FAIRsharing.3gxr9b; Last edited: Sept. 4, 2019, 9:23 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

Other names: SOFT

Using Simple Omnibus Format in Text (SOFT), researchers can readily upload and download data. The resource is text-based so can be compatible with simple spreadsheets and data applications. A SOFT file can simultaneously contain both tabulated data as well as descriptive information for a chain of related Platforms, Samples, and/or Series records.

Webpage:

http://www.ncbi.nlm.nih.gov/geo/info/soft2.html

Publications:

Publications
More detailed information about this field from each metasource.

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository
PMID: 11752295
metasource: Fairsharing.org
version: FAIRsharing.org: SOFT; Simple Omnibus Format in Text; DOI: https://doi.org/10.25504/FAIRsharing.3gxr9b; Last edited: Sept. 4, 2019, 9:23 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

NCBI GEO: mining tens of millions of expression profiles--database and tools update
PMID: 17099226
metasource: Fairsharing.org
version: FAIRsharing.org: SOFT; Simple Omnibus Format in Text; DOI: https://doi.org/10.25504/FAIRsharing.3gxr9b; Last edited: Sept. 4, 2019, 9:23 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

NCBI GEO: mining millions of expression profiles--database and tools
PMID: 15608262
metasource: Fairsharing.org
version: FAIRsharing.org: SOFT; Simple Omnibus Format in Text; DOI: https://doi.org/10.25504/FAIRsharing.3gxr9b; Last edited: Sept. 4, 2019, 9:23 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository PubMed citations: 5825.

5825 articles citing: Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

Cogito: automated and generic comparison of annotated genomic intervals. PMID:35927614
METTL3 preferentially enhances non-m6A translation of epigenetic factors and promotes tumourigenesis. PMID:35927451
Cellular recovery after prolonged warm ischaemia of the whole body. PMID:35922506
Evolutionary Relationships Between Dysregulated Genes in Oral Squamous Cell Carcinoma and Oral Microbiota. PMID:35909962
Cancer-testis antigen KK-LC-1 is a potential biomarker associated with immune cell infiltration in lung adenocarcinoma. PMID:35907786
CC chemokine receptor 7 promotes macrophage recruitment and induces M2-polarization through CC chemokine ligand 19&21 in oral squamous cell carcinoma. PMID:35904690
The lupus susceptibility allele DRB1*03:01 encodes a disease-driving epitope. PMID:35902632
Overexpression of OAS1 Is Correlated With Poor Prognosis in Pancreatic Cancer. PMID:35898870
Global Profiling of Genes Expressed in the Silk Glands of Philippine-Reared Mulberry Silkworms (Bombyx mori). PMID:35893024
Immunomodulatory Responses of Subcapsular Sinus Floor Lymphatic Endothelial Cells in Tumor-Draining Lymph Nodes. PMID:35892863
Stemness Correlates Inversely with MHC Class I Expression in Pediatric Small Round Blue Cell Tumors. PMID:35892842
The Protective Effect of Edaravone on TDP-43 Plus Oxidative Stress-Induced Neurotoxicity in Neuronal Cells: Analysis of Its Neuroprotective Mechanisms Using RNA Sequencing. PMID:35890141
Transcriptional Profiling of Leishmania infantum Infected Dendritic Cells: Insights into the Role of Immunometabolism in Host-Parasite Interaction. PMID:35888991
Prenatal Detection of Novel Compound Heterozygous Splice Site Variants of the KIAA0825 Gene in a Fetus with Postaxial Polydactyly Type A. PMID:35886013
High Oxytocin Receptor Expression Linked to Increased Cell Migration and Reduced Survival in Patients with Triple-Negative Breast Cancer. PMID:35884900
Integrated Clinical and Genomic Models to Predict Optimal Cytoreduction in High-Grade Serous Ovarian Cancer. PMID:35884615
Large-Scale Profiling on lncRNAs in Human Platelets: Correlation with Platelet Reactivity. PMID:35883699
Induced Endothelial Cell-Integrated Liver Assembloids Promote Hepatic Maturation and Therapeutic Effect on Cholestatic Liver Fibrosis. PMID:35883684
In silico discovery of blood cell macromolecular associations. PMID:35879676
Identification of Metabolic Syndrome-Related miRNA-mRNA Regulatory Networks and Key Genes Based on Bioinformatics Analysis. PMID:35877019
Getting Started with LINCS Datasets and Tools. PMID:35876555
Longevity-Promoting Pathways and Transcription Factors Respond to and Control Extracellular Matrix Dynamics During Aging and Disease. PMID:35874275
Unveiling Co-Infection in Cystic Fibrosis Airways: Transcriptomic Analysis of Pseudomonas aeruginosa and Staphylococcus aureus Dual-Species Biofilms. PMID:35873457
The Lack of the TetR-Like Repressor Gene BCG_2177c (Rv2160A) May Help Mycobacteria Overcome Intracellular Redox Stress and Survive Longer Inside Macrophages When Surrounded by a Lipid Environment. PMID:35873160
In silico Identification of Immune Cell-Types and Pathways Involved in Chronic Spontaneous Urticaria. PMID:35872776
EpiVisR: exploratory data analysis and visualization in epigenome-wide association analyses. PMID:35870905
Increased Development of Th1, Th17, and Th1.17 Cells Under T1 Polarizing Conditions in Juvenile Idiopathic Arthritis. PMID:35860254
Un-biased housekeeping gene panel selection for high-validity gene expression analysis. PMID:35853974
An Immunity-Related Gene Model Predicts Prognosis in Cholangiocarcinoma. PMID:35847907
Predicting the Lung Adenocarcinoma and Its Biomarkers by Integrating Gene Expression and DNA Methylation Data. PMID:35846148
Senescent Tumor Cells in the Peritoneal Carcinomatosis Drive Immunosenescence in the Tumor Microenvironment. PMID:35844581
Single-Cell RNA Sequencing Unravels Upregulation of Immune Cell Crosstalk in Relapsed Pediatric Ependymoma. PMID:35844565
Uncovering a Genetic Polymorphism Located in Huntingtin Associated Protein 1 in Modulation of Central Pain Sensitization Signaling Pathways. PMID:35837121
Differential gene screening and bioinformatics analysis of epidermal stem cells and dermal fibroblasts during skin aging. PMID:35835980
Novel roles of luteinizing hormone (LH) in tissue regeneration-associated functions in endometrial stem cells. PMID:35831270
Multivariate competing endogenous RNA network characterization for cancer microRNA biomarker discovery: a novel bioinformatics model with application to prostate cancer metastasis. PMID:35821682
Network Pharmacology and Bioinformatics Methods Reveal the Mechanism of Berberine in the Treatment of Ischaemic Stroke. PMID:35815278
The clinical relevance of unfolded protein response signaling in breast cancer. PMID:35812054
miR-218-5p/RUNX2 Axis Positively Regulates Proliferation and Is Associated with Poor Prognosis in Cervical Cancer. PMID:35805994
DNA methylation fingerprint of hepatocellular carcinoma from tissue and liquid biopsies. PMID:35798798
Vitexin Mitigates Staphylococcus aureus-Induced Mastitis via Regulation of ROS/ER Stress/NF-κB/MAPK Pathway. PMID:35795861
Cytokinin and Its Key Role to Enrich the Plant Nutrients and Growth Under Adverse Conditions-An Update. PMID:35795201
Downregulation of LRRC19 Is Associated with Poor Prognosis in Colorectal Cancer. PMID:35794979
Highly perturbed genes and hub genes associated with type 2 diabetes in different tissues of adult humans: a bioinformatics analytic workflow. PMID:35788821
Integrated Analysis of Immune-Related circRNA-miRNA-mRNA Regulatory Network in Ischemic Stroke. PMID:35785353
Exposure of Keratinocytes to Candida Albicans in the Context of Atopic Milieu Induces Changes in the Surface Glycosylation Pattern of Small Extracellular Vesicles to Enhance Their Propensity to Interact With Inhibitory Siglec Receptors. PMID:35784319
SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. PMID:35776115
The Bioinformatic Study Uncovers Probable Critical Genes Involved in the Pathophysiology of Biliary Atresia. PMID:35774294
FBXO38 Ubiquitin Ligase Controls Sertoli Cell Maturation. PMID:35769260
Methylome-wide analysis of IVF neonates that underwent embryo culture in different media revealed no significant differences. PMID:35768464
Farnesoid X receptor protects against cisplatin-induced acute kidney injury by regulating the transcription of ferroptosis-related genes. PMID:35767918
Network-based machine learning approach to predict immunotherapy response in cancer patients. PMID:35764641
Lymphangiogenesis requires Ang2/Tie/PI3K signaling for VEGFR3 cell-surface expression. PMID:35763346
Context-aware deconvolution of cell-cell communication with Tensor-cell2cell. PMID:35760817
Transcriptomic Profiling of Plaque Psoriasis and Cutaneous T-Cell Subsets during Treatment with Secukinumab. PMID:35757784
Driving innovation for rare skin cancers: utilizing common tumours and machine learning to predict immune checkpoint inhibitor response. PMID:35755000
Pathway importance by graph convolutional network and Shapley additive explanations in gene expression phenotype of diffuse large B-cell lymphoma. PMID:35749395
Model scenarios for cell cycle re-entry in Alzheimer's disease. PMID:35747391
Circulating miRNAs as Potential Biomarkers for Patient Stratification in Bipolar Disorder: A Combined Review and Data Mining Approach. PMID:35741801
Exploring the Core Genes of Schizophrenia Based on Bioinformatics Analysis. PMID:35741729
Identifying the Potential Roles of PBX4 in Human Cancers Based on Integrative Analysis. PMID:35740947
Murine Falcor/LL35 lncRNA Contributes to Glucose and Lipid Metabolism In Vitro and In Vivo. PMID:35740417
Single-cell transcriptome and accessible chromatin dynamics during endocrine pancreas development. PMID:35733248
Host CLIC4 expression in the tumor microenvironment is essential for breast cancer metastatic competence. PMID:35727842
An 8-Gene Signature for Classifying Major Subtypes of Non-Small-Cell Lung Cancer. PMID:35722224
C1QTNF3 is Upregulated During Subcutaneous Adipose Tissue Remodeling and Stimulates Macrophage Chemotaxis and M1-Like Polarization. PMID:35720277
Identification of Differentially Expressed Genes and miRNAs for Ulcerative Colitis Using Bioinformatics Analysis. PMID:35719390
Network Control Models With Personalized Genomics Data for Understanding Tumor Heterogeneity in Cancer. PMID:35712516
Identification of Prognosis-Related Molecular Subgroups and Construction of a Prognostic Prediction Model Using Immune-Related Genes in Pancreatic Cancer. PMID:35712127
Mechanical Strain Induces Transcriptomic Reprogramming of Saphenous Vein Progenitors. PMID:35711359
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
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data. PMID:35710789
T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles. PMID:35710644
Premature Infants Have Normal Maturation of the T Cell Receptor Repertoire at Term. PMID:35707545
Elucidating gene expression patterns across multiple biological contexts through a large-scale investigation of transcriptomic datasets. PMID:35705903
Enhancing the REMBRANDT MRI collection with expert segmentation labels and quantitative radiomic features. PMID:35701399
Host protease activity classifies pneumonia etiology. PMID:35696579
The Olfactory Organ Is a Unique Site for Neutrophils in the Brain. PMID:35693773
Decoding the Mechanism behind the Pathogenesis of the Focal Segmental Glomerulosclerosis. PMID:35693262
SARS-CoV-2 infection impairs the insulin/IGF signaling pathway in the lung, liver, adipose tissue, and pancreatic cells via IRF1. PMID:35688210
Deriving time-concordant event cascades from gene expression data: A case study for Drug-Induced Liver Injury (DILI). PMID:35687583
Role of Nucleolin in Endometrial Precancerous Hyperplasia and Carcinogenesis: Ex Vivo and In Silico Study. PMID:35682908
The AKT1E17K Allele Promotes Breast Cancer in Mice. PMID:35681625
Chronic Chemogenetic Activation of the Superior Colliculus in Glaucomatous Mice: Local and Retrograde Molecular Signature. PMID:35681479
MicroRNAs and other small RNAs in Aedes aegypti saliva and salivary glands following chikungunya virus infection. PMID:35681077
Identification of biomarkers for immunotherapy response in prostate cancer and potential drugs to alleviate immunosuppression. PMID:35680563
An epigenome-wide view of osteoarthritis in primary tissues. PMID:35679866
Gut-derived short-chain fatty acids modulate skin barrier integrity by promoting keratinocyte metabolism and differentiation. PMID:35672452
STAT6 inhibits ferroptosis and alleviates acute lung injury via regulating P53/SLC7A11 pathway. PMID:35668064
Identification of Metabolic Pathways Differentially Regulated in Somatic and Zygotic Embryos of Maritime Pine. PMID:35665168
The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. PMID:35665009
Recapitulation of endogenous 4R tau expression and formation of insoluble tau in directly reprogrammed human neurons. PMID:35659876
Transcriptional profiling of transport mechanisms and regulatory pathways in rat choroid plexus. PMID:35659263
A gene prognostic index from cellular senescence predicting metastasis and radioresistance for prostate cancer. PMID:35658892
Integration of the Salmonella Typhimurium Methylome and Transcriptome Reveals That DNA Methylation and Transcriptional Regulation Are Largely Decoupled under Virulence-Related Conditions. PMID:35658533
The snoGloBe interaction predictor reveals a broad spectrum of C/D snoRNA RNA targets. PMID:35657102
Comprehensive competitive endogenous RNA network analysis reveals EZH2-related axes and prognostic biomarkers in hepatocellular carcinoma. PMID:35656182
JUN and PDGFRA as Crucial Candidate Genes for Childhood Autism Spectrum Disorder. PMID:35655651
Esrrb Regulates Specific Feed-Forward Loops to Transit From Pluripotency Into Early Stages of Differentiation. PMID:35652095
Persister state-directed transitioning and vulnerability in melanoma. PMID:35650266
Characterisation of a nucleo-adhesome. PMID:35650196
Transcriptomic datasets of cancer patients treated with immune-checkpoint inhibitors: a systematic review. PMID:35641998
Target and drug predictions for SARS-CoV-2 infection in hepatocellular carcinoma patients. PMID:35639708
Key gene network related to primary ciliary dyskinesia in hippocampus of patients with Alzheimer's disease revealed by weighted gene co-expression network analysis. PMID:35637434
Single-cell transcriptomics of adult macaque hippocampus reveals neural precursor cell populations. PMID:35637371
LIM Homeobox-2 Suppresses Hallmarks of Adult and Pediatric Liver Cancers by Inactivating MAPK/ERK and Wnt/Beta-Catenin Pathways. PMID:35634422
Chronic Exposure to the Food Additive tBHQ Modulates Expression of Genes Related to SARS-CoV-2 and Influenza Viruses. PMID:35629310
miR-486-5p and miR-22-3p Enable Megakaryocytic Differentiation of Hematopoietic Stem and Progenitor Cells without Thrombopoietin. PMID:35628168
The Circadian Clock in the Retinal Pigment Epithelium Controls the Diurnal Rhythm of Phagocytic Activity. PMID:35628111
miRNA Pattern in Hypoxic Microenvironment of Kidney Cancer-Role of PTEN. PMID:35625614
CDC25C is a prognostic biomarker and correlated with mitochondrial homeostasis in pancreatic adenocarcinoma. PMID:35615982
Identification of Differential Genes of DNA Methylation Associated With Alzheimer's Disease Based on Integrated Bioinformatics and Its Diagnostic Significance. PMID:35615586
Exploration of Potential Biomarker Genes and Pathways in Kawasaki Disease: An Integrated in-Silico Approach. PMID:35615376
Identification and validation of aging-related genes in COPD based on bioinformatics analysis. PMID:35609226
The Overexpression of Fibronectin 1 Promotes Cancer Progression and Associated with M2 Macrophages Polarization in Head and Neck Squamous Cell Carcinoma Patients. PMID:35607361
PqsE Expands and Differentially Modulates the RhlR Quorum Sensing Regulon in Pseudomonas aeruginosa. PMID:35604161
NUF2 Is a Potential Immunological and Prognostic Marker for Non-Small-Cell Lung Cancer. PMID:35600043
Dataset of differentially expressed genes in mouse P12 testes in response to the loss of ATRX in Sertoli cells. PMID:35592768
Adaptation of the gut pathobiont Enterococcus faecalis to deoxycholate and taurocholate bile acids. PMID:35590028
The impact of short-term confinement on human innate immunity. PMID:35589846
Interleukin-4 receptor signaling modulates neuronal network activity. PMID:35587822
Identification and validation of an eight-lncRNA signature that predicts prognosis in patients with esophageal squamous cell carcinoma. PMID:35578166
An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. PMID:35577777
Integrated Analysis of Transcriptome Data Revealed AURKA and KIF20A as Critical Genes in Medulloblastoma Progression. PMID:35574421
High intratumoral dihydrotestosterone is associated with antiandrogen resistance in VCaP prostate cancer xenografts in castrated mice. PMID:35573198
Endophenotype-based in silico network medicine discovery combined with insurance record data mining identifies sildenafil as a candidate drug for Alzheimer's disease. PMID:35572351
NMDA Receptor Antagonists Increase the Release of GLP-1 From Gut Endocrine Cells. PMID:35571112
Immunophenotyping of Acute Inflammatory Exacerbations of Lung Injury Driven by Mutant Surfactant Protein-C: A Role for Inflammatory Eosinophils. PMID:35571100
The Phytotoxin Myrigalone A Triggers a Phased Detoxification Programme and Inhibits Lepidium sativum Seed Germination via Multiple Mechanisms including Interference with Auxin Homeostasis. PMID:35563008
Systems-wide analysis revealed shared and unique responses to moderate and acute high temperatures in the green alga Chlamydomonas reinhardtii. PMID:35562408
Assessing the Potential Prognostic and Immunological Role of TK1 in Prostate Cancer. PMID:35559045
Identification of potential prognostic biomarkers for hepatocellular carcinoma. PMID:35557563
Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. PMID:35549252
Artificial intelligence in cancer target identification and drug discovery. PMID:35538061
Identification of key gene contributing to vitiligo by immune infiltration. PMID:35535201
Profiling senescent cells in human brains reveals neurons with CDKN2D/p19 and tau neuropathology. PMID:35531351
Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation. PMID:35528975
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
3'untranslated regions of tumor suppressor genes evolved specific features to favor cancer resistance. PMID:35523946
Elucidating Human Milk Oligosaccharide biosynthetic genes through network-based multi-omics integration. PMID:35508452
MTG16 regulates colonic epithelial differentiation, colitis, and tumorigenesis by repressing E protein transcription factors. PMID:35503250
Construction of a lncRNA-associated competing endogenous RNA regulatory network after traumatic brain injury in mouse. PMID:35501920
Low Level of PALMD Contributes to the Metastasis of Uveal Melanoma. PMID:35494064
RNA-seq profiling of tubulointerstitial tissue reveals a potential therapeutic role of dual anti-phosphatase 1 in glomerulonephritis. PMID:35488446
Fluorescent tracking identifies key migratory dendritic cells in the lymph node after radiotherapy. PMID:35487695
Temporal and sex-dependent gene expression patterns in a renal ischemia-reperfusion injury and recovery pig model. PMID:35484379
An Arabidopsis mutant deficient in phosphatidylinositol-4-phosphate kinases ß1 and ß2 displays altered auxin-related responses in roots. PMID:35484296
EBAG9 controls CD8+ T cell memory formation responding to tumor challenge in mice. PMID:35482418
lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p. PMID:35480561
Cancer Progression Gene Expression Profiling Identifies the Urokinase Plasminogen Activator Receptor as a Biomarker of Metastasis in Cutaneous Squamous Cell Carcinoma. PMID:35480116
Icariin: A Potential Molecule for Treatment of Knee Osteoarthritis. PMID:35479319
Human placental proteomics and exon variant studies link AAT/SERPINA1 with spontaneous preterm birth. PMID:35477570
Critical contribution of 3' non-seed base pairing to the in vivo function of the evolutionarily conserved let-7a microRNA. PMID:35476978
Alfalfa (Medicago sativa L.) pho2 mutant plants hyperaccumulate phosphate. PMID:35471600
Streptococcus pyogenes Hijacks Host Glutathione for Growth and Innate Immune Evasion. PMID:35467425
Pseudomonas aeruginosa Initiates a Rapid and Specific Transcriptional Response during Surface Attachment. PMID:35467391
Screening of Medications for Idiopathic Membranous Nephropathy Using Glomerular Whole-Genome Sequencing. PMID:35465008
Mitochondria Dysfunction-Mediated Molecular Subtypes and Gene Prognostic Index for Prostate Cancer Patients Undergoing Radical Prostatectomy or Radiotherapy. PMID:35463369
Characterization of transcriptome diversity and in vitro behavior of primary human high-risk breast cells. PMID:35459280
Recognition of a Novel Gene Signature for Human Glioblastoma. PMID:35456975
Transcriptional Profiling and Deriving a Seven-Gene Signature That Discriminates Active and Latent Tuberculosis: An Integrative Bioinformatics Approach. PMID:35456421
Prolonged Cadmium Exposure Alters Migration Dynamics and Increases Heterogeneity of Human Uterine Fibroid Cells-Insights from Time Lapse Analysis. PMID:35453667
Coexpression reveals conserved gene programs that co-vary with cell type across kingdoms. PMID:35451481
Global expression profiling of CD10 + /CD19 + pre-B lymphoblasts from Hispanic B-ALL patients correlates with comparative TARGET database analysis. PMID:35445848
CCNE1 amplification is synthetic lethal with PKMYT1 kinase inhibition. PMID:35444283
3JC48-3 (methyl 4'-methyl-5-(7-nitrobenzo[c][1,2,5]oxadiazol-4-yl)-[1,1'-biphenyl]-3-carboxylate): a novel MYC/MAX dimerization inhibitor reduces prostate cancer growth. PMID:35440696
Global ubiquitinome profiling identifies NEDD4 as a regulator of Profilin 1 and actin remodelling in neural crest cells. PMID:35440627
An evolutionarily conserved stop codon enrichment at the 5' ends of mammalian piRNAs. PMID:35440552
PELO facilitates PLK1-induced the ubiquitination and degradation of Smad4 and promotes the progression of prostate cancer. PMID:35437307
Genome-wide Identification and Expression Analysis of RcMYB Genes in Rhodiola crenulata. PMID:35432456
The human ion channel TRPM2 modulates cell survival in neuroblastoma through E2F1 and FOXM1. PMID:35428820
Systematic Characterization of the Clinical Relevance of KPNA4 in Pancreatic Ductal Adenocarcinoma. PMID:35425701
Construction of a Joint Prediction Model for the Occurrence of Ischemic Stroke and Acute Myocardial Infarction Based on Bioinformatic Analysis. PMID:35419117
The Arabidopsis F-box protein FBW2 targets AGO1 for degradation to prevent spurious loading of illegitimate small RNA. PMID:35417704
Angiopoietin-like 4 governs diurnal lipoprotein lipase activity in brown adipose tissue. PMID:35413480
Neural network modeling of differential binding between wild-type and mutant CTCF reveals putative binding preferences for zinc fingers 1-2. PMID:35410161
ENPP2 Promoter Methylation Correlates with Decreased Gene Expression in Breast Cancer: Implementation as a Liquid Biopsy Biomarker. PMID:35409077
ELK3 Controls Gastric Cancer Cell Migration and Invasion by Regulating ECM Remodeling-Related Genes. PMID:35409069
Construction of MicroRNA-mRNA Regulatory Network in the Molecular Mechanisms of Bleomycin-Induced Pulmonary Fibrosis. PMID:35402615
BTG2 as a tumor target for the treatment of luminal A breast cancer. PMID:35401805
Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs. PMID:35400088
Molecular mechanisms underlying plasticity in a thermally varying environment. PMID:35397190
The interleukin-1 axis and the tumor immune microenvironment in pancreatic ductal adenocarcinoma. PMID:35395492
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Predictive biomarkers for survival benefit with ramucirumab in urothelial cancer in the RANGE trial. PMID:35388003
Comparative functional genomics identifies an iron-limited bottleneck in a Saccharomyces cerevisiae strain with a cytosolic-localized isobutanol pathway. PMID:35387233
Purinergic Receptors in the Airways: Potential Therapeutic Targets for Asthma? PMID:35386996
Translational Analysis of Moderate to Severe Asthma GWAS Signals Into Candidate Causal Genes and Their Functional, Tissue-Dependent and Disease-Related Associations. PMID:35386986
Network-based stage-specific drug repurposing for Alzheimer's disease. PMID:35386099
Downregulation of KRAB zinc finger proteins in 5-fluorouracil resistant colorectal cancer cells. PMID:35379199
High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways. PMID:35372810
Immunopeptidomic analyses of colorectal cancers with and without microsatellite instability. PMID:35367648
Computational analyses of mechanism of action (MoA): data, methods and integration. PMID:35360890
A Link Between Mitochondrial Dysfunction and the Immune Microenvironment of Salivary Glands in Primary Sjogren's Syndrome. PMID:35359935
Nuclear microRNA-466c regulates Vegfa expression in response to hypoxia. PMID:35358280
LKB1 acts as a critical brake for the glucagon-mediated fasting response. PMID:35357082
Transcript and blood-microbiome analysis towards a blood diagnostic tool for goats affected by Haemonchus contortus. PMID:35354850
Cardiac pericyte reprogramming by MEK inhibition promotes arteriologenesis and angiogenesis of the ischemic heart. PMID:35349488
Viral Mimicry of Interleukin-17A by SARS-CoV-2 ORF8. PMID:35343786
Single-Cell Analysis of Refractory Celiac Disease Demonstrates Inter- and Intra-Patient Aberrant Cell Heterogeneity. PMID:35338007
Machine Learning-Based Identification of Colon Cancer Candidate Diagnostics Genes. PMID:35336739
Transcriptomic Stress Response in Streptococcus mutans following Treatment with a Sublethal Concentration of Chlorhexidine Digluconate. PMID:35336136
Expression of cardiovascular-related microRNAs is altered in L-arginine:glycine amidinotransferase deficient mice. PMID:35332188
Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach. PMID:35328380
Screening the Significant Hub Genes by Comparing Tumor Cells, Normoxic and Hypoxic Glioblastoma Stem-like Cell Lines Using Co-Expression Analysis in Glioblastoma. PMID:35328072
Identification of the TF-miRNA-mRNA co-regulatory networks involved in sepsis. PMID:35322335
A flexible model-free prediction-based framework for feature ranking. PMID:35321091
Macrophage mitochondrial bioenergetics and tissue invasion are boosted by an Atossa-Porthos axis in Drosophila. PMID:35319107
Overexpression of CISD1 Predicts Worse Survival in Hepatocarcinoma Patients. PMID:35313629
Nucleoporin107 mediates female sexual differentiation via Dsx. PMID:35311642
Target-Dependent Coordinated Biogenesis of Secondary MicroRNAs by miR-146a Balances Macrophage Activation Processes. PMID:35311564
Blood SSR1: A Possible Biomarker for Early Prediction of Parkinson's Disease. PMID:35310885
Expression of AtWRI1 and AtDGAT1 during soybean embryo development influences oil and carbohydrate metabolism. PMID:35306726
Establishment of a Combined Diagnostic Model of Abdominal Aortic Aneurysm with Random Forest and Artificial Neural Network. PMID:35299890
Indisulam targets RNA splicing and metabolism to serve as a therapeutic strategy for high-risk neuroblastoma. PMID:35296644
Experimental evolution links post-transcriptional regulation to Leishmania fitness gain. PMID:35294501
Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. PMID:35288651
An integrated bioinformatic investigation of mitochondrial solute carrier family 25 (SLC25) in colon cancer followed by preliminary validation of member 5 (SLC25A5) in tumorigenesis. PMID:35288533
A mobile restriction-modification system provides phage defence and resolves an epigenetic conflict with an antagonistic endonuclease. PMID:35286398
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
Exploring the Communal Pathogenesis, Ferroptosis Mechanism, and Potential Therapeutic Targets of Dilated Cardiomyopathy and Hypertrophic Cardiomyopathy via a Microarray Data Analysis. PMID:35282347
Identification of a seven-gene prognostic signature using the gene expression profile of osteosarcoma. PMID:35282067
Restoration of Default Blood Monocyte-Derived Macrophage Polarization With Adalimumab But Not Etanercept in Rheumatoid Arthritis. PMID:35281074
Energy Metabolism-Related Gene Prognostic Index Predicts Biochemical Recurrence for Patients With Prostate Cancer Undergoing Radical Prostatectomy. PMID:35280985
High-Calcium Microenvironment during the Development of Kidney Calculi Can Promote Phenotypic Transformation of NRK-52E Cells by Inhibiting the Expression of Stromal Interaction Molecule-1. PMID:35274024
Formation of the Mouse Internal Capsule and Cerebral Peduncle: A Pioneering Role for Striatonigral Axons as Revealed in Isl1 Conditional Mutants. PMID:35273083
Human Sex Matters: Y-Linked Lysine Demethylase 5D Drives Accelerated Male Craniofacial Osteogenic Differentiation. PMID:35269444
Diurnal and circadian rhythmicity of the human blood transcriptome overlaps with organ- and tissue-specific expression of a non-human primate. PMID:35264172
Melanoma-Secreted Amyloid Beta Suppresses Neuroinflammation and Promotes Brain Metastasis. PMID:35262173
The schizophrenia-associated variant in SLC39A8 alters protein glycosylation in the mouse brain. PMID:35260802
Regulation of chromatin accessibility by hypoxia and HIF. PMID:35258521
RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history. PMID:35253846
A network-based computational and experimental framework for repurposing compounds toward the treatment of non-alcoholic fatty liver disease. PMID:35252807
Genome-Wide Methylation Profiling in the Thalamus of Scrapie Sheep. PMID:35252421
An Integrated Analysis of the Identified PRPF19 as an Onco-immunological Biomarker Encompassing the Tumor Microenvironment, Disease Progression, and Prognoses in Hepatocellular Carcinoma. PMID:35252202
Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light. PMID:35251080
High RAD51 gene expression is associated with aggressive biology and with poor survival in breast cancer. PMID:35249172
In PD-1+ human colon cancer cells NIVOLUMAB promotes survival and could protect tumor cells from conventional therapies. PMID:35246475
Predicting molecular initiating events using chemical target annotations and gene expression. PMID:35246223
Identification of Crucial Genes and Key Functions in Type 2 Diabetic Hearts by Bioinformatic Analysis. PMID:35242109
Identification of novel therapeutic targets for Fuchs' endothelial corneal dystrophy based on gene bioinformatics analysis. PMID:35239706
Disruption of the circadian clock component BMAL1 elicits an endocrine adaption impacting on insulin sensitivity and liver disease. PMID:35238641
i6mA-Vote: Cross-Species Identification of DNA N6-Methyladenine Sites in Plant Genomes Based on Ensemble Learning With Voting. PMID:35237293
PLK1 inhibition selectively induces apoptosis in ARID1A deficient cells through uncoupling of oxygen consumption from ATP production. PMID:35236967
CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. PMID:35236300
Summarizing internal dynamics boosts differential analysis and functional interpretation of super enhancers. PMID:35234924
CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis. PMID:35234914
Contribution of Host miRNA-223-3p to SARS-CoV-Induced Lung Inflammatory Pathology. PMID:35229638
PUCHI represses early meristem formation in developing lateral roots of Arabidopsis thaliana. PMID:35224628
A Ferroptosis-Related Gene Prognostic Index Associated With Biochemical Recurrence and Radiation Resistance for Patients With Prostate Cancer Undergoing Radical Radiotherapy. PMID:35223835
Identification of NUTF2 as a Candidate Diagnostic and Prognostic Biomarker Associated with Immune Infiltration in Head and Neck Squamous Cell Carcinoma. PMID:35221694
Network meta-analysis of transcriptome expression changes in different manifestations of dengue virus infection. PMID:35220956
An in-frame deletion mutation in the degron tail of auxin coreceptor IAA2 confers resistance to the herbicide 2,4-D in Sisymbrium orientale. PMID:35217601
Identification of Nifurtimox and Chrysin as Anti-Influenza Virus Agents by Clinical Transcriptome Signature Reversion. PMID:35216485
Unlike Chloroquine, Mefloquine Inhibits SARS-CoV-2 Infection in Physiologically Relevant Cells. PMID:35215969
Analysing miRNA-Target Gene Networks in Inflammatory Bowel Disease and Other Complex Diseases Using Transcriptomic Data. PMID:35205414
DRPPM-EASY: A Web-Based Framework for Integrative Analysis of Multi-Omics Cancer Datasets. PMID:35205126
Tissular Genomic Responses to Oral FB1 Exposure in Pigs. PMID:35202111
Hsa-miR-183-5p Modulates Cell Adhesion by Repression of ITGB1 Expression in Prostate Cancer. PMID:35202085
Identification of Potential Cytokinin Responsive Key Genes in Rice Treated With Trans-Zeatin Through Systems Biology Approach. PMID:35198001
PI3K-regulated Glycine N-methyltransferase is required for the development of prostate cancer. PMID:35197445
Th1 cells are dispensable for primary clearance of Chlamydia from the female reproductive tract of mice. PMID:35196366
THRSP identified as a potential hepatocellular carcinoma marker by integrated bioinformatics analysis and experimental validation. PMID:35196258
tensorGSEA: Detecting Differential Pathways in Type 2 Diabetes via Tensor-Based Data Reconstruction. PMID:35195883
SEAseq: a portable and cloud-based chromatin occupancy analysis suite. PMID:35193506
FUS-DDIT3 Fusion Oncoprotein Expression Affects JAK-STAT Signaling in Myxoid Liposarcoma. PMID:35186752
Genotypic Variation of Nitrogen Use Efficiency and Amino Acid Metabolism in Barley. PMID:35185958
Elevated Detection of Dual Antibody B Cells Identifies Lupus Patients With B Cell-Reactive VH4-34 Autoantibodies. PMID:35185888
Identification of Transcriptional Pattern Related to Immune Cell Infiltration With Gene Co-Expression Network in Papillary Thyroid Cancer. PMID:35185791
FET fusion oncoproteins interact with BRD4 and SWI/SNF chromatin remodelling complex subtypes in sarcoma. PMID:35182012
Inferring Causation in Yeast Gene Association Networks With Kernel Logistic Regression. PMID:35173404
Placental methylome reveals a 22q13.33 brain regulatory gene locus associated with autism. PMID:35168652
Aureochromes maintain polyunsaturated fatty acid content in Nannochloropsis oceanica. PMID:35166829
Is Cadmium Toxicity Tissue-Specific? Toxicogenomics Studies Reveal Common and Specific Pathways in Pulmonary, Hepatic, and Neuronal Cell Models. PMID:35163690
Spheroid Culture Differentially Affects Cancer Cell Sensitivity to Drugs in Melanoma and RCC Models. PMID:35163092
Cellular and Gene Expression Response to the Combination of Genistein and Kaempferol in the Treatment of Mucopolysaccharidosis Type I. PMID:35162981
Aging Activates the Immune System and Alters the Regenerative Capacity in the Zebrafish Heart. PMID:35159152
gpuZoo: Cost-effective estimation of gene regulatory networks using the Graphics Processing Unit. PMID:35156023
In silico bioinformatics analysis for identification of differentially expressed genes and therapeutic drug molecules in Glucocorticoid-resistant Multiple myeloma. PMID:35150335
Osmotic stress induces long-term biofilm survival in Liberibacter crescens. PMID:35148684
From environmental adaptation to host survival: Attributes that mediate pathogenicity of Candida auris. PMID:35142597
USP25 Expression in Peripheral Blood Mononuclear Cells Is Associated With Bone Mineral Density in Women. PMID:35141233
A framework to predict the applicability of Oncotype DX, MammaPrint, and E2F4 gene signatures for improving breast cancer prognostic prediction. PMID:35140308
Translocated Legionella pneumophila small RNAs mimic eukaryotic microRNAs targeting the host immune response. PMID:35140216
Age-related long-term response in rat thyroid tissue and plasma after internal low dose exposure to 131I. PMID:35136135
Differential interferon-α subtype induced immune signatures are associated with suppression of SARS-CoV-2 infection. PMID:35131898
Identification of Potential Key Genes and Molecular Mechanisms of Medulloblastoma Based on Integrated Bioinformatics Approach. PMID:35127939
Immune Checkpoint Gene Expression Profiling Identifies Programmed Cell Death Ligand-1 Centered Immunologic Subtypes of Oral and Squamous Cell Carcinoma With Favorable Survival. PMID:35127742
Identification of Key Genes and Pathways Involved in Circulating Tumor Cells in Colorectal Cancer. PMID:35127345
Functional New Transcription Factors (TFs) Associated with Cervical Cancer. PMID:35126951
Estrogen modulation of the pronociceptive effects of serotonin on female rat trigeminal sensory neurons is timing dependent and dosage dependent and requires estrogen receptor alpha. PMID:35121697
Antigen cross-presentation in young tumor-bearing hosts promotes CD8+ T cell terminal differentiation. PMID:35119937
Anota2seq Analysis for Transcriptome-Wide Studies of mRNA Translation. PMID:35119670
Identification of biomarkers in colon cancer based on bioinformatic analysis. PMID:35117850
Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer. PMID:35117727
Comprehensive analysis reveals a four-gene signature in colorectal cancer. PMID:35117487
Screening of hub genes associated with prognosis in non-small cell lung cancer by integrated bioinformatics analysis. PMID:35117319
Comprehensive analysis reveals novel gene signature in head and neck squamous cell carcinoma: predicting is associated with poor prognosis in patients. PMID:35117201
Bioinformatic analysis of long non-coding RNA-associated competing endogenous RNA network in adrenocortical carcinoma. PMID:35116967
Alternatively activated NUSAP1 promotes tumor growth and indicates poor prognosis in hepatocellular carcinoma. PMID:35116752
High expression of TXNDC11 indicated unfavorable prognosis of glioma. PMID:35116356
Surgical Trauma in Mice Modifies the Content of Circulating Extracellular Vesicles. PMID:35116043
Molecular Subtyping Resource: a user-friendly tool for rapid biological discovery from transcriptional data. PMID:35112706
Screening and identification of novel candidate biomarkers of focal cortical dysplasia type II via bioinformatics analysis. PMID:35112146
DDX10 promotes the proliferation and metastasis of colorectal cancer cells via splicing RPL35. PMID:35109823
Convergent clonal selection of donor- and recipient-derived CMV-specific T cells in hematopoietic stem cell transplant patients. PMID:35105810
Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease. PMID:35105355
Systems neuroimmunology: a review of multiomics methodologies to characterize neuroimmunological interactions in spinal and cranial diseases. PMID:35104798
Analytical kinetic model of native tandem promoters in E. coli. PMID:35100257
A Gene Prognostic Index Associated With Epithelial-Mesenchymal Transition Predicting Biochemical Recurrence and Tumor Chemoresistance for Prostate Cancer. PMID:35096608
Making sense of the linear genome, gene function and TADs. PMID:35090532
Early downregulation of hsa-miR-144-3p in serum from drug-naïve Parkinson's disease patients. PMID:35079043
Identification of key regulators in Sarcoidosis through multidimensional systems biological approach. PMID:35075176
Overexpression of chaperonin containing TCP1 subunit 7 has diagnostic and prognostic value for hepatocellular carcinoma. PMID:35073517
Identification of key genes associated with esophageal adenocarcinoma based on bioinformatics analysis. PMID:35071405
Immune response pathways enriched in breast cancer samples with brain metastasis. PMID:35070893
Establishment and characterization of NCC-DMM1-C1, a novel patient-derived cell line of desmoplastic malignant pleural mesothelioma. PMID:35069873
Identification of Characteristic Genes in Whole Blood of Intervertebral Disc Degeneration Patients by Weighted Gene Coexpression Network Analysis (WGCNA). PMID:35069789
Implication of Sphingolipid Metabolism Gene Dysregulation and Cardiac Sphingosine-1-Phosphate Accumulation in Heart Failure. PMID:35052814
MicroRNA-Enriched Exosomes from Different Sources of Mesenchymal Stem Cells Can Differentially Modulate Functions of Immune Cells and Neurogenesis. PMID:35052749
The Alzheimer's disease drug candidate J147 decreases blood plasma fatty acid levels via modulation of AMPK/ACC1 signaling in the liver. PMID:35051863
Identification of key genes and microRNAs for multiple sclerosis using bioinformatics analysis. PMID:35049167
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
A cerebrospinal fluid microRNA analysis: Progressive supranuclear palsy. PMID:35039873
Identification of prognostic biomarkers in papillary renal cell carcinoma and PTTG1 may serve as a biomarker for predicting immunotherapy response. PMID:35037540
RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria. PMID:35037022
Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma. PMID:35036167
Key genes associated with prognosis and metastasis of clear cell renal cell carcinoma. PMID:35036081
PD-L1 interacts with Frizzled 6 to activate β-catenin and form a positive feedback loop to promote cancer stem cell expansion. PMID:35034965
Dictionary learning allows model-free pseudotime estimation of transcriptomic data. PMID:35033004
APOE4 confers transcriptomic and functional alterations to primary mouse microglia. PMID:35031484
Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. PMID:35028612
A method for simultaneous detection of small and long RNA biotypes by ribodepleted RNA-Seq. PMID:35022475
Co-expression of cancer-testis antigens of MAGE-A6 and MAGE-A11 is associated with tumor aggressiveness in patients with bladder cancer. PMID:35022469
Mammalian brain glycoproteins exhibit diminished glycan complexity compared to other tissues. PMID:35022400
A lepidic gene signature predicts patient prognosis and sensitivity to immunotherapy in lung adenocarcinoma. PMID:35016696
[Identification of potential hub genes of Alzheimer's disease by weighted gene co-expression network analysis]. PMID:35012905
Enhancer RNA Expression in Response to Glucocorticoid Treatment in Murine Macrophages. PMID:35011590
The Antibiotic Fosfomycin Mimics the Effects of the Intermediate Metabolites Phosphoenolpyruvate and Glyceraldehyde-3-Phosphate on the Stenotrophomonas maltophilia Transcriptome. PMID:35008587
Anticancer Activities of 9-chloro-6-(piperazin-1-yl)-11H-indeno[1,2-c] quinolin-11-one (SJ10) in Glioblastoma Multiforme (GBM) Chemoradioresistant Cell Cycle-Related Oncogenic Signatures. PMID:35008426
IL-27 induces IFN/STAT1-dependent genes and enhances function of TIGIT+ HIVGag-specific T cells. PMID:35005538
ANXA9 as a novel prognostic biomarker associated with immune infiltrates in gastric cancer. PMID:35003923
Searching beyond the streetlight: Neonicotinoid exposure alters the neurogenomic state of worker honey bees. PMID:35003705
Acute sleep deprivation upregulates serotonin 2A receptors in the frontal cortex of mice via the immediate early gene Egr3. PMID:35001075
Human CD206+ macrophages associate with diabetes and adipose tissue lymphoid clusters. PMID:34990410
Integrative blood-derived epigenetic and transcriptomic analysis reveals the potential regulatory role of DNA methylation in ankylosing spondylitis. PMID:34986893
A versatile and robust cell purification system with an RNA-only circuit composed of microRNA-responsive ON and OFF switches. PMID:34985961
CREB1K292 and HINFPK330 as Putative Common Therapeutic Targets in Alzheimer's and Parkinson's Disease. PMID:34984308
Potential biomarkers and therapeutic targets of idiopathic pulmonary arterial hypertension. PMID:34981661
Fluctuating methylation clocks for cell lineage tracing at high temporal resolution in human tissues. PMID:34980912
CRISPR guides induce gene silencing in plants in the absence of Cas. PMID:34980227
The diagnostic and prognostic significance of small nuclear ribonucleoprotein Sm D1 aberrantly high expression in hepatocellular carcinoma. PMID:34976182
Expression profiling of lncRNAs and mRNAs in placental site trophoblastic tumor (PSTT) by microarray. PMID:34975294
Dysregulated BMP2 in the Placenta May Contribute to Early-Onset Preeclampsia by Regulating Human Trophoblast Expression of Extracellular Matrix and Adhesion Molecules. PMID:34970543
The interaction between the Spt6-tSH2 domain and Rpb1 affects multiple functions of RNA Polymerase II. PMID:34967414
High Expression of CEMIP Correlates Poor Prognosis and the Tumur Microenvironment in Breast Cancer as a Promisingly Prognostic Biomarker. PMID:34966410
Bioinformatics study on different gene expression profiles of fibroblasts and vascular endothelial cells in keloids. PMID:34964740
Sustained experimental activation of FGF8/ERK in the developing chicken spinal cord models early events in ERK-mediated tumorigenesis. PMID:34959031
Bacillus subtilis natto Derivatives Inhibit Enterococcal Biofilm Formation via Restructuring of the Cell Envelope. PMID:34956152
HPV16-LINC00393 Integration Alters Local 3D Genome Architecture in Cervical Cancer Cells. PMID:34950609
Autism-Related Transcription Factors Underlying the Sex-Specific Effects of Prenatal Bisphenol A Exposure on Transcriptome-Interactome Profiles in the Offspring Prefrontal Cortex. PMID:34947998
The Solvent Dimethyl Sulfoxide Affects Physiology, Transcriptome and Secondary Metabolism of Aspergillus flavus. PMID:34947037
hsa_circ_0001275 Is One of a Number of circRNAs Dysregulated in Enzalutamide Resistant Prostate Cancer and Confers Enzalutamide Resistance In Vitro. PMID:34945002
A Gene-Based Machine Learning Classifier Associated to the Colorectal Adenoma-Carcinoma Sequence. PMID:34944753
BET Proteins Regulate Expression of Osr1 in Early Kidney Development. PMID:34944697
C4d Deposition after Allogeneic Renal Transplantation in Rats Is Involved in Initial Apoptotic Cell Clearance. PMID:34944007
An episomal DNA vector platform for the persistent genetic modification of pluripotent stem cells and their differentiated progeny. PMID:34942088
Adipose Tissue Dysfunctions in Response to an Obesogenic Diet Are Reduced in Mice after Transgenerational Supplementation with Omega 3 Fatty Acids. PMID:34940596
TIPE polarity proteins are required for mucosal deployment of T lymphocytes and mucosal defense against bacterial infection. PMID:34939151
sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. PMID:34937774
Identification of potential key genes and functional role of CENPF in osteosarcoma using bioinformatics and experimental analysis. PMID:34934449
Identification of Potential Genetic Biomarkers and Target Genes of Peri-Implantitis Using Bioinformatics Tools. PMID:34931168
Carbon nanotube biocompatibility in plants is determined by their surface chemistry. PMID:34930290
Comprehensive analysis identifies IFI16 as a novel signature associated with overall survival and immune infiltration of skin cutaneous melanoma. PMID:34930258
Characterization of Poldip2 knockout mice: Avoiding incorrect gene targeting. PMID:34928942
Parallel Single-Cell Multiomics Analysis of Neonatal Skin Reveals the Transitional Fibroblast States that Restrict Differentiation into Distinct Fates. PMID:34922949
B cell-related gene signature and cancer immunotherapy response. PMID:34921229
Identification of potential biomarkers for diagnosis of hepatocellular carcinoma. PMID:34917180
Mutations in LRRK2 linked to Parkinson disease sequester Rab8a to damaged lysosomes and regulate transferrin-mediated iron uptake in microglia. PMID:34914695
Col6a1+/CD201+ mesenchymal cells regulate intestinal morphogenesis and homeostasis. PMID:34910257
Deletion of TNFAIP6 Gene in Human Keratinocytes Demonstrates a Role for TSG-6 to Retain Hyaluronan Inside Epidermis. PMID:34909750
RANKL Blockade Reduces Cachexia and Bone Loss Induced by Non-Metastatic Ovarian Cancer in Mice. PMID:34904285
Relation Extraction of Protein Complexes from Dynamic Protein-Protein Interaction Network. PMID:34904064
Supervised Methods for Biomarker Detection from Microarray Experiments. PMID:34902125
Navigating Multi-Scale Cancer Systems Biology Towards Model-Driven Clinical Oncology and Its Applications in Personalized Therapeutics. PMID:34900668
Structural Equation Modeling of In silico Perturbations. PMID:34899830
CoRE-ATAC: A deep learning model for the functional classification of regulatory elements from single cell and bulk ATAC-seq data. PMID:34898596
Analysis of a circRNA-, miRNA-, and mRNA-associated ceRNA network reveals potential biomarkers in preeclampsia a ceRNA network in preeclampsia. PMID:34894939
Comparative transcriptomics of the Djungarian hamster hypothalamus during short photoperiod acclimation and spontaneous torpor. PMID:34894101
CAMML: Multi-Label Immune Cell-Typing and Stemness Analysis for Single-Cell RNA-sequencing. PMID:34890149
Canine DUXC: implications for DUX4 retrotransposition and preclinical models of FSHD. PMID:34888646
Organ Specific Copy Number Variations in Visceral Metastases of Human Melanoma. PMID:34885093
(20S) Ginsenoside Rh2 Exerts Its Anti-Tumor Effect by Disrupting the HSP90A-Cdc37 System in Human Liver Cancer Cells. PMID:34884975
Inference with Transposable Data: Modeling the Effects of Row and Column Correlations. PMID:34880705
Hirschsprung's disease: key microRNAs and target genes. PMID:34880446
Intrinsic Antiviral Activity of Optineurin Prevents Hyperproliferation of a Primary Herpes Simplex Virus Type 2 Infection. PMID:34880107
Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis. PMID:34877936
Sparse Regression in Cancer Genomics: Comparing Variable Selection and Predictions in Real World Data. PMID:34866896
Epigenome-wide association studies: current knowledge, strategies and recommendations. PMID:34863305
Manganese transport by Streptococcus sanguinis in acidic conditions and its impact on growth in vitro and in vivo. PMID:34862691
Large Multicohort Study Reveals a Prostate Cancer Susceptibility Allele at 5p15 Regulating TERT via Androgen Signaling-Orchestrated Chromatin Binding of E2F1 and MYC. PMID:34858826
Predicting Bone Metastasis Using Gene Expression-Based Machine Learning Models. PMID:34858485
The impact of fine particulate matter (PM) on various beneficial functions of human endometrial stem cells through its key regulator SERPINB2. PMID:34857902
NEIL1 and NEIL2 DNA glycosylases modulate anxiety and learning in a cooperative manner in mice. PMID:34857879
Genomics and transcriptomics landscapes associated to changes in insulin sensitivity in response to endurance exercise training. PMID:34857871
A computational exploration of resilience and evolvability of protein-protein interaction networks. PMID:34857859
Why Environmental Biomarkers Work: Transcriptome-Proteome Correlations and Modeling of Multistressor Experiments in the Marine Bacterium Trichodesmium. PMID:34855411
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles. PMID:34850907
The SAGA and NuA4 component Tra1 regulates Candida albicans drug resistance and pathogenesis. PMID:34849885
The zinc cluster transcription factor Rha1 is a positive filamentation regulator in Candida albicans. PMID:34849863
Cross-species transcriptomic signatures predict response to MK2 inhibition in mouse models of chronic inflammation. PMID:34849469
Recurrent integration of human papillomavirus genomes at transcriptional regulatory hubs. PMID:34848725
Glutamine deprivation triggers NAGK-dependent hexosamine salvage. PMID:34844667
Diagnostic and Prognostic Implications of Caspase-1 and PD-L1 Co-Expression Patterns in Myelodysplastic Syndromes. PMID:34830867
Osteopontin Deficiency Ameliorates Prostatic Fibrosis and Inflammation. PMID:34830342
Circulatory Endothelin 1-Regulating RNAs Panel: Promising Biomarkers for Non-Invasive NAFLD/NASH Diagnosis and Stratification: Clinical and Molecular Pilot Study. PMID:34828420
The Identification of RNA Modification Gene PUS7 as a Potential Biomarker of Ovarian Cancer. PMID:34827123
Identification of Genes Potentially Associated with Melanoma Tumorigenesis Through Co-Expression Network Analysis. PMID:34824546
Genes and regulatory mechanisms associated with experimentally-induced bovine respiratory disease identified using supervised machine learning methodology. PMID:34824337
Effects of photodeoxygenation on cell biology using dibenzothiophene S-oxide derivatives as O(3P)-precursors. PMID:34822125
Establishment and characterization of prostate organoids from treatment-naïve patients with prostate cancer. PMID:34820005
Automatic cell type identification methods for single-cell RNA sequencing. PMID:34815832
Interleukin-4 and interleukin-13 induce different metabolic profiles in microglia and macrophages that relate with divergent outcomes after spinal cord injury. PMID:34815787
Functionally distinct roles for eEF2K in the control of ribosome availability and p-body abundance. PMID:34815424
Inheritance of gene expression throughout fruit development in chili pepper. PMID:34811443
A Single Human-Relevant Fast Food Meal Rapidly Reorganizes Metabolomic and Transcriptomic Signatures in a Gut Microbiota-Dependent Manner. PMID:34804604
The Macrophage Reprogramming Ability of Antifolates Reveals Soluble CD14 as a Potential Biomarker for Methotrexate Response in Rheumatoid Arthritis. PMID:34804067
Disruption of β-Catenin-Dependent Wnt Signaling in Colon Cancer Cells Remodels the Microenvironment to Promote Tumor Invasion. PMID:34799404
Identification of Immune-Related Genes for Establishment of Prognostic Index in Hepatocellular Carcinoma. PMID:34796177
CircleBase: an integrated resource and analysis platform for human eccDNAs. PMID:34792166
Identification of Cross-Pathway Connections via Protein-Protein Interactions Linked to Altered States of Metabolic Enzymes in Cervical Cancer. PMID:34790674
The Immune Infiltration in HNSCC and Its Clinical Value: A Comprehensive Study Based on the TCGA and GEO Databases. PMID:34790249
Sharing Biomedical Data Obtained Through Government-Funded Research and Development Projects in Korea. PMID:34788906
Human intestinal bitter taste receptors regulate innate immune responses and metabolic regulators in obesity. PMID:34784295
Peptide-YY3-36/glucagon-like peptide-1 combination treatment of obese diabetic mice improves insulin sensitivity associated with recovered pancreatic β-cell function and synergistic activation of discrete hypothalamic and brainstem neuronal circuitries. PMID:34781035
TRIB1 regulates LDL metabolism through CEBPα-mediated effects on the LDL receptor in hepatocytes. PMID:34779419
Machine learning and network medicine approaches for drug repositioning for COVID-19. PMID:34778851
Nanolipoprotein-Mediated Her2 Protein Transfection Induces Malignant Transformation in Human Breast Acinar Cultures. PMID:34778614
Expression Levels of RAD51 Inversely Correlate with Survival of Glioblastoma Patients. PMID:34771522
ENPP2 Methylation in Health and Cancer. PMID:34769391
Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation. PMID:34769335
Classification and Functional Analysis between Cancer and Normal Tissues Using Explainable Pathway Deep Learning through RNA-Sequencing Gene Expression. PMID:34768960
TRPA1 Expression and Pathophysiology in Immune Cells. PMID:34768891
Histone lysine demethylase 4B regulates general and unique gene expression signatures in hypoxic cancer cells. PMID:34766154
Computational methods for protein localization prediction. PMID:34765098
Cigarette smoking-associated isoform switching and 3' UTR lengthening via alternative polyadenylation. PMID:34763026
The Identified Hub Gene GlcN in Osteoarthritis Progression and Treatment. PMID:34754325
Identification of key molecular markers of acute coronary syndrome using peripheral blood transcriptome sequencing analysis and mRNA-lncRNA co-expression network construction. PMID:34753383
Comparing the epigenetic landscape in myonuclei purified with a PCM1 antibody from a fast/glycolytic and a slow/oxidative muscle. PMID:34752468
Epigenetic signature of chronic low back pain in human T cells. PMID:34746619
Aberrant Methylation and Immune Microenvironment Are Associated With Overexpressed Fibronectin 1: A Diagnostic and Prognostic Target in Head and Neck Squamous Cell Carcinoma. PMID:34746236
Identification of an Autophagy-Related Risk Signature Correlates With Immunophenotype and Predicts Immune Checkpoint Blockade Efficacy of Neuroblastoma. PMID:34746127
Evaluation of ATAD2 as a Potential Target in Hepatocellular Carcinoma. PMID:34738187
Mucosal-Associated Invariant T (MAIT) Cell Dysfunction and PD-1 Expression in Prostate Cancer: Implications for Immunotherapy. PMID:34737749
β-caryophyllene enhances the transcriptional upregulation of cholesterol biosynthesis in breast cancer cells. PMID:34733015
Progenitor translatome changes coordinated by Tsc1 increase perception of Wnt signals to end nephrogenesis. PMID:34732708
Integrative genome-wide analysis of dopaminergic neuron-specific PARIS expression in Drosophila dissects recognition of multiple PPAR-γ associated gene regulation. PMID:34728675
Single-cell RNA-sequencing analysis of the ciliary epithelium and contiguous tissues in the mouse eye. PMID:34717927
Microenvironmental IL-6 inhibits anti-cancer immune responses generated by cytotoxic chemotherapy. PMID:34711820
A cis-regulatory element promoting increased transcription at low temperature in cultured ectothermic Drosophila cells. PMID:34711176
Molecular characterization of hematopoietic stem cells after in vitro amplification on biomimetic 3D PDMS cell culture scaffolds. PMID:34707135
Breast cancer dormancy is associated with a 4NG1 state and not senescence. PMID:34707097
Hypomethylation and downregulation of miR-23b-3p are associated with upregulated PLAU: a diagnostic and prognostic biomarker in head and neck squamous cell carcinoma. PMID:34702271
PIM1 phosphorylation of the androgen receptor and 14-3-3 ζ regulates gene transcription in prostate cancer. PMID:34697370
Colon Cancer Progression Is Reflected to Monotonic Differentiation in Gene Expression and Pathway Deregulation Facilitating Stage-specific Drug Repurposing. PMID:34697067
Identification of C3 and FN1 as potential biomarkers associated with progression and prognosis for clear cell renal cell carcinoma. PMID:34688260
Nkx3-1 and Fech genes might be switch genes involved in pituitary non-functioning adenoma invasiveness. PMID:34686726
Nanosecond Pulsed Electric Field Only Transiently Affects the Cellular and Molecular Processes of Leydig Cells. PMID:34681896
Trends in oligomannosylation and α1,2-mannosidase expression in human cancers. PMID:34676051
Construction and Investigation of Competing Endogenous RNA Networks and Candidate Genes Involved in SARS-CoV-2 Infection. PMID:34675627
Proteomic analysis of the host-pathogen interface in experimental cholera. PMID:34675415
Global Histone H3 Lysine 4 Trimethylation (H3K4me3) Landscape Changes in Response to TGFβ. PMID:34671716
Integrated computational analyses reveal novel insights into the stromal microenvironment of SHH-subtype medulloblastoma. PMID:34667228
Nrd1p identifies aberrant and natural exosomal target messages during the nuclear mRNA surveillance in Saccharomyces cerevisiae. PMID:34664673
Identification of key genes for HNSCC from public databases using bioinformatics analysis. PMID:34663338
Pleiotropic Effects of the P5-Type ATPase SpfA on Stress Response Networks Contribute to Virulence in the Pathogenic Mold Aspergillus fumigatus. PMID:34663092
IL-27 Derived From Macrophages Facilitates IL-15 Production and T Cell Maintenance Following Allergic Hypersensitivity Responses. PMID:34659203
Computational Interspecies Translation Between Alzheimer's Disease Mouse Models and Human Subjects Identifies Innate Immune Complement, TYROBP, and TAM Receptor Agonist Signatures, Distinct From Influences of Aging. PMID:34658769
A robust mean and variance test with application to high-dimensional phenotypes. PMID:34651232
Fasting-mimicking diet prevents high-fat diet effect on cardiometabolic risk and lifespan. PMID:34650272
GNG7 and ADCY1 as diagnostic and prognostic biomarkers for pancreatic adenocarcinoma through bioinformatic-based analyses. PMID:34650124
A brain-specific pgc1α fusion transcript affects gene expression and behavioural outcomes in mice. PMID:34649938
Meta-Analysis illustrates possible role of lipopolysaccharide (LPS)-induced tissue injury in nasopharyngeal carcinoma (NPC) pathogenesis. PMID:34648530
A novel m6A-related prognostic signature for predicting the overall survival of hepatocellular carcinoma patients. PMID:34647424
Oestrogen engages brain MC4R signalling to drive physical activity in female mice. PMID:34646010
The network interplay of interferon and Toll-like receptor signaling pathways in the anti-Candida immune response. PMID:34645905
A mouse-specific retrotransposon drives a conserved Cdk2ap1 isoform essential for development. PMID:34644528
Transcriptional Profiling of the Candida auris Response to Exogenous Farnesol Exposure. PMID:34643421
Comparison of the Metastasis Predictive Potential of mRNA and Long Non-Coding RNA Profiling in Systemically Untreated Breast Cancer. PMID:34638391
Evaluation of Comprehensive Gene Expression and NK Cell-Mediated Killing in Glioblastoma Cell Line-Derived Spheroids. PMID:34638384
The Role of miRNAs 340-5p, 92a-3p, and 381-3p in Patients with Endometriosis: A Plasma and Mesenchymal Stem-Like Cell Study. PMID:34631883
SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. PMID:34622168
Identification of immunization-related new prognostic biomarkers for papillary renal cell carcinoma by integrated bioinformatics analysis. PMID:34620162
Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. PMID:34617965
Lipocalin 2 Is a Regulator During Macrophage Polarization Induced by Soluble Worm Antigens. PMID:34616693
A dual-function RNA balances carbon uptake and central metabolism in Vibrio cholerae. PMID:34612526
Antimelanoma Effects of Concomitant Inhibition of SIRT1 and SIRT3 in BrafV600E/PtenNULL Mice. PMID:34597611
The profile analysis of circular RNAs in cervical cancer. PMID:34596168
A 41-Gene Pair Signature for Predicting the Pathological Response of Locally Advanced Rectal Cancer to Neoadjuvant Chemoradiation. PMID:34595195
The Interactions of Small Proline-Rich Proteins with Late Cornified Envelope Proteins are Involved in the Pathogenesis of Psoriasis. PMID:34594126
Transcriptional profiling of macaque microglia reveals an evolutionary preserved gene expression program. PMID:34589771
Protein Aggregation Is an Early Manifestation of Phospholamban p.(Arg14del)-Related Cardiomyopathy: Development of PLN-R14del-Related Cardiomyopathy. PMID:34587756
Transcriptome dataset of ethylene-treated Klutuk Wulung banana. PMID:34584916
Deep learning in cancer diagnosis, prognosis and treatment selection. PMID:34579788
Bioinformatic Analysis for Influential Core Gene Identification and Prognostic Significance in Advanced Serous Ovarian Carcinoma. PMID:34577856
RNA-Seq Provides New Insights into the Gene Expression Changes in Azoarcus olearius BH72 under Nitrogen-Deficient and Replete Conditions beyond the Nitrogen Fixation Process. PMID:34576783
Anaesthesia-Induced Transcriptomic Changes in the Context of Renal Ischemia Uncovered by the Use of a Novel Clamping Device. PMID:34576005
Searching for Biological Function of the Mysterious PA2504 Protein from Pseudomonas aeruginosa. PMID:34575996
Progression Risk Score Estimation Based on Immunostaining Data in Oral Cancer Using Unsupervised Hierarchical Clustering Analysis: A Retrospective Study in Taiwan. PMID:34575686
Dual-Specificity Phosphatase 1 (DUSP1) Has a Central Role in Redox Homeostasis and Inflammation in the Mouse Cochlea. PMID:34572983
The amino acid substitution affects cellular response to mistranslation. PMID:34568909
Position Specific Alternative Splicing and Gene Expression Profiles Along the Tonotopic Axis of Chick Cochlea. PMID:34568429
Limited Impact of Pivalate-Induced Secondary Carnitine Deficiency on Hepatic Transcriptome and Hepatic and Plasma Metabolome in Nursery Pigs. PMID:34564388
Smarca4 Inactivation Promotes Lineage-Specific Transformation and Early Metastatic Features in the Lung. PMID:34561242
Expression and prognosis of CDC45 in cervical cancer based on the GEO database. PMID:34557356
Reciprocal transcription factor networks govern tissue-resident ILC3 subset function and identity. PMID:34556884
ATP-competitive partial antagonists of the IRE1α RNase segregate outputs of the UPR. PMID:34556859
Association between chronic periodontitis and the risk of Alzheimer's disease: combination of text mining and GEO dataset. PMID:34556089
Polymorphic estrogen receptor binding site causes Cd2-dependent sex bias in the susceptibility to autoimmune diseases. PMID:34552089
Elevated Levels of the Escherichia coli nrdAB-Encoded Ribonucleotide Reductase Counteract the Toxicity Caused by an Increased Abundance of the β Clamp. PMID:34543109
The Mutant βE202K Sliding Clamp Protein Impairs DNA Polymerase III Replication Activity. PMID:34543108
Circular RNA repertoires are associated with evolutionarily young transposable elements. PMID:34542406
Programmed Cell Death Protein 1/Programmed Cell Death Ligand-1 Axis activates Intracellular ERK Signaling in Tumor Cells to Mediate Poor Prognosis in T-cell Lymphoma. PMID:34539885
High light and temperature reduce photosynthetic efficiency through different mechanisms in the C4 model Setaria viridis. PMID:34531541
Dynamin-related protein 1 regulates substrate oxidation in skeletal muscle by stabilizing cellular and mitochondrial calcium dynamics. PMID:34529976
Computational drug repositioning of atorvastatin for ulcerative colitis. PMID:34529084
Prognostic impact of a lymphocyte activation-associated gene signature in GBM based on transcriptome analysis. PMID:34527446
Understanding Competitive Endogenous RNA Network Mechanism in Type 1 Diabetes Mellitus Using Computational and Bioinformatics Approaches. PMID:34526791
Meta-analysis of gene expression disease signatures in colonic biopsy tissue from patients with ulcerative colitis. PMID:34521888
The Complex Transcriptional Landscape of Magnetosome Gene Clusters in Magnetospirillum gryphiswaldense. PMID:34519524
Comparative analysis of RNA enrichment methods for preparation of Cryptococcus neoformans RNA sequencing libraries. PMID:34518880
Tissue heterogeneity is prevalent in gene expression studies. PMID:34514392
RNA Sequence Profiling Reveals Unique Immune and Metabolic Features of Breast Cancer Brain Metastases. PMID:34513670
Prediction of the mechanism of miRNAs in laryngeal squamous cell carcinoma based on the miRNA-mRNA regulatory network. PMID:34513340
Identification of Genes Encoding Antimicrobial Proteins in Langerhans Cells. PMID:34512625
Single-Cell RNA Sequencing Reveals Cellular and Transcriptional Changes Associated With M1 Macrophage Polarization in Hidradenitis Suppurativa. PMID:34504848
Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis. PMID:34504668
Mammalian and Invertebrate Models as Complementary Tools for Gaining Mechanistic Insight on Muscle Responses to Spaceflight. PMID:34502375
Investigating the Molecular Processes behind the Cell-Specific Toxicity Response to Titanium Dioxide Nanobelts. PMID:34502343
Herbaspirillum seropedicae expresses non-phosphorylative pathways for D-xylose catabolism. PMID:34499201
Identification of a novel six-gene signature with potential prognostic and therapeutic value in cervical cancer. PMID:34498424
Scanning mutagenesis of RNA-binding protein ProQ reveals a quality control role for the Lon protease. PMID:34497069
An ADAR1-dependent RNA editing event in the cyclin-dependent kinase CDK13 promotes thyroid cancer hallmarks. PMID:34496885
Functional characterization of a highly specific L-arabinose transporter from Trichoderma reesei. PMID:34496831
Dysregulation of KIF14 regulates the cell cycle and predicts poor prognosis in cervical cancer: a study based on integrated approaches. PMID:34495250
Two distinct Sertoli cell states are regulated via germ cell crosstalk†. PMID:34494084
Direct and Indirect Transcriptional Effects of Abiotic Stress in Zea mays Plants Defective in RNA-Directed DNA Methylation. PMID:34489998
Computational challenges and opportunities in spatially resolved transcriptomic data analysis. PMID:34489425
Disrupting biological sensors of force promotes tissue regeneration in large organisms. PMID:34489407
Carcinogenic effect of adenylosuccinate lyase (ADSL) in prostate cancer development and progression through the cell cycle pathway. PMID:34488772
Dataset for: Modeling chemotherapy induced neurotoxicity with human induced pluripotent stem cell (iPSC)-derived sensory neurons. PMID:34485650
Identification of a prognostic 4-mRNA signature in laryngeal squamous cell carcinoma. PMID:34475994
Loss of a 7q gene, CUX1, disrupts epigenetically driven DNA repair and drives therapy-related myeloid neoplasms. PMID:34473231
A computational approach for identification of core modules from a co-expression network and GWAS data. PMID:34467232
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. PMID:34463615
Reproducibility standards for machine learning in the life sciences. PMID:34462593
N6-methyladenosine (m6A) modification and its clinical relevance in cognitive dysfunctions. PMID:34461609
A multi-objective genetic algorithm to find active modules in multiplex biological networks. PMID:34460810
Annotating cell types in human single-cell RNA-seq data with CellO. PMID:34458864
Transcriptome Alterations of an in vitro-Selected, Moderately Resistant, Two-Row Malting Barley in Response to 3ADON, 15ADON, and NIV Chemotypes of Fusarium graminearum. PMID:34456945
New Insights Into Mitochondrial Dysfunction at Disease Susceptibility Loci in the Development of Type 2 Diabetes. PMID:34456865
PCA-based unsupervised feature extraction for gene expression analysis of COVID-19 patients. PMID:34456333
FluB-RAM and FluB-RANS: Genome Rearrangement as Safe and Efficacious Live Attenuated Influenza B Virus Vaccines. PMID:34452022
Screening and identification of NOTCH1, CDKN2A, and NOS3 as differentially expressed autophagy-related genes in erectile dysfunction. PMID:34447638
Exploring the role of monocyte chemoattractant protein-1 in fibroblast-like synovial cells in rheumatoid arthritis. PMID:34447637
HOXB8 Counteracts MAPK/ERK Oncogenic Signaling in a Chicken Embryo Model of Neoplasia. PMID:34445617
Epidermal PPARγ Is a Key Homeostatic Regulator of Cutaneous Inflammation and Barrier Function in Mouse Skin. PMID:34445339
A Novel Approach for the Discovery of Biomarkers of Radiotherapy Response in Breast Cancer. PMID:34442440
Artificial Intelligence for Alzheimer's Disease: Promise or Challenge? PMID:34441407
Two Auxinic Herbicides Affect Brassica napus Plant Hormone Levels and Induce Molecular Changes in Transcription. PMID:34439819
Transcriptome Analysis Identifies Doublesex and Mab-3 Related Transcription Factor (DMRT3) in Nasal Polyp Epithelial Cells of Patients Suffering from Non-Steroidal Anti-Inflammatory Drug-Exacerbated Respiratory Disease (AERD). PMID:34439758
CCL20/TNF/VEGFA Cytokine Secretory Phenotype of Tumor-Associated Macrophages Is a Negative Prognostic Factor in Cutaneous Melanoma. PMID:34439098
The autoimmune signature of hyperinflammatory multisystem inflammatory syndrome in children. PMID:34437303
The related coactivator complexes SAGA and ATAC control embryonic stem cell self-renewal through acetyltransferase-independent mechanisms. PMID:34433046
Perturbed transcriptional profiles after chronic low dose rate radiation in mice. PMID:34428250
Assessment of the Diagnostic Efficiency of a Liquid Biopsy Assay for Early Detection of Gastric Cancer. PMID:34427680
Genotypic Characteristics of Hepatoblastoma as Detected by Next Generation Sequencing and Their Correlation With Clinical Efficacy. PMID:34426785
INFIMA leverages multi-omics model organism data to identify effector genes of human GWAS variants. PMID:34425882
Loss of Mir146b with aging contributes to inflammation and mitochondrial dysfunction in thioglycollate-elicited peritoneal macrophages. PMID:34423778
Identification of JAK2 and FOXM1 expression as novel candidate biomarkers for predicting the benefit of immunotherapy in lung squamous cell carcinoma. PMID:34422993
Hypoxia-Inducible Factor 2-Alpha Mediated Gene Sets Differentiate Pulmonary Arterial Hypertension. PMID:34422822
CD86 Molecule Might Be a Novel Immune-Related Prognostic Biomarker for Patients With Bladder Cancer by Bioinformatics and Experimental Assays. PMID:34422632
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients. PMID:34421903
Transcriptional Time Course After Rotator Cuff Tear. PMID:34421646
Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes. PMID:34417450
RHPN1‑AS1 promotes ovarian carcinogenesis by sponging miR‑6884‑5p thus releasing TOP2A mRNA. PMID:34414458
Large-scale transcriptome-wide profiling of microRNAs in human placenta and maternal plasma at early to mid gestation. PMID:34412547
Cerium Oxide Nanoparticle Administration to Skeletal Muscle Cells under Different Gravity and Radiation Conditions. PMID:34410709
Chronic social isolation signals starvation and reduces sleep in Drosophila. PMID:34408325
Key features of the environment promoting liver cancer in the absence of cirrhosis. PMID:34408183
Long non-coding RNA RP4-694A7.2 Promotes Hepatocellular Carcinoma Cell Proliferation and Metastasis through the Regulation of PSAT1. PMID:34405023
Transcriptomic analysis of the mouse retina after acute and chronic normobaric and hypobaric hypoxia. PMID:34404875
Human iPS-derived pre-epicardial cells direct cardiomyocyte aggregation expansion and organization in vitro. PMID:34404774
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomics. PMID:34404410
The Rsm (Csr) post-transcriptional regulatory pathway coordinately controls multiple CRISPR-Cas immune systems. PMID:34403463
Metabolic preconditioning in CD4+ T cells restores inducible immune tolerance in lupus-prone mice. PMID:34403367
MiR-508-3p promotes proliferation and inhibits apoptosis of middle ear cholesteatoma cells by targeting PTEN/PI3K/AKT pathway. PMID:34400892
Integrated bioinformatics analysis reveals CDK1 and PLK1 as potential therapeutic targets of lung adenocarcinoma. PMID:34397869
Multi-omics network characterization reveals novel microRNA biomarkers and mechanisms for diagnosis and subtyping of kidney transplant rejection. PMID:34389032
ERK signaling controls productive HIF-1 binding to chromatin and cancer cell adaptation to hypoxia through HIF-1α interaction with NPM1. PMID:34388291
The epithelial potassium channel Kir7.1 is stimulated by progesterone. PMID:34387656
NOTUM promotes thermogenic capacity and protects against diet-induced obesity in male mice. PMID:34385484
Replacement of Nitrite in Meat Products by Natural Bioactive Compounds Results in Reduced Exposure to N-Nitroso Compounds: The PHYTOME Project. PMID:34382747
A merged microarray meta-dataset for transcriptionally profiling colorectal neoplasm formation and progression. PMID:34381057
KAT2A-mediated AR translocation into nucleus promotes abiraterone-resistance in castration-resistant prostate cancer. PMID:34381019
Lack of Interferon (IFN) Regulatory Factor 8 Associated with Restricted IFN-γ Response Augmented Japanese Encephalitis Virus Replication in the Mouse Brain. PMID:34379515
KITlow Cells Mediate Imatinib Resistance in Gastrointestinal Stromal Tumor. PMID:34376580
Human Placental Trophoblasts Infected by Listeria monocytogenes Undergo a Pro-Inflammatory Switch Associated With Poor Pregnancy Outcomes. PMID:34367171
Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. PMID:34367154
Volatile Compounds From Bacillus, Serratia, and Pseudomonas Promote Growth and Alter the Transcriptional Landscape of Solanum tuberosum in a Passively Ventilated Growth System. PMID:34367077
Distinct regulation of hippocampal neuroplasticity and ciliary genes by corticosteroid receptors. PMID:34362910
NAT10 as a potential prognostic biomarker and therapeutic target for HNSCC. PMID:34362389
mRNA Inventory of Extracellular Vesicles from Ustilago maydis. PMID:34356940
The Negative Effect of Protein Phosphatase Z1 Deletion on the Oxidative Stress Tolerance of Candida albicans Is Synergistic with Betamethasone Exposure. PMID:34356919
Delayed Contralateral Nephrectomy Halted Post-Ischemic Renal Fibrosis Progression and Inhibited the Ischemia-Induced Fibromir Upregulation in Mice. PMID:34356879
Yippee like 4 (Ypel4) is essential for normal mouse red blood cell membrane integrity. PMID:34354145
Personalized single-cell networks: a framework to predict the response of any gene to any drug for any patient. PMID:34353329
Tomato transcriptomic response to Tuta absoluta infestation. PMID:34348650
Long non-coding RNA profile study identifies a metabolism-related signature for colorectal cancer. PMID:34344319
Spatial transcriptomics analysis of uterine gene expression in enhancer of zeste homolog 2 conditional knockout mice†. PMID:34344022
The ALPK1 pathway drives the inflammatory response to Campylobacter jejuni in human intestinal epithelial cells. PMID:34339468
Does chronic dietary exposure to the mycotoxin deoxynivalenol affect the porcine hepatic transcriptome when an acute-phase response is initiated through first or second-pass LPS challenge of the liver? PMID:34338001
Identification of response signatures for tankyrase inhibitor treatment in tumor cell lines. PMID:34337362
Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis. PMID:34335581
Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. PMID:34330753
Somatic cell hemoglobin modulates nitrogen oxide metabolism in the human airway epithelium. PMID:34326365
RNA sequencing identifies global transcriptional changes in peripheral CD4+ cells during active oesophagitis and following epicutaneous immunotherapy in eosinophilic oesophagitis. PMID:34322233
On the impact of batch effect correction in TCGA isomiR expression data. PMID:34316700
Transcriptional landscape of PTEN loss in primary prostate cancer. PMID:34311724
Identification of novel survival-related lncRNA-miRNA-mRNA competing endogenous RNA network associated with immune infiltration in colorectal cancer. PMID:34306328
Network Pharmacology-Based Mechanistic Investigation of Jinshui Huanxian Formula Acting on Idiopathic Pulmonary Fibrosis. PMID:34306156
A pH-eQTL Interaction at the RIT2-SYT4 Parkinson's Disease Risk Locus in the Substantia Nigra. PMID:34305570
Myeloid Cells Are Enriched in Tonsillar Crypts, Providing Insight into the Viral Tropism of Human Papillomavirus. PMID:34303699
Investigation of Fascin1, a Marker of Mature Dendritic Cells, Reveals a New Role for IL-6 Signaling in CCR7-Mediated Chemotaxis. PMID:34301846
Whole Blood Transcriptome Characterization of 3xTg-AD Mouse and Its Modulation by Transcranial Direct Current Stimulation (tDCS). PMID:34299250
Genomic and clinical characterization of early T-cell precursor lymphoblastic lymphoma. PMID:34297047
Screening of hub genes and evaluation of the growth regulatory role of CD44 in metastatic prostate cancer. PMID:34296309
IL-1B drives opposing responses in primary tumours and bone metastases; harnessing combination therapies to improve outcome in breast cancer. PMID:34290237
Transcriptomic changes in peripheral blood mononuclear cells with weight loss: systematic literature review and primary data synthesis. PMID:34281497
The methyl donor S-adenosyl methionine reverses the DNA methylation signature of chronic neuropathic pain in mouse frontal cortex. PMID:34278163
Effect of Protein O-Mannosyltransferase (MSMEG_5447) on M. smegmatis and Its Survival in Macrophages. PMID:34276591
Differential Packaging Into Outer Membrane Vesicles Upon Oxidative Stress Reveals a General Mechanism for Cargo Selectivity. PMID:34276573
The Progenetix oncogenomic resource in 2021. PMID:34272855
Analysis of the Prognostic Value and Gene Expression Mechanism of SHOX2 in Lung Adenocarcinoma. PMID:34262939
Identification of four key biomarkers and small molecule drugs in nasopharyngeal carcinoma by weighted gene co-expression network analysis. PMID:34261404
Deficiency of Antioxidative Paraoxonase 2 (Pon2) Leads to Increased Number of Phenotypic LT-HSCs and Disturbed Erythropoiesis. PMID:34257800
Linking genotype to phenotype in multi-omics data of small sample. PMID:34256701
CD40L modulates transcriptional signatures of neutrophils in the bone marrow associated with development and trafficking. PMID:34255742
Accurate transcriptome assembly by Nanopore RNA sequencing reveals novel functional transcripts in hepatocellular carcinoma. PMID:34255396
Targeting Bacterial Gyrase with Cystobactamid, Fluoroquinolone, and Aminocoumarin Antibiotics Induces Distinct Molecular Signatures in Pseudomonas aeruginosa. PMID:34254824
Predicting mechanism of action of novel compounds using compound structure and transcriptomic signature coembedding. PMID:34252937
'Single-subject studies'-derived analyses unveil altered biomechanisms between very small cohorts: implications for rare diseases. PMID:34252934
Loss of RND-Type Multidrug Efflux Pumps Triggers Iron Starvation and Lipid A Modifications in Pseudomonas aeruginosa. PMID:34252310
Detecting Differentially Methylated Promoters in Genes Related to Disease Phenotypes Using R. PMID:34250201
Bioinformatics Analysis Reveals Crosstalk Among Platelets, Immune Cells, and the Glomerulus That May Play an Important Role in the Development of Diabetic Nephropathy. PMID:34249963
Role of NRP1 in Bladder Cancer Pathogenesis and Progression. PMID:34249735
Prolonged cadmium exposure alters benign uterine fibroid cell behavior, extracellular matrix components, and TGFB signaling. PMID:34245615
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 viral-mediated pathogenic mechanisms in neurodegenerative diseases using network-based approaches. PMID:34237135
Early inflammation precedes cardiac fibrosis and heart failure in desmoglein 2 murine model of arrhythmogenic cardiomyopathy. PMID:34236518
Combining multiomics and drug perturbation profiles to identify muscle-specific treatments for spinal muscular atrophy. PMID:34236053
DIMEimmune: Robust estimation of infiltrating lymphocytes in CNS tumors from DNA methylation profiles. PMID:34235002
Screening of key biomarkers and immune infiltration in Pulmonary Arterial Hypertension via integrated bioinformatics analysis. PMID:34233597
Active elimination of intestinal cells drives oncogenic growth in organoids. PMID:34233177
Identification of endometriosis-associated genes and pathways based on bioinformatic analysis. PMID:34232189
GNRH1 and LTB4R might be novel immune-related prognostic biomarkers in clear cell renal cell carcinoma (ccRCC). PMID:34229684
Identification of immune-infiltrating cell-related biomarkers in hepatocellular carcinoma based on gene co-expression network analysis. PMID:34218795
Regular football training down-regulates miR-1303 muscle expression in veterans. PMID:34212217
The Placental Response to Guinea Pig Cytomegalovirus Depends Upon the Timing of Maternal Infection. PMID:34211475
Profile of miR-23 Expression and Possible Role in Regulation of Glutamic Acid Decarboxylase during Postnatal Retinal Development. PMID:34209226
Diversity of Rainbow Trout Blood B Cells Revealed by Single Cell RNA Sequencing. PMID:34207643
Cleaning the Medicago Microarray Database to Improve Gene Function Analysis. PMID:34207216
Methylation Status of Corticotropin-Releasing Factor (CRF) Receptor Genes in Colorectal Cancer. PMID:34207031
Serine-Threonine Kinase Receptor-Associated Protein (STRAP) Knockout Decreases the Malignant Phenotype in Neuroblastoma Cell Lines. PMID:34206917
MIR29A Impedes Metastatic Behaviors in Hepatocellular Carcinoma via Targeting LOX, LOXL2, and VEGFA. PMID:34206143
Exploring the Metabolic Heterogeneity of Cancers: A Benchmark Study of Context-Specific Models. PMID:34205912
Statistical Integration of 'Omics Data Increases Biological Knowledge Extracted from Metabolomics Data: Application to Intestinal Exposure to the Mycotoxin Deoxynivalenol. PMID:34205708
Differential Regulation of Gonadotropins as Revealed by Transcriptomes of Distinct LH and FSH Cells of Fish Pituitary. PMID:34204216
TENT4A Non-Canonical Poly(A) Polymerase Regulates DNA-Damage Tolerance via Multiple Pathways That Are Mutated in Endometrial Cancer. PMID:34203408
mRNA-miRNA-lncRNA Regulatory Network in Nonalcoholic Fatty Liver Disease. PMID:34202571
Virus-Host Interaction Gets Curiouser and Curiouser. PART II: Functional Transcriptomics of the E. coli DksA-Deficient Cell upon Phage P1vir Infection. PMID:34200430
Biphasic α2β1 Integrin Expression in Breast Cancer Metastasis to Bone. PMID:34199096
Development of a Novel Live Attenuated Influenza A Virus Vaccine Encoding the IgA-Inducing Protein. PMID:34198994
Tribbles Pseudokinases in Colorectal Cancer. PMID:34198908
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
Genome of the Single Human Chromosome 18 as a "Gold Standard" for Its Transcriptome. PMID:34194472
Pars Pro Toto: Every Single Cell Matters. PMID:34194448
Toll-like receptor 2 induces pathogenicity in Th17 cells and reveals a role for IPCEF in regulating Th17 cell migration. PMID:34192530
Protocol for using heterologous spike-ins to normalize for technical variation in chromatin immunoprecipitation. PMID:34189474
Iron-dependent apoptosis causes embryotoxicity in inflamed and obese pregnancy. PMID:34188052
Conservation genomics reveals pesticide and pathogen exposure in the declining bumble bee Bombus terricola. PMID:34181797
Resistance to different anthracycline chemotherapeutics elicits distinct and actionable primary metabolic dependencies in breast cancer. PMID:34181531
Classifying Medulloblastoma Subgroups Based on Small, Clinically Achievable Gene Sets. PMID:34178626
Predicting Selective RNA Processing and Stabilization Operons in Clostridium spp. PMID:34177856
Bioinformatics analysis of differentially expressed genes and pathways in the development of cervical cancer. PMID:34174849
UniBind: maps of high-confidence direct TF-DNA interactions across nine species. PMID:34174819
Altered expression of SARS-CoV-2 entry and processing genes by Porphyromonas gingivalis-derived lipopolysaccharide, inflammatory cytokines and prostaglandin E2 in human gingival fibroblasts. PMID:34174588
A comprehensive database for integrated analysis of omics data in autoimmune diseases. PMID:34167460
Identification of Independent and Communal Differentially Expressed Genes as Well as Potential Therapeutic Targets in Ischemic Heart Failure and Non-Ischemic Heart Failure. PMID:34163213
Multiomic analysis of the Arabian camel (Camelus dromedarius) kidney reveals a role for cholesterol in water conservation. PMID:34163009
A method to analyze time expression profiles demonstrated in a database of chili pepper fruit development. PMID:34162966
Side effect prediction based on drug-induced gene expression profiles and random forest with iterative feature selection. PMID:34155353
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. PMID:34155239
Duplication and Functional Divergence of Branched-Chain Amino Acid Biosynthesis Genes in Aspergillus nidulans. PMID:34154419
Identification of NAA40 as a Potential Prognostic Marker for Aggressive Liver Cancer Subtypes. PMID:34150665
Identification of a Competing Endogenous RNA Network Related to Immune Signature in Lung Adenocarcinoma. PMID:34149807
Transcriptome Analysis Reveals Putative Target Genes of APETALA3-3 During Early Floral Development in Nigella damascena L. PMID:34149759
hsp-90 and unc-45 depletion induce characteristic transcriptional signatures in coexpression cliques of C. elegans. PMID:34145311
ATP/IL-33-triggered hyperactivation of mast cells results in an amplified production of pro-inflammatory cytokines and eicosanoids. PMID:34142370
Individual B cells transcribe multiple rearranged immunoglobulin light chains in teleost fish. PMID:34142062
DCBLD1 is associated with the integrin signaling pathway and has prognostic value in non-small cell lung and invasive breast carcinoma. PMID:34140574
Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (1): specific signatures of stromal, glandular and luminal epithelial cells. PMID:34139994
Analysis of the transcriptome of bovine endometrial cells isolated by laser micro-dissection (2): impacts of post-partum negative energy balance on stromal, glandular and luminal epithelial cells. PMID:34139988
Transcriptional analysis of sweet corn hybrids in response to crowding stress. PMID:34138910
Endothelial SOCS3 maintains homeostasis and promotes survival in endotoxemic mice. PMID:34138760
The Immunology of Hormone Receptor Positive Breast Cancer. PMID:34135901
The Gene Expression Profile of the Song Control Nucleus HVC Shows Sex Specificity, Hormone Responsiveness, and Species Specificity Among Songbirds. PMID:34135731
Insulin Infusion Is Linked to Increased NPPC Expression in Muscle and Plasma C-type Natriuretic Peptide in Male Dogs. PMID:34131611
Capitalizing on transcriptome profiling to optimize and identify targets for promoting early murine folliculogenesis in vitro. PMID:34131220
Transcriptional drug repositioning and cheminformatics approach for differentiation therapy of leukaemia cells. PMID:34131166
IOAT: an interactive tool for statistical analysis of omics data and clinical data. PMID:34130622
Copy number alterations identify a smoking-associated expression signature predictive of poor outcome in head and neck squamous cell carcinoma. PMID:34130230
AI-guided discovery of the invariant host response to viral pandemics. PMID:34127431
TIMEOR: a web-based tool to uncover temporal regulatory mechanisms from multi-omics data. PMID:34125906
Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers. PMID:34125848
The ChvG-ChvI and NtrY-NtrX Two-Component Systems Coordinately Regulate Growth of Caulobacter crescentus. PMID:34124942
Investigation of the Mechanism of Complement System in Diabetic Nephropathy via Bioinformatics Analysis. PMID:34124269
Murine Blastocysts Release Mature MicroRNAs Into Culture Media That Reflect Developmental Status. PMID:34122510
Exploring the Pathogenesis of Psoriasis Complicated With Atherosclerosis via Microarray Data Analysis. PMID:34122426
Transcriptome Analysis Reveals Cr(VI) Adaptation Mechanisms in Klebsiella sp. Strain AqSCr. PMID:34122372
Identification of Key Biomarkers and Immune Infiltration in Sciatic Nerve of Diabetic Neuropathy BKS-db/db Mice by Bioinformatics Analysis. PMID:34122109
Noncanonical functions of glucocorticoids: A novel role for glucocorticoids in performing multiple beneficial functions in endometrial stem cells. PMID:34120144
Identification of Disease-Specific Hub Biomarkers and Immune Infiltration in Osteoarthritis and Rheumatoid Arthritis Synovial Tissues by Bioinformatics Analysis. PMID:34113405
Exploration of Crucial Mediators for Carotid Atherosclerosis Pathogenesis Through Integration of Microbiome, Metabolome, and Transcriptome. PMID:34108883
Time trajectories in the transcriptomic response to exercise - a meta-analysis. PMID:34108459
Decoding empagliflozin's molecular mechanism of action in heart failure with preserved ejection fraction using artificial intelligence. PMID:34103605
Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation. PMID:34103550
Gene expression changes and DNA damage after ex vivo exposure of peripheral blood cells to various CT photon spectra. PMID:34103547
Type II alveolar epithelial cell-specific loss of RhoA exacerbates allergic airway inflammation through SLC26A4. PMID:34101619
Molecular omics resources should require sex annotation: a call for action. PMID:34099934
A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation. PMID:34099688
HOXA13 in etiology and oncogenic potential of Barrett's esophagus. PMID:34099670
A Dynamic Transcription Factor Signature Along the Colorectal Adenoma-Carcinoma Sequence in Patients With Co-Occurrent Adenoma and Carcinoma. PMID:34094897
Differentially Expressed Genes and Enriched Signaling Pathways in the Adipose Tissue of Obese People. PMID:34093637
Mapping of m6A and Its Regulatory Targets in Prostate Cancer Reveals a METTL3-Low Induction of Therapy Resistance. PMID:34088870
Dynamics of alternative splicing during somatic cell reprogramming reveals functions for RNA-binding proteins CPSF3, hnRNP UL1, and TIA1. PMID:34082786
Continuous Inflammatory Stimulation Leads via Metabolic Plasticity to a Prometastatic Phenotype in Triple-Negative Breast Cancer Cells. PMID:34072893
Transcriptome Profiling of Embryonic Retinal Pigment Epithelium Reprogramming. PMID:34072522
Small RNA-Sequencing: Approaches and Considerations for miRNA Analysis. PMID:34071824
Pivotal Role for Cxcr2 in Regulating Tumor-Associated Neutrophil in Breast Cancer. PMID:34070438
Transcription Factor β-Catenin Plays a Key Role in Fluid Flow Shear Stress-Mediated Glomerular Injury in Solitary Kidney. PMID:34069476
Microarray and qPCR Analysis of Mitochondrial Metabolism Activation during Prenatal and Early Postnatal Development in Rats and Humans with Emphasis on CoQ10 Biosynthesis. PMID:34066731
Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds. PMID:34065673
Application of the Interaction between Tissue Immunohistochemistry Staining and Clinicopathological Factors for Evaluating the Risk of Oral Cancer Progression by Hierarchical Clustering Analysis: A Case-Control Study in a Taiwanese Population. PMID:34063938
Effect of Ecdysterone on the Hepatic Transcriptome and Lipid Metabolism in Lean and Obese Zucker Rats. PMID:34063487
Death Processes in Bovine Theca and Granulosa Cells Modelled and Analysed Using a Systems Biology Approach. PMID:34063056
GeromiRs Are Downregulated in the Tumor Microenvironment during Colon Cancer Colonization of the Liver in a Murine Metastasis Model. PMID:34062897
Deletion of Lats1/2 in adult kidney epithelia leads to renal cell carcinoma. PMID:34060480
GLEANER: a web server for GermLine cycle Expression ANalysis and Epigenetic Roadmap visualization. PMID:34058973
Pro-inflammatory Monocyte Phenotype During Acute Progression of Cerebral Small Vessel Disease. PMID:34055930
Prediction of clinical prognosis in cutaneous melanoma using an immune-related gene pair signature. PMID:34047683
MicroRNA-200c restoration reveals a cytokine profile to enhance M1 macrophage polarization in breast cancer. PMID:34045467
RNA Sequencing Reveals Key Metabolic Pathways Are Modified by Short-Term Whole Egg Consumption. PMID:34041258
In vivo stabilization of endogenous chloroplast RNAs by customized artificial pentatricopeptide repeat proteins. PMID:34037778
MicroRNA in combination with HER2-targeting drugs reduces breast cancer cell viability in vitro. PMID:34035375
Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods. PMID:34031612
NFAT5 Amplifies Antipathogen Responses by Enhancing Chromatin Accessibility, H3K27 Demethylation, and Transcription Factor Recruitment. PMID:34031145
Application of multi-omics data integration and machine learning approaches to identify epigenetic and transcriptomic differences between in vitro and in vivo produced bovine embryos. PMID:34029343
Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome. PMID:34029205
The relationship between cytokine and neutrophil gene network distinguishes SARS-CoV-2-infected patients by sex and age. PMID:34027897
Network-based analysis of key regulatory genes implicated in Type 2 Diabetes Mellitus and Recurrent Miscarriages in Turner Syndrome. PMID:34021221
eVITTA: a web-based visualization and inference toolbox for transcriptome analysis. PMID:34019643
Hub biomarkers for the diagnosis and treatment of glioblastoma based on microarray technology. PMID:34018447
Deep Large-Scale Multitask Learning Network for Gene Expression Inference. PMID:34014778
Identification of the EMT-Related Genes Signature for Predicting Occurrence and Progression in Thyroid Cancer. PMID:34012269
Genome-wide screening of SARS-CoV-2 infection-related genes based on the blood leukocytes sequencing data set of patients with COVID-19. PMID:34009691
Activated mast cells in skeletal muscle can be a potential mediator for cancer-associated cachexia. PMID:34008339
The ApiAP2 factor PfAP2-HC is an integral component of heterochromatin in the malaria parasite Plasmodium falciparum. PMID:33997710
Evaluating the Consistency of Gene Methylation in Liver Cancer Using Bisulfite Sequencing Data. PMID:33996828
Identification of Key Functional Gene Signatures Indicative of Dedifferentiation in Papillary Thyroid Cancer. PMID:33996555
Role of Flt4 in Skin Protection against UVB Radiation: A System Biology Approach. PMID:33995966
Genome-wide analysis of primary microRNA expression using H3K36me3 ChIP-seq data. PMID:33995896
Identifying the Potential Therapeutic Targets for Atopic Dermatitis Through the Immune Infiltration Analysis and Construction of a ceRNA Network. PMID:33994801
Centromere protein N may be a novel malignant prognostic biomarker for hepatocellular carcinoma. PMID:33987018
A surgical method for continuous intraportal infusion of gut microbial metabolites in mice. PMID:33986195
CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity. PMID:33986188
Molecular Regulation of the Melatonin Biosynthesis Pathway in Unipolar and Bipolar Depression. PMID:33981243
Cbl-b deficiency prevents functional but not phenotypic T cell anergy. PMID:33974042
Levels and Characteristics of mRNAs in Spores of Firmicute Species. PMID:33972352
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Interferon-induced degradation of the persistent hepatitis B virus cccDNA form depends on ISG20. PMID:33969602
Role of CCR2+ Myeloid Cells in Inflammation Responses Driven by Expression of a Surfactant Protein-C Mutant in the Alveolar Epithelium. PMID:33968067
Epigenetic dysregulation of immune-related pathways in cancer: bioinformatics tools and visualization. PMID:33963293
Intestinal mucosa-derived DNA methylation signatures in the penetrating intestinal mucosal lesions of Crohn's disease. PMID:33963246
Minimized combinatorial CRISPR screens identify genetic interactions in autophagy. PMID:33956155
Screening and identification of LMNB1 and DLGAP5, two key biomarkers in gliomas. PMID:33956061
Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. PMID:33953180
A cloud-based bioinformatic analytic infrastructure and Data Management Core for the Expanded Program on Immunization Consortium. PMID:33948273
In vivo targets of Salmonella FinO include a FinP-like small RNA controlling copy number of a cohabitating plasmid. PMID:33939833
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. PMID:33937763
Enhancing Fatty Acid Catabolism of Macrophages Within Aberrant Breast Cancer Tumor Microenvironment Can Re-establish Antitumor Function. PMID:33937269
Transcriptome Based Estrogen Related Genes Biomarkers for Diagnosis and Prognosis in Non-small Cell Lung Cancer. PMID:33936178
Leonurine-Repressed miR-18a-5p/SOCS5/JAK2/STAT3 Axis Activity Disrupts CML malignancy. PMID:33935775
SNRPC promotes hepatocellular carcinoma cell motility by inducing epithelial-mesenchymal transition. PMID:33934562
A novel five-gene signature predicts overall survival of patients with hepatocellular carcinoma. PMID:33934539
Induction of stable human FOXP3+ Tregs by a parasite-derived TGF-β mimic. PMID:33929751
Reverse Engineering of Ewing Sarcoma Regulatory Network Uncovers PAX7 and RUNX3 as Master Regulators Associated with Good Prognosis. PMID:33924679
Maternal Heat Stress Alters Expression of Genes Associated with Nutrient Transport Activity and Metabolism in Female Placentae from Mid-Gestating Pigs. PMID:33923747
Hepatic Transcriptome Profiling Reveals Lack of Acsm3 Expression in Polydactylous Rats with High-Fat Diet-Induced Hypertriglyceridemia and Visceral Fat Accumulation. PMID:33923085
Muscle Proteomic and Transcriptomic Profiling of Healthy Aging and Metabolic Syndrome in Men. PMID:33921590
Deciphering the Methylation Landscape in Breast Cancer: Diagnostic and Prognostic Biosignatures through Automated Machine Learning. PMID:33918195
Multi-Layer Picture of Neurodegenerative Diseases: Lessons from the Use of Big Data through Artificial Intelligence. PMID:33917161
Expression Patterns in Reductive Iron Assimilation and Functional Consequences during Phagocytosis of Lichtheimia corymbifera, an Emerging Cause of Mucormycosis. PMID:33916756
Characterization of Type I Interferon-Associated Chemokines and Cytokines in Lacrimal Glands of Nonobese Diabetic Mice. PMID:33916486
Chronic interleukin-1 exposure triggers selection for Cebpa-knockout multipotent hematopoietic progenitors. PMID:33914855
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. PMID:33914028
Identification of therapeutic targets of the hijacked super-enhancer complex in EVI1-rearranged leukemia. PMID:33911178
Transcriptome profiles associated with selenium-deficiency-dependent oxidative stress identify potential diagnostic and therapeutic targets in liver cancer cells. PMID:33907497
VB10, a new blood biomarker for differential diagnosis and recovery monitoring of acute viral and bacterial infections. PMID:33906069
Expression analysis of progesterone‑regulated miRNAs in cells derived from human glioblastoma. PMID:33899118
Immune Subtyping in Latent Tuberculosis. PMID:33897680
eIF4E3 forms an active eIF4F complex during stresses (eIF4FS) targeting mTOR and re-programs the translatome. PMID:33893802
Differences in RNA and microRNA Expression Between PTCH1- and SUFU-mutated Medulloblastoma. PMID:33893086
BdERECTA controls vasculature patterning and phloem-xylem organization in Brachypodium distachyon. PMID:33892630
AGAP2-AS1 May Promote the Occurrence and Development of Glioblastoma by Sponging miR-9-5p: Evidence From a ceRNA Network. PMID:33889541
Identification of transcriptional subtypes in lung adenocarcinoma and squamous cell carcinoma through integrative analysis of microarray and RNA sequencing data. PMID:33888829
ARABIDOPSIS THALIANA HOMEOBOX GENE 1 controls plant architecture by locally restricting environmental responses. PMID:33888582
T cell self-reactivity during thymic development dictates the timing of positive selection. PMID:33884954
Nuclear receptors FXR and SHP regulate protein N-glycan modifications in the liver. PMID:33883138
Transcriptomic alterations in malignant pleural mesothelioma cells in response to long‑term treatment with bullfrog sialic acid‑binding lectin. PMID:33880588
Loss of α2-6 sialylation promotes the transformation of synovial fibroblasts into a pro-inflammatory phenotype in arthritis. PMID:33879788
The bone microenvironment increases phenotypic plasticity of ER+ breast cancer cells. PMID:33878299
A Case of Gene Fragmentation in Plant Mitochondria Fixed by the Selection of a Compensatory Restorer of Fertility-Like PPR Gene. PMID:33878189
Identification of a micropeptide and multiple secondary cell genes that modulate Drosophila male reproductive success. PMID:33876742
Fibroblast-Specific Proteotranscriptomes Reveal Distinct Fibrotic Signatures of Human Sinoatrial Node in Nonfailing and Failing Hearts. PMID:33874740
Prognostic Signature for Lung Adenocarcinoma Patients Based on Cell-Cycle-Related Genes. PMID:33869220
In silico Design for Systems-Based Metabolic Engineering for the Bioconversion of Valuable Compounds From Industrial By-Products. PMID:33868371
Artificial intelligence to deep learning: machine intelligence approach for drug discovery. PMID:33844136
Delta-like 4 is required for pulmonary vascular arborization and alveolarization in the developing lung. PMID:33830085
Altered Responsiveness to TGFβ and BMP and Increased CD45+ Cell Presence in Mitral Valves Are Unique Features of Ischemic Mitral Regurgitation. PMID:33827255
Fibrotic expression profile analysis reveals repurposed drugs with potential anti-fibrotic mode of action. PMID:33826640
The effect of calcium and magnesium on activity, immunogenicity, and efficacy of a recombinant N1/N2 neuraminidase vaccine. PMID:33824333
Sequencing error profiles of Illumina sequencing instruments. PMID:33817639
Screening of Hub Genes Associated with Pulmonary Arterial Hypertension by Integrated Bioinformatic Analysis. PMID:33816621
Different Expressions of Pericardial Fluid MicroRNAs in Patients With Arrhythmogenic Right Ventricular Cardiomyopathy and Ischemic Heart Disease Undergoing Ventricular Tachycardia Ablation. PMID:33816578
Spt4 Promotes Pol I Processivity and Transcription Elongation. PMID:33809333
Transcriptome Analyses Throughout Chili Pepper Fruit Development Reveal Novel Insights into the Domestication Process. PMID:33808668
Feature Selection Using Enhanced Particle Swarm Optimisation for Classification Models. PMID:33807806
TNMplot.com: A Web Tool for the Comparison of Gene Expression in Normal, Tumor and Metastatic Tissues. PMID:33807717
Persistent Inflammatory Stimulation Drives the Conversion of MSCs to Inflammatory CAFs That Promote Pro-Metastatic Characteristics in Breast Cancer Cells. PMID:33806906
Analysis of mir-9 Expression Pattern in Rat Retina during Postnatal Development. PMID:33806574
Voluntary Wheel Running Did Not Alter Gene Expression in 5xfad Mice, but in Wild-Type Animals Exclusively after One-Day of Physical Activity. PMID:33804749
Implication of EZH2 in the Pro-Proliferative and Apoptosis-Resistant Phenotype of Pulmonary Artery Smooth Muscle Cells in PAH: A Transcriptomic and Proteomic Approach. PMID:33803922
Identification of Hub Genes and Key Pathways Associated with Anti-VEGF Resistant Glioblastoma Using Gene Expression Data Analysis. PMID:33803224
The Role of Network Science in Glioblastoma. PMID:33801334
CRISPR-Cas9-Mediated TIM3 Knockout in Human Natural Killer Cells Enhances Growth Inhibitory Effects on Human Glioma Cells. PMID:33800561
Swine Inflammation and Necrosis Syndrome Is Associated with Plasma Metabolites and Liver Transcriptome in Affected Piglets. PMID:33799520
Signal-mediated localization of Candida albicans pheromone response pathway components. PMID:33793759
Effector and regulator: Diverse functions of C. elegans C-type lectin-like domain proteins. PMID:33793670
Proteomics study on the effect of silybin on cardiomyopathy in obese mice. PMID:33785854
Six genes involved in prognosis of hepatocellular carcinoma identified by Cox hazard regression. PMID:33784984
Large-scale labeling and assessment of sex bias in publicly available expression data. PMID:33784977
Randomized Controlled Trial of the Gastrin/CCK2 Receptor Antagonist Netazepide in Patients with Barrett's Esophagus. PMID:33782049
Gene Set Knowledge Discovery with Enrichr. PMID:33780170
Benefits of Airway Androgen Receptor Expression in Human Asthma. PMID:33779531
The Burkholderia pseudomallei intracellular 'TRANSITome'. PMID:33772012
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
Colon epithelial cell TGFβ signaling modulates the expression of tight junction proteins and barrier function in mice. PMID:33759564
Transcriptomic insight into the translational value of two murine models in human atopic dermatitis. PMID:33758305
GAUGE-Annotated Microbial Transcriptomic Data Facilitate Parallel Mining and High-Throughput Reanalysis To Form Data-Driven Hypotheses. PMID:33758032
Overexpression of CCNE1 confers a poorer prognosis in triple-negative breast cancer identified by bioinformatic analysis. PMID:33757543
GPRC5A: An emerging prognostic biomarker for predicting malignancy of Pancreatic Cancer based on bioinformatics analysis. PMID:33753999
Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias. PMID:33753942
Inducible mechanisms of disease tolerance provide an alternative strategy of acquired immunity to malaria. PMID:33752799
Transcriptomic analysis of feminizing somatic stem cells in the Drosophila testis reveals putative downstream effectors of the transcription factor Chinmo. PMID:33751104
Construction of competitive endogenous RNA network reveals regulatory role of long non-coding RNAs in intracranial aneurysm. PMID:33750300
Appyters: Turning Jupyter Notebooks into data-driven web apps. PMID:33748796
Pleiotropic Roles for the Plasmodium berghei RNA Binding Protein UIS12 in Transmission and Oocyst Maturation. PMID:33747980
Comprehensive In Silico Analysis of a Novel Serum Exosome-Derived Competitive Endogenous RNA Network for Constructing a Prognostic Model for Glioblastoma. PMID:33747903
Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis. PMID:33741943
FTO-mediated cytoplasmic m6Am demethylation adjusts stem-like properties in colorectal cancer cell. PMID:33741917
Enhanced insulin signalling ameliorates C9orf72 hexanucleotide repeat expansion toxicity in Drosophila. PMID:33739284
Global miRNA/proteomic analyses identify miRNAs at 14q32 and 3p21, which contribute to features of chronic iron-exposed fallopian tube epithelial cells. PMID:33737539
Identification of New miRNA-mRNA Networks in the Development of Non-syndromic Cleft Lip With or Without Cleft Palate. PMID:33732700
Using Integrated Bioinformatics Analysis to Identify Abnormally Methylated Differentially Expressed Genes in Hepatocellular Carcinoma. PMID:33732011
Juxtapose: a gene-embedding approach for comparing co-expression networks. PMID:33726666
Modulation of the complex regulatory network for methionine biosynthesis in fungi. PMID:33724418
Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants. PMID:33724187
Protein Biomarkers of Autism Spectrum Disorder Identified by Computational and Experimental Methods. PMID:33716802
Increased expression of MCM4 is associated with poor prognosis in patients with hepatocellular carcinoma. PMID:33708433
Correlation Between Immune Lymphoid Cells and Plasmacytoid Dendritic Cells in Human Colon Cancer. PMID:33708200
Burkholderia cenocepacia transcriptome during the early contacts with giant plasma membrane vesicles derived from live bronchial epithelial cells. PMID:33707642
Exovesicular-Shh confers Imatinib resistance by upregulating Bcl2 expression in chronic myeloid leukemia with variant chromosomes. PMID:33707419
Aging and pathological aging signatures of the brain: through the focusing lens of SIRT6. PMID:33690173
TDP-43 maximizes nerve conduction velocity by repressing a cryptic exon for paranodal junction assembly in Schwann cells. PMID:33689679
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. PMID:33677507
Nerve Growth Factor Neutralization Promotes Oligodendrogenesis by Increasing miR-219a-5p Levels. PMID:33669304
Ccdc113/Ccdc96 complex, a novel regulator of ciliary beating that connects radial spoke 3 to dynein g and the nexin link. PMID:33661892
CD74 is a regulator of hematopoietic stem cell maintenance. PMID:33661886
Protein interacting with C-kinase 1 is involved in epithelial-mesenchymal transformation and suppresses progress of gastric cancer. PMID:33660148
Low expression of NLRP1 is associated with a poor prognosis and immune infiltration in lung adenocarcinoma patients. PMID:33658393
Fetal sex modulates placental microRNA expression, potential microRNA-mRNA interactions, and levels of amino acid transporter expression and substrates: INFAT study subpopulation analysis of n-3 LCPUFA intervention during pregnancy and associations with offspring body composition. PMID:33657992
MMP7 as a potential biomarker of colon cancer and its prognostic value by bioinformatics analysis. PMID:33655961
OXPHOS deficiency activates global adaptation pathways to maintain mitochondrial membrane potential. PMID:33655635
Cancer-Associated Fibroblasts Positively Correlate with Dedifferentiation and Aggressiveness of Thyroid Cancer. PMID:33654411
ATF3-Induced Mammary Tumors Exhibit Molecular Features of Human Basal-Like Breast Cancer. PMID:33652981
SSRE: Cell Type Detection Based on Sparse Subspace Representation and Similarity Enhancement. PMID:33647482
Proximity-dependent Mapping of the Androgen Receptor Identifies Kruppel-like Factor 4 as a Functional Partner. PMID:33640491
The TUTase URT1 connects decapping activators and prevents the accumulation of excessively deadenylated mRNAs to avoid siRNA biogenesis. PMID:33637717
Computational screening of potential glioma-related genes and drugs based on analysis of GEO dataset and text mining. PMID:33635875
Transcriptional and Proteomic Characterization of Telomere-Induced Senescence in a Human Alveolar Epithelial Cell Line. PMID:33634147
Recursive ensemble feature selection provides a robust mRNA expression signature for myalgic encephalomyelitis/chronic fatigue syndrome. PMID:33633136
Identification BCL6 and miR-30 family associating with Ibrutinib resistance in activated B-cell-like diffuse large B-cell lymphoma. PMID:33629212
Identification of candidate repurposable drugs to combat COVID-19 using a signature-based approach. PMID:33627767
Dysregulated gene-associated biomarkers for Alzheimer's disease and aging. PMID:33623715
CHARTS: a web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq data sets. PMID:33622236
High-throughput screening and validation of antibodies against synaptic proteins to explore opioid signaling dynamics. PMID:33619305
Bromodomain proteins regulate human cytomegalovirus latency and reactivation allowing epigenetic therapeutic intervention. PMID:33619107
Inferring perturbation profiles of cancer samples. PMID:33617647
Drought-Induced Root Pressure in Sorghum bicolor. PMID:33613594
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. PMID:33611340
Localized EMT reprograms glial progenitors to promote spinal cord repair. PMID:33609461
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters. PMID:33608280
Complex pleiotropic genetic architecture of evolved heat stress and oxidative stress resistance in the nematode Caenorhabditis remanei. PMID:33605401
Peroxisomal Multifunctional Protein 2 Deficiency Perturbs Lipid Homeostasis in the Retina and Causes Visual Dysfunction in Mice. PMID:33604342
Identification of a non-coding RNA and its putative involvement in the regulation of tetanus toxin synthesis in Clostridium tetani. PMID:33603121
Virus infection of the CNS disrupts the immune-neural-synaptic axis via induction of pleiotropic gene regulation of host responses. PMID:33599611
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Systems biology analysis identifies TNFRSF9 as a functional marker of tumor-infiltrating regulatory T-cell enabling clinical outcome prediction in lung cancer. PMID:33598101
Positioning of nucleosomes containing γ-H2AX precedes active DNA demethylation and transcription initiation. PMID:33594057
Joint probabilistic modeling of single-cell multi-omic data with totalVI. PMID:33589839
Decoding the protein composition of whole nucleosomes with Nuc-MS. PMID:33589837
Concordance of Immune-Related Markers in Lymphocytes and Prefrontal Cortex in Schizophrenia. PMID:33585819
Searching for a Putative Mechanism of RIZ2 Tumor-Promoting Function in Cancer Models. PMID:33585202
Identification of key biomarkers and functional pathways in osteosarcomas with lung metastasis: Evidence from bioinformatics analysis. PMID:33578541
Guidelines for biomarker discovery in endometrium: correcting for menstrual cycle bias reveals new genes associated with uterine disorders. PMID:33576824
Identification and analysis of consensus RNA motifs binding to the genome regulator CTCF. PMID:33575587
Functional networks of co-expressed genes to explore iron homeostasis processes in the pathogenic yeast Candida glabrata. PMID:33575583
Depletion of erythropoietic miR-486-5p and miR-451a improves detectability of rare microRNAs in peripheral blood-derived small RNA sequencing libraries. PMID:33575555
Screening and identification of hub genes in bladder cancer by bioinformatics analysis and KIF11 is a potential prognostic biomarker. PMID:33574944
Microarray Data Mining and Preliminary Bioinformatics Analysis of Hepatitis D Virus-Associated Hepatocellular Carcinoma. PMID:33564675
Knockdown of KIF15 promotes cell apoptosis by activating crosstalk of multiple pathways in ovarian cancer: bioinformatic and experimental analysis. PMID:33564360
Integrated bioinformatic analysis identifies COL4A3, COL4A4, and KCNJ1 as key biomarkers in Wilms tumor. PMID:33564352
Wolbachia and Virus Alter the Host Transcriptome at the Interface of Nucleotide Metabolism Pathways. PMID:33563832
A Grad-seq View of RNA and Protein Complexes in Pseudomonas aeruginosa under Standard and Bacteriophage Predation Conditions. PMID:33563827
Family-effects in the epigenomic response of red blood cells to a challenge test in the European sea bass (Dicentrarchus labrax, L.). PMID:33563212
Flow induces barrier and glycocalyx-related genes and negative surface charge in a lab-on-a-chip human blood-brain barrier model. PMID:33563079
Predicting therapeutic drugs for hepatocellular carcinoma based on tissue-specific pathways. PMID:33561121
Association of microbiota-derived propionic acid and Alzheimer's disease; bioinformatics analysis. PMID:33553012
High-Resolution Mapping of Transcription Initiation in the Asexual Stages of Toxoplasma gondii. PMID:33553008
Transcriptome from opaque cornea of Fanconi anemia patient uncovers fibrosis and two connected players. PMID:33552906
E-cadherin is regulated by GATA-2 and marks the early commitment of mouse hematopoietic progenitors to the basophil and mast cell fates. PMID:33547048
Arabidopsis Mitochondrial Transcription Termination Factor mTERF2 Promotes Splicing of Group IIB Introns. PMID:33546419
Development and verification of an immune-related gene pairs prognostic signature in ovarian cancer. PMID:33543590
Transgenerational supplementation with eicosapentaenoic acid reduced the metabolic consequences on the whole body and skeletal muscle in mice receiving an obesogenic diet. PMID:33543364
Identification of Genes Universally Differentially Expressed in Gastric Cancer. PMID:33542925
Metabolic Versatility of Mycobacterium tuberculosis during Infection and Dormancy. PMID:33540752
Sulfatase 2 Is Associated with Steroid Resistance in Childhood Nephrotic Syndrome. PMID:33540508
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
Identification of RCC Subtype-Specific microRNAs-Meta-Analysis of High-Throughput RCC Tumor microRNA Expression Data. PMID:33535553
ViralLink: An integrated workflow to investigate the effect of SARS-CoV-2 on intracellular signalling and regulatory pathways. PMID:33534793
P2X7 Receptor Induces Pyroptotic Inflammation and Cartilage Degradation in Osteoarthritis via NF-κB/NLRP3 Crosstalk. PMID:33532039
Identification of key miRNA-gene pairs in gastric cancer through integrated analysis of mRNA and miRNA microarray. PMID:33527022
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
Acid pH Strategy Adaptation through NRG1 in Ustilago maydis. PMID:33525315
Identification of Key MicroRNAs and Mechanisms in Prostate Cancer Evolution Based on Biomarker Prioritization Model and Carcinogenic Survey. PMID:33519899
AtxA-Controlled Small RNAs of Bacillus anthracis Virulence Plasmid pXO1 Regulate Gene Expression in trans. PMID:33519762
High Throughput Sequencing of MicroRNA in Rainbow Trout Plasma, Mucus, and Surrounding Water Following Acute Stress. PMID:33519501
Role of an ancient light-harvesting protein of PSI in light absorption and photoprotection. PMID:33514722
Polycythemia Vera and Essential Thrombocythemia Patients Exhibit Unique Serum Metabolic Profiles Compared to Healthy Individuals and Secondary Thrombocytosis Patients. PMID:33513807
Identification of hub lncRNA ceRNAs in multiple sclerosis based on ceRNA mechanisms. PMID:33507382
Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene Regulatory Networks. PMID:33505431
Identification of 37 Heterogeneous Drug Candidates for Treatment of COVID-19 via a Rational Transcriptomics-Based Drug Repurposing Approach. PMID:33504008
Genomic Adaption and Mutational Patterns in a HaCaT Subline Resistant to Alkylating Agents and Ionizing Radiation. PMID:33498964
Parallel in vivo analysis of large-effect autism genes implicates cortical neurogenesis and estrogen in risk and resilience. PMID:33497602
Chitosan modulates Pochonia chlamydosporia gene expression during nematode egg parasitism. PMID:33496078
AbaM Regulates Quorum Sensing, Biofilm Formation, and Virulence in Acinetobacter baumannii. PMID:33495249
Cancers in Agreement? Exploring the Cross-Talk of Cancer Metabolomic and Transcriptomic Landscapes Using Publicly Available Data. PMID:33494351
COL1A1 Is a Potential Prognostic Biomarker and Correlated with Immune Infiltration in Mesothelioma. PMID:33490271
Identification of IL10RA by Weighted Correlation Network Analysis and in vitro Validation of Its Association With Prognosis of Metastatic Melanoma. PMID:33490091
Challenge of Bovine Foot Skin Fibroblasts With Digital Dermatitis Treponemes Identifies Distinct Pathogenic Mechanisms. PMID:33489929
A meta-analysis of comorbidities in COVID-19: Which diseases increase the susceptibility of SARS-CoV-2 infection? PMID:33486379
Mining influential genes based on deep learning. PMID:33482718
CF monocyte-derived macrophages have an attenuated response to extracellular vesicles secreted by airway epithelial cells. PMID:33471607
Enrichment and Correlation Analysis of Serum miRNAs in Comorbidity Between Arnold-Chiari and Tourette Syndrome Contribute to Clarify Their Molecular Bases. PMID:33469418
Reiterative infusions of MSCs improve pediatric osteogenesis imperfecta eliciting a pro-osteogenic paracrine response: TERCELOI clinical trial. PMID:33463067
DNA methylome signatures of prenatal exposure to synthetic glucocorticoids in hippocampus and peripheral whole blood of female guinea pigs in early life. PMID:33462183
Significance of serglycin and its binding partners in autocrine promotion of metastasis in esophageal cancer. PMID:33456569
Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles. PMID:33454752
Systematic analysis of differential rhythmic liver gene expression mediated by the circadian clock and feeding rhythms. PMID:33452134
Decreases in different Dnmt3b activities drive distinct development of hematologic malignancies in mice. PMID:33450231
The pioneer and differentiation factor FOXA2 is a key driver of yolk-sac tumour formation and a new biomarker for paediatric and adult yolk-sac tumours. PMID:33448076
SIX2 and SIX3 coordinately regulate functional maturity and fate of human pancreatic β cells. PMID:33446570
JAZF1, A Novel p400/TIP60/NuA4 Complex Member, Regulates H2A.Z Acetylation at Regulatory Regions. PMID:33445503
Endogenous membrane stress induces T6SS activity in Pseudomonas aeruginosa. PMID:33443205
Prognostic significance of KRT19 in Lung Squamous Cancer. PMID:33442422
AlzGPS: a genome-wide positioning systems platform to catalyze multi-omics for Alzheimer's drug discovery. PMID:33441136
Streamlining data-intensive biology with workflow systems. PMID:33438730
Prognosis Prediction for Colorectal Cancer Patients: A Risk Score Based on The Metabolic-Related Genes. PMID:33437216
Inhibition of microbiota-dependent TMAO production attenuates chronic kidney disease in mice. PMID:33436815
STIM1 Mediates Calcium-Dependent Epigenetic Reprogramming in Pancreatic Cancer. PMID:33436389
Exome-wide evaluation of rare coding variants using electronic health records identifies new gene-phenotype associations. PMID:33432171
Droplet-based mRNA sequencing of fixed and permeabilized cells by CLInt-seq allows for antigen-specific TCR cloning. PMID:33431692
Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys. PMID:33431511
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Whole Transcription Profile of Responders to Anti-TNF Drugs in Pediatric Inflammatory Bowel Disease. PMID:33429950
FAK regulates IL-33 expression by controlling chromatin accessibility at c-Jun motifs. PMID:33420223
Dnmt3b catalytic activity is critical for its tumour suppressor function in lymphomagenesis and is associated with c-Met oncogenic signalling. PMID:33418509
Metabolic reprogramming of the myeloid lineage by Schistosoma mansoni infection persists independently of antigen exposure. PMID:33417618
Transcriptomic analysis identifies organ-specific metastasis genes and pathways across different primary sites. PMID:33413400
Biomechanical Forces Regulate Gene Transcription During Stretch-Mediated Growth of Mammalian Neurons. PMID:33408609
STRA8 induces transcriptional changes in germ cells during spermatogonial development. PMID:33400349
Integrated molecular characterisation of the MAPK pathways in human cancers reveals pharmacologically vulnerable mutations and gene dependencies. PMID:33398072
microRNA Sequencing of CD34+ Sorted Adipose Stem Cells Undergoing Endotheliogenesis. PMID:33397204
Personalized beyond Precision: Designing Unbiased Gold Standards to Improve Single-Subject Studies of Personal Genome Dynamics from Gene Products. PMID:33396440
Pan-Cancer Molecular Patterns and Biological Implications Associated with a Tumor-Specific Molecular Signature. PMID:33396205
Specific MiRNAs in naïve T cells associated with Hepatitis C Virus-induced Hepatocellular Carcinoma. PMID:33391397
High-Pressure-Sprayed Double Stranded RNA Does Not Induce RNA Interference of a Reporter Gene. PMID:33391294
Predicting changes in renal metabolism after compound exposure with a genome-scale metabolic model. PMID:33387578
High Levels of Prebiotic Resistant Starch in Diet Modulate a Specific Pattern of miRNAs Expression Profile Associated to a Better Overall Survival in Pancreatic Cancer. PMID:33383727
HeartBioPortal2.0: new developments and updates for genetic ancestry and cardiometabolic quantitative traits in diverse human populations. PMID:33382884
Epstein-Barr virus LMP1 manipulates the content and functions of extracellular vesicles to enhance metastatic potential of recipient cells. PMID:33382850
Long-term transcriptomic and proteomic effects in Sprague Dawley rat thyroid and plasma after internal low dose 131I exposure. PMID:33382739
Adversarial deconfounding autoencoder for learning robust gene expression embeddings. PMID:33381842
A Multi-Pronged Computational Pipeline for Prioritizing Drug Target Strategies for Latent Tuberculosis. PMID:33381491
USP15 Deubiquitinase Safeguards Hematopoiesis and Genome Integrity in Hematopoietic Stem Cells and Leukemia Cells. PMID:33378683
Identifying biomolecules and constructing a prognostic risk prediction model for recurrence in osteosarcoma. PMID:33376666
Effect of let-7c on the PI3K/Akt/FoxO signaling pathway in hepatocellular carcinoma. PMID:33376529
Transcriptional profiling of the stringent response mutant strain E. coli SR reveals enhanced robustness to large-scale conditions. PMID:33369128
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Development and Validation of an Immune-Related Gene Pair Signature in Skin Cutaneous Melanoma. PMID:33364806
MiRNA-Mediated Subpathway Identification and Network Module Analysis to Reveal Prognostic Markers in Human Pancreatic Cancer. PMID:33362865
Acyl-CoA Thioesterase 8 and 11 as Novel Biomarkers for Clear Cell Renal Cell Carcinoma. PMID:33362855
Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. PMID:33357414
MS4A1 expression and function in T cells in the colorectal cancer tumor microenvironment. PMID:33352466
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
Dynamics of transcriptional and post-transcriptional regulation. PMID:33348360
Denoising Autoencoder, A Deep Learning Algorithm, Aids the Identification of A Novel Molecular Signature of Lung Adenocarcinoma. PMID:33346087
Maternal antioxidant treatment prevents the adverse effects of prenatal stress on the offspring's brain and behavior. PMID:33344732
Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data. PMID:33338399
MuscleAtlasExplorer: a web service for studying gene expression in human skeletal muscle. PMID:33338203
Molecular patterns of isolated tubulitis differ from tubulitis with interstitial inflammation in early indication biopsies of kidney allografts. PMID:33335257
The mTOR regulated RNA-binding protein LARP1 requires PABPC1 for guided mRNA interaction. PMID:33332560
Riproximin Exhibits Diversity in Sugar Binding, and Modulates some Metastasis-Related Proteins with Lectin like Properties in Pancreatic Ductal Adenocarcinoma. PMID:33328982
Aortic Gene Expression Profiles Show How ApoA-I Levels Modulate Inflammation, Lysosomal Activity, and Sphingolipid Metabolism in Murine Atherosclerosis. PMID:33327742
Integrated Multichip Analysis Identifies Potential Key Genes in the Pathogenesis of Nonalcoholic Steatohepatitis. PMID:33324350
Cellular and Molecular Response of Macrophages THP-1 during Co-Culture with Inactive Trichophyton rubrum Conidia. PMID:33322794
Tensor-Decomposition-Based Unsupervised Feature Extraction Applied to Prostate Cancer Multiomics Data. PMID:33322492
Toll-Like Receptor 7 Is Required for Lacrimal Gland Autoimmunity and Type 1 Diabetes Development in Male Nonobese Diabetic Mice. PMID:33322152
Revealing Epigenetic Factors of circRNA Expression by Machine Learning in Various Cellular Contexts. PMID:33319172
Endometriosis Is Associated with a Significant Increase in hTERC and Altered Telomere/Telomerase Associated Genes in the Eutopic Endometrium, an Ex-Vivo and In Silico Study. PMID:33317189
Harmine and Piperlongumine Revert TRIB2-Mediated Drug Resistance. PMID:33316942
Sericin inhibits MDA‑MB‑468 cell proliferation via the PI3K/Akt pathway in triple‑negative breast cancer. PMID:33313947
A bioinformatics analysis on the potential role of ACE2 in cardiac impairment of patients with coronavirus disease 2019. PMID:33313148
Requirement of DNMT1 to orchestrate epigenomic reprogramming for NPM-ALK-driven lymphomagenesis. PMID:33310759
Run or Die in the Evolution of New MicroRNAs-Testing the Red Queen Hypothesis on De Novo New Genes. PMID:33306129
Coagulopathy in Malnourished Mice Is Sexually Dimorphic and Regulated by Nutrient-Sensing Nuclear Receptors. PMID:33305154
PDmethDB: A curated Parkinson's disease associated methylation information database. PMID:33304468
Genetic interaction mapping informs integrative structure determination of protein complexes. PMID:33303586
Tnfaip2/exoc3-driven lipid metabolism is essential for stem cell differentiation and organ homeostasis. PMID:33300287
Transmembrane Prolyl 4-Hydroxylase is a Novel Regulator of Calcium Signaling in Astrocytes. PMID:33298456
Transcriptome Remodeling in Gradual Development of Inverse Resistance between Paclitaxel and Cisplatin in Ovarian Cancer Cells. PMID:33287223
Identification of candidate biomarkers correlated with the pathogenesis and prognosis of breast cancer via integrated bioinformatics analysis. PMID:33285689
Differences in key genes in human alveolar macrophages between phenotypically normal smokers and nonsmokers: diagnostic and prognostic value in lung cancer. PMID:33284895
Next generation sequencing of SARS-CoV-2 genomes: challenges, applications and opportunities. PMID:33279989
A review of COVID-19 biomarkers and drug targets: resources and tools. PMID:33279954
Detection of urinary miRNAs for diagnosis of clear cell renal cell carcinoma. PMID:33277569
MethHC 2.0: information repository of DNA methylation and gene expression in human cancer. PMID:33270889
The microRNA miR-29c-5p inhibits cell proliferation and migration by targeting TMEM98 in head and neck carcinoma. PMID:33257597
An Improved, Assay Platform Agnostic, Absolute Single Sample Breast Cancer Subtype Classifier. PMID:33255759
Manganese Depletion Leads to Multisystem Changes in the Transcriptome of the Opportunistic Pathogen Streptococcus sanguinis. PMID:33250881
PAGER-CoV: a comprehensive collection of pathways, annotated gene-lists and gene signatures for coronavirus disease studies. PMID:33245774
Spontaneous intake of essential oils after a negative postnatal experience has long-term effects on blood transcriptome in chickens. PMID:33244117
Bioinformatics Analysis Identifies a Novel Role of GINS1 Gene in Colorectal Cancer. PMID:33235499
Investigation of drugs affecting hypertension in bevacizumab-treated patients and examination of the impact on the therapeutic effect. PMID:33231381
Active Transposition of Insertion Sequences by Oxidative Stress in Deinococcus geothermalis. PMID:33224109
FHOD formin and SRF promote post-embryonic striated muscle growth through separate pathways in C. elegans. PMID:33221314
Transcriptome profiling of laser-captured crown root primordia reveals new pathways activated during early stages of crown root formation in rice. PMID:33211715
Extracellular traps released by antimicrobial TH17 cells contribute to host defense. PMID:33211671
Biophysical and X-ray structural studies of the (GGGTT)3GGG G-quadruplex in complex with N-methyl mesoporphyrin IX. PMID:33206666
Patrolling monocytes inhibit osteosarcoma metastasis to the lung. PMID:33203789
Sarcolipin Exhibits Abundant RNA Transcription and Minimal Protein Expression in Horse Gluteal Muscle. PMID:33202832
Bile Ductal Transcriptome Identifies Key Pathways and Hub Genes in Clonorchis sinensis-Infected Sprague-Dawley Rats. PMID:33202503
ACVR2B antagonism as a countermeasure to multi-organ perturbations in metastatic colorectal cancer cachexia. PMID:33200567
Mutation bias within oncogene families is related to proliferation-specific codon usage. PMID:33199641
iCLIP analysis of RNA substrates of the archaeal exosome. PMID:33198623
Epidermal Growth Factor Is Essential for the Maintenance of Novel Prostate Epithelial Cells Isolated From Patient-Derived Organoids. PMID:33195205
A Novel Signature of 23 Immunity-Related Gene Pairs Is Prognostic of Cutaneous Melanoma. PMID:33193373
Data mining combined with experiments to validate CEP55 as a prognostic biomarker in colorectal cancer. PMID:33190424
Interleukin-6 (IL-6) deficiency enhances intramembranous osteogenesis following stress fracture in mice. PMID:33181349
Distinct regional ontogeny and activation of tumor associated macrophages in human glioblastoma. PMID:33177572
Co‑expression network analysis identified specific miRNAs and genes in association with slow‑transit constipation. PMID:33174045
Systematic Analysis of Protein-Protein and Gene-Environment Interactions to Decipher the Cognitive Mechanisms of Autism Spectrum Disorder. PMID:33165687
A single-cell atlas and lineage analysis of the adult Drosophila ovary. PMID:33159074
Maximizing the reusability of gene expression data by predicting missing metadata. PMID:33156882
Inhibition of inflammatory signaling in Pax5 mutant cells mitigates B-cell leukemogenesis. PMID:33154497
Unsupervised and supervised learning with neural network for human transcriptome analysis and cancer diagnosis. PMID:33154423
Widespread Traces of Lytic Kaposi Sarcoma-Associated Herpesvirus in Primary Effusion Lymphoma at Single-Cell Resolution. PMID:33154001
The RSC (Remodels the Structure of Chromatin) complex of Candida albicans shows compositional divergence with distinct roles in regulating pathogenic traits. PMID:33151931
Investigation of the potential regulator proteins associated with the expression of major surface protein and dentilisin in Treponema denticola. PMID:33149843
Integrative Analysis of miRNAs Identifies Clinically Relevant Epithelial and Stromal Subtypes of Head and Neck Squamous Cell Carcinoma. PMID:33148669
Expression of EMT-Related Genes in Hybrid E/M Colorectal Cancer Cells Determines Fibroblast Activation and Collagen Remodeling. PMID:33143259
The Antiviral Small-Interfering RNA Pathway Induces Zika Virus Resistance in Transgenic Aedes aegypti. PMID:33142991
Utilizing PacBio Iso-Seq for Novel Transcript and Gene Discovery of Abiotic Stress Responses in Oryza sativa L. PMID:33142722
Whole egg consumption increases gene expression within the glutathione pathway in the liver of Zucker Diabetic Fatty rats. PMID:33141822
Correcting for experiment-specific variability in expression compendia can remove underlying signals. PMID:33140829
Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. PMID:33140449
Functional module detection through integration of single-cell RNA sequencing data with protein-protein interaction networks. PMID:33138772
A Systems Biology Approach to Identifying a Master Regulator That Can Transform the Fast Growing Cellular State to a Slowly Growing One in Early Colorectal Cancer Development Model. PMID:33133158
Identification of Novel Potential Type 2 Diabetes Genes Mediating β-Cell Loss and Hyperglycemia Using Positional Cloning. PMID:33133152
SINEUP long non-coding RNA acts via PTBP1 and HNRNPK to promote translational initiation assemblies. PMID:33130894
The birth of a bacterial tRNA gene by large-scale, tandem duplication events. PMID:33124983
Targeting 14-3-3ζ Overcomes Resistance to Epidermal Growth Factor Receptor-Tyrosine Kinase Inhibitors in Lung Adenocarcinoma via BMP2/Smad/ID1 Signaling. PMID:33123465
Changes in Northern Elephant Seal Skeletal Muscle Following Thirty Days of Fasting and Reduced Activity. PMID:33123026
A long noncoding RNA antisense to ICAM-1 is involved in allergic asthma associated hyperreactive response of airway epithelial cells. PMID:33122732
A CRISPR-Cas9 screen identifies mitochondrial translation as an essential process in latent KSHV infection of human endothelial cells. PMID:33122441
Screening and identification of key genes and pathways in metastatic uveal melanoma based on gene expression using bioinformatic analysis. PMID:33120861
Enzymatic Dissociation Induces Transcriptional and Proteotype Bias in Brain Cell Populations. PMID:33114694
Transcriptomic and Phenotypic Analyses of the Sigma B-Dependent Characteristics and the Synergism between Sigma B and Sigma L in Listeria monocytogenes EGD-e. PMID:33114171
Preparation of Multi-omics Grade Extracellular Vesicles by Density-Based Fractionation of Urine. PMID:33111109
Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia. PMID:33108352
ROS networks: designs, aging, Parkinson's disease and precision therapies. PMID:33106503
Genome-wide identification of accessible chromatin regions in bumblebee by ATAC-seq. PMID:33106500
Response of Pseudomonas aeruginosa to the Innate Immune System-Derived Oxidants Hypochlorous Acid and Hypothiocyanous Acid. PMID:33106346
Integrated Microarray to Identify the Hub miRNAs and Constructed miRNA-mRNA Network in Neuroblastoma Via Bioinformatics Analysis. PMID:33104965
Identification of a Twelve-Gene Signature and Establishment of a Prognostic Nomogram Predicting Overall Survival for Medulloblastoma. PMID:33101383
Derivation of Airway Basal Stem Cells from Human Pluripotent Stem Cells. PMID:33098807
Meta-analysis of Transcriptomic Data Reveals Pathophysiological Modules Involved with Atrial Fibrillation. PMID:33095430
Systems analysis of avascular necrosis of femoral head using integrative data analysis and literature mining delineates pathways associated with disease. PMID:33093559
A Semi-Automated Workflow for FAIR Maturity Indicators in the Life Sciences. PMID:33092028
Identification of a nomogram based on an 8-lncRNA signature as a novel diagnostic biomarker for head and neck squamous cell carcinoma. PMID:33091878
Tumor infiltrating immune cells (TIICs) as a biomarker for prognosis benefits in patients with osteosarcoma. PMID:33087099
Improved personalized survival prediction of patients with diffuse large B-cell Lymphoma using gene expression profiling. PMID:33087075
Comparative transcriptomics reveals hidden issues in the plant response to arthropod herbivores. PMID:33085192
Common gene signatures and key pathways in hypopharyngeal and esophageal squamous cell carcinoma: Evidence from bioinformatic analysis. PMID:33080677
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes. PMID:33074331
Oxidative DNA Damage Accelerates Skin Inflammation in Pristane-Induced Lupus Model. PMID:33072095
Transcriptome analysis of Brucella abortus S19∆per immunized mouse spleen revealed activation of MHC-I and MHC-II pathways. PMID:33062939
Whole transcriptomic network analysis using Co-expression Differential Network Analysis (CoDiNA). PMID:33057419
Activation of the CARD8 Inflammasome Requires a Disordered Region. PMID:33053349
Identification of potential key genes and miRNAs involved in Hepatoblastoma pathogenesis and prognosis. PMID:33051830
Maintenance of Cell Fate by the Polycomb Group Gene Sex Combs Extra Enables a Partial Epithelial Mesenchymal Transition in Drosophila. PMID:33051260
Therapeutic Opportunities for Intestinal Angioectasia- Targeting PPARγ and Oxidative Stress. PMID:33048460
Machine learning approach to integrated endometrial transcriptomic datasets reveals biomarkers predicting uterine receptivity in cattle at seven days after estrous. PMID:33046742
Cell-free DNA Methylation and Transcriptomic Signature Prediction of Pregnancies with Adverse Outcomes. PMID:33045922
Silencing KIF18B enhances radiosensitivity: identification of a promising therapeutic target in sarcoma. PMID:33038765
Bioinformatic Identification of Potential Hub Genes in Muscle-Invasive Bladder Urothelial Carcinoma. PMID:33035117
Joint learning of multiple gene networks from single-cell gene expression data. PMID:33033579
Olfactory Stimulation Regulates the Birth of Neurons That Express Specific Odorant Receptors. PMID:33027656
Conditional expression of HGAL leads to the development of diffuse large B-cell lymphoma in mice. PMID:33024996
Network-based identification genetic effect of SARS-CoV-2 infections to Idiopathic pulmonary fibrosis (IPF) patients. PMID:33024988
Survival Strategies of Pathogenic Candida Species in Human Blood Show Independent and Specific Adaptations. PMID:33024045
H. pylori modulates DC functions via T4SS/TNFα/p38-dependent SOCS3 expression. PMID:33023610
Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium. PMID:33022053
Curated gene expression dataset of differentiating 3T3-L1 adipocytes under pharmacological and genetic perturbations. PMID:33016192
Investigating genetic drivers of dermatomyositis pathogenesis using meta-analysis. PMID:33015383
Screening and Identification of Key Biomarkers in Acquired Lapatinib-Resistant Breast Cancer. PMID:33013420
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
Reanalysis of Gene Expression Profiles of CD4+ T Cells Treated with HIV-1 Latency Reversal Agents. PMID:33007800
Integrative Analysis of Membrane Proteome and MicroRNA Reveals Novel Lung Cancer Metastasis Biomarkers. PMID:33005184
Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise. PMID:33003500
The Cu(II) Reductase RclA Protects Escherichia coli against the Combination of Hypochlorous Acid and Intracellular Copper. PMID:32994322
Sex Steroids Induce Membrane Stress Responses and Virulence Properties in Pseudomonas aeruginosa. PMID:32994320
Reconstruction of lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveals functional lncRNAs in skin cutaneous melanoma. PMID:32993558
Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction. PMID:32992050
Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response. PMID:32989321
Tissue-specific usage of transposable element-derived promoters in mouse development. PMID:32988383
Multiple genetic programs contribute to CD4 T cell memory differentiation and longevity by maintaining T cell quiescence. PMID:32987276
A Prognostic Prediction Model Developed Based on Four CpG Sites and Weighted Correlation Network Analysis Identified DNAJB1 as a Novel Biomarker for Pancreatic Cancer. PMID:32984053
STAB: a spatio-temporal cell atlas of the human brain. PMID:32976581
Amphotericin B Specifically Induces the Two-Component System LnrJK: Development of a Novel Whole-Cell Biosensor for the Detection of Amphotericin-Like Polyenes. PMID:32973732
Landscape of Genome-Wide DNA Methylation of Colorectal Cancer Metastasis. PMID:32971738
MondoA regulates gene expression in cholesterol biosynthesis-associated pathways required for zebrafish epiboly. PMID:32969791
Genome Wide Analysis Points towards Subtype-Specific Diseases in Different Genetic Forms of Amyotrophic Lateral Sclerosis. PMID:32967368
Mining genetic and transcriptomic data using machine learning approaches in Parkinson's disease. PMID:32964109
Deconstructing Stepwise Fate Conversion of Human Fibroblasts to Neurons by MicroRNAs. PMID:32961143
Vitamin D3 receptor polymorphisms regulate T cells and T cell-dependent inflammatory diseases. PMID:32958661
Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer. PMID:32958605
High dimensional model representation of log likelihood ratio: binary classification with SNP data. PMID:32957998
Integrated Bioinformatics analysis and clinical validation reveals that high expression of mucin 1 in intrahepatic cholangiocarcinoma predicts recurrence after curative resection. PMID:32952640
Molecular mechanisms underlying altered neurobehavioural development of female offspring of mothers with polycystic ovary syndrome: FOS-mediated regulation of neurotrophins in placenta. PMID:32949999
Cancer gene expression profiles associated with clinical outcomes to chemotherapy treatments. PMID:32948183
A Non-genetic Mechanism Involving the Integrin β4/Paxillin Axis Contributes to Chemoresistance in Lung Cancer. PMID:32947124
Quantitative mapping of transcriptome and proteome dynamics during polarization of human iPSC-derived neurons. PMID:32940601
Hypoxia inducible factor-2α importance for migration, proliferation, and self-renewal of trunk neural crest cells. PMID:32940375
Analyzing Gene Expression Profiles from Ataxia and Spasticity Phenotypes to Reveal Spastic Ataxia Related Pathways. PMID:32937819
Identification, Validation, and Functional Annotations of Genome-Wide Profile Variation between Melanocytic Nevus and Malignant Melanoma. PMID:32934956
Sterol regulatory element-binding protein Sre1 regulates carotenogenesis in the red yeast Xanthophyllomyces dendrorhous. PMID:32933952
The brlA Gene Deletion Reveals That Patulin Biosynthesis Is Not Related to Conidiation in Penicillium expansum. PMID:32932988
A crucial role for Jagunal homolog 1 in humoral immunity and antibody glycosylation in mice and humans. PMID:32930709
The tRNA pseudouridine synthase TruB1 regulates the maturation of let-7 miRNA. PMID:32926445
Are Antisense Proteins in Prokaryotes Functional? PMID:32923454
Identification and validation of novel metastasis-related signatures of clear cell renal cell carcinoma using gene expression databases. PMID:32913492
A gene prioritization method based on a swine multi-omics knowledgebase and a deep learning model. PMID:32913254
An intact gut microbiome protects genetically predisposed mice against leukemia. PMID:32911536
Network Pharmacology to Uncover the Biological Basis of Spleen Qi Deficiency Syndrome and Herbal Treatment. PMID:32908629
TRIM37 controls cancer-specific vulnerability to PLK4 inhibition. PMID:32908304
The neuromuscular junction is a focal point of mTORC1 signaling in sarcopenia. PMID:32908143
Integrated PPI- and WGCNA-Retrieval of Hub Gene Signatures Shared Between Barrett's Esophagus and Esophageal Adenocarcinoma. PMID:32903837
Nrf2 contributes to the weight gain of mice during space travel. PMID:32901092
The Utility of Resolving Asthma Molecular Signatures Using Tissue-Specific Transcriptome Data. PMID:32900903
Serial Passage of Cryptococcus neoformans in Galleria mellonella Results in Increased Capsule and Intracellular Replication in Hemocytes, but Not Increased Resistance to Hydrogen Peroxide. PMID:32899539
RnhP is a plasmid-borne RNase HI that contributes to genome maintenance in the ancestral strain Bacillus subtilis NCIB 3610. PMID:32896031
Bioinformatic analysis reveals hub genes and pathways that promote melanoma metastasis. PMID:32894090
FOXA1 Mutations Reveal Distinct Chromatin Profiles and Influence Therapeutic Response in Breast Cancer. PMID:32888433
Identification of circular RNA hsa_circ_0044556 and its effect on the progression of colorectal cancer. PMID:32884449
Integrative Analysis of MAPK14 as a Potential Biomarker for Cardioembolic Stroke. PMID:32879891
Transcriptomic analysis across liver diseases reveals disease-modulating activation of constitutive androstane receptor in cholestasis. PMID:32875282
Polar Infection of Echovirus-30 Causes Differential Barrier Affection and Gene Regulation at the Blood-Cerebrospinal Fluid Barrier. PMID:32872518
Dysregulated circulating SOCS3 and haptoglobin expression associated with stable coronary artery disease and acute coronary syndrome: An integrated study based on bioinformatics analysis and case-control validation. PMID:32870172
Dorsoventral inversion of the air-filled organ (lungs, gas bladder) in vertebrates: RNAsequencing of laser capture microdissected embryonic tissue. PMID:32864827
Comprehensive analysis of key genes associated with ceRNA networks in nasopharyngeal carcinoma based on bioinformatics analysis. PMID:32863767
Comparative Transcriptomic Analysis of Cerebral Organoids and Cortical Neuron Cultures Derived from Human Induced Pluripotent Stem Cells. PMID:32862797
Machine learning discriminates a movement disorder in a zebrafish model of Parkinson's disease. PMID:32859696
Identification of key differentially expressed mRNAs and microRNAs in non-small cell lung cancer using bioinformatics analysis. PMID:32855723
Comparative Analysis of the Development of Acquired Radioresistance in Canine and Human Mammary Cancer Cell Lines. PMID:32851022
Systematic Evaluation of the Diagnostic and Prognostic Significance of Competitive Endogenous RNA Networks in Prostate Cancer. PMID:32849794
Target Analysis and Mechanism of Podophyllotoxin in the Treatment of Triple-Negative Breast Cancer. PMID:32848800
Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity. PMID:32847508
Whole transcriptome analysis of bovine mammary progenitor cells by P-Cadherin enrichment as a marker in the mammary cell hierarchy. PMID:32843665
An Integrative Omics Approach Reveals Involvement of BRCA1 in Hepatic Metastatic Progression of Colorectal Cancer. PMID:32842712
SARS-CoV-2 infection dynamics in lungs of African green monkeys. PMID:32839775
Cytomegalovirus infection elicits a conserved chemokine response from human and guinea pig amnion cells. PMID:32838950
Microarray Normalization Revisited for Reproducible Breast Cancer Biomarkers. PMID:32832541
Analyzing the lncRNA, miRNA, and mRNA-associated ceRNA networks to reveal potential prognostic biomarkers for glioblastoma multiforme. PMID:32821246
Cancer-Derived Transforming Growth Factor-β Modulates Tumor-Associated Macrophages in Ampullary Cancer. PMID:32821120
Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides. PMID:32817237
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
Human Tregs at the materno-fetal interface show site-specific adaptation reminiscent of tumor Tregs. PMID:32809975
Targeting Hypoxia Sensitizes TNBC to Cisplatin and Promotes Inhibition of Both Bulk and Cancer Stem Cells. PMID:32806648
Construction and Investigation of MicroRNA-mRNA Regulatory Network of Gastric Cancer with Helicobacter pylori Infection. PMID:32802507
The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes. PMID:32798738
Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. PMID:32796535
Transcriptome profiles acquired during cell expansion and licensing validate mesenchymal stromal cell lineage genes. PMID:32795342
Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension. PMID:32793290
Cysteine and Methionine Biosynthetic Enzymes Have Distinct Effects on Seed Nutritional Quality and on Molecular Phenotypes Associated With Accumulation of a Methionine-Rich Seed Storage Protein in Rice. PMID:32793268
Deregulated High Affinity Copper Transport Alters Iron Homeostasis in Arabidopsis. PMID:32793263
Elucidating the fundamental fibrotic processes driving abdominal adhesion formation. PMID:32792541
Interpretation of psychiatric genome-wide association studies with multispecies heterogeneous functional genomic data integration. PMID:32791514
Genome-wide gene expression analysis of a murine model of prostate cancer progression: Deciphering the roles of IL-6 and p38 MAPK as potential therapeutic targets. PMID:32790767
Gene Expression Network Analysis of Precursor Lesions in Familial Pancreatic Cancer. PMID:32783019
The oxytocin receptor signalling system and breast cancer: a critical review. PMID:32782397
Identification of common and divergent gene expression signatures in patients with venous and arterial thrombosis using data from public repositories. PMID:32780732
Identification of Players Controlling Meristem Arrest Downstream of the FRUITFULL-APETALA2 Pathway. PMID:32778534
Computational Identification of Tumor Suppressor Genes Based on Gene Expression Profiles in Normal and Cancerous Gastrointestinal Tissues. PMID:32774369
Molecular Signatures and Networks of Cardiomyocyte Differentiation in Humans and Mice. PMID:32769060
Transcriptional profiling of lung macrophages during pulmonary injury induced by nitrogen mustard. PMID:32767459
Bioinformatics analysis shows that TOP2A functions as a key candidate gene in the progression of cervical cancer. PMID:32765860
Systems Biology Will Direct Vascular-Targeted Therapy for Obesity. PMID:32760294
Characterization of peripheral blood mononuclear cells gene expression profiles of pediatric Staphylococcus aureus persistent and non-carriers using a targeted assay. PMID:32758644
Eight immune-related genes predict survival outcomes and immune characteristics in breast cancer. PMID:32756008
Escherichia coli Has a Unique Transcriptional Program in Long-Term Stationary Phase Allowing Identification of Genes Important for Survival. PMID:32753505
An interspecies translation model implicates integrin signaling in infliximab-resistant inflammatory bowel disease. PMID:32753478
Aberrant methylation and microRNA-target regulation are associated with downregulated NEURL1B: a diagnostic and prognostic target in colon cancer. PMID:32742189
Dynamical gene regulatory networks are tuned by transcriptional autoregulation with microRNA feedback. PMID:32737375
Absence of Plekhg5 Results in Myelin Infoldings Corresponding to an Impaired Schwann Cell Autophagy, and a Reduced T-Cell Infiltration Into Peripheral Nerves. PMID:32733205
The effect of compound kushen injection on cancer cells: Integrated identification of candidate molecular mechanisms. PMID:32730293
Human Nasal Turbinate Tissues in Organ Culture as a Model for Human Cytomegalovirus Infection at the Mucosal Entry Site. PMID:32727881
Time-Dependent miRNA Profile during Septic Acute Kidney Injury in Mice. PMID:32727087
Protamine-2 Deficiency Initiates a Reactive Oxygen Species (ROS)-Mediated Destruction Cascade during Epididymal Sperm Maturation in Mice. PMID:32727081
Insulin-Like Growth Factor 2 mRNA-Binding Protein 3 Modulates Aggressiveness of Ewing Sarcoma by Regulating the CD164-CXCR4 Axis. PMID:32719743
Inflammatory state of lymphatic vessels and miRNA profiles associated with relapse in ovarian cancer patients. PMID:32716937
Preeclamptic placentae release factors that damage neurons: implications for foetal programming of disease. PMID:32714596
Study on the Selection of the Targets of Esophageal Carcinoma and Interventions of Ginsenosides Based on Network Pharmacology and Bioinformatics. PMID:32714406
Integrative Network Biology Framework Elucidates Molecular Mechanisms of SARS-CoV-2 Pathogenesis. PMID:32714115
Absence of cGAS-mediated type I IFN responses in HIV-1-infected T cells. PMID:32709741
Loss of Tdp-43 disrupts the axonal transcriptome of motoneurons accompanied by impaired axonal translation and mitochondria function. PMID:32709255
Pre-Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy. PMID:32708981
Exploring Drug Treatment Patterns Based on the Action of Drug and Multilayer Network Model. PMID:32708644
Cell-Type Specificity of Genomic Imprinting in Cerebral Cortex. PMID:32707083
Membrane budding is a major mechanism of in vivo platelet biogenesis. PMID:32706855
A chemical biology approach to identifying molecular pathways associated with aging. PMID:32705410
Cross‑validation of genes potentially associated with neoadjuvant chemotherapy and platinum‑based chemoresistance in epithelial ovarian carcinoma. PMID:32705213
EGF-mediated reduced miR-92a-1-5p controls HTR-8/SVneo cell invasion through activation of MAPK8 and FAS which in turn increase MMP-2/-9 expression. PMID:32703964
Identification of key genes in calcific aortic valve disease by integrated bioinformatics analysis. PMID:32702920
Identification of new drug treatments to combat COVID19: A signature-based approach using iLINCS. PMID:32702077
Identifying the novel key genes in renal cell carcinoma by bioinformatics analysis and cell experiments. PMID:32699530
Cohesin-Dependent and -Independent Mechanisms Mediate Chromosomal Contacts between Promoters and Enhancers. PMID:32698000
An NMR-based approach reveals the core structure of the functional domain of SINEUP lncRNAs. PMID:32697302
Unique molecular signatures of microRNAs in ocular fluids and plasma in diabetic retinopathy. PMID:32692745
Developmental function and state transitions of a gene expression oscillator in Caenorhabditis elegans. PMID:32687264
Deep Proteomic Deconvolution of Interferons and HBV Transfection Effects on a Hepatoblastoma Cell Line. PMID:32685848
NRF2 is a key regulator of endothelial microRNA expression under proatherogenic stimuli. PMID:32683448
PfMAP-2 is essential for male gametogenesis in the malaria parasite Plasmodium falciparum. PMID:32681115
Reduced Brd1 expression leads to reversible depression-like behaviors and gene-expression changes in female mice. PMID:32681022
TH17 cells require ongoing classic IL-6 receptor signaling to retain transcriptional and functional identity. PMID:32680955
Fetal HLA-G mediated immune tolerance and interferon response in preeclampsia. PMID:32680723
Molecular and clinical characterization of PARP9 in gliomas: A potential immunotherapeutic target. PMID:32678519
Gene expression profiling identifies the role of Zac1 in cervical cancer metastasis. PMID:32678267
Chemical Priming by Isothiocyanates Protects Against Intoxication by Products of the Mustard Oil Bomb. PMID:32676087
Pathogenic Tau Causes a Toxic Depletion of Nuclear Calcium. PMID:32668249
Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation. PMID:32667968
Bioinformatics-based analysis of the lncRNA-miRNA-mRNA and TF regulatory networks reveals functional genes in esophageal squamous cell carcinoma. PMID:32662828
Adenovirus-mediated ubiquitination alters protein-RNA binding and aids viral RNA processing. PMID:32661314
The circular RNA landscape in specific peripheral blood mononuclear cells of critically ill patients with sepsis. PMID:32660590
Extracellular vesicles from Heligmosomoides bakeri and Trichuris muris contain distinct microRNA families and small RNAs that could underpin different functions in the host. PMID:32659276
Global discovery of bacterial RNA-binding proteins by RNase-sensitive gradient profiles reports a new FinO domain protein. PMID:32646969
VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development. PMID:32646368
Identification of key genes for esophageal squamous cell carcinoma via integrated bioinformatics analysis and experimental confirmation. PMID:32642240
Microinjection induces changes in the transcriptome of bovine oocytes. PMID:32641751
RAGE impairs murine diabetic atherosclerosis regression and implicates IRF7 in macrophage inflammation and cholesterol metabolism. PMID:32641587
Characterization of cell-free breast cancer patient-derived scaffolds using liquid chromatography-mass spectrometry/mass spectrometry data and RNA sequencing data. PMID:32637480
Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules. PMID:32636252
Machine Learning-Based Ensemble Recursive Feature Selection of Circulating miRNAs for Cancer Tumor Classification. PMID:32635415
A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program. PMID:32634384
Screening and identification of key gene in sepsis development: Evidence from bioinformatics analysis. PMID:32629654
Array Analysis Manager-An automated DNA microarray analysis tool simplifying microarray data filtering, bias recognition, normalization, and expression analysis. PMID:32624831
Rapid activation of distinct members of multigene families in Plasmodium spp. PMID:32620892
Quiescent stem cell marker genes in glioma gene networks are sufficient to distinguish between normal and glioblastoma (GBM) samples. PMID:32616845
Changes in gene expression in potato meristems treated with the sprout suppressor 1,4-dimethylnaphthalene are dependent on tuber age and dormancy status. PMID:32614863
cnd-1/NeuroD1 Functions with the Homeobox Gene ceh-5/Vax2 and Hox Gene ceh-13/labial To Specify Aspects of RME and DD Neuron Fate in Caenorhabditis elegans. PMID:32601060
Methylation data imputation performances under different representations and missingness patterns. PMID:32600298
Big behavior: challenges and opportunities in a new era of deep behavior profiling. PMID:32599604
PRC2-mediated H3K27me3 modulates shoot iron homeostasis in Arabidopsis thaliana. PMID:32594838
Hub genes and key pathways of traumatic brain injury: bioinformatics analysis and in vivo validation. PMID:32594047
Tryptophanyl-tRNA Synthetase, a Novel Damage-Induced Cytokine, Significantly Increases the Therapeutic Effects of Endometrial Stem Cells. PMID:32592690
An Insulin-Sensitive Circular RNA that Regulates Lifespan in Drosophila. PMID:32592682
Adipose tissue in health and disease through the lens of its building blocks. PMID:32591560
Identification of prognostic risk factors for pancreatic cancer using bioinformatics analysis. PMID:32587798
Minichromosome maintenance 6 complex component identified by bioinformatics analysis and experimental validation in esophageal squamous cell carcinoma. PMID:32583000
The Genetic Regulation of Alternative Splicing in Populus deltoides. PMID:32582229
Short-Term Magnesium Deficiency Triggers Nutrient Retranslocation in Arabidopsis thaliana. PMID:32582226
Adjuvanting Allergen Extracts for Sublingual Immunotherapy: Calcitriol Downregulates CXCL8 Production in Primary Sublingual Epithelial Cells. PMID:32582164
Deciphering the Novel Target Genes Involved in the Epigenetics of Hepatocellular Carcinoma Using Graph Theory Approach. PMID:32581643
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia. PMID:32581241
Construction, analysis and validation of co-expression network to understand stress adaptation in Deinococcus radiodurans R1. PMID:32579573
Signature genes associated with immunological non-responsiveness to anti-retroviral therapy in HIV-1 subtype-c infection. PMID:32579550
The Tomato DELLA Protein PROCERA Promotes Abscisic Acid Responses in Guard Cells by Upregulating an Abscisic Acid Transporter. PMID:32576645
A circular RNA map for human induced pluripotent stem cells of foetal origin. PMID:32574961
Genome-wide transcriptome architecture in a mouse model of Gulf War Illness. PMID:32574576
Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. PMID:32574564
Infection cushions of Fusarium graminearum are fungal arsenals for wheat infection. PMID:32573086
Pervasive changes of mRNA splicing in upf1-deficient zebrafish identify rpl10a as a regulator of T cell development. PMID:32571908
Deletion of Glutathione S-Transferase Omega 1 Activates Type I Interferon Genes and Downregulates Tissue Factor. PMID:32571799
Sequentially induced motor neurons from human fibroblasts facilitate locomotor recovery in a rodent spinal cord injury model. PMID:32571478
Construction and analysis of a lncRNA-miRNA-mRNA network based on competitive endogenous RNA reveal functional lncRNAs in oral cancer. PMID:32571304
Adaptation of the Marine Bacterium Shewanella baltica to Low Temperature Stress. PMID:32570789
Transcriptome analysis of a social caterpillar, Drepana arcuata: De novo assembly, functional annotation and developmental analysis. PMID:32569288
The acute effects of adjuvant radiation and chemotherapy on peripheral blood epigenetic age in early stage breast cancer patients. PMID:32566744
Downregulation of ST3GAL5 is associated with muscle invasion, high grade and a poor prognosis in patients with bladder cancer. PMID:32566010
Identification of key genes associated with the progression of intrahepatic cholangiocarcinoma using weighted gene co-expression network analysis. PMID:32565973
A novel prognostic signature of immune-related genes for patients with colorectal cancer. PMID:32564470
Prognostic characterization of OAS1/OAS2/OAS3/OASL in breast cancer. PMID:32560641
Engineered receptors for human cytomegalovirus that are orthogonal to normal human biology. PMID:32559251
Mitochondrial protein biogenesis in the synapse is supported by local translation. PMID:32558077
An analytical study of neocartilage from microtia and otoplasty surgical remnants: A possible application for BMP7 in microtia development and regeneration. PMID:32555733
Bone marrow adipose tissue is a unique adipose subtype with distinct roles in glucose homeostasis. PMID:32555194
LC-FACSeq is a method for detecting rare clones in leukemia. PMID:32554930
COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. PMID:32554783
An age-independent gene signature for monitoring acute rejection in kidney transplantation. PMID:32550916
Upregulation of Piezo1 Is a Novel Prognostic Indicator in Glioma Patients. PMID:32547190
Identification of Hub Genes in Type 2 Diabetes Mellitus Using Bioinformatics Analysis. PMID:32547141
The Leader Peptide peTrpL Forms Antibiotic-Containing Ribonucleoprotein Complexes for Posttranscriptional Regulation of Multiresistance Genes. PMID:32546623
The novel lncRNA PTTG3P is downregulated and predicts poor prognosis in non-small cell lung cancer. PMID:32542097
TGF-β1-Licensed Murine MSCs Show Superior Therapeutic Efficacy in Modulating Corneal Allograft Immune Rejection In Vivo. PMID:32531237
Bioinformatics analysis of the circRNA-miRNA-mRNA network for non-small cell lung cancer. PMID:32527185
metaRE R Package for Meta-Analysis of Transcriptome Data to Identify the cis-Regulatory Code behind the Transcriptional Reprogramming. PMID:32526881
CPPED1-targeting microRNA-371a-5p expression in human placenta associates with spontaneous delivery. PMID:32520951
KRT8 and KRT19, associated with EMT, are hypomethylated and overexpressed in lung adenocarcinoma and link to unfavorable prognosis. PMID:32519739
Transcriptome-Based Analysis of Tomato Genotypes Resistant to Bacterial Spot (Xanthomonas perforans) Race T4. PMID:32517212
Maternal high-fat diet during lactation reprograms the dopaminergic circuitry in mice. PMID:32510473
Comprehensive identification of a two-genesignature as a novel potential prognostic model for patients with medulloblastoma. PMID:32509164
How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets. PMID:32508872
Identification of immune-related biomarkers associated with tumorigenesis and prognosis in cutaneous melanoma patients. PMID:32508531
Can We Assume the Gene Expression Profile as a Proxy for Signaling Network Activity? PMID:32503292
Integrative analysis of key candidate genes and signaling pathways in autoimmune thyroid dysfunction related to anti-CTLA-4 therapy by bioinformatics. PMID:32500465
Circular RNA HIPK3: A Key Circular RNA in a Variety of Human Cancers. PMID:32500032
poly(UG)-tailed RNAs in genome protection and epigenetic inheritance. PMID:32499657
Expression profiling of small intestinal neuroendocrine tumors identified pathways and gene networks linked to tumorigenesis and metastasis. PMID:32496505
Immune landscapes predict chemotherapy resistance and immunotherapy response in acute myeloid leukemia. PMID:32493790
Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification. PMID:32492250
Leaf tissue specific transcriptome sequence and de novo assembly datasets of Asiatic mangrove Rhizophora mucronata Lam. PMID:32490096
Mutually suppressive roles of KMT2A and KDM5C in behaviour, neuronal structure, and histone H3K4 methylation. PMID:32483278
Prognostic gene expression signature for high-grade serous ovarian cancer. PMID:32473302
Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression. PMID:32471474
Tissue-specific angiogenic and invasive properties of human neonatal thymus and bone MSCs: Role of SLIT3-ROBO1. PMID:32470195
Interaction of YAP with the Myb-MuvB (MMB) complex defines a transcriptional program to promote the proliferation of cardiomyocytes. PMID:32469866
Computational analysis and verification of molecular genetic targets for glioblastoma. PMID:32469390
Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. PMID:32468016
UBR5 regulates proliferation and radiosensitivity in human laryngeal carcinoma via the p38/MAPK signaling pathway. PMID:32468011
Novel Discoveries Targeting Pathogenic Gut Microbes and New Therapies in Pancreatic Cancer: Does Pathogenic E. coli Infection Cause Pancreatic Cancer Progression Modulated by TUBB/Rho/ROCK Signaling Pathway? A Bioinformatic Analysis. PMID:32461969
Genes Involved in Energy Metabolism Are Differentially Expressed During the Day-Night Cycle in Murine Retinal Pigment Epithelium. PMID:32460311
Circular RNA circNRIP1 promotes migration and invasion in cervical cancer by sponging miR-629-3p and regulating the PTP4A1/ERK1/2 pathway. PMID:32457332
Rathke's cleft-like cysts arise from Isl1 deletion in murine pituitary progenitors. PMID:32453714
An up-to-date overview of computational polypharmacology in modern drug discovery. PMID:32452701
A novel risk score model based on eight genes and a nomogram for predicting overall survival of patients with osteosarcoma. PMID:32448271
Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. PMID:32445086
Drought and plant litter chemistry alter microbial gene expression and metabolite production. PMID:32444813
Transcriptomic Evidence of Molecular Mechanisms Underlying the Response of Lactobacillus Plantarum WCFS1 to Hydroxytyrosol. PMID:32443873
Screening and identification of key biomarkers for retinoblastoma: Evidence from bioinformatics analysis. PMID:32443297
Elucidation of the RNA-granule inducing sodium azide stress response through transcriptome analysis. PMID:32437849
A meta-analysis of gene expression data highlights synaptic dysfunction in the hippocampus of brains with Alzheimer's disease. PMID:32433480
Functional Relevance of Citrulline in the Vegetative Tissues of Watermelon During Abiotic Stresses. PMID:32431723
The transition from acute to chronic pain: dynamic epigenetic reprogramming of the mouse prefrontal cortex up to 1 year after nerve injury. PMID:32427748
Dysregulation of Signaling Pathways Due to Differentially Expressed Genes From the B-Cell Transcriptomes of Systemic Lupus Erythematosus Patients - A Bioinformatics Approach. PMID:32426333
Cigarette Smoke Exposure and Inflammatory Signaling Increase the Expression of the SARS-CoV-2 Receptor ACE2 in the Respiratory Tract. PMID:32425701
An NMF-Based Methodology for Selecting Biomarkers in the Landscape of Genes of Heterogeneous Cancer-Associated Fibroblast Populations. PMID:32425511
Comprehensive analysis reveals a six-gene signature and associated drugs in mimic inguinal hernia model. PMID:32424728
TFEB regulates murine liver cell fate during development and regeneration. PMID:32424153
Detecting qualitative changes in biological systems. PMID:32424123
Novel Non-integrating DNA Nano-S/MAR Vectors Restore Gene Function in Isogenic Patient-Derived Pancreatic Tumor Models. PMID:32420409
Screening and Identification of Differentially Expressed Genes Expressed among Left and Right Colon Adenocarcinoma. PMID:32420374
Key genes of renal tubular necrosis: a bioinformatics analysis. PMID:32420172
Hepatotoxic pyrrolizidine alkaloids induce DNA damage response in rat liver in a 28-day feeding study. PMID:32419051
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. PMID:32415191
CSN: unsupervised approach for inferring biological networks based on the genome alone. PMID:32414319
Global Transcriptional Profiling Reveals Novel Autocrine Functions of Interleukin 6 in Human Vascular Endothelial Cells. PMID:32410854
Endoplasmic reticulum stress actively suppresses hepatic molecular identity in damaged liver. PMID:32407006
An EGFR signature predicts cell line and patient sensitivity to multiple tyrosine kinase inhibitors. PMID:32406930
Identification of pathogenic TRAIL-expressing innate immune cells during HIV-1 infection in humanized mice by scRNA-Seq. PMID:32406872
Dietary lipids accumulate in macrophages and stromal cells and change the microarchitecture of mesenteric lymph nodes. PMID:32405435
Correlation-centred variable selection of a gene expression signature to predict breast cancer metastasis. PMID:32404965
MNase Profiling of Promoter Chromatin in Salmonella typhimurium-Stimulated GM12878 Cells Reveals Dynamic and Response-Specific Nucleosome Architecture. PMID:32404364
Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. PMID:32403054
Neuronal activity increases translocator protein (TSPO) levels. PMID:32398717
Transcriptomics in Toxicogenomics, Part II: Preprocessing and Differential Expression Analysis for High Quality Data. PMID:32397130
PPARG Drives Molecular Networks as an Inhibitor for the Pathologic Development and Progression of Lung Adenocarcinoma. PMID:32395124
The Mnemiopsis Genome Project Portal: integrating new gene expression resources and improving data visualization. PMID:32386298
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
A putative competing endogenous RNA network in cisplatin-resistant lung adenocarcinoma cells identifying potentially rewarding research targets. PMID:32382346
Aberrant expression of two miRNAs promotes proliferation, hepatitis B virus amplification, migration and invasion of hepatocellular carcinoma cells: evidence from bioinformatic analysis and experimental validation. PMID:32377460
Kaposi's Sarcoma-Associated Herpesvirus Fine-Tunes the Temporal Expression of Late Genes by Manipulating a Host RNA Quality Control Pathway. PMID:32376621
Construction of an integrated human osteosarcoma database, HOsDb, based on literature mining, microarray analysis, and database retrieval. PMID:32375685
Hdac3 is an epigenetic inhibitor of the cytotoxicity program in CD8 T cells. PMID:32374402
Integrative Analysis for Elucidating Transcriptomics Landscapes of Glucocorticoid-Induced Osteoporosis. PMID:32373610
Mitral valve leaflet response to ischaemic mitral regurgitation: from gene expression to tissue remodelling. PMID:32370692
Differential B-Cell Receptor Signaling Requirement for Adhesion of Mantle Cell Lymphoma Cells to Stromal Cells. PMID:32370190
Multi-Gene Prognostic Signatures and Prediction of Pathological Complete Response to Neoadjuvant Chemotherapy in ER-positive, HER2-negative Breast Cancer Patients. PMID:32369904
The antibiotic bedaquiline activates host macrophage innate immune resistance to bacterial infection. PMID:32369020
Maintaining Myocardial Glucose Utilization in Diabetic Cardiomyopathy Accelerates Mitochondrial Dysfunction. PMID:32366681
CPS1 expression and its prognostic significance in lung adenocarcinoma. PMID:32355785
Promising diagnostic and prognostic value of six genes in human hepatocellular carcinoma. PMID:32355538
The Animal Lectin Galectin-8 Promotes Cytokine Expression and Metastatic Tumor Growth in Mice. PMID:32355198
JAK-STAT Activity in Peripheral Blood Cells and Kidney Tissue in IgA Nephropathy. PMID:32354727
Comparative proteogenomics profiling of non-small and small lung carcinoma cell lines using mass spectrometry. PMID:32351780
Polymorphisms in miRNA binding sites involved in metabolic diseases in mice and humans. PMID:32350386
Long-Term Aberrations To Cerebellar Endocannabinoids Induced By Early-Life Stress. PMID:32350298
EZH2-Deficient T-cell Acute Lymphoblastic Leukemia Is Sensitized to CHK1 Inhibition through Enhanced Replication Stress. PMID:32349972
Integrating SWATH-MS Proteomics and Transcriptome Analysis Identifies CHI3L1 as a Plasma Biomarker for Early Gastric Cancer. PMID:32346614
HMGA1-pseudogene7 transgenic mice develop B cell lymphomas. PMID:32341372
Interactions between DksA and Stress-Responsive Alternative Sigma Factors Control Inorganic Polyphosphate Accumulation in Escherichia coli. PMID:32341074
Identification of Key Genes Related to Lung Squamous Cell Carcinoma Using Bioinformatics Analysis. PMID:32340320
The Construction and Analysis of the Aberrant lncRNA-miRNA-mRNA Network in Adipose Tissue from Type 2 Diabetes Individuals with Obesity. PMID:32337289
GATA2 and Progesterone Receptor Interaction in Endometrial Stromal Cells Undergoing Decidualization. PMID:32335672
PHTF2 regulates lipids metabolism in gastric cancer. PMID:32335542
High dimensional model representation of log-likelihood ratio: binary classification with expression data. PMID:32334509
Differential Effects of the Hormonal and Copper Intrauterine Device on the Endometrial Transcriptome. PMID:32327684
Amyloid Precursor Protein (APP) Controls the Expression of the Transcriptional Activator Neuronal PAS Domain Protein 4 (NPAS4) and Synaptic GABA Release. PMID:32327470
Transcriptomics in Toxicogenomics, Part I: Experimental Design, Technologies, Publicly Available Data, and Regulatory Aspects. PMID:32326418
Comparative Transcriptomic Analysis of Subcutaneous Adipose Tissue from Local Pig Breeds. PMID:32326415
A Study of Gene Expression Changes in Human Spinal and Oculomotor Neurons; Identifying Potential Links to Sporadic ALS. PMID:32325953
Drought Stress Responses in Context-Specific Genome-Scale Metabolic Models of Arabidopsis thaliana. PMID:32325728
Computational Approach to Identifying Universal Macrophage Biomarkers. PMID:32322218
SPEED2: inferring upstream pathway activity from differential gene expression. PMID:32313938
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis. PMID:32312741
Bioinformatics analysis and verification of gene targets for benign tracheal stenosis. PMID:32309912
Transcriptome analysis and functional characterization of cerebral organoids in bipolar disorder. PMID:32306996
The Molecular Processes in the Trabecular Meshwork After Exposure to Corticosteroids and in Corticosteroid-Induced Ocular Hypertension. PMID:32305042
Hepatocyte-specific deletion of Pparα promotes NAFLD in the context of obesity. PMID:32300166
Gene-Specific Control of tRNA Expression by RNA Polymerase II. PMID:32298650
Formation of colorectal liver metastases induces musculoskeletal and metabolic abnormalities consistent with exacerbated cachexia. PMID:32298240
20-Hydroxyecdysone Primes Innate Immune Responses That Limit Bacterial and Malarial Parasite Survival in Anopheles gambiae. PMID:32295874
Differences in the Transcriptomic Response of Campylobacter coli and Campylobacter lari to Heat Stress. PMID:32292399
An epigenetic map of malaria parasite development from host to vector. PMID:32286373
Altered Energy Metabolism During Early Optic Nerve Crush Injury: Implications of Warburg-Like Aerobic Glycolysis in Facilitating Retinal Ganglion Cell Survival. PMID:32277382
iMM1865: A New Reconstruction of Mouse Genome-Scale Metabolic Model. PMID:32277147
Whole-Genome DNA Methylation Profiling of CD14+ Monocytes Reveals Disease Status and Activity Differences in Crohn's Disease Patients. PMID:32276386
ngn-1/neurogenin Activates Transcription of Multiple Terminal Selector Transcription Factors in the Caenorhabditis elegans Nervous System. PMID:32273286
Molecular Fingerprints of Borderline Changes in Kidney Allografts Are Influenced by Donor Category. PMID:32269565
Autophosphorylation at serine 166 regulates RIP kinase 1-mediated cell death and inflammation. PMID:32269263
A Targeted Multi-omic Analysis Approach Measures Protein Expression and Low-Abundance Transcripts on the Single-Cell Level. PMID:32268080
Identification of core genes associated with prostate cancer progression and outcome via bioinformatics analysis in multiple databases. PMID:32266115
Impact of ex vivo Sample Handling on DNA Methylation Profiles in Human Cord Blood and Neonatal Dried Blood Spots. PMID:32265984
Defining the Design Principles of Skin Epidermis Postnatal Growth. PMID:32259486
Landscape of copy number aberrations in esophageal squamous cell carcinoma from a high endemic region of South Africa. PMID:32252688
Role of uL3 in the Crosstalk between Nucleolar Stress and Autophagy in Colon Cancer Cells. PMID:32244996
Wnt signaling regulates neural plate patterning in distinct temporal phases with dynamic transcriptional outputs. PMID:32243887
Chemotherapy exacerbates ovarian cancer cell migration and cancer stem cell-like characteristics through GLI1. PMID:32242101
Geographic assessment of cancer genome profiling studies. PMID:32239182
Endothelialization of arterial vascular grafts by circulating monocytes. PMID:32238801
Epigenetic inhibitors eliminate senescent melanoma BRAFV600E cells that survive long‑term BRAF inhibition. PMID:32236593
LAG3 (LAG-3, CD223) DNA methylation correlates with LAG3 expression by tumor and immune cells, immune cell infiltration, and overall survival in clear cell renal cell carcinoma. PMID:32234847
The immune infiltration in clear cell Renal Cell Carcinoma and their clinical implications: A study based on TCGA and GEO databases. PMID:32231726
Egyptian Rousette IFN-ω Subtypes Elicit Distinct Antiviral Effects and Transcriptional Responses in Conspecific Cells. PMID:32231668
A large-scale comparative study of isoform expressions measured on four platforms. PMID:32228441
Low-Dose Silver Nanoparticle Surface Chemistry and Temporal Effects on Gene Expression in Human Liver Cells. PMID:32227433
Decreased Expression of NUSAP1 Predicts Poor Overall Survival in Cervical Cancer. PMID:32226503
The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. PMID:32219223
Valine-Induced Isoleucine Starvation in Escherichia coli K-12 Studied by Spike-In Normalized RNA Sequencing. PMID:32211022
Evidence of defined temporal expression patterns that lead a gram-negative cell out of dormancy. PMID:32203501
A novel stratification framework for predicting outcome in patients with prostate cancer. PMID:32203215
Fast tree aggregation for consensus hierarchical clustering. PMID:32197576
Tip of the iceberg: roles of circRNAs in hematological malignancies. PMID:32195014
Integrated bioinformatics analysis of the association between apolipoprotein E expression and patient prognosis in papillary thyroid carcinoma. PMID:32194729
IRF1 association with tumor immune microenvironment and use as a diagnostic biomarker for colorectal cancer recurrence. PMID:32194669
Arabidopsis Flippases Cooperate with ARF GTPase Exchange Factors to Regulate the Trafficking and Polarity of PIN Auxin Transporters. PMID:32193204
Neutrophil extracellular traps promote macrophage inflammation and impair atherosclerosis resolution in diabetic mice. PMID:32191637
Deletion of fatty acid transport protein 2 (FATP2) in the mouse liver changes the metabolic landscape by increasing the expression of PPARα-regulated genes. PMID:32188695
Alterations in the methylome of the stromal tumour microenvironment signal the presence and severity of prostate cancer. PMID:32188493
Transcriptomic Landscape and Functional Characterization of Induced Pluripotent Stem Cell-Derived Cerebral Organoids in Schizophrenia. PMID:32186681
Retinal endothelial cell phenotypic modifications during experimental autoimmune uveitis: a transcriptomic approach. PMID:32183784
Identification of key genes and pathways of diagnosis and prognosis in cervical cancer by bioinformatics analysis. PMID:32181600
Dataset of Cavendish banana transcriptome in response to chitosan coating application. PMID:32181300
Analysis of L-arginine:glycine amidinotransferase-, creatine- and homoarginine-dependent gene regulation in the murine heart. PMID:32179820
Enabling population assignment from cancer genomes with SNP2pop. PMID:32179800
Epigenetic Regulation of ABA-Induced Transcriptional Responses in Maize. PMID:32179621
The alarmones (p)ppGpp are part of the heat shock response of Bacillus subtilis. PMID:32176689
RNA-seq Analysis of Wild-Type vs. FOXC2-Deficient Melanoma Cells Reveals a Role for the FOXC2 Transcription Factor in the Regulation of Multiple Oncogenic Pathways. PMID:32175283
A transcriptional landscape of 28 porcine tissues obtained by super deepSAGE sequencing. PMID:32171242
Nitrosative Stress and Lipid Homeostasis as a Mechanism for Zileuton Hepatotoxicity and Resistance in Genetically Sensitive Mice. PMID:32170957
*-DCC: A platform to collect, annotate, and explore a large variety of sequencing experiments. PMID:32170312
Single-cell RNA sequencing reveals a heterogeneous response to Glucocorticoids in breast cancer cells. PMID:32170217
Cystic renal-epithelial derived induced pluripotent stem cells from polycystic kidney disease patients. PMID:32163234
Screening and identification of critical biomarkers in erectile dysfunction: evidence from bioinformatic analysis. PMID:32161689
The Arabidopsis SAFEGUARD1 suppresses singlet oxygen-induced stress responses by protecting grana margins. PMID:32161131
Comprehensive evaluation of the metabolic effects of insect meal from Tenebrio molitor L. in growing pigs by transcriptomics, metabolomics and lipidomics. PMID:32158542
Evaluation of pre-processing on the meta-analysis of DNA methylation data from the Illumina HumanMethylation450 BeadChip platform. PMID:32155174
Whole-Transcriptome Analysis Unveils the Synchronized Activities of Genes for Fructans in Developing Tubers of the Jerusalem Artichoke. PMID:32153609
Deficiency in the endocytic adaptor proteins PHETA1/2 impairs renal and craniofacial development. PMID:32152089
The Application of Deep Learning in Cancer Prognosis Prediction. PMID:32150991
Biocomplexity and Fractality in the Search of Biomarkers of Aging and Pathology: Mitochondrial DNA Profiling of Parkinson's Disease. PMID:32143500
Understanding the Molecular Mechanisms of Asthma through Transcriptomics. PMID:32141255
Assessment of the Mode of Action Underlying the Effects of GenX in Mouse Liver and Implications for Assessing Human Health Risks. PMID:32138627
Evaluation of Seven Different RNA-Seq Alignment Tools Based on Experimental Data from the Model Plant Arabidopsis thaliana. PMID:32138290
Histone H4 dosage modulates DNA damage response in the pathogenic yeast Candida glabrata via homologous recombination pathway. PMID:32134928
Mitochondrial Pyruvate Carrier 1 Promotes Peripheral T Cell Homeostasis through Metabolic Regulation of Thymic Development. PMID:32130894
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Leptin and fractalkine: novel subcutaneous cytokines in burn injury. PMID:32127397
Hypoxia is regulating enzymatic wood decomposition and intracellular carbohydrate metabolism in filamentous white rot fungus. PMID:32123543
Cell Line-, Protein-, and Sialoglycosite-Specific Control of Flux-Based Sialylation in Human Breast Cells: Implications for Cancer Progression. PMID:32117864
Erratum: Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells. PMID:32117464
Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification. PMID:32117426
A TRANSPARENT TESTA Transcriptional Module Regulates Endothelium Polarity. PMID:32117351
The Epipeptide YydF Intrinsically Triggers the Cell Envelope Stress Response of Bacillus subtilis and Causes Severe Membrane Perturbations. PMID:32117169
Adaptive RSK-EphA2-GPRC5A signaling switch triggers chemotherapy resistance in ovarian cancer. PMID:32115889
A reference profile-free deconvolution method to infer cancer cell-intrinsic subtypes and tumor-type-specific stromal profiles. PMID:32111252
Empty SV40 capsids increase survival of septic rats by eliciting numerous host signaling networks that participate in a number of systemic functions. PMID:32110278
Restraining Lysosomal Activity Preserves Hematopoietic Stem Cell Quiescence and Potency. PMID:32109377
Investigation of the quorum-sensing regulon of the biocontrol bacterium Pseudomonas chlororaphis strain PA23. PMID:32109244
Molecular and genetic regulation of pig pancreatic islet cell development. PMID:32108026
Role of miRNA-542-5p in the tumorigenesis of osteosarcoma. PMID:32105410
Integrative module analysis of HCC gene expression landscapes. PMID:32104233
High-Throughput Fluorescence-Based Screen Identifies the Neuronal MicroRNA miR-124 as a Positive Regulator of Alphavirus Infection. PMID:32102877
Functional omics analyses reveal only minor effects of microRNAs on human somatic stem cell differentiation. PMID:32094412
Equivalent change enrichment analysis: assessing equivalent and inverse change in biological pathways between diverse experiments. PMID:32093613
Protein arginine methyltransferase 5 promotes cholesterol biosynthesis-mediated Th17 responses and autoimmunity. PMID:32091410
Transcriptional analysis of arogenate dehydratase genes identifies a link between phenylalanine biosynthesis and lignin biosynthesis. PMID:32090267
Circulating and tissue matricellular RNA and protein expression in calcific aortic valve disease. PMID:32089075
Transcriptomics at Maize Embryo/Endosperm Interfaces Identifies a Transcriptionally Distinct Endosperm Subdomain Adjacent to the Embryo Scutellum. PMID:32086366
RABL6A Is an Essential Driver of MPNSTs that Negatively Regulates the RB1 Pathway and Sensitizes Tumor Cells to CDK4/6 Inhibitors. PMID:32086342
Biosystem Analysis of the Hypoxia Inducible Domain Family Member 2A: Implications in Cancer Biology. PMID:32085461
Development of a four-gene prognostic model for pancreatic cancer based on transcriptome dysregulation. PMID:32081836
Disrupted Gene Networks in Subfertile Hybrid House Mice. PMID:32076722
Data on banana transcriptome in response to blood disease infection. PMID:32071957
Prognostic values of a novel multi-mRNA signature for predicting relapse of cholangiocarcinoma. PMID:32071556
Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression. PMID:32071286
Genome-Wide Analysis of Gene Expression Provides New Insights into Waterlogging Responses in Barley (Hordeum vulgare L.). PMID:32069892
Germ-free and microbiota-associated mice yield small intestinal epithelial organoids with equivalent and robust transcriptome/proteome expression phenotypes. PMID:32068945
IPF pathogenesis is dependent upon TGFβ induction of IGF-1. PMID:32067272
Identification of core biomarkers associated with pathogenesis and prognostic outcomes of laryngeal squamous-cell cancer using bioinformatics analysis. PMID:32067095
A Post-Processing Algorithm for miRNA Microarray Data. PMID:32059403
Computational discovery of therapeutic candidates for preventing preterm birth. PMID:32051340
Inhibition of methyltransferase activity of enhancer of zeste 2 leads to enhanced lipid accumulation and altered chromatin status in zebrafish. PMID:32051014
Robustness and applicability of transcription factor and pathway analysis tools on single-cell RNA-seq data. PMID:32051003
Differential Regulation of circRNA, miRNA, and piRNA during Early Osteogenic and Chondrogenic Differentiation of Human Mesenchymal Stromal Cells. PMID:32050423
Transcriptional Signatures of Tau and Amyloid Neuropathology. PMID:32049030
Using the Gibbs Function as a Measure of Human Brain Development Trends from Fetal Stage to Advanced Age. PMID:32046179
A Functional Landscape of CKD Entities From Public Transcriptomic Data. PMID:32043035
The health status alters the pituitary function and reproduction of mice in a Cxcr2-dependent manner. PMID:32041848
Gene Expression Signature Predictive of Neuroendocrine Transformation in Prostate Adenocarcinoma. PMID:32041153
Distinct cachexia profiles in response to human pancreatic tumours in mouse limb and respiratory muscle. PMID:32039571
Using SNP Weights Derived From Gene Expression Modules to Improve GWAS Power for Feed Efficiency in Pigs. PMID:32038708
APC-β-catenin-TCF signaling silences the intestinal guanylin-GUCY2C tumor suppressor axis. PMID:32037952
Assessing diagnostic value of microRNAs from peripheral blood mononuclear cells and extracellular vesicles in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. PMID:32034172
Determining sequencing depth in a single-cell RNA-seq experiment. PMID:32034137
Combined Use of Three Machine Learning Modeling Methods to Develop a Ten-Gene Signature for the Diagnosis of Ventilator-Associated Pneumonia. PMID:32031163
Comprehensive analysis of tumor necrosis factor receptor TNFRSF9 (4-1BB) DNA methylation with regard to molecular and clinicopathological features, immune infiltrates, and response prediction to immunotherapy in melanoma. PMID:32028068
Synthetic analogues of 2-oxo acids discriminate metabolic contribution of the 2-oxoglutarate and 2-oxoadipate dehydrogenases in mammalian cells and tissues. PMID:32024885
PDGFRα and αSMA mark two distinct mesenchymal cell populations involved in parenchymal and vascular remodeling in pulmonary fibrosis. PMID:32023084
Construction of a prognosis‑associated long noncoding RNA‑mRNA network for multiple myeloma based on microarray and bioinformatics analysis. PMID:32016443
The molecular aetiology of tRNA synthetase depletion: induction of a GCN4 amino acid starvation response despite homeostatic maintenance of charged tRNA levels. PMID:32016368
Exploring the Key Genes and Pathways in the Formation of Corneal Scar Using Bioinformatics Analysis. PMID:32016117
Comparison of DNA methylation profiles from saliva in Coeliac disease and non-coeliac disease individuals. PMID:32014011
Limited utility of qPCR-based detection of tumor-specific circulating mRNAs in whole blood from clear cell renal cell carcinoma patients. PMID:32013938
Identification of differentially expressed protein-coding genes in lung adenocarcinomas. PMID:32010276
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs for discerning baseline expression exclusivity of candidate biomarkers. PMID:32009518
Unveiling ncRNA regulatory axes in atherosclerosis progression. PMID:32009226
Reconstructed Single-Cell Fate Trajectories Define Lineage Plasticity Windows during Differentiation of Human PSC-Derived Distal Lung Progenitors. PMID:32004478
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes. PMID:32000677
Changes in gene expression in human skeletal stem cells transduced with constitutively active Gsα correlates with hallmark histopathological changes seen in fibrous dysplastic bone. PMID:31999703
Triangular correlation (TrC) between cancer aggressiveness, cell uptake capability, and cell deformability. PMID:31998832
Identification of Key Genes and Prognostic Analysis between Chromophobe Renal Cell Carcinoma and Renal Oncocytoma by Bioinformatic Analysis. PMID:31998788
Interleukin-1 Beta-Mediated Sex Differences in Kawasaki Disease Vasculitis Development and Response to Treatment. PMID:31996019
Transcriptional responses of Candida glabrata biofilm cells to fluconazole are modulated by the carbon source. PMID:31993211
Identification of Key Biomarkers in Bladder Cancer: Evidence from a Bioinformatics Analysis. PMID:31991631
Clostridioides difficile-Associated Antibiotics Alter Human Mucosal Barrier Functions by Microbiome-Independent Mechanisms. PMID:31988098
Upregulation of Hallmark Muscle Genes Protects GneM743T/M743T Mutated Knock-In Mice From Kidney and Muscle Phenotype. PMID:31985472
Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PMID:31978041
MicroRNA Biomarker hsa-miR-195-5p for Detecting the Risk of Lung Cancer. PMID:31976313
Integrated, multicohort analysis reveals unified signature of systemic lupus erythematosus. PMID:31971918
MicroRNAs and regulated interaction networks reveal differences between adult and pediatric acute myeloid leukemia. PMID:31966399
CRL4-Cereblon complex in Thalidomide Embryopathy: a translational investigation. PMID:31964914
A qualitative transcriptional signature for predicting the biochemical recurrence risk of prostate cancer patients after radical prostatectomy. PMID:31961962
Ontology-driven integrative analysis of omics data through Onassis. PMID:31959844
Manatee: detection and quantification of small non-coding RNAs from next-generation sequencing data. PMID:31959833
CeRNA regulatory network-based analysis to study the roles of noncoding RNAs in the pathogenesis of intrahepatic cholangiocellular carcinoma. PMID:31956102
Mining the proliferative diabetic retinopathy-associated genes and pathways by integrated bioinformatic analysis. PMID:31953631
Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects. PMID:31953524
Identification of biomarkers in common chronic lung diseases by co-expression networks and drug-target interactions analysis. PMID:31952466
Antiviral activity of interferon-stimulated gene 20, as a putative repressor binding to hepatitis B virus enhancer II and core promoter. PMID:31951295
tRNA 2'-O-methylation by a duo of TRM7/FTSJ1 proteins modulates small RNA silencing in Drosophila. PMID:31943105
Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling. PMID:31942009
Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor. PMID:31940495
The Arabidopsis Protein CGL20 Is Required for Plastid 50S Ribosome Biogenesis. PMID:31937683
Changes in the expression of genes encoding type IV pili-associated proteins are seen when Clostridium perfringens is grown in liquid or on surfaces. PMID:31937237
Comparing DNA methylation profiles across different tissues associated with the diagnosis of pediatric asthma. PMID:31932625
Future of Evidence Synthesis in Precision Oncology: Between Systematic Reviews and Biocuration. PMID:31930186
SCDC: bulk gene expression deconvolution by multiple single-cell RNA sequencing references. PMID:31925417
Array Comparative Genomic Hybridization Analysis Reveals Significantly Enriched Pathways in Canine Oral Melanoma. PMID:31921654
Rainbow Trout IgM+ B Cells Preferentially Respond to Thymus-Independent Antigens but Are Activated by CD40L. PMID:31921163
Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics. PMID:31918046
A pantothenate kinase-deficient mouse model reveals a gene expression program associated with brain coenzyme a reduction. PMID:31918006
DNA hypermethylation associated with upregulated gene expression in prostate cancer demonstrates the diversity of epigenetic regulation. PMID:31914996
Pharmacological inhibition of CSF1R by GW2580 reduces microglial proliferation and is protective against neuroinflammation and dopaminergic neurodegeneration. PMID:31914683
PROP1-Dependent Retinoic Acid Signaling Regulates Developmental Pituitary Morphogenesis and Hormone Expression. PMID:31913463
Evaluation of the 12-Gene Molecular Score and the 21-Gene Recurrence Score as Predictors of Response to Neo-adjuvant Chemotherapy in Estrogen Receptor-Positive, HER2-Negative Breast Cancer. PMID:31907749
Identification and characterization of genes frequently responsive to Xanthomonas oryzae pv. oryzae and Magnaporthe oryzae infections in rice. PMID:31906847
MatchMixeR: a cross-platform normalization method for gene expression data integration. PMID:31904810
Bile and urine peptide marker profiles: access keys to molecular pathways and biological processes in cholangiocarcinoma. PMID:31900160
Differential Expression Gene Explorer (DrEdGE): a tool for generating interactive online visualizations of gene expression datasets. PMID:31899488
Insights into the Gene Expression Profiles of Active and Restricted Red/Green-HIV+ Human Astrocytes: Implications for Shock or Lock Therapies in the Brain. PMID:31896591
Robust hepatitis E virus infection and transcriptional response in human hepatocytes. PMID:31896581
Integrative Gene Expression Profiling Analysis to Investigate Potential Prognostic Biomarkers for Colorectal Cancer. PMID:31893510
A 6-Membrane Protein Gene score for prognostic prediction of cytogenetically normal acute myeloid leukemia in multiple cohorts. PMID:31892991
A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize. PMID:31891625
Estrogen activates Alzheimer's disease genes. PMID:31890855
Integrative Analysis of Axolotl Gene Expression Data from Regenerative and Wound Healing Limb Tissues. PMID:31889169
CD4+ T Cell-Derived NGAL Modifies the Outcome of Ischemic Acute Kidney Injury. PMID:31889023
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis. PMID:31888466
Unique molecular signature in mucolipidosis type IV microglia. PMID:31883529
Increased HLA-DR expression and cortical demyelination in MS links with HLA-DR15. PMID:31882398
Venn-diaNet : venn diagram based network propagation analysis framework for comparing multiple biological experiments. PMID:31881980
PROMO: an interactive tool for analyzing clinically-labeled multi-omic cancer datasets. PMID:31878868
Habitat-Specific Clock Variation and Its Consequence on Reproductive Fitness. PMID:31878828
Arabidopsis EDR1 Protein Kinase Regulates the Association of EDS1 and PAD4 to Inhibit Cell Death. PMID:31876224
A robustness metric for biological data clustering algorithms. PMID:31874625
Syk degradation restrains plasma cell formation and promotes zonal transitions in germinal centers. PMID:31873727
Expression of Alpha-type Platelet-derived Growth Factor Receptor-influenced Genes Predicts Clinical Outcome in Glioma. PMID:31869747
Transcriptional regulation of a gonococcal gene encoding a virulence factor (L-lactate permease). PMID:31860664
StressGenePred: a twin prediction model architecture for classifying the stress types of samples and discovering stress-related genes in arabidopsis. PMID:31856731
Knowledge Base Commons (KBCommons) v1.1: a universal framework for multi-omics data integration and biological discoveries. PMID:31856718
Bioinformatic profiling identifies a platinum-resistant-related risk signature for ovarian cancer. PMID:31856408
Early cold stress responses in post-meiotic anthers from tolerant and sensitive rice cultivars. PMID:31853825
The InsP7 phosphatase Siw14 regulates inositol pyrophosphate levels to control localization of the general stress response transcription factor Msn2. PMID:31848224
Loss of ADAMTS19 causes progressive non-syndromic heart valve disease. PMID:31844321
Supplementation of live yeast based feed additive in early life promotes rumen microbial colonization and fibrolytic potential in lambs. PMID:31844130
Vascular PPARβ/δ Promotes Tumor Angiogenesis and Progression. PMID:31842402
Epigenetic Modifications in T Cells: The Role of DNA Methylation in Salt-Sensitive Hypertension. PMID:31838911
High-resolution chromosomal microarray analysis for copy-number variations in high-functioning autism reveals large aberration typical for intellectual disability. PMID:31838600
Transcriptomic and Proteomic Responses of the Organohalide-Respiring Bacterium Desulfoluna spongiiphila to Growth with 2,6-Dibromophenol as the Electron Acceptor. PMID:31836581
An Integrated Pan-Cancer Analysis and Structure-Based Virtual Screening of GPR15. PMID:31835584
Differences in the intrinsic spatial dynamics of the chromatin contribute to cell differentiation. PMID:31828312
Evolutionarily novel genes are expressed in transgenic fish tumors and their orthologs are involved in development of progressive traits in humans. PMID:31827597
PPP2R2A prostate cancer haploinsufficiency is associated with worse prognosis and a high vulnerability to B55α/PP2A reconstitution that triggers centrosome destabilization. PMID:31822657
Evolutionary transition from degenerate to nonredundant cytokine signaling networks supporting intrathymic T cell development. PMID:31822609
Longitudinal linear combination test for gene set analysis. PMID:31822265
The functional landscape of the human phosphoproteome. PMID:31819260
Distinct patterns of complex rearrangements and a mutational signature of microhomeology are frequently observed in PLP1 copy number gain structural variants. PMID:31818324
Identification of potential core genes in metastatic renal cell carcinoma using bioinformatics analysis. PMID:31814889
GliomaDB: A Web Server for Integrating Glioma Omics Data and Interactive Analysis. PMID:31811943
Comparative transcriptome analysis of hESC- and iPSC-derived lentoid bodies. PMID:31811247
Modelling the gene expression and the DNA-binding in the 3T3-L1 differentiating adipocytes. PMID:31809632
Clinical significance of the immune cell landscape in hepatocellular carcinoma patients with different degrees of fibrosis. PMID:31807510
Infectious stimuli promote malignant B-cell acute lymphoblastic leukemia in the absence of AID. PMID:31804490
Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PMID:31803533
c-Jun overexpression in CAR T cells induces exhaustion resistance. PMID:31802004
mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations. PMID:31799603
Macrophage Coordination of the Interferon Lambda Immune Response. PMID:31798594
aTEMPO: Pathway-Specific Temporal Anomalies for Precision Therapeutics. PMID:31797638
The Transcriptional Profile of Trichophyton rubrum Co-Cultured with Human Keratinocytes Shows New Insights about Gene Modulation by Terbinafine. PMID:31795354
Dynamic regulation of chromatin accessibility by pluripotency transcription factors across the cell cycle. PMID:31794382
Identification of Susceptibility Genes to Allergic Rhinitis by Gene Expression Data Sets. PMID:31794148
Bioinformatics analysis of Ewing's sarcoma: Seeking key candidate genes and pathways. PMID:31788075
Identification of the lncRNA-miRNA-mRNA network associated with gastric cancer via integrated bioinformatics analysis. PMID:31788050
Microarray Gene Expression Dataset Re-analysis Reveals Variability in Influenza Infection and Vaccination. PMID:31787983
Biotin Supplementation Ameliorates Murine Colitis by Preventing NF-κB Activation. PMID:31786364
Gene Expression Value Prediction Based on XGBoost Algorithm. PMID:31781160
Dissection of gene expression datasets into clinically relevant interaction signatures via high-dimensional correlation maximization. PMID:31780653
Histone Lysine Methylation Dynamics Control EGFR DNA Copy-Number Amplification. PMID:31776131
IL-1β Induces SOCS2 Expression in Human Dendritic Cells. PMID:31775389
A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping. PMID:31774481
Commensal microbiota drive the functional diversification of colon macrophages. PMID:31772323
Network Modeling Approaches and Applications to Unravelling Non-Alcoholic Fatty Liver Disease. PMID:31771247
Screening and identification of key biomarkers in nasopharyngeal carcinoma: Evidence from bioinformatic analysis. PMID:31770211
Expression of the BAD pathway is a marker of triple-negative status and poor outcome. PMID:31767884
JASPer controls interphase histone H3S10 phosphorylation by chromosomal kinase JIL-1 in Drosophila. PMID:31767855
Deep Characterization of the Human Antibody Response to Natural Infection Using Longitudinal Immune Repertoire Sequencing. PMID:31767621
BNC1 regulates cell heterogeneity in human pluripotent stem cell-derived epicardium. PMID:31767620
Computational Inference of Gene Co-Expression Networks for the identification of Lung Carcinoma Biomarkers: An Ensemble Approach. PMID:31766738
Bioinformatics analyses of publicly available NEPCa datasets. PMID:31763364
Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia. PMID:31759365
Endothelial Cell-Specific Transcriptome Reveals Signature of Chronic Stress Related to Worse Outcome After Mild Transient Brain Ischemia in Mice. PMID:31758402
Bone marrow adipose tissue does not express UCP1 during development or adrenergic-induced remodeling. PMID:31758074
TACITuS: transcriptomic data collector, integrator, and selector on big data platform. PMID:31757212
The influence of PFK-II overexpression on neuroblastoma patients' survival may be dependent on the particular isoenzyme expressed, PFKFB3 or PFKFB4. PMID:31754349
Monocytes affect bone mineral density in pre- and postmenopausal women through ribonucleoprotein complex biogenesis by integrative bioinformatics analysis. PMID:31754224
iCrotoK-PseAAC: Identify lysine crotonylation sites by blending position relative statistical features according to the Chou's 5-step rule. PMID:31751380
Chaperone-mediated ordered assembly of the SAGA and NuA4 transcription co-activator complexes in yeast. PMID:31748520
Screening and identification of key biomarkers in prostate cancer using bioinformatics. PMID:31746380
A-Lister: a tool for analysis of differentially expressed omics entities across multiple pairwise comparisons. PMID:31744472
Identification of a 6-lncRNA prognostic signature based on microarray re-annotation in gastric cancer. PMID:31743579
Elevating acetyl-CoA levels reduces aspects of brain aging. PMID:31742554
Differences in the importance of microcephaly, dysmorphism, and epilepsy in the detection of pathogenic CNVs in ID and ASD patients. PMID:31741789
The Microalga Nannochloropsis during Transition from Quiescence to Autotrophy in Response to Nitrogen Availability. PMID:31740503
Methylation of drug resistance-related genes in chemotherapy-sensitive Epstein-Barr virus-associated gastric cancer. PMID:31736281
The Gα-interacting vesicle-associated protein interacts with and promotes cell surface localization of GRP78 during endoplasmic reticulum stress. PMID:31736058
Gene expression microarray public dataset reanalysis in chronic obstructive pulmonary disease. PMID:31730674
Identification of key biomarkers associated with development and prognosis in patients with ovarian carcinoma: evidence from bioinformatic analysis. PMID:31729978
Transcriptome analysis of Aspergillus niger xlnR and xkiA mutants grown on corn Stover and soybean hulls reveals a highly complex regulatory network. PMID:31726994
Proteomic and transcriptomic analyses of early and late-chronic Toxoplasma gondii infection shows novel and stage specific transcripts. PMID:31726967
Correlative evidence for co-regulation of phosphorus and carbon exchanges with symbiotic fungus in the arbuscular mycorrhizal Medicago truncatula. PMID:31710651
Assessing the Impact of Sample Heterogeneity on Transcriptome Analysis of Human Diseases Using MDP Webtool. PMID:31708960
Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus. PMID:31708950
Collagen IV (COL4A1, COL4A2), a Component of the Viral Biofilm, Is Induced by the HTLV-1 Oncoprotein Tax and Impacts Virus Transmission. PMID:31708905
Mutation of the PTCH1 gene predicts recurrence of breast cancer. PMID:31704974
Defining the impact of exoribonucleases in the shift between exponential and stationary phases. PMID:31700028
Identification of Hub Genes and Pathways in a Rat Model of Renal Ischemia-Reperfusion Injury Using Bioinformatics Analysis of the Gene Expression Omnibus (GEO) Dataset and Integration of Gene Expression Profiles. PMID:31699960
DNA methylation profiles capturing breast cancer heterogeneity. PMID:31699026
Changes in Calcium Homeostasis and Gene Expression Implicated in Epilepsy in Hippocampi of Mice Overexpressing ORAI1. PMID:31698854
Salt-inducible kinase inhibition suppresses acute myeloid leukemia progression in vivo. PMID:31697837
Genetic Interactions Affect Lung Function in Patients with Systemic Sclerosis. PMID:31694854
The role of nitric oxide during embryonic wound healing. PMID:31694542
Rapid Discovery of Potential Drugs for Osteonecrosis of Femoral Head Based on Gene Expression Omnibus Database and Connectivity Map. PMID:31692295
Development of Tissue-Specific Age Predictors Using DNA Methylation Data. PMID:31690030
NK cell defects in X-linked pigmentary reticulate disorder. PMID:31672938
Non-Invasive Approach for Evaluation of Pulmonary Hypertension Using Extracellular Vesicle-Associated Small Non-Coding RNA. PMID:31671920
Complex Interactions between Cohesin and CTCF in Regulation of Kaposi's Sarcoma-Associated Herpesvirus Lytic Transcription. PMID:31666380
Synchronized replication of genes encoding the same protein complex in fast-proliferating cells. PMID:31662304
Proteasome inhibition preserves longitudinal growth of denervated muscle and prevents neonatal neuromuscular contractures. PMID:31661460
miR‑760 regulates skeletal muscle proliferation in rheumatoid arthritis by targeting Myo18b. PMID:31661144
The FOXC2 Transcription Factor Promotes Melanoma Outgrowth and Regulates Expression of Genes Associated With Drug Resistance and Interferon Responsiveness. PMID:31659103
High Expression of TTYH3 is Related to Poor Clinical Outcomes in Human Gastric Cancer. PMID:31652813
Identification of 15 T Cell Restricted Genes Evaluates T Cell Infiltration of Human Healthy Tissues and Cancers and Shows Prognostic and Predictive Potential. PMID:31652661
Generation and function of progenitor T cells from StemRegenin-1-expanded CD34+ human hematopoietic progenitor cells. PMID:31648315
Acute sprint exercise transcriptome in human skeletal muscle. PMID:31647849
Multi-tissue network analysis for drug prioritization in knee osteoarthritis. PMID:31645614
Network-Based Functional Prediction Augments Genetic Association To Predict Candidate Genes for Histamine Hypersensitivity in Mice. PMID:31645420
Integrated bioinformatics analysis reveals role of the LINC01093/miR-96-5p/ZFAND5/NF-κB signaling axis in hepatocellular carcinoma. PMID:31641376
Size matters: how sample size affects the reproducibility and specificity of gene set analysis. PMID:31639047
ANLN and KDR Are Jointly Prognostic of Breast Cancer Survival and Can Be Modulated for Triple Negative Breast Cancer Control. PMID:31636652
Luteal Lipids Regulate Progesterone Production and May Modulate Immune Cell Function During the Estrous Cycle and Pregnancy. PMID:31636603
TFAP2C regulates carbonic anhydrase XII in human breast cancer. PMID:31636386
Different Pathways Mediate Amphotericin-Lactoferrin Drug Synergy in Cryptococcus and Saccharomyces. PMID:31632362
Global Transcriptional Response of Three Highly Acid-Tolerant Field Strains of Listeria monocytogenes to HCl Stress. PMID:31623206
Identification of prognostic biomarkers for malignant melanoma using microarray datasets. PMID:31620197
Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts. PMID:31620115
Cell Type- and Sex-Dependent Transcriptome Profiles of Rat Anterior Pituitary Cells. PMID:31620083
Long noncoding RNA GAS5 inhibits progression of colorectal cancer by interacting with and triggering YAP phosphorylation and degradation and is negatively regulated by the m6A reader YTHDF3. PMID:31619268
Variance-Preserving Estimation of Intensity Values Obtained From Omics Experiments. PMID:31616468
Peptidoglycan Recognition Protein 4 Limits Bacterial Clearance and Inflammation in Lungs by Control of the Gut Microbiota. PMID:31616404
D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference. PMID:31615113
Electron transport chain biogenesis activated by a JNK-insulin-Myc relay primes mitochondrial inheritance in Drosophila. PMID:31612862
POPDC3 is a potential biomarker for prognosis and radioresistance in patients with head and neck squamous cell carcinoma. PMID:31612055
Screening and authentication of molecular markers in malignant glioblastoma based on gene expression profiles. PMID:31611967
Identification of key biomarkers and potential molecular mechanisms in lung cancer by bioinformatics analysis. PMID:31611952
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
The PedBE clock accurately estimates DNA methylation age in pediatric buccal cells. PMID:31611402
Transcriptional activation of CBFβ by CDK11p110 is necessary to promote osteosarcoma cell proliferation. PMID:31610798
pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. PMID:31608109
Gene expression profiling of whole blood: A comparative assessment of RNA-stabilizing collection methods. PMID:31600258
β-Catenin mutations as determinants of hepatoblastoma phenotypes in mice. PMID:31597698
Enhanced Ex Vivo Generation of Erythroid Cells from Human Induced Pluripotent Stem Cells in a Simplified Cell Culture System with Low Cytokine Support. PMID:31595840
Global gene expression analysis of Escherichia coli K-12 DH5α after exposure to 2.4 GHz wireless fidelity radiation. PMID:31595026
Functional Genomics of the Retina to Elucidate its Construction and Deconstruction. PMID:31590277
Identification of PIKfyve kinase as a target in multiple myeloma. PMID:31582538
Screening and Identification of Potential Prognostic Biomarkers in Adrenocortical Carcinoma. PMID:31572440
Maternal Obesity Alters Neurotrophin-Associated MAPK Signaling in the Hypothalamus of Male Mouse Offspring. PMID:31572115
Degradation of the transcription factors PIF4 and PIF5 under UV-B promotes UVR8-mediated inhibition of hypocotyl growth in Arabidopsis. PMID:31571300
Cytosolic Phospholipase A2 Alpha Regulates TLR Signaling and Migration in Metastatic 4T1 Cells. PMID:31569627
Delineating the role of MITF isoforms in pigmentation and tissue homeostasis. PMID:31562697
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
A Caenorhabditis elegans ortholog of human selenium-binding protein 1 is a pro-aging factor protecting against selenite toxicity. PMID:31557719
ELTD1 facilitates glioma proliferation, migration and invasion by activating JAK/STAT3/HIF-1α signaling axis. PMID:31554859
Targeted transcriptional modulation with type I CRISPR-Cas systems in human cells. PMID:31548729
Screening and identification of biomarkers for systemic sclerosis via microarray technology. PMID:31545397
Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies. PMID:31543463
Similarities and differences in the biotransformation and transcriptomic responses of Caenorhabditis elegans and Haemonchus contortus to five different benzimidazole drugs. PMID:31542693
miR-511-3p protects against cockroach allergen-induced lung inflammation by antagonizing CCL2. PMID:31536479
Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3. PMID:31534498
Myceliophthora thermophila Xyr1 is predominantly involved in xylan degradation and xylose catabolism. PMID:31534479
FPR1 is the plague receptor on host immune cells. PMID:31534221
Comparative transcriptome analysis of the human endocervix and ectocervix during the proliferative and secretory phases of the menstrual cycle. PMID:31530865
Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells. PMID:31523390
Rectal cancer sub-clones respond differentially to neoadjuvant therapy. PMID:31521947
Identification of differentially expressed genes between primary lung cancer and lymph node metastasis via bioinformatic analysis. PMID:31516588
Cross-disease analysis identified novel common genes for both lung adenocarcinoma and lung squamous cell carcinoma. PMID:31516564
Construction of gene causal regulatory networks using microarray data with the coefficient of intrinsic dependence. PMID:31512008
Off-target toxicity is a common mechanism of action of cancer drugs undergoing clinical trials. PMID:31511426
Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data. PMID:31510704
A statistical simulator scDesign for rational scRNA-seq experimental design. PMID:31510652
Model-based optimization of subgroup weights for survival analysis. PMID:31510644
Differences in blastomere totipotency in 2-cell mouse embryos are a maternal trait mediated by asymmetric mRNA distribution. PMID:31504820
SNV identification from single-cell RNA sequencing data. PMID:31504520
Genome-Scale Characterization of Toxicity-Induced Metabolic Alterations in Primary Hepatocytes. PMID:31501904
Seminal fluid compromises visual perception in honeybee queens reducing their survival during additional mating flights. PMID:31500699
Combination of Cannabinoids, Δ9- Tetrahydrocannabinol and Cannabidiol, Ameliorates Experimental Multiple Sclerosis by Suppressing Neuroinflammation Through Regulation of miRNA-Mediated Signaling Pathways. PMID:31497013
p13CMFA: Parsimonious 13C metabolic flux analysis. PMID:31490922
Bioinformatic evidences and analysis of putative biomarkers in pancreatic ductal adenocarcinoma. PMID:31489384
Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy. PMID:31484655
Interrogation of a live-attenuated enterotoxigenic Escherichia coli vaccine highlights features unique to wild-type infection. PMID:31482013
Complex Responses to Hydrogen Peroxide and Hypochlorous Acid by the Probiotic Bacterium Lactobacillus reuteri. PMID:31481604
Modulating Pathogenesis with Mobile-CRISPRi. PMID:31481541
Peripheral blood DNA methylation differences in twin pairs discordant for Alzheimer's disease. PMID:31477183
Dietary Effects on Dahl Salt-Sensitive Hypertension, Renal Damage, and the T Lymphocyte Transcriptome. PMID:31476910
Lymphatic vessels interact dynamically with the hair follicle stem cell niche during skin regeneration in vivo. PMID:31475747
Prospects of genomic resources available at the global databases for the flora of United Arab Emirates. PMID:31475085
A Tridimensional Model for NK Cell-Mediated ADCC of Follicular Lymphoma. PMID:31475004
Screening and identification of potential target genes in head and neck cancer using bioinformatics analysis. PMID:31452775
Identification of aberrantly methylated differentially expressed genes in glioblastoma multiforme and their association with patient survival. PMID:31452706
Calvarial osteoblast gene expression in patients with craniosynostosis leads to novel polygenic mouse model. PMID:31442251
The Inducible Response of the Nematode Caenorhabditis elegans to Members of Its Natural Microbiota Across Development and Adult Life. PMID:31440221
miR-30 Family miRNAs Mediate the Effect of Chronic Social Defeat Stress on Hippocampal Neurogenesis in Mouse Depression Model. PMID:31440139
An elastic-net logistic regression approach to generate classifiers and gene signatures for types of immune cells and T helper cell subsets. PMID:31438843
Statistical genomics in rare cancer. PMID:31437624
Identification of miRNAs involved in fruit ripening by deep sequencing of Olea europaea L. transcriptome. PMID:31437230
Gene networks underlying the early regulation of Paraburkholderia phytofirmans PsJN induced systemic resistance in Arabidopsis. PMID:31437216
FXYD5 (Dysadherin) upregulation predicts shorter survival and reveals platinum resistance in high-grade serous ovarian cancer patients. PMID:31434988
Inhibition of GATA2 restrains cell proliferation and enhances apoptosis and chemotherapy mediated apoptosis in human GATA2 overexpressing AML cells. PMID:31434974
Regulation of Macrophage Foam Cell Formation During Nitrogen Mustard (NM)-Induced Pulmonary Fibrosis by Lung Lipids. PMID:31428777
Dysregulation of DNA methylation patterns may identify patients with breast cancer resistant to endocrine therapy: A predictive classifier based on differentially methylated regions. PMID:31423189
Microglia affect α-synuclein cell-to-cell transfer in a mouse model of Parkinson's disease. PMID:31419995
Moving from Empirical to Rational Vaccine Design in the 'Omics' Era. PMID:31416125
Assessing phenotype order in molecular data. PMID:31409831
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
Oct4 and Hnf4α-induced hepatic stem cells ameliorate chronic liver injury in liver fibrosis model. PMID:31404112
Nascent Polypeptide Domain Topology and Elongation Rate Direct the Cotranslational Hierarchy of Hsp70 and TRiC/CCT. PMID:31400849
Physiological and Transcriptional Responses of Candida parapsilosis to Exogenous Tyrosol. PMID:31399405
Accurate ethnicity prediction from placental DNA methylation data. PMID:31399127
Can Biofilm Be Reversed Through Quorum Sensing in Pseudomonas aeruginosa? PMID:31396166
Folate can promote the methionine-dependent reprogramming of glioblastoma cells towards pluripotency. PMID:31395852
Linker histones are fine-scale chromatin architects modulating developmental decisions in Arabidopsis. PMID:31391082
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Tumour-infiltrating CD8+ lymphocytes and colorectal cancer recurrence by tumour and nodal stage. PMID:31388185
Interaction Among Sex, Aging, and Epigenetic Processes Concerning Visceral Fat, Insulin Resistance, and Dyslipidaemia. PMID:31379754
Epicardial cells derived from human embryonic stem cells augment cardiomyocyte-driven heart regeneration. PMID:31375810
Differential gene expression analysis reveals novel genes and pathways in pediatric septic shock patients. PMID:31375728
Gene Expression Profiling Reveals that PXR Activation Inhibits Hepatic PPARα Activity and Decreases FGF21 Secretion in Male C57Bl6/J Mice. PMID:31374856
Exploring induced pluripotency in human fibroblasts via construction, validation, and application of a gene regulatory network. PMID:31374103
Dysregulation of the histone demethylase KDM6B in alcohol dependence is associated with epigenetic regulation of inflammatory signaling pathways. PMID:31373129
RNA sequencing data of cultured primary rat Müller cells, the spontaneously immortalized rat Müller cell line, SIRMu-1, and the SV40-transformed rat Müller cell line, rMC-1. PMID:31372389
Disparity in Tumor Immune Microenvironment of Breast Cancer and Prognostic Impact: Asian Versus Western Populations. PMID:31371522
The prognostic value of JUNB-positive CTCs in metastatic breast cancer: from bioinformatics to phenotypic characterization. PMID:31370904
Cell-type-specific resolution epigenetics without the need for cell sorting or single-cell biology. PMID:31366909
Daphnia stressor database: Taking advantage of a decade of Daphnia '-omics' data for gene annotation. PMID:31366898
Evaluation of the Common Molecular Basis in Alzheimer's and Parkinson's Diseases. PMID:31366155
Mining of Self-Organizing Map Gene-Expression Portraits Reveals Prognostic Stratification of HPV-Positive Head and Neck Squamous Cell Carcinoma. PMID:31357501
Dramatic changes in gene expression in different forms of Crithidia fasciculata reveal potential mechanisms for insect-specific adhesion in kinetoplastid parasites. PMID:31356610
Identification and Application of Gene Expression Signatures Associated with Lifespan Extension. PMID:31353263
Circular RNAs are differentially expressed in prostate cancer and are potentially associated with resistance to enzalutamide. PMID:31341219
Anti-miRNA Oligonucleotide Therapy for Chondrosarcoma. PMID:31341031
L1TD1 - a prognostic marker for colon cancer. PMID:31337362
Discovery and Validation of Novel Biomarkers for Detection of Epithelial Ovarian Cancer. PMID:31336942
Cultivation and Transcriptional Analysis of a Canonical Nitrospira Under Stable Growth Conditions. PMID:31333593
The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation. PMID:31329950
Data-driven characterization of molecular phenotypes across heterogeneous sample collections. PMID:31329928
AKAP6 and phospholamban colocalize and interact in HEK-293T cells and primary murine cardiomyocytes. PMID:31325238
Profiling microRNA expression in murine bone healing and non-union formation: Role of miR-140 during the early stage of bone healing. PMID:31323027
Identification and characterization of sexual dimorphism‑linked gene expression profile in hepatocellular carcinoma. PMID:31322260
mTORC1/AMPK responses define a core gene set for developmental cell fate switching. PMID:31319820
Transcriptional Regulation of the Glucose-6-Phosphate/Phosphate Translocator 2 Is Related to Carbon Exchange Across the Chloroplast Envelope. PMID:31316533
Changes in nuclear and cytoplasmic microRNA distribution in response to hypoxic stress. PMID:31316122
Density distribution of gene expression profiles and evaluation of using maximal information coefficient to identify differentially expressed genes. PMID:31314810
A Combined Transcriptomic and Genomic Analysis Identifies a Gene Signature Associated With the Response to Anti-TNF Therapy in Rheumatoid Arthritis. PMID:31312201
Regulation of the unfolded protein response through ATF4 and FAM129A in prostate cancer. PMID:31312022
Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma. PMID:31310053
Long Noncoding RNA Expression Profile in BV2 Microglial Cells Exposed to Lipopolysaccharide. PMID:31309106
Anti-inflammatory nutrition with high protein attenuates cardiac and skeletal muscle alterations in a pulmonary arterial hypertension model. PMID:31308383
Clinical update on head and neck cancer: molecular biology and ongoing challenges. PMID:31308358
PRPF40A as a potential diagnostic and prognostic marker is upregulated in pancreatic cancer tissues and cell lines: an integrated bioinformatics data analysis. PMID:31303762
Inferring Regulatory Programs Governing Region Specificity of Neuroepithelial Stem Cells during Early Hindbrain and Spinal Cord Development. PMID:31302154
Retention of paternal DNA methylome in the developing zebrafish germline. PMID:31296860
Evaluating single-subject study methods for personal transcriptomic interpretations to advance precision medicine. PMID:31296218
MCF-7 as a Model for Functional Analysis of Breast Cancer Risk Variants. PMID:31292138
Integration of probabilistic regulatory networks into constraint-based models of metabolism with applications to Alzheimer's disease. PMID:31291905
Septin 9 isoforms promote tumorigenesis in mammary epithelial cells by increasing migration and ECM degradation through metalloproteinase secretion at focal adhesions. PMID:31285548
Genome-scale metabolic model of the rat liver predicts effects of diet restriction. PMID:31285465
Surface PEGylation suppresses pulmonary effects of CuO in allergen-induced lung inflammation. PMID:31277695
Identification of diagnostic markers for major depressive disorder by cross-validation of data from whole blood samples. PMID:31275757
Gene coexpression network for trans-1,4-polyisoprene biosynthesis involving mevalonate and methylerythritol phosphate pathways in Eucommia ulmoides Oliver. PMID:31275023
Context-Specific Transcription Factor Functions Regulate Epigenomic and Transcriptional Dynamics during Cardiac Reprogramming. PMID:31271750
Estimation of Transcription Factor Activity in Knockdown Studies. PMID:31270369
Identification of Genes With Enriched Expression in Early Developing Mouse Cone Photoreceptors. PMID:31260032
L1000 Viewer: A Search Engine and Web Interface for the LINCS Data Repository. PMID:31258549
Quantitative proteomics and single-nucleus transcriptomics of the sinus node elucidates the foundation of cardiac pacemaking. PMID:31253831
Ethylene-mediated improvement in sucrose accumulation in ripening sugarcane involves increased sink strength. PMID:31253103
Inferring Interaction Networks From Multi-Omics Data. PMID:31249591
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
Ethylene causes transcriptomic changes in Synechocystis during phototaxis. PMID:31245714
Dark period transcriptomic and metabolic profiling of two diverse Eutrema salsugineum accessions. PMID:31245703
Cross-species complementation reveals conserved functions for EARLY FLOWERING 3 between monocots and dicots. PMID:31245666
C/EBPβ-LIP induces cancer-type metabolic reprogramming by regulating the let-7/LIN28B circuit in mice. PMID:31240246
Genome-wide methylation in alcohol use disorder subjects: implications for an epigenetic regulation of the cortico-limbic glucocorticoid receptors (NR3C1). PMID:31239533
Pollination Type Recognition from a Distance by the Ovary Is Revealed Through a Global Transcriptomic Analysis. PMID:31238522
Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. PMID:31236944
An Oncogenic Role for Four-Jointed Box 1 (FJX1) in Nasopharyngeal Carcinoma. PMID:31236144
Screening of Candida albicans GRACE library revealed a unique pattern of biofilm formation under repression of the essential gene ILS1. PMID:31235750
Axonal pathology in hPSC-based models of Parkinson's disease results from loss of Nrf2 transcriptional activity at the Map1b gene locus. PMID:31235589
miR-26a-5p is a Stable Reference Gene for miRNA Studies in Chondrocytes from Developing Human Cartilage. PMID:31234552
Core regulon of the global anaerobic regulator Anr targets central metabolism functions in Pseudomonas species. PMID:31227753
Polymorphisms of the cryptochrome 2 and mitoguardin 2 genes are associated with the variation of lipid-related traits in Duroc pigs. PMID:31227735
Next-Generation Sequencing Reveals Increased Anti-oxidant Response and Ecdysone Signaling in STAT Supercompetitors in Drosophila. PMID:31227525
Prophylactic inhibition of soluble epoxide hydrolase delays onset of nephritis and ameliorates kidney damage in NZB/W F1 mice. PMID:31222024
The glycan CA19-9 promotes pancreatitis and pancreatic cancer in mice. PMID:31221853
Genomic knockout of alms1 in zebrafish recapitulates Alström syndrome and provides insight into metabolic phenotypes. PMID:31220269
High similarity of IgG antibody profiles in blood and saliva opens opportunities for saliva based serology. PMID:31220138
BCScreen: A gene panel to test for breast carcinogenesis in chemical safety screening. PMID:31218268
MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature. PMID:31217513
Pseudomonas donghuensis HYS virulence towards Caenorhabditis elegans is regulated by the Cbr/Crc system. PMID:31217473
Methylome-Wide Association Study in Peripheral White Blood Cells Focusing on Central Obesity and Inflammation. PMID:31212707
Carriage of Shiga toxin phage profoundly affects Escherichia coli gene expression and carbon source utilization. PMID:31208335
Insulin Sensitivity Is Associated with Lipoprotein Lipase (LPL) and Catenin Delta 2 (CTNND2) DNA Methylation in Peripheral White Blood Cells in Non-Diabetic Young Women. PMID:31208038
DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes. PMID:31206562
Multi omics analysis of fibrotic kidneys in two mouse models. PMID:31201317
SIMON, an Automated Machine Learning System, Reveals Immune Signatures of Influenza Vaccine Responses. PMID:31201239
Dissecting the Prognostic Significance and Functional Role of Progranulin in Chronic Lymphocytic Leukemia. PMID:31200555
Comprehensive bioinformatics analysis of trabecular meshwork gene expression data to unravel the molecular pathogenesis of primary open-angle glaucoma. PMID:31197946
Risk of spontaneous preterm birth and fetal growth associates with fetal SLIT2. PMID:31194736
Identification of Breast Cancer Stem Cell Related Genes Using Functional Cellular Assays Combined With Single-Cell RNA Sequencing in MDA-MB-231 Cells. PMID:31191614
Identification of novel biomarkers and candidate small molecule drugs in non-small-cell lung cancer by integrated microarray analysis. PMID:31190860
Overexpression of the MYB29 transcription factor affects aliphatic glucosinolate synthesis in Brassica oleracea. PMID:31190320
Cell Cycle-Dependent Regulation and Function of ARGONAUTE1 in Plants. PMID:31189739
Specialized eRpL22 paralogue-specific ribosomes regulate specific mRNA translation in spermatogenesis in Drosophila melanogaster. PMID:31188709
Molecular Signature of Asthma-Enhanced Sensitivity to CuO Nanoparticle Aerosols from 3D Cell Model. PMID:31188557
miR-17-92 and miR-106b-25 clusters regulate beta cell mitotic checkpoint and insulin secretion in mice. PMID:31187215
Dissecting the Stromal Signaling and Regulation of Myeloid Cells and Memory Effector T Cells in Pancreatic Cancer. PMID:31186314
Annotation and Expression of IDN2-like and FDM-like Genes in Sexual and Aposporous Hypericum perforatum L. accessions. PMID:31181659
Genetic resistance to DEHP-induced transgenerational endocrine disruption. PMID:31181066
Ovule Gene Expression Analysis in Sexual and Aposporous Apomictic Hypericum perforatum L. (Hypericaceae) Accessions. PMID:31178879
The role of TNF-α in chordoma progression and inflammatory pathways. PMID:31175552
Identification of microRNAs associated with the aggressiveness of prolactin pituitary tumors using bioinformatic analysis. PMID:31173251
Identification of key candidate genes involved in melanoma metastasis. PMID:31173190
Differentially expressed genes for atrial fibrillation identified by RNA sequencing from paired human left and right atrial appendages. PMID:31172864
Mitochondrial fusion is required for regulation of mitochondrial DNA replication. PMID:31170154
Tertiary lymphoid structures in the choroid plexus in neuropsychiatric lupus. PMID:31167973
Vitamin A Metabolism by Dendritic Cells Triggers an Antimicrobial Response against Mycobacterium tuberculosis. PMID:31167948
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms. PMID:31165139
Toxicity mechanisms of ZnO UV-filters used in sunscreens toward the model cyanobacteria Synechococcus elongatus PCC 7942. PMID:31161548
RNA sequencing of isolated cell populations expressing human APOL1 G2 risk variant reveals molecular correlates of sickle cell nephropathy in zebrafish podocytes. PMID:31158233
PRC2-Mediated H3K27me3 Contributes to Transcriptional Regulation of FIT-Dependent Iron Deficiency Response. PMID:31156682
Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice. PMID:31150625
An overview of publicly available patient-centered prostate cancer datasets. PMID:31143673
Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. PMID:31142855
Map and model-moving from observation to prediction in toxicogenomics. PMID:31140561
Cytochrome P450 Monooxygenase-Mediated Metabolic Utilization of Benzo[a]Pyrene by Aspergillus Species. PMID:31138742
Proton-irradiated breast cells: molecular points of view. PMID:31135901
Cannabinoid Receptor 1 Blockade Attenuates Obesity and Adipose Tissue Type 1 Inflammation Through miR-30e-5p Regulation of Delta-Like-4 in Macrophages and Consequently Downregulation of Th1 Cells. PMID:31134094
Microhomologies are prevalent at Cas9-induced larger deletions. PMID:31127293
Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets. PMID:31122193
MultiPLIER: A Transfer Learning Framework for Transcriptomics Reveals Systemic Features of Rare Disease. PMID:31121115
Acid-Sensitive Ion Channels Are Expressed in Human Induced Pluripotent Stem Cell-Derived Cardiomyocytes. PMID:31119982
Killer-like receptors and GPR56 progressive expression defines cytokine production of human CD4+ memory T cells. PMID:31118448
Transcriptomic responses to diet quality and viral infection in Apis mellifera. PMID:31117959
Cold acclimation triggers major transcriptional changes in Drosophila suzukii. PMID:31117947
The lncRNA SLNCR Recruits the Androgen Receptor to EGR1-Bound Genes in Melanoma and Inhibits Expression of Tumor Suppressor p21. PMID:31116991
ChEA3: transcription factor enrichment analysis by orthogonal omics integration. PMID:31114921
Differentially and Co-expressed Genes in Embryo, Germ-Line and Somatic Tissues of Tribolium castaneum. PMID:31113821
GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data. PMID:31110304
Inactivation of nuclear histone deacetylases by EP300 disrupts the MiCEE complex in idiopathic pulmonary fibrosis. PMID:31110176
The Placental Atlas Tool (PAT): A collaborative research and discovery platform for the placental research community. PMID:31103066
Hexameric NuMA:LGN structures promote multivalent interactions required for planar epithelial divisions. PMID:31101817
Identification of three subtypes of triple-negative breast cancer with potential therapeutic implications. PMID:31101122
CiliaCarta: An integrated and validated compendium of ciliary genes. PMID:31095607
Unbiased Boolean analysis of public gene expression data for cell cycle gene identification. PMID:31091168
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer. PMID:31089686
Differential Effects of Influenza Virus NA, HA Head, and HA Stalk Antibodies on Peripheral Blood Leukocyte Gene Expression during Human Infection. PMID:31088926
Hypoxia-Induced VISTA Promotes the Suppressive Function of Myeloid-Derived Suppressor Cells in the Tumor Microenvironment. PMID:31088847
A possible role for mitochondrial-derived peptides humanin and MOTS-c in patients with Q fever fatigue syndrome and chronic fatigue syndrome. PMID:31088495
Banana (Musa acuminata) transcriptome profiling in response to rhizobacteria: Bacillus amyloliquefaciens Bs006 and Pseudomonas fluorescens Ps006. PMID:31088352
Snf2 controls pulcherriminic acid biosynthesis and antifungal activity of the biocontrol yeast Metschnikowia pulcherrima. PMID:31081214
Strain-selective efficacy of sacubitril/valsartan on carotid fibrosis in response to injury in two inbred mouse strains. PMID:31077344
AKIRIN1: A Potential New Reference Gene in Human Natural Killer Cells and Granulocytes in Sepsis. PMID:31075840
Transcriptome and physiological analyses for revealing genes involved in wheat response to endoplasmic reticulum stress. PMID:31072347
Warburg Effects in Cancer and Normal Proliferating Cells: Two Tales of the Same Name. PMID:31071451
A miR-206 regulated gene landscape enhances mammary epithelial differentiation. PMID:31069797
Data-Driven Analysis of Age, Sex, and Tissue Effects on Gene Expression Variability in Alzheimer's Disease. PMID:31068785
scNPF: an integrative framework assisted by network propagation and network fusion for preprocessing of single-cell RNA-seq data. PMID:31068142
The Hippo Pathway Blocks Mammalian Retinal Müller Glial Cell Reprogramming. PMID:31067451
Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4+ T cells. PMID:31061531
The skin transcriptome in hidradenitis suppurativa uncovers an antimicrobial and sweat gland gene signature which has distinct overlap with wounded skin. PMID:31059533
Clonal evolution patterns in acute myeloid leukemia with NPM1 mutation. PMID:31048683
Mouse models and strain-dependency of Chédiak-Higashi syndrome-associated neurologic dysfunction. PMID:31043676
Characterizing novel olfactory receptors expressed in the murine renal cortex. PMID:31042061
Therapeutic discovery for marrow failure with MDS predisposition using pluripotent stem cells. PMID:31039138
Associations between Maternal Tobacco Smoke Exposure and the Cord Blood [Formula: see text] DNA Methylome. PMID:31039056
Specific chromatin changes mark lateral organ founder cells in the Arabidopsis inflorescence meristem. PMID:31037302
Cyclin C Regulated Oxidative Stress Responsive Transcriptome in Mus musculus Embryonic Fibroblasts. PMID:31036676
Robust pathway-based multi-omics data integration using directed random walks for survival prediction in multiple cancer studies. PMID:31036036
Tumor suppressor SMARCB1 suppresses super-enhancers to govern hESC lineage determination. PMID:31033435
A Novel Joint Gene Set Analysis Framework Improves Identification of Enriched Pathways in Cross Disease Transcriptomic Analysis. PMID:31031796
An Open Science Approach to Artificial Intelligence in Healthcare. PMID:31022753
Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi. PMID:31020039
Two putative MmpL homologs contribute to antimicrobial resistance and nephropathy of enterohemorrhagic E. coli O157:H7. PMID:31019555
Atlas of RNA sequencing profiles for normal human tissues. PMID:31015567
Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. PMID:31015400
Ancestry patterns inferred from massive RNA-seq data. PMID:31010885
A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls. PMID:31000634
OCT4 and PAX6 determine the dual function of SOX2 in human ESCs as a key pluripotent or neural factor. PMID:30999923
Comparison of multi-tissue aging between human and mouse. PMID:30996271
Development and characterisation of acquired radioresistant breast cancer cell lines. PMID:30987655
Variants in KIAA0825 underlie autosomal recessive postaxial polydactyly. PMID:30982135
Sensitive Quantitative Proteomics of Human Hematopoietic Stem and Progenitor Cells by Data-independent Acquisition Mass Spectrometry. PMID:30975897
Identification of Target Genes at Juvenile Idiopathic Arthritis GWAS Loci in Human Neutrophils. PMID:30972099
Gene expression shifts in yellow-bellied marmots prior to natal dispersal. PMID:30971856
Functioning of Mycobacterial Heat Shock Repressors Requires the Master Virulence Regulator PhoP. PMID:30962357
FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex. PMID:30962207
Downregulation of CENPF Remodels Prostate Cancer Cells and Alters Cellular Metabolism. PMID:30957416
Identification of common highly expressed genes of Salmonella Enteritidis by in silico prediction of gene expression and in vitro transcriptomic analysis. PMID:30953073
Influenza A Reinfection in Sequential Human Challenge: Implications for Protective Immunity and "Universal" Vaccine Development. PMID:30953061
exRNA Atlas Analysis Reveals Distinct Extracellular RNA Cargo Types and Their Carriers Present across Human Biofluids. PMID:30951672
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. PMID:30951143
Multi-omics Analysis Reveals Sequential Roles for ABA during Seed Maturation. PMID:30948555
The role of the GATA transcription factor AreB in regulation of nitrogen and carbon metabolism in Aspergillus nidulans. PMID:30939206
Gene set meta-analysis with Quantitative Set Analysis for Gene Expression (QuSAGE). PMID:30939133
Transcriptome Sequence of Antibiotic-Treated Pseudomonas aeruginosa. PMID:30938705
Elevated Plasma microRNA-105-5p Level in Patients With Idiopathic Parkinson's Disease: A Potential Disease Biomarker. PMID:30936821
Progesterone Receptor Attenuates STAT1-Mediated IFN Signaling in Breast Cancer. PMID:30936295
Transcriptional and Chemical Changes in Soybean Leaves in Response to Long-Term Aphid Colonization. PMID:30930925
Accumulating Transcriptome Drift Precedes Cell Aging in Human Umbilical Cord-Derived Mesenchymal Stromal Cells Serially Cultured to Replicative Senescence. PMID:30924318
A Pathway-Based Strategy to Identify Biomarkers for Lung Cancer Diagnosis and Prognosis. PMID:30923439
Characterization of the European Sea Bass (Dicentrarchus labrax) Gonadal Transcriptome During Sexual Development. PMID:30919121
Transcriptional Analysis of the Human IgE-Expressing Plasma Cell Differentiation Pathway. PMID:30915071
let-7 coordinates the transition to adulthood through a single primary and four secondary targets. PMID:30910805
Repression of Germline Genes in Caenorhabditis elegans Somatic Tissues by H3K9 Dimethylation of Their Promoters. PMID:30910798
Advancing Computational Toxicology in the Big Data Era by Artificial Intelligence: Data-Driven and Mechanism-Driven Modeling for Chemical Toxicity. PMID:30907586
Integrated transcriptome interactome study of oncogenes and tumor suppressor genes in breast cancer. PMID:30906836
Inflammatory monocytes are detrimental to the host immune response during acute infection with Cryptococcus neoformans. PMID:30897162
Conformational Engineering of HIV-1 Env Based on Mutational Tolerance in the CD4 and PG16 Bound States. PMID:30894475
Metabolic Regulators Nampt and Sirt6 Serially Participate in the Macrophage Interferon Antiviral Cascade. PMID:30886604
A Systems Vaccinology Approach Reveals the Mechanisms of Immunogenic Responses to Hantavax Vaccination in Humans. PMID:30886186
Identification of Important Effector Proteins in the FOXJ1 Transcriptional Network Associated With Ciliogenesis and Ciliary Function. PMID:30881373
DDOT: A Swiss Army Knife for Investigating Data-Driven Biological Ontologies. PMID:30878356
Copper transporter COPT5 participates in the crosstalk between vacuolar copper and iron pools mobilisation. PMID:30874615
Analysis of differential gene expression and alternative splicing is significantly influenced by choice of reference genome. PMID:30872414
Extracellular Vesicles as Diagnostics and Therapeutics for Structural Epilepsies. PMID:30871144
Clonal analyses of refractory testicular germ cell tumors. PMID:30870501
Herb Target Prediction Based on Representation Learning of Symptom related Heterogeneous Network. PMID:30867892
Bioinformatic exploration of OLFML2B overexpression in gastric cancer base on multiple analyzing tools. PMID:30866865
Glatiramer Acetate modulates ion channels expression and calcium homeostasis in B cell of patients with relapsing-remitting multiple sclerosis. PMID:30862866
Highly Resolved Systems Biology to Dissect the Etioplast-to-Chloroplast Transition in Tobacco Leaves. PMID:30862726
Regulatory network reconstruction of five essential microRNAs for survival analysis in breast cancer by integrating miRNA and mRNA expression datasets. PMID:30859354
Kaiso is required for MTG16-dependent effects on colitis-associated carcinoma. PMID:30858547
Transcriptional Analysis Shows a Robust Host Response to Toxoplasma gondii during Early and Late Chronic Infection in Both Male and Female Mice. PMID:30858341
Identification of Novel Interaction Partners of Ets-1: Focus on DNA Repair. PMID:30857266
The metabolic network coherence of human transcriptomes is associated with genetic variation at the cadherin 18 locus. PMID:30852652
Leveraging Big Data to Transform Drug Discovery. PMID:30848458
Automated exploration of gene ontology term and pathway networks with ClueGO-REST. PMID:30847467
Linking Terpene Synthases to Sesquiterpene Metabolism in Grapevine Flowers. PMID:30846994
A SIR-independent role for cohesin in subtelomeric silencing and organization. PMID:30842278
A new computational drug repurposing method using established disease-drug pair knowledge. PMID:30840053
Lifelong Football Training: Effects on Autophagy and Healthy Longevity Promotion. PMID:30837897
Folate Repletion after Deficiency Induces Irreversible Genomic and Transcriptional Changes in Human Papillomavirus Type 16 (HPV16)-Immortalized Human Keratinocytes. PMID:30836646
Minor Isozymes Tailor Yeast Metabolism to Carbon Availability. PMID:30834327
The Epstein-Barr virus EBNA1 protein modulates the alternative splicing of cellular genes. PMID:30832682
Direct reprogramming to human nephron progenitor-like cells using inducible piggyBac transposon expression of SNAI2-EYA1-SIX1. PMID:30827514
Targetome analysis of chaperone-mediated autophagy in cancer cells. PMID:30821613
Don't brush off buccal data heterogeneity. PMID:30821575
Silicon supply affects the root transcriptome of Brassica napus L. PMID:30820649
Comparing DNA methylation profiles in saliva and intestinal mucosa. PMID:30819108
Rapalog resistance is associated with mesenchymal-type changes in Tsc2-null cells. PMID:30816188
Clinical and research applications of a brain tumor tissue bank in the age of precision medicine. PMID:30816054
FAIRness and Usability for Open-access Omics Data Systems. PMID:30815061
The analysis of a time-course transcriptome profile by systems biology approaches reveals key molecular processes in acute kidney injury. PMID:30815016
hsa-miR-301a- and SOX10-dependent miRNA-TF-mRNA regulatory circuits in breast cancer. PMID:30814872
Loss of Stromal Galectin-1 Enhances Multiple Myeloma Development: Emphasis on a Role in Osteoclasts. PMID:30813402
Podocyte-specific expression of Cre recombinase promotes glomerular basement membrane thickening. PMID:30810063
NADH Dehydrogenases in Pseudomonas aeruginosa Growth and Virulence. PMID:30804898
Circadian regulation in human white adipose tissue revealed by transcriptome and metabolic network analysis. PMID:30804433
Differential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive Tract. PMID:30801031
The prognostic landscape of interactive biological processes presents treatment responses in cancer. PMID:30799199
Circular RNAs are temporospatially regulated throughout development and ageing in the rat. PMID:30796328
Correlation-adjusted regression survival scores for high-dimensional variable selection. PMID:30793795
Epigenome-wide association study in peripheral white blood cells involving insulin resistance. PMID:30792424
Physiological and Transcriptional Responses in Weaned Piglets Fed Diets with Varying Phosphorus and Calcium Levels. PMID:30791512
Global transcriptional regulation of innate immunity by ATF-7 in C. elegans. PMID:30789901
Genetic programming of macrophages generates an in vitro model for the human erythroid island niche. PMID:30787325
Identification of Potential Key Genes and Pathways in Early-Onset Colorectal Cancer Through Bioinformatics Analysis. PMID:30786729
Analysis of the mRNAs in Spores of Bacillus subtilis. PMID:30782632
The Impact of the Wheat Rht-B1b Semi-Dwarfing Allele on Photosynthesis and Seed Development Under Field Conditions. PMID:30778362
Comparative Transcriptomics Between Zebrafish and Mammals: A Roadmap for Discovery of Conserved and Unique Signaling Pathways in Physiology and Disease. PMID:30775367
Unveiling the Link Between Inflammation and Adaptive Immunity in Breast Cancer. PMID:30761130
CD56dim CD16- Natural Killer Cell Profiling in Melanoma Patients Receiving a Cancer Vaccine and Interferon-α. PMID:30761123
Isoprene Acts as a Signaling Molecule in Gene Networks Important for Stress Responses and Plant Growth. PMID:30760638
Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance. PMID:30760637
Mapping Metabolic Events in the Cancer Cell Cycle Reveals Arginine Catabolism in the Committed SG2M Phase. PMID:30759381
IDO1 inhibition potentiates vaccine-induced immunity against pancreatic adenocarcinoma. PMID:30747725
Nuclear import of the DSCAM-cytoplasmic domain drives signaling capable of inhibiting synapse formation. PMID:30745319
Identification of potential blood biomarkers for Parkinson's disease by gene expression and DNA methylation data integration analysis. PMID:30744671
The genetic requirements of fatty acid import by Mycobacterium tuberculosis within macrophages. PMID:30735132
Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. PMID:30733564
Sympathetic nervous system controls resolution of inflammation via regulation of repulsive guidance molecule A. PMID:30733433
Data mining for mutation-specific targets in acute myeloid leukemia. PMID:30728456
An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats. PMID:30728393
The bovine alveolar macrophage DNA methylome is resilient to infection with Mycobacterium bovis. PMID:30728374
Shambhala: a platform-agnostic data harmonizer for gene expression data. PMID:30727942
Boosting γδ T cell-mediated antibody-dependent cellular cytotoxicity by PD-1 blockade in follicular lymphoma. PMID:30723586
Comparison of RNA-Seq and Microarray Gene Expression Platforms for the Toxicogenomic Evaluation of Liver From Short-Term Rat Toxicity Studies. PMID:30723492
Amplified Host Defense by Toll-Like Receptor-Mediated Downregulation of the Glucocorticoid-Induced Leucine Zipper (GILZ) in Macrophages. PMID:30723476
Structural architecture of a dimeric class C GPCR based on co-trafficking of sweet taste receptor subunits. PMID:30723160
Mucor circinelloides Thrives inside the Phagosome through an Atf-Mediated Germination Pathway. PMID:30723131
Characterisation and validation of Mel38; A multi-tissue microRNA signature of cutaneous melanoma. PMID:30721246
Bioinformatic analysis of next‑generation sequencing data to identify dysregulated genes in fibroblasts of idiopathic pulmonary fibrosis. PMID:30720061
Combining data from TCGA and GEO databases and reverse transcription quantitative PCR validation to identify gene prognostic markers in lung cancer. PMID:30718962
Inferring Gene Regulatory Networks from a Population of Yeast Segregants. PMID:30718595
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub. PMID:30718394
Latent network-based representations for large-scale gene expression data analysis. PMID:30717663
Temporal Change of Extracellular Matrix during Vein Arterialization Remodeling in Rats. PMID:30717394
Network-based identification of critical regulators as putative drivers of human cleft lip. PMID:30704473
SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis. PMID:30698691
Loss of CRWN Nuclear Proteins Induces Cell Death and Salicylic Acid Defense Signaling. PMID:30696746
Venous identity requires BMP signalling through ALK3. PMID:30692543
Assessment of weighted topological overlap (wTO) to improve fidelity of gene co-expression networks. PMID:30691386
X-ray irradiation induces subtle changes in the genome-wide distribution of DNA hydroxymethylation with opposing trends in genic and intergenic regions. PMID:30691379
Hypoxia Is Not a Main Stress When Mycobacterium tuberculosis Is in a Dormancy-Like Long-Chain Fatty Acid Environment. PMID:30687646
Drug repositioning for dengue haemorrhagic fever by integrating multiple omics analyses. PMID:30679503
Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PMID:30677026
Identification of Blood Biomarkers for Alzheimer's Disease Through Computational Prediction and Experimental Validation. PMID:30671019
Loss of miR-210 leads to progressive retinal degeneration in Drosophila melanogaster. PMID:30670478
CMEP: a database for circulating microRNA expression profiling. PMID:30668638
IRF4 and IRGs Delineate Clinically Relevant Gene Expression Signatures in Systemic Lupus Erythematosus and Rheumatoid Arthritis. PMID:30666255
Comparative transcriptomic analysis unveils interactions between the regulatory CarS protein and light response in Fusarium. PMID:30665350
Identification of key genes and pathways involved in microsatellite instability in colorectal cancer. PMID:30664178
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
Illuminating spatial A-to-I RNA editing signatures within the Drosophila brain. PMID:30659150
Homoharringtonine deregulates MYC transcriptional expression by directly binding NF-κB repressing factor. PMID:30659143
Oligodendrocyte Progenitor Cells Become Regionally Diverse and Heterogeneous with Age. PMID:30654924
Inhibition of Pannexin 1 Reduces the Tumorigenic Properties of Human Melanoma Cells. PMID:30654593
p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation. PMID:30651074
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. PMID:30649296
MLPA is a practical and complementary alternative to CMA for diagnostic testing in patients with autism spectrum disorders and identifying new candidate CNVs associated with autism. PMID:30647996
Systems Biology Approach to Identify Novel Genomic Determinants for Pancreatic Cancer Pathogenesis. PMID:30644396
ALS-implicated protein TDP-43 sustains levels of STMN2, a mediator of motor neuron growth and repair. PMID:30643292
TULP3: A potential biomarker in colorectal cancer? PMID:30640939
HSP90 inhibitor geldanamycin reverts IL-13- and IL-17-induced airway goblet cell metaplasia. PMID:30640172
Circulating Tumor Cell Clustering Shapes DNA Methylation to Enable Metastasis Seeding. PMID:30633912
Computational translation of genomic responses from experimental model systems to humans. PMID:30629591
Meta-analysis of gene expression profiles in long-term non-progressors infected with HIV-1. PMID:30626383
Transcriptomic profiles of tissues from rats treated with anticancer drug combinations. PMID:30620345
Reciprocal control of motility and biofilm formation by the PdhS2 two-component sensor kinase of Agrobacterium tumefaciens. PMID:30620265
HMGN1 and R848 Synergistically Activate Dendritic Cells Using Multiple Signaling Pathways. PMID:30619338
Iron Regulation in Clostridioides difficile. PMID:30619231
A Longitudinal Study of the Association between Mammographic Density and Gene Expression in Normal Breast Tissue. PMID:30613869
lncRNA-based study of epigenetic regulations in diabetic peripheral neuropathy. PMID:30607320
Re-annotation of eight Drosophila genomes. PMID:30599046
An internal ribosome entry site in the coding region of tyrosyl-DNA phosphodiesterase 2 drives alternative translation start. PMID:30593505
Modeling human prostate cancer progression in vitro. PMID:30590461
Low STYK1 expression indicates poor prognosis in gastric cancer. PMID:30584361
Camphor white oil induces tumor regression through cytotoxic T cell-dependent mechanisms. PMID:30582219
MeDEStrand: an improved method to infer genome-wide absolute methylation levels from DNA enrichment data. PMID:30577750
Impaired immune surveillance accelerates accumulation of senescent cells and aging. PMID:30575733
Downregulation of the Vitamin D Receptor Regulated Gene Set in the Hippocampus After MDMA Treatment. PMID:30559663
RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics. PMID:30558267
Factor cooperation for chromosome discrimination in Drosophila. PMID:30541149
Identification of molecular signatures of cystic fibrosis disease status with plasma-based functional genomics. PMID:30540547
Aberrantly expressed long noncoding RNAs and genes in Parkinson's disease. PMID:30538480
A transcriptomics analysis of the Tbx5 paralogues in zebrafish. PMID:30532148
LCE: an open web portal to explore gene expression and clinical associations in lung cancer. PMID:30532070
CNOT3 targets negative cell cycle regulators in non-small cell lung cancer development. PMID:30531840
A Serum-Induced Transcriptome and Serum Cytokine Signature Obtained at Diagnosis Correlates with the Development of Early Pancreatic Ductal Adenocarcinoma Metastasis. PMID:30530849
Mms21: A Putative SUMO E3 Ligase in Candida albicans That Negatively Regulates Invasiveness and Filamentation, and Is Required for the Genotoxic and Cellular Stress Response. PMID:30530734
SerpinA3N is a novel hypothalamic gene upregulated by a high-fat diet and leptin in mice. PMID:30519364
Danger signals activate a putative innate immune system during regeneration in a filamentous fungus. PMID:30500812
Genome-wide identification of RETINOBLASTOMA RELATED 1 binding sites in Arabidopsis reveals novel DNA damage regulators. PMID:30500810
Tracking microRNA Processing Signals by Degradome Sequencing Data Analysis. PMID:30487815
Two functionally redundant sources of retinoic acid secure spermatogonia differentiation in the seminiferous epithelium. PMID:30487180
PNPase is involved in the coordination of mRNA degradation and expression in stationary phase cells of Escherichia coli. PMID:30486791
Relation between Biofilm and Virulence in Vibrio tapetis: A Transcriptomic Study. PMID:30486310
SkeletalVis: an exploration and meta-analysis data portal of cross-species skeletal transcriptomics data. PMID:30481257
Genetic, Transcriptome, Proteomic, and Epidemiological Evidence for Blood-Brain Barrier Disruption and Polymicrobial Brain Invasion as Determinant Factors in Alzheimer's Disease. PMID:30480234
Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models. PMID:30477446
Identifying cancer-related microRNAs based on subpathways. PMID:30472691
Network Pharmacology to Unveil the Biological Basis of Health-Strengthening Herbal Medicine in Cancer Treatment. PMID:30469422
Differential expression of heat shock and floral regulatory genes in pseudocarpel initials of mantled female inflorescences from Elaeis guineensis Jacq. PMID:30467592
Human Prolactinoma: A View of Protein-Protein Interaction Pattern. PMID:30464775
STE20/PAKA Protein Kinase Gene Releases an Autoinhibitory Domain through Pre-mRNA Alternative Splicing in the Dermatophyte Trichophyton rubrum. PMID:30463281
From sequencing data to gene functions: co-functional network approaches. PMID:30460054
A data citation roadmap for scientific publishers. PMID:30457573
RNase E cleavage shapes the transcriptome of Rhodobacter sphaeroides and strongly impacts phototrophic growth. PMID:30456366
RATEmiRs: the rat atlas of tissue-specific and enriched miRNAs database. PMID:30453895
BioJupies: Automated Generation of Interactive Notebooks for RNA-Seq Data Analysis in the Cloud. PMID:30447998
Screening and clinical significance of tumor markers in head and neck squamous cell carcinoma through bioinformatics analysis. PMID:30431092
Identification of hub genes with diagnostic values in pancreatic cancer by bioinformatics analyses and supervised learning methods. PMID:30428899
Comprehensive bioinformatics analysis identifies several potential diagnostic markers and potential roles of cyclin family members in lung adenocarcinoma. PMID:30425528
Deoxynivalenol Affects Cell Metabolism and Increases Protein Biosynthesis in Intestinal Porcine Epithelial Cells (IPEC-J2): DON Increases Protein Biosynthesis. PMID:30423940
Single cell network analysis with a mixture of Nested Effects Models. PMID:30423100
Conditional generative adversarial network for gene expression inference. PMID:30423066
A Comparison of the TempO-Seq S1500+ Platform to RNA-Seq and Microarray Using Rat Liver Mode of Action Samples. PMID:30420870
Increased sporulation underpins adaptation of Clostridium difficile strain 630 to a biologically-relevant faecal environment, with implications for pathogenicity. PMID:30420658
C/VDdb: A multi-omics expression profiling database for a knowledge-driven approach in cardiovascular disease (CVD). PMID:30419069
Stemformatics: visualize and download curated stem cell data. PMID:30407577
Azithromycin treatment modifies airway and blood gene expression networks in neutrophilic COPD. PMID:30406125
The metabolite BH4 controls T cell proliferation in autoimmunity and cancer. PMID:30405245
LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells. PMID:30404662
Bayesian variable selection for parametric survival model with applications to cancer omics data. PMID:30400837
Enabling precision medicine in neonatology, an integrated repository for preterm birth research. PMID:30398470
Effects of simulated microgravity on the expression profiles of RNA during osteogenic differentiation of human bone marrow mesenchymal stem cells. PMID:30397970
FAM92A Underlies Nonsyndromic Postaxial Polydactyly in Humans and an Abnormal Limb and Digit Skeletal Phenotype in Mice. PMID:30395363
Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans. PMID:30395284
PlantPAN3.0: a new and updated resource for reconstructing transcriptional regulatory networks from ChIP-seq experiments in plants. PMID:30395277
Profiling Immune Escape in Hodgkin's and Diffuse large B-Cell Lymphomas Using the Transcriptome and Immunostaining. PMID:30384489
Identification of grade and origin specific cell populations in serous epithelial ovarian cancer by single cell RNA-seq. PMID:30383866
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
Deep sequencing and miRNA profiles in alcohol-induced neuroinflammation and the TLR4 response in mice cerebral cortex. PMID:30374194
ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks. PMID:30371824
Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data. PMID:30371680
RNA-Seq-Based Analysis Reveals Heterogeneity in Mature 16S rRNA 3' Termini and Extended Anti-Shine-Dalgarno Motifs in Bacterial Species. PMID:30355764
wTO: an R package for computing weighted topological overlap and a consensus network with integrated visualization tool. PMID:30355288
Regulation of human glioma cell migration, tumor growth, and stemness gene expression using a Lck targeted inhibitor. PMID:30353164
Expression of calcium pumps is differentially regulated by histone deacetylase inhibitors and estrogen receptor alpha in breast cancer cells. PMID:30352569
Dietary fibers inhibit obesity in mice, but host responses in the cecum and liver appear unrelated to fiber-specific changes in cecal bacterial taxonomic composition. PMID:30349136
Gene expression profiling in a mouse model of Dravet syndrome. PMID:30347190
Prediction of Target Genes and Pathways Associated With Cetuximab Insensitivity in Colorectal Cancer. PMID:30336768
Single-Cell RNA Sequencing Reveals Novel Markers of Male Pituitary Stem Cells and Hormone-Producing Cell Types. PMID:30335147
A proteasome-resistant fragment of NIK mediates oncogenic NF-κB signaling in schwannomas. PMID:30335132
Comparative Study on Alternative Splicing in Human Fungal Pathogens Suggests Its Involvement During Host Invasion. PMID:30333805
Genome organization and DNA accessibility control antigenic variation in trypanosomes. PMID:30333624
Essential roles of mitochondrial biogenesis regulator Nrf1 in retinal development and homeostasis. PMID:30333037
PWWP2A binds distinct chromatin moieties and interacts with an MTA1-specific core NuRD complex. PMID:30327463
sEst: Accurate Sex-Estimation and Abnormality Detection in Methylation Microarray Data. PMID:30326623
Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium. PMID:30324023
A comparative study of endoderm differentiation in humans and chimpanzees. PMID:30322406
Early IL-10 producing B-cells and coinciding Th/Tr17 shifts during three year grass-pollen AIT. PMID:30318182
WNT signaling memory is required for ACTIVIN to function as a morphogen in human gastruloids. PMID:30311909
Translocated duplication of a targeted chromosomal segment enhances gene expression at the duplicated site and results in phenotypic changes in Aspergillus oryzae. PMID:30305913
Combining Developmental and Perturbation-Seq Uncovers Transcriptional Modules Orchestrating Neuronal Remodeling. PMID:30300589
Identification of gene expression predictors of occupational benzene exposure. PMID:30300410
Multiomics approach reveals metabolic changes in the heart at birth. PMID:30300011
Two Regulators, PA3898 and PA2100, Modulate the Pseudomonas aeruginosa Multidrug Resistance MexAB-OprM and EmrAB Efflux Pumps and Biofilm Formation. PMID:30297364
Proteome and transcriptome profiling of equine myofibrillar myopathy identifies diminished peroxiredoxin 6 and altered cysteine metabolic pathways. PMID:30289745
Early isolated V-lesion may not truly represent rejection of the kidney allograft. PMID:30287520
Identification of key genes involved in the phenotypic alterations of res (restored cell structure by salinity) tomato mutant and its recovery induced by salt stress through transcriptomic analysis. PMID:30285698
Exposure to childhood abuse is associated with human sperm DNA methylation. PMID:30279435
Increased EXT1 gene copy number correlates with increased mRNA level predicts short disease-free survival in hepatocellular carcinoma without vascular invasion. PMID:30278583
New insights into the cellular temporal response to proteostatic stress. PMID:30272558
Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease. PMID:30270042
Divergent Matrix-Remodeling Strategies Distinguish Developmental from Neoplastic Mammary Epithelial Cell Invasion Programs. PMID:30269950
Innate and adaptive signals enhance differentiation and expansion of dual-antibody autoreactive B cells in lupus. PMID:30266981
Glucocorticoid deficiency causes transcriptional and post-transcriptional reprogramming of glutamine metabolism. PMID:30266295
Candida albicans Sfl1/Sfl2 regulatory network drives the formation of pathogenic microcolonies. PMID:30252918
Synergistic combination of flavopiridol and carfilzomib targets commonly dysregulated pathways in adrenocortical carcinoma and has biomarkers of response. PMID:30250647
Fenretinide targeting of human colon cancer sphere cells through cell cycle regulation and stress-responsive activities. PMID:30250604
Comprehensive analysis of gene expression profiles associated with proliferative diabetic retinopathy. PMID:30250524
Robustness by intrinsically disordered C-termini and translational readthrough. PMID:30247639
Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. PMID:30241495
Zingerone Suppresses Tumor Development through Decreasing Cyclin D1 Expression and Inducing Mitotic Arrest. PMID:30235818
Overexpression of an auxin receptor OsAFB6 significantly enhanced grain yield by increasing cytokinin and decreasing auxin concentrations in rice panicle. PMID:30232356
Mannose Alters Gut Microbiome, Prevents Diet-Induced Obesity, and Improves Host Metabolism. PMID:30231992
Subgroup-specific immune and stromal microenvironment in medulloblastoma. PMID:30228931
Integrated Genome-Wide Analysis of Gene Expression and DNA Copy Number Variations Highlights Stem Cell-Related Pathways in Small Cell Esophageal Carcinoma. PMID:30228821
Genome-Wide Association Study Reveals Genetic Link between Diarrhea-Associated Entamoeba histolytica Infection and Inflammatory Bowel Disease. PMID:30228239
Longitudinal transcriptomic characterization of the immune response to acute hepatitis C virus infection in patients with spontaneous viral clearance. PMID:30222771
The topoisomerase 3α zinc-finger domain T1 of Arabidopsis thaliana is required for targeting the enzyme activity to Holliday junction-like DNA repair intermediates. PMID:30222730
Inhibition of neogenin fosters resolution of inflammation and tissue regeneration. PMID:30222138
Effects of hydroxyurea on CNV induction in the mouse germline. PMID:30218578
Assortment of Flowering Time and Immunity Alleles in Natural Arabidopsis thaliana Populations Suggests Immunity and Vegetative Lifespan Strategies Coevolve. PMID:30215800
Systematic Analysis of Gene Expression Profiles Controlled by hnRNP Q and hnRNP R, Two Closely Related Human RNA Binding Proteins Implicated in mRNA Processing Mechanisms. PMID:30214903
Identification of a novel gene fusion in ALT positive osteosarcoma. PMID:30214690
PAX5A and PAX5B isoforms are both efficient to drive B cell differentiation. PMID:30214688
Distinct prognostic values of mRNA expression of glutathione peroxidases in non-small cell lung cancer. PMID:30214294
Whole genome sequencing identifies high-impact variants in well-known pharmacogenomic genes. PMID:30214008
Polarized Entry of Human Parechoviruses in the Airway Epithelium. PMID:30211126
Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus. PMID:30208323
Computational prediction of changes in brain metabolic fluxes during Parkinson's disease from mRNA expression. PMID:30208076
Knockout of the Hmt1p Arginine Methyltransferase in Saccharomyces cerevisiae Leads to the Dysregulation of Phosphate-associated Genes and Processes. PMID:30206180
Genotoxic, Metabolic, and Oxidative Stresses Regulate the RNA Repair Operon of Salmonella enterica Serovar Typhimurium. PMID:30201777
An admixture mapping meta-analysis implicates genetic variation at 18q21 with asthma susceptibility in Latinos. PMID:30201514
Elevated expression of NFE2L3 predicts the poor prognosis of pancreatic cancer patients. PMID:30196752
Characterization of Spleen Transcriptome and Immunity Against Avian Colibacillosis After Immunization With Recombinant Attenuated Salmonella Vaccine Strains. PMID:30186843
A Microarray Study of Articular Cartilage in Relation to Obesity and Severity of Knee Osteoarthritis. PMID:30173558
Feasibility of developing reliable gene expression modules from FFPE derived RNA profiled on Affymetrix arrays. PMID:30169535
Transforming growth factor beta1 targets estrogen receptor signaling in bronchial epithelial cells. PMID:30165855
Post-transcriptional gene regulation by an Hfq-independent small RNA in Caulobacter crescentus. PMID:30165530
Quantitative RNA-seq Analysis Unveils Osmotic and Thermal Adaptation Mechanisms Relevant for Ectoine Production in Chromohalobacter salexigens. PMID:30158907
Differentially expressed proteins in positive versus negative HNSCC lymph nodes. PMID:30157864
Harnessing the biological complexity of Big Data from LINCS gene expression signatures. PMID:30157183
A Chromatin Basis for Cell Lineage and Disease Risk in the Human Pancreas. PMID:30145115
Fate-restricted retinal progenitor cells adopt a molecular profile and spatial position distinct from multipotent progenitor cells. PMID:30145104
Construction and analysis of mRNA, miRNA, lncRNA, and TF regulatory networks reveal the key genes associated with prostate cancer. PMID:30138363
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
Plasma microRNA markers of upper limb recovery following human stroke. PMID:30135469
Transcriptional targeting of oncogene addiction in medullary thyroid cancer. PMID:30135308
Prediction of key genes and pathways involved in trastuzumab-resistant gastric cancer. PMID:30134903
Identification of protein complexes associated with myocardial infarction using a bioinformatics approach. PMID:30132549
Dissecting the expression landscape of mitochondrial genes in lung squamous cell carcinoma and lung adenocarcinoma. PMID:30128019
Identification of genes that predict the biochemical recurrence of prostate cancer. PMID:30127947
Screening and identification of key biomarkers in bladder carcinoma: Evidence from bioinformatics analysis. PMID:30127900
Profiles of immune infiltration in colorectal cancer and their clinical significant: A gene expression-based study. PMID:30117315
Detecting Differentially Variable MicroRNAs via Model-Based Clustering. PMID:30116730
A Spatiotemporal DNA Endoploidy Map of the Arabidopsis Root Reveals Roles for the Endocycle in Root Development and Stress Adaptation. PMID:30115738
Comprehensive integrated analysis of gene expression datasets identifies key anti-cancer targets in different stages of breast cancer. PMID:30112036
QsRNA-seq: a method for high-throughput profiling and quantifying small RNAs. PMID:30107842
Revealing a human p53 universe. PMID:30107566
Machine Learning Based Toxicity Prediction: From Chemical Structural Description to Transcriptome Analysis. PMID:30103448
The effect of Tmem135 overexpression on the mouse heart. PMID:30102730
AMPK activation negatively regulates GDAP1, which influences metabolic processes and circadian gene expression in skeletal muscle. PMID:30093355
JAK-STAT signaling is activated in the kidney and peripheral blood cells of patients with focal segmental glomerulosclerosis. PMID:30093081
Marked disparity of microRNA modulation by cGMP-selective PDE5 versus PDE9 inhibitors in heart disease. PMID:30089721
BART: bioinformatics array research tool. PMID:30089462
Reconstruction of the Protein-Protein Interaction Network for Protein Complexes Identification by Walking on the Protein Pair Fingerprints Similarity Network. PMID:30087694
Myc and ChREBP transcription factors cooperatively regulate normal and neoplastic hepatocyte proliferation in mice. PMID:30087120
Consensus on Molecular Subtypes of High-Grade Serous Ovarian Carcinoma. PMID:30084834
Diagnosis of Kawasaki Disease Using a Minimal Whole-Blood Gene Expression Signature. PMID:30083721
Sensory Neuron Diversity in the Inner Ear Is Shaped by Activity. PMID:30078709
Improving knowledge on the activation of bone marrow fibroblasts in MGUS and MM disease through the automatic extraction of genes via a nonnegative matrix factorization approach on gene expression profiles. PMID:30075788
Douglas-Fir ( Pseudotsuga menziesii (Mirb.) Franco) Transcriptome Profile Changes Induced by Diesel Emissions Generated with CeO2 Nanoparticle Fuel Borne Catalyst. PMID:30075627
Combinatorial Approaches to Viral Attenuation. PMID:30073203
Gene expression analysis indicates reduced memory and cognitive functions in the hippocampus and increase in synaptic reorganization in the frontal cortex 3 weeks after MDMA administration in Dark Agouti rats. PMID:30071829
Parental high dietary arachidonic acid levels modulated the hepatic transcriptome of adult zebrafish (Danio rerio) progeny. PMID:30070994
Male increase in brain gene expression variability is linked to genetic risk for schizophrenia. PMID:30068996
PAK2-c-Myc-PKM2 axis plays an essential role in head and neck oncogenesis via regulating Warburg effect. PMID:30068946
Cardiovascular progenitor cells cultured aboard the International Space Station exhibit altered developmental and functional properties. PMID:30062101
Pattern of DNA Methylation in Daphnia: Evolutionary Perspective. PMID:30060190
The CRISPR/Cas system in Neisseria meningitidis affects bacterial adhesion to human nasopharyngeal epithelial cells. PMID:30059276
Mud2 functions in transcription by recruiting the Prp19 and TREX complexes to transcribed genes. PMID:30053068
A New Bioactive Compound From the Marine Sponge-Derived Streptomyces sp. SBT348 Inhibits Staphylococcal Growth and Biofilm Formation. PMID:30050506
Co-inhibition of mTORC1, HDAC and ESR1α retards the growth of triple-negative breast cancer and suppresses cancer stem cells. PMID:30050079
Requirements for Neurogenin2 during mouse postnatal retinal neurogenesis. PMID:30048641
Automatic extraction of gene-disease associations from literature using joint ensemble learning. PMID:30048465
Analysis of public RNA-sequencing data reveals biological consequences of genetic heterogeneity in cell line populations. PMID:30046134
Enhancer histone-QTLs are enriched on autoimmune risk haplotypes and influence gene expression within chromatin networks. PMID:30046115
Network Rewiring in Cancer: Applications to Melanoma Cell Lines and the Cancer Genome Atlas Patients. PMID:30042785
Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data. PMID:30041657
Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity. PMID:30039798
Construction of Discrete Model of Human Pluripotency in Predicting Lineage-Specific Outcomes and Targeted Knockdowns of Essential Genes. PMID:30038409
The Trithorax group protein dMLL3/4 instructs the assembly of the zygotic genome at fertilization. PMID:30037897
Investigation of epigenetic regulatory networks associated with autism spectrum disorder (ASD) by integrated global LINE-1 methylation and gene expression profiling analyses. PMID:30036398
Using Transcriptomes as Mutant Phenotypes Reveals Functional Regions of a Mediator Subunit in Caenorhabditis elegans. PMID:30030292
Dual RNA-Seq Analysis of Trichophyton rubrum and HaCat Keratinocyte Co-Culture Highlights Important Genes for Fungal-Host Interaction. PMID:30029541
The lincRNA MIRAT binds to IQGAP1 and modulates the MAPK pathway in NRAS mutant melanoma. PMID:30026510
Transcriptional Profiling of Immune-Related Genes in Leishmania infantum-Infected Mice: Identification of Potential Biomarkers of Infection and Progression of Disease. PMID:30013952
Altered Gene Expression in Prefrontal Cortex of a Fabry Disease Mouse Model. PMID:30013462
Dynamics of the Pollen Sequestrome Defined by Subcellular Coupled Omics. PMID:30007911
Integrated Analysis of Quantitative Proteome and Transcriptional Profiles Reveals the Dynamic Function of Maternally Expressed Proteins After Parthenogenetic Activation of Buffalo Oocyte. PMID:30002204
Gene expression profiles in neurological tissues during West Nile virus infection: a critical meta-analysis. PMID:30001706
Alternative empirical Bayes models for adjusting for batch effects in genomic studies. PMID:30001694
Transcriptional Alterations in the Trigeminal Ganglia, Nucleus and Peripheral Blood Mononuclear Cells in a Rat Orofacial Pain Model. PMID:29997476
The association of genomic lesions and PD-1/PD-L1 expression in resected triple-negative breast cancers. PMID:29996881
Novel dual regulators of Pseudomonas aeruginosa essential for productive biofilms and virulence. PMID:29995308
Translational Bioinformatics for Cholangiocarcinoma: Opportunities and Challenges. PMID:29989102
Expression of Adhesive Pili and the Collagen-Binding Adhesin Ace Is Activated by ArgR Family Transcription Factors in Enterococcus faecalis. PMID:29986940
MicroRNAs mediate the senescence-associated decline of NRF2 in endothelial cells. PMID:29986211
Germline DNA replication timing shapes mammalian genome composition. PMID:29986092
Predicting Risk of Postoperative Disease Recurrence in Crohn's Disease: Patients With Indolent Crohn's Disease Have Distinct Whole Transcriptome Profiles at the Time of First Surgery. PMID:29982468
Deletion of Nkx2-5 in trabecular myocardium reveals the developmental origins of pathological heterogeneity associated with ventricular non-compaction cardiomyopathy. PMID:29979676
Arsenic Reduces Gene Expression Response to Changing Salinity in Killifish. PMID:29979584
Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver. PMID:29973619
Maternal obesity has sex-dependent effects on insulin, glucose and lipid metabolism and the liver transcriptome in young adult rat offspring. PMID:29972240
Pirfenidone decreases mesothelioma cell proliferation and migration via inhibition of ERK and AKT and regulates mesothelioma tumor microenvironment in vivo. PMID:29968778
Inhibition of integrin αVβ6 changes fibril thickness of stromal collagen in experimental carcinomas. PMID:29966518
Consistent inverse correlation between DNA methylation of the first intron and gene expression across tissues and species. PMID:29958539
Histology and Transcriptome Profiles of the Mammary Gland across Critical Windows of Development in Sprague Dawley Rats. PMID:29956080
Metabolic Effects of a Chronic Dietary Exposure to a Low-Dose Pesticide Cocktail in Mice: Sexual Dimorphism and Role of the Constitutive Androstane Receptor. PMID:29950287
LONGO: an R package for interactive gene length dependent analysis for neuronal identity. PMID:29950021
GSEA-InContext: identifying novel and common patterns in expression experiments. PMID:29950010
SigMat: a classification scheme for gene signature matching. PMID:29950002
Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population. PMID:29945935
aaquetzalli is required for epithelial cell polarity and neural tissue formation in Drosophila. PMID:29942698
Stable STIM1 Knockdown in Self-Renewing Human Neural Precursors Promotes Premature Neural Differentiation. PMID:29942250
Temporal transcriptomic analysis of metabolic genes in maternal organs and placenta during murine pregnancy. PMID:29939228
Use of Haploid Model of Candida albicans to Uncover Mechanism of Action of a Novel Antifungal Agent. PMID:29938200
Regulatory RNA binding proteins contribute to the transcriptome-wide splicing alterations in human cellular senescence. PMID:29936497
Investigation of Islet2a function in zebrafish embryos: Mutants and morphants differ in morphologic phenotypes and gene expression. PMID:29927984
Co-Expression Network Analysis of AMPK and Autophagy Gene Products during Adipocyte Differentiation. PMID:29921805
Mammary molecular portraits reveal lineage-specific features and progenitor cell vulnerabilities. PMID:29921600
Developments in toxicogenomics: understanding and predicting compound-induced toxicity from gene expression data. PMID:29917034
Presymptomatic change in microRNAs modulates Tau pathology. PMID:29915328
GeNets: a unified web platform for network-based genomic analyses. PMID:29915188
SAMHD1 modulates in vitro proliferation of acute myeloid leukemia-derived THP-1 cells through the PI3K-Akt-p27 axis. PMID:29911928
Damage-associated molecular pattern recognition is required for induction of retinal neuroprotective pathways in a sex-dependent manner. PMID:29904087
MicroRNA-30 modulates metabolic inflammation by regulating Notch signaling in adipose tissue macrophages. PMID:29899524
A data mining paradigm for identifying key factors in biological processes using gene expression data. PMID:29899432
Dietary Intake of Curcumin Improves eIF2 Signaling and Reduces Lipid Levels in the White Adipose Tissue of Obese Mice. PMID:29899429
Transcriptomic immune profiling of ovarian cancers in paraneoplastic cerebellar degeneration associated with anti-Yo antibodies. PMID:29899393
KLRD1-expressing natural killer cells predict influenza susceptibility. PMID:29898768
The Probiotic Escherichia coli Strain Nissle 1917 Combats Lambdoid Bacteriophages stx and λ. PMID:29896160
SSMART: sequence-structure motif identification for RNA-binding proteins. PMID:29893814
Transcriptome analysis highlights nuclear control of chloroplast development in the shoot apex. PMID:29892011
Lmo2 expression defines tumor cell identity during T-cell leukemogenesis. PMID:29880602
The Kinase Complex mTOR Complex 2 Promotes the Follicular Migration and Functional Maturation of Differentiated Follicular Helper CD4+ T Cells During Viral Infection. PMID:29875775
Group A Streptococcus M1T1 Intracellular Infection of Primary Tonsil Epithelial Cells Dampens Levels of Secreted IL-8 Through the Action of SpyCEP. PMID:29868516
Meta-Analysis of Maternal and Fetal Transcriptomic Data Elucidates the Role of Adaptive and Innate Immunity in Preterm Birth. PMID:29867970
SV-BR-1-GM, a Clinically Effective GM-CSF-Secreting Breast Cancer Cell Line, Expresses an Immune Signature and Directly Activates CD4+ T Lymphocytes. PMID:29867922
Strong correlation of downregulated genes related to synaptic transmission and mitochondria in post-mortem autism cerebral cortex. PMID:29859039
Targeted Transcriptional Profiling of Kidney Transplant Biopsies. PMID:29854981
Disease-Specific Integration of Omics Data to Guide Functional Validation of Genetic Associations. PMID:29854229
Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. PMID:29854196
A big data pipeline: Identifying dynamic gene regulatory networks from time-course Gene Expression Omnibus data with applications to influenza infection. PMID:29846143
Identiﬁcation of candidate biomarkers and pathways associated with SCLC by bioinformatics analysis. PMID:29845250
Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data. PMID:29843593
Social interaction-induced activation of RNA splicing in the amygdala of microbiome-deficient mice. PMID:29809134
Supplementation of fructooligosaccharides to suckling piglets affects intestinal microbiota colonization and immune development. PMID:29800418
Identification of genes involved in metabolism and signalling of abscisic acid and gibberellins during Epimedium pseudowushanense B.L.Guo seed morphophysiological dormancy. PMID:29796945
A 2-transcript host cell signature distinguishes viral from bacterial diarrhea and it is influenced by the severity of symptoms. PMID:29795312
BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome. PMID:29792595
Combining NGN2 Programming with Developmental Patterning Generates Human Excitatory Neurons with NMDAR-Mediated Synaptic Transmission. PMID:29791859
Targetable vulnerabilities in T- and NK-cell lymphomas identified through preclinical models. PMID:29789628
CellAtlasSearch: a scalable search engine for single cells. PMID:29788498
Sphingosine-1-Phosphate Signaling and Metabolism Gene Signature in Pediatric Inflammatory Bowel Disease: A Matched-case Control Pilot Study. PMID:29788359
High-fructose diet during adolescent development increases neuroinflammation and depressive-like behavior without exacerbating outcomes after stroke. PMID:29787857
Reversal of siRNA-mediated gene silencing in vivo. PMID:29786096
Identification of brain metastasis genes and therapeutic evaluation of histone deacetylase inhibitors in a clinically relevant model of breast cancer brain metastasis. PMID:29784888
Biomarker microRNAs for prostate cancer metastasis: screened with a network vulnerability analysis model. PMID:29784056
Human plasma and serum extracellular small RNA reference profiles and their clinical utility. PMID:29777089
Targeting invadopodia-mediated breast cancer metastasis by using ABL kinase inhibitors. PMID:29774130
Methylation guide RNA evolution in archaea: structure, function and genomic organization of 110 C/D box sRNA families across six Pyrobaculum species. PMID:29771354
Maternal folate genes and aberrant DNA hypermethylation in pediatric acute lymphoblastic leukemia. PMID:29763473
Immunization Elicits Antigen-Specific Antibody Sequestration in Dorsal Root Ganglia Sensory Neurons. PMID:29755449
Decoding Common Features of Neurodegenerative Disorders: From Differentially Expressed Genes to Pathways. PMID:29755292
Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series. PMID:29750795
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
An integrated view of the role of miR-130b/301b miRNA cluster in prostate cancer. PMID:29744254
UFD1 contributes to MYC-mediated leukemia aggressiveness through suppression of the proapoptotic unfolded protein response. PMID:29743725
Transcriptome analysis in whole blood reveals increased microbial diversity in schizophrenia. PMID:29743478
Paternal developmental toxicant exposure is associated with epigenetic modulation of sperm and placental Pgr and Igf2 in a mouse model. PMID:29741588
MAPK Reliance via Acquired CDK4/6 Inhibitor Resistance in Cancer. PMID:29739788
Time-evolving genetic networks reveal a NAC troika that negatively regulates leaf senescence in Arabidopsis. PMID:29735710
Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia. PMID:29731978
Human serum and platelet lysate are appropriate xeno-free alternatives for clinical-grade production of human MuStem cell batches. PMID:29720259
Identification and characterization of the Komagataella phaffii mating pheromone genes. PMID:29718186
Low-level laser irradiation induces a transcriptional myotube-like profile in C2C12 myoblasts. PMID:29717386
Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). PMID:29709017
DANUBE: Data-driven meta-ANalysis using UnBiased Empirical distributions-applied to biological pathway analysis. PMID:29706661
New perspectives: systems medicine in cardiovascular disease. PMID:29699591
IncGraph: Incremental graphlet counting for topology optimisation. PMID:29698494
Epithelial-Mesenchymal Transition during Metastasis of HPV-Negative Pharyngeal Squamous Cell Carcinoma. PMID:29693014
CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system. PMID:29688349
Community-driven roadmap for integrated disease maps. PMID:29688273
Genome-wide analyses of late pollen-preferred genes conserved in various rice cultivars and functional identification of a gene involved in the key processes of late pollen development. PMID:29687350
Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder. PMID:29686828
Domains within RbpA Serve Specific Functional Roles That Regulate the Expression of Distinct Mycobacterial Gene Subsets. PMID:29686140
The TLR4 Agonist Monophosphoryl Lipid A Drives Broad Resistance to Infection via Dynamic Reprogramming of Macrophage Metabolism. PMID:29686054
Mapping Interaction Sites on Human Chemokine Receptors by Deep Mutational Scanning. PMID:29678950
Specific breast cancer prognosis-subtype distinctions based on DNA methylation patterns. PMID:29675884
Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition. PMID:29674686
BBS9 gene in nonsyndromic craniosynostosis: Role of the primary cilium in the aberrant ossification of the suture osteogenic niche. PMID:29674126
ANLN functions as a key candidate gene in cervical cancer as determined by integrated bioinformatic analysis. PMID:29670400
Global H3.3 dynamic deposition defines its bimodal role in cell fate transition. PMID:29670118
ASB1 differential methylation in ischaemic cardiomyopathy: relationship with left ventricular performance in end-stage heart failure patients. PMID:29667349
Arsenic trioxide-mediated suppression of miR-182-5p is associated with potent anti-oxidant effects through up-regulation of SESN2. PMID:29662624
Activation of TRPV3 by Wood Smoke Particles and Roles in Pneumotoxicity. PMID:29658714
Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks. PMID:29657303
FAR2 is associated with kidney disease in mice and humans. PMID:29652635
Bioinformatic analysis reveals the key pathways and genes in early-onset breast cancer. PMID:29644522
Targeting Sphingosine Kinase Isoforms Effectively Reduces Growth and Survival of Neoplastic Mast Cells With D816V-KIT. PMID:29643855
A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. PMID:29642892
Condition-Specific Modeling of Biophysical Parameters Advances Inference of Regulatory Networks. PMID:29641998
A toolbox of immunoprecipitation-grade monoclonal antibodies to human transcription factors. PMID:29638227
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
Dietary and Endocrine Regulation of Endogenous Hydrogen Sulfide Production: Implications for Longevity. PMID:29634343
Topical application of aminoglycoside antibiotics enhances host resistance to viral infections in a microbiota-independent manner. PMID:29632368
Identification of Prognostic Biomarkers by Combined mRNA and miRNA Expression Microarray Analysis in Pancreatic Cancer. PMID:29631214
TRPM2 promotes the proliferation and invasion of pancreatic ductal adenocarcinoma. PMID:29620272
Identification of key genes in non‑alcoholic fatty liver disease progression based on bioinformatics analysis. PMID:29620197
Rudhira/BCAS3 is essential for mouse development and cardiovascular patterning. PMID:29618843
Differential expression of microRNAs and other small RNAs in muscle tissue of patients with ALS and healthy age-matched controls. PMID:29618798
Global dynamics of stage-specific transcription factor binding during thymocyte development. PMID:29618724
Machine Learning Detects Pan-cancer Ras Pathway Activation in The Cancer Genome Atlas. PMID:29617658
Radiation-Induced Gene Expression Changes in High and Low Grade Breast Cancer Cell Types. PMID:29617354
Expression of the microRNA-143/145 cluster is decreased in hepatitis B virus-associated hepatocellular carcinoma and may serve as a biomarker for tumorigenesis in patients with chronic hepatitis B. PMID:29616093
Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned. PMID:29616078
Pairwise gene GO-based measures for biclustering of high-dimensional expression data. PMID:29610579
Divergence in DNA Specificity among Paralogous Transcription Factors Contributes to Their Differential In Vivo Binding. PMID:29605182
Identification of the key transcription factors in esophageal squamous cell carcinoma. PMID:29600044
Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids. PMID:29593484
GDV1 induces sexual commitment of malaria parasites by antagonizing HP1-dependent gene silencing. PMID:29590075
Heuristic algorithms for feature selection under Bayesian models with block-diagonal covariance structure. PMID:29589558
Methylation-to-Expression Feature Models of Breast Cancer Accurately Predict Overall Survival, Distant-Recurrence Free Survival, and Pathologic Complete Response in Multiple Cohorts. PMID:29581450
Comprehensive analysis of Helicobacter pylori infection-associated diseases based on miRNA-mRNA interaction network. PMID:29579224
Burden-driven feedback control of gene expression. PMID:29578536
IRF8 Regulates Transcription of Naips for NLRC4 Inflammasome Activation. PMID:29576451
Induction of Genes Encoding Plant Cell Wall-Degrading Carbohydrate-Active Enzymes by Lignocellulose-Derived Monosaccharides and Cellobiose in the White-Rot Fungus Dichomitus squalens. PMID:29572208
Lysosomal acid lipase promotes cholesterol ester metabolism and drives clear cell renal cell carcinoma progression. PMID:29569766
Blocking hexose entry into glycolysis activates alternative metabolic conversion of these sugars and upregulates pentose metabolism in Aspergillus nidulans. PMID:29566661
No evidence for association of MTHFR 677C>T and 1298A>C variants with placental DNA methylation. PMID:29564022
A switch in transcription and cell fate governs the onset of an epigenetically-deregulated tumor in Drosophila. PMID:29560857
Bordetella pertussis pertactin knock-out strains reveal immunomodulatory properties of this virulence factor. PMID:29559630
New drug candidates for treatment of atypical meningiomas: An integrated approach using gene expression signatures for drug repurposing. PMID:29558515
Characterization of human dental pulp cells grown in chemically defined serum-free medium. PMID:29556382
Lowered dietary phosphorus affects intestinal and renal gene expression to maintain mineral homeostasis with immunomodulatory implications in weaned piglets. PMID:29554878
Could ALDH2*2 be the reason for low incidence and mortality of ovarian cancer for East Asia women? PMID:29552329
Epigenetic impacts of stress priming of the neuroinflammatory response to sarin surrogate in mice: a model of Gulf War illness. PMID:29549885
Allopregnanolone Alters the Gene Expression Profile of Human Glioblastoma Cells. PMID:29543748
A novel computational approach for drug repurposing using systems biology. PMID:29534151
A regulatory RNA is involved in RNA duplex formation and biofilm regulation in Sulfolobus acidocaldarius. PMID:29529252
p38-MK2 signaling axis regulates RNA metabolism after UV-light-induced DNA damage. PMID:29523821
EAF2 and p53 Co-Regulate STAT3 Activation in Prostate Cancer. PMID:29518696
TRAP-seq identifies cystine/glutamate antiporter as a driver of recovery from liver injury. PMID:29517978
Extracellular vesicle RNAs reflect placenta dysfunction and are a biomarker source for preterm labour. PMID:29516617
Genome-wide transcriptome analysis identifies alternative splicing regulatory network and key splicing factors in mouse and human psoriasis. PMID:29515135
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
A standardized fold change method for microarray differential expression analysis used to reveal genes involved in acute rejection in murine allograft models. PMID:29511625
Protein interaction mapping interpretation of none alcoholic fatty liver disease model of rats after fat diet feeding. PMID:29511485
Association of miR-548c-5p, miR-7-5p, miR-210-3p, miR-128-3p with recurrence in systemically untreated breast cancer. PMID:29507672
Zc3h10 is a novel mitochondrial regulator. PMID:29507079
CRISPR RNA-Dependent Binding and Cleavage of Endogenous RNAs by the Campylobacter jejuni Cas9. PMID:29499139
Computational de novo discovery of distinguishing genes for biological processes and cell types in complex tissues. PMID:29494600
A minimal RNA ligand for potent RIG-I activation in living mice. PMID:29492454
Loss of Pax5 Exploits Sca1-BCR-ABLp190 Susceptibility to Confer the Metabolic Shift Essential for pB-ALL. PMID:29490943
Modulation of the peripheral blood transcriptome by the ingestion of probiotic yoghurt and acidified milk in healthy, young men. PMID:29489876
Functional Genomics and Phylogenetic Evidence Suggest Genus-Wide Cobalamin Production by the Globally Distributed Marine Nitrogen Fixer Trichodesmium. PMID:29487583
Evidence that DNA polymerase δ contributes to initiating leading strand DNA replication in Saccharomyces cerevisiae. PMID:29487291
Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses. PMID:29485625
Transcription factors Tp73, Cebpd, Pax6, and Spi1 rather than DNA methylation regulate chronic transcriptomics changes after experimental traumatic brain injury. PMID:29482641
Novel Dual-Action Targeted Nanomedicine in Mice With Metastatic Thyroid Cancer and Pancreatic Neuroendocrine Tumors. PMID:29481652
A novel joint analysis framework improves identification of differentially expressed genes in cross disease transcriptomic analysis. PMID:29467826
Distinguishing Human Peripheral Blood NK Cells from CD56dimCD16dimCD69+CD103+ Resident Nasal Mucosal Lavage Fluid Cells. PMID:29467466
Epigenome comparisons reveal linkage between gene expression and postnatal remodeling of chromatin domain topology. PMID:29466355
Boolean analysis identifies CD38 as a biomarker of aggressive localized prostate cancer. PMID:29464091
Longitudinal analysis strategies for modelling epigenetic trajectories. PMID:29462323
A hybrid gene selection approach to create the S1500+ targeted gene sets for use in high-throughput transcriptomics. PMID:29462216
Selection of GalNAc-conjugated siRNAs with limited off-target-driven rat hepatotoxicity. PMID:29459660
CEMiTool: a Bioconductor package for performing comprehensive modular co-expression analyses. PMID:29458351
Mixed-species RNAseq analysis of human lymphoma cells adhering to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of mantle cell lymphoma and chronic lymphocytic leukemia patients. PMID:29449436
Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids. PMID:29440725
Small RNAs of Haloferax mediterranei: Identification and Potential Involvement in Nitrogen Metabolism. PMID:29439418
hMENA is a key regulator in endothelin-1/β-arrestin1-induced invadopodial function and metastatic process. PMID:29439204
IKKα is required in the intestinal epithelial cells for tumour stemness. PMID:29438366
Mutational Pleiotropy and the Strength of Stabilizing Selection Within and Between Functional Modules of Gene Expression. PMID:29437825
Combining laser-assisted microdissection (LAM) and RNA-seq allows to perform a comprehensive transcriptomic analysis of epidermal cells of Arabidopsis embryo. PMID:29434651
Up-regulation of hexokinase II contributes to rituximab-chemotherapy resistance and is a clinically relevant target for therapeutic development. PMID:29423101
Signatures of Altered Gene Expression in Dorsal Root Ganglia of a Fabry Disease Mouse Model. PMID:29422837
MELK expression correlates with tumor mitotic activity but is not required for cancer growth. PMID:29417930
Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA. PMID:29416646
Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid. PMID:29410524
PD-1 axis expression in musculoskeletal tumors and antitumor effect of nivolumab in osteosarcoma model of humanized mouse. PMID:29409495
Single-cell profiling of peanut-responsive T cells in patients with peanut allergy reveals heterogeneous effector TH2 subsets. PMID:29408715
Mitochondrial CoQ deficiency is a common driver of mitochondrial oxidants and insulin resistance. PMID:29402381
A practical solution for preserving single cells for RNA sequencing. PMID:29391536
Modified Cross-Linking, Ligation, and Sequencing of Hybrids (qCLASH) Identifies Kaposi's Sarcoma-Associated Herpesvirus MicroRNA Targets in Endothelial Cells. PMID:29386283
Germline contamination and leakage in whole genome somatic single nucleotide variant detection. PMID:29385983
Vital ex vivo tissue labeling and pathology-guided micropunching to characterize cellular heterogeneity in the tissue microenvironment. PMID:29384072
Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signaling and malignant features in vitro and in vivo. PMID:29383126
Transcriptional profiling of NCI/ADR-RES cells unveils a complex network of signaling pathways and molecular mechanisms of drug resistance. PMID:29379303
A Two-Stage Whole-Genome Gene Expression Association Study of Young-Onset Hypertension in Han Chinese Population of Taiwan. PMID:29379041
Additive Effects of Quorum Sensing Anti-Activators on Pseudomonas aeruginosa Virulence Traits and Transcriptome. PMID:29375519
Biofilm formation and transcriptome analysis of Streptococcus gallolyticus subsp. gallolyticus in response to lysozyme. PMID:29373594
Cell-surface marker discovery for lung cancer. PMID:29371917
The Biotrophic Development of Ustilago maydis Studied by RNA-Seq Analysis. PMID:29371439
Comparative analysis of mouse and human placentae across gestation reveals species-specific regulators of placental development. PMID:29361559
The Bioinformatic Analysis of the Dysregulated Genes and MicroRNAs in Entorhinal Cortex, Hippocampus, and Blood for Alzheimer's Disease. PMID:29359159
Gene annotation bias impedes biomedical research. PMID:29358745
The RNA-Binding Protein NONO Coordinates Hepatic Adaptation to Feeding. PMID:29358041
DataMed - an open source discovery index for finding biomedical datasets. PMID:29346583
The GPR120 agonist TUG-891 promotes metabolic health by stimulating mitochondrial respiration in brown fat. PMID:29343498
Identification of bladder cancer prognostic biomarkers using an ageing gene-related competitive endogenous RNA network. PMID:29340088
A novel messenger RNA signature as a prognostic biomarker for predicting relapse in pancreatic ductal adenocarcinoma. PMID:29340021
Application of Weighted Gene Co-expression Network Analysis for Data from Paired Design. PMID:29330528
Base-Resolution Analysis of DNA Methylation Patterns Downstream of Dnmt3a in Mouse Naïve B Cells. PMID:29326230
Omics Assisted N-terminal Proteoform and Protein Expression Profiling On Methionine Aminopeptidase 1 (MetAP1) Deletion. PMID:29317475
Toxoplasma gondii Infection Is Associated with Mitochondrial Dysfunction in-Vitro. PMID:29312892
Integrated Analysis of Gene Expression Differences in Twins Discordant for Disease and Binary Phenotypes. PMID:29311748
Transcriptomic Analysis Reveals Novel Mechanisms Mediating Islet Dysfunction in the Intrauterine Growth-Restricted Rat. PMID:29309562
Boolean network modeling in systems pharmacology. PMID:29307099
POU6f1 Mediates Neuropeptide-Dependent Plasticity in the Adult Brain. PMID:29305536
A novel prospective isolation of murine fetal liver progenitors to study in utero hematopoietic defects. PMID:29300724
ASXL1 and BIM germ line variants predict response and identify CML patients with the greatest risk of imatinib failure. PMID:29296778
Clonal evolution underlying leukemia progression and Richter transformation in patients with ibrutinib-relapsed CLL. PMID:29296715
Identification and validation long non-coding RNAs of oral squamous cell carcinoma by bioinformatics method. PMID:29296179
Impact of Consuming Extra-Virgin Olive Oil or Nuts within a Mediterranean Diet on DNA Methylation in Peripheral White Blood Cells within the PREDIMED-Navarra Randomized Controlled Trial: A Role for Dietary Lipids. PMID:29295516
Mutations in the DNA methylation pathway and number of driver mutations predict response to azacitidine in myelodysplastic syndromes. PMID:29291002
Identification and Functional Validation of a Biomarker for the Diagnosis of Miltefosine Relapse during Visceral Leishmaniasis. PMID:29280431
Cancer transcriptome profiling at the juncture of clinical translation. PMID:29279605
Indian Hedgehog Suppresses a Stromal Cell-Driven Intestinal Immune Response. PMID:29276753
PITX1 promotes chondrogenesis and myogenesis in mouse hindlimbs through conserved regulatory targets. PMID:29273440
Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii. PMID:29269498
Super-delta: a new differential gene expression analysis procedure with robust data normalization. PMID:29268715
Circular RNA expression is abundant and correlated to aggressiveness in early-stage bladder cancer. PMID:29263845
Mining the transcriptome for rare disease therapies: a comparison of the efficiencies of two data mining approaches and a targeted cell-based drug screen. PMID:29263829
Characterization of epithelial-mesenchymal transition intermediate/hybrid phenotypes associated to resistance to EGFR inhibitors in non-small cell lung cancer cell lines. PMID:29262566
Clearance of a persistent picornavirus infection is associated with enhanced pro-apoptotic and cellular immune responses. PMID:29259271
Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus. PMID:29257335
High expression of FLT3 is a risk factor in leukemia. PMID:29257272
Loss of Intercalated Cells (ITCs) in the Mouse Amygdala of Tshz1 Mutants Correlates with Fear, Depression, and Social Interaction Phenotypes. PMID:29255003
FZD4 Marks Lateral Plate Mesoderm and Signals with NORRIN to Increase Cardiomyocyte Induction from Pluripotent Stem Cell-Derived Cardiac Progenitors. PMID:29249665
Potential Diagnostic Power of Blood Circular RNA Expression in Active Pulmonary Tuberculosis. PMID:29248507
Peritoneal tissue-resident macrophages are metabolically poised to engage microbes using tissue-niche fuels. PMID:29234000
Ensemble Modeling Approach Targeting Heterogeneous RNA-Seq data: Application to Melanoma Pseudogenes. PMID:29229974
Noncanonical thyroid hormone signaling mediates cardiometabolic effects in vivo. PMID:29229863
SUV420H2 is an epigenetic regulator of epithelial/mesenchymal states in pancreatic cancer. PMID:29229751
Global gene expression in two potato cultivars in response to 'Candidatus Liberibacter solanacearum' infection. PMID:29228896
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
Annotating gene sets by mining large literature collections with protein networks. PMID:29218918
Advances in Text Mining and Visualization for Precision Medicine. PMID:29218914
Treatment with a DNA methyltransferase inhibitor feminizes zebrafish and induces long-term expression changes in the gonads. PMID:29216900
Systematic integrative analysis of gene expression identifies HNF4A as the central gene in pathogenesis of non-alcoholic steatohepatitis. PMID:29216278
Profiling invasive Plasmodium falciparum merozoites using an integrated omics approach. PMID:29215067
Platelet-rich plasma inhibits RANKL-induced osteoclast differentiation through activation of Wnt pathway during bone remodeling. PMID:29207140
Slam protein dictates subcellular localization and translation of its own mRNA. PMID:29206227
Cross-Laboratory Analysis of Brain Cell Type Transcriptomes with Applications to Interpretation of Bulk Tissue Data. PMID:29204516
Mediator Complex Subunits MED2, MED5, MED16, and MED23 Genetically Interact in the Regulation of Phenylpropanoid Biosynthesis. PMID:29203634
Lymph Node Metastases in Colon Cancer Are Polyclonal. PMID:29203589
Mitochondrial fission is associated with UCP1 activity in human brite/beige adipocytes. PMID:29198749
Protection of macrophages from intracellular pathogens by miR-182-5p mimic-a gene expression meta-analysis approach. PMID:29197182
A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles. PMID:29195078
Transcription Factor-Mediated Control of Anthocyanin Biosynthesis in Vegetative Tissues. PMID:29192027
Genetic variation at the microRNA binding site of CAV1 gene is associated with lung cancer susceptibility. PMID:29190968
The IDO inhibitor 1-methyl tryptophan activates the aryl hydrocarbon receptor response in mesenchymal stromal cells. PMID:29190885
Conditional Loss of Hoxa5 Function Early after Birth Impacts on Expression of Genes with Synaptic Function. PMID:29187810
Integrative Bioinformatic Analysis of Transcriptomic Data Identifies Conserved Molecular Pathways Underlying Ionizing Radiation-Induced Bystander Effects (RIBE). PMID:29186820
Translational bioinformatics in mental health: open access data sources and computational biomarker discovery. PMID:29186302
RNA sequencing reveals candidate genes and polymorphisms related to sperm DNA integrity in testis tissue from boars. PMID:29183316
Selection of internal references for qRT-PCR assays of human hepatocellular carcinoma cell lines. PMID:29180379
Nutrient-Colimited Trichodesmium as a Nitrogen Source or Sink in a Future Ocean. PMID:29180365
ENCoRE: an efficient software for CRISPR screens identifies new players in extrinsic apoptosis. PMID:29178829
A COUP-TFII Human Embryonic Stem Cell Reporter Line to Identify and Select Atrial Cardiomyocytes. PMID:29173897
The histone code reader Spin1 controls skeletal muscle development. PMID:29168801
Novel structural features drive DNA binding properties of Cmr, a CRP family protein in TB complex mycobacteria. PMID:29165665
Inhibition of HOX/PBX dimer formation leads to necroptosis in acute myeloid leukemia cells. PMID:29163771
NRF2 regulates endothelial glycolysis and proliferation with miR-93 and mediates the effects of oxidized phospholipids on endothelial activation. PMID:29161413
Regulation of Sucrose Transporters and Phloem Loading in Response to Environmental Cues. PMID:29158330
Multiplex Proximity Ligation Assay to Identify Potential Prognostic Biomarkers for Improved Survival in Locally Advanced Pancreatic Cancer Patients Treated With Stereotactic Body Radiation Therapy. PMID:29157747
Identification of potential tissue-specific cancer biomarkers and development of cancer versus normal genomic classifiers. PMID:29156751
Comprehensive functional enrichment analysis of male infertility. PMID:29150651
Changes in chromatin state reveal ARNT2 at a node of a tumorigenic transcription factor signature driving glioblastoma cell aggressiveness. PMID:29149419
A transcriptomic insight into the impacts of mast cells in lung, breast, and colon cancers. PMID:29147625
Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children. PMID:29146936
Global analysis of gene expression mediated by OX1 orexin receptor signaling in a hypothalamic cell line. PMID:29145494
Innate Cell-Mediated Cytotoxic Activity of European Sea Bass Leucocytes Against Nodavirus-Infected Cells: A Functional and RNA-seq Study. PMID:29133947
A Novel Mechanism of Inactivating Antibacterial Nitro Compounds in the Human Pathogen Staphylococcus aureus by Overexpression of a NADH-Dependent Flavin Nitroreductase. PMID:29133557
Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development. PMID:29133375
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. PMID:29130882
Isl1 mediates mesenchymal expansion in the developing external genitalia via regulation of Bmp4, Fgf10 and Wnt5a. PMID:29126155
Missing data and technical variability in single-cell RNA-sequencing experiments. PMID:29121214
ADAM9 promotes lung cancer progression through vascular remodeling by VEGFA, ANGPT2, and PLAT. PMID:29118335
Stress hormones promote EGFR inhibitor resistance in NSCLC: Implications for combinations with β-blockers. PMID:29118262
General response of Salmonella enterica serovar Typhimurium to desiccation: A new role for the virulence factors sopD and sseD in survival. PMID:29117268
Crosstalk between Receptor and Non-receptor Mediated Chemical Modes of Action in Rat Livers Converges through a Dysregulated Gene Expression Network at Tumor Suppressor Tp53. PMID:29114260
Restricted Presence of POU6F2 in Human Corneal Endothelial Cells Uncovered by Extension of the Promoter-level Expression Atlas. PMID:29113774
In vivo functional analysis of L-rhamnose metabolic pathway in Aspergillus niger: a tool to identify the potential inducer of RhaR. PMID:29110642
Deep Learning Accurately Predicts Estrogen Receptor Status in Breast Cancer Metabolomics Data. PMID:29110491
Transcriptional responses of wheat and the cereal cyst nematode Heterodera avenae during their early contact stage. PMID:29101332
Cellular, ultrastructural and molecular analyses of epidermal cell development in the planarian Schmidtea mediterranea. PMID:29100657
Gene expression information improves reliability of receptor status in breast cancer patients. PMID:29100391
Autoimmunity and autoinflammation: A systems view on signaling pathway dysregulation profiles. PMID:29099860
A molecular roadmap of the AGM region reveals BMPER as a novel regulator of HSC maturation. PMID:29093060
GPR68, a proton-sensing GPCR, mediates interaction of cancer-associated fibroblasts and cancer cells. PMID:29092903
Post-weaning epiphysiolysis causes distal femur dysplasia and foreshortened hindlimbs in fetuin-A-deficient mice. PMID:29088242
The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline. PMID:29087293
APC downregulated 1 inhibits breast cancer cell invasion by inhibiting the canonical WNT signaling pathway. PMID:29085490
Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. PMID:29085363
Glycosylation-related gene expression in HT29-MTX-E12 cells upon infection by Helicobacter pylori. PMID:29085225
In-silico gene essentiality analysis of polyamine biosynthesis reveals APRT as a potential target in cancer. PMID:29084986
Integrated Proteomic and Transcriptomic Analysis Reveals Long Noncoding RNA HOX Transcript Antisense Intergenic RNA (HOTAIR) Promotes Hepatocellular Carcinoma Cell Proliferation by Regulating Opioid Growth Factor Receptor (OGFr). PMID:29079719
Comparative genomics of geographically distant Fusarium fujikuroi isolates revealed two distinct pathotypes correlating with secondary metabolite profiles. PMID:29073267
Cross-tissue integration of genetic and epigenetic data offers insight into autism spectrum disorder. PMID:29066808
Gene isoforms as expression-based biomarkers predictive of drug response in vitro. PMID:29066719
Ubiquitin-Specific Protease USP6 Regulates the Stability of the c-Jun Protein. PMID:29061731
The SIN3A histone deacetylase complex is required for a complete transcriptional response to hypoxia. PMID:29059365
PpNAC1, a main regulator of phenylalanine biosynthesis and utilization in maritime pine. PMID:29055073
Genome-wide prediction of DNase I hypersensitivity using gene expression. PMID:29051481
A molecular atlas of the developing ectoderm defines neural, neural crest, placode, and nonneural progenitor identity in vertebrates. PMID:29049289
miR-3656 expression enhances the chemosensitivity of pancreatic cancer to gemcitabine through modulation of the RHOF/EMT axis. PMID:29048402
Modulation of Global Transcriptional Regulatory Networks as a Strategy for Increasing Kanamycin Resistance of the Translational Elongation Factor-G Mutants in Escherichia coli. PMID:29046437
Roles of Female and Male Genotype in Post-Mating Responses in Drosophila melanogaster. PMID:29036644
ScanGEO: parallel mining of high-throughput gene expression data. PMID:29036513
Smooth quantile normalization. PMID:29036413
Hedgehog-mesenchyme gene signature identifies bi-modal prognosis in luminal and basal breast cancer sub-types. PMID:29034935
Designing Dietary Recommendations Using System Level Interactomics Analysis and Network-Based Inference. PMID:29033850
Single-cell RNA sequencing reveals developmental heterogeneity among early lymphoid progenitors. PMID:29030486
RBPJ/CBF1 interacts with L3MBTL3/MBT1 to promote repression of Notch signaling via histone demethylase KDM1A/LSD1. PMID:29030483
Human CD8+ EMRA T cells display a senescence-associated secretory phenotype regulated by p38 MAPK. PMID:29024417
Differential gene expression in disease: a comparison between high-throughput studies and the literature. PMID:29020950
Genomic Programming of Human Neonatal Dendritic Cells in Congenital Systemic and In Vitro Cytomegalovirus Infection Reveal Plastic and Robust Immune Pathway Biology Responses. PMID:28993767
Effect of diabetes status and hyperglycemia on global DNA methylation and hydroxymethylation. PMID:28993426
SCENIC: single-cell regulatory network inference and clustering. PMID:28991892
Architectural alterations of the fission yeast genome during the cell cycle. PMID:28991264
Investigating the microRNA-mRNA regulatory network in acute myeloid leukemia. PMID:28989535
Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen. PMID:28987030
Impact of sequencing depth and read length on single cell RNA sequencing data of T cells. PMID:28986563
RNA sequencing identifies novel non-coding RNA and exon-specific effects associated with cigarette smoking. PMID:28985737
A link prediction approach to cancer drug sensitivity prediction. PMID:28984192
Usefulness of Transcriptional Blood Biomarkers as a Non-invasive Surrogate Marker of Mucosal Healing and Endoscopic Response in Ulcerative Colitis. PMID:28981629
IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions. PMID:28977416
Targeting the alternative sigma factor RpoN to combat virulence in Pseudomonas aeruginosa. PMID:28974743
Meta-analysis of transcriptomic datasets identifies genes enriched in the mammalian circadian pacemaker. PMID:28973476
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis. PMID:28968850
A framework for estimating and testing qualitative interactions with applications to predictive biomarkers. PMID:28968765
Identification of candidate genes associated with triple negative breast cancer. PMID:28966727
Transcriptomic responses of the endangered freshwater mussel Margaritifera margaritifera to trace metal contamination in the Dronne River, France. PMID:28963680
Statistically controlled identification of differentially expressed genes in one-to-one cell line comparisons of the CMAP database for drug repositioning. PMID:28962576
Inference and interrogation of a coregulatory network in the context of lipid accumulation in Yarrowia lipolytica. PMID:28955503
Stable Gene Regulatory Network Modeling From Steady-State Data. PMID:28952574
Filamentation Involves Two Overlapping, but Distinct, Programs of Filamentation in the Pathogenic Fungus Candida albicans. PMID:28951491
Pathway and network-based analysis of genome-wide association studies and RT-PCR validation in polycystic ovary syndrome. PMID:28949383
Peroxisome proliferator-activated receptor gamma (PPARγ) regulates lactase expression and activity in the gut. PMID:28947679
Priming and Activation of Inflammasome by Canarypox Virus Vector ALVAC via the cGAS/IFI16-STING-Type I IFN Pathway and AIM2 Sensor. PMID:28947539
Integrated metabolic models for xenobiotic induced mitochondrial toxicity in skeletal muscle. PMID:28942197
Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics. PMID:28941356
Differential expression and co-expression gene networks reveal candidate biomarkers of boar taint in non-castrated pigs. PMID:28939879
The Transcriptome of Estrogen-Independent Mammary Growth in Female Mice Reveals That Not All Mammary Glands Are Created Equally. PMID:28938404
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Light and Plastid Signals Regulate Different Sets of Genes in the Albino Mutant Pap7-1. PMID:28935841
A comprehensive, cell specific microRNA catalogue of human peripheral blood. PMID:28934507
Intercalated disc in failing hearts from patients with dilated cardiomyopathy: Its role in the depressed left ventricular function. PMID:28934278
Comparative transcriptomics of female and male gametocytes in Plasmodium berghei and the evolution of sex in alveolates. PMID:28923023
Complete Circular Genome Sequence and Temperature Independent Adaptation to Anaerobiosis of Listeria weihenstephanensis DSM 24698. PMID:28919887
An HDAC3-PROX1 corepressor module acts on HNF4α to control hepatic triglycerides. PMID:28916805
Data exploration, quality control and statistical analysis of ChIP-exo/nexus experiments. PMID:28911122
Screening and identification of key biomarkers in hepatocellular carcinoma: Evidence from bioinformatic analysis. PMID:28901457
Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation. PMID:28899353
Determining the optimal number of independent components for reproducible transcriptomic data analysis. PMID:28893186
Mining the Volatilomes of Plant-Associated Microbiota for New Biocontrol Solutions. PMID:28890716
MicroRNA Profiling Reveals Distinct Profiles for Tissue-Derived and Cultured Endothelial Cells. PMID:28887500
Integrated expression profiles analysis reveals novel predictive biomarker in pancreatic ductal adenocarcinoma. PMID:28881752
An in-silico approach to predict and exploit synthetic lethality in cancer metabolism. PMID:28878380
FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. PMID:28874813
HT-SuperSAGE of the gut tissue of a Vip3Aa-resistant Heliothis virescens (Lepidoptera: Noctuidae) strain provides insights into the basis of resistance. PMID:28872766
A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research. PMID:28872130
Molecular Analyses Reveal Inflammatory Mediators in the Solid Component and Cyst Fluid of Human Adamantinomatous Craniopharyngioma. PMID:28859336
Retinol saturase coordinates liver metabolism by regulating ChREBP activity. PMID:28855500
Ribosome signatures aid bacterial translation initiation site identification. PMID:28854918
Study on molecular mechanism of ANOS1 promoting development of colorectal cancer. PMID:28854193
Novel evidence for complement system activation in chick myopia and hyperopia models: a meta-analysis of transcriptome datasets. PMID:28852117
Genome-wide expression and response to exposure-based psychological therapy for anxiety disorders. PMID:28850109
Mycobacterium bovis Bacillus Calmette-Guérin Alters Melanoma Microenvironment Favoring Antitumor T Cell Responses and Improving M2 Macrophage Function. PMID:28848560
Expression and Regulatory Network Analysis of miR-140-3p, a New Potential Serum Biomarker for Autism Spectrum Disorder. PMID:28848387
An improved analysis methodology for translational profiling by microarray. PMID:28842509
Heterogeneous Tumor-Immune Microenvironments among Differentially Growing Metastases in an Ovarian Cancer Patient. PMID:28841418
Microbial regulation of microRNA expression in the amygdala and prefrontal cortex. PMID:28838324
Treating the placenta to prevent adverse effects of gestational hypoxia on fetal brain development. PMID:28831049
Measuring mRNA Levels Over Time During the Yeast S. cerevisiae Hypoxic Response. PMID:28829420
DELLA genes restrict inflorescence meristem function independently of plant height. PMID:28827519
A novel SH2 recognition mechanism recruits Spt6 to the doubly phosphorylated RNA polymerase II linker at sites of transcription. PMID:28826505
Ribonucleotide Reductases from Bifidobacteria Contain Multiple Conserved Indels Distinguishing Them from All Other Organisms: In Silico Analysis of the Possible Role of a 43 aa Bifidobacteria-Specific Insert in the Class III RNR Homolog. PMID:28824557
Molecular bases for differential aging programs between flag and second leaves during grain-filling in rice. PMID:28821707
Sources to variability in circulating human miRNA signatures. PMID:28820329
Whole-transcriptome microarray analysis reveals regulation of Rab4 by RBM5 in neurons. PMID:28818525
Analysis of the small non-protein-coding RNA profile of mouse spermatozoa reveals specific enrichment of piRNAs within mature spermatozoa. PMID:28816603
Therapeutic Antibodies to Ganglioside GD2 Evolved from Highly Selective Germline Antibodies. PMID:28813678
Totipotency segregates between the sister blastomeres of two-cell stage mouse embryos. PMID:28811525
Pro- and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages. PMID:28808331
Critical role for arginase 2 in obesity-associated pancreatic cancer. PMID:28808255
DNA Microarray Analysis of Estrogen Responsive Genes in Ishikawa Cells by Glabridin. PMID:28804245
Identification and characterization of a long non-coding RNA up-regulated during HIV-1 infection. PMID:28803142
Transcriptional Analysis of an Ammonium-Excreting Strain of Azotobacter vinelandii Deregulated for Nitrogen Fixation. PMID:28802272
Comprehensive miRNA expression profiling in human T-cell acute lymphoblastic leukemia by small RNA-sequencing. PMID:28801656
EGFR Mutations Compromise Hypoxia-Associated Radiation Resistance through Impaired Replication Fork-Associated DNA Damage Repair. PMID:28801308
The nucleoid protein Dps binds genomic DNA of Escherichia coli in a non-random manner. PMID:28800583
Analytical Strategy to Prioritize Alzheimer's Disease Candidate Genes in Gene Regulatory Networks Using Public Expression Data. PMID:28800327
MicroRNA-132 promotes fibroblast migration via regulating RAS p21 protein activator 1 in skin wound healing. PMID:28798331
Identification and characterization of a new source of adult human neural progenitors. PMID:28796246
Host plant driven transcriptome plasticity in the salivary glands of the cabbage looper (Trichoplusia ni). PMID:28792546
Ventromorphins: A New Class of Small Molecule Activators of the Canonical BMP Signaling Pathway. PMID:28787124
Bioinformatics resources for deciphering the biogenesis and action pathways of plant small RNAs. PMID:28786034
Early involvement of cellular stress and inflammatory signals in the pathogenesis of tubulointerstitial kidney disease due to UMOD mutations. PMID:28785050
Cutting Edge: IL-2-Induced Expression of the Amino Acid Transporters SLC1A5 and CD98 Is a Prerequisite for NKG2D-Mediated Activation of Human NK Cells. PMID:28784848
Developmental disruption of amygdala transcriptome and socioemotional behavior in rats exposed to valproic acid prenatally. PMID:28775827
Transcriptome and Metabolite Changes during Hydrogen Cyanamide-Induced Floral Bud Break in Sweet Cherry. PMID:28769948
Identification of key genes and pathways in Parkinson's disease through integrated analysis. PMID:28765971
Heme and nitric oxide binding by the transcriptional regulator DnrF from the marine bacterium Dinoroseobacter shibae increases napD promoter affinity. PMID:28765283
The metabolic regulator mTORC1 controls terminal myeloid differentiation. PMID:28763796
Integrated diagnostic network construction reveals a 4-gene panel and 5 cancer hallmarks driving breast cancer heterogeneity. PMID:28754978
The Drosophila Duox maturation factor is a key component of a positive feedback loop that sustains regeneration signaling. PMID:28753614
Quantifying Gene Regulatory Relationships with Association Measures: A Comparative Study. PMID:28751908
miR-130b directly targets ARHGAP1 to drive activation of a metastatic CDC42-PAK1-AP1 positive feedback loop in Ewing sarcoma. PMID:28748534
Dissecting the contributions of time and microbe density to variation in immune gene expression. PMID:28747473
Arginase1 Deficiency in Monocytes/Macrophages Upregulates Inducible Nitric Oxide Synthase To Promote Cutaneous Contact Hypersensitivity. PMID:28747341
Whole blood microRNA expression may not be useful for screening non-small cell lung cancer. PMID:28742859
The STAT4/MLL1 Epigenetic Axis Regulates the Antimicrobial Functions of Murine Macrophages. PMID:28733487
ERK/MAPK Signaling Is Required for Pathway-Specific Striatal Motor Functions. PMID:28733355
Chloroplast Redox Status Modulates Genome-Wide Plant Responses during the Non-host Interaction of Tobacco with the Hemibiotrophic Bacterium Xanthomonas campestris pv. vesicatoria. PMID:28725231
Gene expression reversal toward pre-adult levels in the aging human brain and age-related loss of cellular identity. PMID:28724976
Predicting susceptibility to tuberculosis based on gene expression profiling in dendritic cells. PMID:28720766
CLIC, a tool for expanding biological pathways based on co-expression across thousands of datasets. PMID:28719601
Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition. PMID:28716088
Microarray analysis reveals key genes and pathways in Tetralogy of Fallot. PMID:28713939
Identification of Conserved and Novel MicroRNAs in Blueberry. PMID:28713413
Unsupervised Extraction of Stable Expression Signatures from Public Compendia with an Ensemble of Neural Networks. PMID:28711280
The CINSARC signature as a prognostic marker for clinical outcome in multiple neoplasms. PMID:28710396
Biological analysis of cancer specific microRNAs on function modeling in osteosarcoma. PMID:28710380
Profiling Ssb-Nascent Chain Interactions Reveals Principles of Hsp70-Assisted Folding. PMID:28708998
Rv3723/LucA coordinates fatty acid and cholesterol uptake in Mycobacterium tuberculosis. PMID:28708968
Lower Expression of SLC27A1 Enhances Intramuscular Fat Deposition in Chicken via Down-Regulated Fatty Acid Oxidation Mediated by CPT1A. PMID:28706492
Sexual dimorphisms of mRNA and miRNA in human/murine heart disease. PMID:28704447
GT-rich promoters can drive RNA pol II transcription and deposition of H2A.Z in African trypanosomes. PMID:28701485
Deletion of Gas2l3 in mice leads to specific defects in cardiomyocyte cytokinesis during development. PMID:28698371
6S RNA in Rhodobacter sphaeroides: 6S RNA and pRNA transcript levels peak in late exponential phase and gene deletion causes a high salt stress phenotype. PMID:28692405
Reorganization of gene network for degradation of polycyclic aromatic hydrocarbons (PAHs) in Pseudomonas aeruginosa PAO1 under several conditions. PMID:28685384
Genome-wide mapping and analysis of aryl hydrocarbon receptor (AHR)- and aryl hydrocarbon receptor repressor (AHRR)-binding sites in human breast cancer cells. PMID:28681081
A Novel Unsupervised Algorithm for Biological Process-based Analysis on Cancer. PMID:28680165
Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome. PMID:28679547
The methyltransferase SETDB1 regulates a large neuron-specific topological chromatin domain. PMID:28671686
CausalR: extracting mechanistic sense from genome scale data. PMID:28666369
dRNA-seq transcriptional profiling of the FK506 biosynthetic gene cluster in Streptomyces tsukubaensis NRRL18488 and general analysis of the transcriptome. PMID:28665778
KDM2B, an H3K36-specific demethylase, regulates apoptotic response of GBM cells to TRAIL. PMID:28661478
Functional Dissection of the Pol V Largest Subunit CTD in RNA-Directed DNA Methylation. PMID:28658626
Identification of Jak-STAT signaling involvement in sarcoidosis severity via a novel microRNA-regulated peripheral blood mononuclear cell gene signature. PMID:28652588
Deciphering the role of the signal- and Sty1 kinase-dependent phosphorylation of the stress-responsive transcription factor Atf1 on gene activation. PMID:28652406
Protein homeostasis of a metastable subproteome associated with Alzheimer's disease. PMID:28652376
Identifying global expression patterns and key regulators in epithelial to mesenchymal transition through multi-study integration. PMID:28651527
Multivalent binding of PWWP2A to H2A.Z regulates mitosis and neural crest differentiation. PMID:28645917
A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency. PMID:28625162
Safe and Efficient Silencing with a Pol II, but Not a Pol lII, Promoter Expressing an Artificial miRNA Targeting Human Huntingtin. PMID:28624208
TGF-beta/atRA-induced Tregs express a selected set of microRNAs involved in the repression of transcripts related to Th17 differentiation. PMID:28620241
Insights from Global Analyses of Long Noncoding RNAs in Breast Cancer. PMID:28616363
Tricellulin is regulated via interleukin-13-receptor α2, affects macromolecule uptake, and is decreased in ulcerative colitis. PMID:28612843
Involvement of Chromatin Remodeling Genes and the Rho GTPases RhoB and CDC42 in Ovarian Clear Cell Carcinoma. PMID:28611940
Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. PMID:28609292
PHF6 regulates phenotypic plasticity through chromatin organization within lineage-specific genes. PMID:28607179
Neighbours of cancer-related proteins have key influence on pathogenesis and could increase the drug target space for anticancer therapies. PMID:28603644
Hepatic expression profiles in retroviral infection: relevance to drug hypersensitivity risk. PMID:28603631
Uniform neural tissue models produced on synthetic hydrogels using standard culture techniques. PMID:28599598
High-dose maternal folic acid supplementation before conception impairs reversal learning in offspring mice. PMID:28596566
Genetic Dissection of Nutrition-Induced Plasticity in Insulin/Insulin-Like Growth Factor Signaling and Median Life Span in a Drosophila Multiparent Population. PMID:28592498
High-resolution promoter map of human limbal epithelial cells cultured with keratinocyte growth factor and rho kinase inhibitor. PMID:28588247
NaviSE: superenhancer navigator integrating epigenomics signal algebra. PMID:28587674
Identification of the miRNA-target gene regulatory network in intracranial aneurysm based on microarray expression data. PMID:28587396
PA3225 Is a Transcriptional Repressor of Antibiotic Resistance Mechanisms in Pseudomonas aeruginosa. PMID:28584154
Newborn sex-specific transcriptome signatures and gestational exposure to fine particles: findings from the ENVIRONAGE birth cohort. PMID:28583124
Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells. PMID:28575377
Gene Expression (mRNA) Markers for Differentiating between Malignant and Benign Follicular Thyroid Tumours. PMID:28574441
MicroRNA profiling in the dentate gyrus in epileptic rats: The role of miR-187-3p. PMID:28562528
Cooperation between a hierarchical set of recruitment sites targets the X chromosome for dosage compensation. PMID:28562241
Systems-based approach to examine the cytokine responses in primary mouse lung macrophages infected with low pathogenic avian Influenza virus circulating in South East Asia. PMID:28558796
Crops In Silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. PMID:28555150
Non-coding RNAs in the Ovarian Follicle. PMID:28553318
p16 Loss and E2F/cell cycle deregulation in infant posterior fossa ependymoma. PMID:28548702
Transcriptomics technologies. PMID:28545146
eIF1 modulates the recognition of suboptimal translation initiation sites and steers gene expression via uORFs. PMID:28541577
Identifying CpG sites with different differential methylation frequencies in colorectal cancer tissues based on individualized differential methylation analysis. PMID:28537885
RNA-dependent chromatin association of transcription elongation factors and Pol II CTD kinases. PMID:28537551
Induction of resident memory T cells enhances the efficacy of cancer vaccine. PMID:28537262
Genetic variants in the transcription regulatory region of MEGF10 are associated with autism in Chinese Han population. PMID:28536440
Deregulated expression of miR-29a-3p, miR-494-3p and miR-660-5p affects sensitivity to tyrosine kinase inhibitors in CML leukemic stem cells. PMID:28533480
Abnormal expression of ATP1A1 and ATP1A2 in breast cancer. PMID:28529692
Drosophila melanogaster positive transcriptional elongation factors regulate metabolic and sex-biased expression in adults. PMID:28521739
Candidate miRNAs and pathogenesis investigation for hepatocellular carcinoma based on bioinformatics analysis. PMID:28521446
Essential Function of the Serine Hydroxymethyl Transferase (SHMT) Gene During Rapid Syncytial Cell Cycles in Drosophila. PMID:28515048
An RpoHI-Dependent Response Promotes Outgrowth after Extended Stationary Phase in the Alphaproteobacterium Rhodobacter sphaeroides. PMID:28507242
Toxic Electrophiles Induce Expression of the Multidrug Efflux Pump MexEF-OprN in Pseudomonas aeruginosa through a Novel Transcriptional Regulator, CmrA. PMID:28507116
Ranking metrics in gene set enrichment analysis: do they matter? PMID:28499413
Differences in Flower Transcriptome between Grapevine Clones Are Related to Their Cluster Compactness, Fruitfulness, and Berry Size. PMID:28496449
RNA Polymerase III Subunit POLR3G Regulates Specific Subsets of PolyA+ and SmallRNA Transcriptomes and Splicing in Human Pluripotent Stem Cells. PMID:28494942
Relationship between regulatory pattern of gene expression level and gene function. PMID:28494005
In vivo and in vitro ageing results in accumulation of de novo copy number variations in bulls. PMID:28487564
Study of Meta-analysis strategies for network inference using information-theoretic approaches. PMID:28484519
Integration of Immune Cell Populations, mRNA-Seq, and CpG Methylation to Better Predict Humoral Immunity to Influenza Vaccination: Dependence of mRNA-Seq/CpG Methylation on Immune Cell Populations. PMID:28484452
Intermittent glucocorticoid steroid dosing enhances muscle repair without eliciting muscle atrophy. PMID:28481224
Anti-complement component 5 antibody targeting MG4 domain inhibits choroidal neovascularization. PMID:28477014
FnrL and Three Dnr Regulators Are Used for the Metabolic Adaptation to Low Oxygen Tension in Dinoroseobacter shibae. PMID:28473807
High-Throughput Screening Data Interpretation in the Context of In Vivo Transcriptomic Responses to Oral Cr(VI) Exposure. PMID:28472532
Annotating function to differentially expressed LincRNAs in myelodysplastic syndrome using a network-based method. PMID:28472271
EnHERV: Enrichment analysis of specific human endogenous retrovirus patterns and their neighboring genes. PMID:28472109
CTCF and cohesin regulate chromatin loop stability with distinct dynamics. PMID:28467304
Heat shock and prolonged heat stress attenuate neurotoxin and sporulation gene expression in group I Clostridium botulinum strain ATCC 3502. PMID:28464023
Analysis of the in planta transcriptome expressed by the corn pathogen Pantoea stewartii subsp. stewartii via RNA-Seq. PMID:28462040
Expression profile of mitochondrial voltage-dependent anion channel-1 (VDAC1) influenced genes is associated with pulmonary hypertension. PMID:28461778
Gene expression patterns in the progression of canine copper-associated chronic hepatitis. PMID:28459846
DUX-family transcription factors regulate zygotic genome activation in placental mammals. PMID:28459456
Conservation and innovation in the DUX4-family gene network. PMID:28459454
Responses to Hypoxia and Endoplasmic Reticulum Stress Discriminate the Development of Vitreous and Floury Endosperms of Conventional Maize (Zea mays) Inbred Lines. PMID:28450877
Progressive changes in non-coding RNA profile in leucocytes with age. PMID:28448962
Transcriptional response of Escherichia coli to ammonia and glucose fluctuations. PMID:28447391
Differential host gene responses from infection with neurovirulent and partially-neurovirulent strains of Venezuelan equine encephalitis virus. PMID:28446152
Toxicogenomic module associations with pathogenesis: a network-based approach to understanding drug toxicity. PMID:28440344
Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans. PMID:28438122
Mutant uromodulin expression leads to altered homeostasis of the endoplasmic reticulum and activates the unfolded protein response. PMID:28437467
Identification of NTRK3 Fusions in Childhood Melanocytic Neoplasms. PMID:28433076
Cross-disorder comparative analysis of comorbid conditions reveals novel autism candidate genes. PMID:28427329
Expression of the Maize Dof1 Transcription Factor in Wheat and Sorghum. PMID:28424717
Responses of the Housefly, Musca domestica, to the Hytrosavirus Replication: Impacts on Host's Vitellogenesis and Immunity. PMID:28424677
Deciphering the Regulatory Network between the SREBP Pathway and Protein Secretion in Neurospora crassa. PMID:28420736
Genetic sequence-based prediction of long-range chromatin interactions suggests a potential role of short tandem repeat sequences in genome organization. PMID:28420341
The pathway intermediate 2-keto-3-deoxy-L-galactonate mediates the induction of genes involved in D-galacturonic acid utilization in Aspergillus niger. PMID:28417461
High expression of miR-125b-2 and SNORD116 noncoding RNA clusters characterize ERG-related B cell precursor acute lymphoblastic leukemia. PMID:28415578
Transcriptional networks are associated with resistance to Mycobacterium tuberculosis infection. PMID:28414762
goSTAG: gene ontology subtrees to tag and annotate genes within a set. PMID:28413437
Differential gene expression and transport functionality in the bundle sheath versus mesophyll - a potential role in leaf mineral homeostasis. PMID:28407076
Longitudinal peripheral blood transcriptional analysis of a patient with severe Ebola virus disease. PMID:28404864
MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing. PMID:28402935
Nonsense-mediated mRNA decay in Tetrahymena is EJC independent and requires a protozoa-specific nuclease. PMID:28402567
Identification of RUNX1 as a Mediator of Aberrant Retinal Angiogenesis. PMID:28400392
Landscape of histone modifications in a sponge reveals the origin of animal cis-regulatory complexity. PMID:28395144
The integrative omics of white-rot fungus Pycnoporus coccineus reveals co-regulated CAZymes for orchestrated lignocellulose breakdown. PMID:28394946
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
Melanoma-Derived iPCCs Show Differential Tumorigenicity and Therapy Response. PMID:28392221
Coordination of Meristem Doming and the Floral Transition by Late Termination, a Kelch Repeat Protein. PMID:28389586
Recognition memory-induced gene expression in the perirhinal cortex: A transcriptomic analysis. PMID:28389337
Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen. PMID:28383283
Co-expression of AFAP1-AS1 and PD-1 predicts poor prognosis in nasopharyngeal carcinoma. PMID:28380458
Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans. PMID:28376087
Comparison of tissue/disease specific integrated networks using directed graphlet signatures. PMID:28361704
Novel therapeutic effects of sesamin on diabetes-induced cardiac dysfunction. PMID:28358428
Computational Analysis of Specific MicroRNA Biomarkers for Noninvasive Early Cancer Detection. PMID:28357401
Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program. PMID:28357254
Transcription factor Etv5 is essential for the maintenance of alveolar type II cells. PMID:28351980
Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism. PMID:28351387
Modification of the Streptococcus mutans transcriptome by LrgAB and environmental stressors. PMID:28348880
Estimating genome-wide regulatory activity from multi-omics data sets using mathematical optimization. PMID:28347313
WT1 expression in breast cancer disrupts the epithelial/mesenchymal balance of tumour cells and correlates with the metabolic response to docetaxel. PMID:28345629
A Genome-wide Analysis of Human Pluripotent Stem Cell-Derived Endothelial Cells in 2D or 3D Culture. PMID:28343999
Small chromosomal regions position themselves autonomously according to their chromatin class. PMID:28341771
Cross disease analysis of co-functional microRNA pairs on a reconstructed network of disease-gene-microRNA tripartite. PMID:28340554
In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis. PMID:28339466
Analysis of hepatic transcript profile and plasma lipid profile in early lactating dairy cows fed grape seed and grape marc meal extract. PMID:28335726
The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. PMID:28334889
The Wilms tumor protein Wt1 contributes to female fertility by regulating oviductal proteostasis. PMID:28334862
H3.Y discriminates between HIRA and DAXX chaperone complexes and reveals unexpected insights into human DAXX-H3.3-H4 binding and deposition requirements. PMID:28334823
FUNNEL-GSEA: FUNctioNal ELastic-net regression in time-course gene set enrichment analysis. PMID:28334094
Simultaneous analysis of miRNA-mRNA in human meningiomas by integrating transcriptome: A relationship between PTX3 and miR-29c. PMID:28327132
Albugo-imposed changes to tryptophan-derived antimicrobial metabolite biosynthesis may contribute to suppression of non-host resistance to Phytophthora infestans in Arabidopsis thaliana. PMID:28320402
Perturbation of microbiota in one-day old broiler chickens with antibiotic for 24 hours negatively affects intestinal immune development. PMID:28320307
Identification of dysregulated genes in rheumatoid arthritis based on bioinformatics analysis. PMID:28316886
Identification and characterization of a missense mutation in the O-linked β-N-acetylglucosamine (O-GlcNAc) transferase gene that segregates with X-linked intellectual disability. PMID:28302723
Sex differences in the molecular signature of the developing mouse hippocampus. PMID:28302071
sRNA154 a newly identified regulator of nitrogen fixation in Methanosarcina mazei strain Gö1. PMID:28296572
An Exploration of Charge Compensating Ion Channels across the Phagocytic Vacuole of Neutrophils. PMID:28293191
A comparative analytical assay of gene regulatory networks inferred using microarray and RNA-seq datasets. PMID:28293077
Light Modulates Metabolic Pathways and Other Novel Physiological Traits in the Human Pathogen Acinetobacter baumannii. PMID:28289081
Hepatic Transcriptome Profiles of Mice with Diet-Induced Nonalcoholic Steatohepatitis Treated with Astaxanthin and Vitamin E. PMID:28282876
Specific and Novel microRNAs Are Regulated as Response to Fungal Infection in Human Dendritic Cells. PMID:28280489
The within-host dynamics of infection in trans-generationally primed flour beetles. PMID:28277618
miR-193a-3p interaction with HMGB1 downregulates human endothelial cell proliferation and migration. PMID:28276476
De novo computational identification of stress-related sequence motifs and microRNA target sites in untranslated regions of a plant translatome. PMID:28276452
SVMRFE based approach for prediction of most discriminatory gene target for type II diabetes. PMID:28275550
Identifying Novel Transcriptional and Epigenetic Features of Nuclear Lamina-associated Genes. PMID:28273906
Coordination of auxin-triggered leaf initiation by tomato LEAFLESS. PMID:28270611
DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms. PMID:28270217
Rapid Sampling of Escherichia coli After Changing Oxygen Conditions Reveals Transcriptional Dynamics. PMID:28264512
Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge. PMID:28261192
Gene expression profiling in bladder cancer identifies potential therapeutic targets. PMID:28259975
Prostate apoptosis response 4 (PAR4) expression modulates WNT signaling pathways in MCF7 breast cancer cells: A possible mechanism underlying PAR4-mediated docetaxel chemosensitivity. PMID:28259909
Two-way learning with one-way supervision for gene expression data. PMID:28257645
Integrated systems biology analysis of KSHV latent infection reveals viral induction and reliance on peroxisome mediated lipid metabolism. PMID:28257516
Neuroblastoma cells depend on HDAC11 for mitotic cell cycle progression and survival. PMID:28252645
Altered regulation and expression of genes by BET family of proteins in COPD patients. PMID:28248992
ZEB1 regulates glioma stemness through LIF repression. PMID:28246407
Cellulose-Derived Oligomers Act as Damage-Associated Molecular Patterns and Trigger Defense-Like Responses. PMID:28242654
Characterization of bovine embryos cultured under conditions appropriate for sustaining human naïve pluripotency. PMID:28241084
Essentiality of mmpL3 and impact of its silencing on Mycobacterium tuberculosis gene expression. PMID:28240248
Asymmetric interactions between doublesex and tissue- and sex-specific target genes mediate sexual dimorphism in beetles. PMID:28239147
Proteome and Secretome Analysis Reveals Differential Post-transcriptional Regulation of Toll-like Receptor Responses. PMID:28235783
MicroRNA-independent functions of DGCR8 are essential for neocortical development and TBR1 expression. PMID:28232627
Autocrine Loop Involving IL-6 Family Member LIF, LIF Receptor, and STAT4 Drives Sustained Fibroblast Production of Inflammatory Mediators. PMID:28228280
Cross-talk between the glucocorticoid receptor and MyoD family inhibitor domain-containing protein provides a new mechanism for generating tissue-specific responses to glucocorticoids. PMID:28223352
Astrocytic Calcium Waves Signal Brain Injury to Neural Stem and Progenitor Cells. PMID:28216142
Elf5 is a principal cell lineage specific transcription factor in the kidney that contributes to Aqp2 and Avpr2 gene expression. PMID:28215940
Two-stage genome-wide association study identifies a novel susceptibility locus associated with melanoma. PMID:28212542
The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system. PMID:28212376
Short-Chain Chitin Oligomers: Promoters of Plant Growth. PMID:28212295
High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection. PMID:28209632
Making life difficult for Clostridium difficile: augmenting the pathogen's metabolic model with transcriptomic and codon usage data for better therapeutic target characterization. PMID:28209199
Aurora A regulates expression of AR-V7 in models of castrate resistant prostate cancer. PMID:28205582
Pistil Transcriptome Analysis to Disclose Genes and Gene Products Related to Aposporous Apomixis in Hypericum perforatum L. PMID:28203244
Using global gene expression to discriminate thin melanomas with poor outcomes. PMID:28197532
Biocomplexity and Fractality in the Search of Biomarkers of Aging and Pathology: Focus on Mitochondrial DNA and Alzheimer's Disease. PMID:28197358
Transcription Profiling of Bacillus subtilis Cells Infected with AR9, a Giant Phage Encoding Two Multisubunit RNA Polymerases. PMID:28196958
Analysis of miRNA, mRNA, and TF interactions through network-based methods. PMID:28194173
Simultaneous identification of robust synergistic subnetwork markers for effective cancer prognosis. PMID:28194169
Transcriptional Mechanisms of Resistance to Anti-PD-1 Therapy. PMID:28193624
A novel point mutation in RpoB improves osmotolerance and succinic acid production in Escherichia coli. PMID:28193207
A novel RNA sequencing data analysis method for cell line authentication. PMID:28192450
Upregulation of FAM84B during prostate cancer progression. PMID:28186973
An empirically driven data reduction method on the human 450K methylation array to remove tissue specific non-variable CpGs. PMID:28184257
Transcriptomic Profiling of Egg Quality in Sea Bass (Dicentrarchus labrax) Sheds Light on Genes Involved in Ubiquitination and Translation. PMID:28181038
Individualized analysis reveals CpG sites with methylation aberrations in almost all lung adenocarcinoma tissues. PMID:28178989
Mouse Dux is myotoxic and shares partial functional homology with its human paralog DUX4. PMID:28173143
Unique genetic responses revealed in RNA-seq of the spleen of chickens stimulated with lipopolysaccharide and short-term heat. PMID:28166270
TGF-β1 along with other platelet contents augments Treg cells to suppress anti-FVIII immune responses in hemophilia A mice. PMID:28164173
Loss of CD44dim Expression from Early Progenitor Cells Marks T-Cell Lineage Commitment in the Human Thymus. PMID:28163708
Physiological Responses and Gene Co-Expression Network of Mycorrhizal Roots under K+ Deprivation. PMID:28159827
Genome-Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans. PMID:28154810
A scalable algorithm for structure identification of complex gene regulatory network from temporal expression data. PMID:28143596
Unsupervised detection of regulatory gene expression information in different genomic regions enables gene expression ranking. PMID:28143396
Transcriptional Profiling in Experimental Visceral Leishmaniasis Reveals a Broad Splenic Inflammatory Environment that Conditions Macrophages toward a Disease-Promoting Phenotype. PMID:28141856
Impact of Neutron Exposure on Global Gene Expression in a Human Peripheral Blood Model. PMID:28140791
Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization. PMID:28133571
Vitiligo blood transcriptomics provides new insights into disease mechanisms and identifies potential novel therapeutic targets. PMID:28129744
A Systematic Framework for Drug Repositioning from Integrated Omics and Drug Phenotype Profiles Using Pathway-Drug Network. PMID:28127549
Regulation of myeloid cells by activated T cells determines the efficacy of PD-1 blockade. PMID:28123870
A systematic comparative evaluation of biclustering techniques. PMID:28114903
Transcriptome profiling of gene expression during immunisation trial against Fasciola hepatica: identification of genes and pathways involved in conferring immunoprotection in a murine model. PMID:28114888
RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. PMID:28108657
A Common Variant of IL-6R is Associated with Elevated IL-6 Pathway Activity in Alzheimer's Disease Brains. PMID:28106546
Characterization and in vivo regulon determination of an ECF sigma factor and its cognate anti-sigma factor in Nostoc punctiforme. PMID:28105698
Splenic CD4+ T Cells in Progressive Visceral Leishmaniasis Show a Mixed Effector-Regulatory Phenotype and Impair Macrophage Effector Function through Inhibitory Receptor Expression. PMID:28103263
Role of miR-34a-5p in Hematopoietic Progenitor Cells Proliferation and Fate Decision: Novel Insights into the Pathogenesis of Primary Myelofibrosis. PMID:28098757
MultiDataSet: an R package for encapsulating multiple data sets with application to omic data integration. PMID:28095799
iGC-an integrated analysis package of gene expression and copy number alteration. PMID:28088185
MicroRNA based Pan-Cancer Diagnosis and Treatment Recommendation. PMID:28086747
RYK promotes the stemness of glioblastoma cells via the WNT/ β-catenin pathway. PMID:28086236
Testicular Dysgenesis Syndrome and Long-Lasting Epigenetic Silencing of Mouse Sperm Genes Involved in the Reproductive System after Prenatal Exposure to DEHP. PMID:28085963
Sequential Targeting of CD52 and TNF Allows Early Minimization Therapy in Kidney Transplantation: From a Biomarker to Targeting in a Proof-Of-Concept Trial. PMID:28085915
Vps33b is crucial for structural and functional hepatocyte polarity. PMID:28082148
Establishment of a integrative multi-omics expression database CKDdb in the context of chronic kidney disease (CKD). PMID:28079125
From the Cover: Embryonic Exposure to TCDD Impacts Osteogenesis of the Axial Skeleton in Japanese medaka, Oryzias latipes. PMID:28077779
Muscle developmental defects in heterogeneous nuclear Ribonucleoprotein A1 knockout mice. PMID:28077597
Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. PMID:28076869
Pax-5 is a potent regulator of E-cadherin and breast cancer malignant processes. PMID:28076843
Targeting BET proteins improves the therapeutic efficacy of BCL-2 inhibition in T-cell acute lymphoblastic leukemia. PMID:28074072
Expression of CD14, IL10, and Tolerogenic Signature in Dendritic Cells Inversely Correlate with Clinical and Immunologic Response to TARP Vaccination in Prostate Cancer Patients. PMID:28073842
Breast Cancer Malignant Processes are Regulated by Pax-5 Through the Disruption of FAK Signaling Pathways. PMID:28070224
Mutant U2AF1-expressing cells are sensitive to pharmacological modulation of the spliceosome. PMID:28067246
DNA methylation assessment from human slow- and fast-twitch skeletal muscle fibers. PMID:28057818
Identification of Biomarkers for Breast Cancer Using Databases. PMID:28053957
Myoblast replication is reduced in the IUGR fetus despite maintained proliferative capacity in vitro. PMID:28053000
Linking Hematopoietic Differentiation to Co-Expressed Sets of Pluripotency-Associated and Imprinted Genes and to Regulatory microRNA-Transcription Factor Motifs. PMID:28052084
Batch effects and the effective design of single-cell gene expression studies. PMID:28045081
Novel Biomarker MicroRNAs for Subtyping of Acute Coronary Syndrome: A Bioinformatics Approach. PMID:28044128
Comparative "Omics" of the Fusarium fujikuroi Species Complex Highlights Differences in Genetic Potential and Metabolite Synthesis. PMID:28040774
Quantitative assessment of the diagnostic role of FHIT promoter methylation in non-small cell lung cancer. PMID:28036263
Neuroblastoma, a Paradigm for Big Data Science in Pediatric Oncology. PMID:28035989
Activating transcription factor 3 is crucial for antitumor activity and to strengthen the antiviral properties of Onconase. PMID:28035074
PML-RARA-associated cooperating mutations belong to a transcriptional network that is deregulated in myeloid leukemias. PMID:28025581
Alternative splicing in tomato pollen in response to heat stress. PMID:28025318
Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping. PMID:28024297
Function of AP2/ERF Transcription Factors Involved in the Regulation of Specialized Metabolism in Ophiorrhiza pumila Revealed by Transcriptomics and Metabolomics. PMID:28018397
Changing POU dimerization preferences converts Oct6 into a pluripotency inducer. PMID:28007765
Knowledge-Guided Bioinformatics Model for Identifying Autism Spectrum Disorder Diagnostic MicroRNA Biomarkers. PMID:28000768
Identification of Polycystic Ovary Syndrome (PCOS) Specific Genes in Cumulus and Mural Granulosa Cells. PMID:27997581
Aberrant methylation of CDH13 can be a diagnostic biomarker for lung adenocarcinoma. PMID:27994665
Inducible super-enhancers are organized based on canonical signal-specific transcription factor binding elements. PMID:27994038
Circulating cell-free DNA-based epigenetic assay can detect early breast cancer. PMID:27993161
Exposure of Bacterial Biofilms to Electrical Current Leads to Cell Death Mediated in Part by Reactive Oxygen Species. PMID:27992529
PAX2 function, regulation and targeting in fallopian tube-derived high-grade serous ovarian cancer. PMID:27991925
Gene Expression Correlated with Severe Asthma Characteristics Reveals Heterogeneous Mechanisms of Severe Disease. PMID:27984699
Sepsis Diagnostics: From Discovery to Application. PMID:27984279
Evaluating side effects of nanoparticle-mediated siRNA delivery to mesenchymal stem cells using next generation sequencing and enrichment analysis. PMID:27981244
"Gap hunting" to characterize clustered probe signals in Illumina methylation array data. PMID:27980682
Comparative analyses of super-enhancers reveal conserved elements in vertebrate genomes. PMID:27965291
Prior knowledge guided eQTL mapping for identifying candidate genes. PMID:27964730
Synergistic drug combinations from electronic health records and gene expression. PMID:27940607
Stromal hedgehog signaling maintains smooth muscle and hampers micro-invasive prostate cancer. PMID:27935821
Computing and Applying Atomic Regulons to Understand Gene Expression and Regulation. PMID:27933038
Expression of Cav1.3 calcium channel in the human and mouse colon: posttranscriptional inhibition by IFNγ. PMID:27932504
miR-17∼92 family clusters control iNKT cell ontogenesis via modulation of TGF-β signaling. PMID:27930306
Cellular and molecular characterization of a stem rust resistance locus on wheat chromosome 7AL. PMID:27927228
Transcriptional Network Architecture of Breast Cancer Molecular Subtypes. PMID:27920729
Advax, a Delta Inulin Microparticle, Potentiates In-built Adjuvant Property of Co-administered Vaccines. PMID:27919753
TRPM2 SNP genotype previously associated with susceptibility to Rhodococcus equi pneumonia in Quarter Horse foals displays differential gene expression identified using RNA-Seq. PMID:27919223
Human Intervention Study to Assess the Effects of Supplementation with Olive Leaf Extract on Peripheral Blood Mononuclear Cell Gene Expression. PMID:27918443
Cyanobacteria as Chassis for Industrial Biotechnology: Progress and Prospects. PMID:27916886
Complex genetics architecture contributes to Salmonella resistance in AcB60 mice. PMID:27913859
Chromatin landscapes and genetic risk in systemic lupus. PMID:27906046
Identification of biomarker microRNAs for predicting the response of colorectal cancer to neoadjuvant chemoradiotherapy based on microRNA regulatory network. PMID:27903980
Transcriptomics of Environmental Enrichment Reveals a Role for Retinoic Acid Signaling in Addiction. PMID:27899881
MEF2 transcription factors are key regulators of sprouting angiogenesis. PMID:27898394
EMPOWERING MULTI-COHORT GENE EXPRESSION ANALYSIS TO INCREASE REPRODUCIBILITY. PMID:27896970
Enhancers and super-enhancers have an equivalent regulatory role in embryonic stem cells through regulation of single or multiple genes. PMID:27895109
Identification of genes and signaling pathways associated with diabetic neuropathy using a weighted correlation network analysis: A consort study. PMID:27893688
Whole-Cell Cancer Vaccines Induce Large Antibody Responses to Carbohydrates and Glycoproteins. PMID:27889407
Time-Course Analysis of Gene Expression During the Saccharomyces cerevisiae Hypoxic Response. PMID:27883312
The microRNA toolkit of insects. PMID:27883064
Three distinct cell populations express extracellular matrix proteins and increase in number during skeletal muscle fibrosis. PMID:27881411
Forward Genetic Screens in Zebrafish Identify Pre-mRNA-Processing Pathways Regulating Early T Cell Development. PMID:27880902
High-specificity bioinformatics framework for epigenomic profiling of discordant twins reveals specific and shared markers for ACPA and ACPA-positive rheumatoid arthritis. PMID:27876072
Myeloid-Specific Gene Deletion of Protein Phosphatase 2A Magnifies MyD88- and TRIF-Dependent Inflammation following Endotoxin Challenge. PMID:27872207
Conservation of immune gene signatures in solid tumors and prognostic implications. PMID:27871313
Dietary Intake Influences Adult Fertility and Offspring Fitness in Zebrafish. PMID:27870856
The histone demethylase KDM4B regulates peritoneal seeding of ovarian cancer. PMID:27869162
Reprogramming mouse fibroblasts into engraftable myeloerythroid and lymphoid progenitors. PMID:27869129
Global transcriptome responses including small RNAs during mixed-species interactions with methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa. PMID:27868360
Genome-wide DNA methylation analysis identifies MEGF10 as a novel epigenetically repressed candidate tumor suppressor gene in neuroblastoma. PMID:27862318
Transcriptomic responses in the oral cavity of F344 rats and B6C3F1 mice following exposure to Cr(VI): Implications for risk assessment. PMID:27859739
Identification of an Efficient Gene Expression Panel for Glioblastoma Classification. PMID:27855170
In silico Pathway Activation Network Decomposition Analysis (iPANDA) as a method for biomarker development. PMID:27848968
A meta-analysis of public microarray data identifies gene regulatory pathways deregulated in peripheral blood mononuclear cells from individuals with Systemic Lupus Erythematosus compared to those without. PMID:27846842
GEN3VA: aggregation and analysis of gene expression signatures from related studies. PMID:27846806
Proliferation rates and gene expression profiles in human lymphoblastoid cell lines from patients with depression characterized in response to antidepressant drug therapy. PMID:27845776
Discriminating cancer-related and cancer-unrelated chemoradiation-response genes for locally advanced rectal cancers. PMID:27845363
Integrative analysis of genetic data sets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. PMID:27842596
VRS2 regulates hormone-mediated inflorescence patterning in barley. PMID:27841879
Transcriptome profiling of NIH3T3 cell lines expressing opsin and the P23H opsin mutant identifies candidate drugs for the treatment of retinitis pigmentosa. PMID:27838510
OTX015 (MK-8628), a novel BET inhibitor, exhibits antitumor activity in non-small cell and small cell lung cancer models harboring different oncogenic mutations. PMID:27835869
NUAK1 (ARK5) Is Associated with Poor Prognosis in Ovarian Cancer. PMID:27833898
Arnica montana Stimulates Extracellular Matrix Gene Expression in a Macrophage Cell Line Differentiated to Wound-Healing Phenotype. PMID:27832158
Potential molecular characteristics in situ in response to repetitive UVB irradiation. PMID:27829444
Different tissue phagocytes sample apoptotic cells to direct distinct homeostasis programs. PMID:27828940
Pubertal and adult windows of susceptibility to a high animal fat diet in Trp53-null mammary tumorigenesis. PMID:27825136
Ankyrin-3 as a molecular marker of early-life stress and vulnerability to psychiatric disorders. PMID:27824361
Discovery and replication of a peripheral tissue DNA methylation biosignature to augment a suicide prediction model. PMID:27822318
Group B Streptococcus circumvents neutrophils and neutrophil extracellular traps during amniotic cavity invasion and preterm labor. PMID:27819066
Gene expression profiles and protein-protein interaction networks in amyotrophic lateral sclerosis patients with C9orf72 mutation. PMID:27814735
Integrative analysis for identification of shared markers from various functional cells/tissues for rheumatoid arthritis. PMID:27812736
Comparative Gene Expression Profiling of Primary and Metastatic Renal Cell Carcinoma Stem Cell-Like Cancer Cells. PMID:27812180
Changes in mammary histology and transcriptome profiles by low-dose exposure to environmental phenols at critical windows of development. PMID:27810681
A map of mobile DNA insertions in the NCI-60 human cancer cell panel. PMID:27807467
Transcriptional Analysis of serk1 and serk3 Coreceptor Mutants. PMID:27803191
The Conserved Dcw Gene Cluster of R. sphaeroides Is Preceded by an Uncommonly Extended 5' Leader Featuring the sRNA UpsM. PMID:27802301
Identifying reproducible cancer-associated highly expressed genes with important functional significances using multiple datasets. PMID:27796338
Hepatic transcriptome implications for palm fruit juice deterrence of type 2 diabetes mellitus in young male Nile rats. PMID:27795741
CPI-17 drives oncogenic Ras signaling in human melanomas via Ezrin-Radixin-Moesin family proteins. PMID:27793041
Single cell lineage tracing reveals a role for TgfβR2 in intestinal stem cell dynamics and differentiation. PMID:27791005
Cistrome Data Browser: a data portal for ChIP-Seq and chromatin accessibility data in human and mouse. PMID:27789702
Exploring the intrinsic differences among breast tumor subtypes defined using immunohistochemistry markers based on the decision tree. PMID:27786176
A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. PMID:27782827
CLIP-GENE: a web service of the condition specific context-laid integrative analysis for gene prioritization in mouse TF knockout experiments. PMID:27776539
Computational Analysis of G-Quadruplex Forming Sequences across Chromosomes Reveals High Density Patterns Near the Terminal Ends. PMID:27776185
Gene expression analysis reveals important pathways for drought response in leaves and roots of a wheat cultivar adapted to rainfed cropping in the Cerrado biome. PMID:27768155
Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes. PMID:27764126
The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1. PMID:27760161
Deficiency of base excision repair enzyme NEIL3 drives increased predisposition to autoimmunity. PMID:27760045
Characterization of Transient Receptor Potential Vanilloid-1 (TRPV1) Variant Activation by Coal Fly Ash Particles and Associations with Altered Transient Receptor Potential Ankyrin-1 (TRPA1) Expression and Asthma. PMID:27758864
Methylome analysis for spina bifida shows SOX18 hypomethylation as a risk factor with evidence for a complex (epi)genetic interplay to affect neural tube development. PMID:27757173
RhoA controls retinoid signaling by ROCK dependent regulation of retinol metabolism. PMID:27754752
Diabetes-linked transcription factor HNF4α regulates metabolism of endogenous methylarginines and β-aminoisobutyric acid by controlling expression of alanine-glyoxylate aminotransferase 2. PMID:27752141
Coordinated Activities of Multiple Myc-dependent and Myc-independent Biosynthetic Pathways in Hepatoblastoma. PMID:27738108
CNARA: reliability assessment for genomic copy number profiles. PMID:27733115
Comprehensive Cross-Population Analysis of High-Grade Serous Ovarian Cancer Supports No More Than Three Subtypes. PMID:27729437
Genome-Wide Interaction Analyses between Genetic Variants and Alcohol Consumption and Smoking for Risk of Colorectal Cancer. PMID:27723779
Convergent transcriptomics and proteomics of environmental enrichment and cocaine identifies novel therapeutic strategies for addiction. PMID:27717806
Exploring timing activation of functional pathway based on differential co-expression analysis in preimplantation embryogenesis. PMID:27705919
Self-Antigen-Driven Thymic B Cell Class Switching Promotes T Cell Central Tolerance. PMID:27705788
Neuronal Splicing Regulator RBFOX3 (NeuN) Regulates Adult Hippocampal Neurogenesis and Synaptogenesis. PMID:27701470
A cytotoxic anti-IL-3Rα antibody targets key cells and cytokines implicated in systemic lupus erythematosus. PMID:27699260
Safety and efficacy of the JAK inhibitor tofacitinib citrate in patients with alopecia areata. PMID:27699252
Upregulation of IFN-Inducible and Damage-Response Pathways in Chronic Graft-versus-Host Disease. PMID:27694491
Characterisation of equine satellite cell transcriptomic profile response to β-hydroxy-β-methylbutyrate (HMB). PMID:27691998
A penicillin-binding protein inhibits selection of colistin-resistant, lipooligosaccharide-deficient Acinetobacter baumannii. PMID:27681618
Characterization and phosphoproteomic analysis of a human immortalized podocyte model of Fabry disease generated using CRISPR/Cas9 technology. PMID:27681560
In search for geroprotectors: in silico screening and in vitro validation of signalome-level mimetics of young healthy state. PMID:27677171
Data-Driven Metabolic Pathway Compositions Enhance Cancer Survival Prediction. PMID:27673682
Novel ABCG2 Antagonists Reverse Topotecan-Mediated Chemotherapeutic Resistance in Ovarian Carcinoma Xenografts. PMID:27671528
Characteristics of Pos19 - A Small Coding RNA in the Oxidative Stress Response of Rhodobacter sphaeroides. PMID:27669425
The Challenge of Stability in High-Throughput Gene Expression Analysis: Comprehensive Selection and Evaluation of Reference Genes for BALB/c Mice Spleen Samples in the Leishmania infantum Infection Model. PMID:27668434
Modelling TFE renal cell carcinoma in mice reveals a critical role of WNT signaling. PMID:27668431
Data set for transcriptome analysis of Escherichia coli exposed to nickel. PMID:27668277
Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis. PMID:27666746
Finding lost genes in GWAS via integrative-omics analysis reveals novel sub-networks associated with preterm birth. PMID:27664809
Transcriptomic analysis of the highly efficient oil-degrading bacterium Acinetobacter venetianus RAG-1 reveals genes important in dodecane uptake and utilization. PMID:27664055
Systematically characterizing dysfunctional long intergenic non-coding RNAs in multiple brain regions of major psychosis. PMID:27661005
Detecting cognizable trends of gene expression in a time series RNA-sequencing experiment: a bootstrap approach. PMID:27659329
Trinitrobenzene sulfonic acid-induced intestinal injury in neonatal mice activates transcriptional networks similar to those seen in human necrotizing enterocolitis. PMID:27656771
Expression and methylation data from SLE patient and healthy control blood samples subdivided with respect to ARID3a levels. PMID:27656675
miR-125b affects mitochondrial biogenesis and impairs brite adipocyte formation and function. PMID:27656399
Uncovering synthetic lethal interactions for therapeutic targets and predictive markers in lung adenocarcinoma. PMID:27655641
DNA Microarray Platform for Detection and Surveillance of Viruses Transmitted by Small Mammals and Arthropods. PMID:27654806
Global transcriptome dysregulation in second trimester fetuses with FMR1 expansions. PMID:27646161
Diverse fates of uracilated HIV-1 DNA during infection of myeloid lineage cells. PMID:27644592
Global analysis of transcription in castration-resistant prostate cancer cells uncovers active enhancers and direct androgen receptor targets. PMID:27641228
Functional roles of MMP14 and MMP15 in early postnatal mammary gland development. PMID:27633994
Subpathway-CorSP: Identification of metabolic subpathways via integrating expression correlations and topological features between metabolites and genes of interest within pathways. PMID:27625019
Large-scale microarray profiling reveals four stages of immune escape in non-Hodgkin lymphomas. PMID:27622044
Investigating the Control of Chlorophyll Degradation by Genomic Correlation Mining. PMID:27618630
Portraying breast cancers with long noncoding RNAs. PMID:27617288
Regulatory Cross-Talks and Cascades in Rice Hormone Biosynthesis Pathways Contribute to Stress Signaling. PMID:27617021
Pramipexole induced place preference after L-dopa therapy and nigral dopaminergic loss: linking behavior to transcriptional modifications. PMID:27614895
A robust data scaling algorithm to improve classification accuracies in biomedical data. PMID:27612635
Ultrasonic Surgical Aspirate is a Reliable Source For Culturing Glioblastoma Stem Cells. PMID:27605047
Unbiased identification of signal-activated transcription factors by barcoded synthetic tandem repeat promoter screening (BC-STAR-PROM). PMID:27601530
Cancer Biomarkers from Genome-Scale DNA Methylation: Comparison of Evolutionary and Semantic Analysis Methods. PMID:27600245
Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. PMID:27600081
Global Profiling of the Cellular Alternative RNA Splicing Landscape during Virus-Host Interactions. PMID:27598998
A Mycobacterium avium subsp. paratuberculosis Predicted Serine Protease Is Associated with Acid Stress and Intraphagosomal Survival. PMID:27597934
Genotypes of cancer stem cells characterized by epithelial-to-mesenchymal transition and proliferation related functions. PMID:27597445
Identification and Characterization of the Dermal Panniculus Carnosus Muscle Stem Cells. PMID:27594590
Identification of BCL11B as a regulator of adipogenesis. PMID:27586877
Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex. PMID:27585846
A Small Protein Associated with Fungal Energy Metabolism Affects the Virulence of Cryptococcus neoformans in Mammals. PMID:27583447
A novel method for the identification of conserved structural patterns in RNA: From small scale to high-throughput applications. PMID:27580722
Epigenetic Loss of MLH1 Expression in Normal Human Hematopoietic Stem Cell Clones is Defined by the Promoter CpG Methylation Pattern Observed by High-Throughput Methylation Specific Sequencing. PMID:27570841
The transcriptional and splicing landscape of intestinal organoids undergoing nutrient starvation or endoplasmic reticulum stress. PMID:27561422
Characterization of Gene Expression Patterns among Artificially Developed Cancer Stem Cells Using Spherical Self-Organizing Map. PMID:27559294
EpiTracer - an algorithm for identifying epicenters in condition-specific biological networks. PMID:27556637
Systematic selection of small molecules to promote differentiation of embryonic stem cells and experimental validation for generating cardiomyocytes. PMID:27551501
fluff: exploratory analysis and visualization of high-throughput sequencing data. PMID:27547532
Exocytosis of polyubiquitinated proteins in bortezomib-resistant leukemia cells: a role for MARCKS in acquired resistance to proteasome inhibitors. PMID:27542283
Genome-wide association study identifies 14 novel risk alleles associated with basal cell carcinoma. PMID:27539887
MiR-4653-3p and its target gene FRS2 are prognostic biomarkers for hormone receptor positive breast cancer patients receiving tamoxifen as adjuvant endocrine therapy. PMID:27533459
A single nucleotide polymorphism genotyping platform for the authentication of patient derived xenografts. PMID:27528024
Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq). PMID:27519343
Transcriptome analysis of copper homeostasis genes reveals coordinated upregulation of SLC31A1,SCO1, and COX11 in colorectal cancer. PMID:27516958
The human olfactory transcriptome. PMID:27515280
Time-course gene expression data on the transcriptional effects of Aminaphtone on ECV304 endothelial cells. PMID:27508230
Differential expression of skeletal muscle genes following administration of clenbuterol to exercised horses. PMID:27506674
Regulation of proinflammatory genes by the circulating microRNA hsa-miR-939. PMID:27498764
RNA expression profile of calcified bicuspid, tricuspid, and normal human aortic valves by RNA sequencing. PMID:27495158
A long noncoding RNA signature for ulcerative colitis identifies IFNG-AS1 as an enhancer of inflammation. PMID:27492330
Backmasking in the yeast genome: encoding overlapping information for protein-coding and RNA degradation. PMID:27492286
White Adipose Tissue Browning in the R6/2 Mouse Model of Huntington's Disease. PMID:27486903
Transcriptomic profile adaptations following exposure of equine satellite cells to nutriactive phytochemical gamma-oryzanol. PMID:27482297
Using ILP to Identify Pathway Activation Patterns in Systems Biology. PMID:27478883
New Cell Adhesion Molecules in Human Ischemic Cardiomyopathy. PCDHGA3 Implications in Decreased Stroke Volume and Ventricular Dysfunction. PMID:27472518
The Landscape of A-to-I RNA Editome Is Shaped by Both Positive and Purifying Selection. PMID:27467689
Inverse association between carbohydrate consumption and plasma adropin concentrations in humans. PMID:27460714
Machine Learning of Protein Interactions in Fungal Secretory Pathways. PMID:27441920
Targeted genomic analysis reveals widespread autoimmune disease association with regulatory variants in the TNF superfamily cytokine signalling network. PMID:27435189
Coordinate Regulation of Metabolite Glycosylation and Stress Hormone Biosynthesis by TT8 in Arabidopsis. PMID:27432888
Comparison of In Vivo Gene Expression Profiling of RPE/Choroid following Intravitreal Injection of Dexamethasone and Triamcinolone Acetonide. PMID:27429799
Gremlin-1 Overexpression in Mouse Lung Reduces Silica-Induced Lymphocyte Recruitment - A Link to Idiopathic Pulmonary Fibrosis through Negative Correlation with CXCL10 Chemokine. PMID:27428020
Molecular signatures of neural connectivity in the olfactory cortex. PMID:27426965
Efficient generation of patient-matched malignant and normal primary cell cultures from clear cell renal cell carcinoma patients: clinically relevant models for research and personalized medicine. PMID:27422173
Regulation of a polyamine transporter by the conserved 3' UTR-derived sRNA SorX confers resistance to singlet oxygen and organic hydroperoxides in Rhodobacter sphaeroides. PMID:27420112
Calreticulin mediates an invasive breast cancer phenotype through the transcriptional dysregulation of p53 and MAPK pathways. PMID:27418879
miRNA Profile in Three Different Normal Human Ocular Tissues by miRNA-Seq. PMID:27415791
Polycomb-Mediated Repression and Sonic Hedgehog Signaling Interact to Regulate Merkel Cell Specification during Skin Development. PMID:27414999
Type IV collagen drives alveolar epithelial-endothelial association and the morphogenetic movements of septation. PMID:27412481
Obtaining Human Ischemic Stroke Gene Expression Biomarkers from Animal Models: A Cross-species Validation Study. PMID:27407070
The biofilm inhibitor Carolacton inhibits planktonic growth of virulent pneumococci via a conserved target. PMID:27404808
Non-canonical NF-κB pathway activation predicts outcome in borderline oestrogen receptor positive breast carcinoma. PMID:27404455
A consolidated analysis of the physiologic and molecular responses induced under acid stress in the legume-symbiont model-soil bacterium Sinorhizobium meliloti. PMID:27404346
Overcoming the matched-sample bottleneck: an orthogonal approach to integrate omic data. PMID:27403564
Developmental regulation of myeloerythroid progenitor function by the Lin28b-let-7-Hmga2 axis. PMID:27401346
Integrated Omic Analysis of a Guinea Pig Model of Heart Failure and Sudden Cardiac Death. PMID:27399916
NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease. PMID:27392431
Algorithms for differential splicing detection using exon arrays: a comparative assessment. PMID:27391904
Non-myogenic tumors display altered expression of dystrophin (DMD) and a high frequency of genetic alterations. PMID:27391342
Transition of an Anaerobic Escherichia coli Culture to Aerobiosis: Balancing mRNA and Protein Levels in a Demand-Directed Dynamic Flux Balance Analysis. PMID:27384956
Embryonic lethal abnormal vision proteins and adenine and uridine-rich element mRNAs after global cerebral ischemia and reperfusion in the rat. PMID:27381823
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
Type IV pili promote early biofilm formation by Clostridium difficile. PMID:27369898
Proteomic Screening and Lasso Regression Reveal Differential Signaling in Insulin and Insulin-like Growth Factor I (IGF1) Pathways. PMID:27364358
Prior knowledge transfer across transcriptional data sets and technologies using compositional statistics yields new mislabelled ovarian cell line. PMID:27353327
Identification of miRNA/mRNA-Negative Regulation Pairs in Nasopharyngeal Carcinoma. PMID:27350400
Knock-down of the methyltransferase Kmt6 relieves H3K27me3 and results in induction of cryptic and otherwise silent secondary metabolite gene clusters in Fusarium fujikuroi. PMID:27348741
FOXR2 Interacts with MYC to Promote Its Transcriptional Activities and Tumorigenesis. PMID:27346356
Filtered selection coupled with support vector machines generate a functionally relevant prediction model for colorectal cancer. PMID:27330311
Biomarkers of Tolerance in Kidney Transplantation: Are We Predicting Tolerance or Response to Immunosuppressive Treatment? PMID:27328267
A Mechanistic Beta-Binomial Probability Model for mRNA Sequencing Data. PMID:27326762
Transcriptional Profiling of Mycobacterium tuberculosis Exposed to In Vitro Lysosomal Stress. PMID:27324481
Gene expression prediction using low-rank matrix completion. PMID:27317252
AKT isoforms modulate Th1-like Treg generation and function in human autoimmune disease. PMID:27312110
Analysis of aggregated cell-cell statistical distances within pathways unveils therapeutic-resistance mechanisms in circulating tumor cells. PMID:27307648
What time is it? Deep learning approaches for circadian rhythms. PMID:27307647
The Regulation of rRNA Gene Transcription during Directed Differentiation of Human Embryonic Stem Cells. PMID:27299313
A Novel Mechanism of Host-Pathogen Interaction through sRNA in Bacterial Outer Membrane Vesicles. PMID:27295279
Folic acid induces cell type-specific changes in the transcriptome of breast cancer cell lines: a proof-of-concept study. PMID:27293554
Human Argonaute 2 Is Tethered to Ribosomal RNA through MicroRNA Interactions. PMID:27288410
Phorbol ester-mediated re-expression of endogenous LAT adapter in J.CaM2 cells: a model for dissecting drivers and blockers of LAT transcription. PMID:27278128
SSX2 regulates focal adhesion but does not drive the epithelial to mesenchymal transition in prostate cancer. PMID:27276714
Analysis of the Microprocessor in Dictyostelium: The Role of RbdB, a dsRNA Binding Protein. PMID:27272207
Bioinformatics resources for pollen. PMID:27271281
Long-lived antigen-induced IgM plasma cells demonstrate somatic mutations and contribute to long-term protection. PMID:27270306
Transcriptomic comparison of Drosophila snRNP biogenesis mutants reveals mutant-specific changes in pre-mRNA processing: implications for spinal muscular atrophy. PMID:27268418
Defining the identity of mouse embryonic dermal fibroblasts. PMID:27265328
Defining the Minimal Factors Required for Erythropoiesis through Direct Lineage Conversion. PMID:27264182
Transcriptome Profiling Identifies Multiplexin as a Target of SAGA Deubiquitinase Activity in Glia Required for Precise Axon Guidance During Drosophila Visual Development. PMID:27261002
Selection for reduced translation costs at the intronic 5' end in fungi. PMID:27260512
Breast cancer subtype predictors revisited: from consensus to concordance? PMID:27259591
Chemotherapy-related cachexia is associated with mitochondrial depletion and the activation of ERK1/2 and p38 MAPKs. PMID:27259276
Diagnostic value of microRNAs in asbestos exposure and malignant mesothelioma: systematic review and qualitative meta-analysis. PMID:27259231
Integrated omics approaches provide strategies for rapid erythromycin yield increase in Saccharopolyspora erythraea. PMID:27255285
Minor intron splicing is regulated by FUS and affected by ALS-associated FUS mutants. PMID:27252488
Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line. PMID:27245205
Coronary artery disease susceptibility gene ADTRP regulates cell cycle progression, proliferation, and apoptosis by global gene expression regulation. PMID:27235449
Deleterious assembly of the lamin A/C mutant p.S143P causes ER stress in familial dilated cardiomyopathy. PMID:27235420
The CsrA-FliW network controls polar localization of the dual-function flagellin mRNA in Campylobacter jejuni. PMID:27229370
Glucocorticoid receptor isoforms direct distinct mitochondrial programs to regulate ATP production. PMID:27226058
The Regulation of Cytokine Networks in Hippocampal CA1 Differentiates Extinction from Those Required for the Maintenance of Contextual Fear Memory after Recall. PMID:27224427
klf2a couples mechanotransduction and zebrafish valve morphogenesis through fibronectin synthesis. PMID:27221222
Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution. PMID:27220911
Identification of FRA-1 as a novel player in pancreatic cancer in cooperation with a MUC1: ERK signaling axis. PMID:27220889
A robust (re-)annotation approach to generate unbiased mapping references for RNA-seq-based analyses of differential expression across closely related species. PMID:27220689
Transcriptomic and proteomic analyses of core metabolism in Clostridium termitidis CT1112 during growth on α-cellulose, xylan, cellobiose and xylose. PMID:27215540
The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region. PMID:27210747
Altered gene expression in the lower respiratory tract of Car6 (-/-) mice. PMID:27209317
DNetDB: The human disease network database based on dysfunctional regulation mechanism. PMID:27209279
Cartography of Pathway Signal Perturbations Identifies Distinct Molecular Pathomechanisms in Malignant and Chronic Lung Diseases. PMID:27200087
Prevention of antipsychotic-induced hyperglycaemia by vitamin D: a data mining prediction followed by experimental exploration of the molecular mechanism. PMID:27199286
Identification of the long, edited dsRNAome of LPS-stimulated immune cells. PMID:27197207
Immunogenic Subtypes of Breast Cancer Delineated by Gene Classifiers of Immune Responsiveness. PMID:27197066
Identification of polycystic ovary syndrome potential drug targets based on pathobiological similarity in the protein-protein interaction network. PMID:27191267
Pervasive Effects of Aging on Gene Expression in Wild Wolves. PMID:27189566
Whole-transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases. PMID:27189340
A critical role for the Drosophila dopamine D1-like receptor Dop1R2 at the onset of metamorphosis. PMID:27184815
U2AF35(S34F) Promotes Transformation by Directing Aberrant ATG7 Pre-mRNA 3' End Formation. PMID:27184077
Associations between whole peripheral blood fatty acids and DNA methylation in humans. PMID:27181711
High Persister Mutants in Mycobacterium tuberculosis. PMID:27176494
The transcriptional activator GaaR of Aspergillus niger is required for release and utilization of d-galacturonic acid from pectin. PMID:27174630
Microarray Gene Expression Analysis to Evaluate Cell Type Specific Expression of Targets Relevant for Immunotherapy of Hematological Malignancies. PMID:27171398
The arabidopsis cyclic nucleotide interactome. PMID:27170143
Negative control of CSL gene transcription by stress/DNA damage response and p53. PMID:27163456
Uptake of dietary milk miRNAs by adult humans: a validation study. PMID:27158459
MiR-16 mediates trastuzumab and lapatinib response in ErbB-2-positive breast and gastric cancer via its novel targets CCNJ and FUBP1. PMID:27157613
Transcriptional signatures of brain aging and Alzheimer's disease: What are our rodent models telling us? PMID:27155503
Cerebellar neurodegeneration in a new rat model of episodic hepatic encephalopathy. PMID:27154504
Molecular characterization of Gleason patterns 3 and 4 prostate cancer using reverse Warburg effect-associated genes. PMID:27152194
In vivo gene expression in a Staphylococcus aureus prosthetic joint infection characterized by RNA sequencing and metabolomics: a pilot study. PMID:27150914
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
Integrating DNA Methylation and Gene Expression Data in the Development of the Soybean-Bradyrhizobium N2-Fixing Symbiosis. PMID:27148207
Reconstructed Metabolic Network Models Predict Flux-Level Metabolic Reprogramming in Glioblastoma. PMID:27147948
Assessment of FBA Based Gene Essentiality Analysis in Cancer with a Fast Context-Specific Network Reconstruction Method. PMID:27145226
Ontology-based annotations and semantic relations in large-scale (epi)genomics data. PMID:27142216
Identification of the BRD1 interaction network and its impact on mental disorder risk. PMID:27142060
Deletion of inositol hexakisphosphate kinase 1 (IP6K1) reduces cell migration and invasion, conferring protection from aerodigestive tract carcinoma in mice. PMID:27140681
Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. PMID:27138000
Interferon Regulatory Factor 8 (IRF8) Impairs Induction of Interferon Induced with Tetratricopeptide Repeat Motif (IFIT) Gene Family Members. PMID:27137933
Identification of key regulators of pancreatic cancer progression through multidimensional systems-level analysis. PMID:27137215
2,3,7,8 Tetrachlorodibenzo-p-dioxin-induced RNA abundance changes identify Ackr3, Col18a1, Cyb5a and Glud1 as candidate mediators of toxicity. PMID:27136898
Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats. PMID:27135913
Low Dimensionality in Gene Expression Data Enables the Accurate Extraction of Transcriptional Programs from Shallow Sequencing. PMID:27135536
Keeping Control: The Role of Senescence and Development in Plant Pathogenesis and Defense. PMID:27135337
Mitochondrial Stress Induces Chromatin Reorganization to Promote Longevity and UPR(mt). PMID:27133166
Age-Dependent Pancreatic Gene Regulation Reveals Mechanisms Governing Human β Cell Function. PMID:27133132
Establishing an analytic pipeline for genome-wide DNA methylation. PMID:27127542
Characterization of key triacylglycerol biosynthesis processes in rhodococci. PMID:27126051
Genetics of PCOS: A systematic bioinformatics approach to unveil the proteins responsible for PCOS. PMID:27114910
Immune activation of the host cell induces drug tolerance in Mycobacterium tuberculosis both in vitro and in vivo. PMID:27114608
Genome-wide transcription start site mapping of Bradyrhizobium japonicum grown free-living or in symbiosis - a rich resource to identify new transcripts, proteins and to study gene regulation. PMID:27107716
Cisplatin selects for stem-like cells in osteosarcoma by activating Notch signaling. PMID:27102300
Survival in acute myeloid leukemia is associated with NKp44 splice variants. PMID:27102296
CIP2A Promotes T-Cell Activation and Immune Response to Listeria monocytogenes Infection. PMID:27100879
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
The Influence of the Global Gene Expression Shift on Downstream Analyses. PMID:27092944
Learning from Co-expression Networks: Possibilities and Challenges. PMID:27092161
Arachidonic and oleic acid exert distinct effects on the DNA methylome. PMID:27088456
Identification and Evolutionary Analysis of Potential Candidate Genes in a Human Eating Disorder. PMID:27088090
Two sets of RNAi components are required for heterochromatin formation in trans triggered by truncated transgenes. PMID:27085807
Pathway activation strength is a novel independent prognostic biomarker for cetuximab sensitivity in colorectal cancer patients. PMID:27081524
s-SHIP expression identifies a subset of murine basal prostate cells as neonatal stem cells. PMID:27081082
In silico methods for drug repurposing and pharmacology. PMID:27080087
Fatty Acid Oxidation is Impaired in An Orthologous Mouse Model of Autosomal Dominant Polycystic Kidney Disease. PMID:27077126
Data set for transcriptional response to depletion of the Shoc2 scaffolding protein. PMID:27077079
Transcriptomic and metabolomic profiling of ionic liquid stimuli unveils enhanced secondary metabolism in Aspergillus nidulans. PMID:27072538
Contrasting invertebrate immune defense behaviors caused by a single gene, the Caenorhabditis elegans neuropeptide receptor gene npr-1. PMID:27066825
Comprehensive Transcriptome Meta-analysis to Characterize Host Immune Responses in Helminth Infections. PMID:27058578
RegenBase: a knowledge base of spinal cord injury biology for translational research. PMID:27055827
Mga2 Transcription Factor Regulates an Oxygen-responsive Lipid Homeostasis Pathway in Fission Yeast. PMID:27053105
Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs. PMID:27050376
Genome-Wide Expression Profiling Reveals S100B as Biomarker for Invasive Aspergillosis. PMID:27047454
Reconstruction of the Regulatory Network for Bacillus subtilis and Reconciliation with Gene Expression Data. PMID:27047450
A Thermodynamic-Based Interpretation of Protein Expression Heterogeneity in Different Glioblastoma Multiforme Tumors Identifies Tumor-Specific Unbalanced Processes. PMID:27035264
Assessing Concordance of Drug-Induced Transcriptional Response in Rodent Liver and Cultured Hepatocytes. PMID:27028627
Overexpression of Ran GTPase Components Regulating Nuclear Export, but not Mitotic Spindle Assembly, Marks Chromosome Instability and Poor Prognosis in Breast Cancer. PMID:27023921
UV-B Perception and Acclimation in Chlamydomonas reinhardtii. PMID:27020958
Integrative network modeling approaches to personalized cancer medicine. PMID:27019658
Linker histone variant H1T targets rDNA repeats. PMID:27018843
Can data repositories help find effective treatments for complex diseases? PMID:27018167
Androgen deprivation therapy sensitizes triple negative breast cancer cells to immune-mediated lysis through androgen receptor independent modulation of osteoprotegerin. PMID:27015557
The retinoblastoma protein regulates hypoxia-inducible genetic programs, tumor cell invasiveness and neuroendocrine differentiation in prostate cancer cells. PMID:27015368
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. PMID:27013077
Condensin I and II behaviour in interphase nuclei and cells undergoing premature chromosome condensation. PMID:27008552
The Gene Expression Omnibus Database. PMID:27008011
An individualized prognostic signature and multi‑omics distinction for early stage hepatocellular carcinoma patients with surgical resection. PMID:27006471
Polysome Profiling Links Translational Control to the Radioresponse of Glioblastoma Stem-like Cells. PMID:27005284
UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data. PMID:27001340
Spatiotemporal transcriptome provides insights into early fruit development of tomato (Solanum lycopersicum). PMID:26988970
Bifidobacterium thermophilum RBL67 impacts on growth and virulence gene expression of Salmonella enterica subsp. enterica serovar Typhimurium. PMID:26988691
Human adaptation and population differentiation in the light of ancient genomes. PMID:26988143
GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data. PMID:26983021
Transcriptional analysis of antiviral small molecule therapeutics as agonists of the RLR pathway. PMID:26981429
Computational gene expression profiling under salt stress reveals patterns of co-expression. PMID:26981411
Transcriptional profile of immediate response to ionizing radiation exposure. PMID:26981369
Identification and Characterization of msf, a Novel Virulence Factor in Haemophilus influenzae. PMID:26977929
Patterns of Transcriptional Response to 1,25-Dihydroxyvitamin D3 and Bacterial Lipopolysaccharide in Primary Human Monocytes. PMID:26976439
Cellular Tracking and Gene Profiling of Fusarium graminearum during Maize Stalk Rot Disease Development Elucidates Its Strategies in Confronting Phosphorus Limitation in the Host Apoplast. PMID:26974960
RNA-binding protein IGF2BP3 targeting of oncogenic transcripts promotes hematopoietic progenitor proliferation. PMID:26974154
Transcriptomic Analysis Using Olive Varieties and Breeding Progenies Identifies Candidate Genes Involved in Plant Architecture. PMID:26973682
Gene expression changes in damaged osteoarthritic cartilage identify a signature of non-chondrogenic and mechanical responses. PMID:26973327
Comorbidities of Psoriasis - Exploring the Links by Network Approach. PMID:26966903
Programming of Plant Leaf Senescence with Temporal and Inter-Organellar Coordination of Transcriptome in Arabidopsis. PMID:26966169
12-HETER1/GPR31, a high-affinity 12(S)-hydroxyeicosatetraenoic acid receptor, is significantly up-regulated in prostate cancer and plays a critical role in prostate cancer progression. PMID:26965684
Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo. PMID:26964064
Toward improved phosphorus efficiency in monogastrics-interplay of serum, minerals, bone, and immune system after divergent dietary phosphorus supply in swine. PMID:26962023
Integrated mRNA and miRNA expression profiling in blood reveals candidate biomarkers associated with endurance exercise in the horse. PMID:26960911
Comparative transcriptome analysis of Gastrodia elata (Orchidaceae) in response to fungus symbiosis to identify gastrodin biosynthesis-related genes. PMID:26960548
Translational Meta-analytical Methods to Localize the Regulatory Patterns of Neurological Disorders in the Human Brain. PMID:26958307
Combining Human Disease Genetics and Mouse Model Phenotypes towards Drug Repositioning for Parkinson's disease. PMID:26958284
The TGF-β pathway is activated by 5-fluorouracil treatment in drug resistant colorectal carcinoma cells. PMID:26956045
Serological and Genetic Evidence for Altered Complement System Functionality in Systemic Lupus Erythematosus: Findings of the GAPAID Consortium. PMID:26950932
Comparative evaluation of isoform-level gene expression estimation algorithms for RNA-seq and exon-array platforms. PMID:26944083
Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. PMID:26944061
The Brewed Rice Vinegar Kurozu Increases HSPA1A Expression and Ameliorates Cognitive Dysfunction in Aged P8 Mice. PMID:26943920
High-throughput discovery of post-transcriptional cis-regulatory elements. PMID:26941072
The transcriptome of NaCl-treated Limonium bicolor leaves reveals the genes controlling salt secretion of salt gland. PMID:26936070
Quantitative assessment of ribosome drop-off in E. coli. PMID:26935582
Integrated analysis of DNA methylation profiles and gene expression profiles to identify genes associated with pilocytic astrocytomas. PMID:26934913
Alternatively Activated Macrophages Boost Induced Regulatory T and Th17 Cell Responses during Immunotherapy for Colitis. PMID:26927797
An interactive environment for agile analysis and visualization of ChIP-sequencing data. PMID:26926434
The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium. PMID:26924983
An integrated genomics analysis of epigenetic subtypes in human breast tumors links DNA methylation patterns to chromatin states in normal mammary cells. PMID:26923702
GATA3-dependent cellular reprogramming requires activation-domain dependent recruitment of a chromatin remodeler. PMID:26922637
Distribution of miRNA expression across human tissues. PMID:26921406
Thymic stromal lymphopoietin (TSLP) inhibits human colon tumor growth by promoting apoptosis of tumor cells. PMID:26919238
A nuclear-directed human pancreatic ribonuclease (PE5) targets the metabolic phenotype of cancer cells. PMID:26918450
Reduced-representation Phosphosignatures Measured by Quantitative Targeted MS Capture Cellular States and Enable Large-scale Comparison of Drug-induced Phenotypes. PMID:26912667
Early-branching gut fungi possess a large, comprehensive array of biomass-degrading enzymes. PMID:26912365
Quantitative analysis by next generation sequencing of hematopoietic stem and progenitor cells (LSK) and of splenic B cells transcriptomes from wild-type and Usp3-knockout mice. PMID:26909367
Using Multi-objective Optimization to Identify Dynamical Network Biomarkers as Early-warning Signals of Complex Diseases. PMID:26906975
αCP binding to a cytosine-rich subset of polypyrimidine tracts drives a novel pathway of cassette exon splicing in the mammalian transcriptome. PMID:26896798
Interleukin-6 is a potential therapeutic target in interleukin-6 dependent, estrogen receptor-α-positive breast cancer. PMID:26893580
Positional proteomics reveals differences in N-terminal proteoform stability. PMID:26893308
Discovering gene re-ranking efficiency and conserved gene-gene relationships derived from gene co-expression network analysis on breast cancer data. PMID:26892392
Role of miR-222-3p in c-Src-Mediated Regulation of Osteoclastogenesis. PMID:26891296
MiR-449a Affects Epithelial Proliferation during the Pseudoglandular and Canalicular Phases of Avian and Mammal Lung Development. PMID:26891231
DNA methylation variation of human-specific Alu repeats. PMID:26890526
Oestrogen receptor β regulates epigenetic patterns at specific genomic loci through interaction with thymine DNA glycosylase. PMID:26889208
Profiling placental and fetal DNA methylation in human neural tube defects. PMID:26889207
Microarray Analysis of Gene Expression in Saccharomyces cerevisiae kap108Δ Mutants upon Addition of Oxidative Stress. PMID:26888869
miR-182 Modulates Myocardial Hypertrophic Response Induced by Angiogenesis in Heart. PMID:26888314
New tools for studying microglia in the mouse and human CNS. PMID:26884166
Physiological evidence for diversification of IFNα- and IFNβ-mediated response programs in different autoimmune diseases. PMID:26882897
ZBIT Bioinformatics Toolbox: A Web-Platform for Systems Biology and Expression Data Analysis. PMID:26882475
Therapeutic potential of targeting microRNA-10b in established intracranial glioblastoma: first steps toward the clinic. PMID:26881967
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice. PMID:26881867
Genomic and transcriptomic hallmarks of poorly differentiated and anaplastic thyroid cancers. PMID:26878173
Translational bioinformatics in the era of real-time biomedical, health care and wellness data streams. PMID:26876889
Single-cell Transcriptome Study as Big Data. PMID:26876720
RONIN Is an Essential Transcriptional Regulator of Genes Required for Mitochondrial Function in the Developing Retina. PMID:26876175
Gene expression inference with deep learning. PMID:26873929
Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes. PMID:26872257
Social threat exposure in juvenile mice promotes cocaine-seeking by altering blood clotting and brain vasculature. PMID:26870906
Regulation of the tumour suppressor PDCD4 by miR-499 and miR-21 in oropharyngeal cancers. PMID:26867589
Identification of Targets of CUG-BP, Elav-Like Family Member 1 (CELF1) Regulation in Embryonic Heart Muscle. PMID:26866591
A genome-wide search for epigenetically [corrected] regulated genes in zebra finch using MethylCap-seq and RNA-seq. PMID:26864856
Differential Expression of Genes and DNA Methylation associated with Prenatal Protein Undernutrition by Albumen Removal in an avian model. PMID:26861190
New insights into the Plasmodium vivax transcriptome using RNA-Seq. PMID:26858037
Loss of the transcription factor Meis1 prevents sympathetic neurons target-field innervation and increases susceptibility to sudden cardiac death. PMID:26857994
Integrative Genomic Analyses Yield Cell-Cycle Regulatory Programs with Prognostic Value. PMID:26856934
Dictyocaulus viviparus genome, variome and transcriptome elucidate lungworm biology and support future intervention. PMID:26856411
JAK-STAT and G-protein-coupled receptor signaling pathways are frequently altered in epitheliotropic intestinal T-cell lymphoma. PMID:26854024
Gene set analysis using sufficient dimension reduction. PMID:26852017
Identification of CdnL, a Putative Transcriptional Regulator Involved in Repair and Outgrowth of Heat-Damaged Bacillus cereus Spores. PMID:26849219
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay. PMID:26846207
The Role of DNA Methylation in Cardiovascular Risk and Disease: Methodological Aspects, Study Design, and Data Analysis for Epidemiological Studies. PMID:26837743
Benchmarking Procedures for High-Throughput Context Specific Reconstruction Algorithms. PMID:26834640
Chemical Inhibition of Wild-Type p53-Induced Phosphatase 1 (WIP1/PPM1D) by GSK2830371 Potentiates the Sensitivity to MDM2 Inhibitors in a p53-Dependent Manner. PMID:26832796
IgG Glycome in Colorectal Cancer. PMID:26831718
A multiplex immunoassay for the non-invasive detection of bladder cancer. PMID:26830497
Reduced CYFIP1 in Human Neural Progenitors Results in Dysregulation of Schizophrenia and Epilepsy Gene Networks. PMID:26824476
Long non-coding RNAs display higher natural expression variation than protein-coding genes in healthy humans. PMID:26821746
Missing value imputation for microRNA expression data by using a GO-based similarity measure. PMID:26818962
MatP regulates the coordinated action of topoisomerase IV and MukBEF in chromosome segregation. PMID:26818444
Prediction of drugs having opposite effects on disease genes in a directed network. PMID:26818006
PMD: A Resource for Archiving and Analyzing Protein Microarray data. PMID:26813635
Gene signature of the post-Chernobyl papillary thyroid cancer. PMID:26810418
Identification of factors involved in target RNA-directed microRNA degradation. PMID:26809675
Accelerating Adverse Outcome Pathway Development Using Publicly Available Data Sources. PMID:26809562
Estrogen Receptor Alpha (ESR1)-Dependent Regulation of the Mouse Oviductal Transcriptome. PMID:26808832
RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis. PMID:26808730
A Novel Biomarker Panel Examining Response to Gemcitabine with or without Erlotinib for Pancreatic Cancer Therapy in NCIC Clinical Trials Group PA.3. PMID:26808546
A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha. PMID:26798136
Identification of Crowding Stress Tolerance Co-Expression Networks Involved in Sweet Corn Yield. PMID:26796516
Transcriptome Changes in Hirschfeldia incana in Response to Lead Exposure. PMID:26793211
Global Regulation of Gene Expression by the MafR Protein of Enterococcus faecalis. PMID:26793169
CD28 Deficiency Enhances Type I IFN Production by Murine Plasmacytoid Dendritic Cells. PMID:26773151
New players in heterochromatin silencing: histone variant H3.3 and the ATRX/DAXX chaperone. PMID:26773061
Postponing the Hypoglycemic Response to Partial Hepatectomy Delays Mouse Liver Regeneration. PMID:26772417
Transcriptome responses in alfalfa associated with tolerance to intensive animal grazing. PMID:26763747
Novel insights into human respiratory syncytial virus-host factor interactions through integrated proteomics and transcriptomics analysis. PMID:26760927
The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP. PMID:26755627
Testing the kinship theory of intragenomic conflict in honey bees (Apis mellifera). PMID:26755583
Whole Blood Transcriptomics Is Relevant to Identify Molecular Changes in Response to Genetic Selection for Feed Efficiency and Nutritional Status in the Pig. PMID:26752050
Type III Methyltransferase M.NgoAX from Neisseria gonorrhoeae FA1090 Regulates Biofilm Formation and Interactions with Human Cells. PMID:26733970
Transcriptional profiling and muscle cross-section analysis reveal signs of ischemia reperfusion injury following total knee arthroplasty with tourniquet. PMID:26733251
ChainRank, a chain prioritisation method for contextualisation of biological networks. PMID:26729273
Multiple Transcriptome Data Analysis Reveals Biologically Relevant Atopic Dermatitis Signature Genes and Pathways. PMID:26717000
Improving Cancer Gene Expression Data Quality through a TCGA Data-Driven Evaluation of Identifier Filtering. PMID:26715829
EntropyExplorer: an R package for computing and comparing differential Shannon entropy, differential coefficient of variation and differential expression. PMID:26714840
Patients with Dilated Cardiomyopathy and Sustained Monomorphic Ventricular Tachycardia Show Up-Regulation of KCNN3 and KCNJ2 Genes and CACNG8-Linked Left Ventricular Dysfunction. PMID:26710323
The Macrophage Inhibitor CNI-1493 Blocks Metastasis in a Mouse Model of Ewing Sarcoma through Inhibition of Extravasation. PMID:26709919
WheatExp: an RNA-seq expression database for polyploid wheat. PMID:26705106
Comparative analysis of blood and saliva expression profiles in chronic and refractory periodontitis patients. PMID:26705104
The human milk oligosaccharide 2'-fucosyllactose augments the adaptive response to extensive intestinal. PMID:26702137
Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model. PMID:26697387
Assessment of microRNA expression in mouse epididymal epithelial cells and spermatozoa by next generation sequencing. PMID:26697376
Prediction of Druggable Proteins Using Machine Learning and Systems Biology: A Mini-Review. PMID:26696900
Conserved and highly expressed tRNA derived fragments in zebrafish. PMID:26694924
iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function. PMID:26694817
Neurospora crassa transcriptomics reveals oxidative stress and plasma membrane homeostasis biology genes as key targets in response to chitosan. PMID:26694141
Prediction of tissue-specific effects of gene knockout on apoptosis in different anatomical structures of human brain. PMID:26693857
Interleukin-1 antagonism moderates the inflammatory state associated with Type 1 diabetes during clinical trials conducted at disease onset. PMID:26692253
MiR-338-5p sensitizes glioblastoma cells to radiation through regulation of genes involved in DNA damage response. PMID:26692101
Understanding gene expression in coronary artery disease through global profiling, network analysis and independent validation of key candidate genes. PMID:26690514
Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner. PMID:26684652
Expression Profiling after Prolonged Experimental Febrile Seizures in Mice Suggests Structural Remodeling in the Hippocampus. PMID:26684451
Molecular analysis of pediatric brain tumors identifies microRNAs in pilocytic astrocytomas that target the MAPK and NF-κB pathways. PMID:26682910
Infection by Herpes Simplex Virus 1 Causes Near-Complete Loss of RNA Polymerase II Occupancy on the Host Cell Genome. PMID:26676778
Targeting Innate Immunity for Antiviral Therapy through Small Molecule Agonists of the RLR Pathway. PMID:26676770
A human haploid gene trap collection to study lncRNAs with unusual RNA biology. PMID:26670263
Actin remodeling confers BRAF inhibitor resistance to melanoma cells through YAP/TAZ activation. PMID:26668268
Immune modulators in disease: integrating knowledge from the biomedical literature and gene expression. PMID:26661719
Intermittent Hypoxia Alters Gene Expression in Peripheral Blood Mononuclear Cells of Healthy Volunteers. PMID:26657991
A genome-scale screen reveals context-dependent ovarian cancer sensitivity to miRNA overexpression. PMID:26655797
Diguanylate Cyclases AdrA and STM1987 Regulate Salmonella enterica Exopolysaccharide Production during Plant Colonization in an Environment-Dependent Manner. PMID:26655751
iRDA: a new filter towards predictive, stable, and enriched candidate genes. PMID:26647162
Rapid Increase in frequency of gene copy-number variants during experimental evolution in Caenorhabditis elegans. PMID:26645535
Identifying Novel Transcriptional Regulators with Circadian Expression. PMID:26644408
AKT Inhibition Promotes Nonautonomous Cancer Cell Survival. PMID:26637368
Intra-Gene DNA Methylation Variability Is a Clinically Independent Prognostic Marker in Women's Cancers. PMID:26629914
Genetic architecture of early pre-inflammatory stage transcription signatures of autoimmune diabetes in the pancreatic lymph nodes of the NOD mouse reveals significant gene enrichment on chromosomes 6 and 7. PMID:26629415
BRAFV600E-Associated Gene Expression Profile: Early Changes in the Transcriptome, Based on a Transgenic Mouse Model of Papillary Thyroid Carcinoma. PMID:26625260
Loss of Ezh2 promotes a midbrain-to-forebrain identity switch by direct gene derepression and Wnt-dependent regulation. PMID:26621269
σ Factor and Anti-σ Factor That Control Swarming Motility and Biofilm Formation in Pseudomonas aeruginosa. PMID:26620262
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. PMID:26619358
C-terminal domains of a histone demethylase interact with a pair of transcription factors and mediate specific chromatin association. PMID:26617990
Increased collagen cross-linking is a signature of dystrophin-deficient muscle. PMID:26616495
Data standards can boost metabolomics research, and if there is a will, there is a way. PMID:26612985
Gatekeeper role of brain antigen-presenting CD11c+ cells in neuroinflammation. PMID:26612827
A novel xenograft model to study the role of TSLP-induced CRLF2 signals in normal and malignant human B lymphopoiesis. PMID:26611474
Identification of sample annotation errors in gene expression datasets. PMID:26608184
The sialyl-glycolipid stage-specific embryonic antigen 4 marks a subpopulation of chemotherapy-resistant breast cancer cells with mesenchymal features. PMID:26607327
Impact of SNPs on methylation readouts by Illumina Infinium HumanMethylation450 BeadChip Array: implications for comparative population studies. PMID:26607064
Transcriptome analysis of GVHD reveals aurora kinase A as a targetable pathway for disease prevention. PMID:26606970
Gene expression profiles and protein-protein interaction network analysis in AIDS patients with HIV-associated encephalitis and dementia. PMID:26604827
Telomere binding protein TRB1 is associated with promoters of translation machinery genes in vivo. PMID:26597966
Isolation and characterization of circulating lymphatic endothelial colony forming cells. PMID:26597759
Gene-expression signature functional annotation of breast cancer tumours in function of age. PMID:26597277
Nuclear factor, erythroid 2-like 2-associated molecular signature predicts lung cancer survival. PMID:26596768
Precision Subtypes of T Cell-Mediated Rejection Identified by Molecular Profiles. PMID:26594210
SBR-Blood: systems biology repository for hematopoietic cells. PMID:26590403
Mycobacterial infection induces a specific human innate immune response. PMID:26586179
Transcriptome analysis reveals regulatory networks underlying differential susceptibility to Botrytis cinerea in response to nitrogen availability in Solanum lycopersicum. PMID:26583019
Ectodysplasin/NF-κB Promotes Mammary Cell Fate via Wnt/β-catenin Pathway. PMID:26581094
De novo transcriptome profiling of cold-stressed siliques during pod filling stages in Indian mustard (Brassica juncea L.). PMID:26579175
Combined Genome-Wide CSF Aβ-42's Associations and Simple Network Properties Highlight New Risk Factors for Alzheimer's Disease. PMID:26576771
Mining for novel candidate clock genes in the circadian regulatory network. PMID:26576534
An Effective Method to Identify Shared Pathways and Common Factors among Neurodegenerative Diseases. PMID:26575483
Five omic technologies are concordant in differentiating the biochemical characteristics of the berries of five grapevine (Vitis vinifera L.) cultivars. PMID:26573226
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
Gene expression and immunochemical localization of major cytochrome P450 drug-metabolizing enzymes in bovine nasal olfactory and respiratory mucosa. PMID:26572092
The effects of long-term daily folic acid and vitamin B12 supplementation on genome-wide DNA methylation in elderly subjects. PMID:26568774
Intra-tumor genetic heterogeneity in rectal cancer. PMID:26568296
A comprehensive multiomics approach toward understanding the relationship between aging and dementia. PMID:26564964
Dysregulation of bile acid homeostasis in parenteral nutrition mouse model. PMID:26564717
From System-Wide Differential Gene Expression to Perturbed Regulatory Factors: A Combinatorial Approach. PMID:26562430
Survival analysis and microarray profiling identify Cd40 as a candidate for the Salmonella susceptibility locus, Ity5. PMID:26562079
Primary Amine Oxidase of Escherichia coli Is a Metabolic Enzyme that Can Use a Human Leukocyte Molecule as a Substrate. PMID:26556595
Transcriptome-wide analysis supports environmental adaptations of two Pinus pinaster populations from contrasting habitats. PMID:26545587
CXCL1 is elevated in the urine of bladder cancer patients. PMID:26543745
Identification and functional studies of regulatory variants responsible for the association of NRG3 with a delusion phenotype in schizophrenia. PMID:26528484
IRAK1 is a novel DEK transcriptional target and is essential for head and neck cancer cell survival. PMID:26527316
Puberty-specific promotion of mammary tumorigenesis by a high animal fat diet. PMID:26526858
NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program. PMID:26516211
Novel gene sets improve set-level classification of prokaryotic gene expression data. PMID:26511329
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data. PMID:26511205
Prior infection with Type A Francisella tularensis antagonizes the pulmonary transcriptional response to an aerosolized Toll-like receptor 4 agonist. PMID:26510639
Transcriptomic Changes Due to Cytoplasmic TDP-43 Expression Reveal Dysregulation of Histone Transcripts and Nuclear Chromatin. PMID:26510133
Specific inhibition by synthetic analogs of pyruvate reveals that the pyruvate dehydrogenase reaction is essential for metabolism and viability of glioblastoma cells. PMID:26503465
Quercetin suppresses immune cell accumulation and improves mitochondrial gene expression in adipose tissue of diet-induced obese mice. PMID:26499876
Transcriptional profiles of pilocytic astrocytoma are related to their three different locations, but not to radiological tumor features. PMID:26497896
Oct4-induced oligodendrocyte progenitor cells enhance functional recovery in spinal cord injury model. PMID:26497893
Inhibition of the miR-155 target NIAM phenocopies the growth promoting effect of miR-155 in B-cell lymphoma. PMID:26497687
Tumor-host signaling interaction reveals a systemic, age-dependent splenic immune influence on tumor development. PMID:26497558
MtiBase: a database for decoding microRNA target sites located within CDS and 5'UTR regions from CLIP-Seq and expression profile datasets. PMID:26490638
A functional module-based exploration between inflammation and cancer in esophagus. PMID:26489668
New global analysis of the microRNA transcriptome of primary tumors and lymph node metastases of papillary thyroid cancer. PMID:26487287
A mutation in the nucleoporin-107 gene causes XX gonadal dysgenesis. PMID:26485283
Time-series analysis of the transcriptome of the re-establishment of desiccation tolerance by ABA in germinated Arabidopsis thaliana seeds. PMID:26484244
A ChIP-on-chip tiling array approach detects functional histone-free regions associated with boundaries at vertebrate HOX genes. PMID:26484075
Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis. PMID:26482908
NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases. PMID:26475471
Identification of two mutations increasing the methanol tolerance of Corynebacterium glutamicum. PMID:26474849
Potential involvement of miR-375 in the premalignant progression of oral squamous cell carcinoma mediated via transcription factor KLF5. PMID:26474386
Different exercise modalities have distinct effects on the integrin-linked kinase (ILK) and Ca2+ signaling pathways in the male rat bone. PMID:26471755
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize. PMID:26470872
Gene-expression profiling of buccal epithelium among non-smoking women exposed to household air pollution from smoky coal. PMID:26468118
Whole transcriptome profiling reveals the RNA content of motor axons. PMID:26464439
Sample size reassessment for a two-stage design controlling the false discovery rate. PMID:26461844
Broad-spectrum antibodies against self-antigens and cytokines in RAG deficiency. PMID:26457731
Molecular adaptation of Lactobacillus plantarum WCFS1 to gallic acid revealed by genome-scale transcriptomic signature and physiological analysis. PMID:26453568
A cross-cancer differential co-expression network reveals microRNA-regulated oncogenic functional modules. PMID:26448606
Whole Genome Expression Microarray Analysis of Highly Versus Poorly Tumorigenic Murine Melanoma Cell Lines Provides Insights into Factors That Regulate Tumor Growth, Metastasis, and Immunogenicity. PMID:26441959
Mammary Stem Cell Self-Renewal Is Regulated by Slit2/Robo1 Signaling through SNAI1 and mINSC. PMID:26440891
Synergistic Gene Expression Signature Observed in TK6 Cells upon Co-Exposure to UVC-Irradiation and Protein Kinase C-Activating Tumor Promoters. PMID:26431317
A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq. PMID:26427366
The idiopathic preterm delivery methylation profile in umbilical cord blood DNA. PMID:26419829
Vigilant keratinocytes trigger pathogen-associated molecular pattern signaling in response to streptococcal M1 protein. PMID:26416902
The decrease in histone methyltransferase EZH2 in response to fluid shear stress alters endothelial gene expression and promotes quiescence. PMID:26416763
MicroRNAs and Their Targets Are Differentially Regulated in Adult and Neonatal Mouse CD8+ T Cells. PMID:26416483
Molecular portraits revealing the heterogeneity of breast tumor subtypes defined using immunohistochemistry markers. PMID:26404658
Transcriptomics Profiling of Alzheimer's Disease Reveal Neurovascular Defects, Altered Amyloid-β Homeostasis, and Deregulated Expression of Long Noncoding RNAs. PMID:26402107
Whose Gene Is It Anyway? The Effect of Preparation Purity on Neutrophil Transcriptome Studies. PMID:26401909
Modulation of MicroRNA Cluster miR-183-96-182 Expression by Epstein-Barr Virus Latent Membrane Protein 1. PMID:26401047
ATM deficiency promotes development of murine B-cell lymphomas that resemble diffuse large B-cell lymphoma in humans. PMID:26400962
Translational compensation of genomic instability in neuroblastoma. PMID:26399178
Enhanced virome sequencing using targeted sequence capture. PMID:26395152
Autism-like syndrome is induced by pharmacological suppression of BET proteins in young mice. PMID:26392221
Merkel cell polyomavirus T antigens promote cell proliferation and inflammatory cytokine gene expression. PMID:26385761
Extracting tumor tissue immune status from expression profiles: correlating renal cancer prognosis with tumor-associated immunome. PMID:26384298
1918 pandemic influenza virus and Streptococcus pneumoniae co-infection results in activation of coagulation and widespread pulmonary thrombosis in mice and humans. PMID:26383585
MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies. PMID:26380270
DNA Damage Response Checkpoint Activation Drives KP1019 Dependent Pre-Anaphase Cell Cycle Delay in S. cerevisiae. PMID:26375390
Cross-Talk in the Female Rat Mammary Gland: Influence of Aryl Hydrocarbon Receptor on Estrogen Receptor Signaling. PMID:26372666
Identification of transcripts regulated by CUG-BP, Elav-like family member 1 (CELF1) in primary embryonic cardiomyocytes by RNA-seq. PMID:26366374
Epigenetic synergy between decitabine and platinum derivatives. PMID:26366234
Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases. PMID:26362267
High-fructose diet during periadolescent development increases depressive-like behavior and remodels the hypothalamic transcriptome in male rats. PMID:26356038
WDR5 Expression Is Prognostic of Breast Cancer Outcome. PMID:26355959
Cross Platform Standardisation of an Experimental Pipeline for Use in the Identification of Dysregulated Human Circulating MiRNAs. PMID:26355751
DKK1 is a potential novel mediator of cisplatin-refractoriness in non-small cell lung cancer cell lines. PMID:26353782
Biochemical isolation of Argonaute protein complexes by Ago-APP. PMID:26351695
Growth-Phase-Specific Modulation of Cell Morphology and Gene Expression by an Archaeal Histone Protein. PMID:26350964
New Technologies for Studying Biofilms. PMID:26350329
Turning publicly available gene expression data into discoveries using gene set context analysis. PMID:26350211
RNA sequencing provides exquisite insight into the manipulation of the alveolar macrophage by tubercle bacilli. PMID:26346536
Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease. PMID:26342919
A distinct gene expression signature characterizes human neuroblastoma cancer stem cells. PMID:26342562
ABO blood type correlates with survival on prostate cancer vaccine therapy. PMID:26338967
Seq-ing improved gene expression estimates from microarrays using machine learning. PMID:26338512
Global analysis of asymmetric RNA enrichment in oocytes reveals low conservation between closely related Xenopus species. PMID:26337391
Na+/K+-ATPase α1 subunit, a novel therapeutic target for hepatocellular carcinoma. PMID:26334094
Comparative Analysis of Label-Free and 8-Plex iTRAQ Approach for Quantitative Tissue Proteomic Analysis. PMID:26331617
Deciphering Cis-Regulatory Element Mediated Combinatorial Regulation in Rice under Blast Infected Condition. PMID:26327607
Microarray Analysis of Copy Number Variants on the Human Y Chromosome Reveals Novel and Frequent Duplications Overrepresented in Specific Haplogroups. PMID:26322892
Lhx5 controls mamillary differentiation in the developing hypothalamus of the mouse. PMID:26321924
The histone variant H2A.Z is an important regulator of enhancer activity. PMID:26319018
Citing a Data Repository: A Case Study of the Protein Data Bank. PMID:26317409
Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways. PMID:26313928
The RNA-binding protein Sam68 regulates expression and transcription function of the androgen receptor splice variant AR-V7. PMID:26310125
Mitochondrial uncoupling links lipid catabolism to Akt inhibition and resistance to tumorigenesis. PMID:26310111
Immune cell subsets and their gene expression profiles from human PBMC isolated by Vacutainer Cell Preparation Tube (CPT™) and standard density gradient. PMID:26307036
Integrating Gene Regulatory Networks to identify cancer-specific genes. PMID:26306224
The Pacific Northwest National Laboratory library of bacterial and archaeal proteomic biodiversity. PMID:26306205
Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa. PMID:26305928
Cis-acting signals modulate the efficiency of programmed DNA elimination in Paramecium tetraurelia. PMID:26304543
Perivascular Mesenchymal Stem Cells From the Adult Human Brain Harbor No Instrinsic Neuroectodermal but High Mesodermal Differentiation Potential. PMID:26304036
Finding mouse models of human lymphomas and leukemia's using the Jackson laboratory mouse tumor biology database. PMID:26302176
Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica. PMID:26296338
DIS3 shapes the RNA polymerase II transcriptome in humans by degrading a variety of unwanted transcripts. PMID:26294688
Evaluation of Left Ventricle Function by Regional Fractional Area Change (RFAC) in a Mouse Model of Myocardial Infarction Secondary to Valsartan Treatment. PMID:26291973
Dipeptide species regulate p38MAPK-Smad3 signalling to maintain chronic myelogenous leukaemia stem cells. PMID:26289811
Macrophage cell death and transcriptional response are actively triggered by the fungal virulence factor Cbp1 during H. capsulatum infection. PMID:26288377
Exercise-mimetic AICAR transiently benefits brain function. PMID:26286955
Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case. PMID:26286638
Uterine overdistention induces preterm labor mediated by inflammation: observations in pregnant women and nonhuman primates. PMID:26284599
aRrayLasso: a network-based approach to microarray interconversion. PMID:26283699
EphA2 Expression Is a Key Driver of Migration and Invasion and a Poor Prognostic Marker in Colorectal Cancer. PMID:26283684
Simultaneous Host-Pathogen Transcriptome Analysis during Granulibacter bethesdensis Infection of Neutrophils from Healthy Subjects and Patients with Chronic Granulomatous Disease. PMID:26283340
Functional Analysis and Characterization of Differential Coexpression Networks. PMID:26282208
Analysis of Polygenic Mutants Suggests a Role for Mediator in Regulating Transcriptional Activation Distance in Saccharomyces cerevisiae. PMID:26281848
ApiAP2 Factors as Candidate Regulators of Stochastic Commitment to Merozoite Production in Theileria annulata. PMID:26273826
Gene Coexpression and Evolutionary Conservation Analysis of the Human Preimplantation Embryos. PMID:26273607
Derivation of a fifteen gene prognostic panel for six cancers. PMID:26272668
Next Generation Sequencing Analysis Reveals Segmental Patterns of microRNA Expression in Mouse Epididymal Epithelial Cells. PMID:26270822
Modulator of apoptosis 1 (MOAP-1) is a tumor suppressor protein linked to the RASSF1A protein. PMID:26269600
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
Transcription Factor Repertoire of Homeostatic Eosinophilopoiesis. PMID:26268651
Systems biology approach to studying proliferation-dependent prognostic subnetworks in breast cancer. PMID:26257336
Proton irradiation impacts age-driven modulations of cancer progression influenced by immune system transcriptome modifications from splenic tissue. PMID:26253138
Potential roles of microRNA-29a in the molecular pathophysiology of T-cell acute lymphoblastic leukemia. PMID:26251039
Gene Expression Profile in the Liver of BALB/c Mice Infected with Fasciola hepatica. PMID:26247779
Self-renewing diploid Axin2(+) cells fuel homeostatic renewal of the liver. PMID:26245375
Prenatal Exposure to DEHP Affects Spermatogenesis and Sperm DNA Methylation in a Strain-Dependent Manner. PMID:26244509
Understanding the aristolochic acid toxicities in rat kidneys with regulatory networks. PMID:26243830
A transcriptomal analysis of bovine oviductal epithelial cells collected during the follicular phase versus the luteal phase of the estrous cycle. PMID:26242217
Tissue Remodelling following Resection of Porcine Liver. PMID:26240819
Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages. PMID:26239120
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
mRIN for direct assessment of genome-wide and gene-specific mRNA integrity from large-scale RNA-sequencing data. PMID:26234653
Identification of Oxygen-Responsive Transcripts in the Silage Inoculant Lactobacillus buchneri CD034 by RNA Sequencing. PMID:26230316
Differential miRNA expression in inherently high- and low-active inbred mice. PMID:26229004
Integrated genomic analyses identify KDM1A's role in cell proliferation via modulating E2F signaling activity and associate with poor clinical outcome in oral cancer. PMID:26225839
Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing. PMID:26225632
Differential gene methylation in paired glioblastomas suggests a role of immune response pathways in tumor progression. PMID:26224161
Small molecule and RNAi induced phenotype transition of expanded and primary colonic epithelial cells. PMID:26223582
Biological processes and pathway changes in isoflurane-induced anesthesia revealed by bioinformatics analysis of gene expression profiles. PMID:26223573
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
Integrated systems approach identifies risk regulatory pathways and key regulators in coronary artery disease. PMID:26208504
Gene Expression in Experimental Aortic Coarctation and Repair: Candidate Genes for Therapeutic Intervention? PMID:26207811
Copy-number variations in hepatoblastoma associate with unique clinical features. PMID:26201635
Empirical comparison of structure-based pathway methods. PMID:26197809
MDA-MB-231 breast cancer cells overexpressing single VEGF isoforms display distinct colonisation characteristics. PMID:26196186
A tuberculosis ontology for host systems biology. PMID:26190839
Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown. PMID:26186542
Pharyngeal Satellite Cells Undergo Myogenesis Under Basal Conditions and Are Required for Pharyngeal Muscle Maintenance. PMID:26178867
Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PMID:26177267
Systemic and Ocular Long Pentraxin 3 in Patients with Age-Related Macular Degeneration. PMID:26176960
Identification of reproducible drug-resistance-related dysregulated genes in small-scale cancer cell line experiments. PMID:26173481
LXRs link metabolism to inflammation through Abca1-dependent regulation of membrane composition and TLR signaling. PMID:26173179
Characteristic expression of MSX1, MSX2, TBX2 and ENTPD1 in dental pulp cells. PMID:26171167
Methylating micronutrient supplementation during pregnancy influences foetal hepatic gene expression and IGF signalling and increases foetal weight. PMID:26169873
Transcriptional fingerprinting of "browning" white fat identifies NRG4 as a novel adipokine. PMID:26167402
Olfactomedin 4 Serves as a Marker for Disease Severity in Pediatric Respiratory Syncytial Virus (RSV) Infection. PMID:26162090
Simulated Microgravity Exerts an Age-Dependent Effect on the Differentiation of Cardiovascular Progenitors Isolated from the Human Heart. PMID:26161778
Using gene expression signatures to identify novel treatment strategies in gulf war illness. PMID:26156520
Survival Rate and Transcriptional Response upon Infection with the Generalist Parasite Beauveria bassiana in a World-Wide Sample of Drosophila melanogaster. PMID:26154519
NKX2-5 mutations causative for congenital heart disease retain functionality and are directed to hundreds of targets. PMID:26146939
Immunobiotic Lactobacillus administered post-exposure averts the lethal sequelae of respiratory virus infection. PMID:26145728
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
An Integrated Prognostic Classifier for Stage I Lung Adenocarcinoma Based on mRNA, microRNA, and DNA Methylation Biomarkers. PMID:26134223
Genetic Analysis of T Cell Lymphomas in Carbon Ion-Irradiated Mice Reveals Frequent Interstitial Chromosome Deletions: Implications for Second Cancer Induction in Normal Tissues during Carbon Ion Radiotherapy. PMID:26125582
A second trigeminal CGRP receptor: function and expression of the AMY1 receptor. PMID:26125036
MicroRNA-132 enhances transition from inflammation to proliferation during wound healing. PMID:26121747
Identification of Cyclobutane Pyrimidine Dimer-Responsive Genes Using UVB-Irradiated Human Keratinocytes Transfected with In Vitro-Synthesized Photolyase mRNA. PMID:26121660
Kidney Regeneration: Lessons from Development. PMID:26120499
IL-10 Production in Macrophages Is Regulated by a TLR-Driven CREB-Mediated Mechanism That Is Linked to Genes Involved in Cell Metabolism. PMID:26116503
Expression quantitative trait locus analysis for translational medicine. PMID:26110023
In Pursuit of New Imprinting Syndromes by Epimutation Screening in Idiopathic Neurodevelopmental Disorder Patients. PMID:26106604
Synaptic microRNAs Coordinately Regulate Synaptic mRNAs: Perturbation by Chronic Alcohol Consumption. PMID:26105134
A salt-regulated peptide derived from the CAP superfamily protein negatively regulates salt-stress tolerance in Arabidopsis. PMID:26093145
A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. PMID:26089837
Extensive rewiring of epithelial-stromal co-expression networks in breast cancer. PMID:26087699
Evidence for Immune Response, Axonal Dysfunction and Reduced Endocytosis in the Substantia Nigra in Early Stage Parkinson's Disease. PMID:26087293
Selection for Improved Energy Use Efficiency and Drought Tolerance in Canola Results in Distinct Transcriptome and Epigenome Changes. PMID:26082400
Targeting PBK/TOPK decreases growth and survival of glioma initiating cells in vitro and attenuates tumor growth in vivo. PMID:26081429
Autoantigen microarrays reveal autoantibodies associated with proliferative nephritis and active disease in pediatric systemic lupus erythematosus. PMID:26081107
Genome-wide transcriptomic analysis of a superior biomass-degrading strain of A. fumigatus revealed active lignocellulose-degrading genes. PMID:26076650
Silencing of Essential Genes within a Highly Coordinated Operon in Escherichia coli. PMID:26070674
Strand-specific RNA sequencing in Plasmodium falciparum malaria identifies developmentally regulated long non-coding RNA and circular RNA. PMID:26070627
Identification of Gene and MicroRNA Signatures for Oral Cancer Developed from Oral Leukoplakia. PMID:26064958
The TF-miRNA Coregulation Network in Oral Lichen Planus. PMID:26064947
Lysosome and Cytoskeleton Pathways Are Robustly Enriched in the Blood of Septic Patients: A Meta-Analysis of Transcriptomic Data. PMID:26063982
A Pitx2-MicroRNA Pathway Modulates Cell Proliferation in Myoblasts and Skeletal-Muscle Satellite Cells and Promotes Their Commitment to a Myogenic Cell Fate. PMID:26055324
Differential MicroRNA Expression in Human Macrophages with Mycobacterium tuberculosis Infection of Beijing/W and Non-Beijing/W Strain Types. PMID:26053546
E2F8 promotes hepatic steatosis through FABP3 expression in diet-induced obesity in zebrafish. PMID:26052340
An integrated genomic analysis of papillary renal cell carcinoma type 1 uncovers the role of focal adhesion and extracellular matrix pathways. PMID:26051997
The pervasiveness and plasticity of circadian oscillations: the coupled circadian-oscillators framework. PMID:26049162
Impact of microfluidic processing on bacterial ribonucleic acid expression. PMID:26045727
High mobility group protein-mediated transcription requires DNA damage marker γ-H2AX. PMID:26045162
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
Integrative analyses of cancer data: a review from a statistical perspective. PMID:26041968
quantro: a data-driven approach to guide the choice of an appropriate normalization method. PMID:26040460
Identification of novel gene targets and putative regulators of arsenic-associated DNA methylation in human urothelial cells and bladder cancer. PMID:26039340
FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro. PMID:26036639
Deletion of the App-Runx1 region in mice models human partial monosomy 21. PMID:26035870
Transcription factor p63 bookmarks and regulates dynamic enhancers during epidermal differentiation. PMID:26034101
Dietary MicroRNA Database (DMD): An Archive Database and Analytic Tool for Food-Borne microRNAs. PMID:26030752
Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. PMID:26023099
Whole Genome Sequence of Multiple Myeloma-Prone C57BL/KaLwRij Mouse Strain Suggests the Origin of Disease Involves Multiple Cell Types. PMID:26020268
GECluster: a novel protein complex prediction method. PMID:26019559
The combination of HDAC and aminopeptidase inhibitors is highly synergistic in myeloma and leads to disruption of the NFκB signalling pathway. PMID:26015393
Low folate and selenium in the mouse maternal diet alters liver gene expression patterns in the offspring after weaning. PMID:26007332
RasGRP1 opposes proliferative EGFR-SOS1-Ras signals and restricts intestinal epithelial cell growth. PMID:26005835
In Vivo imaging reveals extracellular vesicle-mediated phenocopying of metastatic behavior. PMID:26000481
The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells. PMID:25998054
Gene set enrichment analysis of pathways and transcription factors associated with diabetic retinopathy using a microarray dataset. PMID:25997411
A Combined Omics Approach to Generate the Surface Atlas of Human Naive CD4+ T Cells during Early T-Cell Receptor Activation. PMID:25991687
Significant expansion of the REST/NRSF cistrome in human versus mouse embryonic stem cells: potential implications for neural development. PMID:25990720
Identification of targets for rational pharmacological therapy in childhood craniopharyngioma. PMID:25990246
The fission yeast MTREC complex targets CUTs and unspliced pre-mRNAs to the nuclear exosome. PMID:25989903
Reverse enGENEering of Regulatory Networks from Big Data: A Roadmap for Biologists. PMID:25983554
Repression by H-NS of genes required for the biosynthesis of the Vibrio cholerae biofilm matrix is modulated by the second messenger cyclic diguanylic acid. PMID:25982817
Latent Pathways Identification by Microarray Expression Profiles in Thyroid-Associated Ophthalmopathy Patients. PMID:25982257
A ranking-based meta-analysis reveals let-7 family as a meta-signature for grade classification in breast cancer. PMID:25978727
Cell Cycle Control by the Master Regulator CtrA in Sinorhizobium meliloti. PMID:25978424
GEO2Enrichr: browser extension and server app to extract gene sets from GEO and analyze them for biological functions. PMID:25971742
Genome-wide gene expression analysis for target genes to differentiate patients with intestinal tuberculosis and Crohn's disease and discriminative value of FOXP3 mRNA expression. PMID:25969456
Interleukin-6/STAT3 Pathway Signaling Drives an Inflammatory Phenotype in Group A Ependymoma. PMID:25968456
Probe Region Expression Estimation for RNA-Seq Data for Improved Microarray Comparability. PMID:25966034
Mutant U2AF1 Expression Alters Hematopoiesis and Pre-mRNA Splicing In Vivo. PMID:25965570
Revisiting the transcriptional analysis of primary tumours and associated nodal metastases with enhanced biological and statistical controls: application to thyroid cancer. PMID:25965298
Revealing the Molecular Portrait of Triple Negative Breast Tumors in an Understudied Population through Omics Analysis of Formalin-Fixed and Paraffin-Embedded Tissues. PMID:25961742
Investigation into the annotation of protocol sequencing steps in the sequence read archive. PMID:25960871
Genome-wide mapping of histone H3 lysine 4 trimethylation in Eucalyptus grandis developing xylem. PMID:25957781
Gene expression profiling of porcine mammary epithelial cells after challenge with Escherichia coli and Staphylococcus aureus in vitro. PMID:25948480
Activation of defence pathways in Scots pine bark after feeding by pine weevil (Hylobius abietis). PMID:25943104
Bias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure. PMID:25942392
Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells. PMID:25928846
Identification of sample-specific regulations using integrative network level analysis. PMID:25928379
New Noncoding Lytic Transcripts Derived from the Epstein-Barr Virus Latency Origin of Replication, oriP, Are Hyperedited, Bind the Paraspeckle Protein, NONO/p54nrb, and Support Viral Lytic Transcription. PMID:25926645
Argonaute 2 Binds Directly to tRNA Genes and Promotes Gene Repression in cis. PMID:25918241
Tracking the Elusive Function of Bacillus subtilis Hfq. PMID:25915524
Protein microarrays: a new tool for the study of autoantibodies in immunodeficiency. PMID:25904912
A technology platform to assess multiple cancer agents simultaneously within a patient's tumor. PMID:25904742
Re-replication of a centromere induces chromosomal instability and aneuploidy. PMID:25901968
Functional and mechanistic studies of XPC DNA-repair complex as transcriptional coactivator in embryonic stem cells. PMID:25901318
Modulation of dendritic cell alternative activation and function by the vitamin A metabolite retinoic acid. PMID:25899567
ChiNet uncovers rewired transcription subnetworks in tolerant yeast for advanced biofuels conversion. PMID:25897127
Histone modifications induced by MDV infection at early cytolytic and latency phases. PMID:25896894
Anti-repulsive Guidance Molecule C (RGMc) Antibodies Increases Serum Iron in Rats and Cynomolgus Monkeys by Hepcidin Downregulation. PMID:25896304
Gene Expression Analyses during Spontaneous Reversal of Cardiomyopathy in Mice with Repressed Nuclear CUG-BP, Elav-Like Family (CELF) Activity in Heart Muscle. PMID:25894229
Integrated compensatory network is activated in the absence of NCC phosphorylation. PMID:25893600
Systems medicine: evolution of systems biology from bench to bedside. PMID:25891169
Kinetics of gene expression and bone remodelling in the clinical phase of collagen-induced arthritis. PMID:25889670
miR-10b-5p expression in Huntington's disease brain relates to age of onset and the extent of striatal involvement. PMID:25889241
Combinatorial Conflicting Homozygosity (CCH) analysis enables the rapid identification of shared genomic regions in the presence of multiple phenocopies. PMID:25888400
A mRNA landscape of bovine embryos after standard and MAPK-inhibited culture conditions: a comparative analysis. PMID:25888366
Identifying module biomarker in type 2 diabetes mellitus by discriminative area of functional activity. PMID:25888350
Copy number variations in high and low fertility breeding boars. PMID:25888238
Identification of active miRNA and transcription factor regulatory pathways in human obesity-related inflammation. PMID:25887648
Common binding by redundant group B Sox proteins is evolutionarily conserved in Drosophila. PMID:25887553
Copy number variation in Y chromosome multicopy genes is linked to a paternal parent-of-origin effect on CNS autoimmune disease in female offspring. PMID:25886764
Denoising perturbation signatures reveal an actionable AKT-signaling gene module underlying a poor clinical outcome in endocrine-treated ER+ breast cancer. PMID:25886003
The role of HGF/MET and FGF/FGFR in fibroblast-derived growth stimulation and lapatinib-resistance of esophageal squamous cell carcinoma. PMID:25884729
The ependymal region of the adult human spinal cord differs from other species and shows ependymoma-like features. PMID:25882650
Bicluster Sampled Coherence Metric (BSCM) provides an accurate environmental context for phenotype predictions. PMID:25881257
Nourishment level affects caste-related gene expression in Polistes wasps. PMID:25880983
Advanced age is associated with worsened outcomes and a unique genomic response in severely injured patients with hemorrhagic shock. PMID:25880307
Global gene expression in granulosa cells of growing, plateau and atretic dominant follicles in cattle. PMID:25879740
Transcriptional programming of human macrophages: on the way to systems immunology. PMID:25877862
Understanding developmental and adaptive cues in pine through metabolite profiling and co-expression network analysis. PMID:25873654
Molecular mechanism of flocculation self-recognition in yeast and its role in mating and survival. PMID:25873380
Metabolic reprogramming in triple-negative breast cancer through Myc suppression of TXNIP. PMID:25870263
GWAS for executive function and processing speed suggests involvement of the CADM2 gene. PMID:25869804
Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state. PMID:25865119
Retinoic acid-independent expression of Meis2 during autopod patterning in the developing bat and mouse limb. PMID:25861444
Modeling discrete survival time using genomic feature data. PMID:25861216
MYB controls erythroid versus megakaryocyte lineage fate decision through the miR-486-3p-mediated downregulation of MAF. PMID:25857263
Histone methyltransferase Setd8 represses Gata2 expression and regulates erythroid maturation. PMID:25848090
Regulatory network inferred using expression data of small sample size: application and validation in erythroid system. PMID:25840044
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine. PMID:25834725
Disease-Associated Single-Nucleotide Polymorphisms From Noncoding Regions in Juvenile Idiopathic Arthritis Are Located Within or Adjacent to Functional Genomic Elements of Human Neutrophils and CD4+ T Cells. PMID:25833190
A comparative study of improvements Pre-filter methods bring on feature selection using microarray data. PMID:25825671
Expression profiles of 151 pediatric low-grade gliomas reveal molecular differences associated with location and histological subtype. PMID:25825052
Conditioned medium from human amniotic mesenchymal stromal cells limits infarct size and enhances angiogenesis. PMID:25824141
Transcriptomics of maternal and fetal membranes can discriminate between gestational-age matched preterm neonates with and without cognitive impairment diagnosed at 18-24 months. PMID:25822971
Transcriptome analysis of post-hatch breast muscle in legacy and modern broiler chickens reveals enrichment of several regulators of myogenic growth. PMID:25821972
RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition. PMID:25820424
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
Biomarker-based classification of bacterial and fungal whole-blood infections in a genome-wide expression study. PMID:25814982
Parallel epigenomic and transcriptomic responses to viral infection in honey bees (Apis mellifera). PMID:25811620
Dual RNA sequencing reveals the expression of unique transcriptomic signatures in lipopolysaccharide-induced BV-2 microglial cells. PMID:25811458
Herb-Partitioned Moxibustion and the miRNAs Related to Crohn's Disease: A Study Based on Rat Models. PMID:25810742
A gene co-expression network predicts functional genes controlling the re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds. PMID:25809152
Discovery of molecular markers to discriminate corneal endothelial cells in the human body. PMID:25807145
SRD: a Staphylococcus regulatory RNA database. PMID:25805861
Gene expression profiling to investigate tyrosol-induced lifespan extension in Caenorhabditis elegans. PMID:25804201
Identification of a microRNA signature for the diagnosis of fibromyalgia. PMID:25803872
T-cell activation and early gene response in dogs. PMID:25803042
Loss of Lrig1 leads to expansion of Brunner glands followed by duodenal adenomas with gastric metaplasia. PMID:25794708
IP3 3-kinase B controls hematopoietic stem cell homeostasis and prevents lethal hematopoietic failure in mice. PMID:25788703
HSET overexpression fuels tumor progression via centrosome clustering-independent mechanisms in breast cancer patients. PMID:25788277
Optimal drug prediction from personal genomics profiles. PMID:25781964
Functional analysis of sirtuin genes in multiple Plasmodium falciparum strains. PMID:25780929
The carbon starvation response of the ectomycorrhizal fungus Paxillus involutus. PMID:25778509
A cluster of four homologous small RNAs modulates C1 metabolism and the pyruvate dehydrogenase complex in Rhodobacter sphaeroides under various stress conditions. PMID:25777678
The Sinorhizobium meliloti SyrM regulon: effects on global gene expression are mediated by syrA and nodD3. PMID:25777671
Microbial forensics: predicting phenotypic characteristics and environmental conditions from large-scale gene expression profiles. PMID:25774498
A New Augmentation Based Algorithm for Extracting Maximal Chordal Subgraphs. PMID:25767331
Haploinsufficiency of Hedgehog interacting protein causes increased emphysema induced by cigarette smoke through network rewiring. PMID:25763110
A novel miRNA-based predictive model for biochemical failure following post-prostatectomy salvage radiation therapy. PMID:25760964
Expression of three topologically distinct membrane proteins elicits unique stress response pathways in the yeast Saccharomyces cerevisiae. PMID:25759377
Next generation sequencing analysis reveals that the ribonucleases RNase II, RNase R and PNPase affect bacterial motility and biofilm formation in E. coli. PMID:25757888
Tracking the best reference genes for RT-qPCR data normalization in filamentous fungi. PMID:25757610
Language workbench user interfaces for data analysis. PMID:25755929
Histone Deacetylase Inhibitors (HDACi) Cause the Selective Depletion of Bromodomain Containing Proteins (BCPs). PMID:25755299
Arabidopsis flower specific defense gene expression patterns affect resistance to pathogens. PMID:25750645
A continuous molecular roadmap to iPSC reprogramming through progression analysis of single-cell mass cytometry. PMID:25748935
A melanoma subtype with intrinsic resistance to BRAF inhibition identified by receptor tyrosine kinases gene-driven classification. PMID:25742786
Systems biology approaches for advancing the discovery of effective drug combinations. PMID:25741385
Toxicogenomics profiling of bone marrow from rats treated with topotecan in combination with oxaliplatin: a mechanistic strategy to inform combination toxicity. PMID:25729387
Potent degradation of neuronal miRNAs induced by highly complementary targets. PMID:25724380
Early telomerase inactivation accelerates aging independently of telomere length. PMID:25723167
Gateways to the FANTOM5 promoter level mammalian expression atlas. PMID:25723102
Lysosomal calcium signalling regulates autophagy through calcineurin and TFEB. PMID:25720963
A MEIG1/PACRG complex in the manchette is essential for building the sperm flagella. PMID:25715396
Synergistic and antagonistic interplay between myostatin gene expression and physical activity levels on gene expression patterns in triceps Brachii muscles of C57/BL6 mice. PMID:25710176
Gene expression in obliterative bronchiolitis-like lesions in 2,3-pentanedione-exposed rats. PMID:25710175
CD14 and complement crosstalk and largely mediate the transcriptional response to Escherichia coli in human whole blood as revealed by DNA microarray. PMID:25706641
Oncogenic properties of apoptotic tumor cells in aggressive B cell lymphoma. PMID:25702581
The PDZ-domain protein Whirlin facilitates mechanosensory signaling in mammalian proprioceptors. PMID:25698744
Functions of BET proteins in erythroid gene expression. PMID:25696920
Transcriptional attenuation controls macrolide inducible efflux and resistance in Streptococcus pneumoniae and in other Gram-positive bacteria containing mef/mel(msr(D)) elements. PMID:25695510
The arabidopsis DNA polymerase δ has a role in the deposition of transcriptionally active epigenetic marks, development and flowering. PMID:25693187
Comparison of drought stress response and gene expression between a GM maize variety and a near-isogenic non-GM variety. PMID:25692547
Evidence-based translation for the genomic responses of murine models for the study of human immunity. PMID:25680113
Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PMID:25679813
Transcriptome and metabolome analysis of plant sulfate starvation and resupply provides novel information on transcriptional regulation of metabolism associated with sulfur, nitrogen and phosphorus nutritional responses in Arabidopsis. PMID:25674096
A statistically inferred microRNA network identifies breast cancer target miR-940 as an actin cytoskeleton regulator. PMID:25673565
Ribosomal and immune transcripts associate with relapse in acquired ADAMTS13-deficient thrombotic thrombocytopenic purpura. PMID:25671313
FlowerNet: a gene expression correlation network for anther and pollen development. PMID:25667314
Identification and validation of the methylation biomarkers of non-small cell lung cancer (NSCLC). PMID:25657825
microRNA profiling in the zoonotic parasite Echinococcus canadensis using a high-throughput approach. PMID:25656283
A whole-genome microarray study of Arabidopsis thaliana semisolid callus cultures exposed to microgravity and nonmicrogravity related spaceflight conditions for 5 days on board of Shenzhou 8. PMID:25654111
Antigen expression determines adenoviral vaccine potency independent of IFN and STING signaling. PMID:25642773
Human promoters are intrinsically directional. PMID:25639469
Messenger RNA processing is altered in autosomal dominant leukodystrophy. PMID:25637521
Prioritizing causal disease genes using unbiased genomic features. PMID:25633252
Using the canary genome to decipher the evolution of hormone-sensitive gene regulation in seasonal singing birds. PMID:25631560
PhenomeExpress: a refined network analysis of expression datasets by inclusion of known disease phenotypes. PMID:25631385
Evolutionary adaptation of an AraC-like regulatory protein in Citrobacter rodentium and Escherichia species. PMID:25624355
A systems-level approach to parental genomic imprinting: the imprinted gene network includes extracellular matrix genes and regulates cell cycle exit and differentiation. PMID:25614607
Memory T cells specific for murine cytomegalovirus re-emerge after multiple challenges and recapitulate immunity in various adoptive transfer scenarios. PMID:25595792
Peax: interactive visual analysis and exploration of complex clinical phenotype and gene expression association. PMID:25592601
Contribution of non-reference alleles in mtDNA of Alzheimer's disease patients. PMID:25590040
Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. PMID:25586221
Sublethal concentrations of carbapenems alter cell morphology and genomic expression of Klebsiella pneumoniae biofilms. PMID:25583711
Targeted exploration and analysis of large cross-platform human transcriptomic compendia. PMID:25581801
A subcutaneous adipose tissue-liver signalling axis controls hepatic gluconeogenesis. PMID:25581158
A survey of computational intelligence techniques in protein function prediction. PMID:25574395
The dam replacing gene product enhances Neisseria gonorrhoeae FA1090 viability and biofilm formation. PMID:25566225
Gene regulatory network analysis reveals differences in site-specific cell fate determination in mammalian brain. PMID:25565969
The naked endosperm genes encode duplicate INDETERMINATE domain transcription factors required for maize endosperm cell patterning and differentiation. PMID:25552497
SUMO ligase PIAS1 functions as a target gene selective androgen receptor coregulator on prostate cancer cell chromatin. PMID:25552417
Expression of tumor necrosis factor-alpha-mediated genes predicts recurrence-free survival in lung cancer. PMID:25548907
Transcriptional analysis of micro-dissected articular cartilage in post-traumatic murine osteoarthritis. PMID:25545425
Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state. PMID:25545155
Analysis of the basal chordate Botryllus schlosseri reveals a set of genes associated with fertility. PMID:25542255
Bioinformatic identification of connective tissue growth factor as an osteogenic protein within skeletal muscle. PMID:25539834
Reproducibility enhancement and differential expression of non predefined functional gene sets in human genome. PMID:25539829
TSLP expression: analysis with a ZsGreen TSLP reporter mouse. PMID:25539812
Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor. PMID:25539760
The relative importance of DNA methylation and Dnmt2-mediated epigenetic regulation on Wolbachia densities and cytoplasmic incompatibility. PMID:25538866
Global analysis of methylation profiles from high resolution CpG data. PMID:25537884
MicroRNA-7 inhibits multiple oncogenic pathways to suppress HER2Δ16 mediated breast tumorigenesis and reverse trastuzumab resistance. PMID:25532106
RNA-seq analysis reveals significant transcriptome changes in turbot (Scophthalmus maximus) suffering severe enteromyxosis. PMID:25526753
Assessment of cancer cell line representativeness using microarrays for Merkel cell carcinoma. PMID:25521454
Protein acetylation affects acetate metabolism, motility and acid stress response in Escherichia coli. PMID:25518064
Genes associated with thermosensitive genic male sterility in rice identified by comparative expression profiling. PMID:25512054
MicroRNA Profiling of Laser-Microdissected Hepatocellular Carcinoma Reveals an Oncogenic Phenotype of the Tumor Capsule. PMID:25500075
MiR-score: a novel 6-microRNA signature that predicts survival outcomes in patients with malignant pleural mesothelioma. PMID:25497279
RNA-seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature. PMID:25494716
Natural Variation in Fish Transcriptomes: Comparative Analysis of the Fathead Minnow (Pimephales promelas) and Zebrafish (Danio rerio). PMID:25493933
Meta-analysis of human methylomes reveals stably methylated sequences surrounding CpG islands associated with high gene expression. PMID:25493099
Pathomx: an interactive workflow-based tool for the analysis of metabolomic data. PMID:25490956
Establishment of the neurogenic boundary of the mouse retina requires cooperation of SOX2 and WNT signaling. PMID:25488119
Gene Expression Characterization of HPV Positive Head and Neck Cancer to Predict Response to Chemoradiation. PMID:25481760
Human Hematopoietic Signal peptide-containing Secreted 1 (hHSS1) modulates genes and pathways in glioma: implications for the regulation of tumorigenicity and angiogenesis. PMID:25481245
Genetic variants modify the effect of age on APOE methylation in the Genetics of Lipid Lowering Drugs and Diet Network study. PMID:25476875
The COPD Knowledge Base: enabling data analysis and computational simulation in translational COPD research. PMID:25471253
TRIM37 is a new histone H2A ubiquitin ligase and breast cancer oncoprotein. PMID:25470042
Comparative gene expression of Wigglesworthia inhabiting non-infected and Trypanosoma brucei gambiense-infected Glossina palpalis gambiensis flies. PMID:25452752
The novel small leucine-rich protein chondroadherin-like (CHADL) is expressed in cartilage and modulates chondrocyte differentiation. PMID:25451920
Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants. PMID:25443390
Functional characterization of a Nudix hydrolase AtNUDX8 upon pathogen attack indicates a positive role in plant immune responses. PMID:25436909
Impact of analytic provenance in genome analysis. PMID:25435180
Gene expression microarray analysis of the sciatic nerve of mice with diabetic neuropathy. PMID:25435094
Tissue-aware data integration approach for the inference of pathway interactions in metazoan organisms. PMID:25431329
Transcriptional evidence for the role of chronic venlafaxine treatment in neurotrophic signaling and neuroplasticity including also Glutamatergic [corrected] - and insulin-mediated neuronal processes. PMID:25423262
The phenotypic manifestations of rare genic CNVs in autism spectrum disorder. PMID:25421404
SHMT1 knockdown induces apoptosis in lung cancer cells by causing uracil misincorporation. PMID:25412303
Shift in GATA3 functions, and GATA3 mutations, control progression and clinical presentation in breast cancer. PMID:25410484
Uromodulin retention in thick ascending limb of Henle's loop affects SCD1 in neighboring proximal tubule: renal transcriptome studies in mouse models of uromodulin-associated kidney disease. PMID:25409434
Transcriptional profiling of human epithelial cells infected with plasmid-bearing and plasmid-deficient Chlamydia trachomatis. PMID:25404022
Glucose tolerance is associated with differential expression of microRNAs in skeletal muscle: results from studies of twins with and without type 2 diabetes. PMID:25403480
Genomic landscape of metastatic colorectal cancer. PMID:25394515
The Aspergillus nidulans metZ gene encodes a transcription factor involved in regulation of sulfur metabolism in this fungus and other Eurotiales. PMID:25391366
Genomic characterization of variable surface antigens reveals a telomere position effect as a prerequisite for RNA interference-mediated silencing in Paramecium tetraurelia. PMID:25389173
CpG preconditioning regulates miRNA expression that modulates genomic reprogramming associated with neuroprotection against ischemic injury. PMID:25388675
Prolonged growth of a clinical Staphylococcus aureus strain selects for a stable small-colony-variant cell type. PMID:25385795
Sustained β-catenin activity in dermal fibroblasts promotes fibrosis by up-regulating expression of extracellular matrix protein-coding genes. PMID:25385294
Broad integration of expression maps and co-expression networks compassing novel gene functions in the brain. PMID:25382412
Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation. PMID:25381334
Proteomics for systems toxicology. PMID:25379146
Current advances in systems and integrative biology. PMID:25379142
Identification of under-detected periodicity in time-series microarray data by using empirical mode decomposition. PMID:25372711
Exonic variants associated with development of aspirin exacerbated respiratory diseases. PMID:25372592
How difficult is inference of mammalian causal gene regulatory networks? PMID:25369032
Comprehensive characterization and RNA-Seq profiling of the HD-Zip transcription factor family in soybean (Glycine max) during dehydration and salt stress. PMID:25362847
Systems analysis reveals down-regulation of a network of pro-survival miRNAs drives the apoptotic response in dilated cardiomyopathy. PMID:25361207
STAT3 inhibition suppresses proliferation of retinoblastoma through down-regulation of positive feedback loop of STAT3/miR-17-92 clusters. PMID:25359779
Genome-wide distribution of RNA-DNA hybrids identifies RNase H targets in tRNA genes, retrotransposons and mitochondria. PMID:25357144
Argonaute proteins affect siRNA levels and accumulation of a novel extrachromosomal DNA from the Dictyostelium retrotransposon DIRS-1. PMID:25352599
Topic modeling for cluster analysis of large biological and medical datasets. PMID:25350106
A novel peptide interferes with Mycobacterium tuberculosis virulence and survival. PMID:25349777
Transcriptome profiling of developing photoreceptor subtypes reveals candidate genes involved in avian photoreceptor diversification. PMID:25349106
Human placental transcriptome shows sexually dimorphic gene expression and responsiveness to maternal dietary n-3 long-chain polyunsaturated fatty acid intervention during pregnancy. PMID:25348288
Mineralocorticoid effects in the late gestation ovine fetal lung. PMID:25347852
A composite model for subgroup identification and prediction via bicluster analysis. PMID:25347824
MitProNet: A knowledgebase and analysis platform of proteome, interactome and diseases for mammalian mitochondria. PMID:25347823
Expression profile of Caenorhabditis elegans mutant for the Werner syndrome gene ortholog reveals the impact of vitamin C on development to increase life span. PMID:25346348
Transcriptomic profiling facilitates classification of response to influenza challenge. PMID:25345603
The Notch driven long non-coding RNA repertoire in T-cell acute lymphoblastic leukemia. PMID:25344525
Topographical transcriptome mapping of the mouse medial ganglionic eminence by spatially resolved RNA-seq. PMID:25344199
Transcriptomics of desiccation tolerance in the streptophyte green alga Klebsormidium reveal a land plant-like defense reaction. PMID:25340847
The nuclear immune receptor RPS4 is required for RRS1SLH1-dependent constitutive defense activation in Arabidopsis thaliana. PMID:25340333
Integrative investigation on breast cancer in ER, PR and HER2-defined subgroups using mRNA and miRNA expression profiling. PMID:25338681
Analysis of gene expression in induced pluripotent stem cell-derived human neurons exposed to botulinum neurotoxin A subtype 1 and a type A atoxic derivative. PMID:25337697
Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy. PMID:25333715
Identification of antigenic proteins of the nosocomial pathogen Klebsiella pneumoniae. PMID:25333280
Removing batch effects for prediction problems with frozen surrogate variable analysis. PMID:25332844
Profound impact of Hfq on nutrient acquisition, metabolism and motility in the plant pathogen Agrobacterium tumefaciens. PMID:25330313
GroupRank: rank candidate genes in PPI network by differentially expressed gene groups. PMID:25330105
An integrated cell purification and genomics strategy reveals multiple regulators of pancreas development. PMID:25330008
Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana. PMID:25326238
Hidden treasures in "ancient" microarrays: gene-expression portrays biology and potential resistance pathways of major lung cancer subtypes and normal tissue. PMID:25325012
A novel class of somatic small RNAs similar to germ cell pachytene PIWI-interacting small RNAs. PMID:25320077
Inhalation of rod-like carbon nanotubes causes unconventional allergic airway inflammation. PMID:25318534
Increased CYFIP1 dosage alters cellular and dendritic morphology and dysregulates mTOR. PMID:25311365
Generation of mice lacking DUF1220 protein domains: effects on fecundity and hyperactivity. PMID:25308000
Comprehensive characterization of cancer subtype associated long non-coding RNAs and their clinical implications. PMID:25307233
Identification and characterization of Wilt and salt stress-responsive microRNAs in chickpea through high-throughput sequencing. PMID:25295754
Whole-genome expression profile in zebrafish embryos after chronic exposure to morphine: identification of new genes associated with neuronal function and mu opioid receptor expression. PMID:25294025
Development and validation of an Haemophilus influenzae supragenome hybridization (SGH) array for transcriptomic analyses. PMID:25290153
Comparing bacterial community composition of healthy and dark spot-affected Siderastrea siderea in Florida and the Caribbean. PMID:25289937
Comparative study of computational methods for reconstructing genetic networks of cancer-related pathways. PMID:25288880
Comparative network analysis via differential graphlet communities. PMID:25283527
Detecting temporal protein complexes from dynamic protein-protein interaction networks. PMID:25282536
RING finger protein RNF207, a novel regulator of cardiac excitation. PMID:25281747
Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. PMID:25281301
Joint genetic analysis of hippocampal size in mouse and human identifies a novel gene linked to neurodegenerative disease. PMID:25280473
Coronavirus non-structural protein 16: evasion, attenuation, and possible treatments. PMID:25278144
Retrotransposon-based profiling of mammalian epigenomes: DNA methylation of IAP LTRs in embryonic stem, somatic and cancer cells. PMID:25277721
Transcriptome-wide characterization of the eIF4A signature highlights plasticity in translation regulation. PMID:25273840
Treatment of potato tubers with the synthetic cytokinin 1-(α-ethylbenzyl)-3-nitroguanidine results in rapid termination of endodormancy and induction of transcripts associated with cell proliferation and growth. PMID:25270889
Identification of co-expression gene networks, regulatory genes and pathways for obesity based on adipose tissue RNA Sequencing in a porcine model. PMID:25270054
DupChecker: a bioconductor package for checking high-throughput genomic data redundancy in meta-analysis. PMID:25267467
Characterization of p-hydroxycinnamate catabolism in a soil Actinobacterium. PMID:25266382
Hybrid Bayesian-rank integration approach improves the predictive power of genomic dataset aggregation. PMID:25266226
Translational control of the oogenic program by components of OMA ribonucleoprotein particles in Caenorhabditis elegans. PMID:25261697
Subcellular transcriptome alterations in a cell culture model of spinal muscular atrophy point to widespread defects in axonal growth and presynaptic differentiation. PMID:25246652
Population- and sex-biased gene expression in the excretion organs of Drosophila melanogaster. PMID:25246242
G9a/GLP-dependent H3K9me2 patterning alters chromatin structure at CpG islands in hematopoietic progenitors. PMID:25237399
SNP-guided identification of monoallelic DNA-methylation events from enrichment-based sequencing data. PMID:25237057
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. PMID:25236618
IL-5 triggers a cooperative cytokine network that promotes eosinophil precursor maturation. PMID:25230753
Molecular subtyping of serous ovarian tumors reveals multiple connections to intrinsic breast cancer subtypes. PMID:25226589
Growth-promoting and tumourigenic activity of c-Myc is suppressed by Hhex. PMID:25220416
Role of oxygen and the OxyR protein in the response to iron limitation in Rhodobacter sphaeroides. PMID:25220182
Glial enriched gene expression profiling identifies novel factors regulating the proliferation of specific glial subtypes in the Drosophila brain. PMID:25217886
Discovery and validation of new potential biomarkers for early detection of colon cancer. PMID:25215506
Plasmodium falciparum infection induces expression of a mosquito salivary protein (Agaphelin) that targets neutrophil function and inhibits thrombosis without impairing hemostasis. PMID:25211214
Uterine epithelial cell estrogen receptor alpha-dependent and -independent genomic profiles that underlie estrogen responses in mice. PMID:25210133
Cloning and characterization of an apolipoprotein C2 promoter in the mouse central nervous system. PMID:25206486
Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing. PMID:25204630
PDE7B is a novel, prognostically significant mediator of glioblastoma growth whose expression is regulated by endothelial cells. PMID:25203500
Modulation of intestinal microbiota by the probiotic VSL#3 resets brain gene expression and ameliorates the age-related deficit in LTP. PMID:25202975
Performance evaluation of DNA copy number segmentation methods. PMID:25202135
The concentrations of EGFR, LRG1, ITIH4, and F5 in serum correlate with the number of colonic adenomas in ApcPirc/+ rats. PMID:25200834
Biological network exploration with Cytoscape 3. PMID:25199793
Genome-wide binding and transcriptome analysis of human farnesoid X receptor in primary human hepatocytes. PMID:25198545
Blood-gene expression reveals reduced circadian rhythmicity in individuals resistant to sleep deprivation. PMID:25197809
Identification of gene expression biomarkers for predicting radiation exposure. PMID:25189756
Interaction of age and mechanical stability on bone defect healing: an early transcriptional analysis of fracture hematoma in rat. PMID:25187955
KIT is a frequent target for epigenetic silencing in cutaneous melanoma. PMID:25178104
Dietary fatty acids alter left ventricular myocardial gene expression in Wistar rats. PMID:25172377
Mucosal transcriptomics implicates under expression of BRINP3 in the pathogenesis of ulcerative colitis. PMID:25171508
Systems-based analyses of brain regions functionally impacted in Parkinson's disease reveals underlying causal mechanisms. PMID:25170892
Synovial phenotypes in rheumatoid arthritis correlate with response to biologic therapeutics. PMID:25167216
Microarray R-based analysis of complex lysate experiments with MIRACLE. PMID:25161257
Dynamic gene expression patterns in animal models of early and late heart failure reveal biphasic-bidirectional transcriptional activation of signaling pathways. PMID:25159852
HrrF is the Fur-regulated small RNA in nontypeable Haemophilus influenzae. PMID:25157846
A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. PMID:25156699
RNA-sequencing analysis of HepG2 cells treated with atorvastatin. PMID:25153832
IL-17/Th17 pathway is activated in acne lesions. PMID:25153527
Characterization of wastewater treatment plant microbial communities and the effects of carbon sources on diversity in laboratory models. PMID:25148472
Expression of nicotinamide phosphoribosyltransferase-influenced genes predicts recurrence-free survival in lung and breast cancers. PMID:25146220
Effects of GWAS-associated genetic variants on lncRNAs within IBD and T1D candidate loci. PMID:25144376
Germ cell nuclear factor regulates gametogenesis in developing gonads. PMID:25140725
Functional networks of nucleocytoplasmic transport-related genes differentiate ischemic and dilated cardiomyopathies. A new therapeutic opportunity. PMID:25137373
Genetic and pharmacological reactivation of the mammalian inactive X chromosome. PMID:25136103
A Plasmodium falciparum histone deacetylase regulates antigenic variation and gametocyte conversion. PMID:25121747
RNAseq analysis of cassava reveals similar plant responses upon infection with pathogenic and non-pathogenic strains of Xanthomonas axonopodis pv. manihotis. PMID:25120000
Modeling dynamic functional relationship networks and application to ex vivo human erythroid differentiation. PMID:25115705
Tight regulation of ubiquitin-mediated DNA damage response by USP3 preserves the functional integrity of hematopoietic stem cells. PMID:25113974
Characterization of BPSS1521 (bprD), a regulator of Burkholderia pseudomallei virulence gene expression in the mouse model. PMID:25111708
Comparison of molecular signatures from multiple skin diseases identifies mechanisms of immunopathogenesis. PMID:25111617
Stress response of Salmonella enterica serovar typhimurium to acidified nitrite. PMID:25107963
Preliminary characterization of IL32 in basal-like/triple negative compared to other types of breast cell lines and tissues. PMID:25100201
Semantic Web repositories for genomics data using the eXframe platform. PMID:25093072
BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. PMID:25089180
Whole-genome analysis of muscle founder cells implicates the chromatin regulator Sin3A in muscle identity. PMID:25088419
A thyroid hormone challenge in hypothyroid rats identifies T3 regulated genes in the hypothalamus and in models with altered energy balance and glucose homeostasis. PMID:25087834
Gene set enrichment analysis for multiple continuous phenotypes. PMID:25086605
Glucocorticoid receptor binds half sites as a monomer and regulates specific target genes. PMID:25085117
The RNA editing enzyme APOBEC1 induces somatic mutations and a compatible mutational signature is present in esophageal adenocarcinomas. PMID:25085003
DEAD-box helicase DP103 defines metastatic potential of human breast cancers. PMID:25083991
Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. PMID:25082855
Transcriptional correlates of disease outcome in anticoagulant-treated non-human primates infected with ebolavirus. PMID:25079789
Antifungal drug resistance evoked via RNAi-dependent epimutations. PMID:25079329
Functional and genetic analysis of the colon cancer network. PMID:25079297
Profiling dose-dependent activation of p53-mediated signaling pathways by chemicals with distinct mechanisms of DNA damage. PMID:25078064
Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation. PMID:25074712
Inactivation of thyA in Staphylococcus aureus attenuates virulence and has a strong impact on metabolism and virulence gene expression. PMID:25073642
Functionally diverse dendritic mRNAs rapidly associate with ribosomes following a novel experience. PMID:25072471
Toward a systems-level understanding of gene regulatory, protein interaction, and metabolic networks in cyanobacteria. PMID:25071821
CRTC1/MAML2 gain-of-function interactions with MYC create a gene signature predictive of cancers with CREB-MYC involvement. PMID:25071166
Activin A balance regulates epithelial invasiveness and tumorigenesis. PMID:25068654
Gene expression profiling reveals similarities between the spatial architectures of postnatal articular and growth plate cartilage. PMID:25068449
Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice. PMID:25063675
Proteasome function is required for platelet production. PMID:25061876
Cannabidiol exerts sebostatic and antiinflammatory effects on human sebocytes. PMID:25061872
Genomic profiling of rice roots with short- and long-term chromium stress. PMID:25056418
Interrogation of allelic chromatin states in human cells by high-density ChIP-genotyping. PMID:25055051
Genes involved in the osteoarthritis process identified through genome wide expression analysis in articular cartilage; the RAAK study. PMID:25054223
Hypoxia represses microRNA biogenesis proteins in breast cancer cells. PMID:25052766
Gene expression profiling of peri-implant healing of PLGA-Li+ implants suggests an activated Wnt signaling pathway in vivo. PMID:25047349
Transcription factor Sp4 regulates expression of nervous wreck 2 to control NMDAR1 levels and dendrite patterning. PMID:25045015
Elucidating how the saprophytic fungus Aspergillus nidulans uses the plant polyester suberin as carbon source. PMID:25043916
Identifying mouse models for skin cancer using the Mouse Tumor Biology Database. PMID:25040013
Exome sequencing identifies highly recurrent MED12 somatic mutations in breast fibroadenoma. PMID:25038752
LANA binds to multiple active viral and cellular promoters and associates with the H3K4methyltransferase hSET1 complex. PMID:25033463
Data integration in the era of omics: current and future challenges. PMID:25032990
Genome-wide analysis reveals divergent patterns of gene expression during zygotic and somatic embryo maturation of Theobroma cacao L., the chocolate tree. PMID:25030026
KIFCI, a novel putative prognostic biomarker for ovarian adenocarcinomas: delineating protein interaction networks and signaling circuitries. PMID:25028599
Intercellular network structure and regulatory motifs in the human hematopoietic system. PMID:25028490
Genetic targets of hydrogen sulfide in ventilator-induced lung injury--a microarray study. PMID:25025333
Reproducible combinatorial regulatory networks elucidate novel oncogenic microRNAs in non-small cell lung cancer. PMID:25024357
An improved method for computing q-values when the distribution of effect sizes is asymmetric. PMID:25024290
Comprehensive identification of essential pathways and transcription factors related to epilepsy by gene set enrichment analysis on microarray datasets. PMID:25016997
A large-scale RNAi-based mouse tumorigenesis screen identifies new lung cancer tumor suppressors that repress FGFR signaling. PMID:25015643
Transcriptional network control of normal and leukaemic haematopoiesis. PMID:25014893
Degree-adjusted algorithm for prioritisation of candidate disease genes from gene expression and protein interactome. PMID:25014224
Life on the edge: functional genomic response of Ignicoccus hospitalis to the presence of Nanoarchaeum equitans. PMID:25012904
Stability of the CpG island methylator phenotype during glioma progression and identification of methylated loci in secondary glioblastomas. PMID:25012071
Genome-wide profiling of 8-oxoguanine reveals its association with spatial positioning in nucleus. PMID:25008760
Alterations in circulating miRNA levels following early-stage estrogen receptor-positive breast cancer resection in post-menopausal women. PMID:25004125
Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. PMID:25003194
An integrative analysis of meningioma tumors reveals the determinant genes and pathways of malignant transformation. PMID:25003081
RNA sequencing analysis of the broad-host-range strain Sinorhizobium fredii NGR234 identifies a large set of genes linked to quorum sensing-dependent regulation in the background of a traI and ngrI deletion mutant. PMID:25002423
Developmental cell fate and virulence are linked to trehalose homeostasis in Cryptococcus neoformans. PMID:25001408
Comparing reference-based RNA-Seq mapping methods for non-human primate data. PMID:25001289
piRNAQuest: searching the piRNAome for silencers. PMID:24997126
Transcriptome analysis reveals signature of adaptation to landscape fragmentation. PMID:24988207
Clinic-genomic association mining for colorectal cancer using publicly available datasets. PMID:24987669
Gene response in rice plants treated with continuous fog influenced by pH, was similar to that treated with biotic stress. PMID:24987489
Transforming growth factor beta receptor type III is a tumor promoter in mesenchymal-stem like triple negative breast cancer. PMID:24985072
SUMOylation modulates the transcriptional activity of androgen receptor in a target gene and pathway selective manner. PMID:24981513
Comprehensive transcriptome analysis unravels the existence of crucial genes regulating primary metabolism during adventitious root formation in Petunia hybrida. PMID:24978694
The inferred cardiogenic gene regulatory network in the mammalian heart. PMID:24971943
Batch effect confounding leads to strong bias in performance estimates obtained by cross-validation. PMID:24967636
Novel insights into the regulatory architecture of CD4+ T cells in rheumatoid arthritis. PMID:24959711
Human enteroendocrine cell responses to infection with Chlamydia trachomatis: a microarray study. PMID:24959205
Detection of expressional changes induced by intrauterine growth restriction in the developing rat mammary gland via exploratory pathways analysis. PMID:24955840
Supplemental carnitine affects the microRNA expression profile in skeletal muscle of obese Zucker rats. PMID:24952657
Breast cancer prognosis risk estimation using integrated gene expression and clinical data. PMID:24949450
CSNK1E/CTNNB1 are synthetic lethal to TP53 in colorectal cancer and are markers for prognosis. PMID:24947187
Glycogen Synthase Kinase 3β in Pancreatic Cancer and its Implications in Chemotherapy and Radiation Therapy. PMID:24944842
A method for detecting long non-coding RNAs with tiled RNA expression microarrays. PMID:24937006
Bone marrow endosteal mesenchymal progenitors depend on HIF factors for maintenance and regulation of hematopoiesis. PMID:24936467
Phenotype prediction based on genome-wide DNA methylation data. PMID:24934728
Interruption of KLF5 acetylation converts its function from tumor suppressor to tumor promoter in prostate cancer cells. PMID:24931571
RNase J is required for processing of a small number of RNAs in Rhodobacter sphaeroides. PMID:24922065
External validation of a multiplex urinary protein panel for the detection of bladder cancer in a multicenter cohort. PMID:24920641
Expression profiling of the wheat pathogen Zymoseptoria tritici reveals genomic patterns of transcription and host-specific regulatory programs. PMID:24920004
Mesenchymal precursor cells maintain the differentiation and proliferation potentials of breast epithelial cells. PMID:24916766
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
Quality control on the frontier. PMID:24904650
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Allen Brain Atlas-Driven Visualizations: a web-based gene expression energy visualization tool. PMID:24904397
Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)-infected cynomolgus macaques. PMID:24898206
Peroxidasin is essential for eye development in the mouse. PMID:24895407
Identification of genomic loci associated with Rhodococcus equi susceptibility in foals. PMID:24892408
Maternal experience with predation risk influences genome-wide embryonic gene expression in threespined sticklebacks (Gasterosteus aculeatus). PMID:24887438
Intergenerational genomic DNA methylation patterns in mouse hybrid strains. PMID:24887417
Amerindian-specific regions under positive selection harbour new lipid variants in Latinos. PMID:24886709
EXPRSS: an Illumina based high-throughput expression-profiling method to reveal transcriptional dynamics. PMID:24884414
CD80 and PD-L2 define functionally distinct memory B cell subsets that are independent of antibody isotype. PMID:24880458
The Emerging Role of Reactive Oxygen Species Signaling during Lateral Root Development. PMID:24879433
Impact of gene dosage on gene expression, biological processes and survival in cervical cancer: a genome-wide follow-up study. PMID:24879114
Differential Shannon entropy and differential coefficient of variation: alternatives and augmentations to differential expression in the search for disease-related genes. PMID:24878729
Hypoxia-mediated retinal neovascularization and vascular leakage in diabetic retina is suppressed by HIF-1α destabilization by SH-1242 and SH-1280, novel hsp90 inhibitors. PMID:24875598
The PhoP-dependent ncRNA Mcr7 modulates the TAT secretion system in Mycobacterium tuberculosis. PMID:24874799
Mechanisms for the adverse effects of late gestational increases in maternal cortisol on the heart revealed by transcriptomic analyses of the fetal septum. PMID:24867915
β-Cryptoxanthin alleviates diet-induced nonalcoholic steatohepatitis by suppressing inflammatory gene expression in mice. PMID:24858832
RNA-Seq and expression microarray highlight different aspects of the fetal amniotic fluid transcriptome. PMID:24852236
Genus beta human papillomavirus E6 proteins vary in their effects on the transactivation of p53 target genes. PMID:24850740
Rapid proliferation and differentiation impairs the development of memory CD8+ T cells in early life. PMID:24850719
MiRNome and transcriptome aided pathway analysis in human regulatory T cells. PMID:24848933
Distinct gene expression profiles in ovarian cancer linked to Lynch syndrome. PMID:24848881
Niacin in pharmacological doses alters microRNA expression in skeletal muscle of obese Zucker rats. PMID:24847987
Global adaptation to a lipid environment triggers the dormancy-related phenotype of Mycobacterium tuberculosis. PMID:24846381
The epigenetic bivalency of core pancreatic β-cell transcription factor genes within mouse pluripotent embryonic stem cells is not affected by knockdown of the polycomb repressive complex 2, SUZ12. PMID:24845830
MiRNAting control of DNA methylation. PMID:24845501
Targeted tandem duplication of a large chromosomal segment in Aspergillus oryzae. PMID:24837372
DNA replication is an integral part of the mouse oocyte's reprogramming machinery. PMID:24836291
Exploiting a Reference Genome in Terms of Duplications: The Network of Paralogs and Single Copy Genes in Arabidopsis thaliana. PMID:24833233
Importance of the RNA secondary structure for the relative accumulation of clustered viral microRNAs. PMID:24831544
Striking differences between knockout and wild-type mice in global gene expression variability. PMID:24830645
Cross-platform toxicogenomics for the prediction of non-genotoxic hepatocarcinogenesis in rat. PMID:24830643
Identification of heparin-binding EGF-like growth factor (HB-EGF) as a biomarker for lysophosphatidic acid receptor type 1 (LPA1) activation in human breast and prostate cancers. PMID:24828490
Cell competition is a tumour suppressor mechanism in the thymus. PMID:24828041
A naturally occurring, noncanonical GTP aptamer made of simple tandem repeats. PMID:24824832
Genome-wide characterization reveals complex interplay between TP53 and TP63 in response to genotoxic stress. PMID:24823795
Chronic unpredictable stress regulates visceral adipocyte-mediated glucose metabolism and inflammatory circuits in male rats. PMID:24819750
Lipid profiling and transcriptomic analysis reveals a functional interplay between estradiol and growth hormone in liver. PMID:24816529
Genetic dissection of the Drosophila melanogaster female head transcriptome reveals widespread allelic heterogeneity. PMID:24810915
Palmdelphin, a novel target of p53 with Ser46 phosphorylation, controls cell death in response to DNA damage. PMID:24810057
Identification of miRNA-mediated core gene module for glioma patient prediction by integrating high-throughput miRNA, mRNA expression and pathway structure. PMID:24809850
Genome-defence small RNAs exapted for epigenetic mating-type inheritance. PMID:24805235
Involvement of endocytosis and alternative splicing in the formation of the pathological process in the early stages of Parkinson's disease. PMID:24804238
Integrating omics technologies to study pulmonary physiology and pathology at the systems level. PMID:24802001
Effect of chronic valproic Acid treatment on hepatic gene expression profile in wfs1 knockout mouse. PMID:24799886
Genetic analysis of the assimilation of C5-dicarboxylic acids in Pseudomonas aeruginosa PAO1. PMID:24794562
Pleiotropic mutations are subject to strong stabilizing selection. PMID:24793289
Evolutionary approach for relative gene expression algorithms. PMID:24790574
Single nucleotide variants in transcription factors associate more tightly with phenotype than with gene expression. PMID:24784239
Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures. PMID:24780077
TGF-beta signalling in the adult neurogenic niche promotes stem cell quiescence as well as generation of new neurons. PMID:24779367
Dissection of estrogen receptor alpha signaling pathways in osteoblasts using RNA-sequencing. PMID:24776842
Air toxics and epigenetic effects: ozone altered microRNAs in the sputum of human subjects. PMID:24771714
The bromodomain protein BRD4 regulates the KEAP1/NRF2-dependent oxidative stress response. PMID:24763052
Molecular signatures differentiate immune states in type 1 diabetic families. PMID:24760139
Wolbachia infection modifies the profile, shuttling and structure of microRNAs in a mosquito cell line. PMID:24759922
Breast tumor specific mutation in GATA3 affects physiological mechanisms regulating transcription factor turnover. PMID:24758297
Gene expression pattern of cells from inflamed and normal areas of osteoarthritis synovial membrane. PMID:24757147
Expression microarray identifies the unliganded glucocorticoid receptor as a regulator of gene expression in mammary epithelial cells. PMID:24755251
Oncogene-like induction of cellular invasion from centrosome amplification. PMID:24739973
Transcriptional dissection of pancreatic tumors engrafted in mice. PMID:24739241
Expression of a truncated ATHB17 protein in maize increases ear weight at silking. PMID:24736658
MLL fusion-driven activation of CDK6 potentiates proliferation in MLL-rearranged infant ALL. PMID:24736461
Identification of mRNAs and lincRNAs associated with lung cancer progression using next-generation RNA sequencing from laser micro-dissected archival FFPE tissue specimens. PMID:24735754
The very low density lipoprotein receptor attenuates house dust mite-induced airway inflammation by suppressing dendritic cell-mediated adaptive immune responses. PMID:24733846
A family of nonclassical class I MHC genes contributes to ultrasensitive chemodetection by mouse vomeronasal sensory neurons. PMID:24719092
Fatty acid elongation in non-alcoholic steatohepatitis and hepatocellular carcinoma. PMID:24714086
Urinary protein biomarker panel for the detection of recurrent bladder cancer. PMID:24714076
Pulsatile exposure to simulated reflux leads to changes in gene expression in a 3D model of oesophageal mucosa. PMID:24713057
SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. PMID:24712981
Patient-derived xenografts of triple-negative breast cancer reproduce molecular features of patient tumors and respond to mTOR inhibition. PMID:24708766
Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions. PMID:24708602
A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. PMID:24708151
Critical role of extracellular vesicles in modulating the cellular effects of cytokines. PMID:24705984
Parallel clustering algorithm for large-scale biological data sets. PMID:24705246
Extensively self-renewing erythroblasts derived from transgenic β-yac mice is a novel model system for studying globin switching and erythroid maturation. PMID:24704162
Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci. PMID:24693880
Relationship of gene expression in the injured human meniscus to body mass index: a biologic connection between obesity and osteoarthritis. PMID:24692131
DNA methylome profiling of human tissues identifies global and tissue-specific methylation patterns. PMID:24690455
CD36 deletion improves recovery from spinal cord injury. PMID:24690303
Biomarker signature identification in "omics" data with multi-class outcome. PMID:24688712
Simultaneous multi-analyte urinary protein assay for bladder cancer detection. PMID:24684904
Identification of novel reference genes based on MeSH categories. PMID:24682035
SLC25A1, or CIC, is a novel transcriptional target of mutant p53 and a negative tumor prognostic marker. PMID:24681808
Signaling by IL-6 promotes alternative activation of macrophages to limit endotoxemia and obesity-associated resistance to insulin. PMID:24681566
Plant systems biology: insights, advances and challenges. PMID:24671625
Global gene expression in endometrium of high and low fertility heifers during the mid-luteal phase of the estrous cycle. PMID:24669966
Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription. PMID:24668167
Hmga2 is required for canonical WNT signaling during lung development. PMID:24661562
TLR4 ligands lipopolysaccharide and monophosphoryl lipid a differentially regulate effector and memory CD8+ T Cell differentiation. PMID:24659688
TDP2 protects transcription from abortive topoisomerase activity and is required for normal neural function. PMID:24658003
Remodeling of the sarcomeric cytoskeleton in cardiac ventricular myocytes during heart failure and after cardiac resynchronization therapy. PMID:24657727
INsPeCT: INtegrative Platform for Cancer Transcriptomics. PMID:24653643
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PMID:24651478
Tissue specific DNA methylation in normal human breast epithelium and in breast cancer. PMID:24651077
Gene regulatory and metabolic adaptation processes of Dinoroseobacter shibae DFL12T during oxygen depletion. PMID:24648520
Systematic assessment of prognostic gene signatures for breast cancer shows distinct influence of time and ER status. PMID:24645668
Evolutionary conservation of the eumetazoan gene regulatory landscape. PMID:24642862
Extreme sensitivity of gene expression in human SH-SY5Y neurocytes to ultra-low doses of Gelsemium sempervirens. PMID:24642002
Genome-wide copy number variant discovery in dogs using the CanineHD genotyping array. PMID:24640994
Negative elongation factor is required for the maintenance of proviral latency but does not induce promoter-proximal pausing of RNA polymerase II on the HIV long terminal repeat. PMID:24636995
Navigating and mining modENCODE data. PMID:24636835
Gene expression differences predict treatment outcome of merkel cell carcinoma patients. PMID:24634783
A BRCA1 deficient-like signature is enriched in breast cancer brain metastases and predicts DNA damage-induced poly (ADP-ribose) polymerase inhibitor sensitivity. PMID:24625110
Arabidopsis thaliana RALF1 opposes brassinosteroid effects on root cell elongation and lateral root formation. PMID:24620000
A personalized committee classification approach to improving prediction of breast cancer metastasis. PMID:24618465
Combinatorial cytokine code generates anti-viral state in dendritic cells. PMID:24616721
Extracellular vesicles in luminal fluid of the ovine uterus. PMID:24614226
Exploring the molecular causes of hepatitis B virus vaccination response: an approach with epigenomic and transcriptomic data. PMID:24612962
The functional consequences of variation in transcription factor binding. PMID:24603674
A network pharmacology approach to understanding the mechanisms of action of traditional medicine: Bushenhuoxue formula for treatment of chronic kidney disease. PMID:24598793
Modeling the Drosophila gene cluster regulation network for muscle development. PMID:24594656
A systems biological approach reveals multiple crosstalk mechanism between gram-positive and negative bacterial infections: an insight into core mechanism and unique molecular signatures. PMID:24587173
Automated detection of off-label drug use. PMID:24586689
Altered miRNA expression in canine retinas during normal development and in models of retinal degeneration. PMID:24581223
Abandon the mouse research ship? Not just yet! PMID:24569509
Statistical insights into major human muscular diseases. PMID:24569163
Identification of a BET family bromodomain/casein kinase II/TAF-containing complex as a regulator of mitotic condensin function. PMID:24565511
Weighted set enrichment of gene expression data. PMID:24565001
A novel approach to minimize false discovery rate in genome-wide data analysis. PMID:24564975
Systematically profiling and annotating long intergenic non-coding RNAs in human embryonic stem cell. PMID:24564552
Application of microRNA and mRNA expression profiling on prognostic biomarker discovery for hepatocellular carcinoma. PMID:24564407
MaTSE: the gene expression time-series explorer. PMID:24564291
Improving reliability and absolute quantification of human brain microarray data by filtering and scaling probes using RNA-Seq. PMID:24564186
A splicing-dependent transcriptional checkpoint associated with prespliceosome formation. PMID:24560925
Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes. PMID:24558399
BiNA: a visual analytics tool for biological network data. PMID:24551056
The gene regulatory network for breast cancer: integrated regulatory landscape of cancer hallmarks. PMID:24550935
Immunological Outcome in Haploidentical-HSC Transplanted Patients Treated with IL-10-Anergized Donor T Cells. PMID:24550909
Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice. PMID:24549398
Fenofibrate induces apoptosis of triple-negative breast cancer cells via activation of NF-κB pathway. PMID:24529079
Derivation and maintenance of murine trophoblast stem cells under defined conditions. PMID:24527396
Translational Bioinformatics Approaches to Drug Development. PMID:24527359
High-Throughput Single-Cell Analysis for Wound Healing Applications. PMID:24527358
CXCL10 is critical for the progression and maintenance of depigmentation in a mouse model of vitiligo. PMID:24523323
Gene expression profiling reveals GC and CEACAM1 as new tools in the diagnosis of lung carcinoids. PMID:24518592
Global miRNA expression analysis of serous and clear cell ovarian carcinomas identifies differentially expressed miRNAs including miR-200c-3p as a prognostic marker. PMID:24512620
Cytokinin as a mediator for regulating root system architecture in response to environmental cues. PMID:24509549
Pristane-induced arthritis loci interact with the Slc11a1 gene to determine susceptibility in mice selected for high inflammation. PMID:24505471
Loss of FTO antagonises Wnt signaling and leads to developmental defects associated with ciliopathies. PMID:24503721
All-trans retinoic acid-triggered antimicrobial activity against Mycobacterium tuberculosis is dependent on NPC2. PMID:24501203
De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PMID:24499931
A GNAS mutation found in pancreatic intraductal papillary mucinous neoplasms induces drastic alterations of gene expression profiles with upregulation of mucin genes. PMID:24498386
De novo synthesis of milk triglycerides in humans. PMID:24496312
KDM5B focuses H3K4 methylation near promoters and enhancers during embryonic stem cell self-renewal and differentiation. PMID:24495580
Accounting for cellular heterogeneity is critical in epigenome-wide association studies. PMID:24495553
Statistical analysis of differential gene expression relative to a fold change threshold on NanoString data of mouse odorant receptor genes. PMID:24495268
Mutant p53-associated myosin-X upregulation promotes breast cancer invasion and metastasis. PMID:24487586
Hunting complex differential gene interaction patterns across molecular contexts. PMID:24482443
The interplay of light and oxygen in the reactive oxygen stress response of Chlamydomonas reinhardtii dissected by quantitative mass spectrometry. PMID:24482124
Transcriptome analysis of Vibrio parahaemolyticus in type III secretion system 1 inducing conditions. PMID:24478989
Attenuation and restoration of severe acute respiratory syndrome coronavirus mutant lacking 2'-o-methyltransferase activity. PMID:24478444
Minimum information about a biofilm experiment (MIABiE): standards for reporting experiments and data on sessile microbial communities living at interfaces. PMID:24478124
Transcriptomic meta-analysis of multiple sclerosis and its experimental models. PMID:24475162
Comprehensive analysis of β-catenin target genes in colorectal carcinoma cell lines with deregulated Wnt/β-catenin signaling. PMID:24467841
Microarray analysis of rat pancreas reveals altered expression of Alox15 and regenerating islet-derived genes in response to iron deficiency and overload. PMID:24465846
The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs. PMID:24465553
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
Nutrient limitation governs Staphylococcus aureus metabolism and niche adaptation in the human nose. PMID:24453967
A generic tool for transcription factor target gene discovery in Arabidopsis cell suspension cultures based on tandem chromatin affinity purification. PMID:24453163
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. PMID:24451627
Differential gene expression in small and large rainbow trout derived from two seasonal spawning groups. PMID:24450799
Fast-evolving microRNAs are highly expressed in the early embryo of Drosophila virilis. PMID:24448446
GATA2 as a potential metastasis-driving gene in prostate cancer. PMID:24448395
AMPK agonist AICAR improves cognition and motor coordination in young and aged mice. PMID:24443745
Types of DNA methylation status of the interspersed repetitive sequences for LINE-1, Alu, HERV-E and HERV-K in the neutrophils from systemic lupus erythematosus patients and healthy controls. PMID:24430577
Genes showing altered expression in the medial preoptic area in the highly social maternal phenotype are related to autism and other disorders with social deficits. PMID:24423034
Salicylic acid is an indispensable component of the Ny-1 resistance-gene-mediated response against Potato virus Y infection in potato. PMID:24420577
CD44 is a negative cell surface marker for pluripotent stem cell identification during human fibroblast reprogramming. PMID:24416407
Mutation screening and array comparative genomic hybridization using a 180K oligonucleotide array in VACTERL association. PMID:24416387
RSK2 is a modulator of craniofacial development. PMID:24416220
DevMouse, the mouse developmental methylome database and analysis tools. PMID:24408217
A long-term demasculinization of X-linked intergenic noncoding RNAs in Drosophila melanogaster. PMID:24407956
The nature and extent of mutational pleiotropy in gene expression of male Drosophila serrata. PMID:24402375
Global regulation of mRNA translation and stability in the early Drosophila embryo by the Smaug RNA-binding protein. PMID:24393533
Spatial control of adult stem cell fate using nanotopographic cues. PMID:24388388
Characterization of the yehUT two-component regulatory system of Salmonella enterica Serovar Typhi and Typhimurium. PMID:24386394
Protein complex identification by integrating protein-protein interaction evidence from multiple sources. PMID:24386289
MicroRNA-132 is enriched in developing axons, locally regulates Rasa1 mRNA, and promotes axon extension. PMID:24381269
Gene expression analysis indicates CB1 receptor upregulation in the hippocampus and neurotoxic effects in the frontal cortex 3 weeks after single-dose MDMA administration in Dark Agouti rats. PMID:24378229
IpsA, a novel LacI-type regulator, is required for inositol-derived lipid formation in Corynebacteria and Mycobacteria. PMID:24377418
Partitioning the human transcriptome using HKera, a novel classifier of housekeeping and tissue-specific genes. PMID:24376628
An emerging picture of the seed desiccome: confirmed regulators and newcomers identified using transcriptome comparison. PMID:24376450
Homology modeling and molecular docking for the science curriculum. PMID:24376157
Structural polymorphism in the promoter of pfmrp2 confers Plasmodium falciparum tolerance to quinoline drugs. PMID:24372851
Leukocyte transcriptome from chickens infected with avian pathogenic Escherichia coli identifies pathways associated with resistance. PMID:24371566
Identification of reproducible gene expression signatures in lung adenocarcinoma. PMID:24369726
Mantle cell lymphoma in cyclin D1 transgenic mice with Bim-deficient B cells. PMID:24352880
Transcriptional profiling of hilar nodes from pigs after experimental infection with Actinobacillus pleuropneumoniae. PMID:24351863
Biased gene expression in early honeybee larval development. PMID:24350621
Microarray analysis of transcriptome of medulla identifies potential biomarkers for Parkinson's disease. PMID:24350239
Curcumin intake affects miRNA signature in murine melanoma with mmu-miR-205-5p most significantly altered. PMID:24349037
Power and stability properties of resampling-based multiple testing procedures with applications to gene oncology studies. PMID:24348741
Integrative DNA methylation and gene expression analysis in high-grade soft tissue sarcomas. PMID:24345474
Identification of expressed and conserved human noncoding RNAs. PMID:24344320
Transcriptome analysis of leaf and root of rice seedling to acute dehydration. PMID:24341907
Bcl-xL silencing induces alterations in hsa-miR-608 expression and subsequent cell death in A549 and SK-LU1 human lung adenocarcinoma cells. PMID:24339958
Efficient keratinocyte differentiation strictly depends on JNK-induced soluble factors in fibroblasts. PMID:24335928
Can transcriptomics provide insight into the chemopreventive mechanisms of complex mixtures of phytochemicals in humans? PMID:24328558
Prenatal arsenic exposure and the epigenome: altered microRNAs associated with innate and adaptive immune signaling in newborn cord blood. PMID:24327377
Whole transcriptome characterization of the effects of dehydration and rehydration on Cladonia rangiferina, the grey reindeer lichen. PMID:24325588
Microarray and morphological analysis of early postnatal CRB2 mutant retinas on a pure C57BL/6J genetic background. PMID:24324803
Simultaneous transcriptional profiling of bacteria and their host cells. PMID:24324615
SIOMICS: a novel approach for systematic identification of motifs in ChIP-seq data. PMID:24322294
The oncogenic properties of EWS/WT1 of desmoplastic small round cell tumors are unmasked by loss of p53 in murine embryonic fibroblasts. PMID:24321497
Evolutionary history of mitogen-activated protein kinase (MAPK) genes in Lotus, Medicago, and Phaseolus. PMID:24317362
Protein microarray analysis of antibody responses to Plasmodium falciparum in western Kenyan highland sites with differing transmission levels. PMID:24312649
A machine learned classifier that uses gene expression data to accurately predict estrogen receptor status. PMID:24312637
Assessing differential expression in two-color microarrays: a resampling-based empirical Bayes approach. PMID:24312198
A multi-level multi-scale approach to study essential genes in Mycobacterium tuberculosis. PMID:24308365
HEFT: eQTL analysis of many thousands of expressed genes while simultaneously controlling for hidden factors. PMID:24307700
Lipopolysaccharide activates Toll-like receptor 4 (TLR4)-mediated NF-κB signaling pathway and proinflammatory response in human pericytes. PMID:24307174
Formaldehyde-associated changes in microRNAs: tissue and temporal specificity in the rat nose, white blood cells, and bone marrow. PMID:24304932
CellFinder: a cell data repository. PMID:24304896
Non-growing Rhodopseudomonas palustris increases the hydrogen gas yield from acetate by shifting from the glyoxylate shunt to the tricarboxylic acid cycle. PMID:24302724
Ribosome profiling reveals pervasive and regulated stop codon readthrough in Drosophila melanogaster. PMID:24302569
Comparative transcript profiling by SuperSAGE identifies novel candidate genes for controlling potato quantitative resistance to late blight not compromised by late maturity. PMID:24294214
Array data extractor (ADE): a LabVIEW program to extract and merge gene array data. PMID:24289243
Identification of breast cancer patients based on human signaling network motifs. PMID:24284521
FOXD1 promotes nephron progenitor differentiation by repressing decorin in the embryonic kidney. PMID:24284212
BORIS/CTCFL is an RNA-binding protein that associates with polysomes. PMID:24279897
The microRNAome of pregnancy: deciphering miRNA networks at the maternal-fetal interface. PMID:24278102
Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. PMID:24274116
Slit2-Robo4 pathway modulates lipopolysaccharide-induced endothelial inflammation and its expression is dysregulated during endotoxemia. PMID:24272999
Abnormalities in glycogen metabolism in a patient with alpers' syndrome presenting with hypoglycemia. PMID:24272679
The Gene Expression Barcode 3.0: improved data processing and mining tools. PMID:24271388
MultiFacTV: module detection from higher-order time series biological data. PMID:24268038
Characterization of chromosomal architecture in Arabidopsis by chromosome conformation capture. PMID:24267747
Global bidirectional transcription of the Epstein-Barr virus genome during reactivation. PMID:24257595
Identification of RNase L-dependent, 3'-end-modified, viral small RNAs in Sindbis virus-infected mammalian cells. PMID:24255120
Downregulation of Max dimerization protein 3 is involved in decreased visceral adipose tissue by inhibiting adipocyte differentiation in zebrafish and mice. PMID:24254064
Iron-binding haemerythrin RING ubiquitin ligases regulate plant iron responses and accumulation. PMID:24253678
Deep sequencing identification of novel glucocorticoid-responsive miRNAs in apoptotic primary lymphocytes. PMID:24250753
Combinatory microarray and SuperSAGE analyses identify pairing-dependently transcribed genes in Schistosoma mansoni males, including follistatin. PMID:24244773
Prediction of drug-target interactions for drug repositioning only based on genomic expression similarity. PMID:24244130
Molecular sub-group-specific immunophenotypic changes are associated with outcome in recurrent posterior fossa ependymoma. PMID:24240813
The transcription factor ATOH8 is regulated by erythropoietic activity and regulates HAMP transcription and cellular pSMAD1,5,8 levels. PMID:24236640
MicroRNA-20a constrains p300-driven myocardial angiogenic transcription by direct targeting of p300. PMID:24236097
Quantitative network measures as biomarkers for classifying prostate cancer disease states: a systems approach to diagnostic biomarkers. PMID:24236006
Integrating in silico resources to map a signaling network. PMID:24233784
Protein expression profiles of intestinal epithelial co-cultures: effect of functionalised carbon nanotube exposure. PMID:24228069
In search of epigenetic marks in testes and sperm cells of differentially fed boars. PMID:24223838
Phosphorylation-dependent derepression by the response regulator HnoC in the Shewanella oneidensis nitric oxide signaling network. PMID:24218564
Wnt signaling in triple negative breast cancer is associated with metastasis. PMID:24209998
Transcriptome-wide mapping of pea seed ageing reveals a pivotal role for genes related to oxidative stress and programmed cell death. PMID:24205239
Microarray analysis of tomato's early and late wound response reveals new regulatory targets for Leucine aminopeptidase A. PMID:24205013
Human neonatal cardiovascular progenitors: unlocking the secret to regenerative ability. PMID:24204836
Ten simple rules for reproducible computational research. PMID:24204232
A genome-wide survey of maternal and embryonic transcripts during Xenopus tropicalis development. PMID:24195446
High-throughput 3D screening reveals differences in drug sensitivities between culture models of JIMT1 breast cancer cells. PMID:24194875
Functional analysis of sporophytic transcripts repressed by the female gametophyte in the ovule of Arabidopsis thaliana. PMID:24194852
Bivalve omics: state of the art and potential applications for the biomonitoring of harmful marine compounds. PMID:24189277
Molecular mechanisms of system responses to novel stimuli are predictable from public data. PMID:24185701
The BET family of proteins targets moloney murine leukemia virus integration near transcription start sites. PMID:24183673
HypoxiaDB: a database of hypoxia-regulated proteins. PMID:24178989
Analysis of expressed SNPs identifies variable extents of expression from the human inactive X chromosome. PMID:24176135
Promoters maintain their relative activity levels under different growth conditions. PMID:24169404
Divergent compensatory responses to high-fat diet between C57BL6/J and C57BLKS/J inbred mouse strains. PMID:24169046
Inference of sigma factor controlled networks by using numerical modeling applied to microarray time series data of the germinating prokaryote. PMID:24157841
The ESX-3 secretion system is necessary for iron and zinc homeostasis in Mycobacterium tuberculosis. PMID:24155985
Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates. PMID:24154525
Relationship between gene responses and symptoms induced by Rice grassy stunt virus. PMID:24151491
Positively correlated miRNA-mRNA regulatory networks in mouse frontal cortex during early stages of alcohol dependence. PMID:24148570
PhysioSpace: relating gene expression experiments from heterogeneous sources using shared physiological processes. PMID:24147039
F11R is a novel monocyte prognostic biomarker for malignant glioma. PMID:24147027
Identifying genes relevant to specific biological conditions in time course microarray experiments. PMID:24146889
Hsp70-Hsp40 chaperone complex functions in controlling polarized growth by repressing Hsf1-driven heat stress-associated transcription. PMID:24146635
Analysis of cell surface markers specific for transplantable rod photoreceptors. PMID:24146539
The Ets transcription factor EHF as a regulator of cornea epithelial cell identity. PMID:24142692
Construction of the influenza A virus infection-induced cell-specific inflammatory regulatory network based on mutual information and optimization. PMID:24138989
The housekeeping gene hypoxanthine guanine phosphoribosyltransferase (HPRT) regulates multiple developmental and metabolic pathways of murine embryonic stem cell neuronal differentiation. PMID:24130677
Manipulation of the HIF-Vegf pathway rescues methyl tert-butyl ether (MTBE)-induced vascular lesions. PMID:24128854
Decreased bone formation and increased osteoclastogenesis cause bone loss in mucolipidosis II. PMID:24127423
Genetically engineered transvestites reveal novel mating genes in budding yeast. PMID:24121774
Integrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots. PMID:24119003
Inferring tumour purity and stromal and immune cell admixture from expression data. PMID:24113773
Spt6 regulates intragenic and antisense transcription, nucleosome positioning, and histone modifications genome-wide in fission yeast. PMID:24100010
Silver nanowire exposure results in internalization and toxicity to Daphnia magna. PMID:24099093
Canonical Nlrp3 inflammasome links systemic low-grade inflammation to functional decline in aging. PMID:24093676
Downregulation of 14q32 microRNAs in Primary Human Desmoplastic Medulloblastoma. PMID:24093088
SLIT3-ROBO4 activation promotes vascular network formation in human engineered tissue and angiogenesis in vivo. PMID:24090675
From genes to milk: genomic organization and epigenetic regulation of the mammary transcriptome. PMID:24086428
Root transcript profiling of two Rorippa species reveals gene clusters associated with extreme submergence tolerance. PMID:24077074
Mass fingerprinting of complex mixtures: protein inference from high-resolution peptide masses and predicted retention times. PMID:24074221
Network-based inference framework for identifying cancer genes from gene expression data. PMID:24073403
Differential host response, rather than early viral replication efficiency, correlates with pathogenicity caused by influenza viruses. PMID:24073225
Enabling transparent and collaborative computational analysis of 12 tumor types within The Cancer Genome Atlas. PMID:24071850
RNA-Seq reveals spliceosome and proteasome genes as most consistent transcripts in human cancer cells. PMID:24069164
A genome-wide systematic analysis reveals different and predictive proliferation expression signatures of cancerous vs. non-cancerous cells. PMID:24068970
Expression signature as a biomarker for prenatal diagnosis of trisomy 21. PMID:24066117
Small RNA profiling of Xenopus embryos reveals novel miRNAs and a new class of small RNAs derived from intronic transposable elements. PMID:24065776
Genome-wide transcriptional response of Trichoderma reesei to lignocellulose using RNA sequencing and comparison with Aspergillus niger. PMID:24060058
BD-Func: a streamlined algorithm for predicting activation and inhibition of pathways. PMID:24058887
Plasticity of blood- and lymphatic endothelial cells and marker identification. PMID:24058540
Knockdown of human TCF4 affects multiple signaling pathways involved in cell survival, epithelial to mesenchymal transition and neuronal differentiation. PMID:24058414
Snf1 is a regulator of lipid accumulation in Yarrowia lipolytica. PMID:24056466
Role of type II pneumocyte senescence in radiation-induced lung fibrosis. PMID:24052614
Human cell toxicogenomic analysis linking reactive oxygen species to the toxicity of monohaloacetic acid drinking water disinfection byproducts. PMID:24050308
A kinetic analysis of the auxin transcriptome reveals cell wall remodeling proteins that modulate lateral root development in Arabidopsis. PMID:24045021
The membrane-bound NAC transcription factor ANAC013 functions in mitochondrial retrograde regulation of the oxidative stress response in Arabidopsis. PMID:24045019
An immunological fingerprint differentiates muscular lymphatics from arteries and veins. PMID:24044756
LEA polypeptide profiling of recalcitrant and orthodox legume seeds reveals ABI3-regulated LEA protein abundance linked to desiccation tolerance. PMID:24043848
Stem cells isolated from adipose tissue of obese patients show changes in their transcriptomic profile that indicate loss in stemcellness and increased commitment to an adipocyte-like phenotype. PMID:24040759
Genome-wide study of the adaptation of Saccharomyces cerevisiae to the early stages of wine fermentation. PMID:24040173
Role and regulation of the Flp/Tad pilus in the virulence of Pectobacterium atrosepticum SCRI1043 and Pectobacterium wasabiae SCC3193. PMID:24040039
Global features of gene expression on the proteome and transcriptome levels in S. coelicolor during germination. PMID:24039809
Altered expression of cyclin A 1 in muscle of patients with facioscapulohumeral muscle dystrophy (FSHD-1). PMID:24019929
Analysis of the RelA:CBP/p300 interaction reveals its involvement in NF-κB-driven transcription. PMID:24019758
DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals. PMID:24013725
The Oct1 homolog Nubbin is a repressor of NF-κB-dependent immune gene expression that increases the tolerance to gut microbiota. PMID:24010524
Standardization of sample collection, isolation and analysis methods in extracellular vesicle research. PMID:24009894
A nuclear calcium-sensing pathway is critical for gene regulation and salt stress tolerance in Arabidopsis. PMID:24009530
Small RNAs derived from lncRNA RNase MRP have gene-silencing activity relevant to human cartilage-hair hypoplasia. PMID:24009312
Inferring Boolean network states from partial information. PMID:24006954
Developmental arrest of Drosophila survival motor neuron (Smn) mutants accounts for differences in expression of minor intron-containing genes. PMID:24006466
Essential role for Dnmt1 in the prevention and maintenance of MYC-induced T-cell lymphomas. PMID:24001767
Arabidopsis Polycomb Repressive Complex 2 binding sites contain putative GAGA factor binding motifs within coding regions of genes. PMID:24001316
Microarray-assisted fine mapping of quantitative trait loci on chromosome 15 for susceptibility to seizure-induced cell death in mice. PMID:24001120
Regulated expression of polysaccharide utilization and capsular biosynthesis loci in biofilm and planktonic Bacteroides thetaiotaomicron during growth in chemostats. PMID:23996813
Extensive cooperation of immune master regulators IRF3 and NFκB in RNA Pol II recruitment and pause release in human innate antiviral transcription. PMID:23994473
Pleiotropic effects of the trichloroethylene-associated P81S VHL mutation on metabolism, apoptosis, and ATM-mediated DNA damage response. PMID:23990666
PhenDisco: phenotype discovery system for the database of genotypes and phenotypes. PMID:23989082
RNA-Seq effectively monitors gene expression in Eutrema salsugineum plants growing in an extreme natural habitat and in controlled growth cabinet conditions. PMID:23984645
Screening biomarkers of prostate cancer by integrating microRNA and mRNA microarrays. PMID:23984644
Review of processing and analysis methods for DNA methylation array data. PMID:23982603
Retinoic acid-dependent regulation of miR-19 expression elicits vertebrate axis defects. PMID:23975936
Count-based differential expression analysis of RNA sequencing data using R and Bioconductor. PMID:23975260
Transposon mutagenesis identified chromosomal and plasmid genes essential for adaptation of the marine bacterium Dinoroseobacter shibae to anaerobic conditions. PMID:23974024
ARX regulates cortical intermediate progenitor cell expansion and upper layer neuron formation through repression of Cdkn1c. PMID:23968833
Expansion of multipotent stem cells from the adult human brain. PMID:23967194
Elucidation of how cancer cells avoid acidosis through comparative transcriptomic data analysis. PMID:23967163
Global expression profiling reveals genetic programs underlying the developmental divergence between mouse and human embryogenesis. PMID:23961710
Microenvironment-Dependent Phenotypic Changes in a SCID Mouse Model for Malignant Mesothelioma. PMID:23951555
Combining evidence of preferential gene-tissue relationships from multiple sources. PMID:23950964
Defining cell-type specificity at the transcriptional level in human disease. PMID:23950145
Gentrepid V2.0: a web server for candidate disease gene prediction. PMID:23947436
Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity. PMID:23945942
New network topology approaches reveal differential correlation patterns in breast cancer. PMID:23945349
Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis. PMID:23942234
A network integration approach to predict conserved regulators related to pathogenicity of influenza and SARS-CoV respiratory viruses. PMID:23935999
A strong anti-inflammatory signature revealed by liver transcription profiling of Tmprss6-/- mice. PMID:23922777
The tumour suppressor miR-34c targets MET in prostate cancer cells. PMID:23922103
Integrated genetic and epigenetic analysis of childhood acute lymphoblastic leukemia. PMID:23921123
Identification and systematic annotation of tissue-specific differentially methylated regions using the Illumina 450k array. PMID:23919675
Uterine NK cells regulate endometrial bleeding in women and are suppressed by the progesterone receptor modulator asoprisnil. PMID:23913972
Methodological approaches for using synchrotron X-ray fluorescence (SXRF) imaging as a tool in ionomics: examples from Arabidopsis thaliana. PMID:23912758
Serum from humans on long-term calorie restriction enhances stress resistance in cell culture. PMID:23912304
The molecular components of the extracellular protein-degradation pathways of the ectomycorrhizal fungus Paxillus involutus. PMID:23902518
Immune response of the Caribbean sea fan, Gorgonia ventalina, exposed to an Aplanochytrium parasite as revealed by transcriptome sequencing. PMID:23898300
Submergence confers immunity mediated by the WRKY22 transcription factor in Arabidopsis. PMID:23897923
Cold-induced changes in gene expression in brown adipose tissue, white adipose tissue and liver. PMID:23894377
Influenza A/Hong Kong/156/1997(H5N1) virus NS1 gene mutations F103L and M106I both increase IFN antagonism, virulence and cytoplasmic localization but differ in binding to RIG-I and CPSF30. PMID:23886034
Discovery of structural alterations in solid tumor oligodendroglioma by single molecule analysis. PMID:23885787
Microarray characterization of gene expression changes in blood during acute ethanol exposure. PMID:23883607
Identification of genes critical for resistance to infection by West Nile virus using RNA-Seq analysis. PMID:23881275
Regulation of lipid synthesis genes and milk fat production in human mammary epithelial cells during secretory activation. PMID:23880316
High-throughput identification of reference genes for research and clinical RT-qPCR analysis of breast cancer samples. PMID:23876162
Corruption of the intra-gene DNA methylation architecture is a hallmark of cancer. PMID:23874574
High-throughput miRNA and mRNA sequencing of paired colorectal normal, tumor and metastasis tissues and bioinformatic modeling of miRNA-1 therapeutic applications. PMID:23874421
LifeMap Discovery™: the embryonic development, stem cells, and regenerative medicine research portal. PMID:23874394
Effects of the plant growth-promoting bacterium Burkholderia phytofirmans PsJN throughout the life cycle of Arabidopsis thaliana. PMID:23869243
Insights into TREM2 biology by network analysis of human brain gene expression data. PMID:23855984
Conditional deletion of PTEN in peripheral T cells augments TCR-mediated activation but does not abrogate CD28 dependency or prevent anergy induction. PMID:23851688
Dynamic expression of 3' UTRs revealed by Poisson hidden Markov modeling of RNA-Seq: implications in gene expression profiling. PMID:23845781
Differences in the degree of cerulein-induced chronic pancreatitis in C57BL/6 mouse substrains lead to new insights in identification of potential risk factors in the development of chronic pancreatitis. PMID:23845568
Connectivity Mapping for Candidate Therapeutics Identification Using Next Generation Sequencing RNA-Seq Data. PMID:23840550
Impact of heat shock transcription factor 1 on global gene expression profiles in cells which induce either cytoprotective or pro-apoptotic response following hyperthermia. PMID:23834426
DNA methylation in nasal epithelial cells from smokers: identification of ULBP3-related effects. PMID:23831618
Utilization of never-medicated bipolar disorder patients towards development and validation of a peripheral biomarker profile. PMID:23826396
Assessing Global Transcriptome Changes in Response to South African Cassava Mosaic Virus [ZA-99] Infection in Susceptible Arabidopsis thaliana. PMID:23826319
Inferring epitopes of a polymorphic antigen amidst broadly cross-reactive antibodies using protein microarrays: a study of OspC proteins of Borrelia burgdorferi. PMID:23826301
Modeling exon expression using histone modifications. PMID:23825663
Genomic Stability of Aggregatibacter actinomycetemcomitans during Persistent Oral Infection in Human. PMID:23824402
microRNAs Involved in Regulating Spontaneous Recovery in Embolic Stroke Model. PMID:23823624
Integrative "omics"-approach discovers dynamic and regulatory features of bacterial stress responses. PMID:23818867
Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding. PMID:23818864
Linear combination test for gene set analysis of a continuous phenotype. PMID:23815123
Elevation of Eosinophil-Derived Neurotoxin in Plasma of the Subjects with Aspirin-Exacerbated Respiratory Disease: A Possible Peripheral Blood Protein Biomarker. PMID:23805255
The Y chromosome as a regulatory element shaping immune cell transcriptomes and susceptibility to autoimmune disease. PMID:23800453
Mining breast cancer genes with a network based noise-tolerant approach. PMID:23799982
A comparative analysis of transcription factor expression during metazoan embryonic development. PMID:23799133
eFG: an electronic resource for Fusarium graminearum. PMID:23798489
GeneMANIA prediction server 2013 update. PMID:23794635
Combined small RNA and degradome sequencing reveals novel miRNAs and their targets in response to low nitrate availability in maize. PMID:23788746
Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus. PMID:23788332
ATG4B/autophagin-1 regulates intestinal homeostasis and protects mice from experimental colitis. PMID:23782979
Inhibition of TGF-β and EGF pathway gene expression and migration of oral carcinoma cells by mucosa-associated lymphoid tissue 1. PMID:23778523
Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization. PMID:23777981
Role of the aryl hydrocarbon receptor in carcinogenesis and potential as a drug target. PMID:23771949
Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions. PMID:23771142
A Prader-Willi locus lncRNA cloud modulates diurnal genes and energy expenditure. PMID:23771028
Multiplex protein signature for the detection of bladder cancer in voided urine samples. PMID:23764080
Novel Integrative Genomics Approach for Associating GWAS Information with Intrinsic Subtypes of Breast Cancer. PMID:23761956
Molecular mechanisms of toxicity of silver nanoparticles in zebrafish embryos. PMID:23758687
The responses of Vitreoscilla hemoglobin-expressing hybrid aspen (Populus tremula × tremuloides) exposed to 24-h herbivory: expression of hemoglobin and stress-related genes in exposed and nonorthostichous leaves. PMID:23744275
A rapid transcriptome response is associated with desiccation resistance in aerially-exposed killifish embryos. PMID:23741328
Temporal induction of immunoregulatory processes coincides with age-dependent resistance to viral-induced type 1 diabetes. PMID:23739610
Selective tropism of Seneca Valley virus for variant subtype small cell lung cancer. PMID:23739064
Distinct roles of KAP1, HP1 and G9a/GLP in silencing of the two-cell-specific retrotransposon MERVL in mouse ES cells. PMID:23735015
A task-based approach for Gene Ontology evaluation. PMID:23734599
Rapid identification of novel immunodominant proteins and characterization of a specific linear epitope of Campylobacter jejuni. PMID:23734261
Drosophila host model reveals new enterococcus faecalis quorum-sensing associated virulence factors. PMID:23734216
Lytic infection of Lactococcus lactis by bacteriophages Tuc2009 and c2 triggers alternative transcriptional host responses. PMID:23728817
PMTED: a plant microRNA target expression database. PMID:23725466
Phenotypic characterization of retinoic acid differentiated SH-SY5Y cells by transcriptional profiling. PMID:23724009
Large scale expression changes of genes related to neuronal signaling and developmental processes found in lateral septum of postpartum outbred mice. PMID:23717492
Small RNA sequencing-microarray analyses in Parkinson leukocytes reveal deep brain stimulation-induced splicing changes that classify brain region transcriptomes. PMID:23717260
Recapitulating maladaptive, multiscale remodeling of failing myocardium on a chip. PMID:23716679
FeoB-mediated uptake of iron by Francisella tularensis. PMID:23716605
Metal dyshomeostasis and inflammation in Alzheimer's and Parkinson's diseases: possible impact of environmental exposures. PMID:23710288
Genes and pathways underlying regional and cell type changes in Alzheimer's disease. PMID:23705665
Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid. PMID:23705659
Ptc6 is required for proper rapamycin-induced down-regulation of the genes coding for ribosomal and rRNA processing proteins in S. cerevisiae. PMID:23704987
The genomic landscape of cohesin-associated chromatin interactions. PMID:23704192
Gene expression changes in the colon epithelium are similar to those of intact colon during late inflammation in interleukin-10 gene deficient mice. PMID:23700416
Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription. PMID:23699410
Cells surviving fractional killing by TRAIL exhibit transient but sustainable resistance and inflammatory phenotypes. PMID:23699397
Transcriptional profiling of swine lung tissue after experimental infection with Actinobacillus pleuropneumoniae. PMID:23698783
High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PMID:23696746
Probiotics VSL#3 protect against development of visceral pain in murine model of irritable bowel syndrome. PMID:23691109
Francisella tularensis subsp. tularensis induces a unique pulmonary inflammatory response: role of bacterial gene expression in temporal regulation of host defense responses. PMID:23690939
The neurotrophic compound J147 reverses cognitive impairment in aged Alzheimer's disease mice. PMID:23673233
Cross-platform microarray meta-analysis for the mouse jejunum selects novel reference genes with highly uniform levels of expression. PMID:23671661
Differences in gastric carcinoma microenvironment stratify according to EBV infection intensity: implications for possible immune adjuvant therapy. PMID:23671415
Effect of avian influenza A H5N1 infection on the expression of microRNA-141 in human respiratory epithelial cells. PMID:23663545
p63 attenuates epithelial to mesenchymal potential in an experimental prostate cell model. PMID:23658742
Female bias in Rhox6 and 9 regulation by the histone demethylase KDM6A. PMID:23658530
Targeting the treponemal microbiome of digital dermatitis infections by high-resolution phylogenetic analyses and comparison with fluorescent in situ hybridization. PMID:23658264
Iterative rank-order normalization of gene expression microarray data. PMID:23647742
Adaptation of the hydrocarbonoclastic bacterium Alcanivorax borkumensis SK2 to alkanes and toxic organic compounds: a physiological and transcriptomic approach. PMID:23645199
Genome-wide analysis of the GH3 family in apple (Malus × domestica). PMID:23638690
Age-mediated transcriptomic changes in adult mouse substantia nigra. PMID:23638090
The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates. PMID:23637639
Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PMID:23637631
Candidate cancer-targeting agents identified by expression-profiling arrays. PMID:23637543
Chapter 15: disease gene prioritization. PMID:23633938
Cluster analysis reveals differential transcript profiles associated with resistance training-induced human skeletal muscle hypertrophy. PMID:23632419
Chronic carvedilol treatment partially reverses the right ventricular failure transcriptional profile in experimental pulmonary hypertension. PMID:23632417
miR-222 contributes to sex-dimorphic cardiac eNOS expression via ets-1. PMID:23632416
A comprehensive analysis of adiponectin QTLs using SNP association, SNP cis-effects on peripheral blood gene expression and gene expression correlation identified novel metabolic syndrome (MetS) genes with potential role in carcinogenesis and systemic inflammation. PMID:23628382
Parity induces differentiation and reduces Wnt/Notch signaling ratio and proliferation potential of basal stem/progenitor cells isolated from mouse mammary epithelium. PMID:23621987
Interactions between immunity, proliferation and molecular subtype in breast cancer prognosis. PMID:23618380
Serum biomarkers for neurofibromatosis type 1 and early detection of malignant peripheral nerve-sheath tumors. PMID:23618374
Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge. PMID:23613991
Proteomic profiling of halloysite clay nanotube exposure in intestinal cell co-culture. PMID:23606564
MePR: a novel human mesenchymal progenitor model with characteristics of pluripotency. PMID:23597129
Drug target prediction and repositioning using an integrated network-based approach. PMID:23593264
The transcriptional response to nonself in the fungus Podospora anserina. PMID:23589521
Visualizing time-related data in biology, a review. PMID:23585583
An integrated approach to uncover driver genes in breast cancer methylation genomes. PMID:23579546
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves. PMID:23578292
Correction of spatial bias in oligonucleotide array data. PMID:23573083
miR-205 negatively regulates the androgen receptor and is associated with adverse outcome of prostate cancer patients. PMID:23571738
Key role for the alternative sigma factor, SigH, in the intracellular life of Mycobacterium avium subsp. paratuberculosis during macrophage stress. PMID:23569115
High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity. PMID:23565725
Next-generation sequencing and microarray-based interrogation of microRNAs from formalin-fixed, paraffin-embedded tissue: preliminary assessment of cross-platform concordance. PMID:23562991
Functional requirements for bacteriophage growth: gene essentiality and expression in mycobacteriophage Giles. PMID:23560716
Zebularine regulates early stages of mESC differentiation: effect on cardiac commitment. PMID:23559004
DNA copy number profiling reveals extensive genomic loss in hereditary BRCA1 and BRCA2 ovarian carcinomas. PMID:23558894
Global gene expression analysis reveals pathway differences between teratogenic and non-teratogenic exposure concentrations of bisphenol A and 17β-estradiol in embryonic zebrafish. PMID:23557687
Differential network analysis reveals genetic effects on catalepsy modules. PMID:23555609
Strong EGFR signaling in cell line models of ERBB2-amplified breast cancer attenuates response towards ERBB2-targeting drugs. PMID:23552733
curatedOvarianData: clinically annotated data for the ovarian cancer transcriptome. PMID:23550061
Following the 'tracks': Tramtrack69 regulates epithelial tube expansion in the Drosophila ovary through Paxillin, Dynamin, and the homeobox protein Mirror. PMID:23545328
Effect of acute stressor and serotonin transporter genotype on amygdala first wave transcriptome in mice. PMID:23536833
Stem cell-like gene expression in ovarian cancer predicts type II subtype and prognosis. PMID:23536770
Temozolomide-mediated DNA methylation in human myeloid precursor cells: differential involvement of intrinsic and extrinsic apoptotic pathways. PMID:23536437
Identification of Robust Pathway Markers for Cancer through Rank-Based Pathway Activity Inference. PMID:23533400
The computational analysis of human testis transcriptome reveals closer ties to pluripotency. PMID:23531778
Molars and incisors: show your microarray IDs. PMID:23531410
Genes associated with the cis-regulatory functions of intragenic LINE-1 elements. PMID:23530910
Key role for a glutathione transferase in multiple-herbicide resistance in grass weeds. PMID:23530204
Normalizing gene expression by quantitative PCR during somatic embryogenesis in two representative conifer species: Pinus pinaster and Picea abies. PMID:23529547
The neuron-specific chromatin regulatory subunit BAF53b is necessary for synaptic plasticity and memory. PMID:23525042
Differential expression analysis for pathways. PMID:23516350
PQBP1, a factor linked to intellectual disability, affects alternative splicing associated with neurite outgrowth. PMID:23512658
Post-weaning selenium and folate supplementation affects gene and protein expression and global DNA methylation in mice fed high-fat diets. PMID:23497688
Global mapping of transcription start sites and promoter motifs in the symbiotic α-proteobacterium Sinorhizobium meliloti 1021. PMID:23497287
AUREA: an open-source software system for accurate and user-friendly identification of relative expression molecular signatures. PMID:23496976
An inferential framework for biological network hypothesis tests. PMID:23496778
Arabidopsis copper transport protein COPT2 participates in the cross talk between iron deficiency responses and low-phosphate signaling. PMID:23487432
Altered subcellular localization of heat shock protein 90 is associated with impaired expression of the aryl hydrocarbon receptor pathway in dogs. PMID:23472125
MicroRNA-762 is upregulated in human corneal epithelial cells in response to tear fluid and Pseudomonas aeruginosa antigens and negatively regulates the expression of host defense genes encoding RNase7 and ST2. PMID:23469087
Delineating the cytogenomic and epigenomic landscapes of glioma stem cell lines. PMID:23468990
Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates. PMID:23467541
A sympathetic neuron autonomous role for Egr3-mediated gene regulation in dendrite morphogenesis and target tissue innervation. PMID:23467373
FBH1 protects melanocytes from transformation and is deregulated in melanomas. PMID:23466708
virtualArray: a R/bioconductor package to merge raw data from different microarray platforms. PMID:23452776
Aberrant gene expression in dogs with portosystemic shunts. PMID:23451256
Estrogen signalling and the metabolic syndrome: targeting the hepatic estrogen receptor alpha action. PMID:23451233
Genetic and genomic analysis of Rhizoctonia solani interactions with Arabidopsis; evidence of resistance mediated through NADPH oxidases. PMID:23451091
Cytosolic streaming in vegetative mycelium and aerial structures of Aspergillus niger. PMID:23450745
The effect of natamycin on the transcriptome of conidia of Aspergillus niger. PMID:23449730
Germination of conidia of Aspergillus niger is accompanied by major changes in RNA profiles. PMID:23449598
Two-way AIC: detection of differentially expressed genes from large scale microarray meta-dataset. PMID:23445621
Molecular characterisation of colour formation in the prawn Fenneropenaeus merguiensis. PMID:23441225
Loss of T cell progenitor checkpoint control underlies leukemia initiation in Rag1-deficient nonobese diabetic mice. PMID:23440410
Gene expression analyses implicate an alternative splicing program in regulating contractile gene expression and serum response factor activity in mice. PMID:23437181
Oil palm phenolics confer neuroprotective effects involving cognitive and motor functions in mice. PMID:23433062
Active subnetwork recovery with a mechanism-dependent scoring function; with application to angiogenesis and organogenesis studies. PMID:23432934
Effect of the leptin receptor Q223R polymorphism on the host transcriptome following infection with Entamoeba histolytica. PMID:23429533
MetaSeq: privacy preserving meta-analysis of sequencing-based association studies. PMID:23424140
Interpreting personal transcriptomes: personalized mechanism-scale profiling of RNA-seq data. PMID:23424121
Comparison of the transcriptomes of long-term label retaining-cells and control cells microdissected from mammary epithelium: an initial study to characterize potential stem/progenitor cells. PMID:23423481
Epigenetic epistatic interactions constrain the evolution of gene expression. PMID:23423319
An Integrative Genomics Approach for Associating GWAS Information with Triple-Negative Breast Cancer. PMID:23423317
Cross-species transcriptional network analysis reveals conservation and variation in response to metal stress in cyanobacteria. PMID:23421563
canEvolve: a web portal for integrative oncogenomics. PMID:23418540
Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq. PMID:23409192
Low-density lipoprotein receptor-related protein 1 variant interacts with saturated fatty acids in Puerto Ricans. PMID:23404896
The investigational Aurora kinase A inhibitor MLN8237 induces defects in cell viability and cell-cycle progression in malignant bladder cancer cells in vitro and in vivo. PMID:23403633
Frequencies and prognostic impact of RAS mutations in MLL-rearranged acute lymphoblastic leukemia in infants. PMID:23403319
Common bean (Phaseolus vulgaris L.) PvTIFY orchestrates global changes in transcript profile response to jasmonate and phosphorus deficiency. PMID:23402340
The mouse cytosine-5 RNA methyltransferase NSun2 is a component of the chromatoid body and required for testis differentiation. PMID:23401851
A local genetic algorithm for the identification of condition-specific microRNA-gene modules. PMID:23401666
Genomic responses in mouse models poorly mimic human inflammatory diseases. PMID:23401516
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. PMID:23396134
Developmental and environmental regulation of Aquaporin gene expression across Populus species: divergence or redundancy? PMID:23393587
Constitutive activation of NOTCH1 signaling in Sertoli cells causes gonocyte exit from quiescence. PMID:23391689
Characterization of transcriptional changes in ERG rearrangement-positive prostate cancer identifies the regulation of metabolic sensors such as neuropeptide Y. PMID:23390522
Novel genes underlying beta cell survival in metabolic stress. PMID:23390342
Borrelia host adaptation Regulator (BadR) regulates rpoS to modulate host adaptation and virulence factors in Borrelia burgdorferi. PMID:23387366
Feeder-free generation and long-term culture of human induced pluripotent stem cells using pericellular matrix of decidua derived mesenchymal cells. PMID:23383118
The 3D organization of the yeast genome correlates with co-expression and reflects functional relations between genes. PMID:23382942
Whole genome gene expression analysis reveals casiopeína-induced apoptosis pathways. PMID:23382936
Molecular profiling of cutaneous squamous cell carcinomas and actinic keratoses from organ transplant recipients. PMID:23379751
A DEAD box RNA helicase is critical for pre-mRNA splicing, cold-responsive gene regulation, and cold tolerance in Arabidopsis. PMID:23371945
A novel method for the normalization of microRNA RT-PCR data. PMID:23369279
Discovery and analysis of consistent active sub-networks in cancers. PMID:23368093
An antiviral role for antimicrobial peptides during the arthropod response to alphavirus replication. PMID:23365449
Release of severe acute respiratory syndrome coronavirus nuclear import block enhances host transcription in human lung cells. PMID:23365422
Serum antibodies to blood group A predict survival on PROSTVAC-VF. PMID:23362327
Gene expression profiling of early intervertebral disc degeneration reveals a down-regulation of canonical Wnt signaling and caveolin-1 expression: implications for development of regenerative strategies. PMID:23360510
Data submission and quality in microarray-based microRNA profiling. PMID:23358751
Centromere-like regions in the budding yeast genome. PMID:23349633
Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy. PMID:23344181
Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells. PMID:23341978
Alterations in cardiac DNA methylation in human dilated cardiomyopathy. PMID:23341106
MicroRNA paraffin-based studies in osteosarcoma reveal reproducible independent prognostic profiles at 14q32. PMID:23339462
Exact statistical tests for the intersection of independent lists of genes. PMID:23335952
Transcriptional profiling of the Arabidopsis abscission mutant hae hsl2 by RNA-Seq. PMID:23327667
Transcriptome profile analysis of young floral buds of fertile and sterile plants from the self-pollinated offspring of the hybrid between novel restorer line NR1 and Nsa CMS line in Brassica napus. PMID:23324545
Comparative gene expression between two yeast species. PMID:23324262
Formaldehyde and epigenetic alterations: microRNA changes in the nasal epithelium of nonhuman primates. PMID:23322811
MicroRNA expression profiling of peripheral blood samples predicts resistance to first-line sunitinib in advanced renal cell carcinoma patients. PMID:23308047
Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. PMID:23302187
Chapter 2: Data-driven view of disease biology. PMID:23300408
Chapter 3: Small molecules and disease. PMID:23300405
Deregulation of lipid metabolism pathway genes in nasopharyngeal carcinoma cells. PMID:23292678
StRAP: an integrated resource for profiling high-throughput cancer genomic data from stress response studies. PMID:23284744
A synthetic interaction screen identifies factors selectively required for proliferation and TERT transcription in p53-deficient human cancer cells. PMID:23284306
Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function. PMID:23284291
Meta-analytical biomarker search of EST expression data reveals three differentially expressed candidates. PMID:23282184
Elevated levels of circulating microRNA-200 family members correlate with serous epithelial ovarian cancer. PMID:23272653
Reuse of public genome-wide gene expression data. PMID:23269463
Pressure-overload hypertrophy of the developing heart reveals activation of divergent gene and protein pathways in the left and right ventricular myocardium. PMID:23262132
Unlocking the potential of publicly available microarray data using inSilicoDb and inSilicoMerging R/Bioconductor packages. PMID:23259851
A microRNA network regulates proliferative timing and extracellular matrix synthesis during cellular quiescence in fibroblasts. PMID:23259597
Cutoff Finder: a comprehensive and straightforward Web application enabling rapid biomarker cutoff optimization. PMID:23251644
Transcriptome profiling of rabbit parthenogenetic blastocysts developed under in vivo conditions. PMID:23251477
Chromosome 19 annotations with disease speciation: a first report from the Global Research Consortium. PMID:23249167
Toward a molecular pathogenic pathway for Yersinia pestis YopM. PMID:23248776
Microarray analysis of gene expression profiles in ripening pineapple fruits. PMID:23245313
ChIP-on-chip analysis identifies IL-22 as direct target gene of ectopically expressed FOXP3 transcription factor in human T cells. PMID:23244505
Whole-genome reconstruction and mutational signatures in gastric cancer. PMID:23237666
Validation of MIMGO: a method to identify differentially expressed GO terms in a microarray dataset. PMID:23232071
Clarifying off-target effects for torcetrapib using network pharmacology and reverse docking approach. PMID:23228038
Coral thermal tolerance: tuning gene expression to resist thermal stress. PMID:23226355
Temporal colonic gene expression profiling in the recurrent colitis model identifies early and chronic inflammatory processes. PMID:23226271
Exploiting parallel R in the cloud with SPRINT. PMID:23223611
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis. PMID:23222129
Identification of avian RIG-I responsive genes during influenza infection. PMID:23220072
Systems approaches to influenza-virus host interactions and the pathogenesis of highly virulent and pandemic viruses. PMID:23218769
Piwi-interacting RNAs protect DNA against loss during Oxytricha genome rearrangement. PMID:23217708
miRNA profiles of monocyte-lineage cells are consistent with complicated roles in HIV-1 restriction. PMID:23202444
Whole miRNome-wide differential co-expression of microRNAs. PMID:23200138
Using genome-wide expression profiling to define gene networks relevant to the study of complex traits: from RNA integrity to network topology. PMID:23195313
Comparative genomic hybridization and transcriptome analysis with a pan-genome microarray reveal distinctions between JP2 and non-JP2 genotypes of Aggregatibacter actinomycetemcomitans. PMID:23194436
NCBI GEO: archive for functional genomics data sets--update. PMID:23193258
Zic3 is required in the extra-cardiac perinodal region of the lateral plate mesoderm for left-right patterning and heart development. PMID:23184148
Identification of maternally-loaded RNA transcripts in unfertilized eggs of Tribolium castaneum. PMID:23181844
Correlation networks visualization. PMID:23181065
RiceFREND: a platform for retrieving coexpressed gene networks in rice. PMID:23180784
RiceXPro version 3.0: expanding the informatics resource for rice transcriptome. PMID:23180765
Vitamin D receptor signaling mechanisms: integrated actions of a well-defined transcription factor. PMID:23178257
Salinomycin induces cell death and differentiation in head and neck squamous cell carcinoma stem cells despite activation of epithelial-mesenchymal transition and Akt. PMID:23176396
Impact of Lactobacillus plantarum sortase on target protein sorting, gastrointestinal persistence, and host immune response modulation. PMID:23175652
Identification of novel genes involved in DNA damage response by screening a genome-wide Schizosaccharomyces pombe deletion library. PMID:23173672
Impact of 4 Lactobacillus plantarum capsular polysaccharide clusters on surface glycan composition and host cell signaling. PMID:23170998
Association of genes with physiological functions by comparative analysis of pooled expression microarray data. PMID:23170034
Building a statistical model for predicting cancer genes. PMID:23166609
The genetic regulation of the terminating phase of liver regeneration. PMID:23164283
Visual analysis of transcriptome data in the context of anatomical structures and biological networks. PMID:23162564
Identifying reference genes with stable expression from high throughput sequence data. PMID:23162540
Genomic profiling of rectal adenoma and carcinoma by array-based comparative genomic hybridization. PMID:23158542
Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs. PMID:23153069
Non-canonical TAF complexes regulate active promoters in human embryonic stem cells. PMID:23150797
Quality controls in cellular immunotherapies: rapid assessment of clinical grade dendritic cells by gene expression profiling. PMID:23147403
Maternal diets trigger sex-specific divergent trajectories of gene expression and epigenetic systems in mouse placenta. PMID:23144842
A characterization of the oral microbiome in allogeneic stem cell transplant patients. PMID:23144704
Computer-assisted annotation of murine Sertoli cell small RNA transcriptome. PMID:23136297
A Steiner tree-based method for biomarker discovery and classification in breast cancer metastasis. PMID:23134806
Pregnancy induces transcriptional activation of the peripheral innate immune system and increases oxidative DNA damage among healthy third trimester pregnant women. PMID:23133592
Theory on the coupled stochastic dynamics of transcription and splice-site recognition. PMID:23133354
miR-10b*, a master inhibitor of the cell cycle, is down-regulated in human breast tumours. PMID:23125021
DNA methylation profile of Aire-deficient mouse medullary thymic epithelial cells. PMID:23116172
Selective gene-expression profiling of migratory tumor cells in vivo predicts clinical outcome in breast cancer patients. PMID:23113900
Transcriptomic markers meet the real world: finding diagnostic signatures of corticosteroid treatment in commercial beef samples. PMID:23110699
An integrative computational systems biology approach identifies differentially regulated dynamic transcriptome signatures which drive the initiation of human T helper cell differentiation. PMID:23110343
Ultrastructural observation and gene expression profiling of Schistosoma japonicum derived from two natural reservoir hosts, water buffalo and yellow cattle. PMID:23110087
Carabin deficiency in B cells increases BCR-TLR9 costimulation-induced autoimmunity. PMID:23109291
Arabidopsis bZIP16 transcription factor integrates light and hormone signaling pathways to regulate early seedling development. PMID:23104829
Large-scale functional organization of long-range chromatin interaction networks. PMID:23103170
Revisiting global gene expression analysis. PMID:23101621
A candidate molecular biomarker panel for the detection of bladder cancer. PMID:23097579
Transcription factor ATF5 is required for terminal differentiation and survival of olfactory sensory neurons. PMID:23090999
The effect of curcumin on human bronchial epithelial cells exposed to fine particulate matter: a predictive analysis. PMID:23090021
Embedding siRNA sequences targeting apolipoprotein B100 in shRNA and miRNA scaffolds results in differential processing and in vivo efficacy. PMID:23089734
Gene expression anti-profiles as a basis for accurate universal cancer signatures. PMID:23088656
Comparative transcriptome analysis of tobacco (Nicotiana tabacum) leaves to identify aroma compound-related genes expressed in different cultivated regions. PMID:23079704
Molecular deregulation induced by silencing of the high mobility group protein A2 gene in retinoblastoma cells. PMID:23077401
Inflammatory mediators alter the astrocyte transcriptome and calcium signaling elicited by multiple G-protein-coupled receptors. PMID:23077035
Conserved DNA methylation patterns in healthy blood cells and extensive changes in leukemia measured by a new quantitative technique. PMID:23075513
Inference of temporally varying Bayesian networks. PMID:23074260
Gene expression profiling unravels cancer-related hepatic molecular signatures in steatohepatitis but not in steatosis. PMID:23071592
Proteomic analysis of mouse models of Niemann-Pick C disease reveals alterations in the steady-state levels of lysosomal proteins within the brain. PMID:23070805
Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays. PMID:23062031
DAMTC regulates cytoskeletal reorganization and cell motility in human lung adenocarcinoma cell line: an integrated proteomics and transcriptomics approach. PMID:23059821
Integrating constitutive gene expression and chemoactivity: mining the NCI60 anticancer screen. PMID:23056181
Gene expression responses to FUS, EWS, and TAF15 reduction and stress granule sequestration analyses identifies FET-protein non-redundant functions. PMID:23049996
miR-BAG: bagging based identification of microRNA precursors. PMID:23049860
PAGED: a pathway and gene-set enrichment database to enable molecular phenotype discoveries. PMID:23046413
Precise probes of type II interferon activity define the origin of interferon signatures in target tissues in rheumatic diseases. PMID:23045702
The zinc-responsive regulon of Neisseria meningitidis comprises 17 genes under control of a Zur element. PMID:23043002
ZNF385B and VEGFA are strongly differentially expressed in serous ovarian carcinomas and correlate with survival. PMID:23029477
MicroRNA expression profiles of whole blood in lung adenocarcinoma. PMID:23029380
Analyzing gene expression from whole tissue vs. different cell types reveals the central role of neurons in predicting severity of Alzheimer's disease. PMID:23029292
Cooperativity of stress-responsive transcription factors in core hypoxia-inducible factor binding regions. PMID:23029193
Melanoma-associated cancer-testis antigen 16 (CT16) regulates the expression of apoptotic and antiapoptotic genes and promotes cell survival. PMID:23028975
Transcriptome tomography for brain analysis in the web-accessible anatomical space. PMID:23028969
Microarray analysis of microRNA expression during axolotl limb regeneration. PMID:23028429
Convergence of the transcriptional responses to heat shock and singlet oxygen stresses. PMID:23028346
Tissue-specific functional networks for prioritizing phenotype and disease genes. PMID:23028291
Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity. PMID:23025749
Rhesus monkey cumulus cells revert to a mural granulosa cell state after an ovulatory stimulus. PMID:23008515
Exposure to solute stress affects genome-wide expression but not the polycyclic aromatic hydrocarbon-degrading activity of Sphingomonas sp. strain LH128 in biofilms. PMID:23001650
Transcriptome-wide analysis of exosome targets. PMID:23000172
Evolutionary insights into scleractinian corals using comparative genomic hybridizations. PMID:22994626
Poplar wood rays are involved in seasonal remodeling of tree physiology. PMID:22992511
Cis-regulatory signatures of orthologous stress-associated bZIP transcription factors from rice, sorghum and Arabidopsis based on phylogenetic footprints. PMID:22992304
Transcriptional profiling in facioscapulohumeral muscular dystrophy to identify candidate biomarkers. PMID:22988124
Transcriptomic changes and signalling pathways induced by arsenic stress in rice roots. PMID:22987115
Bioinformatics for cancer immunology and immunotherapy. PMID:22986455
Myelin-derived lipids modulate macrophage activity by liver X receptor activation. PMID:22984598
Immune complex signatures of patients with active and inactive SLE revealed by multiplex protein binding analysis on antigen microarrays. PMID:22984570
MMP7 is a target of the tumour-associated antigen EpCAM. PMID:22974215
oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets. PMID:22973536
Transcriptional signatures as a disease-specific and predictive inflammatory biomarker for type 1 diabetes. PMID:22972474
Microarray and proteomic analysis of the cardioprotective effects of cold blood cardioplegia in the mature and aged male and female. PMID:22968637
Global analysis of genome, transcriptome and proteome reveals the response to aneuploidy in human cells. PMID:22968442
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Integrative systems biology approaches in asthma pharmacogenomics. PMID:22966888
Transcriptional regulation of the GPX1 gene by TFAP2C and aberrant CpG methylation in human breast cancer. PMID:22964634
Transcriptome analysis of rice root responses to potassium deficiency. PMID:22963580
Proteomic profiling identifies dysregulated pathways in small cell lung cancer and novel therapeutic targets including PARP1. PMID:22961666
Short-term erythropoietin treatment does not substantially modulate monocyte transcriptomes of patients with combined heart and renal failure. PMID:22957013
ATXN2-CAG42 sequesters PABPC1 into insolubility and induces FBXW8 in cerebellum of old ataxic knock-in mice. PMID:22956915
Sperm mRNA transcripts are indicators of sub-chronic low dose testicular injury in the Fischer 344 rat. PMID:22952946
Expression profile of telomere-associated genes in multiple myeloma. PMID:22947336
Glucosylated hydroxymethyluracil, DNA base J, prevents transcriptional readthrough in Leishmania. PMID:22939620
Identification of the Streptococcus mutans LytST two-component regulon reveals its contribution to oxidative stress tolerance. PMID:22937869
Gene isoform specificity through enhancer-associated antisense transcription. PMID:22937057
Urinary BTA: indicator of bladder cancer or of hematuria. PMID:22932760
Gelsolin induces colorectal tumor cell invasion via modulation of the urokinase-type plasminogen activator cascade. PMID:22927998
Arabinose is metabolized via a phosphoketolase pathway in Clostridium acetobutylicum ATCC 824. PMID:22922942
Prediction of gene network models in limb muscle precursors. PMID:22917675
Systematic prediction of cis-regulatory elements in the Chlamydomonas reinhardtii genome using comparative genomics. PMID:22915576
Global changes in gene expression during compatible and incompatible interactions of cowpea (Vigna unguiculata L.) with the root parasitic angiosperm Striga gesnerioides. PMID:22900582
Emerging putative biomarkers: the role of alpha 2 and 6 integrins in susceptibility, treatment, and prognosis. PMID:22900191
A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia. PMID:22898401
H2.0-like homeobox regulates early hematopoiesis and promotes acute myeloid leukemia. PMID:22897850
Assessing numerical dependence in gene expression summaries with the jackknife expression difference. PMID:22876276
Snf1-related kinase inhibits colon cancer cell proliferation through calcyclin-binding protein-dependent reduction of β-catenin. PMID:22874833
miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets. PMID:22870325
Regulation and gene expression profiling of NKG2D positive human cytomegalovirus-primed CD4+ T-cells. PMID:22870231
Detection of biomarkers for hepatocellular carcinoma using a hybrid univariate gene selection methods. PMID:22867264
CD8 lineage-specific regulation of interleukin-7 receptor expression by the transcriptional repressor Gfi1. PMID:22865857
Genome-wide responses of the model archaeon Halobacterium sp. strain NRC-1 to oxygen limitation. PMID:22865851
Comparative transcriptional analysis of clinically relevant heat stress response in Clostridium difficile strain 630. PMID:22860125
Discovery and validation of gene classifiers for endocrine-disrupting chemicals in zebrafish (danio rerio). PMID:22849515
Genome-wide transcriptional response of the archaeon Thermococcus gammatolerans to cadmium. PMID:22848664
One Hand Clapping: detection of condition-specific transcription factor interactions from genome-wide gene activity data. PMID:22844089
Coex-Rank: An approach incorporating co-expression information for combined analysis of microarray data. PMID:22842118
Subnetwork-based analysis of chronic lymphocytic leukemia identifies pathways that associate with disease progression. PMID:22837534
GRHL3/GET1 and trithorax group members collaborate to activate the epidermal progenitor differentiation program. PMID:22829784
A microRNA activity map of human mesenchymal tumors: connections to oncogenic pathways; an integrative transcriptomic study. PMID:22823907
The emerging paradigm of network medicine in the study of human disease. PMID:22821909
C3KO mouse expression analysis: downregulation of the muscular dystrophy Ky protein and alterations in muscle aging. PMID:22820870
Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides. PMID:22815952
Role of heat-stable enterotoxins in the induction of early immune responses in piglets after infection with enterotoxigenic Escherichia coli. PMID:22815904
Twist1 transcriptional targets in the developing atrio-ventricular canal of the mouse. PMID:22815831
Gene Expression Commons: an open platform for absolute gene expression profiling. PMID:22815738
Microarray analysis of Xenopus endoderm expressing Ptf1a. PMID:22815262
Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes. PMID:22808168
Transcriptomes reveal genetic signatures underlying physiological variations imposed by different fermentation conditions in Lactobacillus plantarum. PMID:22802930
Increased immune gene expression and immune cell infiltration in high-grade astrocytoma distinguish long-term from short-term survivors. PMID:22802421
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
Differences in gene expression between strabismic and normal human extraocular muscles. PMID:22786898
An automated bayesian framework for integrative gene expression analysis and predictive medicine. PMID:22779059
Dual RpoH sigma factors and transcriptional plasticity in a symbiotic bacterium. PMID:22773790
Cytotoxic mechanisms employed by mouse T cells to destroy pancreatic β-cells. PMID:22773667
A comparative analysis of biclustering algorithms for gene expression data. PMID:22772837
SFTA2--a novel secretory peptide highly expressed in the lung--is modulated by lipopolysaccharide but not hyperoxia. PMID:22768197
A retinoblastoma orthologue is a major regulator of S-phase, mitotic, and developmental gene expression in Dictyostelium. PMID:22768168
A single promoter inversion switches Photorhabdus between pathogenic and mutualistic states. PMID:22767929
HP1a targets the Drosophila KDM4A demethylase to a subset of heterochromatic genes to regulate H3K36me3 levels. PMID:22761891
The maximum clique enumeration problem: algorithms, applications, and implementations. PMID:22759429
The Choice between MapMan and Gene Ontology for Automated Gene Function Prediction in Plant Science. PMID:22754563
The chemoattractant chemerin suppresses melanoma by recruiting natural killer cell antitumor defenses. PMID:22753924
Computational tools for prioritizing candidate genes: boosting disease gene discovery. PMID:22751426
Insertion-deletions in a FADS2 intron 1 conserved regulatory locus control expression of fatty acid desaturases 1 and 2 and modulate response to simvastatin. PMID:22748975
Conserved rules govern genetic interaction degree across species. PMID:22747640
Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. PMID:22740638
Toxicogenomic profiles in relation to maternal immunotoxic exposure and immune functionality in newborns. PMID:22738990
Linking the transcriptional profiles and the physiological states of Mycobacterium tuberculosis during an extended intracellular infection. PMID:22737072
Potassium starvation in yeast: mechanisms of homeostasis revealed by mathematical modeling. PMID:22737060
Identification of androgen-regulated genes in human prostate. PMID:22735730
WhiB5, a transcriptional regulator that contributes to Mycobacterium tuberculosis virulence and reactivation. PMID:22733573
Identification of yeast genes that confer resistance to chitosan oligosaccharide (COS) using chemogenomics. PMID:22727066
The heterotrimeric laminin coiled-coil domain exerts anti-adhesive effects and induces a pro-invasive phenotype. PMID:22723936
Detection of simultaneous group effects in microRNA expression and related target gene sets. PMID:22723856
Generation of Calhm1 knockout mouse and characterization of calhm1 gene expression. PMID:22723178
Prenatal arsenic exposure alters gene expression in the adult liver to a proinflammatory state contributing to accelerated atherosclerosis. PMID:22719926
Down-weighting overlapping genes improves gene set analysis. PMID:22713124
Cancer/testis antigens and urological malignancies. PMID:22710665
ERK5 protein promotes, whereas MEK1 protein differentially regulates, the Toll-like receptor 2 protein-dependent activation of human endothelial cells and monocytes. PMID:22707717
Long noncoding RNAs in C. elegans. PMID:22707570
Labellum transcriptome reveals alkene biosynthetic genes involved in orchid sexual deception and pollination-induced senescence. PMID:22706647
Genetic variation in T-box binding element functionally affects SCN5A/SCN10A enhancer. PMID:22706305
The application of nonsense-mediated mRNA decay inhibition to the identification of breast cancer susceptibility genes. PMID:22703186
Gene expression changes in the septum: possible implications for microRNAs in sculpting the maternal brain. PMID:22701680
Extensive gene-specific translational reprogramming in a model of B cell differentiation and Abl-dependent transformation. PMID:22693568
MiR-146a as marker of senescence-associated pro-inflammatory status in cells involved in vascular remodelling. PMID:22692818
Global gene profiling of VCP-associated inclusion body myopathy. PMID:22686199
Insecticide resistance mechanisms in the green peach aphid Myzus persicae (Hemiptera: Aphididae) I: A transcriptomic survey. PMID:22685538
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. PMID:22685160
Neonatal diethylstilbestrol exposure alters the metabolic profile of uterine epithelial cells. PMID:22679223
Identifying dysregulated pathways in cancers from pathway interaction networks. PMID:22676414
A new mouse model for mania shares genetic correlates with human bipolar disorder. PMID:22675514
Genomic islands as a marker to differentiate between clinical and environmental Burkholderia pseudomallei. PMID:22675491
Phthalate exposure changes the metabolic profile of cardiac muscle cells. PMID:22672789
Coculture with hematopoietic stem cells protects cardiomyocytes against apoptosis via paracrine activation of AKT. PMID:22672705
Gene regulation of UDP-galactose synthesis and transport: potential rate-limiting processes in initiation of milk production in humans. PMID:22649065
A systems biology approach reveals common metastatic pathways in osteosarcoma. PMID:22640921
Gene regulation by cytokinin in Arabidopsis. PMID:22639635
SLocX: Predicting Subcellular Localization of Arabidopsis Proteins Leveraging Gene Expression Data. PMID:22639594
Differential gene expression in the EphA4 knockout spinal cord and analysis of the inflammatory response following spinal cord injury. PMID:22629434
Systems biology approach to identify gene network signatures for colorectal cancer. PMID:22629282
The practical effect of batch on genomic prediction. PMID:22611599
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. PMID:22609849
Comparative transcriptomic analysis of streptococcus pseudopneumoniae with viridans group streptococci. PMID:22607240
Genome-wide recruitment to Polycomb-modified chromatin and activity regulation of the synovial sarcoma oncogene SYT-SSX2. PMID:22594313
Observation of dually decoded regions of the human genome using ribosome profiling data. PMID:22593554
Hypocotyl transcriptome reveals auxin regulation of growth-promoting genes through GA-dependent and -independent pathways. PMID:22590525
Learning transcriptional regulatory relationships using sparse graphical models. PMID:22586449
miRFANs: an integrated database for Arabidopsis thaliana microRNA function annotations. PMID:22583976
Genome-wide analysis of p63 binding sites identifies AP-2 factors as co-regulators of epidermal differentiation. PMID:22573176
Growth factor TGF-β induces intestinal epithelial cell (IEC-6) differentiation: miR-146b as a regulatory component in the negative feedback loop. PMID:22570175
Identity by descent mapping of founder mutations in cancer using high-resolution tumor SNP data. PMID:22567117
Defining the limits of physiological plasticity: how gene expression can assess and predict the consequences of ocean change. PMID:22566679
Identification of genes with a correlation between copy number and expression in gastric cancer. PMID:22559327
Regulation of motility of myogenic cells in filling limb muscle anlagen by Pitx2. PMID:22558231
Utilizing RNA-Seq data for de novo coexpression network inference. PMID:22556371
Genomic analysis of reactive astrogliosis. PMID:22553043
Paternal Benzo[a]pyrene Exposure Modulates MicroRNA Expression Patterns in the Developing Mouse Embryo. PMID:22548065
A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. PMID:22546241
mRNA-Seq analysis of the Pseudoperonospora cubensis transcriptome during cucumber (Cucumis sativus L.) infection. PMID:22545137
Expression profiling of Cucumis sativus in response to infection by Pseudoperonospora cubensis. PMID:22545095
Erythroid-specific transcriptional changes in PBMCs from pulmonary hypertension patients. PMID:22545094
NLRP10 is a NOD-like receptor essential to initiate adaptive immunity by dendritic cells. PMID:22538615
Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR. PMID:22537494
Characterization of the transcriptome profiles related to globin gene switching during in vitro erythroid maturation. PMID:22537182
Chemocentric informatics approach to drug discovery: identification and experimental validation of selective estrogen receptor modulators as ligands of 5-hydroxytryptamine-6 receptors and as potential cognition enhancers. PMID:22537153
Modulation of activation-associated host cell gene expression by the apicomplexan parasite Theileria annulata. PMID:22533473
Transcriptional portrait of Actinobacillus pleuropneumoniae during acute disease--potential strategies for survival and persistence in the host. PMID:22530048
Oil palm phenolics attenuate changes caused by an atherogenic diet in mice. PMID:22527284
Dynamic antagonism between phytochromes and PIF family basic helix-loop-helix factors induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis. PMID:22517317
Microarray analysis of gene expression in West Nile virus-infected human retinal pigment epithelium. PMID:22509103
How can microarrays unlock asthma? PMID:22500180
Continuous infusion of 20-hydroxyecdysone increased mass of triceps brachii in C57BL/6 mice. PMID:22495969
Neuronal and epithelial cell rescue resolves chronic systemic inflammation in the lipid storage disorder Niemann-Pick C. PMID:22493001
Comparative analysis of Lactobacillus plantarum WCFS1 transcriptomes by using DNA microarray and next-generation sequencing technologies. PMID:22492454
A novel class of cysteine protease receptors that mediate lysosomal transport. PMID:22486861
Integrated inference and analysis of regulatory networks from multi-level measurements. PMID:22482944
Population differences in transcript-regulator expression quantitative trait loci. PMID:22479588
Critical evaluation of imprinted gene expression by RNA-Seq: a new perspective. PMID:22479196
Virulence regulator EspR of Mycobacterium tuberculosis is a nucleoid-associated protein. PMID:22479184
The ectomycorrhizal fungus Paxillus involutus converts organic matter in plant litter using a trimmed brown-rot mechanism involving Fenton chemistry. PMID:22469289
Epigenetic variability in cells of normal cytology is associated with the risk of future morphological transformation. PMID:22453031
A previously unknown oxalyl-CoA synthetase is important for oxalate catabolism in Arabidopsis. PMID:22447686
Transcriptional architecture of the primate neocortex. PMID:22445337
T-2 toxin induced Salmonella Typhimurium intoxication results in decreased Salmonella numbers in the cecum contents of pigs, despite marked effects on Salmonella-host cell interactions. PMID:22440148
Isoniazid resistance without a loss of fitness in Mycobacterium tuberculosis. PMID:22434196
The Saccharomyces cerevisiae Nrd1-Nab3 transcription termination pathway acts in opposition to Ras signaling and mediates response to nutrient depletion. PMID:22431520
Old and new stories: revelations from functional analysis of the bovine mammary transcriptome during the lactation cycle. PMID:22428004
Sleeping Beauty mutagenesis reveals cooperating mutations and pathways in pancreatic adenocarcinoma. PMID:22421440
Role of the gut endoderm in relaying left-right patterning in mice. PMID:22412348
A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs. PMID:22408077
Translation initiation factor eIF4E is a target for tumor cell radiosensitization. PMID:22397984
Function-based discovery of significant transcriptional temporal patterns in insulin stimulated muscle cells. PMID:22396763
Genetic basis of hidden phenotypic variation revealed by increased translational readthrough in yeast. PMID:22396662
Deciphering the molecular basis of wine yeast fermentation traits using a combined genetic and genomic approach. PMID:22384338
Identification of new genes involved in human adipogenesis and fat storage. PMID:22384002
Ten years of pathway analysis: current approaches and outstanding challenges. PMID:22383865
Plastids are major regulators of light signaling in Arabidopsis. PMID:22383539
Nrf2 links epidermal barrier function with antioxidant defense. PMID:22383093
Antimicrobial effect and mode of action of terpeneless cold-pressed Valencia orange essential oil on methicillin-resistant Staphylococcus aureus. PMID:22372962
Low red/far-red ratios reduce Arabidopsis resistance to Botrytis cinerea and jasmonate responses via a COI1-JAZ10-dependent, salicylic acid-independent mechanism. PMID:22371506
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. PMID:22369646
Genetic copy number variants in myocardial infarction patients with hyperlipidemia. PMID:22369086
Expression of the Arabidopsis thaliana BBX32 gene in soybean increases grain yield. PMID:22363475
Investigations on transgenerational epigenetic response down the male line in F2 pigs. PMID:22359544
Identifying neighborhoods of coordinated gene expression and metabolite profiles. PMID:22355360
Genome-Wide Scale-Free Network Inference for Candida albicans. PMID:22355294
DNA replication stress differentially regulates G1/S genes via Rad53-dependent inactivation of Nrm1. PMID:22333915
Gene expression profiling of primary male breast cancers reveals two unique subgroups and identifies N-acetyltransferase-1 (NAT1) as a novel prognostic biomarker. PMID:22333393
Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. PMID:22328084
Strain-related differences in antibody-mediated changes in gene expression are associated with differences in capsule and location of binding. PMID:22327012
Regulation of microRNA expression in the heart by the ATF6 branch of the ER stress response. PMID:22326432
The latent membrane protein 1 (LMP1) oncogene of Epstein-Barr virus can simultaneously induce and inhibit apoptosis in B cells. PMID:22318153
Genome-wide definition of the SigF regulon in Mycobacterium tuberculosis. PMID:22307756
MYC-driven tumorigenesis is inhibited by WRN syndrome gene deficiency. PMID:22301954
Expressed sequences and polymorphisms in rohu carp (Labeo rohita, Hamilton) revealed by mRNA-seq. PMID:22298294
A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PMID:22295108
Genome-wide repression of NF-κB target genes by transcription factor MIBP1 and its modulation by O-linked β-N-acetylglucosamine (O-GlcNAc) transferase. PMID:22294689
Widespread RNA 3'-end oligouridylation in mammals. PMID:22291204
Colorectal adenoma to carcinoma progression is accompanied by changes in gene expression associated with ageing, chromosomal instability, and fatty acid metabolism. PMID:22278361
Functional genomics resources for the North Atlantic copepod, Calanus finmarchicus: EST database and physiological microarray. PMID:22277925
Interleukin-1 receptor-associated kinase-3 is a key inhibitor of inflammation in obesity and metabolic syndrome. PMID:22272346
Toxicogenomic biomarkers for liver toxicity. PMID:22271975
The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. PMID:22267485
Integrating heterogeneous high-throughput data for meta-dimensional pharmacogenomics and disease-related studies. PMID:22256870
Nearest hyperplane distance neighbor clustering algorithm applied to gene co-expression analysis in Alzheimer's disease. PMID:22255598
Measures of association for identifying microRNA-mRNA pairs of biological interest. PMID:22253745
MicroRNAs control neurobehavioral development and function in zebrafish. PMID:22253472
Widespread translational control contributes to the regulation of Arabidopsis photomorphogenesis. PMID:22252389
Hyperthermophilic Thermotoga species differ with respect to specific carbohydrate transporters and glycoside hydrolases. PMID:22247137
Ars2 promotes proper replication-dependent histone mRNA 3' end formation. PMID:22244333
The absence of P2X7 receptors (P2rx7) on non-haematopoietic cells leads to selective alteration in mood-related behaviour with dysregulated gene expression and stress reactivity in mice. PMID:22243662
Global gene expression analysis of the interaction between cancer cells and osteoblasts to predict bone metastasis in breast cancer. PMID:22235336
Systems-based approaches to cardiovascular disease. PMID:22231714
Combination of a novel gene expression signature with a clinical nomogram improves the prediction of survival in high-risk bladder cancer. PMID:22228636
GATA4 expression is primarily regulated via a miR-26b-dependent post-transcriptional mechanism during cardiac hypertrophy. PMID:22219180
Differential gene expression from microarray analysis distinguishes woven and lamellar bone formation in the rat ulna following mechanical loading. PMID:22216249
Preservation of ranking order in the expression of human Housekeeping genes. PMID:22216246
Affymetrix GeneChip microarray preprocessing for multivariate analyses. PMID:22210854
Deletion of KDM6A, a histone demethylase interacting with MLL2, in three patients with Kabuki syndrome. PMID:22197486
The re-establishment of desiccation tolerance in germinated Arabidopsis thaliana seeds and its associated transcriptome. PMID:22195004
Insights into hypoxic systemic responses based on analyses of transcriptional regulation in Arabidopsis. PMID:22194941
Influence of 17β-estradiol on gene expression of Paracoccidioides during mycelia-to-yeast transition. PMID:22194832
Activation of endothelial TLR2 by bacterial lipoprotein upregulates proteins specific for the neutrophil response. PMID:22186927
Identification of proprotein convertase substrates using genome-wide expression correlation analysis. PMID:22185580
Complex human glucocorticoid receptor dim mutations define glucocorticoid induced apoptotic resistance in bone cells. PMID:22174376
Small interfering RNA against transcription factor STAT6 leads to increased cholesterol synthesis in lung cancer cell lines. PMID:22162773
Histone deacetylase inhibition decreases proliferation and potentiates the effect of ionizing radiation in atypical teratoid/rhabdoid tumor cells. PMID:22156471
Changes in transcriptional orientation are associated with increases in evolutionary rates of enterobacterial genes. PMID:22152004
Stress induced Salmonella Typhimurium recrudescence in pigs coincides with cortisol induced increased intracellular proliferation in macrophages. PMID:22151081
Segmental chromosomal alterations lead to a higher risk of relapse in infants with MYCN-non-amplified localised unresectable/disseminated neuroblastoma (a SIOPEN collaborative study). PMID:22146831
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
Loss of Dnmt3b function upregulates the tumor modifier Ment and accelerates mouse lymphomagenesis. PMID:22133874
Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments. PMID:22133085
Genome-wide identification of microRNAs in response to low nitrate availability in maize leaves and roots. PMID:22132192
Transcriptomic analyses during the transition from biomass production to lipid accumulation in the oleaginous yeast Yarrowia lipolytica. PMID:22132183
Strategies to explore functional genomics data sets in NCBI's GEO database. PMID:22130872
Isolation of novel multipotent neural crest-derived stem cells from adult human inferior turbinate. PMID:22128806
Gene expression and network-based analysis reveals a novel role for hsa-miR-9 and drug control over the p38 network in glioblastoma multiforme progression. PMID:22122801
MetaQC: objective quality control and inclusion/exclusion criteria for genomic meta-analysis. PMID:22116060
FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomas. PMID:22113614
Antisense suppression of the small chloroplast protein CP12 in tobacco: a transcriptional viewpoint. PMID:22112458
RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew. PMID:22112294
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PMID:22110609
eXframe: reusable framework for storage, analysis and visualization of genomics experiments. PMID:22103807
Average rank-based score to measure deregulation of molecular pathway gene sets. PMID:22096597
Evaluation of the NOD/SCID xenograft model for glucocorticoid-regulated gene expression in childhood B-cell precursor acute lymphoblastic leukemia. PMID:22093874
Perturbation of FliL interferes with Proteus mirabilis swarmer cell gene expression and differentiation. PMID:22081397
Tbx20 regulates a genetic program essential to adult mouse cardiomyocyte function. PMID:22080862
Integrated transcriptome and binding sites analysis implicates E2F in the regulation of self-renewal in human pluripotent stem cells. PMID:22076139
Evolutionary history and functional characterization of the amphibian xenosensor CAR. PMID:22074953
Genome-wide binding map of the HIV-1 Tat protein to the human genome. PMID:22073215
Identification and characterization of Hoxa9 binding sites in hematopoietic cells. PMID:22072553
Modeling the transcriptional consequences of epidermal growth factor receptor ablation in Ras-initiated squamous cancer. PMID:22068661
Identification of transcriptome profiles and signaling pathways for the allelochemical juglone in rice roots. PMID:22065257
Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar. PMID:22058225
PlantNATsDB: a comprehensive database of plant natural antisense transcripts. PMID:22058132
Effect of rickettsial toxin VapC on its eukaryotic host. PMID:22046301
An integrated transcriptomic and meta-analysis of hepatoma cells reveals factors that influence susceptibility to HCV infection. PMID:22046242
Network based consensus gene signatures for biomarker discovery in breast cancer. PMID:22046239
Effect of L-carnitine on the hepatic transcript profile in piglets as animal model. PMID:22040461
Anthrax lethal toxin-induced gene expression changes in mouse lung. PMID:22039574
Targeted gene-silencing reveals the functional significance of myocardin signaling in the failing heart. PMID:22028870
Transcriptome-wide binding sites for components of the Saccharomyces cerevisiae non-poly(A) termination pathway: Nrd1, Nab3, and Sen1. PMID:22028667
Graph constrained discriminant analysis: a new method for the integration of a graph into a classification process. PMID:22022543
The molecular signature underlying the thymic migration and maturation of TCRαβ+ CD4+ CD8 thymocytes. PMID:22022412
A non-canonical DNA structure is a binding motif for the transcription factor SP1 in vitro. PMID:22021377
Transcriptional regulation of co-expressed microRNA target genes. PMID:22002038
Expression of FACT in mammalian tissues suggests its role in maintaining of undifferentiated state of cells. PMID:21998152
Reprogramming of mesenchymal stem cells by the synovial sarcoma-associated oncogene SYT-SSX2. PMID:21996728
Systematic mapping of two component response regulators to gene targets in a model sulfate reducing bacterium. PMID:21992415
Microarray analysis of genes associated with cell surface NIS protein levels in breast cancer. PMID:21989294
A gene signature in histologically normal surgical margins is predictive of oral carcinoma recurrence. PMID:21989116
Skin healing and scale regeneration in fed and unfed sea bream, Sparus auratus. PMID:21981800
Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in maize. PMID:21980173
Sildenafil improves epicenter vascular perfusion but not hindlimb functional recovery after contusive spinal cord injury in mice. PMID:21970599
Molecular profiling of stomatal meristemoids reveals new component of asymmetric cell division and commonalities among stem cell populations in Arabidopsis. PMID:21963668
Classification of unknown primary tumors with a data-driven method based on a large microarray reference database. PMID:21955394
Regulation of IL-2 gene expression by Siva and FOXP3 in human T cells. PMID:21955384
Yeast Nrd1, Nab3, and Sen1 transcriptome-wide binding maps suggest multiple roles in post-transcriptional RNA processing. PMID:21954178
The transcriptome of a human polar body accurately reflects its sibling oocyte. PMID:21953461
Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. PMID:21951686
Discovering biological connections between experimental conditions based on common patterns of differential gene expression. PMID:21951600
Integrated analyses of copy number variations and gene expression in lung adenocarcinoma. PMID:21935476
Transcriptional profiling of chondrodysplasia growth plate cartilage reveals adaptive ER-stress networks that allow survival but disrupt hypertrophy. PMID:21935428
Ligand-independent phosphorylation of the glucocorticoid receptor integrates cellular stress pathways with nuclear receptor signaling. PMID:21930780
High IGFBP2 expression correlates with tumor severity in pediatric rhabdomyosarcoma. PMID:21924226
Insights into eyestalk ablation mechanism to induce ovarian maturation in the black tiger shrimp. PMID:21915325
Ehrlichia chaffeensis transcriptome in mammalian and arthropod hosts reveals differential gene expression and post transcriptional regulation. PMID:21915290
Ranking candidate disease genes from gene expression and protein interaction: a Katz-centrality based approach. PMID:21912686
A promoter DNA demethylation landscape of human hematopoietic differentiation. PMID:21911366
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. PMID:21911355
Deep brain stimulation induces rapidly reversible transcript changes in Parkinson's leucocytes. PMID:21910823
The mycotoxin deoxynivalenol potentiates intestinal inflammation by Salmonella typhimurium in porcine ileal loops. PMID:21909370
Integrative cancer genomics (IntOGen) in Biomart. PMID:21903633
Toward the blood-borne miRNome of human diseases. PMID:21892151
Soybean homologs of MPK4 negatively regulate defense responses and positively regulate growth and development. PMID:21878550
An integrative genomics approach to biomarker discovery in breast cancer. PMID:21869864
Host regulatory network response to infection with highly pathogenic H5N1 avian influenza virus. PMID:21865398
Differential transcriptomic profiles effected by oil palm phenolics indicate novel health outcomes. PMID:21864415
Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment. PMID:21862625
mir-11 limits the proapoptotic function of its host gene, dE2f1. PMID:21856777
High-throughput identification of potential minor histocompatibility antigens by MHC tetramer-based screening: feasibility and limitations. PMID:21850230
Discovery and preclinical validation of drug indications using compendia of public gene expression data. PMID:21849665
The need for the pathology community to sponsor a whole slide imaging repository with technical guidance from the pathology informatics community. PMID:21845229
Antibacterial mechanism of action of arylamide foldamers. PMID:21844313
Resistance to Plasmopara viticola in a grapevine segregating population is associated with stilbenoid accumulation and with specific host transcriptional responses. PMID:21838877
Fibrogenic and redox-related but not proinflammatory genes are upregulated in Lewis rat model of chronic silicosis. PMID:21830856
Genome-wide integration on transcription factors, histone acetylation and gene expression reveals genes co-regulated by histone modification patterns. PMID:21829453
Reciprocal transcriptional regulation of metabolic and signaling pathways correlates with disease severity in heart failure. PMID:21828333
Eliminating SF-1 (NR5A1) sumoylation in vivo results in ectopic hedgehog signaling and disruption of endocrine development. PMID:21820362
Single cell transcriptomics of neighboring hyphae of Aspergillus niger. PMID:21816052
DAF-12 regulates a connected network of genes to ensure robust developmental decisions. PMID:21814518
Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. PMID:21810278
Characterization of early host responses in adults with dengue disease. PMID:21810247
3'UTR elements inhibit Ras-induced C/EBPβ post-translational activation and senescence in tumour cells. PMID:21804532
STIM1 as a key regulator for Ca2+ homeostasis in skeletal-muscle development and function. PMID:21798093
Crx broadly modulates the pineal transcriptome. PMID:21797868
In vivo neuronal subtype-specific targets of Atoh1 (Math1) in dorsal spinal cord. PMID:21795538
Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation. PMID:21791600
Predictive and prognostic molecular markers for cancer medicine. PMID:21789130
Large-scale methylation domains mark a functional subset of neuronally expressed genes. PMID:21784875
DMRT1 prevents female reprogramming in the postnatal mammalian testis. PMID:21775990
Similarity of mouse perivascular and brown adipose tissues and their resistance to diet-induced inflammation. PMID:21765057
Post-transcription initiation function of the ubiquitous SAGA complex in tissue-specific gene activation. PMID:21764853
An evaluation protocol for subtype-specific breast cancer event prediction. PMID:21760900
Remodeling lipid metabolism and improving insulin responsiveness in human primary myotubes. PMID:21760887
A toxicogenomic comparison of primary and photochemically altered air pollutant mixtures. PMID:21757418
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. PMID:21750106
A screening assay based on host-pathogen interaction models identifies a set of novel antifungal benzimidazole derivatives. PMID:21746957
Genome-wide gene expression profiling of fertilization competent mycelium in opposite mating types in the heterothallic fungus Podospora anserina. PMID:21738678
Positive outcomes of oil palm phenolics on degenerative diseases in animal models. PMID:21736778
Meta-analysis of multiple microarray datasets reveals a common gene signature of metastasis in solid tumors. PMID:21736749
miRNA studies in in vitro and in vivo activated hepatic stellate cells. PMID:21734783
Bile salts induce resistance to polymyxin in enterohemorrhagic Escherichia coli O157:H7. PMID:21725004
Transcriptional profiling of Medicago truncatula under salt stress identified a novel CBF transcription factor MtCBF4 that plays an important role in abiotic stress responses. PMID:21718548
Copy number variants in candidate genes are genetic modifiers of Hirschsprung disease. PMID:21712996
Comparative kinetic analyses of gene profiles of naïve CD4+ and CD8+ T cells from young and old animals reveal novel age-related alterations. PMID:21711441
Chromatin structure characteristics of pre-miRNA genomic sequences. PMID:21702984
BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. PMID:21702939
A genome-wide DNA methylation study in colorectal carcinoma. PMID:21699707
Integrative computational biology for cancer research. PMID:21691773
The role of bioinformatics in studying rheumatic and autoimmune disorders. PMID:21691330
Nab2 functions in the metabolism of RNA driven by polymerases II and III. PMID:21680710
Genome-wide association study of schizophrenia in Japanese population. PMID:21674006
The characterisation of piRNA-related 19mers in the mouse. PMID:21672259
Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation. PMID:21672225
Inflammatory gene regulatory networks in amnion cells following cytokine stimulation: translational systems approach to modeling human parturition. PMID:21655103
An atlas of tissue-specific conserved coexpression for functional annotation and disease gene prediction. PMID:21654723
PREDICT: a method for inferring novel drug indications with application to personalized medicine. PMID:21654673
Genome-scale analysis of replication timing: from bench to bioinformatics. PMID:21637205
Absence of repellents in Ustilago maydis induces genes encoding small secreted proteins. PMID:21626092
The plant cuticle is required for osmotic stress regulation of abscisic acid biosynthesis and osmotic stress tolerance in Arabidopsis. PMID:21610183
The transcriptome of human epicardial, mediastinal and subcutaneous adipose tissues in men with coronary artery disease. PMID:21603615
Integrative mRNA profiling comparing cultured primary cells with clinical samples reveals PLK1 and C20orf20 as therapeutic targets in cutaneous squamous cell carcinoma. PMID:21602893
Prospecting for genes involved in transcriptional regulation of plant defenses, a bioinformatics approach. PMID:21595873
Transcriptome analysis by GeneTrail revealed regulation of functional categories in response to alterations of iron homeostasis in Arabidopsis thaliana. PMID:21592396
Identification and replication of loci involved in camptothecin-induced cytotoxicity using CEPH pedigrees. PMID:21573211
Tat RNA silencing suppressor activity contributes to perturbation of lymphocyte miRNA by HIV-1. PMID:21569500
Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability. PMID:21562599
The role of indirect connections in gene networks in predicting function. PMID:21551147
Assessing affymetrix GeneChip microarray quality. PMID:21548974
EXORDIUM-LIKE1 promotes growth during low carbon availability in Arabidopsis. PMID:21543728
Human cytomegalovirus IE1 protein elicits a type II interferon-like host cell response that depends on activated STAT1 but not interferon-γ. PMID:21533215
Aberrant epigenetic and genetic marks are seen in myelodysplastic leukocytes and reveal Dock4 as a candidate pathogenic gene on chromosome 7q. PMID:21532034
Tracheal occlusion modulates the gene expression profile of the medial thalamus in anesthetized rats. PMID:21527662
Gene expression profiles from discordant monozygotic twins suggest that molecular pathways are shared among multiple systemic autoimmune diseases. PMID:21521520
Epigenomic and RNA structural correlates of polyadenylation. PMID:21508683
Methylation and loss of Secreted Frizzled-Related Protein 3 enhances melanoma cell migration and invasion. PMID:21494614
Extensive effects of in vitro oocyte maturation on rhesus monkey cumulus cell transcriptome. PMID:21487073
H3 lysine 4 is acetylated at active gene promoters and is regulated by H3 lysine 4 methylation. PMID:21483810
Integration of transcriptomics, proteomics, and microRNA analyses reveals novel microRNA regulation of targets in the mammalian inner ear. PMID:21483685
Immediate reduction of Salmonella enterica serotype typhimurium viability via membrane destabilization following exposure to multiple-hurdle treatments with heated, acidified organic acid salt solutions. PMID:21478311
Identification of SERPINA1 as single marker for papillary thyroid carcinoma through microarray meta analysis and quantification of its discriminatory power in independent validation. PMID:21470421
Crosstalk between c-Jun and TAp73alpha/beta contributes to the apoptosis-survival balance. PMID:21459846
Alignment of gene expression profiles from test samples against a reference database: New method for context-specific interpretation of microarray data. PMID:21453538
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. PMID:21447789
A 44K microarray dataset of the changing transcriptome in developing Atlantic salmon (Salmo salar L.). PMID:21447175
Relationship between symptoms and gene expression induced by the infection of three strains of Rice dwarf virus. PMID:21445363
PlaNet: combined sequence and expression comparisons across plant networks derived from seven species. PMID:21441431
Meta-analysis of gene expression microarrays with missing replicates. PMID:21435268
COP1-mediated degradation of BBX22/LZF1 optimizes seedling development in Arabidopsis. PMID:21427283
Apolipoproteins in the brain: implications for neurological and psychiatric disorders. PMID:21423873
Hypomethylation of intragenic LINE-1 represses transcription in cancer cells through AGO2. PMID:21423624
The human TTAGGG repeat factors 1 and 2 bind to a subset of interstitial telomeric sequences and satellite repeats. PMID:21423270
Effect of Xpcl1 activation and p27(Kip1) loss on gene expression in murine lymphoma. PMID:21412408
Use of transcriptional signatures induced in lymphoid and myeloid cell lines as an inflammatory biomarker in Type 1 diabetes. PMID:21406607
Making sense of cancer genomic data. PMID:21406553
Shmt1 heterozygosity impairs folate-dependent thymidylate synthesis capacity and modifies risk of Apc(min)-mediated intestinal cancer risk. PMID:21406397
Identification of genes involved in cell wall biogenesis in grasses by differential gene expression profiling of elongating and non-elongating maize internodes. PMID:21402660
The impact of quantitative optimization of hybridization conditions on gene expression analysis. PMID:21401920
Phosphoproteomic analysis reveals an intrinsic pathway for the regulation of histone deacetylase 7 that controls the function of cytotoxic T lymphocytes. PMID:21399638
Population-genetic properties of differentiated human copy-number polymorphisms. PMID:21397061
Role of p53 serine 46 in p53 target gene regulation. PMID:21394211
Interorgan coordination of the murine adaptive response to fasting. PMID:21393243
Rat diaphragm mitochondria have lower intrinsic respiratory rates than mitochondria in limb muscles. PMID:21389333
Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PMID:21386892
The expanded human disease network combining protein-protein interaction information. PMID:21386875
Identification of microRNA-mRNA modules using microarray data. PMID:21375780
Reconstruction of the regulatory network of Lactobacillus plantarum WCFS1 on basis of correlated gene expression and conserved regulatory motifs. PMID:21375715
Microarray analysis of differential gene expression profile in peripheral blood cells of patients with human essential hypertension. PMID:21369372
Peripheral blood gene expression profiles in metabolic syndrome, coronary artery disease and type 2 diabetes. PMID:21368773
MicroRNA-183 family expression in hair cell development and requirement of microRNAs for hair cell maintenance and survival. PMID:21360794
Distinct early molecular responses to mutations causing vLINCL and JNCL presage ATP synthase subunit C accumulation in cerebellar cells. PMID:21359198
Association of FABP5 expression with poor survival in triple-negative breast cancer: implication for retinoic acid therapy. PMID:21356353
Gene expression throughout a vertebrate's embryogenesis. PMID:21356103
In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis. PMID:21352611
Kaposi's sarcoma-associated herpesvirus viral interferon regulatory factor 3 inhibits gamma interferon and major histocompatibility complex class II expression. PMID:21345951
IL-17-induced NF-kappaB activation via CIKS/Act1: physiologic significance and signaling mechanisms. PMID:21335551
Meta-analysis of muscle transcriptome data using the MADMuscle database reveals biologically relevant gene patterns. PMID:21324190
Translocation of the cytoplasmic domain of ADAM13 to the nucleus is essential for Calpain8-a expression and cranial neural crest cell migration. PMID:21316592
Brain perihematoma genomic profile following spontaneous human intracerebral hemorrhage. PMID:21311749
Histone deacetylase inhibitors in the treatment of muscular dystrophies: epigenetic drugs for genetic diseases. PMID:21308150
Identification of candidate small-molecule therapeutics to cancer by gene-signature perturbation in connectivity mapping. PMID:21305029
Gene expression meta-analysis identifies VDAC1 as a predictor of poor outcome in early stage non-small cell lung cancer. PMID:21297950
PERP regulates enamel formation via effects on cell-cell adhesion and gene expression. PMID:21285247
Detecting cancer gene networks characterized by recurrent genomic alterations in a population. PMID:21283511
Identification of Tat-SF1 cellular targets by exon array analysis reveals dual roles in transcription and splicing. PMID:21282347
Isolation and characterization of progenitor-like cells from human renal proximal tubules. PMID:21281815
Loss of subcellular lipid transport due to ARV1 deficiency disrupts organelle homeostasis and activates the unfolded protein response. PMID:21266578
Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene. PMID:21266089
MicroRNA controlled adenovirus mediates anti-cancer efficacy without affecting endogenous microRNA activity. PMID:21264344
Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. PMID:21261984
Indole and 7-hydroxyindole diminish Pseudomonas aeruginosa virulence. PMID:21261883
Lyngbyoic acid, a "tagged" fatty acid from a marine cyanobacterium, disrupts quorum sensing in Pseudomonas aeruginosa. PMID:21258753
Biological assessment of robust noise models in microarray data analysis. PMID:21252077
Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. PMID:21247874
Transcriptome profiling of the rice blast fungus during invasive plant infection and in vitro stresses. PMID:21247492
MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms. PMID:21244711
A Bayesian framework for inference of the genotype-phenotype map for segregating populations. PMID:21242536
Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice. PMID:21226959
Selenium toxicity but not deficient or super-nutritional selenium status vastly alters the transcriptome in rodents. PMID:21226930
A ß-D: -xylosidase and a PR-4B precursor identified as genes accounting for differences in peach cold storage tolerance. PMID:21221699
Microarray analysis of XOPS-mCFP zebrafish retina identifies genes associated with rod photoreceptor degeneration and regeneration. PMID:21217106
Functional specialization of Piwi proteins in Paramecium tetraurelia from post-transcriptional gene silencing to genome remodelling. PMID:21216825
Functional analysis of Rfx6 and mutant variants associated with neonatal diabetes. PMID:21215266
Mammalian stem cells reprogramming in response to terahertz radiation. PMID:21209821
Short-term administration of rhGH increases markers of cellular proliferation but not milk protein gene expression in normal lactating women. PMID:21205870
Matrix metalloproteinase-8 deficiency increases joint inflammation and bone erosion in the K/BxN serum-transfer arthritis model. PMID:21190566
Comprehensive gene-expression survey identifies wif1 as a modulator of cardiomyocyte differentiation. PMID:21179454
The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes. PMID:21177656
Silicon enhances suberization and lignification in roots of rice (Oryza sativa). PMID:21172812
Association of tissue lineage and gene expression: conservatively and differentially expressed genes define common and special functions of tissues. PMID:21172044
Expression profiling of formalin-fixed paraffin-embedded primary breast tumors using cancer-specific and whole genome gene panels on the DASL® platform. PMID:21172013
A scalable approach for discovering conserved active subnetworks across species. PMID:21170309
CD47 knockout mice exhibit improved recovery from spinal cord injury. PMID:21168495
Mthfd1 is a modifier of chemically induced intestinal carcinogenesis. PMID:21156972
Systematic identification of placental epigenetic signatures for the noninvasive prenatal detection of Edwards syndrome. PMID:21152411
A transcription factor map as revealed by a genome-wide gene expression analysis of whole-blood mRNA transcriptome in multiple sclerosis. PMID:21152067
Analysis of kinase gene expression patterns across 5681 human tissue samples reveals functional genomic taxonomy of the kinome. PMID:21151926
Global gene expression profiling of a population exposed to a range of benzene levels. PMID:21147609
Epigenetic changes induced by air toxics: formaldehyde exposure alters miRNA expression profiles in human lung cells. PMID:21147603
Fine-scale genetic mapping of a hybrid sterility factor between Drosophila simulans and D. mauritiana: the varied and elusive functions of "speciation genes". PMID:21144061
Comparative profiling of the transcriptional response to iron restriction in six serotypes of Actinobacillus pleuropneumoniae with different virulence potential. PMID:21143895
Structure and expression of the maize (Zea mays L.) SUN-domain protein gene family: evidence for the existence of two divergent classes of SUN proteins in plants. PMID:21143845
FBG1 is a promiscuous ubiquitin ligase that sequesters APC2 and causes S-phase arrest. PMID:21135578
Chronic intermittent hypoxia induces lung growth in adult mice. PMID:21131398
Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. PMID:21130701
Mining Affymetrix microarray data for long non-coding RNAs: altered expression in the nucleus accumbens of heroin abusers. PMID:21128942
GAMMA-BASED CLUSTERING VIA ORDERED MEANS WITH APPLICATION TO GENE-EXPRESSION ANALYSIS. PMID:21113321
NCBI GEO: archive for functional genomics data sets--10 years on. PMID:21097893
Primosomal proteins DnaD and DnaB are recruited to chromosomal regions bound by DnaA in Bacillus subtilis. PMID:21097613
Deducing corticotropin-releasing hormone receptor type 1 signaling networks from gene expression data by usage of genetic algorithms and graphical Gaussian models. PMID:21092110
The transcriptional regulator Rok binds A+T-rich DNA and is involved in repression of a mobile genetic element in Bacillus subtilis. PMID:21085634
Escherichia coli global gene expression in urine from women with urinary tract infection. PMID:21085611
Physiology of Pseudomonas aeruginosa in biofilms as revealed by transcriptome analysis. PMID:21083928
Proteomics and transcriptomics characterization of bile stress response in probiotic Lactobacillus rhamnosus GG. PMID:21078892
Feasibility of using gene expression analysis to study canine soft tissue sarcomas. PMID:21076837
Algorithm-driven artifacts in median polish summarization of microarray data. PMID:21070630
A comparative analysis of gene-expression data of multiple cancer types. PMID:21060876
Identification and optimization of classifier genes from multi-class earthworm microarray dataset. PMID:21060837
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media. PMID:21057108
IGRhCellID: integrated genomic resources of human cell lines for identification. PMID:21051335
Specified species in gingival crevicular fluid predict bacterial diversity. PMID:21049043
Ancestral centriole and flagella proteins identified by analysis of Naegleria differentiation. PMID:21045110
Integrative systems biology for data-driven knowledge discovery. PMID:21044756
Stromal microenvironment processes unveiled by biological component analysis of gene expression in xenograft tumor models. PMID:21044358
Prioritizing genes associated with prostate cancer development. PMID:21044312
Myogenin regulates exercise capacity and skeletal muscle metabolism in the adult mouse. PMID:21042574
Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection. PMID:21041446
eXtraembryonic ENdoderm (XEN) stem cells produce factors that activate heart formation. PMID:20975998
CaSNP: a database for interrogating copy number alterations of cancer genome from SNP array data. PMID:20972221
The role of epidermal growth factor in the healing tympanic membrane following perforation in rats. PMID:20967565
Seasonal changes in bacterial and archaeal gene expression patterns across salinity gradients in the Columbia River coastal margin. PMID:20967204
Comparative survival analysis of breast cancer microarray studies identifies important prognostic genetic pathways. PMID:20964848
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. PMID:20958970
Practical application of toxicogenomics for profiling toxicant-induced biological perturbations. PMID:20957103
Temporal gene expression profiling during rat femoral marrow ablation-induced intramembranous bone regeneration. PMID:20957030
Hal4 and Hal5 protein kinases are required for general control of carbon and nitrogen uptake and metabolism. PMID:20952580
CancerResource: a comprehensive database of cancer-relevant proteins and compound interactions supported by experimental knowledge. PMID:20952398
Epigenetic antagonism between polycomb and SWI/SNF complexes during oncogenic transformation. PMID:20951942
RB-pathway disruption in breast cancer: differential association with disease subtypes, disease-specific prognosis and therapeutic response. PMID:20948315
Alkaline-stress response in Glycine soja leaf identifies specific transcription factors and ABA-mediated signaling factors. PMID:20938706
Gene expression in a paleopolyploid: a transcriptome resource for the ciliate Paramecium tetraurelia. PMID:20932287
Ontology-based meta-analysis of global collections of high-throughput public data. PMID:20927376
Robust assignment of cancer subtypes from expression data using a uni-variate gene expression average as classifier. PMID:20925936
Multi-species integrative biclustering. PMID:20920250
Features of cryptic promoters and their varied reliance on bromodomain-containing factors. PMID:20886085
Gene expression study of monocytes/macrophages during early foreign body reaction and identification of potential precursors of myofibroblasts. PMID:20886081
Dysregulation of the mitogen granulin in human cancer through the miR-15/107 microRNA gene group. PMID:20884628
Nutrient-regulated transcriptional responses in the brown tide-forming alga Aureococcus anophagefferens. PMID:20880332
Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis. PMID:20876091
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. PMID:20875095
A Brassica exon array for whole-transcript gene expression profiling. PMID:20862292
BAFF receptor signaling aids the differentiation of immature B cells into transitional B cells following tonic BCR signaling. PMID:20861359
Girafe--an R/Bioconductor package for functional exploration of aligned next-generation sequencing reads. PMID:20861030
Characterization of a novel Lactobacillus species closely related to Lactobacillus johnsonii using a combination of molecular and comparative genomics methods. PMID:20849602
The forkhead transcription factor Hcm1 promotes mitochondrial biogenesis and stress resistance in yeast. PMID:20847055
Gene and noncoding RNA regulation underlying photoreceptor protection: microarray study of dietary antioxidant saffron and photobiomodulation in rat retina. PMID:20844572
A systems biology approach to identify effective cocktail drugs. PMID:20840734
Systemic gut microbial modulation of bile acid metabolism in host tissue compartments. PMID:20837534
In silico models of cancer. PMID:20836040
MitoGenesisDB: an expression data mining tool to explore spatio-temporal dynamics of mitochondrial biogenesis. PMID:20833631
Genomic distance entrained clustering and regression modelling highlights interacting genomic regions contributing to proliferation in breast cancer. PMID:20825665
Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PMID:20824171
Using expression genetics to study the neurobiology of ethanol and alcoholism. PMID:20813241
Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs. PMID:20813047
Genome-wide profiling of p63 DNA-binding sites identifies an element that regulates gene expression during limb development in the 7q21 SHFM1 locus. PMID:20808887
A maternal low protein diet has pronounced effects on mitochondrial gene expression in offspring liver and skeletal muscle; protective effect of taurine. PMID:20804614
Analyzing schizophrenia by DNA microarrays. PMID:20801428
The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. PMID:20797886
Current concepts of follicle-stimulating hormone receptor gene regulation. PMID:20739665
Molecular analysis of ex-vivo CD133+ GBM cells revealed a common invasive and angiogenic profile but different proliferative signatures among high grade gliomas. PMID:20735813
Transcriptional regulation by CHIP/LDB complexes. PMID:20730086
Gene Expression Browser: large-scale and cross-experiment microarray data integration, management, search & visualization. PMID:20727159
Molecular and functional characterization of allogantigen-specific anergic T cells suitable for cell therapy. PMID:20713457
Alpha-synuclein deficiency leads to increased glyoxalase I expression and glycation stress. PMID:20711648
A comparative analysis of extra-embryonic endoderm cell lines. PMID:20711519
Integration of metabolism and virulence by Clostridium difficile CodY. PMID:20709897
Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655. PMID:20709841
Transcription profiling of fertilization and early seed development events in a solanaceous species using a 7.7 K cDNA microarray from Solanum chacoense ovules. PMID:20704744
Microarray meta-analysis database (M(2)DB): a uniformly pre-processed, quality controlled, and manually curated human clinical microarray database. PMID:20698961
Transcriptional profiling of intrinsic PNS factors in the postnatal mouse. PMID:20696251
Identification of testis-relevant genes using in silico analysis from testis ESTs and cDNA microarray in the black tiger shrimp (Penaeus monodon). PMID:20696033
Detecting novel genes with sparse arrays. PMID:20691772
Integrative analysis of large scale expression profiles reveals core transcriptional response and coordination between multiple cellular processes in a cyanobacterium. PMID:20678200
Transcriptome analysis of alkali shock and alkali adaptation in Listeria monocytogenes 10403S. PMID:20677981
Reconstruction of the core and extended regulons of global transcription factors. PMID:20661434
Characterization of a Clp protease gene regulator and the reaeration response in Mycobacterium tuberculosis. PMID:20661284
Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. PMID:20660011
Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment. PMID:20653984
Genome-wide expression profiling deciphers host responses altered during dengue shock syndrome and reveals the role of innate immunity in severe dengue. PMID:20652028
Effective knowledge management in translational medicine. PMID:20642836
Power training and postmenopausal hormone therapy affect transcriptional control of specific co-regulated gene clusters in skeletal muscle. PMID:20640546
Identification of primary gene targets of TFAP2C in hormone responsive breast carcinoma cells. PMID:20629094
Functional genetic diversity among Mycobacterium tuberculosis complex clinical isolates: delineation of conserved core and lineage-specific transcriptomes during intracellular survival. PMID:20628579
Neighborhood rough set reduction-based gene selection and prioritization for gene expression profile analysis and molecular cancer classification. PMID:20625410
Independent component analysis: mining microarray data for fundamental human gene expression modules. PMID:20619355
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways. PMID:20616000
High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection. PMID:20610602
Small RNAs, DNA methylation and transposable elements in wheat. PMID:20584339
Increased mutation frequency in redox-impaired Escherichia coli due to RelA- and RpoS-mediated repression of DNA repair. PMID:20581184
Innate immune processes are sufficient for driving silicosis in mice. PMID:20576854
Immature cell populations and an erythropoiesis gene-expression signature in systemic juvenile idiopathic arthritis: implications for pathogenesis. PMID:20576155
Transcriptional profile analysis of RPGRORF15 frameshift mutation identifies novel genes associated with retinal degeneration. PMID:20574030
Elevated cyclic AMP levels in T lymphocytes transformed by human T-cell lymphotropic virus type 1. PMID:20573814
Alternative splicing is frequent during early embryonic development in mouse. PMID:20573213
Global transcriptional response to carbonic anhydrase IX deficiency in the mouse stomach. PMID:20573196
Molecular subtypes of breast cancer are associated with characteristic DNA methylation patterns. PMID:20565864
A general framework for optimization of probes for gene expression microarray and its application to the fungus Podospora anserina. PMID:20565839
Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing. PMID:20562853
Metatranscriptomic analysis of the response of river biofilms to pharmaceutical products, using anonymous DNA microarrays. PMID:20562274
Identification of novel epithelial ovarian cancer biomarkers by cross-laboratory microarray analysis. PMID:20556581
A gene network switch enhances the oxidative capacity of ovine skeletal muscle during late fetal development. PMID:20546621
Lactobacillus acidophilus induces virus immune defence genes in murine dendritic cells by a Toll-like receptor-2-dependent mechanism. PMID:20545783
The lytic transcriptome of Kaposi's sarcoma-associated herpesvirus reveals extensive transcription of noncoding regions, including regions antisense to important genes. PMID:20534856
UFFizi: a generic platform for ranking informative features. PMID:20525252
Response of the mouse lung transcriptome to welding fume: effects of stainless and mild steel fumes on lung gene expression in A/J and C57BL/6J mice. PMID:20525249
Deletion of von Hippel-Lindau in glomerular podocytes results in glomerular basement membrane thickening, ectopic subepithelial deposition of collagen {alpha}1{alpha}2{alpha}1(IV), expression of neuroglobin, and proteinuria. PMID:20522651
Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila. PMID:20515475
The correlation pattern of acquired copy number changes in 164 ETV6/RUNX1-positive childhood acute lymphoblastic leukemias. PMID:20513752
Changes in DnaA-dependent gene expression contribute to the transcriptional and developmental response of Bacillus subtilis to manganese limitation in Luria-Bertani medium. PMID:20511500
Induction of neuro-protective/regenerative genes in stem cells infiltrating post-ischemic brain tissue. PMID:20509949
Fast integration of heterogeneous data sources for predicting gene function with limited annotation. PMID:20507895
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset. PMID:20507584
Gene expression profile in circulating mononuclear cells after exposure to ultrafine carbon particles. PMID:20507211
An eScience-Bayes strategy for analyzing omics data. PMID:20504364
Benzo(a)pyrene induces similar gene expression changes in testis of DNA repair proficient and deficient mice. PMID:20504355
Functional and gene network analyses of transcriptional signatures characterizing pre-weaned bovine mammary parenchyma or fat pad uncovered novel inter-tissue signaling networks during development. PMID:20504330
Development of a cross-platform biomarker signature to detect renal transplant tolerance in humans. PMID:20501943
Prediction of breast cancer prognosis using gene set statistics provides signature stability and biological context. PMID:20500821
Re-annotation is an essential step in systems biology modeling of functional genomics data. PMID:20498845
Drawing networks of rejection - a systems biological approach to the identification of candidate genes in heart transplantation. PMID:20497491
Expression of miR-196b is not exclusively MLL-driven but is especially linked to activation of HOXA genes in pediatric acute lymphoblastic leukemia. PMID:20494936
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PMID:20485568
The relationship among gene expression, the evolution of gene dosage, and the rate of protein evolution. PMID:20485561
The RNA binding protein Tudor-SN is essential for stress tolerance and stabilizes levels of stress-responsive mRNAs encoding secreted proteins in Arabidopsis. PMID:20484005
Detecting microRNA activity from gene expression data. PMID:20482775
Identification of components associated with thermal acclimation of photosystem II in Synechocystis sp. PCC6803. PMID:20463904
Genome-wide changes accompanying the knockdown of Ep-CAM in retinoblastoma. PMID:20461151
Hedgehog pathway-regulated gene networks in cerebellum development and tumorigenesis. PMID:20460306
Thiamine biosynthesis in Saccharomyces cerevisiae is regulated by the NAD+-dependent histone deacetylase Hst1. PMID:20439498
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
Gene expression atlas for human embryogenesis. PMID:20430792
Alternate protein kinase A activity identifies a unique population of stromal cells in adult bone. PMID:20421483
Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. PMID:20410506
MicroRNA gene evolution in Arabidopsis lyrata and Arabidopsis thaliana. PMID:20407027
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. PMID:20406493
Proliferation and pluripotency of human embryonic stem cells maintained on type I collagen. PMID:20367282
Using pre-existing microarray datasets to increase experimental power: application to insulin resistance. PMID:20361040
Bayesian approach to transforming public gene expression repositories into disease diagnosis databases. PMID:20360561
Onecut-2 knockout mice fail to thrive during early postnatal period and have altered patterns of gene expression in small intestine. PMID:20354101
Dissecting interferon-induced transcriptional programs in human peripheral blood cells. PMID:20339534
Reciprocal regulation of metabolic and signaling pathways. PMID:20334672
Widespread transcriptional autosomal dosage compensation in Drosophila correlates with gene expression level. PMID:20333221
Significance of light, sugar, and amino acid supply for diurnal gene regulation in developing barley caryopses. PMID:20304969
Global and unbiased detection of splice junctions from RNA-seq data. PMID:20236510
High-resolution genomic profiling of human papillomavirus-associated vulval neoplasia. PMID:20234371
Analysis of the genome content of Lactococcus garvieae by genomic interspecies microarray hybridization. PMID:20233401
RNA isolation method for single embryo transcriptome analysis in zebrafish. PMID:20233395
MiDReG: a method of mining developmentally regulated genes using Boolean implications. PMID:20231483
Systematic planning of genome-scale experiments in poorly studied species. PMID:20221257
Array-based transcript profiling and limiting-dilution reverse transcription-PCR analysis identify additional latent genes in Kaposi's sarcoma-associated herpesvirus. PMID:20219929
Homozygous deletion mapping in myeloma samples identifies genes and an expression signature relevant to pathogenesis and outcome. PMID:20215539
Conserved regulatory motifs at phenylethanolamine N-methyltransferase (PNMT) are disrupted by common functional genetic variation: an integrated computational/experimental approach. PMID:20204374
MicroRNAs of Bombyx mori identified by Solexa sequencing. PMID:20199675
Neonatal maternal deprivation response and developmental changes in gene expression revealed by hypothalamic gene expression profiling in mice. PMID:20195375
Role of the Sinorhizobium meliloti global regulator Hfq in gene regulation and symbiosis. PMID:20192823
Multiple common variants for celiac disease influencing immune gene expression. PMID:20190752
Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits. PMID:20185544
Differential gene expression in adipose stem cells cultured in allogeneic human serum versus fetal bovine serum. PMID:20184435
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PMID:20169069
Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function. PMID:20167116
High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. PMID:20165882
Broad spectrum microarray for fingerprint-based bacterial species identification. PMID:20163710
Transcription of proteinase 3 and related myelopoiesis genes in peripheral blood mononuclear cells of patients with active Wegener's granulomatosis. PMID:20155833
Increased sinusoidal flow is not the primary stimulus to liver regeneration. PMID:20148099
Classification of genes and putative biomarker identification using distribution metrics on expression profiles. PMID:20140228
Regulation of gene expression in hepatic cells by the mammalian Target of Rapamycin (mTOR). PMID:20140209
Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. PMID:20130013
Inferring the functions of longevity genes with modular subnetwork biomarkers of Caenorhabditis elegans aging. PMID:20128910
Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats. PMID:20128895
MicroRNAs show diverse and dynamic expression patterns in multiple tissues of Bombyx mori. PMID:20122259
Functional genomic study of exogenous n-butanol stress in Escherichia coli. PMID:20118358
Alternative route for glyoxylate consumption during growth on two-carbon compounds by Methylobacterium extorquens AM1. PMID:20118267
Changes in gene expression in regions of the extended amygdala of alcohol-preferring rats after binge-like alcohol drinking. PMID:20116196
The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. PMID:20107022
Modeling complex genetic and environmental influences on comorbid bipolar disorder with tobacco use disorder. PMID:20102619
Copy number variation in the genomes of twelve natural isolates of Caenorhabditis elegans. PMID:20100350
ChIP-chip designs to interrogate the genome of Xenopus embryos for transcription factor binding and epigenetic regulation. PMID:20098671
Frozen robust multiarray analysis (fRMA). PMID:20097884
Expanded multilocus sequence typing and comparative genomic hybridization of Campylobacter coli isolates from multiple hosts. PMID:20097815
Spatial and temporal regulation of gene expression in the mammalian growth plate. PMID:20096814
Expression profiling of S. pombe acetyltransferase mutants identifies redundant pathways of gene regulation. PMID:20096118
Gene expression profiling of peripheral blood cells for early detection of breast cancer. PMID:20078854
PepD participates in the mycobacterial stress response mediated through MprAB and SigE. PMID:20061478
Genome-wide identification of hypoxia-inducible factor binding sites and target genes by a probabilistic model integrating transcription-profiling data and in silico binding site prediction. PMID:20061373
DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. PMID:20060365
Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. PMID:20053754
Effects of moderate drinking during pregnancy on placental gene expression. PMID:20053520
IGF-I induced genes in stromal fibroblasts predict the clinical outcome of breast and lung cancer patients. PMID:20051100
Cardiovascular networks: systems-based approaches to cardiovascular disease. PMID:20048233
Novel early response genes in osteoblasts exposed to dynamic fluid flow. PMID:20047941
Correlating measurements across samples improves accuracy of large-scale expression profile experiments. PMID:20042104
A gene expression signature of invasive potential in metastatic melanoma cells. PMID:20041153
Effects of temperature on gene expression in embryos of the coral Montastraea faveolata. PMID:20030803
Androgen regulated genes in human prostate xenografts in mice: relation to BPH and prostate cancer. PMID:20027305
Chimeric mouse tumor models reveal differences in pathway activation between ERBB family- and KRAS-dependent lung adenocarcinomas. PMID:20023657
Discovering collectively informative descriptors from high-throughput experiments. PMID:20021653
Mixture-model based estimation of gene expression variance from public database improves identification of differentially expressed genes in small sized microarray data. PMID:20015947
Molecular evolution of sex-biased genes in the Drosophila ananassae subgroup. PMID:20015359
Developmental profiling of postnatal dentate gyrus progenitors provides evidence for dynamic cell-autonomous regulation. PMID:20014381
Estradiol stimulates vasodilatory and metabolic pathways in cultured human endothelial cells. PMID:20011585
Sialic acid utilisation and synthesis in the neonatal rat revisited. PMID:20011510
ConceptGen: a gene set enrichment and gene set relation mapping tool. PMID:20007254
Systems biology of embryogenesis. PMID:20003850
Dissecting the dynamics of dysregulation of cellular processes in mouse mammary gland tumor. PMID:20003387
The pitfalls of platform comparison: DNA copy number array technologies assessed. PMID:19995423
Biomarker detection in the integration of multiple multi-class genomic studies. PMID:19965884
Two-transcript gene expression classifiers in the diagnosis and prognosis of human diseases. PMID:19961616
A model selection approach to discover age-dependent gene expression patterns using quantile regression models. PMID:19958479
Consensus miRNA expression profiles derived from interplatform normalization of microarray data. PMID:19948767
Novel rank-based statistical methods reveal microRNAs with differential expression in multiple cancer types. PMID:19946373
Detection call algorithms for high-throughput gene expression microarray data. PMID:19939941
Data reporting standards: making the things we use better. PMID:19939294
p38gamma mitogen-activated protein kinase is a key regulator in skeletal muscle metabolic adaptation in mice. PMID:19936205
A genome-wide characterization of microRNA genes in maize. PMID:19936050
Exon array analysis of head and neck cancers identifies a hypoxia related splice variant of LAMA3 associated with a poor prognosis. PMID:19936049
Members of the LBD family of transcription factors repress anthocyanin synthesis and affect additional nitrogen responses in Arabidopsis. PMID:19933203
Differentially expressed genes for aggressive pecking behaviour in laying hens. PMID:19925670
The Drosophila PGC-1 homologue Spargel coordinates mitochondrial activity to insulin signalling. PMID:19910925
FoxJ1-dependent gene expression is required for differentiation of radial glia into ependymal cells and a subset of astrocytes in the postnatal brain. PMID:19906869
An expression database for roots of the model legume Medicago truncatula under salt stress. PMID:19906315
CITED2 and NCOR2 in anti-oestrogen resistance and progression of breast cancer. PMID:19904269
Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling. PMID:19901961
Analysis of chromosomal aberration (1, 3, and 8) and association of microRNAs in uveal melanoma. PMID:19898689
Matrix factorization for recovery of biological processes from microarray data. PMID:19897089
Use of microarray hybridization to identify Brugia genes involved in mosquito infectivity. PMID:19894065
Alternative splicing in the differentiation of human embryonic stem cells into cardiac precursors. PMID:19893621
Analysis of gene expression and physiological responses in three Mexican maize landraces under drought stress and recovery irrigation. PMID:19888455
Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants. PMID:19888323
Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression. PMID:19887574
ArrayMining: a modular web-application for microarray analysis combining ensemble and consensus methods with cross-study normalization. PMID:19863798
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays. PMID:19860899
Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura. PMID:19859648
Transcriptional regulation of membrane lipid homeostasis in Escherichia coli. PMID:19854834
Comprehensive gene and microRNA expression profiling reveals a role for microRNAs in human liver development. PMID:19841744
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PMID:19834616
Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data. PMID:19828070
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. PMID:19828039
Rapamycin response in tumorigenic and non-tumorigenic hepatic cell lines. PMID:19816606
Genoproteomic mining of urothelial cancer suggests {gamma}-glutamyl hydrolase and diazepam-binding inhibitor as putative urinary markers of outcome after chemotherapy. PMID:19815704
Facilitating functional annotation of chicken microarray data. PMID:19811685
MicroRNAs show mutually exclusive expression patterns in the brain of adult male rats. PMID:19806225
Early over expression of messenger RNA for multiple genes, including insulin, in the Pancreatic Lymph Nodes of NOD mice is associated with Islet Autoimmunity. PMID:19799787
AP-2gamma promotes proliferation in breast tumour cells by direct repression of the CDKN1A gene. PMID:19798054
Global transcriptional response to Hfe deficiency and dietary iron overload in mouse liver and duodenum. PMID:19787063
MicroRNA expression profiling during the life cycle of the silkworm (Bombyx mori). PMID:19785751
A secretory phospholipase A2-mediated neuroprotection and anti-apoptosis. PMID:19775433
Global identification of targets of the Arabidopsis MADS domain protein AGAMOUS-Like15. PMID:19767455
A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. PMID:19758566
New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis. PMID:19754951
Glucocorticoids with different chemical structures but similar glucocorticoid receptor potency regulate subsets of common and unique genes in human trabecular meshwork cells. PMID:19744340
Nutrition controls mitochondrial biogenesis in the Drosophila adipose tissue through Delg and cyclin D/Cdk4. PMID:19742324
Meta-coexpression conservation analysis of microarray data: a "subset" approach provides insight into brain-derived neurotrophic factor regulation. PMID:19737418
A high throughput experimental approach to identify miRNA targets in human cells. PMID:19734348
Human TCR-alpha beta+ CD4- CD8- T cells can derive from CD8+ T cells and display an inflammatory effector phenotype. PMID:19734235
The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. PMID:19732946
Plasmodium falciparum heterochromatin protein 1 marks genomic loci linked to phenotypic variation of exported virulence factors. PMID:19730695
GEM-TREND: a web tool for gene expression data mining toward relevant network discovery. PMID:19728865
Systems-level modeling of cancer-fibroblast interaction. PMID:19727395
Evolution of sex-dependent gene expression in three recently diverged species of Drosophila. PMID:19720861
NF-E2-related factor 2 regulates the stress response to UVA-1-oxidized phospholipids in skin cells. PMID:19720622
Penetration of the stigma and style elicits a novel transcriptome in pollen tubes, pointing to genes critical for growth in a pistil. PMID:19714218
A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis. PMID:19713416
A reliable measure of similarity based on dependency for short time series: an application to gene expression networks. PMID:19712487
BMP signaling induces cell-type-specific changes in gene expression programs of human keratinocytes and fibroblasts. PMID:19710687
Peripheral blood T cells in acute myeloid leukemia (AML) patients at diagnosis have abnormal phenotype and genotype and form defective immune synapses with AML blasts. PMID:19710498
GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. PMID:19703314
Gene regulation in parthenocarpic tomato fruit. PMID:19700496
Identification of brain transcriptional variation reproduced in peripheral blood: an approach for mapping brain expression traits. PMID:19692348
Microarray and real-time PCR analyses of the responses of high-arctic soil bacteria to hydrocarbon pollution and bioremediation treatments. PMID:19684169
Targeted deletion of Dicer disrupts lens morphogenesis, corneal epithelium stratification, and whole eye development. PMID:19681134
Impact of the TCR signal on regulatory T cell homeostasis, function, and trafficking. PMID:19668367
Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. PMID:19666046
Rapid and spontaneous loss of phthiocerol dimycocerosate (PDIM) from Mycobacterium tuberculosis grown in vitro: implications for virulence studies. PMID:19661177
Limb immobilization induces a coordinate down-regulation of mitochondrial and other metabolic pathways in men and women. PMID:19654872
Moderate strength (0.23-0.28 T) static magnetic fields (SMF) modulate signaling and differentiation in human embryonic cells. PMID:19653909
Increased local expression of coagulation factor X contributes to the fibrotic response in human and murine lung injury. PMID:19652365
MDS and secondary AML display unique patterns and abundance of aberrant DNA methylation. PMID:19652201
Differential response of C57BL/6J mouse and DBA/2J mouse to optic nerve crush. PMID:19643015
Chromosome aberrations resulting from double-strand DNA breaks at a naturally occurring yeast fragile site composed of inverted ty elements are independent of Mre11p and Sae2p. PMID:19635935
NeuroD6 genomic signature bridging neuronal differentiation to survival via the molecular chaperone network. PMID:19610105
Low-risk susceptibility alleles in 40 human breast cancer cell lines. PMID:19607694
Leukemia inhibitory factor regulates the timing of oligodendrocyte development and myelination in the postnatal optic nerve. PMID:19598242
Microarray analysis of lymphatic tissue reveals stage-specific, gene expression signatures in HIV-1 infection. PMID:19596987
Array-based DNA methylation profiling in follicular lymphoma. PMID:19587707
NCBI Peptidome: a new public repository for mass spectrometry peptide identifications. PMID:19587658
The RNA-binding motif protein 15B (RBM15B/OTT3) acts as cofactor of the nuclear export receptor NXF1. PMID:19586903
Subtype-specific peripheral blood gene expression profiles in recent-onset juvenile idiopathic arthritis. PMID:19565513
FOXP3 inhibits activation-induced NFAT2 expression in T cells thereby limiting effector cytokine expression. PMID:19564342
A gene signature for post-infectious chronic fatigue syndrome. PMID:19555476
Impact of animal strain on gene expression in a rat model of acute cardiac rejection. PMID:19552812
Physiological and toxicological transcriptome changes in HepG2 cells exposed to copper. PMID:19549813
Unsupervised assessment of microarray data quality using a Gaussian mixture model. PMID:19545436
HOXA3 modulates injury-induced mobilization and recruitment of bone marrow-derived cells. PMID:19544454
HORMONOMETER: a tool for discerning transcript signatures of hormone action in the Arabidopsis transcriptome. PMID:19535475
Lasp1 gene disruption is linked to enhanced cell migration and tumor formation. PMID:19531578
Placenta-derived fetal specific mRNA is more readily detectable in maternal plasma than in whole blood. PMID:19516908
Role of cholesterol pathways in norovirus replication. PMID:19515767
An exploratory pathways analysis of temporal changes induced by spinal cord injury in the rat bladder wall: insights on remodeling and inflammation. PMID:19513121
Gene expression profiling of intestinal regeneration in the sea cucumber. PMID:19505337
Pilin regulation in the pilT mutant of Neisseria gonorrhoeae strain MS11. PMID:19486161
Profile of estrogen-responsive genes in an estrogen-specific mammary gland outgrowth model. PMID:19484750
Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. PMID:19480707
Identification of gene co-regulatory modules and associated cis-elements involved in degenerative heart disease. PMID:19476647
PathExpress update: the enzyme neighbourhood method of associating gene-expression data with metabolic pathways. PMID:19474337
An rtt109-independent role for vps75 in transcription-associated nucleosome dynamics. PMID:19470761
Ripening-regulated susceptibility of tomato fruit to Botrytis cinerea requires NOR but not RIN or ethylene. PMID:19465579
Gene expression profiles of sporadic canine hemangiosarcoma are uniquely associated with breed. PMID:19461996
A novel information retrieval model for high-throughput molecular medicine modalities. PMID:19458790
Epigenomic profiling indicates a role for DNA methylation in early postnatal liver development. PMID:19457928
Transcriptomic and proteomic analysis of global ischemia and cardioprotection in the rabbit heart. PMID:19454556
Transcriptional signatures of Itk-deficient CD3+, CD4+ and CD8+ T-cells. PMID:19450280
Assessing reliability of protein-protein interactions by integrative analysis of data in model organisms. PMID:19426453
Integration of tomato reproductive developmental landmarks and expression profiles, and the effect of SUN on fruit shape. PMID:19422692
High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors. PMID:19419571
Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers. PMID:19412622
Convergence of biomarkers, bioinformatics and nanotechnology for individualized cancer treatment. PMID:19409634
Genomic DNA microarray comparison of gene expression patterns in Paracoccidioides brasiliensis mycelia and yeasts in vitro. PMID:19406900
The tetraspanin Tm4sf3 is localized to the ventral pancreas and regulates fusion of the dorsal and ventral pancreatic buds. PMID:19403659
Web-queryable large-scale data sets for hypothesis generation in plant biology. PMID:19401381
Absence of SPARC leads to impaired lens circulation. PMID:19401199
GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. PMID:19398447
Repertoire of microRNAs in epithelial ovarian cancer as determined by next generation sequencing of small RNA cDNA libraries. PMID:19390579
Grape seed extract acting on astrocytes reveals neuronal protection against oxidative stress via interleukin-6-mediated mechanisms. PMID:19381798
Increased antibiotic resistance of Escherichia coli in mature biofilms. PMID:19376922
A specialized outer layer of the primary cell wall joins elongating cotton fibers into tissue-like bundles. PMID:19369592
Biologic and immunologic effects of knockout of human cytomegalovirus pp65 nuclear localization signal. PMID:19369477
Thymic OX40 expression discriminates cells undergoing strong responses to selection ligands. PMID:19342632
Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. PMID:19341625
Hexosamine template. A platform for modulating gene expression and for sugar-based drug discovery. PMID:19326913
Estrogen receptor beta is required for optimal cAMP production in mouse granulosa cells. PMID:19324971
Detection of genomic deletions in rice using oligonucleotide microarrays. PMID:19320995
A cross-study transcriptional analysis of Parkinson's disease. PMID:19305504
Transcriptome analysis of synaptoneurosomes identifies neuroplasticity genes overexpressed in incipient Alzheimer's disease. PMID:19295912
T7-based linear amplification of low concentration mRNA samples using beads and microfluidics for global gene expression measurements. PMID:19294302
ebTrack: an environmental bioinformatics system built upon ArrayTrack. PMID:19278561
Chromatin state marks cell-type- and gender-specific replication of the Drosophila genome. PMID:19270159
Depletion of the cullin Cdc53p induces morphogenetic changes in Candida albicans. PMID:19270112
SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. PMID:19265543
Cellular expression of midkine-a and midkine-b during retinal development and photoreceptor regeneration in zebrafish. PMID:19263476
BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource. PMID:19259398
Prediction and verification of mouse tRNA gene families. PMID:19246989
Effects of differential glycosylation of glycodelins on lymphocyte survival. PMID:19240032
Salicylic acid confers resistance to a biotrophic rust pathogen, Puccinia substriata, in pearl millet (Pennisetum glaucum). PMID:19236576
PVY(NTN) elicits a diverse gene expression response in different potato genotypes in the first 12 h after inoculation. PMID:19236574
Analysis of variance components reveals the contribution of sample processing to transcript variation. PMID:19233957
Using differential gene expression to study Entamoeba histolytica pathogenesis. PMID:19217826
Gene expression profiling of the tumor microenvironment during breast cancer progression. PMID:19187537
Expression diversity and evolutionary dynamics of rice duplicate genes. PMID:19184107
Repeatability of published microarray gene expression analyses. PMID:19174838
Infection and genotype remodel the entire soybean transcriptome. PMID:19171053
Genome-wide epigenetic analysis delineates a biologically distinct immature acute leukemia with myeloid/T-lymphoid features. PMID:19168792
Reconfiguring the quorum-sensing regulator SdiA of Escherichia coli to control biofilm formation via indole and N-acylhomoserine lactones. PMID:19168658
Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. PMID:19159457
Gene expression patterns induced by HPV-16 L1 virus-like particles in leukocytes from vaccine recipients. PMID:19155521
A subtype of childhood acute lymphoblastic leukaemia with poor treatment outcome: a genome-wide classification study. PMID:19138562
Differentially expressed genes during malting and correlation with malting quality phenotypes in barley (Hordeum vulgare L.). PMID:19132335
Acute mixed lineage leukemia in children: the experience of St Jude Children's Research Hospital. PMID:19131545
Using pathway signatures as means of identifying similarities among microarray experiments. PMID:19125200
Origins of the Xylella fastidiosa prophage-like regions and their impact in genome differentiation. PMID:19116666
Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling. PMID:19103603
Pleiotropic effects in Eya3 knockout mice. PMID:19102749
GeneTrailExpress: a web-based pipeline for the statistical evaluation of microarray experiments. PMID:19099609
TATA-binding protein variants that bypass the requirement for Mot1 in vivo. PMID:19098311
Complex fate of paralogs. PMID:19094234
A protein interaction based model for schizophrenia study. PMID:19091023
Identification of G1-regulated genes in normally cycling human cells. PMID:19079774
Co-inhibition of Plasmodium falciparum S-adenosylmethionine decarboxylase/ornithine decarboxylase reveals perturbation-specific compensatory mechanisms by transcriptome, proteome, and metabolome analyses. PMID:19073607
Gene expression profile in pelvic organ prolapse. PMID:19056808
Analyzing ChIP-chip data using bioconductor. PMID:19043553
Changes in gene expression pattern of human primary macrophages induced by carbosilane dendrimer 2G-NN16. PMID:19034630
EMAAS: an extensible grid-based rich internet application for microarray data analysis and management. PMID:19032776
A comparison of four clustering methods for brain expression microarray data. PMID:19032745
Synaptogenesis in purified cortical subplate neurons. PMID:19029062
Gene expression in the human mammary epithelium during lactation: the milk fat globule transcriptome. PMID:19018045
Expression profiles of switch-like genes accurately classify tissue and infectious disease phenotypes in model-based classification. PMID:19014681
Gene set analyses for interpreting microarray experiments on prokaryotic organisms. PMID:18986519
Boolean implication networks derived from large scale, whole genome microarray datasets. PMID:18973690
A chemical genomics study identifies Snf1 as a repressor of GCN4 translation. PMID:18955495
NCBI GEO: archive for high-throughput functional genomic data. PMID:18940857
Experimental analysis of oligonucleotide microarray design criteria to detect deletions by comparative genomic hybridization. PMID:18940006
Norvaline is accumulated after a down-shift of oxygen in Escherichia coli W3110. PMID:18940002
SVD-based anatomy of gene expressions for correlation analysis in Arabidopsis thaliana. PMID:18931094
Loss of RNase R induces competence development in Legionella pneumophila. PMID:18849432
Targets of the Entamoeba histolytica transcription factor URE3-BP. PMID:18846235
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. PMID:18842599
Glycogen synthase kinase 3beta-mediated serine phosphorylation of the human glucocorticoid receptor redirects gene expression profiles. PMID:18838540
Organogenic nodule development in hop (Humulus lupulus L.): transcript and metabolic responses. PMID:18823540
Bioinformatic and statistical analysis of the optic nerve head in a primate model of ocular hypertension. PMID:18822132
Single-species microarrays and comparative transcriptomics. PMID:18815615
Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. PMID:18806003
Systematic bioinformatic analysis of expression levels of 17,330 human genes across 9,783 samples from 175 types of healthy and pathological tissues. PMID:18803840
Transcriptome analyses show changes in gene expression to accompany pollen germination and tube growth in Arabidopsis. PMID:18775970
Key issues in conducting a meta-analysis of gene expression microarray datasets. PMID:18767902
Cdc7-Dbf4 kinase overexpression in multiple cancers and tumor cell lines is correlated with p53 inactivation. PMID:18714392
Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs. PMID:18713869
Differential regulation of Listeria monocytogenes internalin and internalin-like genes by sigmaB and PrfA as revealed by subgenomic microarray analyses. PMID:18713061
A decade of genome-wide gene expression profiling in acute myeloid leukemia: flashback and prospects. PMID:18703705
Microarray analysis of human monocytes infected with Francisella tularensis identifies new targets of host response subversion. PMID:18698339
Superposition of transcriptional behaviors determines gene state. PMID:18682855
The Arabidopsis NFYA5 transcription factor is regulated transcriptionally and posttranscriptionally to promote drought resistance. PMID:18682547
Two new clock proteins, LWD1 and LWD2, regulate Arabidopsis photoperiodic flowering. PMID:18676661
Molecular credentialing of rodent bladder carcinogenesis models. PMID:18670642
Accessing and integrating data and knowledge for biomedical research. PMID:18660883
Gene expression patterns of sulfur starvation in Synechocystis sp. PCC 6803. PMID:18644144
Global gene expression profiles suggest an important role for nutrient acquisition in early pathogenesis in a plant model of Pseudomonas aeruginosa infection. PMID:18641163
MN1 affects expression of genes involved in hematopoiesis and can enhance as well as inhibit RAR/RXR-induced gene expression. PMID:18632758
Standardization Initiatives in the (eco)toxicogenomics domain: a review. PMID:18629184
Navigating public microarray databases. PMID:18629145
A bistable gene switch for antibiotic biosynthesis: the butyrolactone regulon in Streptomyces coelicolor. PMID:18628968
MAIDS resistance-associated gene expression patterns in secondary lymphoid organs. PMID:18612634
Differential variability analysis of gene expression and its application to human diseases. PMID:18586739
Genome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome. PMID:18567666
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PMID:18560577
Id1 is a common downstream target of oncogenic tyrosine kinases in leukemic cells. PMID:18559972
Whole genome assessment of the retinal response to diabetes reveals a progressive neurovascular inflammatory response. PMID:18554398
Transcriptional repression of c-Myb and GATA-2 is involved in the biologic effects of C/EBPalpha in p210BCR/ABL-expressing cells. PMID:18550858
Protein translation and cell death: the role of rare tRNAs in biofilm formation and in activating dormant phage killer genes. PMID:18545668
Combined analysis of murine and human microarrays and ChIP analysis reveals genes associated with the ability of MYC to maintain tumorigenesis. PMID:18535662
Calprotectin is released from human skeletal muscle tissue during exercise. PMID:18511485
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. PMID:18487259
HCLS 2.0/3.0: health care and life sciences data mashup using Web 2.0/3.0. PMID:18487092
Individual mRNA expression profiles reveal the effects of specific microRNAs. PMID:18485210
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. PMID:18463138
Global transcription in pluripotent embryonic stem cells. PMID:18462694
Identification of woolliness response genes in peach fruit after post-harvest treatments. PMID:18453640
Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots. PMID:18442363
Conserved co-expression for candidate disease gene prioritization. PMID:18433471
Uncovering signal transduction networks from high-throughput data by integer linear programming. PMID:18411207
Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats. PMID:18405950
Genome wide transcriptional profiling in breast cancer cells reveals distinct changes in hormone receptor target genes and chromatin modifying enzymes after proteasome inhibition. PMID:18381591
A software framework for microarray and gene expression object model (MAGE-OM) array design annotation. PMID:18366695
The R1 conjugative plasmid increases Escherichia coli biofilm formation through an envelope stress response. PMID:18344336
A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PMID:18320038
Temporal transcriptomic microarray analysis of "Dehalococcoides ethenogenes" strain 195 during the transition into stationary phase. PMID:18310438
Gene expression by the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough grown on an iron electrode under cathodic protection conditions. PMID:18310429
Discovery of agents that eradicate leukemia stem cells using an in silico screen of public gene expression data. PMID:18305216
A new perspective on transcriptional system regulation (TSR): towards TSR profiling. PMID:18297136
Activation of counter-regulatory mechanisms in a rat renal acute rejection model. PMID:18261221
Up regulation in gene expression of chromatin remodelling factors in cervical intraepithelial neoplasia. PMID:18248679
Pathways change in expression during replicative aging in Saccharomyces cerevisiae. PMID:18245757
Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis. PMID:18221554
EzArray: a web-based highly automated Affymetrix expression array data management and analysis system. PMID:18218103
The role of particulate matter-associated zinc in cardiac injury in rats. PMID:18197293
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. PMID:18177501
Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. PMID:18154662
Computational prediction of protein-protein interactions. PMID:18095187
AffyTrees: facilitating comparative analysis of Affymetrix plant microarray chips. PMID:18065560
Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. PMID:18053145
BioCAD: an information fusion platform for bio-network inference and analysis. PMID:18047703
Characterization of zfs1 as an mRNA-binding and -destabilizing protein in Schizosaccharomyces pombe. PMID:18042546
Comparative analysis of the sigma B-dependent stress responses in Listeria monocytogenes and Listeria innocua strains exposed to selected stress conditions. PMID:18024685
Demasculinization of X chromosomes in the Drosophila genus. PMID:17994090
Host pathogen protein interactions predicted by comparative modeling. PMID:17965183
Prediction potential of candidate biomarker sets identified and validated on gene expression data from multiple datasets. PMID:17963508
CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. PMID:17962311
miRGator: an integrated system for functional annotation of microRNAs. PMID:17942429
Weighted analysis of general microarray experiments. PMID:17937807
Phenotypic and transcriptomic analyses demonstrate interactions between the transcriptional regulators CtsR and Sigma B in Listeria monocytogenes. PMID:17933929
Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors. PMID:17925016
Gene expression trees in lymphoid development. PMID:17925013
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. PMID:17925008
Sharing and reusing gene expression profiling data in neuroscience. PMID:17917127
Cadmium triggers an integrated reprogramming of the metabolism of Synechocystis PCC6803, under the control of the Slr1738 regulator. PMID:17910763
Linking microarray reporters with protein functions. PMID:17897448
Reversible and permanent effects of tobacco smoke exposure on airway epithelial gene expression. PMID:17894889
SAGETTARIUS: a program to reduce the number of tags mapped to multiple transcripts and to plan SAGE sequencing stages. PMID:17884916
Evidence based selection of housekeeping genes. PMID:17878933
EDISA: extracting biclusters from multiple time-series of gene expression profiles. PMID:17850657
The embryonic muscle transcriptome of Caenorhabditis elegans. PMID:17848203
Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. PMID:17765265
PARE: a tool for comparing protein abundance and mRNA expression data. PMID:17718915
Genetic and molecular epidemiology. PMID:17699527
An "Electronic Fluorescent Pictograph" browser for exploring and analyzing large-scale biological data sets. PMID:17684564
Statistical analysis and significance testing of serial analysis of gene expression data using a Poisson mixture model. PMID:17683533
Selective regulation of bone cell apoptosis by translational isoforms of the glucocorticoid receptor. PMID:17682054
Meta-analysis of microarray results: challenges, opportunities, and recommendations for standardization. PMID:17651921
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. PMID:17645793
Identification of novel genes expressed during mouse tooth development by microarray gene expression analysis. PMID:17626284
Cell-specific microarray profiling experiments reveal a comprehensive picture of gene expression in the C. elegans nervous system. PMID:17612406
Strategy for encoding and comparison of gene expression signatures. PMID:17612401
Function of periplasmic hydrogenases in the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. PMID:17601789
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. PMID:17567993
Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. PMID:17559689
An efficient pseudomedian filter for tiling microrrays. PMID:17555595
PrestOMIC, an open source application for dissemination of proteomic datasets by individual laboratories. PMID:17553161
Molecular evidence for a link between the N363S glucocorticoid receptor polymorphism and altered gene expression. PMID:17535992
Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. PMID:17517326
Indole is an inter-species biofilm signal mediated by SdiA. PMID:17511876
Enterohemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin. PMID:17483266
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans. PMID:17472752
Functional dissection of the ash2 and ash1 transcriptomes provides insights into the transcriptional basis of wing phenotypes and reveals conserved protein interactions. PMID:17466076
Molecular characterisation of the early response in pigs to experimental infection with Actinobacillus pleuropneumoniae using cDNA microarrays. PMID:17466061
Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains. PMID:17451403
Identification of genes implicated in methapyrilene-induced hepatotoxicity by comparing differential gene expression in target and nontarget tissue. PMID:17450226
Up-regulation of tissue factor in human pulmonary artery endothelial cells after ultrafine particle exposure. PMID:17450221
The genopolis microarray database. PMID:17430566
DNA microarray data integration by ortholog gene analysis reveals potential molecular mechanisms of estrogen-dependent growth of human uterine fibroids. PMID:17407572
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. PMID:17400893
Graph-based identification of cancer signaling pathways from published gene expression signatures using PubLiME. PMID:17389643
Sharing detailed research data is associated with increased citation rate. PMID:17375194
Temperature-dependent expression of Listeria monocytogenes internalin and internalin-like genes suggests functional diversity of these proteins among the listeriae. PMID:17337561
From bytes to bedside: data integration and computational biology for translational cancer research. PMID:17319736
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PMID:17299599
Genome-wide profiling and analysis of Arabidopsis siRNAs. PMID:17298187
YcfR (BhsA) influences Escherichia coli biofilm formation through stress response and surface hydrophobicity. PMID:17293424
A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains. PMID:17270048
Global reconstruction of the human metabolic network based on genomic and bibliomic data. PMID:17267599
Human glucocorticoid receptor beta binds RU-486 and is transcriptionally active. PMID:17242213
DiscoverySpace: an interactive data analysis application. PMID:17210078
RINGdb: an integrated database for G protein-coupled receptors and regulators of G protein signaling. PMID:17173697
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it. PMID:17169146
Databases of free expression. PMID:17143588
Localization of a long-range cis-regulatory element of IL13 by allelic transcript ratio mapping. PMID:17135570
ArrayExpress--a public database of microarray experiments and gene expression profiles. PMID:17132828
Absolute enrichment: gene set enrichment analysis for homeostatic systems. PMID:17130162
NCBI GEO: mining tens of millions of expression profiles--database and tools update. PMID:17099226
Mining expressed sequence tags identifies cancer markers of clinical interest. PMID:17078886
Signatures from tissue-specific MPSS libraries identify transcripts preferentially expressed in the mouse inner ear. PMID:17049805
Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts. PMID:17030620
A new locus for autosomal dominant amelogenesis imperfecta on chromosome 8q24.3. PMID:17024372
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. PMID:17010196
The reactive oxygen species network pathways:an essential prerequisite for perception of pathogen attack and the acquired disease resistance in plants. PMID:17006022
Global comparative transcriptome analysis identifies gene network regulating secondary xylem development in Arabidopsis thaliana. PMID:16969662
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. PMID:16939800
Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. PMID:16888359
An open-access long oligonucleotide microarray resource for analysis of the human and mouse transcriptomes. PMID:16855282
An alpha-galactosidase with an essential function during leaf development. PMID:16845526
Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression. PMID:16776839
Expression profiling of the mouse early embryo: reflections and perspectives. PMID:16739220
Early days: genomics and human responses to infection. PMID:16679048
Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. PMID:16623940
YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. PMID:16597943
Modulation of the transcription regulatory program in yeast cells committed to sporulation. PMID:16542486
NABP1, a novel RORgamma-regulated gene encoding a single-stranded nucleic-acid-binding protein. PMID:16533169
Meeting report: Validation of toxicogenomics-based test systems: ECVAM-ICCVAM/NICEATM considerations for regulatory use. PMID:16507466
Global analysis of X-chromosome dosage compensation. PMID:16507155
The PowerAtlas: a power and sample size atlas for microarray experimental design and research. PMID:16504070
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. PMID:16465594
The Arabidopsis zinc finger-homeodomain genes encode proteins with unique biochemical properties that are coordinately expressed during floral development. PMID:16428600
A molecular signature of epithelial host defense: comparative gene expression analysis of cultured bronchial epithelial cells and keratinocytes. PMID:16420688
Recent applications of DNA microarray technology to toxicology and ecotoxicology. PMID:16393650
Biased alternative polyadenylation in human tissues. PMID:16356263
Mining published lists of cancer related microarray experiments: identification of a gene expression signature having a critical role in cell-cycle control. PMID:16351740
A quantization method based on threshold optimization for microarray short time series. PMID:16351737
Reverse-engineering gene-regulatory networks using evolutionary algorithms and grid computing. PMID:16328947
MiMiR: a comprehensive solution for storage, annotation and exchange of microarray data. PMID:16280078
MyoD induces myogenic differentiation through cooperation of its NH2- and COOH-terminal regions. PMID:16275751
Transformation of expression intensities across generations of Affymetrix microarrays using sequence matching and regression modeling. PMID:16224098
Unexpectedly high bacterial diversity in arctic tundra relative to boreal forest soils, revealed by serial analysis of ribosomal sequence tags. PMID:16204479
L2L: a simple tool for discovering the hidden significance in microarray expression data. PMID:16168088
XenDB: full length cDNA prediction and cross species mapping in Xenopus laevis. PMID:16162280
Storing, linking, and mining microarray databases using SRS. PMID:16048644
Reproducible clusters from microarray research: whither? PMID:16026595
Transcript copy number estimation using a mouse whole-genome oligonucleotide microarray. PMID:15998450
Regulation of mouse hepatic genes in response to diet induced obesity, insulin resistance and fasting induced weight reduction. PMID:15985155
Evaluation of the similarity of gene expression data estimated with SAGE and Affymetrix GeneChips. PMID:15955238
Local coexpression domains of two to four genes in the genome of Arabidopsis. PMID:15923337
Loss-of-function mutations in chitin responsive genes show increased susceptibility to the powdery mildew pathogen Erysiphe cichoracearum. PMID:15923325
Novel response to microtubule perturbation in meiosis. PMID:15899877
The Arabidopsis AtRaptor genes are essential for post-embryonic plant growth. PMID:15845148
MARS: microarray analysis, retrieval, and storage system. PMID:15836795
Profile of changes in gene expression in cultured hippocampal neurones evoked by the GABAB receptor agonist baclofen. PMID:15784695
Quantitative inference of dynamic regulatory pathways via microarray data. PMID:15748298
Can Zipf's law be adapted to normalize microarrays? PMID:15727680
Evolutionary significance of gene expression divergence. PMID:15716085
Presenilin-1-dependent transcriptome changes. PMID:15703411
Microarray analysis confirms the specificity of a Chlamydomonas reinhardtii chloroplast RNA stability mutant. PMID:15665248
BarleyBase--an expression profiling database for plant genomics. PMID:15608273
The Stanford Microarray Database accommodates additional microarray platforms and data formats. PMID:15608265
NCBI GEO: mining millions of expression profiles--database and tools. PMID:15608262
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:15608260
FlyBase: genes and gene models. PMID:15608223
CLOE: identification of putative functional relationships among genes by comparison of expression profiles between two species. PMID:15550177
Comparative profiling of lipid-soluble antioxidants and transcripts reveals two phases of photo-oxidative stress in a xanthophyll-deficient mutant of Chlamydomonas reinhardtii. PMID:15517390
Combining gene expression data from different generations of oligonucleotide arrays. PMID:15504239
In control: systematic assessment of microarray performance. PMID:15459748
PEDRo: a database for storing, searching and disseminating experimental proteomics data. PMID:15377392
GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. PMID:15375207
Handling multiple testing while interpreting microarrays with the Gene Ontology Database. PMID:15350198
Standards for microarray data: an open letter. PMID:15345376
Improving identification of differentially expressed genes in microarray studies using information from public databases. PMID:15345054
Performance evaluation of commercial short-oligonucleotide microarrays and the impact of noise in making cross-platform correlations. PMID:15345031
Submission of microarray data to public repositories. PMID:15340489
Selective and mutational patterns associated with gene expression in humans: influences on synonymous composition and intron presence. PMID:15280243
GOAL: automated Gene Ontology analysis of expression profiles. PMID:15215435
KARMA: a web server application for comparing and annotating heterogeneous microarray platforms. PMID:15215426
CARRIE web service: automated transcriptional regulatory network inference and interactive analysis. PMID:15215383
A survey of ovary-, testis-, and soma-biased gene expression in Drosophila melanogaster adults. PMID:15186491
Coexpression analysis of human genes across many microarray data sets. PMID:15173114
A bioinformatics analysis of memory consolidation reveals involvement of the transcription factor c-rel. PMID:15102909
Charting gene regulatory networks: strategies, challenges and perspectives. PMID:15080794
A gene atlas of the mouse and human protein-encoding transcriptomes. PMID:15075390
MiCoViTo: a tool for gene-centric comparison and visualization of yeast transcriptome states. PMID:15053844
Database development in toxicogenomics: issues and efforts. PMID:15033600
FlyGEM, a full transcriptome array platform for the Drosophila community. PMID:15003122
Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. PMID:14962989
Expression array annotation using the BioMediator biological data integration system and the BioConductor analytic platform. PMID:14728212
Scratching the (T cell) surface. PMID:14709166
The PEPR GeneChip data warehouse, and implementation of a dynamic time series query tool (SGQT) with graphical interface. PMID:14681485
NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. PMID:14681484
CleanEx: a database of heterogeneous gene expression data based on a consistent gene nomenclature. PMID:14681477
The Mouse SAGE Site: database of public mouse SAGE libraries. PMID:14681462
yMGV: a cross-species expression data mining tool. PMID:14681424
Database resources of the National Center for Biotechnology Information: update. PMID:14681353
ArrayTrack--supporting toxicogenomic research at the U.S. Food and Drug Administration National Center for Toxicological Research. PMID:14630514
Evaluation of gene expression measurements from commercial microarray platforms. PMID:14500831
Rapid evolution of male-biased gene expression in Drosophila. PMID:12907700
SOURCE: a unified genomic resource of functional annotations, ontologies, and gene expression data. PMID:12519986
ArrayExpress--a public repository for microarray gene expression data at the EBI. PMID:12519949
Database resources of the National Center for Biotechnology. PMID:12519941
Paucity of genes on the Drosophila X chromosome showing male-biased expression. PMID:12511656
Gene expression profiling with DNA microarrays: advancing our understanding of psychiatric disorders. PMID:12462404
BioArray Software Environment (BASE): a platform for comprehensive management and analysis of microarray data. PMID:12186655
Database resources of the National Center for Biotechnology Information: 2002 update. PMID:11752242
NCBI GEO: mining tens of millions of expression profiles--database and tools update PubMed citations: 656.

656 articles citing: NCBI GEO: mining tens of millions of expression profiles--database and tools update

Hsa-let-7c-5p, hsa-miR-130b-3p, and hsa-miR-142-3p as Novel miRNA Biomarkers for Melanoma Progression. PMID:35903462
Gene Expression Characteristics of Tumor and Adjacent Non-Tumor Tissues of Pancreatic Ductal Adenocarcinoma (PDAC) In-Silico. PMID:35891953
Identification of Immune-Related Gene Signature in Stanford Type A Aortic Dissection. PMID:35795203
Construction of a Prognostic Immune-Related LncRNA Risk Model for Gastric Cancer. PMID:35794986
From drug repositioning to target repositioning: prediction of therapeutic targets using genetically perturbed transcriptomic signatures. PMID:35758779
Comprehensive Analysis of m5C Methylation Regulatory Genes and Tumor Microenvironment in Prostate Cancer. PMID:35757739
CLP1 is a Prognosis-Related Biomarker and Correlates With Immune Infiltrates in Rheumatoid Arthritis. PMID:35721104
Identification of Core Genes and Screening of Potential Targets in Intervertebral Disc Degeneration Using Integrated Bioinformatics Analysis. PMID:35711934
Omics-based integrated analysis identified IKZF2 as a biomarker associated with lupus nephritis. PMID:35688845
Glomerular Expression of S100A8 in Lupus Nephritis: An Integrated Bioinformatics Analysis. PMID:35572531
Comprehensive Analysis of N6-Methyladenosine Regulators in the Subcluster Classification and Drug Candidates Prediction of Severe Obstructive Sleep Apnea. PMID:35559050
A Qualitative Signature to Identify TERT Promoter Mutant High-Risk Tumors in Low-Grade Gliomas. PMID:35495630
Identification of a Ferroptosis-Related Prognostic Gene PTGS2 Based on Risk Modeling and Immune Microenvironment of Early-Stage Cervical Cancer. PMID:35432535
Development of Tumor Mutation Burden-Related Prognostic Model and Novel Biomarker Identification in Stomach Adenocarcinoma. PMID:35399509
Screening of Potential Key Biomarkers for Ewing Sarcoma: Evidence from Gene Array Analysis. PMID:35342299
ECO: An Integrated Gene Expression Omnibus for Mouse Endothelial Cells In Vivo. PMID:35309132
Integrative Analyses of Genes Associated With Otologic Disorders in Turner Syndrome. PMID:35273637
Augmentation of Transcriptomic Data for Improved Classification of Patients with Respiratory Diseases of Viral Origin. PMID:35269624
CD44-Mediated Poor Prognosis in Glioma Is Associated With M2-Polarization of Tumor-Associated Macrophages and Immunosuppression. PMID:35187044
Aldehyde Dehydrogenase 2 Family Member (ALDH2) Is a Therapeutic Index for Oxaliplatin Response on Colorectal Cancer Therapy with Dysfunction p53. PMID:35178443
Clinical and molecular assessment of an onco-immune signature with prognostic significance in patients with colorectal cancer. PMID:35137551
Dysfunctional Network and Mutation Genes of Hypertrophic Cardiomyopathy. PMID:35126952
Down-regulated hsa_circ_0067934 facilitated the progression of gastric cancer by sponging hsa-mir-4705 to downgrade the expression of BMPR1B. PMID:35117027
Genome-wide methylation analyses identifies Non-coding RNA genes dysregulated in breast tumours that metastasise to the brain. PMID:35058523
Human α-defensin 6 (HD6) suppresses CRC proliferation and metastasis through abolished EGF/EGFR signaling pathway. PMID:34975297
Identification of Potential Genetic Biomarkers and Target Genes of Peri-Implantitis Using Bioinformatics Tools. PMID:34931168
Effects of Serum Metabolites on the Pancreatic Transcriptome in Acute Acalculous Cholecystitis. PMID:34925503
The Construction and Comprehensive Analysis of a ceRNA Immunoregulatory Network and Tissue-Infiltrating Immune Cells in Atrial Fibrillation. PMID:34876841
LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine. PMID:34850125
Identification of circRNA-miRNA-mRNA Regulatory Network and Autophagy Interaction Network in Atrial Fibrillation Based on Bioinformatics Analysis. PMID:34848999
Integrating network pharmacological and experimental models to investigate the therapeutic effects of baicalein in glaucoma. PMID:34823561
A five-gene methylation signature predicts overall survival of patients with clear cell renal cell carcinoma. PMID:34716619
Regulation of Tumor Metabolism and Extracellular Acidosis by the TIMP-10-CD63 Axis in Breast Carcinoma. PMID:34685701
The Identification of Childhood Asthma Progression-Related lncRNAs and mRNAs Suitable as Biomarkers Using Weighted Gene Coexpression Network Analysis. PMID:34456632
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
Network-based approach to identify prognosis-related genes in tamoxifen-treated patients with estrogen receptor-positive breast cancer. PMID:34406386
A ferroptosis-related gene signature for graft loss prediction following renal allograft. PMID:34338139
Identification of Key Genes Involved in Pancreatic Ductal Adenocarcinoma with Diabetes Mellitus Based on Gene Expression Profiling Analysis. PMID:34257566
Revisiting social MPE: an integration of molecular pathological epidemiology and social science in the new era of precision medicine. PMID:34253130
Identification of Macrophage Polarization-Related Genes as Biomarkers of Chronic Obstructive Pulmonary Disease Based on Bioinformatics Analyses. PMID:34250093
Overexpression of HPRT1 is associated with poor prognosis in head and neck squamous cell carcinoma. PMID:34231338
StrongestPath: a Cytoscape application for protein-protein interaction analysis. PMID:34187355
Insights into how environment shapes post-mortem RNA transcription in mouse brain. PMID:34155272
TTSurv: Exploring the Multi-Gene Prognosis in Thousands of Tumors. PMID:34113575
Reconciling multiple connectivity scores for drug repurposing. PMID:34013329
Signature RNAS and related regulatory roles in type 1 diabetes mellitus based on competing endogenous RNA regulatory network analysis. PMID:34006268
Identify potential miRNA-mRNA regulatory networks contributing to high-risk neuroblastoma. PMID:33666785
A novel prognostic prediction model based on seven immune-related RNAs for predicting overall survival of patients in early cervical squamous cell carcinoma. PMID:33588862
Identification of Three Significant Genes Associated with Immune Cells Infiltration in Dysfunctional Adipose Tissue-Induced Insulin-Resistance of Obese Patients via Comprehensive Bioinformatics Analysis. PMID:33564304
Potential biomarkers and lncRNA-mRNA regulatory networks in invasive growth hormone-secreting pituitary adenomas. PMID:33559847
LAPTM5 Plays a Key Role in the Diagnosis and Prognosis of Testicular Germ Cell Tumors. PMID:33521125
Screening and identification of potential biomarkers and therapeutic drugs in melanoma via integrated bioinformatics analysis. PMID:33501609
Profiling transcriptomic changes and signaling pathways in atopic dermatitis by integrative analyses on multiple databases. PMID:33438050
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
Clinical significance and potential mechanisms of miR-223-3p and miR-204-5p in squamous cell carcinoma of head and neck: a study based on TCGA and GEO. PMID:33336030
Immune-Related Four-lncRNA Signature for Patients with Cervical Cancer. PMID:33274204
Tumor Suppressive Maspin-Sensitized Prostate Cancer to Drug Treatment Through Negative Regulating Androgen Receptor Expression. PMID:33195208
Screening and Identification of Potential Biomarkers in Hepatitis B Virus-Related Hepatocellular Carcinoma by Bioinformatics Analysis. PMID:33193629
CGPE: an integrated online server for Cancer Gene and Pathway Exploration. PMID:33185687
Pan-transcriptome-based candidate therapeutic discovery for idiopathic pulmonary fibrosis. PMID:33167785
Combining bioinformatics techniques to explore the molecular mechanisms involved in pancreatic cancer metastasis and prognosis. PMID:33164330
Bioinformatics Gene Analysis of Potential Biomarkers and Therapeutic Targets for Unstable Atherosclerotic Plaque-Related Stroke. PMID:33155176
A connectivity map-based drug repurposing study and integrative analysis of transcriptomic profiling of SARS-CoV-2 infection. PMID:33130005
Identification of Hub Genes and Potential Molecular Mechanisms in Patients with HBV-Associated Acute Liver Failure. PMID:33100826
Weighted gene co-expression network analysis revealed key biomarkers associated with the diagnosis of hypertrophic cardiomyopathy. PMID:33099311
A review of systems biology research of anxiety disorders. PMID:33053074
Identification of Parkinson's disease-related pathways and potential risk factors. PMID:33021140
An Integrated Analysis of mRNAs and miRNAs Microarray Profiles to Screen miRNA Signatures Involved in Nasopharyngeal Carcinoma. PMID:32985354
Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. PMID:32967266
A seven-gene signature model predicts overall survival in kidney renal clear cell carcinoma. PMID:32883362
Identification of potential biomarkers and candidate small molecule drugs in glioblastoma. PMID:32874133
Six-Gene Signature Associated with Immune Cells in the Progression of Atherosclerosis Discovered by Comprehensive Bioinformatics Analyses. PMID:32821283
Analysis and identification of novel biomarkers involved in neuroblastoma via integrated bioinformatics. PMID:32772341
Characterization of Glycolysis-Associated Molecules in the Tumor Microenvironment Revealed by Pan-Cancer Tissues and Lung Cancer Single Cell Data. PMID:32635458
Bioinformatics Analysis of Prognostic miRNA Signature and Potential Critical Genes in Colon Cancer. PMID:32582275
COnTORT: COmprehensive Transcriptomic ORganizational Tool for Simultaneously Retrieving and Organizing Numerous Gene Expression Data Sets from the NCBI Gene Expression Omnibus Database. PMID:32554783
Interaction between ACOT7 and LncRNA NMRAL2P via Methylation Regulates Gastric Cancer Progression. PMID:32469171
Identification of Prognostic miRNA Signature and Lymph Node Metastasis-Related Key Genes in Cervical Cancer. PMID:32457603
Characterizing the Role of SMYD2 in Mammalian Embryogenesis-Future Directions. PMID:32408548
BIOMEX: an interactive workflow for (single cell) omics data interpretation and visualization. PMID:32392297
Identification of Potential Biomarkers Associated with Basal Cell Carcinoma. PMID:32382535
A putative competing endogenous RNA network in cisplatin-resistant lung adenocarcinoma cells identifying potentially rewarding research targets. PMID:32382346
Diagnostic model of combined ceRNA and DNA methylation related genes in esophageal carcinoma. PMID:32266120
Differential expression of AURKA/PLK4 in quiescence and senescence of osteosarcoma U2OS cells. PMID:32200684
Investigation of Potential Genetic Biomarkers and Molecular Mechanism of Ulcerative Colitis Utilizing Bioinformatics Analysis. PMID:32190668
LncRNA profile study reveals a seven-lncRNA signature predicts the prognosis of patients with colorectal cancer. PMID:32128213
Pathogenic Gene Prediction Algorithm Based on Heterogeneous Information Fusion. PMID:32117433
The lysine methyltransferase SMYD2 is required for normal lymphocyte development and survival of hematopoietic leukemias. PMID:32115575
Network-Based Genetic Profiling Reveals Cellular Pathway Differences Between Follicular Thyroid Carcinoma and Follicular Thyroid Adenoma. PMID:32093341
Curcumin Inhibits ERK/c-Jun Expressions and Phosphorylation against Endometrial Carcinoma. PMID:32083122
Integrative network modeling reveals mechanisms underlying T cell exhaustion. PMID:32024856
Network Pharmacology Approach Reveals the Potential Immune Function Activation and Tumor Cell Apoptosis Promotion of Xia Qi Decoction in Lung Cancer. PMID:31905767
Repurposing Drugs by In Silico Methods to Target BCR Kinase Domain in Chronic Myeloid Leukemia. PMID:31759365
Common Gene Expression Patterns in Environmental Model Organisms Exposed to Engineered Nanomaterials: A Meta-Analysis. PMID:31752483
Screening potential prognostic biomarkers of long non-coding RNAs for predicting the risk of chronic kidney disease. PMID:31721901
Multi-omics Analysis of Microenvironment Characteristics and Immune Escape Mechanisms of Hepatocellular Carcinoma. PMID:31681571
Significantly different expression levels of microRNAs associated with vascular invasion in hepatocellular carcinoma and their prognostic significance after surgical resection. PMID:31513595
Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm. PMID:31510663
Drug repurposing for Alzheimer's disease based on transcriptional profiling of human iPSC-derived cortical neurons. PMID:31492831
A five-gene signature to predict the overall survival time of patients with esophageal squamous cell carcinoma. PMID:31423201
Clinical value of microRNA-198-5p downregulation in lung adenocarcinoma and its potential pathways. PMID:31402959
Network Pharmacology-Based Prediction and Verification of the Targets and Mechanism for Panax Notoginseng Saponins against Coronary Heart Disease. PMID:31354855
Circular RNA Signature in Hepatocellular Carcinoma. PMID:31293639
Identification of key candidate genes for pancreatic cancer by bioinformatics analysis. PMID:31281439
Identification and in vivo Efficacy Assessment of Approved Orally Bioavailable Human Host Protein-Targeting Drugs With Broad Anti-influenza A Activity. PMID:31244822
Gene set enrichment analysis and meta-analysis identified 12 key genes regulating and controlling the prognosis of lung adenocarcinoma. PMID:31186783
Differentially Expressed Gene Screening, Biological Function Enrichment, and Correlation with Prognosis in Non-Small Cell Lung Cancer. PMID:31181055
Dysregulation of Mesenchymal Cell Survival Pathways in Severe Fibrotic Lung Disease: The Effect of Nintedanib Therapy. PMID:31156440
Plasticity of intestinal gene expression profile signatures reflected by nutritional interventions in piglets. PMID:31122193
Analysis of Effect of Schisandra in the Treatment of Myocardial Infarction Based on Three-Mode Gene Ontology Network. PMID:30949047
Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO). PMID:30922293
Mechanism-based disease similarity. PMID:30854526
Recent advances in gene function prediction using context-specific coexpression networks in plants. PMID:30800290
Leukemia multiclass assessment and classification from Microarray and RNA-seq technologies integration at gene expression level. PMID:30753220
The Association of rs1670533 Polymorphism in RNF212 Gene With the Risk of Down Syndrome in Young Women. PMID:30647754
Circulating miR-3659 may be a potential biomarker of dyslipidemia in patients with obesity. PMID:30642348
Identification of key genes and signaling pathways during Sendai virus infection in vitro. PMID:30637656
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. PMID:30576493
Gene set enrichment analysis and meta-analysis to identify six key genes regulating and controlling the prognosis of esophageal squamous cell carcinoma. PMID:30505479
Screening and clinical significance of tumor markers in head and neck squamous cell carcinoma through bioinformatics analysis. PMID:30431092
EndoDB: a database of endothelial cell transcriptomics data. PMID:30357379
Candidate Biomarkers and Molecular Mechanism Investigation for Glioblastoma Multiforme Utilizing WGCNA. PMID:30356407
Computational analysis of mRNA expression profiles identifies a novel triple-biomarker model as prognostic predictor of stage II and III colorectal adenocarcinoma patients. PMID:30214289
Multiclass classification for skin cancer profiling based on the integration of heterogeneous gene expression series. PMID:29750795
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
The Pathway Coexpression Network: Revealing pathway relationships. PMID:29554099
Construction and Analysis of Gene Co-Expression Networks in Escherichia coli. PMID:29518040
The mRNA, miRNA and lncRNA networks in hepatocellular carcinoma: An integrative transcriptomic analysis from Gene Expression Omnibus. PMID:29512731
Construction of key signal regulatory network in metastatic colorectal cancer. PMID:29464057
A new approach for interpreting Random Forest models and its application to the biology of ageing. PMID:29462247
SEMA3C drives cancer growth by transactivating multiple receptor tyrosine kinases via Plexin B1. PMID:29348142
Prediction of novel target genes and pathways involved in bevacizumab-resistant colorectal cancer. PMID:29342159
An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench). PMID:29273003
Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling. PMID:29157215
Gene expression information improves reliability of receptor status in breast cancer patients. PMID:29100391
Application of a co‑expression network for the analysis of aggressive and non‑aggressive breast cancer cell lines to predict the clinical outcome of patients. PMID:28944917
From Saccharomyces cerevisiae to human: The important gene co-expression modules. PMID:28804628
Integrated diagnostic network construction reveals a 4-gene panel and 5 cancer hallmarks driving breast cancer heterogeneity. PMID:28754978
Diagnostic MicroRNA Biomarker Discovery for Non-Small-Cell Lung Cancer Adenocarcinoma by Integrative Bioinformatics Analysis. PMID:28698868
Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula. PMID:28698354
Using Coexpression Protein Interaction Network Analysis to Identify Mechanisms of Danshensu Affecting Patients with Coronary Heart Disease. PMID:28629174
Prediction of lncRNA-protein interactions using HeteSim scores based on heterogeneous networks. PMID:28623317
Influenza-Omics and the Host Response: Recent Advances and Future Prospects. PMID:28604586
Multi-class computational evolution: development, benchmark evaluation and application to RNA-Seq biomarker discovery. PMID:28450890
Identification of Biomarkers for Schistosoma-Associated Pulmonary Arterial Hypertension Based on RNA-Seq Data of Mouse Whole Lung Tissues. PMID:28393260
LncFunNet: an integrated computational framework for identification of functional long noncoding RNAs in mouse skeletal muscle cells. PMID:28379566
A clustering-based approach for efficient identification of microRNA combinatorial biomarkers. PMID:28361698
Hsp90 regulation of fibroblast activation in pulmonary fibrosis. PMID:28239659
Fused Lasso Additive Model. PMID:28239246
Elucidating the modes of action for bioactive compounds in a cell-specific manner by large-scale chemically-induced transcriptomics. PMID:28071740
Androgen receptor transcriptionally regulates semaphorin 3C in a GATA2-dependent manner. PMID:28038451
Prediction of key genes and miRNAs responsible for loss of muscle force in patients during an acute exacerbation of chronic obstructive pulmonary disease. PMID:28025995
Perspectives on the history of evo-devo and the contemporary research landscape in the genomics era. PMID:27994116
Growth hormone-releasing hormone receptor antagonists inhibit human gastric cancer through downregulation of PAK1-STAT3/NF-κB signaling. PMID:27930339
Identification of potential biomarkers and drugs for papillary thyroid cancer based on gene expression profile analysis. PMID:27779685
KLHL21, a novel gene that contributes to the progression of hepatocellular carcinoma. PMID:27769251
The Role of Neutrophil Proteins on the Amyloid Beta-RAGE Axis. PMID:27676391
THBS2 is a Potential Prognostic Biomarker in Colorectal Cancer. PMID:27632935
Genomic-Wide Analysis with Microarrays in Human Oncology. PMID:27600234
Expression deregulation of mir31 and CXCL12 in two types of oral precancers and cancer: importance in progression of precancer and cancer. PMID:27597234
Repositioning of a cyclin-dependent kinase inhibitor GW8510 as a ribonucleotide reductase M2 inhibitor to treat human colorectal cancer. PMID:27551518
Comparison of the compatible solute pool of two slightly halophilic planctomycetes species, Gimesia maris and Rubinisphaera brasiliensis. PMID:27502056
Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach. PMID:27446133
Approaches to uncovering cancer diagnostic and prognostic molecular signatures. PMID:27308330
A network-driven approach for genome-wide association mapping. PMID:27307613
The role of drug profiles as similarity metrics: applications to repurposing, adverse effects detection and drug-drug interactions. PMID:27273288
Systematic discovery of drug action mechanisms by an integrated chemical genomics approach: identification of functional disparities between azacytidine and decitabine. PMID:27036028
Weighted gene co-expression network analysis identifies specific modules and hub genes related to coronary artery disease. PMID:26944061
Integrated analysis of DNA methylation profiles and gene expression profiles to identify genes associated with pilocytic astrocytomas. PMID:26934913
Prediction of Candidate Drugs for Treating Pancreatic Cancer by Using a Combined Approach. PMID:26910401
Identification of key genes associated with gastric cancer based on DNA microarray data. PMID:26870242
A semi-parametric statistical model for integrating gene expression profiles across different platforms. PMID:26818110
A Novel Biomarker Panel Examining Response to Gemcitabine with or without Erlotinib for Pancreatic Cancer Therapy in NCIC Clinical Trials Group PA.3. PMID:26808546
Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation. PMID:26795250
The Molecular Signatures Database (MSigDB) hallmark gene set collection. PMID:26771021
CrossNorm: a novel normalization strategy for microarray data in cancers. PMID:26732145
Transcriptional profiling of the leaves of near-isogenic rice lines with contrasting drought tolerance at the reproductive stage in response to water deficit. PMID:26715311
Genome-wide profiling to analyze the effects of FXR activation on mouse renal proximal tubular cells. PMID:26697325
MERAV: a tool for comparing gene expression across human tissues and cell types. PMID:26626150
A comparison of human and mouse gene co-expression networks reveals conservation and divergence at the tissue, pathway and disease levels. PMID:26589719
Identification of hub genes of pneumocyte senescence induced by thoracic irradiation using weighted gene co‑expression network analysis. PMID:26572216
The MAP3K ZAK, a novel modulator of ERK-dependent migration, is upregulated in colorectal cancer. PMID:26522728
Methods for biological data integration: perspectives and challenges. PMID:26490630
The influence of cancer tissue sampling on the identification of cancer characteristics. PMID:26490514
A respiratory chain controlled signal transduction cascade in the mitochondrial intermembrane space mediates hydrogen peroxide signaling. PMID:26438848
Pathogen-regulated genes in wheat isogenic lines differing in resistance to brown rust Puccinia triticina. PMID:26438375
Downregulation of ASPP2 in pancreatic cancer cells contributes to increased resistance to gemcitabine through autophagy activation. PMID:26438046
Enhanced MAF Oncogene Expression and Breast Cancer Bone Metastasis. PMID:26376684
Seq-ing improved gene expression estimates from microarrays using machine learning. PMID:26338512
MGFM: a novel tool for detection of tissue and cell specific marker genes from microarray gene expression data. PMID:26314578
Identification of Gene Biomarkers for Distinguishing Small-Cell Lung Cancer from Non-Small-Cell Lung Cancer Using a Network-Based Approach. PMID:26290870
Identification of autophagy signaling network that contributes to stroke in the ischemic rodent brain via gene expression. PMID:26254060
Functional analysis of the nasopharyngeal carcinoma primary tumor‑associated gene interaction network. PMID:26238040
Microarray Analysis of the Major Depressive Disorder mRNA Profile Data. PMID:26207134
ATM regulation of IL-8 links oxidative stress to cancer cell migration and invasion. PMID:26030852
BioMiner: Paving the Way for Personalized Medicine. PMID:26005322
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
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs. PMID:25972521
Identify the signature genes for diagnose of uveal melanoma by weight gene co-expression network analysis. PMID:25938039
cMonkey2: Automated, systematic, integrated detection of co-regulated gene modules for any organism. PMID:25873626
A software tool for the input and management of phenotypic data using personal digital assistants and other mobile devices. PMID:25866550
NexGenEx-Tom: a gene expression platform to investigate the functionalities of the tomato genome. PMID:25849067
Traits and types of health data repositories. PMID:25825668
The HMGB1-RAGE Inflammatory Pathway: Implications for Brain Injury-Induced Pulmonary Dysfunction. PMID:25751601
Machine learning applications in cancer prognosis and prediction. PMID:25750696
Meta-Analysis of Gene Expression in Autism Spectrum Disorder. PMID:25720351
Database of Gene Co-Regulation (dGCR): A Web Tool for Analysing Patterns of Gene Co-regulation across Publicly Available Expression Data. PMID:25628763
Identification of key genes associated with colorectal cancer based on the transcriptional network. PMID:25613817
Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. PMID:25477382
Diversity, expression and mRNA targeting abilities of Argonaute-targeting miRNAs among selected vascular plants. PMID:25443390
Predicting the potential ankylosing spondylitis-related genes utilizing bioinformatics approaches. PMID:25432079
Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data. PMID:25414366
Revealing the potential pathogenesis of glioma by utilizing a glioma associated protein-protein interaction network. PMID:25410026
Ectopic lignification in the flax lignified bast fiber1 mutant stem is associated with tissue-specific modifications in gene expression and cell wall composition. PMID:25381351
CLUH regulates mitochondrial biogenesis by binding mRNAs of nuclear-encoded mitochondrial proteins. PMID:25349259
Understanding disease mechanisms with models of signaling pathway activities. PMID:25344409
Network-based analysis of comorbidities risk during an infection: SARS and HIV case studies. PMID:25344230
Cyberinfrastructure for the digital brain: spatial standards for integrating rodent brain atlases. PMID:25309417
Biological network exploration with Cytoscape 3. PMID:25199793
MYLK and MYL9 expression in non-small cell lung cancer identified by bioinformatics analysis of public expression data. PMID:25179839
Dynamic modularity of host protein interaction networks in Salmonella Typhi infection. PMID:25144185
Identification of collaboration patterns of dysfunctional pathways in breast cancer. PMID:25120762
Toward effective sharing of high-dimensional immunology data. PMID:25101748
Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum. PMID:25063396
Bioinformatics on the cloud computing platform Azure. PMID:25050811
Large-scale investigation of human TF-miRNA relations based on coexpression profiles. PMID:24995316
Exploring the optimal strategy to predict essential genes in microbes. PMID:24970124
Deconvolution of the gene expression profiles of valuable banked blood specimens for studying the prognostic values of altered peripheral immune cell proportions in cancer patients. PMID:24959668
LINCS Canvas Browser: interactive web app to query, browse and interrogate LINCS L1000 gene expression signatures. PMID:24906883
Mycoplasma contamination in the 1000 Genomes Project. PMID:24872843
Correlation between PDZK1, Cdc37, Akt and breast cancer malignancy: the role of PDZK1 in cell growth through Akt stabilization by increasing and interacting with Cdc37. PMID:24869908
RARRES3 suppresses breast cancer lung metastasis by regulating adhesion and differentiation. PMID:24867881
Transduction motif analysis of gastric cancer based on a human signaling network. PMID:24838641
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. PMID:24771658
On integrating multi-experiment microarray data. PMID:24751870
Quantitative transcriptional changes associated with chlorosis severity in mosaic leaves of tobacco plants infected with Cucumber mosaic virus. PMID:24745045
Unexpectedly low nitrogen acquisition and absence of root architecture adaptation to nitrate supply in a Medicago truncatula highly branched root mutant. PMID:24706718
Refining gold from existing data. PMID:24625777
Translational research platforms integrating clinical and omics data: a review of publicly available solutions. PMID:24608524
Differential enrichment of regulatory motifs in the composite network of protein-protein and gene regulatory interactions. PMID:24576339
Meta-analysis and gene set analysis of archived microarrays suggest implication of the spliceosome in metastatic and hypoxic phenotypes. PMID:24497970
Is gene transcription involved in seed dry after-ripening? PMID:24466101
A Sorghum bicolor expression atlas reveals dynamic genotype-specific expression profiles for vegetative tissues of grain, sweet and bioenergy sorghums. PMID:24456189
Expression sensitivity analysis of human disease related genes. PMID:24350280
Identification of unstable network modules reveals disease modules associated with the progression of Alzheimer's disease. PMID:24348898
Hierarchical clustering of high-throughput expression data based on general dependences. PMID:24334400
DeGNServer: deciphering genome-scale gene networks through high performance reverse engineering analysis. PMID:24328032
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. PMID:24304892
Integrating in silico resources to map a signaling network. PMID:24233784
SPIEDw: a searchable platform-independent expression database web tool. PMID:24199845
GPLEXUS: enabling genome-scale gene association network reconstruction and analysis for very large-scale expression data. PMID:24178033
Genes and co-expression modules common to drought and bacterial stress responses in Arabidopsis and rice. PMID:24130868
Metastasis tumor-associated protein 2 enhances metastatic behavior and is associated with poor outcomes in estrogen receptor-negative breast cancer. PMID:24077732
ExpressionBlast: mining large, unstructured expression databases. PMID:24076985
Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data. PMID:24067414
Metadata management and semantics in microarray repositories. PMID:24052712
Functional comparison between genes dysregulated in ulcerative colitis and colorectal carcinoma. PMID:23991021
Differential expression analysis with global network adjustment. PMID:23968143
Key pathways and genes controlling the development and progression of clear cell renal cell carcinoma (ccRCC) based on gene set enrichment analysis. PMID:23943374
Genome-wide survey and comparative analysis of LTR retrotransposons and their captured genes in rice and sorghum. PMID:23923055
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data. PMID:23895370
Analysis of differentially expressed genes in abiotic stress response and their role in signal transduction pathways. PMID:23893304
Pathprinting: An integrative approach to understand the functional basis of disease. PMID:23890051
Assessing Global Transcriptome Changes in Response to South African Cassava Mosaic Virus [ZA-99] Infection in Susceptible Arabidopsis thaliana. PMID:23826319
PDZK1 is a novel factor in breast cancer that is indirectly regulated by estrogen through IGF-1R and promotes estrogen-mediated growth. PMID:23821363
iPcc: a novel feature extraction method for accurate disease class discovery and prediction. PMID:23761440
ChIPXpress: using publicly available gene expression data to improve ChIP-seq and ChIP-chip target gene ranking. PMID:23758851
Identification of novel tissue-specific genes by analysis of microarray databases: a human and mouse model. PMID:23741331
PLANEX: the plant co-expression database. PMID:23688397
Pax6 expressed in osteocytes inhibits canonical Wnt signaling. PMID:23529217
Target identification and mechanism of action in chemical biology and drug discovery. PMID:23508189
Dissection of regulatory networks that are altered in disease via differential co-expression. PMID:23505361
Screening key genes and pathways in glioma based on gene set enrichment analysis and meta-analysis. PMID:23494636
Pitfalls in experimental designs for characterizing the transcriptional, methylational and copy number changes of oncogenes and tumor suppressor genes. PMID:23472150
Drug target inference through pathway analysis of genomics data. PMID:23369829
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments. PMID:23307556
Reverse engineering: a key component of systems biology to unravel global abiotic stress cross-talk. PMID:23293646
Overview of DNA microarrays: types, applications, and their future. PMID:23288464
A measure of the signal-to-noise ratio of microarray samples and studies using gene correlations. PMID:23251415
Transcriptome analysis reveals unique metabolic features in the Cryptosporidium parvum Oocysts associated with environmental survival and stresses. PMID:23171372
Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PMID:23166598
Distributional fold change test - a statistical approach for detecting differential expression in microarray experiments. PMID:23122055
Non-gaussian distributions affect identification of expression patterns, functional annotation, and prospective classification in human cancer genomes. PMID:23118863
A gene-phenotype network based on genetic variability for drought responses reveals key physiological processes in controlled and natural environments. PMID:23056196
GeneFriends: an online co-expression analysis tool to identify novel gene targets for aging and complex diseases. PMID:23039964
TARGETgene: a tool for identification of potential therapeutic targets in cancer. PMID:22952662
Different gene expression profiles in normo- and dyslipidemic men after fish oil supplementation: results from a randomized controlled trial. PMID:22929118
Group normalization for genomic data. PMID:22912661
Motif effects in Affymetrix GeneChips seriously affect probe intensities. PMID:22904084
Integrating external biological knowledge in the construction of regulatory networks from time-series expression data. PMID:22898396
Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes. PMID:22838965
Histone H2B monoubiquitination facilitates the rapid modulation of gene expression during Arabidopsis photomorphogenesis. PMID:22829781
[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
'MicroRNA Targets', a new AthaMap web-tool for genome-wide identification of miRNA targets in Arabidopsis thaliana. PMID:22800758
Progression to adrenocortical tumorigenesis in mice and humans through insulin-like growth factor 2 and β-catenin. PMID:22800756
The core regulation module of stress-responsive regulatory networks in yeast. PMID:22784859
Gemma: a resource for the reuse, sharing and meta-analysis of expression profiling data. PMID:22782548
Proteome-wide prediction of protein-protein interactions from high-throughput data. PMID:22729399
Silencing of enzymes involved in ceramide biosynthesis causes distinct global alterations of lipid homeostasis and gene expression. PMID:22628619
Comparative genome analysis of central nitrogen metabolism and its control by GlnR in the class Bacilli. PMID:22607086
Inferring a protein interaction map of Mycobacterium tuberculosis based on sequences and interologs. PMID:22595003
Comprehensive gene expression analysis of the NAC gene family under normal growth conditions, hormone treatment, and drought stress conditions in rice using near-isogenic lines (NILs) generated from crossing Aday Selection (drought tolerant) and IR64. PMID:22526427
Galectins in hematological malignancies. PMID:22432074
Genomic analysis of wig-1 pathways. PMID:22347364
Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments. PMID:22325809
Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction. PMID:22319178
Bioinformatics tools and novel challenges in long non-coding RNAs (lncRNAs) functional analysis. PMID:22312241
Medicago truncatula transporter database: a comprehensive database resource for M. truncatula transporters. PMID:22309450
ChIP sequencing of cyclin D1 reveals a transcriptional role in chromosomal instability in mice. PMID:22307325
A comparative study of gene-expression data of basal cell carcinoma and melanoma reveals new insights about the two cancers. PMID:22295108
A searchable cross-platform gene expression database reveals connections between drug treatments and disease. PMID:22233519
Normalized Affymetrix expression data are biased by G-quadruplex formation. PMID:22199258
Genomic approach to study floral development genes in Rosa sp. PMID:22194838
Systematic identification of functional modules and cis-regulatory elements in Arabidopsis thaliana. PMID:22168340
Comparative analysis of root transcriptome profiles of two pairs of drought-tolerant and susceptible rice near-isogenic lines under different drought stress. PMID:22136218
Hyperactivation of oxidative mitochondrial metabolism in epithelial cancer cells in situ: visualizing the therapeutic effects of metformin in tumor tissue. PMID:22134189
Complex trait subtypes identification using transcriptome profiling reveals an interaction between two QTL affecting adiposity in chicken. PMID:22103296
Comparative transcriptome analysis of AP2/EREBP gene family under normal and hormone treatments, and under two drought stresses in NILs setup by Aday Selection and IR64. PMID:22102215
High Expression of Complement Component 5 (C5) at Tumor Site Associates with Superior Survival in Ewing's Sarcoma Family of Tumour Patients. PMID:22084725
Construction of regulatory networks using expression time-series data of a genotyped population. PMID:22084118
GeneWeaver: a web-based system for integrative functional genomics. PMID:22080549
ENCODE whole-genome data in the UCSC Genome Browser: update 2012. PMID:22075998
Composite effects of gene determinants on the translation speed and density of ribosomes. PMID:22050731
The transcriptome of the reference potato genome Solanum tuberosum Group Phureja clone DM1-3 516R44. PMID:22046362
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
Multi-membership gene regulation in pathway based microarray analysis. PMID:21939531
Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair. PMID:21878096
Analysis of human meiotic recombination events with a parent-sibling tracing approach. PMID:21867557
Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data. PMID:21864367
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
PTEN, NHERF1 and PHLPP form a tumor suppressor network that is disabled in glioblastoma. PMID:21804599
Who shares? Who doesn't? Factors associated with openly archiving raw research data. PMID:21765886
Systemic response to Campylobacter jejuni infection by profiling gene transcription in the spleens of two genetic lines of chickens. PMID:21748442
An evolutionary trade-off between protein turnover rate and protein aggregation favors a higher aggregation propensity in fast degrading proteins. PMID:21731483
KIAA0101 interacts with BRCA1 and regulates centrosome number. PMID:21673012
Computationally translating molecular discoveries into tools for medicine: translational bioinformatics articles now featured in JAMIA. PMID:21672904
Dissecting the oncogenic and tumorigenic potential of differentiated human induced pluripotent stem cells and human embryonic stem cells. PMID:21646469
Targeted mRNA oxidation regulates sunflower seed dormancy alleviation during dry after-ripening. PMID:21642546
D-MaPs - DNA-microarray projects: Web-based software for multi-platform microarray analysis. PMID:21637530
A comparison of machine learning techniques for survival prediction in breast cancer. PMID:21569330
Evidence for a stromal-epithelial "lactate shuttle" in human tumors: MCT4 is a marker of oxidative stress in cancer-associated fibroblasts. PMID:21558814
Molecular profiling of a lethal tumor microenvironment, as defined by stromal caveolin-1 status in breast cancers. PMID:21521946
Ketones and lactate increase cancer cell "stemness," driving recurrence, metastasis and poor clinical outcome in breast cancer: achieving personalized medicine via Metabolo-Genomics. PMID:21512313
Characterization of a cinnamoyl-CoA reductase 1 (CCR1) mutant in maize: effects on lignification, fibre development, and global gene expression. PMID:21493812
ROS-DET: robust detector of switching mechanisms in gene expression. PMID:21459849
hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. PMID:21450710
HOCTAR database: a unique resource for microRNA target prediction. PMID:21435384
A method for visualization of "omic" datasets for sphingolipid metabolism to predict potentially interesting differences. PMID:21415121
AnyExpress: integrated toolkit for analysis of cross-platform gene expression data using a fast interval matching algorithm. PMID:21410990
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
The phosphoinositide kinase PIKfyve is vital in early embryonic development: preimplantation lethality of PIKfyve-/- embryos but normality of PIKfyve+/- mice. PMID:21349843
BiC: a web server for calculating bimodality of coexpression between gene and protein networks. PMID:21345871
Public sharing of research datasets: a pilot study of associations. PMID:21339841
Rapid diagnosis of medulloblastoma molecular subgroups. PMID:21325292
GCOD - GeneChip Oncology Database. PMID:21291543
Epigenetic regulation of human β-defensin 2 and CC chemokine ligand 20 expression in gingival epithelial cells in response to oral bacteria. PMID:21248725
The TB Structural Genomics Consortium: a decade of progress. PMID:21247804
ATTED-II updates: condition-specific gene coexpression to extend coexpression analyses and applications to a broad range of flowering plants. PMID:21217125
A two-step site and mRNA-level model for predicting microRNA targets. PMID:21194446
BiologicalNetworks 2.0--an integrative view of genome biology data. PMID:21190573
SVM classifier to predict genes important for self-renewal and pluripotency of mouse embryonic stem cells. PMID:21176149
Validation and characterization of DNA microarray gene expression data distribution and associated moments. PMID:21092329
The DNA methylome of human peripheral blood mononuclear cells. PMID:21085693
COXPRESdb: a database to compare gene coexpression in seven model animals. PMID:21081562
An SF1 affinity model to identify branch point sequences in human introns. PMID:21071404
Integrative analysis correlates donor transcripts to recipient autoantibodies in primary graft dysfunction after lung transplantation. PMID:21070236
Density based pruning for identification of differentially expressed genes from microarray data. PMID:21047384
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants. PMID:21044364
Prioritizing genes associated with prostate cancer development. PMID:21044312
RegPhos: a system to explore the protein kinase-substrate phosphorylation network in humans. PMID:21037261
RBPDB: a database of RNA-binding specificities. PMID:21036867
MediPlEx - a tool to combine in silico & experimental gene expression profiles of the model legume Medicago truncatula. PMID:20958970
Genome-wide expression patterns in physiological cardiac hypertrophy. PMID:20937113
Multi-species integrative biclustering. PMID:20920250
Toward a complete in silico, multi-layered embryonic stem cell regulatory network. PMID:20890967
Differentially expressed RNA from public microarray data identifies serum protein biomarkers for cross-organ transplant rejection and other conditions. PMID:20885780
Asymmetric microarray data produces gene lists highly predictive of research literature on multiple cancer types. PMID:20875095
Investigating the predictability of essential genes across distantly related organisms using an integrative approach. PMID:20870748
Motif prediction to distinguish LPS-stimulated pro-inflammatory vs. antibacterial macrophage genes. PMID:20858252
Candidate gene prioritization by network analysis of differential expression using machine learning approaches. PMID:20840752
A systems biology approach to identify effective cocktail drugs. PMID:20840734
Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana. PMID:20840729
Current concepts of follicle-stimulating hormone receptor gene regulation. PMID:20739665
Translational bioinformatics in the cloud: an affordable alternative. PMID:20691073
Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PMID:20676366
Quantitative gene expression profiles in real time from expressed sequence tag databases. PMID:20635574
Stability of ranked gene lists in large microarray analysis studies. PMID:20625502
Connecting mutations of the RNA polymerase II C-terminal domain to complex phenotypic changes using combined gene expression and network analyses. PMID:20613981
The gene expression profile in the synovium as a predictor of the clinical response to infliximab treatment in rheumatoid arthritis. PMID:20593016
Meta-analysis of kindling-induced gene expression changes in the rat hippocampus. PMID:20582280
UFFizi: a generic platform for ranking informative features. PMID:20525252
Genome-wide identification of new Wnt/beta-catenin target genes in the human genome using CART method. PMID:20515496
Detecting microRNA activity from gene expression data. PMID:20482775
A differentiation-based phylogeny of cancer subtypes. PMID:20463876
A Bayesian framework to account for complex non-genetic factors in gene expression levels greatly increases power in eQTL studies. PMID:20463871
Predicting environmental chemical factors associated with disease-related gene expression data. PMID:20459635
Molecular signaling in zebrafish development and the vertebrate phylotypic period. PMID:20433455
Systems biology in heart diseases. PMID:20411053
Identification of responsive gene modules by network-based gene clustering and extending: application to inflammation and angiogenesis. PMID:20406493
Signal pathways JNK and NF-kappaB, identified by global gene expression profiling, are involved in regulation of TNFalpha-induced mPGES-1 and COX-2 expression in gingival fibroblasts. PMID:20398340
Robin: an intuitive wizard application for R-based expression microarray quality assessment and analysis. PMID:20388663
Coexpression landscape in ATTED-II: usage of gene list and gene network for various types of pathways. PMID:20383554
Semantic relations for interpreting DNA microarray data. PMID:20351860
Recall and bias of retrieving gene expression microarray datasets through PubMed identifiers. PMID:20349403
Vascular endothelial growth factor B controls endothelial fatty acid uptake. PMID:20228789
TiSGeD: a database for tissue-specific genes. PMID:20223836
TC-motifs at the TATA-box expected position in plant genes: a novel class of motifs involved in the transcription regulation. PMID:20222994
Increasing alternative promoter repertories is positively associated with differential expression and disease susceptibility. PMID:20208995
Statistical expression deconvolution from mixed tissue samples. PMID:20202973
Gene expression prediction by soft integration and the elastic net-best performance of the DREAM3 gene expression challenge. PMID:20169069
Tight junction-associated MARVEL proteins marveld3, tricellulin, and occludin have distinct but overlapping functions. PMID:20164257
The receptor for advanced glycation end products (RAGE) and the lung. PMID:20145712
Network-based elucidation of human disease similarities reveals common functional modules enriched for pluripotent drug targets. PMID:20140234
Classification of genes and putative biomarker identification using distribution metrics on expression profiles. PMID:20140228
Gene expression profiling and network analysis reveals lipid and steroid metabolism to be the most favored by TNFalpha in HepG2 cells. PMID:20140224
Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. PMID:20126639
An integrative modular approach to systematically predict gene-phenotype associations. PMID:20122238
The submergence tolerance regulator Sub1A mediates stress-responsive expression of AP2/ERF transcription factors. PMID:20107022
Translation efficiency in humans: tissue specificity, global optimization and differences between developmental stages. PMID:20097653
Does replication groups scoring reduce false positive rate in SNP interaction discovery? PMID:20092660
Near-isogenic cotton germplasm lines that differ in fiber-bundle strength have temporal differences in fiber gene expression patterns as revealed by comparative high-throughput profiling. PMID:20087569
A censored beta mixture model for the estimation of the proportion of non-differentially expressed genes. PMID:20080506
NetPath: a public resource of curated signal transduction pathways. PMID:20067622
Antibodies specifically target AML antigen NuSAP1 after allogeneic bone marrow transplantation. PMID:20053754
Prediction of microRNAs affecting mRNA expression during retinal development. PMID:20053268
REDD1 is a major target of testosterone action in preventing dexamethasone-induced muscle loss. PMID:20032058
Genetic variation at the FTO locus influences RBL2 gene expression. PMID:20009087
ConceptGen: a gene set enrichment and gene set relation mapping tool. PMID:20007254
Mutation patterns in cancer genomes. PMID:19995982
deepBase: a database for deeply annotating and mining deep sequencing data. PMID:19966272
Mining for coexpression across hundreds of datasets using novel rank aggregation and visualization methods. PMID:19961599
The polyamine metabolism genes ornithine decarboxylase and antizyme 2 predict aggressive behavior in neuroblastomas with and without MYCN amplification. PMID:19960435
Improving gene expression similarity measurement using pathway-based analytic dimension. PMID:19958478
Using transcriptome profiling to characterize QTL regions on chicken chromosome 5. PMID:19954542
Consensus miRNA expression profiles derived from interplatform normalization of microarray data. PMID:19948767
Colorectal cancer cell-derived microvesicles are enriched in cell cycle-related mRNAs that promote proliferation of endothelial cells. PMID:19930720
Genetic resources for maize cell wall biology. PMID:19926802
The use of neuroproteomics in drug abuse research. PMID:19926406
HAMSTER: visualizing microarray experiments as a set of minimum spanning trees. PMID:19925686
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. PMID:19923232
Dynamism in gene expression across multiple studies. PMID:19920211
Illumina WG-6 BeadChip strips should be normalized separately. PMID:19903361
Identification of microRNA activity by Targets' Reverse EXpression. PMID:19897564
The ferroportin metal efflux proteins function in iron and cobalt homeostasis in Arabidopsis. PMID:19861554
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. PMID:19828039
AntigenDB: an immunoinformatics database of pathogen antigens. PMID:19820110
Genoproteomic mining of urothelial cancer suggests {gamma}-glutamyl hydrolase and diazepam-binding inhibitor as putative urinary markers of outcome after chemotherapy. PMID:19815704
Unsupervised meta-analysis on diverse gene expression datasets allows insight into gene function and regulation. PMID:19812781
T-bet-dependent S1P5 expression in NK cells promotes egress from lymph nodes and bone marrow. PMID:19808259
Extensive structural renovation of retrogenes in the evolution of the Populus genome. PMID:19789289
Beyond element-wise interactions: identifying complex interactions in biological processes. PMID:19774090
Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression. PMID:19767600
Genetic analysis of variation in human meiotic recombination. PMID:19763160
Towards large-scale sample annotation in gene expression repositories. PMID:19761579
Exploratory and inferential analysis of gene cluster neighborhood graphs. PMID:19751523
Efficiently finding genome-wide three-way gene interactions from transcript- and genotype-data. PMID:19736252
Meta-analysis of glioblastoma multiforme versus anaplastic astrocytoma identifies robust gene markers. PMID:19732454
Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach. PMID:19728875
Identification of a novel function of PiT1 critical for cell proliferation and independent of its phosphate transport activity. PMID:19726692
Transcriptional response of the model planctomycete Rhodopirellula baltica SH1(T) to changing environmental conditions. PMID:19725962
Expression of Wnt receptors in adult spiral ganglion neurons: frizzled 9 localization at growth cones of regenerating neurites. PMID:19716861
Mapping accessible chromatin regions using Sono-Seq. PMID:19706456
Network-assisted protein identification and data interpretation in shotgun proteomics. PMID:19690572
A computational screen for regulators of oxidative phosphorylation implicates SLIRP in mitochondrial RNA homeostasis. PMID:19680543
Impaired uptake and/or utilization of leucine by Saccharomyces cerevisiae is suppressed by the SPT15-300 allele of the TATA-binding protein gene. PMID:19666729
Human disease-drug network based on genomic expression profiles. PMID:19657382
Discovery of genes essential for heme biosynthesis through large-scale gene expression analysis. PMID:19656490
Assessing individual differences in genome-wide gene expression in human whole blood: reliability over four hours and stability over 10 months. PMID:19653838
Therapeutic effect of CD137 immunomodulation in lymphoma and its enhancement by Treg depletion. PMID:19641184
An integrative network approach to map the transcriptome to the phenome. PMID:19630539
Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis. PMID:19620096
TileProbe: modeling tiling array probe effects using publicly available data. PMID:19592393
Comparative analysis of protein-protein interactions in cancer-associated genes. PMID:19591789
Automated multidimensional phenotypic profiling using large public microarray repositories. PMID:19590007
Virus-host interactions: from systems biology to translational research. PMID:19576841
Comparison of sequence-dependent tiling array normalization approaches. PMID:19566918
Translational bioinformatics applications in genome medicine. PMID:19566916
The impact of incomplete knowledge on evaluation: an experimental benchmark for protein function prediction. PMID:19561015
Expansion mechanisms and functional annotations of hypothetical genes in the rice genome. PMID:19535473
Expression pattern divergence of duplicated genes in rice. PMID:19534757
Meta Analysis of Gene Expression Data within and Across Species. PMID:19516959
Splicing factors PTBP1 and PTBP2 promote proliferation and migration of glioma cell lines. PMID:19506066
VisHiC--hierarchical functional enrichment analysis of microarray data. PMID:19483095
Functional analysis of transcription factors in Arabidopsis. PMID:19478073
A novel information retrieval model for high-throughput molecular medicine modalities. PMID:19458790
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
A global meta-analysis of microarray expression data to predict unknown gene functions and estimate the literature-data divide. PMID:19447786
plantsUPS: a database of plants' Ubiquitin Proteasome System. PMID:19445698
Effects of sample size on robustness and prediction accuracy of a prognostic gene signature. PMID:19445687
Network analysis of differential expression for the identification of disease-causing genes. PMID:19436755
Insights into the regulation of intrinsically disordered proteins in the human proteome by analyzing sequence and gene expression data. PMID:19432952
Differential gene expression signatures for cell wall integrity found in chitin synthase II (chs2Delta) and myosin II (myo1Delta) deficient cytokinesis mutants of Saccharomyces cerevisiae. PMID:19426543
Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping. PMID:19421373
Transcriptional profiling of cattle infected with Trypanosoma congolense highlights gene expression signatures underlying trypanotolerance and trypanosusceptibility. PMID:19409086
Discovering structural cis-regulatory elements by modeling the behaviors of mRNAs. PMID:19401680
Gene set internal coherence in the context of functional profiling. PMID:19397819
PrognoScan: a new database for meta-analysis of the prognostic value of genes. PMID:19393097
Choosing the right path: enhancement of biologically relevant sets of genes or proteins using pathway structure. PMID:19393085
Ranking differentially expressed genes from Affymetrix gene expression data: methods with reproducibility, sensitivity, and specificity. PMID:19386098
Severe zinc depletion of Escherichia coli: roles for high affinity zinc binding by ZinT, zinc transport and zinc-independent proteins. PMID:19377097
Application and evaluation of automated semantic annotation of gene expression experiments. PMID:19376825
Single feature polymorphisms between two rice cultivars detected using a median polish method. PMID:19370320
SysPTM: a systematic resource for proteomic research on post-translational modifications. PMID:19366988
A compendium of potential biomarkers of pancreatic cancer. PMID:19360088
Systems pharmacology and genome medicine: a future perspective. PMID:19348698
Function annotation of an SBP-box gene in Arabidopsis based on analysis of co-expression networks and promoters. PMID:19333437
Phenotypes and gene expression profiles of Saccharopolyspora erythraea rifampicin-resistant (rif) mutants affected in erythromycin production. PMID:19331655
A national clinical decision support infrastructure to enable the widespread and consistent practice of genomic and personalized medicine. PMID:19309514
Evolving DNA motifs to predict GeneChip probe performance. PMID:19298675
Microarray labeling extension values: laboratory signatures for Affymetrix GeneChips. PMID:19295132
DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli. PMID:19265557
SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. PMID:19265543
BRB-ArrayTools Data Archive for human cancer gene expression: a unique and efficient data sharing resource. PMID:19259398
Identifying compartment-specific non-HLA targets after renal transplantation by integrating transcriptome and "antibodyome" measures. PMID:19251643
Massive transcriptional start site analysis of human genes in hypoxia cells. PMID:19237398
Integrating sequence, evolution and functional genomics in regulatory genomics. PMID:19226437
Asymmetric relationships between proteins shape genome evolution. PMID:19216750
Tuberculosis drug resistance mutation database. PMID:19209951
Human gene expression sensitivity according to large scale meta-analysis. PMID:19208159
Integrative disease classification based on cross-platform microarray data. PMID:19208125
Meta-analysis of age-related gene expression profiles identifies common signatures of aging. PMID:19189975
Expression diversity and evolutionary dynamics of rice duplicate genes. PMID:19184107
Data-driven methods to discover molecular determinants of serious adverse drug events. PMID:19177064
Expression of genes associated with carbohydrate metabolism in cotton stems and roots. PMID:19161628
Transcriptomic and proteomic profiling of two porcine tissues using high-throughput technologies. PMID:19152685
Molecular classification and prognostication of adrenocortical tumors by transcriptome profiling. PMID:19147773
The origins of breast cancer prognostic gene expression profiles. PMID:19118016
A role for MEIS1 in MLL-fusion gene leukemia. PMID:19109563
TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PMID:19104654
GeneChaser: identifying all biological and clinical conditions in which genes of interest are differentially expressed. PMID:19094235
G-spots cause incorrect expression measurement in Affymetrix microarrays. PMID:19094220
MicroRNA target prediction by expression analysis of host genes. PMID:19088304
A snapshot of CNVs in the pig genome. PMID:19079605
CleanEx: new data extraction and merging tools based on MeSH term annotation. PMID:19073704
A cross-species transcriptomics approach to identify genes involved in leaf development. PMID:19061504
FitSNPs: highly differentially expressed genes are more likely to have variants associated with disease. PMID:19061490
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
c-REDUCE: incorporating sequence conservation to detect motifs that correlate with expression. PMID:19040743
Gene expression profiles in HPV-immortalized human cervical cells treated with the nicotine-derived carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone. PMID:19038236
Clustering cancer gene expression data: a comparative study. PMID:19038021
A comparison of four clustering methods for brain expression microarray data. PMID:19032745
Synaptogenesis in purified cortical subplate neurons. PMID:19029062
Genome adaptation to chemical stress: clues from comparative transcriptomics in Saccharomyces cerevisiae and Candida glabrata. PMID:19025642
Cataloguing the HIV type 1 human protein interaction network. PMID:19025396
sRNAMap: genomic maps for small non-coding RNAs, their regulators and their targets in microbial genomes. PMID:19015153
ArrayExpress update--from an archive of functional genomics experiments to the atlas of gene expression. PMID:19015125
Gene-L'EXPO: a tool to extract knowledge From transcriptomes and find 'Literature-Sparse' relationships between genes and tissues. PMID:18999036
Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44 K Agilent microarray. PMID:18990222
Differential gene expression associated with postnatal equine articular cartilage maturation. PMID:18986532
The prediction of protein-protein interaction networks in rice blast fungus. PMID:18976500
The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. PMID:18971253
Coincidence between transcriptome analyses on different microarray platforms using a parametric framework. PMID:18958174
ATTED-II provides coexpressed gene networks for Arabidopsis. PMID:18953027
Database resources of the National Center for Biotechnology Information. PMID:18940862
NCBI GEO: archive for high-throughput functional genomic data. PMID:18940857
Expression-based Pathway Signature Analysis (EPSA): mining publicly available microarray data for insight into human disease. PMID:18937865
Selected reaction monitoring for quantitative proteomics: a tutorial. PMID:18854821
AthaMap, integrating transcriptional and post-transcriptional data. PMID:18842622
GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus. PMID:18842599
DroID: the Drosophila Interactions Database, a comprehensive resource for annotated gene and protein interactions. PMID:18840285
Network evaluation from the consistency of the graph structure with the measured data. PMID:18828895
Antigen stimulation of peripheral blood mononuclear cells from Mycobacterium bovis infected cattle yields evidence for a novel gene expression program. PMID:18823559
Global transcription and metabolic flux analysis of Escherichia coli in glucose-limited fed-batch cultivations. PMID:18806003
MiMiR--an integrated platform for microarray data sharing, mining and analysis. PMID:18801157
Identification of Arx transcriptional targets in the developing basal forebrain. PMID:18799476
Effect of single nucleotide polymorphisms on Affymetrix match-mismatch probe pairs. PMID:18795114
GeneSpeed Beta Cell: an online genomics data repository and analysis resource tailored for the islet cell biologist. PMID:18795106
In silico analysis and verification of S100 gene expression in gastric cancer. PMID:18793447
Identifying cognate binding pairs among a large set of paralogs: the case of PE/PPE proteins of Mycobacterium tuberculosis. PMID:18787688
Meta-analysis and profiling of cardiac expression modules. PMID:18780758
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia. PMID:18779235
Gene expression variation to predict 10-year survival in lymph-node-negative breast cancer. PMID:18778486
Translational bioinformatics: coming of age. PMID:18755990
Gene Vector Analysis (Geneva): a unified method to detect differentially-regulated gene sets and similar microarray experiments. PMID:18721468
Molecular credentialing of rodent bladder carcinogenesis models. PMID:18670642
Accessing and integrating data and knowledge for biomedical research. PMID:18660883
Genes regulated by caloric restriction have unique roles within transcriptional networks. PMID:18634819
A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness. PMID:18628962
Meta-analysis of nasopharyngeal carcinoma microarray data explores mechanism of EBV-regulated neoplastic transformation. PMID:18605998
Strong position-dependent effects of sequence mismatches on signal ratios measured using long oligonucleotide microarrays. PMID:18598341
A weighted average difference method for detecting differentially expressed genes from microarray data. PMID:18578891
Molecular analysis of the vaginal response to estrogens in the ovariectomized rat and postmenopausal woman. PMID:18578861
Predicting transcriptional regulatory interactions with artificial neural networks applied to E. coli multidrug resistance efflux pumps. PMID:18565227
The incredible shrinking world of DNA microarrays. PMID:18563246
Functional annotation and identification of candidate disease genes by computational analysis of normal tissue gene expression data. PMID:18560577
Transcriptome analyses in normal prostate epithelial cells exposed to low-dose cadmium: oncogenic and immunomodulations involving the action of tumor necrosis factor. PMID:18560533
Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. PMID:18528524
Identification of Pou5f1, Sox2, and Nanog downstream target genes with statistical confidence by applying a novel algorithm to time course microarray and genome-wide chromatin immunoprecipitation data. PMID:18522731
Genome-wide survey of allele-specific splicing in humans. PMID:18518984
DiRE: identifying distant regulatory elements of co-expressed genes. PMID:18487623
Individual mRNA expression profiles reveal the effects of specific microRNAs. PMID:18485210
Context-specific metabolic networks are consistent with experiments. PMID:18483554
Expansion of signaling genes for adaptive immune system evolution in early vertebrates. PMID:18479507
Domain-specific data sharing in neuroscience: what do we have to learn from each other? PMID:18473189
Microarray retriever: a web-based tool for searching and large scale retrieval of public microarray data. PMID:18463138
Global transcription in pluripotent embryonic stem cells. PMID:18462694
GraphWeb: mining heterogeneous biological networks for gene modules with functional significance. PMID:18460544
RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina. PMID:18457592
Genome-wide assessments reveal extremely high levels of polymorphism of two active families of mouse endogenous retroviral elements. PMID:18454193
An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thaliana. PMID:18433503
Inferring microRNA activities by combining gene expression with microRNA target prediction. PMID:18431476
How many human genes can be defined as housekeeping with current expression data? PMID:18416810
Myeloid ecotropic viral integration site 1 (MEIS) 1 involvement in embryonic implantation. PMID:18408019
Engineering and analysis of a Saccharomyces cerevisiae strain that uses formaldehyde as an auxiliary substrate. PMID:18378663
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome. PMID:18375597
Annotating genes of known and unknown function by large-scale coexpression analysis. PMID:18354039
Mapping translocation breakpoints by next-generation sequencing. PMID:18326688
BAF250B-associated SWI/SNF chromatin-remodeling complex is required to maintain undifferentiated mouse embryonic stem cells. PMID:18323406
A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PMID:18320038
Insulin-like growth factor-1 promoter polymorphisms and colorectal cancer: a functional genomics approach. PMID:18308828
Transcriptional and metabolic adjustments in ADP-glucose pyrophosphorylase-deficient bt2 maize kernels. PMID:18287491
The Ehrlich pathway for fusel alcohol production: a century of research on Saccharomyces cerevisiae metabolism. PMID:18281432
Bioinformatics and cancer research: building bridges for translational research. PMID:18258507
Characterization of a newly developed chicken 44K Agilent microarray. PMID:18237426
A process for analysis of microarray comparative genomics hybridisation studies for bacterial genomes. PMID:18230148
Transcriptomic identification of candidate genes involved in sunflower responses to chilling and salt stresses based on cDNA microarray analysis. PMID:18221554
Pollution-affected fish hepatic transcriptome and its expression patterns on exposure to cadmium. PMID:18213484
Strand bias structure in mouse DNA gives a glimpse of how chromatin structure affects gene expression. PMID:18194530
Switch-like genes populate cell communication pathways and are enriched for extracellular proteins. PMID:18177501
Comparative analysis of microarray data identifies common responses to caloric restriction among mouse tissues. PMID:18155270
Microarray analysis of iron deficiency chlorosis in near-isogenic soybean lines. PMID:18154662
Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data. PMID:18053145
Database resources of the National Center for Biotechnology Information. PMID:18045790
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PMID:18043742
Characterization of zfs1 as an mRNA-binding and -destabilizing protein in Schizosaccharomyces pombe. PMID:18042546
microRNAs in viral oncogenesis. PMID:18036240
Microarray expression profiles of 20.000 genes across 23 healthy porcine tissues. PMID:18030337
The origin and function of calmodulin regulated Ca2+ pumps in plants. PMID:18000746
Gene expression profiling suggests primary central nervous system lymphomas to be derived from a late germinal center B cell. PMID:17989719
Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome. PMID:17980019
Innate gene repression associated with Mycobacterium bovis infection in cattle: toward a gene signature of disease. PMID:17974019
AILUN: reannotating gene expression data automatically. PMID:17971777
CEBS--Chemical Effects in Biological Systems: a public data repository integrating study design and toxicity data with microarray and proteomics data. PMID:17962311
CATdb: a public access to Arabidopsis transcriptome data from the URGV-CATMA platform. PMID:17940091
COXPRESdb: a database of coexpressed gene networks in mammals. PMID:17932064
CanGEM: mining gene copy number changes in cancer. PMID:17932056
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. PMID:17932051
High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer. PMID:17925008
Sharing and reusing gene expression profiling data in neuroscience. PMID:17917127
Gene expression profiling of long-lived dwarf mice: longevity-associated genes and relationships with diet, gender and aging. PMID:17915019
The PhenoGen informatics website: tools for analyses of complex traits. PMID:17760997
PARE: a tool for comparing protein abundance and mRNA expression data. PMID:17718915
Computation of significance scores of unweighted Gene Set Enrichment Analyses. PMID:17683603
Genes overexpressed in different human solid cancers exhibit different tissue-specific expression profiles. PMID:17664417
Large-scale integration of cancer microarray data identifies a robust common cancer signature. PMID:17663766
TrED: the Trichophyton rubrum Expression Database. PMID:17650345
Strategy for encoding and comparison of gene expression signatures. PMID:17612401
A transversal approach to predict gene product networks from ontology-based similarity. PMID:17605807
Challenges and standards in integrating surveys of structural variation. PMID:17597783
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. PMID:17586824
Global gene expression profiling reveals similarities and differences among mouse pluripotent stem cells of different origins and strains. PMID:17560561
Comprehensive serial analysis of gene expression of the cervical transcriptome. PMID:17543121
g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments. PMID:17478515
Database resources of the National Center for Biotechnology Information. PMID:17170002
NCBI GEO: mining millions of expression profiles--database and tools PubMed citations: 460.

460 articles citing: NCBI GEO: mining millions of expression profiles--database and tools

Stemness Correlates Inversely with MHC Class I Expression in Pediatric Small Round Blue Cell Tumors. PMID:35892842
An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. PMID:35884419
SERPINE1 Gene Is a Reliable Molecular Marker for the Early Diagnosis of Aortic Dissection. PMID:35836829
Novel roles of luteinizing hormone (LH) in tissue regeneration-associated functions in endometrial stem cells. PMID:35831270
Upregulation of Cartilage Oligomeric Matrix Protein Predicts Poor Prognosis in Urothelial Carcinoma. PMID:35795328
Comprehensive Bioinformatics Analysis to Reveal Key RNA Targets and Hub Competitive Endogenous RNA Network of Keratoconus. PMID:35747602
Integrated Analysis of Glutathione Metabolic Pathway in Pancreatic Cancer. PMID:35721499
Identification of potential gene markers in gestational diabetes mellitus. PMID:35718998
Computational epigenetic landscape analysis reveals association of CACNA1G-AS1, F11-AS1, NNT-AS1, and MSC-AS1 lncRNAs in prostate cancer progression through aberrant methylation. PMID:35715447
The intestinal microbiota influences the microenvironment of metastatic colon cancer by targeting miRNAs. PMID:35712898
The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. PMID:35665009
Analysis of the lncRNA-Associated Competing Endogenous RNA (ceRNA) Network for Tendinopathy. PMID:35645614
NUF2 Is a Potential Immunological and Prognostic Marker for Non-Small-Cell Lung Cancer. PMID:35600043
Identification and validation of an eight-lncRNA signature that predicts prognosis in patients with esophageal squamous cell carcinoma. PMID:35578166
An Artificial Intelligence-guided signature reveals the shared host immune response in MIS-C and Kawasaki disease. PMID:35577777
Immune-Related Biomarkers Associated with Lung Metastasis from the Colorectal Cancer Microenvironment. PMID:35576491
Identification and validation of EMT-immune-related prognostic biomarkers CDKN2A, CMTM8 and ILK in colon cancer. PMID:35429970
Bioinformatical analysis identifies PDLIM3 as a potential biomarker associated with immune infiltration in patients with endometriosis. PMID:35378934
Artificial intelligence-rationalized balanced PPARα/γ dual agonism resets dysregulated macrophage processes in inflammatory bowel disease. PMID:35288651
Identification of Hub Genes in Pancreatic Ductal Adenocarcinoma Using Bioinformatics Analysis. PMID:35223598
Novel insight into pancreatic adenocarcinoma pathogenesis using liquid association analysis. PMID:35180880
Screening and Identification of Muscle-Specific Candidate Genes via Mouse Microarray Data Analysis. PMID:34966817
Influence of N6-Methyladenosine Modification Gene HNRNPC on Cell Phenotype in Parkinson's Disease. PMID:34966539
Colon Cancer-Related Genes Identification and Function Study Based on Single-Cell Multi-Omics Integration. PMID:34901030
The impact of fine particulate matter (PM) on various beneficial functions of human endometrial stem cells through its key regulator SERPINB2. PMID:34857902
Identification of key regulators in parathyroid adenoma using an integrative gene network analysis. PMID:34803267
Transcriptomic Biomarkers for Tuberculosis: Validation of NPC2 as a Single mRNA Biomarker to Diagnose TB, Predict Disease Progression, and Monitor Treatment Response. PMID:34685683
Targeting CDC7 potentiates ATR-CHK1 signaling inhibition through induction of DNA replication stress in liver cancer. PMID:34663432
Genetic interaction between RLM1 and F-box motif encoding gene SAF1 contributes to stress response in Saccharomyces cerevisiae. PMID:34627408
SPT6 loss permits the transdifferentiation of keratinocytes into an intestinal fate that resembles Barrett's metaplasia. PMID:34622168
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization. PMID:34596551
Identifying key genes and screening therapeutic agents associated with diabetes mellitus and HCV-related hepatocellular carcinoma by bioinformatics analysis. PMID:34588861
Screening and discrimination of optimal prognostic genes for pancreatic cancer based on a prognostic prediction model. PMID:34499727
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Adult stem cell-derived complete lung organoid models emulate lung disease in COVID-19. PMID:34463615
Four Prognosis-Associated lncRNAs Serve as Biomarkers in Ovarian Cancer. PMID:34367239
Prediction of Disease Genes Based on Stage-Specific Gene Regulatory Networks in Breast Cancer. PMID:34335705
AI-guided discovery of the invariant host response to viral pandemics. PMID:34127431
Noncanonical functions of glucocorticoids: A novel role for glucocorticoids in performing multiple beneficial functions in endometrial stem cells. PMID:34120144
Hypoxia Constructing the Prognostic Model of Colorectal Adenocarcinoma and Related to the Immune Microenvironment. PMID:33959617
CBCR: A Curriculum Based Strategy For Chromosome Reconstruction. PMID:33923653
Coronary artery disease: differential expression of ceRNAs and interaction analyses. PMID:33708856
Prognostic Gene Expression, Stemness and Immune Microenvironment in Pediatric Tumors. PMID:33670534
Identification of the hub gene BUB1B in hepatocellular carcinoma via bioinformatic analysis and in vitro experiments. PMID:33665036
Identification of Crucial Genes and Pathways Associated with Atherosclerotic Plaque in Diabetic Patients. PMID:33568933
Inhibitory effect of sodium butyrate on colorectal cancer cells and construction of the related molecular network. PMID:33549042
Multiple microarray analyses identify key genes associated with the development of Non-Small Cell Lung Cancer from Chronic Obstructive Pulmonary Disease. PMID:33442399
Artificial Intelligence in Drug Discovery: A Comprehensive Review of Data-driven and Machine Learning Approaches. PMID:33437151
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions. PMID:33431024
Identification and analysis of circRNA-miRNA-mRNA regulatory network in hepatocellular carcinoma. PMID:33399102
Identification of Hub Genes of Mesio Temporal Lobe Epilepsy and Prognostic Biomarkers of Brain Low-grade Gliomas Based on Bioinformatics Analysis. PMID:33327771
The Association between the Usage of Non-Steroidal Anti-Inflammatory Drugs and Cognitive Status: Analysis of Longitudinal and Cross-Sectional Studies from the Global Alzheimer's Association Interactive Network and Transcriptomic Data. PMID:33321871
Identification of potential circRNAs and circRNA-miRNA-mRNA regulatory network in the development of diabetic foot ulcers by integrated bioinformatics analysis. PMID:33314661
TTK, CDC25A, and ESPL1 as Prognostic Biomarkers for Endometrial Cancer. PMID:33282948
Tumor Suppressive Maspin-Sensitized Prostate Cancer to Drug Treatment Through Negative Regulating Androgen Receptor Expression. PMID:33195208
PRAP1 is a novel lipid-binding protein that promotes lipid absorption by facilitating MTTP-mediated lipid transport. PMID:33168624
Comprehensive Analysis of Prognostic Markers for Acute Myeloid Leukemia Based on Four Metabolic Genes. PMID:33117716
Oxidative DNA Damage Accelerates Skin Inflammation in Pristane-Induced Lupus Model. PMID:33072095
Early-pregnancy transcriptome signatures of preeclampsia: from peripheral blood to placenta. PMID:33046794
Long non-coding RNA LPP-AS2 promotes glioma tumorigenesis via miR-7-5p/EGFR/PI3K/AKT/c-MYC feedback loop. PMID:32962742
Identification of potential biomarkers and candidate small molecule drugs in glioblastoma. PMID:32874133
GEO Data Sets Analysis Identifies COX-2 and Its Related Micro RNAs as Biomarkers for Non-Ischemic Heart Failure. PMID:32848764
Computational repositioning of dimethyl fumarate for treating alcoholic liver disease. PMID:32811823
Identification of potential crucial genes associated with the pathogenesis and prognosis of pancreatic adenocarcinoma. PMID:32793313
MAGPEL: an autoMated pipeline for inferring vAriant-driven Gene PanEls from the full-length biomedical literature. PMID:32703994
Identification of potential crucial genes and key pathways in osteosarcoma. PMID:32665038
Exploring the Molecular Mechanisms of Pterygium by Constructing lncRNA-miRNA-mRNA Regulatory Network. PMID:32645133
Tryptophanyl-tRNA Synthetase, a Novel Damage-Induced Cytokine, Significantly Increases the Therapeutic Effects of Endometrial Stem Cells. PMID:32592690
Upregulation of cGMP-dependent Protein Kinase (PRKG1) in the Development of Adolescent Idiopathic Scoliosis. PMID:32558266
Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. PMID:32468016
Computational Approach to Identifying Universal Macrophage Biomarkers. PMID:32322218
Early Diagnosis of Hepatocellular Carcinoma Using Machine Learning Method. PMID:32292778
Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer. PMID:32195055
A review of computational drug repurposing. PMID:32055582
Screening of Prognostic Factors in Early-Onset Breast Cancer. PMID:32028860
Integrated Bioinformatics Analysis for the Identification of Key Molecules and Pathways in the Hippocampus of Rats After Traumatic Brain Injury. PMID:31997105
UGM: a more stable procedure for large-scale multiple testing problems, new solutions to identify oncogene. PMID:31865918
PPP2R2A prostate cancer haploinsufficiency is associated with worse prognosis and a high vulnerability to B55α/PP2A reconstitution that triggers centrosome destabilization. PMID:31822657
Stress-induced changes in the expression of antioxidant system genes for rice (Oryza sativa L.) and bread wheat (Triticum aestivum L.). PMID:31803533
Candidate lncRNA-miRNA-mRNA network in predicting hepatocarcinogenesis with cirrhosis: an integrated bioinformatics analysis. PMID:31758243
Prognostic profiling of the immune cell microenvironment in Ewing´s Sarcoma Family of Tumors. PMID:31741777
The Gα-interacting vesicle-associated protein interacts with and promotes cell surface localization of GRP78 during endoplasmic reticulum stress. PMID:31736058
The assessment of efficient representation of drug features using deep learning for drug repositioning. PMID:31726977
LDAPred: A Method Based on Information Flow Propagation and a Convolutional Neural Network for the Prediction of Disease-Associated lncRNAs. PMID:31510011
circMYBL2, a circRNA from MYBL2, regulates FLT3 translation by recruiting PTBP1 to promote FLT3-ITD AML progression. PMID:31387917
GSMA: an approach to identify robust global and test Gene Signatures using Meta-Analysis. PMID:31329248
Circular RNA Signature in Hepatocellular Carcinoma. PMID:31293639
Identification of gene expression logical invariants in Arabidopsis. PMID:31245766
Differentially Expressed Gene Screening, Biological Function Enrichment, and Correlation with Prognosis in Non-Small Cell Lung Cancer. PMID:31181055
Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells. PMID:31098409
OSlms: A Web Server to Evaluate the Prognostic Value of Genes in Leiomyosarcoma. PMID:30984618
A Multi-Cohort and Multi-Omics Meta-Analysis Framework to Identify Network-Based Gene Signatures. PMID:30941158
Investigation of molecular biomarker candidates for diagnosis and prognosis of chronic periodontitis by bioinformatics analysis of pooled microarray gene expression datasets in Gene Expression Omnibus (GEO). PMID:30922293
Integration of Transcriptomic Data Identifies Global and Cell-Specific Asthma-Related Gene Expression Signatures. PMID:30815178
Pancreatic cancer biomarker detection by two support vector strategies for recursive feature elimination. PMID:30767554
Decentralized Learning Framework of Meta-Survival Analysis for Developing Robust Prognostic Signatures. PMID:30657395
Investigation into the underlying molecular mechanisms of white adipose tissue through comparative transcriptome analysis of multiple tissues. PMID:30569103
Long non-coding RNA H19 promotes TDRG1 expression and cisplatin resistance by sequestering miRNA-106b-5p in seminoma. PMID:30430771
Identification of candidate genes or microRNAs associated with the lymph node metastasis of SCLC. PMID:30364292
Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis. PMID:30261835
Identification of biomarkers for Barcelona Clinic Liver Cancer staging and overall survival of patients with hepatocellular carcinoma. PMID:30138346
Bioinformatics analysis of microarray data to reveal the pathogenesis of diffuse intrinsic pontine glioma. PMID:30124166
Changing Trends in Computational Drug Repositioning. PMID:29874824
Computational approaches for predicting key transcription factors in targeted cell reprogramming (Review). PMID:29845286
Integrative analysis of gene expression profiles reveals specific signaling pathways associated with pancreatic duct adenocarcinoma. PMID:29764514
Bioinformatics analysis of microarray data to reveal the pathogenesis of brain ischemia. PMID:29749511
Coding and Non-coding RNAs, the Frontier Has Never Been So Blurred. PMID:29720998
Bioinformatics-based identification of potential microRNA biomarkers in frequent and non-frequent exacerbators of COPD. PMID:29713155
Microarray Analysis of the Molecular Mechanism Involved in Parkinson's Disease. PMID:29686831
Key signaling pathways, genes and transcription factors associated with hepatocellular carcinoma. PMID:29658607
Cartilage oligomeric matrix protein: COMPopathies and beyond. PMID:29530484
Construction of key signal regulatory network in metastatic colorectal cancer. PMID:29464057
Potential effect of tumor-specific Treg-targeted antibodies in the treatment of human cancers: A bioinformatics analysis. PMID:29308313
Genome expression profiling predicts the molecular mechanism of peripheral myelination. PMID:29286075
Drug repurposing for the treatment of glioblastoma multiforme. PMID:29179732
Biomarker MicroRNAs for Diagnosis of Oral Squamous Cell Carcinoma Identified Based on Gene Expression Data and MicroRNA-mRNA Network Analysis. PMID:29098014
A new method to study the change of miRNA-mRNA interactions due to environmental exposures. PMID:28881990
Extracting genotype information of Arabidopsis thaliana recombinant inbred lines from transcript profiles established with high-density oligonucleotide arrays. PMID:28856445
Using omics approaches to understand pulmonary diseases. PMID:28774304
T2DiACoD: A Gene Atlas of Type 2 Diabetes Mellitus Associated Complex Disorders. PMID:28761062
Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds. PMID:28626466
Ribosomal protein L23 negatively regulates cellular apoptosis via the RPL23/Miz-1/c-Myc circuit in higher-risk myelodysplastic syndrome. PMID:28539603
Tailoring high-density oligonucleotide arrays for transcript profiling of different Arabidopsis thaliana accessions using a sequence-based approach. PMID:28534065
Identifying biologically relevant putative mechanisms in a given phenotype comparison. PMID:28486531
Screening of Tumor Suppressor Genes in Metastatic Colorectal Cancer. PMID:28473981
The physical characteristics of human proteins in different biological functions. PMID:28459865
GSNFS: Gene subnetwork biomarker identification of lung cancer expression data. PMID:28117655
Central Nodes in Protein Interaction Networks Drive Critical Functions in Transforming Growth Factor Beta-1 Stimulated Kidney Cells. PMID:28042536
MICRORNA-AUGMENTED PATHWAYS (mirAP) AND THEIR APPLICATIONS TO PATHWAY ANALYSIS AND DISEASE SUBTYPING. PMID:27896992
Alpha-2 macroglobulin in Alzheimer's disease: a marker of neuronal injury through the RCAN1 pathway. PMID:27872486
Learning Latent Variable Gaussian Graphical Model for Biomolecular Network with Low Sample Complexity. PMID:27843485
Thrombospondin-targeting TAX2 peptide impairs tumor growth in preclinical mouse models of childhood neuroblastoma. PMID:27842053
RNA-Seq Count Data Modelling by Grey Relational Analysis and Nonparametric Gaussian Process. PMID:27783633
Positive Selection Linked with Generation of Novel Mammalian Dentition Patterns. PMID:27613398
Quality Visualization of Microarray Datasets Using Circos. PMID:27605337
A genetic algorithm-based weighted ensemble method for predicting transposon-derived piRNAs. PMID:27578422
Emerging role of bioinformatics tools and software in evolution of clinical research. PMID:27453827
Bioinformatics analysis of differentially expressed pathways related to the metastatic characteristics of osteosarcoma. PMID:27353415
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. PMID:27114493
Cartilage oligomeric matrix protein contributes to the development and metastasis of breast cancer. PMID:27065333
Antitumour activity of the novel flavonoid Oncamex in preclinical breast cancer models. PMID:27031849
Cross-Clustering: A Partial Clustering Algorithm with Automatic Estimation of the Number of Clusters. PMID:27015427
The Gene Expression Omnibus Database. PMID:27008011
Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis. PMID:27000948
NABIC Microarray: an integrated database of high throughput data for gene expression profiles. PMID:26912952
Systems Perturbation Analysis of a Large-Scale Signal Transduction Model Reveals Potentially Influential Candidates for Cancer Therapeutics. PMID:26904540
Sevoflurane exerts a more marked influence compared with propofol on gene expression in patients undergoing coronary artery bypass graft surgery. PMID:26893629
Integrated, Multi-cohort Analysis Identifies Conserved Transcriptional Signatures across Multiple Respiratory Viruses. PMID:26682989
A computational method for drug repositioning using publicly available gene expression data. PMID:26679199
Intermittent Hypoxia Alters Gene Expression in Peripheral Blood Mononuclear Cells of Healthy Volunteers. PMID:26657991
CardioGenBase: A Literature Based Multi-Omics Database for Major Cardiovascular Diseases. PMID:26624015
LegumeIP 2.0--a platform for the study of gene function and genome evolution in legumes. PMID:26578557
Gene Network Rewiring to Study Melanoma Stage Progression and Elements Essential for Driving Melanoma. PMID:26558755
Using shRNA experiments to validate gene regulatory networks. PMID:26484195
Genome-wide gene expression profiling of acute metal exposures in male zebrafish. PMID:26484131
Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors. PMID:26484094
Human miRNome profiling in colorectal cancer and liver metastasis development. PMID:26484092
CTCF regulates positioning of the human cystic fibrosis gene in association with a histone deacetylase. PMID:26484076
Genome-wide profiling to analyze the effects of high fat diet induced obesity on renal gene expression in mouse with reduced renal mass. PMID:26484066
Genome-wide gene expression profiling to predict resistance to anthracyclines in breast cancer patients. PMID:26484051
BubbleGUM: automatic extraction of phenotype molecular signatures and comprehensive visualization of multiple Gene Set Enrichment Analyses. PMID:26481321
A Semi-Supervised Approach for Refining Transcriptional Signatures of Drug Response and Repositioning Predictions. PMID:26452147
Screening of feature genes in distinguishing different types of breast cancer using support vector machine. PMID:26347014
DLAT subunit of the pyruvate dehydrogenase complex is upregulated in gastric cancer-implications in cancer therapy. PMID:26279757
Tissue Remodelling following Resection of Porcine Liver. PMID:26240819
Gene expression profiling of ovarian carcinomas and prognostic analysis of outcome. PMID:26228058
How Many Genes Are Expressed in a Transcriptome? Estimation and Results for RNA-Seq. PMID:26107654
Multiple signatures of a disease in potential biomarker space: Getting the signatures consensus and identification of novel biomarkers. PMID:26100469
Every Site Counts: Submitting Transcription Factor-Binding Site Information through the CollecTF Portal. PMID:26013488
BAG2 Is Repressed by NF-κB Signaling, and Its Overexpression Is Sufficient to Shift Aβ1-42 from Neurotrophic to Neurotoxic in Undifferentiated SH-SY5Y Neuroblastoma. PMID:25985852
Identification of CTLA2A, DEFB29, WFDC15B, SERPINA1F and MUP19 as Novel Tissue-Specific Secretory Factors in Mouse. PMID:25946105
Evaluation of public cancer datasets and signatures identifies TP53 mutant signatures with robust prognostic and predictive value. PMID:25886164
A survey of current trends in computational drug repositioning. PMID:25832646
Small RNA sequencing for profiling microRNAs in long-term preserved formalin-fixed and paraffin-embedded non-small cell lung cancer tumor specimens. PMID:25812157
Correcting positional correlations in Affymetrix® genome chips. PMID:25767049
Integrated regulatory mechanisms of miRNAs and targeted genes involved in colorectal cancer. PMID:25755742
Analysis of mechanical ventilation and lipopolysaccharide‑induced acute lung injury using DNA microarray analysis. PMID:25672411
ToxDBScan: Large-scale similarity screening of toxicological databases for drug candidates. PMID:25338045
Vitamin D receptor and RXR in the post-genomic era. PMID:25335912
Relevance of different prior knowledge sources for inferring gene interaction networks. PMID:25009552
Keratinocyte detachment-differentiation connection revisited, or anoikis-pityriasi nexus redux. PMID:24960166
Identification of potential therapeutic targets in a model of neuropathic pain. PMID:24904634
Vitamin D and the RNA transcriptome: more than mRNA regulation. PMID:24860511
The joint graphical lasso for inverse covariance estimation across multiple classes. PMID:24817823
Expression data analysis to identify biomarkers associated with asthma in children. PMID:24790987
Glucagon regulates hepatic kisspeptin to impair insulin secretion. PMID:24703698
Inference and validation of predictive gene networks from biomedical literature and gene expression data. PMID:24691108
Navigating and mining modENCODE data. PMID:24636835
Review of biological network data and its applications. PMID:24465231
Leukaemogenesis induced by an activating β-catenin mutation in osteoblasts. PMID:24429522
The human sodium-dependent ascorbic acid transporters SLC23A1 and SLC23A2 do not mediate ascorbic acid release in the proximal renal epithelial cell. PMID:24400138
Target genes discovery through copy number alteration analysis in human hepatocellular carcinoma. PMID:24379610
Transcriptional profiling of hilar nodes from pigs after experimental infection with Actinobacillus pleuropneumoniae. PMID:24351863
Network based elucidation of drug response: from modulators to targets. PMID:24330611
Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. PMID:24135138
Using random walks to identify cancer-associated modules in expression data. PMID:24128261
scnRCA: a novel method to detect consistent patterns of translational selection in mutationally-biased genomes. PMID:24116094
Drug repositioning for orphan genetic diseases through Conserved Anticoexpressed Gene Clusters (CAGCs). PMID:24088245
Drug repositioning framework by incorporating functional information. PMID:24067419
Analysis of differentially expressed genes in abiotic stress response and their role in signal transduction pathways. PMID:23893304
Detecting and comparing non-coding RNAs in the high-throughput era. PMID:23887659
Penalized unsupervised learning with outliers. PMID:23875057
Transcriptional profiling of swine lung tissue after experimental infection with Actinobacillus pleuropneumoniae. PMID:23698783
HMGA1: a master regulator of tumor progression in triple-negative breast cancer cells. PMID:23658826
D-Light on promoters: a client-server system for the analysis and visualization of cis-regulatory elements. PMID:23617301
A fully scalable online pre-processing algorithm for short oligonucleotide microarray atlases. PMID:23563154
The landscape of host transcriptional response programs commonly perturbed by bacterial pathogens: towards host-oriented broad-spectrum drug targets. PMID:23516507
A data similarity-based strategy for meta-analysis of transcriptional profiles in cancer. PMID:23383020
SKINOMICS: Transcriptional Profiling in Dermatology and Skin Biology. PMID:23372422
Inferring evolution of gene duplicates using probabilistic models and nonparametric belief propagation. PMID:23368094
Recent developments in plant zinc homeostasis and the path toward improved biofortification and phytoremediation programs. PMID:23221755
Gene expression changes in response to aging compared to heat stress, oxidative stress and ionizing radiation in Drosophila melanogaster. PMID:23211361
The genetic regulation of the terminating phase of liver regeneration. PMID:23164283
Gene expression signatures of angiocidin and darapladib treatment connect to therapy options in cervical cancer. PMID:23052694
Transcriptional data: a new gateway to drug repositioning? PMID:22897878
The presence of tumor associated macrophages in tumor stroma as a prognostic marker for breast cancer patients. PMID:22824040
Integrative approach to pain genetics identifies pain sensitivity loci across diseases. PMID:22685391
Using functional signatures to identify repositioned drugs for breast, myelogenous leukemia and prostate cancer. PMID:22346740
Cell-to-cell signaling influences the fate of prostate cancer stem cells and their potential to generate more aggressive tumors. PMID:22328933
Penalized classification using Fisher's linear discriminant. PMID:22323898
Cyclophilin B expression is associated with in vitro radioresistance and clinical outcome after radiotherapy. PMID:22241958
Quantifying the white blood cell transcriptome as an accessible window to the multiorgan transcriptome. PMID:22219206
Predicting gene ontology from a global meta-analysis of 1-color microarray experiments. PMID:22166114
High-throughput processing and normalization of one-color microarrays for transcriptional meta-analyses. PMID:22166002
The genetic signature of perineuronal oligodendrocytes reveals their unique phenotype. PMID:22132705
Hormone receptor and ERBB2 status in gene expression profiles of human breast tumor samples. PMID:22022496
G-DOC: a systems medicine platform for personalized oncology. PMID:21969811
Knowledge sharing and collaboration in translational research, and the DC-THERA Directory. PMID:21969471
TGFβ superfamily signaling regulators are differentially expressed in the developing and adult mouse testis. PMID:21866277
Computational repositioning of the anticonvulsant topiramate for inflammatory bowel disease. PMID:21849664
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
The microRNA miR-29 controls innate and adaptive immune responses to intracellular bacterial infection by targeting interferon-γ. PMID:21785411
Integrative computational biology for cancer research. PMID:21691773
Gene expression profiling of the brain: pondering facts and fiction. PMID:21689753
mirAct: a web tool for evaluating microRNA activity based on gene expression data. PMID:21596785
Exploring genomic profiles of hepatocellular carcinoma. PMID:21465573
Gene-expression signatures can distinguish gastric cancer grades and stages. PMID:21445269
Comparison of automated and human assignment of MeSH terms on publicly-available molecular datasets. PMID:21420508
Rat diaphragm mitochondria have lower intrinsic respiratory rates than mitochondria in limb muscles. PMID:21389333
Data standards for Omics data: the basis of data sharing and reuse. PMID:21370078
In depth analysis of genes and pathways of the mammary gland involved in the pathogenesis of bovine Escherichia coli-mastitis. PMID:21352611
Accurate quantification of functional analogy among close homologs. PMID:21304936
easyDAS: automatic creation of DAS servers. PMID:21244646
Tumor endothelin-1 enhances metastatic colonization of the lung in mouse xenograft models of bladder cancer. PMID:21183790
Periodicity detection method for small-sample time series datasets. PMID:21151841
Assessing the quality of annotations in asthma gene expression experiments. PMID:21044366
A doublecortin containing microtubule-associated protein is implicated in mechanotransduction in Drosophila sensory cilia. PMID:20975667
An integrated transcriptomic and computational analysis for biomarker identification in gastric cancer. PMID:20965966
A comprehensive and universal method for assessing the performance of differential gene expression analyses. PMID:20844739
Identification of transcription factor's targets using tissue-specific transcriptomic data in Arabidopsis thaliana. PMID:20840729
A Comparative Study of the Impact of G-Stack Probes on Various Affymetrix GeneChips of Mammalia. PMID:20725627
Identifying modules of coexpressed transcript units and their organization of Saccharopolyspora erythraea from time series gene expression profiles. PMID:20711345
Intracellular localization of GASP/ECOP/VOPP1. PMID:20571887
Dynamic changes in gene expression in vivo predict prognosis of tamoxifen-treated patients with breast cancer. PMID:20569502
An information-flow-based model with dissipation, saturation and direction for active pathway inference. PMID:20504374
DSGeo: software tools for cross-platform analysis of gene expression data in GEO. PMID:20435161
Large scale analysis of positional effects of single-base mismatches on microarray gene expression data. PMID:20429935
Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group. PMID:20406941
Identifying common prognostic factors in genomic cancer studies: a novel index for censored outcomes. PMID:20334636
RNA isolation method for single embryo transcriptome analysis in zebrafish. PMID:20233395
Gene expression profiles of lung adenocarcinoma linked to histopathological grading and survival but not to EGF-R status: a microarray study. PMID:20196851
High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. PMID:20165882
Increased sinusoidal flow is not the primary stimulus to liver regeneration. PMID:20148099
Candidate genes for alcohol preference identified by expression profiling in alcohol-preferring and -nonpreferring reciprocal congenic rats. PMID:20128895
Changes in gene expression in regions of the extended amygdala of alcohol-preferring rats after binge-like alcohol drinking. PMID:20116196
The G protein-coupled receptor GPR30 inhibits proliferation of estrogen receptor-positive breast cancer cells. PMID:20086172
Members of the Entamoeba histolytica transmembrane kinase family play non-redundant roles in growth and phagocytosis. PMID:20083116
Genomics Portals: integrative web-platform for mining genomics data. PMID:20070909
Effects of moderate drinking during pregnancy on placental gene expression. PMID:20053520
A taxonomy of epithelial human cancer and their metastases. PMID:20017941
Web-based interrogation of gene expression signatures using EXALT. PMID:20003458
Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. PMID:19956698
Meta-analysis of transcripts associated with race-specific resistance to stripe rust in wheat demonstrates common induction of blue copper-binding protein, heat-stress transcription factor, pathogen-induced WIR1A protein, and ent-kaurene synthase transcripts. PMID:19937262
Automatic policing of biochemical annotations using genomic correlations. PMID:19935659
Differentially expressed genes for aggressive pecking behaviour in laying hens. PMID:19925670
NCR-PCOPGene: An Exploratory Tool for Analysis of Sample-Classes Effect on Gene-Expression Relationships. PMID:19920990
Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes. PMID:19828069
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. PMID:19786482
Towards large-scale sample annotation in gene expression repositories. PMID:19761579
Evaluation of a large-scale biomedical data annotation initiative. PMID:19761564
Integrating multiple microarray data for cancer pathway analysis using bootstrapping K-S test. PMID:19704919
Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis. PMID:19689821
Allergen databases: current status and perspectives. PMID:19671381
Gene expression changes in the nucleus accumbens of alcohol-preferring rats following chronic ethanol consumption. PMID:19666046
Construction and use of gene expression covariation matrix. PMID:19594909
Identification of global transcriptional dynamics. PMID:19593450
Revealing system-level correlations between aging and calorie restriction using a mouse transcriptome. PMID:19590981
Protein engineering of the transcriptional activator FhlA To enhance hydrogen production in Escherichia coli. PMID:19581479
Increased microRNA activity in human cancers. PMID:19557174
Internet Resources for Gene Expression Analysis in Arabidopsis thaliana. PMID:19506727
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. PMID:19491311
Bioinformatics resources for cancer research with an emphasis on gene function and structure prediction tools. PMID:19458756
MIMAS 3.0 is a Multiomics Information Management and Annotation System. PMID:19450266
PCOPGene-Net: holistic characterisation of cellular states from microarray data based on continuous and non-continuous analysis of gene-expression relationships. PMID:19426548
Identification of differentially expressed subnetworks based on multivariate ANOVA. PMID:19405941
Chronic lymphocytic leukemia and B and T cells differ in their response to cyclic nucleotide phosphodiesterase inhibitors. PMID:19380787
Generating genome-scale candidate gene lists for pharmacogenomics. PMID:19369935
Influence of fatty acid diets on gene expression in rat mammary epithelial cells. PMID:19351911
Recent developments in parameter estimation and structure identification of biochemical and genomic systems. PMID:19327372
SiPaGene: A new repository for instant online retrieval, sharing and meta-analyses of GeneChip expression data. PMID:19265543
Exploring the human genome with functional maps. PMID:19246570
High mobility group box2 promoter-controlled suicide gene expression enables targeted glioblastoma treatment. PMID:19240692
Identification of discriminating biomarkers for human disease using integrative network biology. PMID:19209693
Assessing and selecting gene expression signals based upon the quality of the measured dynamics. PMID:19208252
Benchmarks for identification of ordinary differential equations from time series data. PMID:19176548
Consistency analysis of redundant probe sets on affymetrix three-prime expression arrays and applications to differential mRNA processing. PMID:19165320
A novel regulatory event-based gene set analysis method for exploring global functional changes in heterogeneous genomic data sets. PMID:19146704
Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. PMID:19137102
Identification of G1-regulated genes in normally cycling human cells. PMID:19079774
Annotating breast cancer microarray samples using ontologies. PMID:18999108
Silencing of directional migration in roundabout4 knockdown endothelial cells. PMID:18980679
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. PMID:18945703
Using a 3D virtual muscle model to link gene expression changes during myogenesis to protein spatial location in muscle. PMID:18945372
Physical protein-protein interactions predicted from microarrays. PMID:18829707
The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets - improving meta-analysis and prediction of prognosis. PMID:18803878
Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression. PMID:18769540
The proteogenomic path towards biomarker discovery. PMID:18764911
Differential regulation of Listeria monocytogenes internalin and internalin-like genes by sigmaB and PrfA as revealed by subgenomic microarray analyses. PMID:18713061
Tissue-specific splicing factor gene expression signatures. PMID:18653532
A comparative study of survival models for breast cancer prognostication based on microarray data: does a single gene beat them all? PMID:18635567
Inferring mouse gene functions from genomic-scale data using a combined functional network/classification strategy. PMID:18613949
T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. PMID:18605991
ArrayWiki: an enabling technology for sharing public microarray data repositories and meta-analyses. PMID:18541053
Bioinformatic tools for inferring functional information from plant microarray data: tools for the first steps. PMID:18528524
Identification of SNPs and INDELS in swine transcribed sequences using short oligonucleotide microarrays. PMID:18510738
Recurrent design patterns in the feedback regulation of the mammalian signalling network. PMID:18463614
Improved grading and survival prediction of human astrocytic brain tumors by artificial neural network analysis of gene expression microarray data. PMID:18445660
Myeloid ecotropic viral integration site 1 (MEIS) 1 involvement in embryonic implantation. PMID:18408019
Differential gene expression in the nucleus accumbens with ethanol self-administration in inbred alcohol-preferring rats. PMID:18405950
Enabling integrative genomic analysis of high-impact human diseases through text mining. PMID:18229717
In silico approach to identify the expression of the undiscovered molecules from microarray public database: identification of odorant receptors expressed in non-olfactory tissues. PMID:18228002
The impact of horizontal gene transfer in shaping operons and protein interaction networks--direct evidence of preferential attachment. PMID:18218112
Transcriptional profiling of MnSOD-mediated lifespan extension in Drosophila reveals a species-general network of aging and metabolic genes. PMID:18067683
Using protein complexes to predict phenotypic effects of gene mutation. PMID:18042286
Prepubertal onset of diabetes prevents expression of renal cortical connective tissue growth factor. PMID:18030501
Application of a correlation correction factor in a microarray cross-platform reproducibility study. PMID:18005444
From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis. PMID:17916261
A gene expression bar code for microarray data. PMID:17906632
Identification of novel stem cell markers using gap analysis of gene expression data. PMID:17875203
DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data. PMID:17868443
Orthologous transcription factors in bacteria have different functions and regulate different genes. PMID:17845071
Structure and function of the Escherichia coli protein YmgB: a protein critical for biofilm formation and acid-resistance. PMID:17765265
The PhenoGen informatics website: tools for analyses of complex traits. PMID:17760997
Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells. PMID:17720827
Quantitative genomics of locomotor behavior in Drosophila melanogaster. PMID:17708775
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
PHIDIAS: a pathogen-host interaction data integration and analysis system. PMID:17663773
A statistical framework for expression quantitative trait loci mapping. PMID:17660576
Classification of heterogeneous microarray data by maximum entropy kernel. PMID:17651507
Arabidopsis Gene Family Profiler (aGFP)--user-oriented transcriptomic database with easy-to-use graphic interface. PMID:17645793
Faster rates of post-puberty kidney deterioration in males is correlated with elevated oxidative stress in males vs females at early puberty. PMID:17620128
Probabilistic prediction and ranking of human protein-protein interactions. PMID:17615067
Strategy for encoding and comparison of gene expression signatures. PMID:17612401
Using biomarker signature patterns for an mRNA molecular diagnostic of mouse embryonic stem cell differentiation state. PMID:17605829
Integrated olfactory receptor and microarray gene expression databases. PMID:17603910
Integrative analysis of the mouse embryonic transcriptome. PMID:17597930
New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures. PMID:17587440
Celsius: a community resource for Affymetrix microarray data. PMID:17570842
DGEM--a microarray gene expression database for primary human disease tissues. PMID:17570735
The ENCODEdb portal: simplified access to ENCODE Consortium data. PMID:17568011
Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. PMID:17562008
High-sensitivity transcriptome data structure and implications for analysis and biologic interpretation. PMID:17531797
Cross-study analysis of gene expression data for intermediate neuroblastoma identifies two biological subtypes. PMID:17531100
Inhibition of hydrogen uptake in Escherichia coli by expressing the hydrogenase from the cyanobacterium Synechocystis sp. PCC 6803. PMID:17521447
Functional gene expression differences between inbred alcohol-preferring and -non-preferring rats in five brain regions. PMID:17517326
Indole is an inter-species biofilm signal mediated by SdiA. PMID:17511876
Unexpected observations after mapping LongSAGE tags to the human genome. PMID:17504516
Enterohemorrhagic Escherichia coli biofilms are inhibited by 7-hydroxyindole and stimulated by isatin. PMID:17483266
Molecular characterisation of the early response in pigs to experimental infection with Actinobacillus pleuropneumoniae using cDNA microarrays. PMID:17466061
Identification of candidate genes for alcohol preference by expression profiling of congenic rat strains. PMID:17451403
The genopolis microarray database. PMID:17430566
Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. PMID:17400893
A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection. PMID:17395691
Spotted cotton oligonucleotide microarrays for gene expression analysis. PMID:17389046
Evidence of spatially bound gene regulation in Mus musculus: decreased gene expression proximal to microRNA genomic location. PMID:17360362
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. PMID:17356713
Temperature-dependent expression of Listeria monocytogenes internalin and internalin-like genes suggests functional diversity of these proteins among the listeriae. PMID:17337561
The (in)dependence of alternative splicing and gene duplication. PMID:17335345
Intercenter reliability and validity of the rhesus macaque GeneChip. PMID:17328815
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PMID:17299599
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. PMID:17298663
Genome-wide profiling and analysis of Arabidopsis siRNAs. PMID:17298187
Improved precision and accuracy for microarrays using updated probe set definitions. PMID:17288599
Pathways and genes differentially expressed in the motor cortex of patients with sporadic amyotrophic lateral sclerosis. PMID:17244347
Interpretation of multiple probe sets mapping to the same gene in Affymetrix GeneChips. PMID:17224057
CYCLONET--an integrated database on cell cycle regulation and carcinogenesis. PMID:17202170
SIGMA: a system for integrative genomic microarray analysis of cancer genomes. PMID:17192189
The Stanford Microarray Database: implementation of new analysis tools and open source release of software. PMID:17182626
PageMan: an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments. PMID:17176458
Tumor-specific and proliferation-specific gene expression typifies murine transgenic B cell lymphomagenesis. PMID:17166848
NCBI GEO standards and services for microarray data. PMID:17160034
AthaMap web tools for the analysis and identification of co-regulated genes. PMID:17148485
Absolute enrichment: gene set enrichment analysis for homeostatic systems. PMID:17130162
The mouse Gene Expression Database (GXD): 2007 update. PMID:17130151
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. PMID:17130150
Expression profiling of drug response--from genes to pathways. PMID:17117610
Modification of gene expression of the small airway epithelium in response to cigarette smoking. PMID:17115125
PolymiRTS Database: linking polymorphisms in microRNA target sites with complex traits. PMID:17099235
PathoPlant: a platform for microarray expression data to analyze co-regulated genes involved in plant defense responses. PMID:17099232
NCBI GEO: mining tens of millions of expression profiles--database and tools update. PMID:17099226
SAGE detects microRNA precursors. PMID:17090314
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB. PMID:17087822
Unraveling transcriptional control and cis-regulatory codes using the software suite GeneACT. PMID:17064417
Too much data, but little inter-changeability: a lesson learned from mining public data on tissue specificity of gene expression. PMID:17064414
A summarization approach for Affymetrix GeneChip data using a reference training set from a large, biologically diverse database. PMID:17059591
Transcriptional response to alcohol exposure in Drosophila melanogaster. PMID:17054780
Signatures from tissue-specific MPSS libraries identify transcripts preferentially expressed in the mouse inner ear. PMID:17049805
Novel mRNA targets for tristetraprolin (TTP) identified by global analysis of stabilized transcripts in TTP-deficient fibroblasts. PMID:17030620
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. PMID:17010196
Identification of a novel oligodendrocyte cell adhesion protein using gene expression profiling. PMID:17005852
MicroArray Facility: a laboratory information management system with extended support for Nylon based technologies. PMID:16987406
Genomes as geography: using GIS technology to build interactive genome feature maps. PMID:16984652
When transcriptome meets metabolome: fast cellular responses of yeast to sudden relief of glucose limitation. PMID:16969341
Scientific software development is not an oxymoron. PMID:16965174
Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. PMID:16939800
Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). PMID:16901231
Mining microarray data at NCBI's Gene Expression Omnibus (GEO)*. PMID:16888359
Global gene expression analysis of the heat shock response in the phytopathogen Xylella fastidiosa. PMID:16885450
An alpha-galactosidase with an essential function during leaf development. PMID:16845526
GEPS: the Gene Expression Pattern Scanner. PMID:16845057
DyNAVacS: an integrative tool for optimized DNA vaccine design. PMID:16845007
Sequence biases in large scale gene expression profiling data. PMID:16840527
One hundred years of high-throughput Drosophila research. PMID:16821132
Global transcriptome analysis of Tropheryma whipplei in response to temperature stresses. PMID:16816195
The microarray data analysis process: from raw data to biological significance. PMID:16815220
Web-based analysis of the mouse transcriptome using Genevestigator. PMID:16790046
Genomic analysis of Xenopus organizer function. PMID:16756679
An analysis of intra array repeats: the good, the bad and the non informative. PMID:16753054
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. PMID:16685651
A universal reference sample derived from clone vector for improved detection of differential gene expression. PMID:16677381
The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. PMID:16675512
Assessment of the relationship between pre-chip and post-chip quality measures for Affymetrix GeneChip expression data. PMID:16623940
Biologically relevant effects of mRNA amplification on gene expression profiles. PMID:16608515
YliH (BssR) and YceP (BssS) regulate Escherichia coli K-12 biofilm formation by influencing cell signaling. PMID:16597943
STEM: a tool for the analysis of short time series gene expression data. PMID:16597342
MIMAS: an innovative tool for network-based high density oligonucleotide microarray data management and annotation. PMID:16597336
Modulation of the transcription regulatory program in yeast cells committed to sporulation. PMID:16542486
Characteristics and clustering of human ribosomal protein genes. PMID:16504170
BayGO: Bayesian analysis of ontology term enrichment in microarray data. PMID:16504085
Arabidopsis PEN3/PDR8, an ATP binding cassette transporter, contributes to nonhost resistance to inappropriate pathogens that enter by direct penetration. PMID:16473969
Expression profiling identifies novel candidate genes for ethanol sensitivity QTLs. PMID:16465594
ITTACA: a new database for integrated tumor transcriptome array and clinical data analysis. PMID:16381943
HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. PMID:16381942
Database resources of the National Center for Biotechnology Information. PMID:16381840
Avoiding inconsistencies over time and tracking difficulties in Applied Biosystems AB1700/Panther probe-to-gene annotations. PMID:16372901
MicroGen: a MIAME compliant web system for microarray experiment information and workflow management. PMID:16351755
GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. PMID:16343346
Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. PMID:16284200
Analysis of microarray studies performed in the neurosciences. PMID:16280595
Chipper: discovering transcription-factor targets from chromatin immunoprecipitation microarrays using variance stabilization. PMID:16277751
MyoD induces myogenic differentiation through cooperation of its NH2- and COOH-terminal regions. PMID:16275751
Consistent across-tissue signatures of differential gene expression in Crohn's disease. PMID:16189665
Cross-platform comparability of microarray technology: intra-platform consistency and appropriate data analysis procedures are essential. PMID:16026597
Plant genome resources at the national center for biotechnology information. PMID:16010002
Identification of the iron-responsive genes of Neisseria gonorrhoeae by microarray analysis in defined medium. PMID:15995201
Storage and retrieval of microarray data and open source microarray database software. PMID:15988049
T-profiler: scoring the activity of predefined groups of genes using gene expression data. PMID:15980543
Natural antisense transcripts with coding capacity in Arabidopsis may have a regulatory role that is not linked to double-stranded RNA degradation. PMID:15960803
The European Bioinformatics Institute's data resources: towards systems biology. PMID:15608238
Database resources of the National Center for Biotechnology Information. PMID:15608222

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version: FAIRsharing.org: SOFT; Simple Omnibus Format in Text; DOI: https://doi.org/10.25504/FAIRsharing.3gxr9b; Last edited: Sept. 4, 2019, 9:23 p.m.; Last accessed: Jan 03 2022 7:10 p.m.

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