
Therapeutic opportunities within the DNA damage response. PMID:25709118
EXPath: a database of comparative expression analysis inferring metabolic pathways for plants. PMID:25708775
Relevance Epistasis Network of Gastritis for Intra-chromosomes in the Korea Associated Resource (KARE) Cohort Study. PMID:25705161
Current state of genome-scale modeling in filamentous fungi. PMID:25700817
CHOPER filters enable rare mutation detection in complex mutagenesis populations by next-generation sequencing. PMID:25692681
Deconstruction of archaeal genome depict strategic consensus in core pathways coding sequence assembly. PMID:25674789
Crystallization and preliminary crystallographic analysis of the putative sugar-binding protein Msmeg_0515 (AgaE) from Mycobacterium smegmatis. PMID:25664794
Regulation of toll-like receptor signaling by the SF3a mRNA splicing complex. PMID:25658809
A genome-wide association study for clinical mastitis in first parity US Holstein cows using single-step approach and genomic matrix re-weighting procedure. PMID:25658712
Regulation of ICAM-1 in cells of the monocyte/macrophage system in microgravity. PMID:25654110
Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome. PMID:25638282
Prednisolone-induced predisposition to femoral head separation and the accompanying plasma protein changes in chickens. PMID:25635167
Whole transcriptome responses among females of the filariasis and arbovirus vector mosquito Culex pipiens implicate TGF-β signaling and chromatin modification as key drivers of diapause induction. PMID:25634120
TNF-α and IGF1 modify the microRNA signature in skeletal muscle cell differentiation. PMID:25630602
Metabolome profiling by HRMAS NMR spectroscopy of pheochromocytomas and paragangliomas detects SDH deficiency: clinical and pathophysiological implications. PMID:25622899
A Coxiella-like endosymbiont is a potential vitamin source for the Lone Star tick. PMID:25618142
ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways. PMID:25617415
Chemoselective detection and discrimination of carbonyl-containing compounds in metabolite mixtures by 1H-detected 15N nuclear magnetic resonance. PMID:25616249
RNA synthesis by in vitro selected ribozymes for recreating an RNA world. PMID:25610978
The genomic landscape of fibrolamellar hepatocellular carcinoma: whole genome sequencing of ten patients. PMID:25605237
Functional analysis of Girardia tigrina transcriptome seeds pipeline for anthelmintic target discovery. PMID:25600302
Genome sequence of Coxiella burnetii strain Namibia. PMID:25593636
The BioJS article collection of open source components for biological data visualisation. PMID:25580221
Efficient metabolic exchange and electron transfer within a syntrophic trichloroethene-degrading coculture of Dehalococcoides mccartyi 195 and Syntrophomonas wolfei. PMID:25576615
Stratified pathway analysis to identify gene sets associated with oral contraceptive use and breast cancer. PMID:25574128
Global coordination in adaptation to gene rewiring. PMID:25564530
Exploration of molecular pathways mediating electric field-directed Schwann cell migration by RNA-seq. PMID:25557037
Loss of ion transporters and increased unfolded protein response in Fuchs' dystrophy. PMID:25548511
RNA-Seq data mining: downregulation of NeuroD6 serves as a possible biomarker for alzheimer's disease brains. PMID:25548427
Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state. PMID:25545155
Microalgal Metabolic Network Model Refinement through High-Throughput Functional Metabolic Profiling. PMID:25540776
DCDB 2.0: a major update of the drug combination database. PMID:25539768
Synthetic biology outside the cell: linking computational tools to cell-free systems. PMID:25538941
Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions. PMID:25523622
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation. PMID:25520953
Plant Omics Data Center: an integrated web repository for interspecies gene expression networks with NLP-based curation. PMID:25505034
MOROKOSHI: transcriptome database in Sorghum bicolor. PMID:25505007
Visnagin protects against doxorubicin-induced cardiomyopathy through modulation of mitochondrial malate dehydrogenase. PMID:25504881
Browning of human adipocytes requires KLF11 and reprogramming of PPARγ superenhancers. PMID:25504365
New mode of energy metabolism in the seventh order of methanogens as revealed by comparative genome analysis of “Candidatus methanoplasma termitum”. PMID:25501486
A novel phosphatidylinositol 3-kinase (PI3K) inhibitor directs a potent FOXO-dependent, p53-independent cell cycle arrest phenotype characterized by the differential induction of a subset of FOXO-regulated genes. PMID:25488803
Microbiome changes in healthy volunteers treated with GSK1322322, a novel antibiotic targeting bacterial peptide deformylase. PMID:25487798
Transcriptomic analysis of the lesser spotted catshark (Scyliorhinus canicula) pancreas, liver and brain reveals molecular level conservation of vertebrate pancreas function. PMID:25480530
High-resolution genetic analysis of the requirements for horizontal transmission of the ESBL plasmid from Escherichia coli O104:H4. PMID:25477379
Comparative transcriptomics and metabolomics in a rhesus macaque drug administration study. PMID:25453034
Pin-Align: a new dynamic programming approach to align protein-protein interaction networks. PMID:25435900
Rewiring of genetic networks in response to modification of genetic background. PMID:25432942
The BioGRID interaction database: 2015 update. PMID:25428363
Plasmids of psychrophilic and psychrotolerant bacteria and their role in adaptation to cold environments. PMID:25426110
Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells. PMID:25418962
rrnDB: improved tools for interpreting rRNA gene abundance in bacteria and archaea and a new foundation for future development. PMID:25414355
BioModels: ten-year anniversary. PMID:25414348
Integrated network analysis and effective tools in plant systems biology. PMID:25408696
I-GSEA4GWAS v2: a web server for functional analysis of SNPs in trait-associated pathways identified from genome-wide association study. PMID:25407412
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
Identifying feasible metabolic routes in Mycobacterium smegmatis and possible alterations under diverse nutrient conditions. PMID:25403821
Potential microRNA-mediated oncogenic intercellular communication revealed by pan-cancer analysis. PMID:25403569
dbSNO 2.0: a resource for exploring structural environment, functional and disease association and regulatory network of protein S-nitrosylation. PMID:25399423
Short-term airborne particulate matter exposure alters the epigenetic landscape of human genes associated with the mitogen-activated protein kinase network: a cross-sectional study. PMID:25395096
Helminth.net: expansions to Nematode.net and an introduction to Trematode.net. PMID:25392426
CeCaFDB: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13C-fluxomics. PMID:25392417
iPathCons and iPathDB: an improved insect pathway construction tool and the database. PMID:25388589
A deep transcriptomic analysis of pod development in the vanilla orchid (Vanilla planifolia). PMID:25380694
Proteomics for systems toxicology. PMID:25379146
MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae. PMID:25378328
Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes. PMID:25375929
A pan-cancer modular regulatory network analysis to identify common and cancer-specific network components. PMID:25374456
Global metabolomic and isobaric tagging capillary liquid chromatography-tandem mass spectrometry approaches for uncovering pathway dysfunction in diabetic mouse aorta. PMID:25368974
Quantitative phosphoproteomic analysis of IL-33-mediated signaling. PMID:25367039
From molecular signatures to predictive biomarkers: modeling disease pathophysiology and drug mechanism of action. PMID:25364744
ADReCS: an ontology database for aiding standardization and hierarchical classification of adverse drug reaction terms. PMID:25361966
Polyreactivity and autoreactivity among HIV-1 antibodies. PMID:25355869
Gene: a gene-centered information resource at NCBI. PMID:25355515
STRING v10: protein-protein interaction networks, integrated over the tree of life. PMID:25352553
Cancer in silico drug discovery: a systems biology tool for identifying candidate drugs to target specific molecular tumor subtypes. PMID:25349306
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data. PMID:25348409
Folic acid induces salicylic acid-dependent immunity in Arabidopsis and enhances susceptibility to Alternaria brassicicola. PMID:25348251
Ketogenesis prevents diet-induced fatty liver injury and hyperglycemia. PMID:25347470
Ecophysiology of Thioploca ingrica as revealed by the complete genome sequence supplemented with proteomic evidence. PMID:25343513
ToxDBScan: Large-scale similarity screening of toxicological databases for drug candidates. PMID:25338045
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
Updates in Rhea--a manually curated resource of biochemical reactions. PMID:25332395
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PMID:25330313
ImmuCo: a database of gene co-expression in immune cells. PMID:25326331
EzCatDB: the enzyme reaction database, 2015 update. PMID:25324316
EpilepsyGene: a genetic resource for genes and mutations related to epilepsy. PMID:25324312
A curated C. difficile strain 630 metabolic network: prediction of essential targets and inhibitors. PMID:25315994
TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. PMID:25300491
Super Natural II--a database of natural products. PMID:25300487
Statistical measures of transcriptional diversity capture genomic heterogeneity of cancer. PMID:25294321
Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. PMID:25280501
Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease. PMID:25252782
Assessing the metabolic impact of nitrogen availability using a compartmentalized maize leaf genome-scale model. PMID:25248718
Generalized portrait of cancer metabolic pathways inferred from a list of genes overexpressed in cancer. PMID:25243088
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. PMID:25231498
Characterizing the pocketome of Mycobacterium tuberculosis and application in rationalizing polypharmacological target selection. PMID:25220818
Variations in metabolic pathways create challenges for automated metabolic reconstructions: Examples from the tetrahydrofolate synthesis pathway. PMID:25210598
Insilico analysis of hypothetical proteins unveils putative metabolic pathways and essential genes in Leishmania donovani. PMID:25206363
Genomic analysis of Skermanella stibiiresistens type strain SB22 (T.). PMID:25197493
The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice. PMID:25190456
A thirteen-gene expression signature predicts survival of patients with pancreatic cancer and identifies new genes of interest. PMID:25180633
An overview of the neurobiology of suicidal behaviors as one meta-system. PMID:25178164
Developmentally-Dynamic Murine Brain Proteomes and Phosphoproteomes Revealed by Quantitative Proteomics. PMID:25177544
KEGGscape: a Cytoscape app for pathway data integration. PMID:25177485
DawnRank: discovering personalized driver genes in cancer. PMID:25177370
Switchgrass (Panicum virgatum L) flag leaf transcriptomes reveal molecular signatures of leaf development, senescence, and mineral dynamics. PMID:25173486
Gene transfers shaped the evolution of de novo NAD+ biosynthesis in eukaryotes. PMID:25169983
Enumeration of ring-chain tautomers based on SMIRKS rules. PMID:25158156
Functional and genomic context in pathway analysis of GWAS data. PMID:25154796
MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. PMID:25136443
Alzheimer's disease: relevant molecular and physiopathological events affecting amyloid-β brain balance and the putative role of PPARs. PMID:25120477
Arabidopsis ENHANCED DISEASE SUSCEPTIBILITY1 promotes systemic acquired resistance via azelaic acid and its precursor 9-oxo nonanoic acid. PMID:25114016
Lean Big Data integration in systems biology and systems pharmacology. PMID:25109570
Composition and applications of focus libraries to phenotypic assays. PMID:25104937
Comparison of gene expression patterns across 12 tumor types identifies a cancer supercluster characterized by TP53 mutations and cell cycle defects. PMID:25088195
The associations between immunity-related genes and breast cancer prognosis in Korean women. PMID:25075970
Personalized medicine approaches for colon cancer driven by genomics and systems biology: OncoTrack. PMID:25074435
The draft genome and transcriptome of Amaranthus hypochondriacus: a C4 dicot producing high-lysine edible pseudo-cereal. PMID:25071079
The dynamics of a family's gut microbiota reveal variations on a theme. PMID:25061514
Differential hippocampal gene expression and pathway analysis in an etiology-based mouse model of major depressive disorder. PMID:25059218
Text-mining-assisted biocuration workflows in Argo. PMID:25037308
Genomic profiling of human Leishmania braziliensis lesions identifies transcriptional modules associated with cutaneous immunopathology. PMID:25036052
Nonlinear quantitative radiation sensitivity prediction model based on NCI-60 cancer cell lines. PMID:25032244
A phage tail-derived element with wide distribution among both prokaryotic domains: a comparative genomic and phylogenetic study. PMID:25015235
Identification and characterization of long intergenic non-coding RNAs related to mouse liver development. PMID:25012394
ChiloDB: a genomic and transcriptome database for an important rice insect pest Chilo suppressalis. PMID:24997141
An introduction to the analysis of shotgun metagenomic data. PMID:24982662
Functional annotation and structural characterization of a novel lactonase hydrolyzing D-xylono-1,4-lactone-5-phosphate and L-arabino-1,4-lactone-5-phosphate. PMID:24955762
Lynx web services for annotations and systems analysis of multi-gene disorders. PMID:24948611
Multicilin drives centriole biogenesis via E2f proteins. PMID:24934224
TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants. PMID:24930145
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network. PMID:24861622
mzGroupAnalyzer--predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data. PMID:24846183
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. PMID:24829452
Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features. PMID:24827998
Isolation and characterization of mammalian cells expressing the Arf promoter during eye development. PMID:24806224
Evolution and communication of subcellular compartments: An integrated approach. PMID:24786592
A comparison of the rest complex binding patterns in embryonic stem cells and epiblast stem cells. PMID:24752154
What's that gene (or protein)? Online resources for exploring functions of genes, transcripts, and proteins. PMID:24723265
Extracellular vesicles in luminal fluid of the ovine uterus. PMID:24614226
Toward understanding the origin and evolution of cellular organisms PubMed citations: 630.

630 articles citing: Toward understanding the origin and evolution of cellular organisms

Mito-nuclear coevolution and phylogenetic artifacts: the case of bivalve mollusks. PMID:35773462
Survival-related indicators ALOX12B and SPRR1A are associated with DNA damage repair and tumor microenvironment status in HPV 16-negative head and neck squamous cell carcinoma patients. PMID:35768785
Transcriptome analysis of SerpinB2-deficient breast tumors provides insight into deciphering SerpinB2-mediated roles in breast cancer progression. PMID:35768767
Differential proteomics of placentas reveals metabolic disturbance and oxidative damage participate yak spontaneous miscarriage during late pregnancy. PMID:35761325
Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea. PMID:35751094
Machine-learning algorithms based on personalized pathways for a novel predictive model for the diagnosis of hepatocellular carcinoma. PMID:35739471
A cerumenolomic approach to bovine trypanosomosis diagnosis. PMID:35739279
Exploring the potential mechanism of emetine against coronavirus disease 2019 combined with lung adenocarcinoma: bioinformatics and molecular simulation analyses. PMID:35733175
Antennal transcriptome analysis of olfactory genes and tissue expression profiling of odorant binding proteins in Semanotus bifasciatus (cerambycidae: coleoptera). PMID:35733103
Transcriptional changes in the peripheral blood leukocytes from Brangus cattle before and after tick challenge with Rhipicephalus australis. PMID:35725367
Genome-wide association mapping and genomic prediction for pre‑harvest sprouting resistance, low α-amylase and seed color in Iranian bread wheat. PMID:35715737
Integrated bioinformatics analysis reveals marker genes and immune infiltration for pulmonary arterial hypertension. PMID:35710932
Integrated analysis reveals the pivotal interactions between immune cells in the melanoma tumor microenvironment. PMID:35710862
Identification of HOX signatures contributing to oral cancer phenotype. PMID:35710803
CF-Seq, an accessible web application for rapid re-analysis of cystic fibrosis pathogen RNA sequencing studies. PMID:35710652
miRNA-mRNA analysis of sheep adrenal glands reveals the network regulating reproduction. PMID:35710353
Identification of ferroptosis-related genes for overall survival prediction in hepatocellular carcinoma. PMID:35705729
Advances in understanding Norway spruce natural resistance to needle bladder rust infection: transcriptional and secondary metabolites profiling. PMID:35692040
Semaphorin 4B promotes tumor progression and associates with immune infiltrates in lung adenocarcinoma. PMID:35676688
Integrative analysis of expression profile indicates the ECM receptor and LTP dysfunction in the glioma-related epilepsy. PMID:35676651
Exploring the mechanism and experimental verification of puerarin in the treatment of endometrial carcinoma based on network pharmacology and bioinformatics analysis. PMID:35672846
Potential prognosis index for m6A-related mRNA in cholangiocarcinoma. PMID:35672673
Developing a bioinformatics pipeline for comparative protein classification analysis. PMID:35668373
Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus. PMID:35659263
The correlation of EZH2 expression with the progression and prognosis of hepatocellular carcinoma. PMID:35659256
Pyroptosis is related to immune infiltration and predictive for survival of colon adenocarcinoma patients. PMID:35655081
Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions. PMID:35650424
Comparative transcriptome analysis of heat-induced domesticated zebrafish during gonadal differentiation. PMID:35641933
Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations. PMID:35637371
Effect of berberine on global modulation of lncRNAs and mRNAs expression profiles in patients with stable coronary heart disease. PMID:35619068
Autoreactive CD8+ T cells are restrained by an exhaustion-like program that is maintained by LAG3. PMID:35618829
Integrative Analysis of lncRNA-miRNA-mRNA Regulatory Network Reveals the Key lncRNAs Implicated Potentially in the Differentiation of Adipocyte in Goats. PMID:35600305
Combined use of specific length amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) for rapid identification of genes influencing fiber content of hemp (Cannabis sativa L.). PMID:35596150
KDM3A-mediated SP1 activates PFKFB4 transcription to promote aerobic glycolysis in osteosarcoma and augment tumor development. PMID:35590288
Transcriptome sequencing reveals the differentially expressed lncRNAs and mRNAs in response to cold acclimation and cold stress in Pomacea canaliculata. PMID:35590244
Exploring the underlying molecular mechanism of liver cancer cells under hypoxia based on RNA sequencing. PMID:35590240
Identification of AKIRIN2 as a potential biomarker and correlation with immunotherapy in gastric adenocarcinoma by integrated bioinformatics analysis. PMID:35589807
Comparative genome analysis among Variovorax species and genome guided aromatic compound degradation analysis emphasizing 4-hydroxybenzoate degradation in Variovorax sp. PAMC26660. PMID:35585492
SYNJ2 is a novel and potential biomarker for the prediction and treatment of cancers: from lung squamous cell carcinoma to pan-cancer. PMID:35581615
An immune gene signature to predict prognosis and immunotherapeutic response in lung adenocarcinoma. PMID:35581376
Identification of miRNA biomarkers for stomach adenocarcinoma. PMID:35578189
Prediction of gestational age using urinary metabolites in term and preterm pregnancies. PMID:35577875
Microbiota-Associated Biofilm Regulation Leads to Vibrio cholerae Resistance Against Intestinal Environmental Stress. PMID:35573801
Modelling liver cancer microenvironment using a novel 3D culture system. PMID:35568708
Diagnostic and prognostic values of pyroptosis-related genes for the hepatocellular carcinoma. PMID:35562678
Role of CD68 in tumor immunity and prognosis prediction in pan-cancer. PMID:35550532
Role of tRNA derived fragments in renal ischemia-reperfusion injury. PMID:35546262
The transcriptome-wide N6-methyladenosine (m6A) map profiling reveals the regulatory role of m6A in the yak ovary. PMID:35538402
Integrated transcriptome and endogenous hormone analysis provides new insights into callus proliferation in Osmanthus fragrans. PMID:35534621
Integrated analysis of lncRNAs and mRNAs by RNA-Seq in secondary hair follicle development and cycling (anagen, catagen and telogen) of Jiangnan cashmere goat (Capra hircus). PMID:35524260
The identification of miRNA and mRNA expression profiles associated with pediatric atypical teratoid/rhabdoid tumor. PMID:35524230
A deep learning approach for orphan gene identification in moso bamboo (Phyllostachys edulis) based on the CNN + Transformer model. PMID:35513802
Survival strategies of an anoxic microbial ecosystem in Lake Untersee, a potential analog for Enceladus. PMID:35513542
Different effects of hydrogen-rich water intake and hydrogen gas inhalation on gut microbiome and plasma metabolites of rats in health status. PMID:35508571
Network pharmacology combined with molecular docking to explore the potential mechanisms for the antioxidant activity of Rheum tanguticum seeds. PMID:35505340
Integrative analysis of circRNA, miRNA, and mRNA profiles to reveal ceRNA regulation in chicken muscle development from the embryonic to post-hatching periods. PMID:35505302
Circulating microRNA sequencing revealed miRNome patterns in hematology and oncology patients aiding the prognosis of invasive aspergillosis. PMID:35504997
High MICAL-L2 expression and its role in the prognosis of colon adenocarcinoma. PMID:35501725
Bacterial communities associated with silage of different forage crops in Malaysian climate analysed using 16S amplicon metagenomics. PMID:35501317
Differential expression of circulating miRNAs after alemtuzumab induction therapy in lung transplantation. PMID:35490174
Signature transcriptome analysis of stage specific atherosclerotic plaques of patients. PMID:35488341
Identification of an autophagy-related gene signature for predicting prognosis and immune activity in pancreatic adenocarcinoma. PMID:35488119
Network pharmacology analysis and experimental validation to explore the mechanism of Bushao Tiaozhi capsule (BSTZC) on hyperlipidemia. PMID:35484204
The identification of liver metastasis- and prognosis-associated genes in pancreatic ductal adenocarcinoma. PMID:35477379
Comparative study on gut microbiota in three Anura frogs from a mountain stream. PMID:35475186
Effect of acute high-intensity exercise on myocardium metabolic profiles in rat and human study via metabolomics approach. PMID:35473956
Trans-cinnamaldehyde protects against phenylephrine-induced cardiomyocyte hypertrophy through the CaMKII/ERK pathway. PMID:35468773
ADAM12 is an independent predictor of poor prognosis in liver cancer. PMID:35459884
A cross-sectional analysis about bacterial vaginosis, high-risk human papillomavirus infection, and cervical intraepithelial neoplasia in Chinese women. PMID:35459771
Key Signaling in Alcohol-Associated Liver Disease: The Role of Bile Acids. PMID:35456053
HREM, RNAseq and Cell Cycle Analyses Reveal the Role of the G2/M-Regulatory Protein, WEE1, on the Survivability of Chicken Embryos during Diapause. PMID:35453529
Single-cell transcriptomics identifies Mcl-1 as a target for senolytic therapy in cancer. PMID:35449130
Profiling the lncRNA-miRNA-mRNA interaction network in the submandibular gland of diabetic mice. PMID:35449001
Comparative transcriptomic analyses of citrus cold-resistant vs. sensitive rootstocks might suggest a relevant role of ABA signaling in triggering cold scion adaption. PMID:35448939
The Effects of Sesquiterpene Lactones on the Differentiation of Human or Animal Cells Cultured In-Vitro: A Critical Systematic Review. PMID:35444549
Identification of ubiquitin-specific protease 32 as an oncogene in glioblastoma and the underlying mechanisms. PMID:35440702
Tanshinone I attenuates fibrosis in fibrotic kidneys through down-regulation of inhibin beta-A. PMID:35439976
Transcriptome profiling of flower buds of male-sterile lines provides new insights into male sterility mechanism in alfalfa. PMID:35428186
Proteomics analysis: inhibiting the expression of P62 protein by chloroquine combined with dacarbazine can reduce the malignant progression of uveal melanoma. PMID:35421957
MicroRNA profiles in aqueous humor between pseudoexfoliation glaucoma and normal tension glaucoma patients in a Korean population. PMID:35418653
Vero cells gain renal tubule markers in low-calcium and magnesium chemically defined media. PMID:35418617
Molecular signatures of tumor progression in pancreatic adenocarcinoma identified by energy metabolism characteristics. PMID:35418066
Unravelling the neuroprotective mechanisms of carotenes in differentiated human neural cells: Biochemical and proteomic approaches. PMID:35415676
Clone and Function Verification of the OPR gene in Brassica napus Related to Linoleic Acid Synthesis. PMID:35410118
TIA1 Loss Exacerbates Fatty Liver Disease but Exerts a Dual Role in Hepatocarcinogenesis. PMID:35406476
Identification of microRNA-mRNA-TF regulatory networks in periodontitis by bioinformatics analysis. PMID:35397550
TGF-β induced reprogramming and drug resistance in triple-negative breast cells. PMID:35395809
Zinc supplementation modifies brain tissue transcriptome of Apis mellifera honeybees. PMID:35395723
Large-scale analysis of MicroRNA expression in motor neuron-like cells derived from human umbilical cord blood mesenchymal stem cells. PMID:35393444
CircUBE2Q2 promotes differentiation of cattle muscle stem cells and is a potential regulatory molecule of skeletal muscle development. PMID:35387588
Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa. PMID:35384379
Feedlot diets containing different starch levels and additives change the cecal proteome involved in cattle's energy metabolism and inflammatory response. PMID:35383279
TMT-based proteomic analysis reveals integrins involved in the synergistic infection of reticuloendotheliosis virus and avian leukosis virus subgroup J. PMID:35379256
Transcriptome analysis of blastoderms exposed to prolonged egg storage and short periods of incubation during egg storage. PMID:35379173
Correlation between intestinal flora disruption and protein-energy wasting in patients with end-stage renal disease. PMID:35369865
Parthenolide leads to proteomic differences in thyroid cancer cells and promotes apoptosis. PMID:35366876
Based on multiple machine learning to identify the ENO2 as diagnosis biomarkers of glaucoma. PMID:35366826
Predict the role of lncRNA in kidney aging based on RNA sequencing. PMID:35366793
Metabolomics approach to assess the effect of siphonal autotomy on metabolic characteristics of razor clam Solen grandis. PMID:35365742
Molecular mechanisms of Huanglian jiedu decoction on ulcerative colitis based on network pharmacology and molecular docking. PMID:35365737
Compositions of gut microbiota before and shortly after hepatitis C viral eradication by direct antiviral agents. PMID:35361930
Black pepper and tarragon essential oils suppress the lipolytic potential and the type II secretion system of P. psychrophila KM02. PMID:35361821
Evaluation of Early Biomarkers of Atherosclerosis Associated with Polychlorinated Biphenyl Exposure: An in Vitro and in Vivo Study. PMID:35349355
Integrative analyses of biomarkers and pathways for heart failure. PMID:35346191
Transcriptome-wide N6-methyladenine methylation in granulosa cells of women with decreased ovarian reserve. PMID:35346019
MicroRNA-mediated post-transcriptional regulation of Pinus pinaster response and resistance to pinewood nematode. PMID:35338210
Effects of varicocele and microsurgical varicocelectomy on the metabolites in semen. PMID:35338186
Metabolomic strategies and biochemical analysis of the effect of processed Rehmanniae radix extract on a blood-deficient rat model. PMID:35337319
Comprehensive analysis of tumor immune microenvironment and prognosis of m6A-related lncRNAs in gastric cancer. PMID:35331183
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data. PMID:35323700
Comparative transcriptome analysis of heat stress responses of Clematis lanuginosa and Clematis crassifolia. PMID:35321648
Identification of co-expression hub genes for ferroptosis in kidney renal clear cell carcinoma based on weighted gene co-expression network analysis and The Cancer Genome Atlas clinical data. PMID:35314744
Temporally Selective Modification of the Tomato Rhizosphere and Root Microbiome by Volcanic Ash Fertilizer Containing Micronutrients. PMID:35311513
Beta-blocker/ACE inhibitor therapy differentially impacts the steady state signaling landscape of failing and non-failing hearts. PMID:35306519
Identification of hub genes and transcription factors in patients with rheumatoid arthritis complicated with atherosclerosis. PMID:35304503
Bioinformatical analysis of the key differentially expressed genes and associations with immune cell infiltration in development of endometriosis. PMID:35303800
Integrative analysis identifies key genes related to metastasis and a robust gene-based prognostic signature in uveal melanoma. PMID:35300699
Species composition and overall diversity are significantly correlated between the tongue coating and gastric fluid microbiomes in gastritis patients. PMID:35300688
An Oxidative Stress-Related Genes Signature for Predicting Survival in Bladder Cancer: Based on TCGA Database and Bioinformatics. PMID:35300137
Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum. PMID:35287589
Cold stress tolerance of the intertidal red alga Neoporphyra haitanensis. PMID:35287582
Salicylic Acid-Mediated Disturbance Increases Bacterial Diversity in the Phyllosphere but Is Overcome by a Dominant Core Community. PMID:35283825
Gut microbial composition in developmental stages of gall inducing thrips Gynaikothrips uzeli and associated plant pathogenesis. PMID:35280592
Nicotinamide (niacin) supplement increases lipid metabolism and ROS-induced energy disruption in triple-negative breast cancer: potential for drug repositioning as an anti-tumor agent. PMID:35278276
Novel alleles gained during the Beringian isolation period. PMID:35277570
Maize plant architecture trait QTL mapping and candidate gene identification based on multiple environments and double populations. PMID:35277127
Hydrolyzed Proteins and Vegetable Peptides: Anti-Inflammatory Mechanisms in Obesity and Potential Therapeutic Targets. PMID:35277049
Exposure to Trypanosoma parasites induces changes in the microbiome of the Chagas disease vector Rhodnius prolixus. PMID:35272716
Comparative analysis of the daily brain transcriptomes of Asian particolored bat. PMID:35264653
MicroRNome analysis generates a blood-based signature for endometriosis. PMID:35260677
6-Hydroxydopamine Induces Neurodegeneration in Terminally Differentiated SH-SY5Y Neuroblastoma Cells via Enrichment of the Nucleosomal Degradation Pathway: a Global Proteomics Approach. PMID:35258800
Patients with low muscle mass have characteristic microbiome with low potential for amino acid synthesis in chronic liver disease. PMID:35256716
Shared genetic loci for body fat storage and adipocyte lipolysis in humans. PMID:35256633
High-content analysis of microRNAs involved in the phenotype regulation of vascular smooth muscle cells. PMID:35241704
Network pharmacology-based predictions of active components and pharmacological mechanisms of Artemisia annua L. for the treatment of the novel Corona virus disease 2019 (COVID-19). PMID:35241045
Prognostic value and immune relevancy of a combined autophagy-, apoptosis- and necrosis-related gene signature in glioblastoma. PMID:35241019
Combination of ferroptosis and pyroptosis to construct a prognostic classifier and predict immune landscape, chemotherapeutic efficacy and immunosuppressive molecules in hepatocellular carcinoma. PMID:35236323
Discovery and characterization of differentially expressed soybean miRNAs and their targets during soybean mosaic virus infection unveils novel insight into Soybean-SMV interaction. PMID:35236286
Comprehensive analysis of ferroptosis-related genes and prognosis of cutaneous melanoma. PMID:35232428
Potential biomarkers in the fibrosis progression of nonalcoholic steatohepatitis (NASH). PMID:35226336
Extracellular circulating miRNAs as stress-related signature to search and rescue dogs. PMID:35217704
MicroRNA editing patterns in Huntington's disease. PMID:35210471
Multi-Omics Analysis of Multiple Glucose-Sensing Receptor Systems in Yeast. PMID:35204676
Amniotic Fluid microRNA in Severe Twin-Twin Transfusion Syndrome Cardiomyopathy-Identification of Differences and Predicting Demise. PMID:35200691
Protein and miRNA profile of circulating extracellular vesicles in patients with primary sclerosing cholangitis. PMID:35194091
Clinical implications and molecular mechanisms of Cyclin-dependent kinases 4 for patients with hepatocellular carcinoma. PMID:35193513
Endothelial Phospholipase Cγ2 Improves Outcomes of Diabetic Ischemic Limb Rescue Following VEGF Therapy. PMID:35192691
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
Comprehensive analysis of the expression and significance of CXCLs in human diffuse large B-cell lymphoma. PMID:35181719
Transcriptomic and metabolomic analysis reveals the difference between large and small flower taxa of Herba Epimedii during flavonoid accumulation. PMID:35177764
Exosomes derived from human placental mesenchymal stem cells ameliorate myocardial infarction via anti-inflammation and restoring gut dysbiosis. PMID:35172728
HIV-1 Tat and cocaine coexposure impacts piRNAs to affect astrocyte energy metabolism. PMID:35170353
Transcriptome analysis of genes associated with autolysis of Coprinus comatus. PMID:35169137
Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior. PMID:35163386
Genome Mining and Gene Expression Reveal Maytansine Biosynthetic Genes from Endophytic Communities Living inside Gymnosporia heterophylla (Eckl. and Zeyh.) Loes. and the Relationship with the Plant Biosynthetic Gene, Friedelin Synthase. PMID:35161302
Cerebrospinal fluid purinomics as a biomarker approach to predict outcome after severe traumatic brain injury. PMID:35157328
ILF2 enhances the DNA cytosine deaminase activity of tumor mutator APOBEC3B in multiple myeloma cells. PMID:35145187
Combined transcriptomic and metabolomic analysis reveals the potential mechanism of seed germination and young seedling growth in Tamarix hispida. PMID:35135479
Exploring the total flavones of Abelmoschus manihot against IAV-induced lung inflammation by network pharmacology. PMID:35123452
Construction and comprehensive analysis of the competing endogenous RNA network in endometrial adenocarcinoma. PMID:35123404
Identification and validation of an autophagy-related gene signature for predicting prognosis in patients with esophageal squamous cell carcinoma. PMID:35121801
Single cell RNA sequencing reveals differentiation related genes with drawing implications in predicting prognosis and immunotherapy response in gliomas. PMID:35115572
RNA-seq of nine canine prostate cancer cell lines reveals diverse therapeutic target signatures. PMID:35109825
Amphioxus muscle transcriptomes reveal vertebrate-like myoblast fusion genes and a highly conserved role of insulin signalling in the metabolism of muscle. PMID:35105312
Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. PMID:35099752
The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. PMID:35096646
Gene Expression in Embryos From Norwegian Red Bulls With High or Low Non Return Rate: An RNA-Seq Study of in vivo-Produced Single Embryos. PMID:35096004
Bioinformatics screening the novel and promising targets of curcumin in hepatocellular carcinoma chemotherapy and prognosis. PMID:35078445
Fungal and ciliate protozoa are the main rumen microbes associated with methane emissions in dairy cattle. PMID:35077540
A simple guide to de novo transcriptome assembly and annotation. PMID:35076693
Construction and validation of a novel gene signature for predicting the prognosis of osteosarcoma. PMID:35075228
Potential biomarkers of acute myocardial infarction based on co-expression network analysis. PMID:35069843
Insight Into the Anti-staphylococcal Activity of JBC 1847 at Sub-Inhibitory Concentration. PMID:35069485
Dietary Correlates of Oral and Gut Microbiota in the Water Monitor Lizard, Varanus salvator (Laurenti, 1768). PMID:35069477
Single-cell multi-omics reveals dyssynchrony of the innate and adaptive immune system in progressive COVID-19. PMID:35064122
Pcyt2 deficiency causes age-dependant development of nonalcoholic steatohepatitis and insulin resistance that could be attenuated with phosphoethanolamine. PMID:35058529
A potential target gene CD63 for different degrees of intervertebral disc degeneration. PMID:35046480
Revealing potential diagnostic gene biomarkers of septic shock based on machine learning analysis. PMID:35045818
N6-Methyladenosine-Related lncRNAs as potential biomarkers for predicting prognoses and immune responses in patients with cervical cancer. PMID:35042477
Elevational Constraints on the Composition and Genomic Attributes of Microbial Communities in Antarctic Soils. PMID:35040702
Two novel prognostic models for ovarian cancer respectively based on ferroptosis and necroptosis. PMID:35039008
Intestinal Claudin-7 deficiency impacts the intestinal microbiota in mice with colitis. PMID:35039003
An integrative analysis of DNA methylation and transcriptome showed the dysfunction of MAPK pathway was involved in the damage of human chondrocyte induced by T-2 toxin. PMID:35038982
Identification of a ferroptosis-related gene pair biomarker with immune infiltration landscapes in ischemic stroke: a bioinformatics-based comprehensive study. PMID:35033021
NETME: on-the-fly knowledge network construction from biomedical literature. PMID:35013714
Transplantation of umbilical cord-derived mesenchymal stem cells promotes the recovery of thin endometrium in rats. PMID:35013490
RNAseq reveals extensive metabolic disruptions in the sensitive SF-295 cell line treated with schweinfurthins. PMID:35013404
Comprehensive analysis of expression profile and prognostic significance of interferon regulatory factors in pancreatic cancer. PMID:35012444
Local ancestry prediction with PyLAE. PMID:35003914
Membrane tension sensing molecule-FNBP1 is a prognostic biomarker related to immune infiltration in BRCA, LUAD and STAD. PMID:34998385
Objective to identify and verify the regulatory mechanism of DTNBP1 as a prognostic marker for hepatocellular carcinoma. PMID:34997064
Maize/peanut intercropping improves nutrient uptake of side-row maize and system microbial community diversity. PMID:34996375
Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome. PMID:34996356
Genome-wide association study identifies SNPs for growth performance and serum indicators in Valgus-varus deformity broilers (Gallus gallus) using ddGBS sequencing. PMID:34991478
Transcriptomics analysis reveals the signal transduction mechanism of brassinolides in tea leaves and its regulation on the growth and development of Camellia sinensis. PMID:34991475
Prediction of trehalose-metabolic pathway and comparative analysis of KEGG, MetaCyc, and RAST databases based on complete genome of Variovorax sp. PAMC28711. PMID:34991451
Marine pollutant exposures and human milk extracellular vesicle-microRNAs in a mother-infant cohort from the Faroe Islands. PMID:34991248
Transcriptional analysis of Bemisia tabaci MEAM1 cryptic species under the selection pressure of neonicotinoids imidacloprid, acetamiprid and thiamethoxam. PMID:34983398
Transcriptome analysis to identify the downstream genes of androgen receptor in dermal papilla cells. PMID:34983378
Genome-wide identification and functional analysis of circRNAs in Trichophyton rubrum conidial and mycelial stages. PMID:34983376
Comprehensive analysis of the long noncoding RNA-associated competitive endogenous RNA network in the osteogenic differentiation of periodontal ligament stem cells. PMID:34979896
Comparative de novo transcriptome analysis identifies salinity stress responsive genes and metabolic pathways in sugarcane and its wild relative Erianthus arundinaceus [Retzius] Jeswiet. PMID:34972826
Plasma metabolomic profiling of hypertrophic cardiomyopathy patients before and after surgical myectomy suggests postoperative improvement in metabolic function. PMID:34961475
Microsporidian Infection in Mosquitoes (Culicidae) Is Associated with Gut Microbiome Composition and Predicted Gut Microbiome Functional Content. PMID:34939130
MYCL promotes iPSC-like colony formation via MYC Box 0 and 2 domains. PMID:34930932
Recurring exposure to low humidity induces transcriptional and protein level changes in the vocal folds of rabbits. PMID:34921171
The effect of lipocalin-2 (LCN2) on apoptosis: a proteomics analysis study in an LCN2 deficient mouse model. PMID:34903175
iTRAQ based protein profile analysis revealed key proteins involved in regulation of drought-tolerance during seed germination in Adzuki bean. PMID:34887505
Transcriptomic and metabolomic changes triggered by Macrosiphum rosivorum in rose (Rosa longicuspis). PMID:34886808
A Computational Analysis in a Cohort of Parkinson's Disease Patients and Clock-Modified Colorectal Cancer Cells Reveals Common Expression Alterations in Clock-Regulated Genes. PMID:34885088
Identification of an epithelial-mesenchymal transition-related lncRNA prognostic signature for patients with glioblastoma. PMID:34880375
reString: an open-source Python software to perform automatic functional enrichment retrieval, results aggregation and data visualization. PMID:34873191
Integrated metabolic and microbial analysis reveals host-microbial interactions in IgE-mediated childhood asthma. PMID:34862469
Identification of the ferroptosis-related long non-coding RNAs signature to improve the prognosis prediction and immunotherapy response in patients with NSCLC. PMID:34861872
Bacterial challenge-associated metabolic phenotypes in Hermetia illucens defining nutritional and functional benefits. PMID:34857836
Multiomics analysis of soybean meal induced marine fish enteritis in juvenile pearl gentian grouper, Epinephelus fuscoguttatus ♀ × Epinephelus lanceolatus ♂. PMID:34857775
Transcriptomic Profiling and Microsatellite Identification in Cobia (Rachycentron canadum), Using High-Throughput RNA Sequencing. PMID:34855031
Investigation of hub gene associated with the infection of Staphylococcus aureus via weighted gene co-expression network analysis. PMID:34852788
Combined transcriptome and metabolome integrated analysis of Acer mandshuricum to reveal candidate genes involved in anthocyanin accumulation. PMID:34848790
The impact of bacterial diversity on resistance to biocides in oilfields. PMID:34845279
Cluster analysis and profiling of airway fluid metabolites in pediatric acute hypoxemic respiratory failure. PMID:34836982
Identification of transcriptomics biomarkers for the early prediction of the prognosis of septic shock from pneumopathies. PMID:34836493
Vaccine Hyporesponse Induced by Individual Antibiotic Treatment in Mice and Non-Human Primates Is Diminished upon Recovery of the Gut Microbiome. PMID:34835271
Mycorrhiza-Induced Alterations in Metabolome of Medicago lupulina Leaves during Symbiosis Development. PMID:34834870
PI3K/AKT/mTOR Signaling Pathway Is Required for JCPyV Infection in Primary Astrocytes. PMID:34831441
MicroRNA Sequencing Analysis in Obstructive Sleep Apnea and Depression: Anti-Oxidant and MAOA-Inhibiting Effects of miR-15b-5p and miR-92b-3p through Targeting PTGS1-NF-κB-SP1 Signaling. PMID:34829725
Corticosterone-Mediated Physiological Stress Alters Liver, Kidney, and Breast Muscle Metabolomic Profiles in Chickens. PMID:34827788
Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes. PMID:34827437
Mechanism of quercetin therapeutic targets for Alzheimer disease and type 2 diabetes mellitus. PMID:34824300
Heterogeneous recruitment abilities to RNA polymerases generate nonlinear scaling of gene expression with cell volume. PMID:34824198
The Hitchhiker's Guide to Untargeted Lipidomics Analysis: Practical Guidelines. PMID:34822371
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
Metabolomic and lipidomic characterization of an X-chromosome deletion disorder in neural progenitor cells by UHPLC-HRMS. PMID:34820667
Urinary peptidomics reveals proteases involved in idiopathic membranous nephropathy. PMID:34819020
Rapidly evolving genetic features for desert adaptations in Stipagrostis pennata. PMID:34814836
Nomogram based on autophagy related genes for predicting the survival in melanoma. PMID:34809598
A pan-cancer analysis revealing the role of TIGIT in tumor microenvironment. PMID:34795387
De novo transcriptome and tissue specific expression analysis of genes associated with biosynthesis of secondary metabolites in Operculina turpethum (L.). PMID:34795371
Transcriptome provides potential insights into how calcium affects the formation of stone cell in Pyrus. PMID:34789145
Temperature-induced reorganisation of Schistocephalus solidus (Cestoda) proteome during the transition to the warm-blooded host. PMID:34787304
Toward modeling metabolic state from single-cell transcriptomics. PMID:34785394
Plant height heterosis is quantitatively associated with expression levels of plastid ribosomal proteins. PMID:34782463
Hub microRNAs and genes in the development of atrial fibrillation identified by weighted gene co-expression network analysis. PMID:34781940
Systems pharmacology to reveal multi-scale mechanisms of traditional Chinese medicine for gastric cancer. PMID:34773055
Factors that influence the quality of metabolomics data in in vitro cell toxicity studies: a systematic survey. PMID:34764412
The effects of exosomes derived from trabecular meshwork cells on Schlemm's canal endothelial cells. PMID:34754027
A dry immersion model of microgravity modulates platelet phenotype, miRNA signature, and circulating plasma protein biomarker profile. PMID:34753989
Impact of spaceflight and artificial gravity on sulfur metabolism in mouse liver: sulfur metabolomic and transcriptomic analysis. PMID:34750416
A genetic screen in macrophages identifies new regulators of IFNγ-inducible MHCII that contribute to T cell activation. PMID:34747695
MCLR-elicited hepatic fibrosis and carcinogenic gene expression changes persist in rats with diet-induced nonalcoholic steatohepatitis through a 4-week recovery period. PMID:34740672
Selenium-enriched Bacillus subtilis yb-114246 improved growth and immunity of broiler chickens through modified ileal bacterial composition. PMID:34737359
Nitecap: An Exploratory Circadian Analysis Web Application. PMID:34724846
Characterizing the breast cancer lipidome and its interaction with the tissue microbiota. PMID:34707244
Nutritional restriction during the peri-conceptional period alters the myometrial transcriptome during the peri-implantation period. PMID:34707153
Preparation of an anti-NEK2 monoclonal antibody and its application in liver cancer. PMID:34706700
RNA-Seq analysis in giant pandas reveals the differential expression of multiple genes involved in cataract formation. PMID:34706646
A Markov random field model for network-based differential expression analysis of single-cell RNA-seq data. PMID:34702190
Transcriptomic Response Analysis of Escherichia coli to Palladium Stress. PMID:34690987
Identification of C3 and FN1 as potential biomarkers associated with progression and prognosis for clear cell renal cell carcinoma. PMID:34688260
The Changes in Endogenous Metabolites in Hyperlipidemic Rats Treated with Herbal Mixture Containing Lemon, Apple Cider, Garlic, Ginger, and Honey. PMID:34684574
Structural Protein Analysis of Driver Gene Mutations in Conjunctival Melanoma. PMID:34681018
Periostin Exon-21 Antibody Neutralization of Triple-Negative Breast Cancer Cell-Derived Periostin Regulates Tumor-Associated Macrophage Polarization and Angiogenesis. PMID:34680221
Cell Wall Proteomics Reveal Phenotypic Adaption of Drug-Resistant Mycobacterium smegmatis to Subinhibitory Rifampicin Exposure. PMID:34676224
The nomogram based on the 6-lncRNA model can promote the prognosis prediction of patients with breast invasive carcinoma. PMID:34675301
Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens. PMID:34675224
SPRY4-AS1, A Novel Enhancer RNA, Is a Potential Novel Prognostic Biomarker and Therapeutic Target for Hepatocellular Carcinoma. PMID:34671565
Pseudomonas aeruginosa transcriptome adaptations from colonization to biofilm infection of skin wounds. PMID:34667187
Extracellular calcium alters calcium-sensing receptor network integrating intracellular calcium-signaling and related key pathway. PMID:34663830
Functional glyco-metagenomics elucidates the role of glycan-related genes in environments. PMID:34663219
Non-coding RNA in raw and commercially processed milk and putative targets related to growth and immune-response. PMID:34657595
Transcriptomics Reveals the Putative Mycoparasitic Strategy of the Mushroom Entoloma abortivum on Species of the Mushroom Genus Armillaria. PMID:34636668
Identification of biomarkers of brown adipose tissue aging highlights the role of dysfunctional energy and nucleotide metabolism pathways. PMID:34620947
Applying PICRUSt and 16S rRNA functional characterisation to predicting co-digestion strategies of various animal manures for biogas production. PMID:34620937
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. PMID:34592166
Insights into the gut bacterial communities of spider from wild with no evidence of phylosymbiosis. PMID:34588907
Oxysterol binding protein-like 3 (OSBPL3) is a novel driver gene that promotes tumor growth in part through R-Ras/Akt signaling in gastric cancer. PMID:34584127
Exploration of the lactation function of protein phosphorylation sites in goat mammary tissues by phosphoproteome analysis. PMID:34583635
Short-term transcriptomic response to plasma membrane injury. PMID:34580330
The MAPK/ERK Pathway and the Role of DUSP1 in JCPyV Infection of Primary Astrocytes. PMID:34578413
NetCom: A Network-Based Tool for Predicting Metabolic Activities of Microbial Communities Based on Interpretation of Metagenomics Data. PMID:34576734
Personalised Medicine for Colorectal Cancer Using Mechanism-Based Machine Learning Models. PMID:34576133
Mammary Tumorigenesis and Metabolome in Male Adipose Specific Monocyte Chemotactic Protein-1 Deficient MMTV-PyMT Mice Fed a High-Fat Diet. PMID:34568008
CD49a Identifies Polyfunctional Memory CD8 T Cell Subsets that Persist in the Lungs After Influenza Infection. PMID:34566986
Profiles of microRNA in aqueous humor of normal tension glaucoma patients using RNA sequencing. PMID:34561506
Circulating microRNAs as biomarkers in bile-derived exosomes of cholangiocarcinoma. PMID:34549037
Activin-A impedes the establishment of CD4+ T cell exhaustion and enhances anti-tumor immunity in the lung. PMID:34548096
Transcriptome profiling of Malus sieversii under freezing stress after being cold-acclimated. PMID:34548013
Pre- versus post-operative untargeted plasma nuclear magnetic resonance spectroscopy metabolomics of pheochromocytoma and paraganglioma. PMID:34536194
Integrative analyses of targeted metabolome and transcriptome of Isatidis Radix autotetraploids highlighted key polyploidization-responsive regulators. PMID:34535080
Protective mechanism of Erigeron breviscapus injection on blood-brain barrier injury induced by cerebral ischemia in rats. PMID:34531475
Metabolic effect of drought stress on the leaves of young oil palm (Elaeis guineensis) plants using UHPLC-MS and multivariate analysis. PMID:34521943
Immunoregulatory mechanism studies of ginseng leaves on lung cancer based on network pharmacology and molecular docking. PMID:34521875
In silico predictions of protein interactions between Zika virus and human host. PMID:34513323
Cabazitaxel suppresses colorectal cancer cell growth via enhancing the p53 antitumor pathway. PMID:34496154
Gelatin methacrylate hydrogels culture model for glioblastoma cells enriches for mesenchymal-like state and models interactions with immune cells. PMID:34489494
Dectin-2 mediates phagocytosis of Lactobacillus paracasei KW3110 and IL-10 production by macrophages. PMID:34489491
Proteome analysis identified proteins associated with mitochondrial function and inflammation activation crucially regulating the pathogenesis of fatty liver disease. PMID:34481473
Transcriptome analysis provides genome annotation and expression profiles in the central nervous system of Lymnaea stagnalis at different ages. PMID:34479505
A ferroptosis-associated gene signature for the prediction of prognosis and therapeutic response in luminal-type breast carcinoma. PMID:34475496
Transcriptional expression of ZICs as an independent indicator of survival in gliomas. PMID:34475426
Metabolomics reveal alterations in arachidonic acid metabolism in Schistosoma mekongi after exposure to praziquantel. PMID:34473691
Microvesicles transfer mitochondria and increase mitochondrial function in brain endothelial cells. PMID:34450196
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes. PMID:34442314
Overexpression and Activation of αvβ3 Integrin Differentially Affects TGFβ2 Signaling in Human Trabecular Meshwork Cells. PMID:34440692
Genotypic and phenotypic diversity of Mycobacterium tuberculosis complex genotypes prevalent in West Africa. PMID:34437584
Functional Annotation of MicroRNAs Using Existing Resources. PMID:34432273
Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide. PMID:34430812
KEGG mapping tools for uncovering hidden features in biological data. PMID:34423492
HIV-1 Tat and cocaine impact astrocytic energy reservoir influence on miRNA epigenetic regulation. PMID:34418497
Identification of PLA2G7 as a novel biomarker of diffuse large B cell lymphoma. PMID:34404374
Revealing the role of Plant Growth Promoting Rhizobacteria in suppressive soils against Fusarium oxysporum f.sp. cubense based on metagenomic analysis. PMID:34401567
Identification of novel biomarkers in Hunner's interstitial cystitis using the CIBERSORT, an algorithm based on machine learning. PMID:34399738
Contrasting gut microbiota in captive Eurasian otters (Lutra lutra) by age. PMID:34398307
Identification of prognostic biomarkers related to the tumor microenvironment in thyroid carcinoma. PMID:34376710
Comparative transcriptome analysis of the gills and hepatopancreas from Macrobrachium rosenbergii exposed to the heavy metal Cadmium (Cd2+). PMID:34373575
FcγR engagement reprograms neutrophils into antigen cross-presenting cells that elicit acquired anti-tumor immunity. PMID:34373452
Resilience of Microbial Communities after Hydrogen Peroxide Treatment of a Eutrophic Lake to Suppress Harmful Cyanobacterial Blooms. PMID:34361929
Interstrain Variability of Human Vaginal Lactobacillus crispatus for Metabolism of Biogenic Amines and Antimicrobial Activity against Urogenital Pathogens. PMID:34361691
Exploring the genes involved in biosynthesis of dihydroquercetin and dihydromyricetin in Ampelopsis grossedentata. PMID:34341423
Aurora kinase A (AURKA) promotes the progression and imatinib resistance of advanced gastrointestinal stromal tumors. PMID:34332577
Pyroptosis-Related Gene Signatures Can Robustly Diagnose Skin Cutaneous Melanoma and Predict the Prognosis. PMID:34327145
Analysis of long intergenic non-coding RNAs transcriptomic profiling in skeletal muscle growth during porcine embryonic development. PMID:34315913
Construction of a novel mRNA-signature prediction model for prognosis of bladder cancer based on a statistical analysis. PMID:34315402
Integrative analysis reveals the prognostic value and functions of splicing factors implicated in hepatocellular carcinoma. PMID:34312475
The role of strigolactones in P deficiency induced transcriptional changes in tomato roots. PMID:34301182
Hedgehog/GLI Signaling Pathway: Transduction, Regulation, and Implications for Disease. PMID:34298625
Systemic characterization of alternative splicing related to prognosis and immune infiltration in malignant mesothelioma. PMID:34294080
Mesenchymal stem cell-derived exosomes protect trabecular meshwork from oxidative stress. PMID:34290351
Genome-wide chromatin accessibility analyses provide a map for enhancing optic nerve regeneration. PMID:34290335
Interspecific variation and functional traits of the gut microbiome in spiders from the wild: The largest effort so far. PMID:34288947
Comparative transcriptomic analysis of two Saccharopolyspora spinosa strains reveals the relationships between primary metabolism and spinosad production. PMID:34285307
Untargeted metabolomics and transcriptomics identified glutathione metabolism disturbance and PCS and TMAO as potential biomarkers for ER stress in lung. PMID:34282162
Prediction of combination therapies based on topological modeling of the immune signaling network in multiple sclerosis. PMID:34271980
Physiological and transcriptome analyses for assessing the effects of exogenous uniconazole on drought tolerance in hemp (Cannabis sativa L.). PMID:34262091
Mechanisms of Antiviral Cytotoxic CD4 T Cell Differentiation. PMID:34260270
A HML6 endogenous retrovirus on chromosome 3 is upregulated in amyotrophic lateral sclerosis motor cortex. PMID:34253796
The 2021 update of the EPA's adverse outcome pathway database. PMID:34253739
MicroRNA-378a-3p is overexpressed in psoriasis and modulates cell cycle arrest in keratinocytes via targeting BMP2 gene. PMID:34244572
Integrative analysis of key candidate genes and signaling pathways in acute coronary syndrome related to obstructive sleep apnea by bioinformatics. PMID:34239024
Identification of anticancer drug target genes using an outside competitive dynamics model on cancer signaling networks. PMID:34238960
TBX5-AS1, an enhancer RNA, is a potential novel prognostic biomarker for lung adenocarcinoma. PMID:34238250
ORA , FCS , and PT Strategies in Functional Enrichment Analysis. PMID:34236661
A metabolomics comparison of plant-based meat and grass-fed meat indicates large nutritional differences despite comparable Nutrition Facts panels. PMID:34226581
Holocene life and microbiome profiling in ancient tropical Lake Chalco, Mexico. PMID:34226571
Intestinal Microbiota Mediates High-Fructose and High-Fat Diets to Induce Chronic Intestinal Inflammation. PMID:34222037
SERPINE1 associated with remodeling of the tumor microenvironment in colon cancer progression: a novel therapeutic target. PMID:34215248
Multi-omics analysis of glucose-mediated signaling by a moonlighting Gβ protein Asc1/RACK1. PMID:34214075
Machine learning compensates fold-change method and highlights oxidative phosphorylation in the brain transcriptome of Alzheimer's disease. PMID:34211065
Ganoderma lucidum promotes sleep through a gut microbiota-dependent and serotonin-involved pathway in mice. PMID:34211003
SurvCNN: A Discrete Time-to-Event Cancer Survival Estimation Framework Using Image Representations of Omics Data. PMID:34206288
Impact of Nosema Disease and American Foulbrood on Gut Bacterial Communities of Honeybees Apis mellifera. PMID:34204079
Five Metagenome-Assembled Genomes of the Rare Phylum CSSED10-310 from Zodletone Spring (Oklahoma, USA). PMID:34197190
The maintenance of microbial community in human fecal samples by a cost effective preservation buffer. PMID:34188136
A mouse model of prenatal exposure to Interleukin-6 to study the developmental origin of health and disease. PMID:34168254
Transmitting silks of maize have a complex and dynamic microbiome. PMID:34168223
M5C regulator-mediated methylation modification patterns and tumor microenvironment infiltration characterization in lung adenocarcinoma. PMID:34164268
Anticancer gold(iii)-bisphosphine complex alters the mitochondrial electron transport chain to induce in vivo tumor inhibition. PMID:34163837
Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease. PMID:34162989
Differences in molecular phenotype in mouse and human hypertrophic cardiomyopathy. PMID:34162896
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Soil metabolome response to whole-ecosystem warming at the Spruce and Peatland Responses under Changing Environments experiment. PMID:34161254
Heterotrophic euglenid Rhabdomonas costata resembles its phototrophic relatives in many aspects of molecular and cell biology. PMID:34158556
The risk of pancreatic adenocarcinoma following SARS-CoV family infection. PMID:34155232
Composition and stage dynamics of mitochondrial complexes in Plasmodium falciparum. PMID:34155201
Microbiomes attached to fresh perennial ryegrass are temporally resilient and adapt to changing ecological niches. PMID:34154659
Host-Parasite Interaction of Atlantic salmon (Salmo salar) and the Ectoparasite Neoparamoeba perurans in Amoebic Gill Disease. PMID:34135900
Doxycycline host-directed therapy in human pulmonary tuberculosis. PMID:34128838
Meta-analysis of gene signatures and key pathways indicates suppression of JNK pathway as a regulator of chemo-resistance in AML. PMID:34127725
Melatonin influences the early growth stage in Zoysia japonica Steud. by regulating plant oxidation and genes of hormones. PMID:34117332
Age related gene DST represents an independent prognostic factor for MYCN non-amplified neuroblastoma. PMID:34116676
Integrated proteomic and transcriptomic profiling identifies aberrant gene and protein expression in the sarcomere, mitochondrial complex I, and the extracellular matrix in Warmblood horses with myofibrillar myopathy. PMID:34112090
Transcriptome and metabolome analyses revealing the potential mechanism of seed germination in Polygonatum cyrtonema. PMID:34108536
Effects of FUdR on gene expression in the C. elegans bacterial diet OP50. PMID:34103088
Cancer cell-selective modulation of mitochondrial respiration and metabolism by potent organogold(iii) dithiocarbamates. PMID:34094305
TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes. PMID:34090334
Metabolomics analysis of the soapberry (Sapindus mukorossi Gaertn.) pericarp during fruit development and ripening based on UHPLC-HRMS. PMID:34079016
Unsupervised logic-based mechanism inference for network-driven biological processes. PMID:34077417
Comparative analyses of transcriptional responses of Dectes texanus LeConte (Coleoptera: Cerambycidae) larvae fed on three different host plants and artificial diet. PMID:34075134
A novel ferroptosis related gene signature is associated with prognosis in patients with ovarian serous cystadenocarcinoma. PMID:34075060
Aspergillus Metabolome Database for Mass Spectrometry Metabolomics. PMID:34063531
Highly heterogeneous-related genes of triple-negative breast cancer: potential diagnostic and prognostic biomarkers. PMID:34053447
Aging affects artemisinin synthesis in Artemisia annua. PMID:34050229
Transcriptome analysis of potential candidate genes and molecular pathways in colitis-associated colorectal cancer of Mkp-1-deficient mice. PMID:34034704
Health monitoring in birds using bio-loggers and whole blood transcriptomics. PMID:34031452
Multiscale-omic assessment of EWSR1-NFATc2 fusion positive sarcomas identifies the mTOR pathway as a potential therapeutic target. PMID:34021224
Upregulated functional gene expression programmes in tumour pericytes mark progression in patients with low-grade glioma. PMID:34018679
imPlatelet classifier: image-converted RNA biomarker profiles enable blood-based cancer diagnostics. PMID:34013585
Next‑generation sequencing analysis reveals that MTH‑3, a novel curcuminoid derivative, suppresses the invasion of MDA‑MB‑231 triple‑negative breast adenocarcinoma cells. PMID:34013378
Decreased vascular smooth muscle contractility in Hutchinson-Gilford Progeria Syndrome linked to defective smooth muscle myosin heavy chain expression. PMID:34012019
Revealing the developmental dynamics in male strobilus transcriptome of Gnetum luofuense using nanopore sequencing technology. PMID:34006996
Alternative splicing acts as an independent prognosticator in ovarian carcinoma. PMID:34001978
Thymic transcriptome analysis after Newcastle disease virus inoculation in chickens and the influence of host small RNAs on NDV replication. PMID:33986327
Species and population specific gene expression in blood transcriptomes of marine turtles. PMID:33985425
Integrated Genomic and Functional Characterization of the Anti-diabetic Potential of Arthrobacter sp. SW1. PMID:33983483
Discovery and validation of novel protein markers in mucosa of portal hypertensive gastropathy. PMID:33971821
Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast. PMID:33967978
Immunohistochemical analysis of Nuclear Factor-kappa B (NF-κB) between follicular and plexiform ameloblastomas: A pilot study. PMID:33967482
Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn's disease. PMID:33963246
Metabolomic and phenotypic implications of the application of fertilization products containing microcontaminants in lettuce (Lactuca sativa). PMID:33958645
MicroRNA Expression in Extracellular Vesicles from Nasal Lavage Fluid in Chronic Rhinosinusitis. PMID:33925835
Knock out of specific maternal vitellogenins in zebrafish (Danio rerio) evokes vital changes in egg proteomic profiles that resemble the phenotype of poor quality eggs. PMID:33910518
Gene network and biological pathways associated with susceptibility to differentiated thyroid carcinoma. PMID:33903625
SCD5 expression correlates with prognosis and response to neoadjuvant chemotherapy in breast cancer. PMID:33903614
Transgenic mice overexpressing the LH receptor in the female reproductive system spontaneously develop endometrial tumour masses. PMID:33893331
Transcriptome analysis reveals gene responses to herbicide, tribenuron methyl, in Brassica napus L. during seed germination. PMID:33892633
Investigating the effects of chronic perinatal alcohol and combined nicotine and alcohol exposure on dopaminergic and non-dopaminergic neurons in the VTA. PMID:33888815
scSensitiveGeneDefine: sensitive gene detection in single-cell RNA sequencing data by Shannon entropy. PMID:33888056
Transcriptome profiling of immune response to Yersinia ruckeri in spleen of rainbow trout (Oncorhynchus mykiss). PMID:33882827
Novel, non-invasive markers for detecting therapy induced neuroendocrine differentiation in castration-resistant prostate cancer patients. PMID:33859239
Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs. PMID:33856433
Transcriptome-wide study revealed m6A regulation of embryonic muscle development in Dingan goose (Anser cygnoides orientalis). PMID:33853538
A long non-coding RNAs expression signature to improve prognostic prediction of Wilms tumor in children. PMID:33850811
Whole-exome sequencing with targeted analysis and epilepsy after acute symptomatic neonatal seizures. PMID:33846556
Identification of co-expression network correlated with different periods of adipogenic and osteogenic differentiation of BMSCs by weighted gene co-expression network analysis (WGCNA). PMID:33836657
An order independent algorithm for inferring gene regulatory network using quantile value for conditional independence tests. PMID:33828122
Metabolic Capacity of the Antarctic Cyanobacterium Phormidium pseudopriestleyi That Sustains Oxygenic Photosynthesis in the Presence of Hydrogen Sulfide. PMID:33809699
Corynebacterium diphtheriae Proteome Adaptation to Cell Culture Medium and Serum. PMID:33805816
A Detailed Catalogue of Multi-Omics Methodologies for Identification of Putative Biomarkers and Causal Molecular Networks in Translational Cancer Research. PMID:33802234
Indole-3-Acetic Acid Is Synthesized by the Endophyte Cyanodermella asteris via a Tryptophan-Dependent and -Independent Way and Mediates the Interaction with a Non-Host Plant. PMID:33800748
Biosyntheses characterization of alkaloids and flavonoids in Sophora flavescens by combining metabolome and transcriptome. PMID:33795823
Network pharmacology and molecular docking study on the active ingredients of qidengmingmu capsule for the treatment of diabetic retinopathy. PMID:33795817
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq). PMID:33793824
Proteomics study on the effect of silybin on cardiomyopathy in obese mice. PMID:33785854
Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function in mice. PMID:33767339
Dynamic transcriptome analysis identifies genes related to fatty acid biosynthesis in the seeds of Prunus pedunculata Pall. PMID:33761884
Mitochondrial genotype alters the impact of rapamycin on the transcriptional response to nutrients in Drosophila. PMID:33761878
Herb-target virtual screening and network pharmacology for prediction of molecular mechanism of Danggui Beimu Kushen Wan for prostate cancer. PMID:33758314
Transcriptomic insight into the translational value of two murine models in human atopic dermatitis. PMID:33758305
Expression profiling of Echinococcus multilocularis miRNAs throughout metacestode development in vitro. PMID:33750964
Comparative transcriptome analysis during developmental stages of direct somatic embryogenesis in Tilia amurensis Rupr. PMID:33737673
Application of text mining to develop AOP-based mucus hypersecretion genesets and confirmation with in vitro and clinical samples. PMID:33731770
Potential benefits of L. acidophilus in dyslipidemic rats. PMID:33731756
Chronic villitis of unknown etiology: Investigations into viral pathogenesis. PMID:33730616
The Effect of hsa-miR-451b Knockdown on Biological Functions of Gastric Cancer Stem-Like Cells. PMID:33725258
A systematic analysis of hypermucoviscosity and capsule reveals distinct and overlapping genes that impact Klebsiella pneumoniae fitness. PMID:33720976
Human milk extracellular vesicle miRNA expression and associations with maternal characteristics in a population-based cohort from the Faroe Islands. PMID:33712635
Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells. PMID:33707642
Major ceRNA regulation and key metabolic signature analysis of intervertebral disc degeneration. PMID:33676464
Single-cell differential splicing analysis reveals high heterogeneity of liver tumor-infiltrating T cells. PMID:33674641
Starvation Alters Gut Microbiome in Black Soldier Fly (Diptera: Stratiomyidae) Larvae. PMID:33664713
Pharmacological inhibition of tumor anabolism and host catabolism as a cancer therapy. PMID:33664364
Resequencing and SNP discovery of Amur ide (Leuciscus waleckii) provides insights into local adaptations to extreme environments. PMID:33658614
B2M overexpression correlates with malignancy and immune signatures in human gliomas. PMID:33658560
Novel gene signatures for stage classification of the squamous cell carcinoma of the lung. PMID:33649335
Interspecies chimeric conditions affect the developmental rate of human pluripotent stem cells. PMID:33647016
The role of gut microbiota and amino metabolism in the effects of improvement of islet β-cell function after modified jejunoileal bypass. PMID:33637880
Crystal structure of acetoacetyl-CoA reductase from Rickettsia felis. PMID:33620038
Lysosome repositioning as an autophagy escape mechanism by Mycobacterium tuberculosis Beijing strain. PMID:33619301
Modulating the unfolded protein response with ONC201 to impact on radiation response in prostate cancer cells. PMID:33608585
Novel signaling pathways regulate SARS-CoV and SARS-CoV-2 infectious disease. PMID:33607766
Cerebrospinal fluid proteome shows disrupted neuronal development in multiple sclerosis. PMID:33602999
Identification of biomarkers and pathogenesis in severe asthma by coexpression network analysis. PMID:33602227
Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation. PMID:33602141
Mitochondrial Inhibitor Atovaquone Increases Tumor Oxygenation and Inhibits Hypoxic Gene Expression in Patients with Non-Small Cell Lung Cancer. PMID:33597271
Digital gene expression analysis of the response to Ralstonia solanacearum between resistant and susceptible tobacco varieties. PMID:33594109
In Esophageal Squamous Cells From Eosinophilic Esophagitis Patients, Th2 Cytokines Increase Eotaxin-3 Secretion Through Effects on Intracellular Calcium and a Non-Gastric Proton Pump. PMID:33581123
Effects of glyphosate residues and different concentrate feed proportions in dairy cow rations on hepatic gene expression, liver histology and biochemical blood parameters. PMID:33577576
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
Small RNAs and their targets are associated with the transgenerational effects of water-deficit stress in durum wheat. PMID:33574419
Transcriptome analysis of genes involved in starch biosynthesis in developing Chinese chestnut (Castanea mollissima Blume) seed kernels. PMID:33574357
Functionally selective activation of the dopamine receptor D2 is mirrored by the protein expression profiles. PMID:33568753
Integrated analysis identifies oxidative stress genes associated with progression and prognosis in gastric cancer. PMID:33558567
Meta-analysis cum machine learning approaches address the structure and biogeochemical potential of marine copepod associated bacteriobiomes. PMID:33558540
Arrayed CRISPR reveals genetic regulators of tau aggregation, autophagy and mitochondria in Alzheimer's disease model. PMID:33536571
Immature symbiotic system between horizontally transmitted green algae and brown hydra. PMID:33536483
Metabolic dysfunction in pregnancy: Fingerprinting the maternal metabolome using proton nuclear magnetic resonance spectroscopy. PMID:33532625
Transcriptomic and Functional Analyses of Mitochondrial Dysfunction in Pressure Overload-Induced Right Ventricular Failure. PMID:33522250
American lobster postlarvae alter gene regulation in response to ocean warming and acidification. PMID:33520168
High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. PMID:33519501
A novel microbiome metabolic modulator improves the growth performance of broiler chickens in multiple trials and modulates targeted energy and amino acid metabolic pathways in the cecal metagenome. PMID:33518302
Comparative gene expression analysis reveals that multiple mechanisms regulate the weeping trait in Prunus mume. PMID:33514804
Transcriptome analysis reveals the long intergenic noncoding RNAs contributed to skeletal muscle differences between Yorkshire and Tibetan pig. PMID:33514792
Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. PMID:33513807
Reporting on the Role of miRNAs and Affected Pathways on the Molecular Backbone of Ovarian Insufficiency: A Systematic Review and Critical Analysis Mapping of Future Research. PMID:33511114
Genome-wide comparative analyses reveal selection signatures underlying adaptation and production in Tibetan and Poll Dorset sheep. PMID:33510350
Identifying RNA Biomarkers and Molecular Pathways Involved in Multiple Subtypes of Uveitis. PMID:33503442
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia. PMID:33500463
Metagenomic analysis of the cow, sheep, reindeer and red deer rumen. PMID:33479378
Acetyl-CoA flux from the cytosol to the ER regulates engagement and quality of the secretory pathway. PMID:33479349
Targeted metabolomics analysis of postoperative delirium. PMID:33452279
Combined transcriptomic and lipidomic analysis reveals aberrant lipid metabolism in central nervous system hemangioblastomas. PMID:33446752
Genomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece. PMID:33446715
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Immune modulation resulting from MR-guided high intensity focused ultrasound in a model of murine breast cancer. PMID:33441763
MicroRNA expression profiling after recurrent febrile seizures in rat and emerging role of miR-148a-3p/SYNJ1 axis. PMID:33441699
Uncovering multi-faceted taxonomic and functional diversity of soil bacteriomes in tropical Southeast Asian countries. PMID:33436774
Comparative genomics and metabolomics analysis of Riemerella anatipestifer strain CH-1 and CH-2. PMID:33436670
R-2-hydroxyglutarate attenuates aerobic glycolysis in leukemia by targeting the FTO/m6A/PFKP/LDHB axis. PMID:33434505
Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism. PMID:33431991
An Optimized Protein Extraction Method for Gel-Free Proteomic Analysis of Opuntia Ficus-Indica. PMID:33429847
Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. PMID:33426377
Computational analysis to repurpose drugs for COVID-19 based on transcriptional response of host cells to SARS-CoV-2. PMID:33413329
MicrobeAnnotator: a user-friendly, comprehensive functional annotation pipeline for microbial genomes. PMID:33407081
Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. PMID:33384856
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
Inflammatory Proteins HMGA2 and PRTN3 as Drivers of Vulvar Squamous Cell Carcinoma Progression. PMID:33374674
Genome-scale reconstructions to assess metabolic phylogeny and organism clustering. PMID:33373364
Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair. PMID:33339161
MicroRNA-451a prevents cutaneous squamous cell carcinoma progression via the 3-phosphoinositide-dependent protein kinase-1-mediated PI3K/AKT signaling pathway. PMID:33335579
Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions. PMID:33335165
GAS2L1 Is a Potential Biomarker of Circulating Tumor Cells in Pancreatic Cancer. PMID:33333841
Impact of Staphylococcus aureus Small Colony Variants on Human Lung Epithelial Cells with Subsequent Influenza Virus Infection. PMID:33333815
Frameshift Variant in Novel Adenosine-A1-Receptor Homolog Associated With Bovine Spastic Syndrome/Late-Onset Bovine Spastic Paresis in Holstein Sires. PMID:33329738
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
Trypanosoma cruzi Modulates PIWI-Interacting RNA Expression in Primary Human Cardiac Myocytes during the Early Phase of Infection. PMID:33322418
Sericin inhibits MDA‑MB‑468 cell proliferation via the PI3K/Akt pathway in triple‑negative breast cancer. PMID:33313947
Understanding Mechanisms Underlying Non-Alcoholic Fatty Liver Disease (NAFLD) in Mental Illness: Risperidone and Olanzapine Alter the Hepatic Proteomic Signature in Mice. PMID:33302598
An animal model study on the gene expression profile of meniscal degeneration. PMID:33293598
Multi-omics integration in biomedical research - A metabolomics-centric review. PMID:33248648
Single cell profiling of capillary blood enables out of clinic human immunity studies. PMID:33239690
Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L. PMID:33235240
Associations of the gut microbiome and clinical factors with acute GVHD in allogeneic HSCT recipients. PMID:33232475
Unique maternal immune and functional microbial profiles during prenatal stress. PMID:33219314
Circulating miRNA-181b-5p, miRNA-223-3p, miRNA-210-3p, let 7i-5p, miRNA-21-5p and miRNA-29a-3p in patients with localized scleroderma as potential biomarkers. PMID:33214624
LOXL2 promotes aggrecan and gender-specific anabolic differences to TMJ cartilage. PMID:33214607
The attachment process and physiological properties of Escherichia coli O157:H7 on quartz. PMID:33213384
Variable Selection in Untargeted Metabolomics and the Danger of Sparsity. PMID:33213095
The effect of hypoxia on the proteomic signature of pig adipose-derived stromal/stem cells (pASCs). PMID:33208768
The invasive red-eared slider turtle is more successful than the native Chinese three-keeled pond turtle: evidence from the gut microbiota. PMID:33194431
Mechanisms of EGFR Resistance in Glioblastoma. PMID:33187135
UPLC/MS-based untargeted metabolomics reveals the changes of metabolites profile of Salvia miltiorrhiza bunge during Sweating processing. PMID:33177654
Narasin inhibits tumor metastasis and growth of ERα‑positive breast cancer cells by inactivation of the TGF‑β/SMAD3 and IL‑6/STAT3 signaling pathways. PMID:33174044
Using mRNA deep sequencing to analyze differentially expressed genes during Panax notoginseng saponin treatment of ischemic stroke. PMID:33173991
Cytokines CCL2 and CXCL1 may be potential novel predictors of early bone loss. PMID:33173955
Omics approaches for conservation biology research on the bivalve Chamelea gallina. PMID:33154500
Comparative physiological and transcriptomic analysis of pear leaves under distinct training systems. PMID:33144674
β-Barrels covalently link peptidoglycan and the outer membrane in the α-proteobacterium Brucella abortus. PMID:33139884
From sequence to information. PMID:33131436
Higher miR-543 levels correlate with lower STK31 expression and longer pancreatic cancer survival. PMID:33128354
KEGG: integrating viruses and cellular organisms. PMID:33125081
The Oncometabolite 5'-Deoxy-5'-Methylthioadenosine Blocks Multiple Signaling Pathways of NK Cell Activation. PMID:33123121
Differential Gene Expression in Brain and Liver Tissue of Wistar Rats after Rapid Eye Movement Sleep Deprivation. PMID:33114225
Integrated Proteomic and Glycoproteomic Characterization of Human High-Grade Serous Ovarian Carcinoma. PMID:33086064
Complementary Tendencies in the Use of Regulatory Elements (Transcription Factors, Sigma Factors, and Riboswitches) in Bacteria and Archaea. PMID:33077635
Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. PMID:33076907
SP_0916 Is an Arginine Decarboxylase That Catalyzes the Synthesis of Agmatine, Which Is Critical for Capsule Biosynthesis in Streptococcus pneumoniae. PMID:33072045
IL-4-BATF signaling directly modulates IL-9 producing mucosal mast cell (MMC9) function in experimental food allergy. PMID:33069715
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell. PMID:33067542
Present and Future of Anti-Glioblastoma Therapies: A Deep Look into Molecular Dependencies/Features. PMID:33053763
Inhibition of O-GlcNAc transferase activates tumor-suppressor gene expression in tamoxifen-resistant breast cancer cells. PMID:33046784
Quantitative Proteomic Analysis of Porcine Intestinal Epithelial Cells Infected with Porcine Deltacoronavirus Using iTRAQ-Coupled LC-MS/MS. PMID:33045833
The interplay between host genetics and the gut microbiome reveals common and distinct microbiome features for complex human diseases. PMID:33032658
Integrated transcriptomic and metabolomic data reveal the flavonoid biosynthesis metabolic pathway in Perilla frutescens (L.) leaves. PMID:33004940
Expression of fatty acid and triacylglycerol synthesis genes in interspecific hybrids of oil palm. PMID:33004875
miR‑592 acts as an oncogene and promotes medullary thyroid cancer tumorigenesis by targeting cyclin‑dependent kinase 8. PMID:32945439
Immunotyping of tumor-infiltrating lymphocytes in triple-negative breast cancer and genetic characterization. PMID:32934708
Investigating the influence of perinatal nicotine and alcohol exposure on the genetic profiles of dopaminergic neurons in the VTA using miRNA-mRNA analysis. PMID:32929144
Teleological role of L-2-hydroxyglutarate dehydrogenase in the kidney. PMID:32928875
Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals. PMID:32917913
The overexpression of OsACBP5 protects transgenic rice against necrotrophic, hemibiotrophic and biotrophic pathogens. PMID:32913218
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
iTRAQ‑based proteomic analysis reveals potential regulatory networks in dust mite‑related asthma treated with subcutaneous allergen immunotherapy. PMID:32901873
Sterile Spikelets Contribute to Yield in Sorghum and Related Grasses. PMID:32873633
RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva. PMID:32859978
The small compound, TD-198946, protects against intervertebral degeneration by enhancing glycosaminoglycan synthesis in nucleus pulposus cells. PMID:32843678
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics. PMID:32813693
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. PMID:32810438
Actinobacteria from Antarctica as a source for anticancer discovery. PMID:32807803
Comparative Genomics Underlines Multiple Roles of Profftella, an Obligate Symbiont of Psyllids: Providing Toxins, Vitamins, and Carotenoids. PMID:32797185
Characterization of an acid rock drainage microbiome and transcriptome at the Ely Copper Mine Superfund site. PMID:32785287
MDM2-Dependent Rewiring of Metabolomic and Lipidomic Profiles in Dedifferentiated Liposarcoma Models. PMID:32759684
Hepatopancreas immune response during molt cycle in the mud crab, Scylla paramamosain. PMID:32753724
A Network-Based Approach to Explore the Mechanism and Bioactive Compounds of Erzhi Pill against Metabolic Dysfunction-Associated Fatty Liver Disease. PMID:32724826
GGCT promotes colorectal cancer migration and invasion via epithelial-mesenchymal transition. PMID:32724344
The Potential of Metabolomics in the Diagnosis of Thyroid Cancer. PMID:32722293
A carbohydrate-active enzyme (CAZy) profile links successful metabolic specialization of Prevotella to its abundance in gut microbiota. PMID:32709972
IL-21 Stimulates the expression and activation of cell cycle regulators and promotes cell proliferation in EBV-positive diffuse large B cell lymphoma. PMID:32704112
A G-quadruplex-binding compound shows potent activity in human gemcitabine-resistant pancreatic cancer cells. PMID:32699225
Plasma Phospholipid Metabolites Associate With Functional Outcomes Following Mild Traumatic Brain Injury in Older Adults. PMID:32696677
MAF1 is a chronic repressor of RNA polymerase III transcription in the mouse. PMID:32686713
Gene expression profiling identifies the role of Zac1 in cervical cancer metastasis. PMID:32678267
Peroxisome proliferator-activated receptor alpha is involved in the temperature-induced sex differentiation of a vertebrate. PMID:32669596
DNA Methylation Epigenetically Regulates Gene Expression in Burkholderia cenocepacia and Controls Biofilm Formation, Cell Aggregation, and Motility. PMID:32669472
Impact of Sacbrood Virus on Larval Microbiome of Apis mellifera and Apis cerana. PMID:32668740
Captivity affects diversity, abundance, and functional pathways of gut microbiota in the northern grass lizard Takydromus septentrionalis. PMID:32666685
Toxicology of tramadol following chronic exposure based on metabolomics of the cerebrum in mice. PMID:32636435
CYP1B1 gene: Implications in glaucoma and cancer. PMID:32626511
Isolation, identification, and whole genome sequence analysis of the alginate-degrading bacterium Cobetia sp. cqz5-12. PMID:32616809
Comparative transcriptome analysis of a taxol-producing endophytic fungus, Aspergillus aculeatinus Tax-6, and its mutant strain. PMID:32601443
The chromatin landscape at the HIV-1 provirus integration site determines viral expression. PMID:32597987
The seed water content as a time-independent physiological trait during germination in wild tree species such as Ceiba aesculifolia. PMID:32591557
Prognostic Biomarkers in Endometrial Cancer: A Systematic Review and Meta-Analysis. PMID:32560580
Wnt Signaling in Gynecologic Malignancies. PMID:32560059
CRISPR/Cas9 knockout of human arylamine N-acetyltransferase 1 in MDA-MB-231 breast cancer cells suggests a role in cellular metabolism. PMID:32555504
Increased Connexin36 Phosphorylation in AII Amacrine Cell Coupling of the Mouse Myopic Retina. PMID:32547367
Screening and functional identification of lncRNAs in antler mesenchymal and cartilage tissues using high-throughput sequencing. PMID:32528134
NetMet: A Network-Based Tool for Predicting Metabolic Capacities of Microbial Species and their Interactions. PMID:32503277
RNA-Seq Analyses Reveal That Endothelial Activation and Fibrosis Are Induced Early and Progressively by Besnoitia besnoiti Host Cell Invasion and Proliferation. PMID:32500038
A Translational In Vivo and In Vitro Metabolomic Study Reveals Altered Metabolic Pathways in Red Blood Cells of Type 2 Diabetes. PMID:32471219
Bioinformatics analysis of the network of histone H3 lysine 9 trimethylation in acute myeloid leukaemia. PMID:32468066
Follicular extracellular vesicles enhance meiotic resumption of domestic cat vitrified oocytes. PMID:32451384
A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimer's disease. PMID:32433480
Characterization of Stem-like Circulating Tumor Cells in Pancreatic Cancer. PMID:32429174
In Vitro Effects of Streptococcus oralis Biofilm on Peri-Implant Soft Tissue Cells. PMID:32429151
Transcriptomic evidence that insulin signalling pathway regulates the ageing of subterranean termite castes. PMID:32424344
Detecting qualitative changes in biological systems. PMID:32424123
Metabolomics analyses to characterize metabolic alterations in Korean native calves by oral vitamin A supplementation. PMID:32415141
Lysine Acetyltransferase p300/CBP Plays an Important Role in Reproduction, Embryogenesis and Longevity of the Pea Aphid Acyrthosiphon pisum. PMID:32357443
Are Pathogenic Germline Variants in Metastatic Melanoma Associated with Resistance to Combined Immunotherapy? PMID:32354124
Charcot-Marie-Tooth Type 2B: A New Phenotype Associated with a Novel RAB7A Mutation and Inhibited EGFR Degradation. PMID:32326241
Transcriptional analyses of differential cultivars during resistant and susceptible interactions with Peronospora effusa, the causal agent of spinach downy mildew. PMID:32317662
Hemocyte phagosomal proteome is dynamically shaped by cytoskeleton remodeling and interorganellar communication with endoplasmic reticulum during phagocytosis in a marine invertebrate, Crassostrea gigas. PMID:32313134
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Comprehensive immunogenomic landscape analysis of prognosis-related genes in head and neck cancer. PMID:32286381
Leveraging host metabolism for bisdemethoxycurcumin production in Pseudomonas putida. PMID:32280587
Metabolic disturbance in hippocampus and liver of mice: A primary response to imidacloprid exposure. PMID:32235887
Proteomic mapping of Drosophila transgenic elav.L-GAL4/+ brain as a tool to illuminate neuropathology mechanisms. PMID:32214222
MetaBridge: An Integrative Multi-Omics Tool for Metabolite-Enzyme Mapping. PMID:32199034
Coxsackievirus B3 Infection of Human Neural Progenitor Cells Results in Distinct Expression Patterns of Innate Immune Genes. PMID:32192194
PDGFD induces ibrutinib resistance of diffuse large B‑cell lymphoma through activation of EGFR. PMID:32186759
Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis. PMID:32161689
Novel pathways of HIV latency reactivation revealed by integrated analysis of transcriptome and target profile of bryostatin. PMID:32103135
Association between MIR499A rs3746444 polymorphism and breast cancer susceptibility: a meta-analysis. PMID:32103099
Transcriptome Analysis Reveals Biosynthesis of Important Bioactive Constituents and Mechanism of Stem Formation of Dendrobium huoshanense. PMID:32071345
Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families. PMID:32066727
Cytokinins Are Abundant and Widespread Among Insect Species. PMID:32041320
Imputation of Gene Expression Data in Blood Cancer and Its Significance in Inferring Biological Pathways. PMID:31970084
MicroRNA and mRNA interactions coordinate the immune response in non-lethal heat stressed Litopenaeus vannamei against AHPND-causing Vibrio parahaemolyticus. PMID:31964916
Genome Sequence of Lignin-Degrading Arthrobacter sp. Strain RT-1, Isolated from Termite Gut and Rumen Fluid. PMID:31948970
Gambogenic acid exerts anticancer effects in cisplatin‑resistant non‑small cell lung cancer cells. PMID:31922223
Weighted gene co‑expression network analysis to identify key modules and hub genes associated with atrial fibrillation. PMID:31894294
Identification of circulating microRNA signatures as potential biomarkers in the serum of elk infected with chronic wasting disease. PMID:31873177
A network pharmacology approach to reveal the protective mechanism of Salvia miltiorrhiza-Dalbergia odorifera coupled-herbs on coronary heart disease. PMID:31852981
Bacillus amyloliquefaciens MBI600 differentially induces tomato defense signaling pathways depending on plant part and dose of application. PMID:31836790
Transcription modulation by CDK9 regulates inflammatory genes and RIPK3-MLKL-mediated necroptosis in periodontitis progression. PMID:31758083
LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer. PMID:31746401
Extracellular vesicles from endothelial progenitor cells prevent steroid-induced osteoporosis by suppressing the ferroptotic pathway in mouse osteoblasts based on bioinformatics evidence. PMID:31695092
DNA methylation of antisense noncoding RNA in the INK locus (ANRIL) is associated with coronary artery disease in a Chinese population. PMID:31653960
S‑allyl‑cysteine sulfoxide (alliin) alleviates myocardial infarction by modulating cardiomyocyte necroptosis and autophagy. PMID:31573046

KEGG: integrating viruses and cellular organisms PubMed citations: 614.

The KEGG database PubMed citations: 456.

KEGG Atlas mapping for global analysis of metabolic pathways PubMed citations: 188.

Medical subject headings PubMed citations: 81.

Using the KEGG database resource PubMed citations: 75.

Tags:

Tags
More detailed information about this field from each metasource.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: KEGG; Kyoto Encyclopedia of Genes and Genomes; DOI: https://doi.org/10.25504/FAIRsharing.327nbg; Last edited: April 23, 2020, 1:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

molecular interaction
metasource: Fairsharing.org
version: FAIRsharing.org: KEGG; Kyoto Encyclopedia of Genes and Genomes; DOI: https://doi.org/10.25504/FAIRsharing.327nbg; Last edited: April 23, 2020, 1:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

rna sequencing
metasource: Fairsharing.org
version: FAIRsharing.org: KEGG; Kyoto Encyclopedia of Genes and Genomes; DOI: https://doi.org/10.25504/FAIRsharing.327nbg; Last edited: April 23, 2020, 1:55 p.m.; Last accessed: Jan 03 2022 7:05 p.m.

covid-19
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

biochemistry
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

bioinformatics
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

cells
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

chemistry
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

drugs
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

ecosystem
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

health
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

molecular interaction networks
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

organism
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

systemic functions
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

systems biology
metasource: re3data.org
version: re3data.org: Kyoto Encyclopedia of Genes and Genomes; editing status 2021-08-25; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3792T last accessed: 2022-11-04

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

endocrinology and metabolism
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

protein interactions
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:24:12.882125

genome molecular interaction rna sequence covid-19 biochemistry bioinformatics cells chemistry drugs ecosystem genetics genomics health molecular interaction networks organism systemic functions systems biology molecular interactions, pathways and networks endocrinology and metabolism mapping protein interaction model organisms

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