Gene Ontology (GO) Gene Association File Format 2.1
Names
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Gene Ontology (GO) Gene Association File Format 2.1
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
GAF 2.1
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
Gene Ontology (GO) Gene Association File Format 2.1
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
GAF 2.1
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Names
More detailed information about this field from each metasource.
Gene Ontology (GO) Gene Association File Format 2.1
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
GAF 2.1
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.1 (GAF 2.1). The annotation flat file format is comprised of 17 tab-delimited fields. This format is preferred over the GAF 2.0 format.
Description
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Ontology-based annotation data can be submitted to the Gene Ontology Consortium and other projects (e.g. the Planteome project) in the Gene Association Format 2.1 (GAF 2.1). The annotation flat file format is comprised of 17 tab-delimited fields. This format is preferred over the GAF 2.0 format.
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Webpage:
http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/Webpage
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http://geneontology.org/docs/go-annotation-file-gaf-format-2.1/
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
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Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Licence URL
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https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications:
Publications
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The Gene Ontology Resource: 20 years and still GOing strong
PMID: 30395331
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Publications
More detailed information about this field from each metasource.
The Gene Ontology Resource: 20 years and still GOing strong
PMID: 30395331
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
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The Gene Ontology Resource: 20 years and still GOing strong
PubMed citations: 1480.
1480 articles citing: The Gene Ontology Resource: 20 years and still GOing strong
Evolutionary Relationships Between Dysregulated Genes in Oral Squamous Cell Carcinoma and Oral Microbiota. PMID:35909962
Bioinformatics Analysis of the Mechanisms of Diabetic Nephropathy via Novel Biomarkers and Competing Endogenous RNA Network. PMID:35909518
Shared Genetics and Causality Between Decaffeinated Coffee Consumption and Neuropsychiatric Diseases: A Large-Scale Genome-Wide Cross-Trait Analysis and Mendelian Randomization Analysis. PMID:35898629
Challenges and Limitations of Biological Network Analysis. PMID:35892929
Computational modeling and analysis of the morphogenetic domain signaling networks regulating C. elegans embryogenesis. PMID:35891777
A Current Encyclopedia of Bioinformatics Tools, Data Formats and Resources for Mass Spectrometry Lipidomics. PMID:35888710
Large-Scale Multi-Omics Studies Provide New Insights into Blood Pressure Regulation. PMID:35886906
An Integrated Bioinformatics Analysis towards the Identification of Diagnostic, Prognostic, and Predictive Key Biomarkers for Urinary Bladder Cancer. PMID:35884419
Getting Started with LINCS Datasets and Tools. PMID:35876555
Venom composition of Trimeresurus albolabris, T. insularis, T. puniceus and T. purpureomaculatus from Indonesia. PMID:35875602
Identification of circRNA-miRNA-mRNA Regulatory Network and Crucial Signaling Pathway Axis Involved in Tetralogy of Fallot. PMID:35873466
Genetic Pathways Associated With Sleep Problems in Children With Autism Spectrum Disorder. PMID:35873241
orsum: a Python package for filtering and comparing enrichment analyses using a simple principle. PMID:35870894
Identification of Immune-Associated Genes in Diagnosing Aortic Valve Calcification With Metabolic Syndrome by Integrated Bioinformatics Analysis and Machine Learning. PMID:35865542
ORIGINS: A protein network-based approach to quantify cell pluripotency from scRNA-seq data. PMID:35855951
A genome-wide comparative evolutionary analysis of zinc finger-BED transcription factor genes in land plants. PMID:35853967
Integrated Analysis Revealing the Senescence-Mediated Immune Heterogeneity of HCC and Construction of a Prognostic Model Based on Senescence-Related Non-Coding RNA Network. PMID:35847928
Favoring Expression of Yak Alleles in Interspecies F1 Hybrids of Cattle and Yak Under High-Altitude Environments. PMID:35847643
Variations of SARS-CoV-2 in the Iranian population and candidate putative drug-like compounds to inhibit the mutated proteins. PMID:35847618
Excessive Sodium Intake Leads to Cardiovascular Disease by Promoting Sex-Specific Dysfunction of Murine Heart. PMID:35845798
The Mechanism of Wnt Pathway Regulated by Telocytes to Promote the Regeneration and Repair of Intrauterine Adhesions. PMID:35844454
A TP53 Related Immune Prognostic Model for the Prediction of Clinical Outcomes and Therapeutic Responses in Lung Adenocarcinoma. PMID:35837383
Selective expression of variant surface antigens enables Plasmodium falciparum to evade immune clearance in vivo. PMID:35831417
Identification of the shared gene signatures and pathways between polycystic ovary syndrome and endometrial cancer: An omics data based combined approach. PMID:35830453
Systems biology models to identify the influence of SARS-CoV-2 infections to the progression of human autoimmune diseases. PMID:35818398
Identification and Validation of Candidate Gene Module Along With Immune Cells Infiltration Patterns in Atherosclerosis Progression to Plaque Rupture via Transcriptome Analysis. PMID:35811739
Genetic variation associated with condensate dysregulation in disease. PMID:35809564
Lipolysis regulates major transcriptional programs in brown adipocytes. PMID:35803907
Identification of molecular mechanisms underlying the therapeutic effects of Xintong granule in coronary artery disease by a network pharmacology and molecular docking approach. PMID:35801781
A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection. PMID:35794133
Increased CSF-decorin predicts brain pathological changes driven by Alzheimer's Aβ amyloidosis. PMID:35787306
A consensus view of the proteome of the last universal common ancestor. PMID:35784055
Bioinformatics Analysis Highlights Five Differentially Expressed Genes as Prognostic Biomarkers of Cervical Cancer and Novel Option for Anticancer Treatment. PMID:35782114
Identification of pyroptosis-related long non-coding RNAs with prognosis and therapy in lung squamous cell carcinoma. PMID:35778526
An automatic integrative method for learning interpretable communities of biological pathways. PMID:35769343
DeepGOZero: improving protein function prediction from sequence and zero-shot learning based on ontology axioms. PMID:35758802
Calculating genetic risk for dysfunction in pleiotropic biological processes using whole exome sequencing data. PMID:35751013
Metabolome and Transcriptome Analyses of Cucurbitacin Biosynthesis in Luffa (Luffa acutangula). PMID:35747880
Differences and Similarities between the Lung Transcriptomic Profiles of COVID-19, COPD, and IPF Patients: A Meta-Analysis Study of Pathophysiological Signaling Pathways. PMID:35743918
TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer. PMID:35743803
Molecular alterations in human milk in simulated maternal nasal mucosal infection with live attenuated influenza vaccination. PMID:35739193
Expression and prognosis analysis of mitochondrial ribosomal protein family in breast cancer. PMID:35739158
Many kinds of oxidized proteins are present more in the urine of the elderly. PMID:35733114
Human follicular mites: Ectoparasites becoming symbionts. PMID:35724423
Screening and Identification of Hub Genes in the Development of Early Diabetic Kidney Disease Based on Weighted Gene Co-Expression Network Analysis. PMID:35721731
Identification of a neural development gene expression signature in colon cancer stem cells reveals a role for EGR2 in tumorigenesis. PMID:35720265
Identification and Validation of Genomic Subtypes and a Prognostic Model Based on Antigen-Presenting Cells and Tumor Microenvironment Infiltration Characteristics in Hepatocellular Carcinoma. PMID:35720008
SFARI genes and where to find them; modelling Autism Spectrum Disorder specific gene expression dysregulation with RNA-seq data. PMID:35710789
A hexa-species transcriptome atlas of mammalian embryogenesis delineates metabolic regulation across three different implantation modes. PMID:35710749
The DNA methylation landscape of five pediatric-tumor types. PMID:35707123
Analysis and pharmacological modulation of senescence in human epithelial stem cells. PMID:35706382
Proteome analysis of urinary biomarkers in a cigarette smoke-induced COPD rat model. PMID:35705945
Nutrient Availability Does Not Affect Community Assembly in Root-Associated Fungi but Determines Fungal Effects on Plant Growth. PMID:35695510
Decoding the Mechanism behind the Pathogenesis of the Focal Segmental Glomerulosclerosis. PMID:35693262
Novel App knock-in mouse model shows key features of amyloid pathology and reveals profound metabolic dysregulation of microglia. PMID:35690868
Comparative transcriptome analysis reveals a rapid response to phosphorus deficiency in a phosphorus-efficient rice genotype. PMID:35676419
Neuropilin-1 is present on Foxp3+ T regulatory cell-derived small extracellular vesicles and mediates immunity against skin transplantation. PMID:35676234
Digital Cell Atlas of Mouse Uterus: From Regenerative Stage to Maturational Stage. PMID:35669188
The impact of genetic modifiers on variation in germline mutation rates within and among human populations. PMID:35666194
Gene Expression Profile Analysis of Human Epidermal Keratinocytes Expressing Human Papillomavirus Type 8 E7. PMID:35665406
SSRTool: A web tool for evaluating RNA secondary structure predictions based on species-specific functional interpretability. PMID:35664227
Brain proteome profiling implicates the complement and coagulation cascade in multiple system atrophy brain pathology. PMID:35657417
Exploring the Genetic Associations Between the Use of Statins and Alzheimer's Disease. PMID:35656152
A Novel lncRNA Panel for Risk Stratification and Immune Landscape in Breast Cancer Patients. PMID:35655656
Expediting knowledge acquisition by a web framework for Knowledge Graph Exploration and Visualization (KGEV): case studies on COVID-19 and Human Phenotype Ontology. PMID:35655307
Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex. PMID:35653398
Characterisation of a nucleo-adhesome. PMID:35650196
Potential biomarkers and molecular mechanisms in preeclampsia progression. PMID:35647297
Cystatin SN promotes epithelial-mesenchymal transition and serves as a prognostic biomarker in lung adenocarcinoma. PMID:35637432
Correlation Between Serum 25-Hydroxyvitamin D Levels in Albuminuria Progression of Diabetic Kidney Disease and Underlying Mechanisms By Bioinformatics Analysis. PMID:35634488
Flavivirus Capsid Proteins Inhibit the Interferon Response. PMID:35632712
Transcriptomics Integrated with Metabolomics Reveals 2-Methoxy-1, 4-Naphthoquinone-Based Carbon Dots Induced Molecular Shifts in Penicillium italicum. PMID:35628676
Epigenetic Silencing of PTEN and Epi-Transcriptional Silencing of MDM2 Underlied Progression to Secondary Acute Myeloid Leukemia in Myelodysplastic Syndrome Treated with Hypomethylating Agents. PMID:35628480
Trifluoperazine and Its Analog Suppressed the Tumorigenicity of Non-Small Cell Lung Cancer Cell; Applicability of Antipsychotic Drugs to Lung Cancer Treatment. PMID:35625784
CRISPR Library Screening in Cultured Cardiomyocytes. PMID:35618895
A preliminary, observational study using whole-blood RNA sequencing reveals differential expression of inflammatory and bone markers post-implantation of percutaneous osseointegrated prostheses. PMID:35617338
OncoboxPD: human 51 672 molecular pathways database with tools for activity calculating and visualization. PMID:35615022
An Myh11 single lysine deletion causes aortic dissection by reducing aortic structural integrity and contractility. PMID:35614093
Gene co-expression network based on part mutual information for gene-to-gene relationship and gene-cancer correlation analysis. PMID:35610556
Blood transcriptomics identifies immune signatures indicative of infectious complications in childhood cancer patients with febrile neutropenia. PMID:35602885
The ceRNA Crosstalk between mRNAs and lncRNAs in Diabetes Myocardial Infarction. PMID:35592708
DAB2IP down-regulates HSP90AA1 to inhibit the malignant biological behaviors of colorectal cancer. PMID:35590292
Local chromatin context regulates the genetic requirements of the heterochromatin spreading reaction. PMID:35584134
GenePlexus: a web-server for gene discovery using network-based machine learning. PMID:35580053
Transcription elongation is finely tuned by dozens of regulatory factors. PMID:35575476
Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins. PMID:35575460
Identification of significant genes with a poor prognosis in skin cutaneous malignant melanoma based on a bioinformatics analysis. PMID:35571409
Pan-Cancer Bioinformatics Analysis of Gene UBE2C. PMID:35571064
Cancer Metabolic Subtypes and Their Association with Molecular and Clinical Features. PMID:35565274
Close Related Drug-Resistance Beijing Isolates of Mycobacterium tuberculosis Reveal a Different Transcriptomic Signature in a Murine Disease Progression Model. PMID:35563545
Identification of a novel lipid metabolism-related gene signature within the tumour immune microenvironment for breast cancer. PMID:35562758
CrowdGO: Machine learning and semantic similarity guided consensus Gene Ontology annotation. PMID:35560159
Revealing the Mechanism of Huazhi Rougan Granule in the Treatment of Nonalcoholic Fatty Liver Through Intestinal Flora Based on 16S rRNA, Metagenomic Sequencing and Network Pharmacology. PMID:35559233
Role of tRNA derived fragments in renal ischemia-reperfusion injury. PMID:35546262
SubcellulaRVis: a web-based tool to simplify and visualise subcellular compartment enrichment. PMID:35536291
Transcriptomic profile of the predatory mite Amblyseius swirskii (Acari: Phytoseiidae) on different host plants. PMID:35534782
An approach for evaluating the effects of dietary fiber polysaccharides on the human gut microbiome and plasma proteome. PMID:35533274
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
The macrophage-associated microRNA-4715-3p / Gasdermin D axis potentially indicates fibrosis progression in nonalcoholic fatty liver disease: evidence from transcriptome and biological data. PMID:35521691
Signatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades. PMID:35510788
Survival-related genes are diversified across cancers but generally enriched in cancer hallmark pathways. PMID:35508961
Ox-LDL-mediated ILF3 overexpression in gastric cancer progression by activating the PI3K/AKT/mTOR signaling pathway. PMID:35507914
Analysis of host-pathogen gene association networks reveals patient-specific response to streptococcal and polymicrobial necrotising soft tissue infections. PMID:35505341
Identification of Inflammation-Related Biomarkers in Diabetes of the Exocrine Pancreas With the Use of Weighted Gene Co-Expression Network Analysis. PMID:35498402
Knowledge integration and decision support for accelerated discovery of antibiotic resistance genes. PMID:35487919
Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. PMID:35484513
Proteomic networks associated with tumor-educated macrophage polarization and cytotoxicity potentiated by heat-killed tuberculosis. PMID:35477732
Lupus Susceptibility Loci Predispose Mice to Clonal Lymphocytic Responses and Myeloid Expansion. PMID:35477687
Comprehensive enhancer-target gene assignments improve gene set level interpretation of genome-wide regulatory data. PMID:35473573
Cell type and gene expression deconvolution with BayesPrism enables Bayesian integrative analysis across bulk and single-cell RNA sequencing in oncology. PMID:35469013
Bioinformatics and System Biology Approach to Identify the Influences of COVID-19 on Rheumatoid Arthritis. PMID:35464423
Identification of a Four-Gene Metabolic Signature to Evaluate the Prognosis of Colon Adenocarcinoma Patients. PMID:35462848
Estimating RNA dynamics using one time point for one sample in a single-pulse metabolic labeling experiment. PMID:35459101
A Bayesian framework to integrate multi-level genome-scale data for Autism risk gene prioritization. PMID:35459094
Identification of Novel Genes and Associated Drugs in Cervical Cancer by Bioinformatics Methods. PMID:35428744
Identification and Validation of Immune Cells and Hub Genes in Gastric Cancer Microenvironment. PMID:35422890
Research and experimental verification of the molecular mechanism of berberine in improving premature ovarian failure based on network pharmacology. PMID:35420511
An evidence-based lexical pattern approach for quality assurance of Gene Ontology relations. PMID:35419584
Analysis of human brain tissue derived from DBS surgery. PMID:35418104
A systematic review and functional bioinformatics analysis of genes associated with Crohn's disease identify more than 120 related genes. PMID:35418025
Transcriptional and Distributional Profiling of Microglia in Retinal Angiomatous Proliferation. PMID:35408803
An alternative UPF1 isoform drives conditional remodeling of nonsense-mediated mRNA decay. PMID:35403729
Multifaced regulator: RNA binding proteins and their roles in hematopoiesis. PMID:35402803
Machine learning-based screening of the diagnostic genes and their relationship with immune-cell infiltration in patients with lung adenocarcinoma. PMID:35399247
Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs. PMID:35395709
Human pluripotent stem cell-derived myogenic progenitors undergo maturation to quiescent satellite cells upon engraftment. PMID:35395188
Predicted mouse interactome and network-based interpretation of differentially expressed genes. PMID:35390003
Hierarchical multi-label classification based on LSTM network and Bayesian decision theory for LncRNA function prediction. PMID:35388048
SuperDendrix algorithm integrates genetic dependencies and genomic alterations across pathways and cancer types. PMID:35382456
MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. PMID:35380657
Transcriptome-wide association study for postpartum depression implicates altered B-cell activation and insulin resistance. PMID:35365803
NeuroSCORE is a genome-wide omics-based model that identifies candidate disease genes of the central nervous system. PMID:35361823
ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS. PMID:35361110
Chicken Peripheral Blood Mononuclear Cells Response to Avian Leukosis Virus Subgroup J Infection Assessed by Single-Cell RNA Sequencing. PMID:35359721
Genomic heterogeneity underlies multidrug resistance in Pseudomonas aeruginosa: A population-level analysis beyond susceptibility testing. PMID:35358221
Computational methods, databases and tools for synthetic lethality prediction. PMID:35352098
Mechanism of Zhen Wu Decoction in the Treatment of Heart Failure Based on Network Pharmacology and Molecular Docking. PMID:35341142
Evolution of Protein Functional Annotation: Text Mining Study. PMID:35330478
Functional Enrichment Analysis of Regulatory Elements. PMID:35327392
GOing Forward With the Cardiac Conduction System Using Gene Ontology. PMID:35309148
Transcriptome Analyses of Senecavirus A-Infected PK-15 Cells: RIG-I and IRF7 Are the Important Factors in Inducing Type III Interferons. PMID:35308346
Machine Learning of All Mycobacterium tuberculosis H37Rv RNA-seq Data Reveals a Structured Interplay between Metabolism, Stress Response, and Infection. PMID:35306876
Transcriptomic analysis of human sensory neurons in painful diabetic neuropathy reveals inflammation and neuronal loss. PMID:35304484
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:35300459
Protocol for isolation and functional validation of label-retaining quiescent colorectal cancer stem cells from patient-derived organoids for RNA-seq. PMID:35300001
Contributions of Artificial Intelligence Reported in Obstetrics and Gynecology Journals: Systematic Review. PMID:35297766
Whole genome sequencing delineates regulatory, copy number, and cryptic splice variants in early onset cardiomyopathy. PMID:35288587
The Key Genes Underlying Pathophysiology Correlation Between the Acute Myocardial Infarction and COVID-19. PMID:35282650
HCK is a Potential Prognostic Biomarker that Correlates with Immune Cell Infiltration in Acute Myeloid Leukemia. PMID:35280440
GATA4/5/6 family transcription factors are conserved determinants of cardiac versus pharyngeal mesoderm fate. PMID:35275720
Proteome Analysis of Urinary Biomarkers in a Bovine IRBP-Induced Uveitis Rat Model via Data-Independent Acquisition and Parallel Reaction Monitoring Proteomics. PMID:35274006
Transcriptomics of Parental Care in the Hypothalamic-Septal Region of Female Zebra Finch Brain. PMID:35269661
A non-canonical tricarboxylic acid cycle underlies cellular identity. PMID:35264789
CRISPR/Cas9-Mediated Insertion of HIV Long Terminal Repeat within BACH2 Promotes Expansion of T Regulatory-like Cells. PMID:35264460
Broad domains of histone marks in the highly compact Paramecium macronuclear genome. PMID:35264449
E2F4 may be a core transcription factor in the lncRNA-TF regulatory network in cervical cancer. PMID:35262965
Expression and regulatory network of long noncoding RNA in rats after spinal cord hemisection injury. PMID:35259853
Human biliary epithelial cells from discarded donor livers rescue bile duct structure and function in a mouse model of biliary disease. PMID:35245467
Considerations for constructing a protein sequence database for metaproteomics. PMID:35242286
Upregulated YB-1 protein promotes glioblastoma growth through a YB-1/CCT4/mLST8/mTOR pathway. PMID:35239512
Multi-omic rejuvenation of naturally aged tissues by a single cycle of transient reprogramming. PMID:35235716
PSINDB: the postsynaptic protein-protein interaction database. PMID:35234850
LINC00665 regulates hepatocellular carcinoma by modulating mRNA via the m6A enzyme. PMID:35233461
Landscape genomics of the streamside salamander: Implications for species management in the face of environmental change. PMID:35233244
Growth-rate-dependent and nutrient-specific gene expression resource allocation in fission yeast. PMID:35228260
MHC-II Signature Correlates With Anti-Tumor Immunity and Predicts anti-PD-L1 Response of Bladder Cancer. PMID:35223828
Student biocuration projects as a learning environment. PMID:35211294
Differential Expression of RAD51AP1 in Ovarian Cancer: Effects of siRNA In Vitro. PMID:35207688
Development of Gene Expression-Based Random Forest Model for Predicting Neoadjuvant Chemotherapy Response in Triple-Negative Breast Cancer. PMID:35205629
The Transcription Factor FgAtrR Regulates Asexual and Sexual Development, Virulence, and DON Production and Contributes to Intrinsic Resistance to Azole Fungicides in Fusarium graminearum. PMID:35205191
A Review on Transcriptional Responses of Interactions between Insect Vectors and Plant Viruses. PMID:35203347
Identification of Potential Immune Checkpoint Inhibitor Targets in Gliomas via Bioinformatic Analyses. PMID:35198632
Proteome-defined changes in cellular pathways for decidua and trophoblast tissues associated with location and viability of early-stage pregnancy. PMID:35189928
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
Cancer/Testis Antigen 55 is required for cancer cell proliferation and mitochondrial DNA maintenance. PMID:35189384
Wei2GO: weighted sequence similarity-based protein function prediction. PMID:35186498
DrugShot: querying biomedical search terms to retrieve prioritized lists of small molecules. PMID:35183110
Transcriptional changes in dendritic cells underlying allergen specific induced tolerance in a mouse model. PMID:35181694
Quantitative multiplexed proteomics analysis reveals reshaping of the lysine 2-hydroxyisobutyrylome in Fusarium graminearum by tebuconazole. PMID:35180840
Clinical and molecular characteristics of estrogen receptor-positive ultralow risk breast cancer tumors identified by the 70-gene signature. PMID:35179782
Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes. PMID:35178025
The m6A(m)-independent role of FTO in regulating WNT signaling pathways. PMID:35169043
Zebrafish information network, the knowledgebase for Danio rerio research. PMID:35166825
Transcriptomic Profile of Canine DH82 Macrophages Infected by Leishmania infantum Promastigotes with Different Virulence Behavior. PMID:35163386
Investigating changes of proteome in the bovine milk serum after retort processing using proteomics techniques. PMID:35154669
Gene-Interaction-Sensitive enrichment analysis in congenital heart disease. PMID:35151364
Multimodal reasoning based on knowledge graph embedding for specific diseases. PMID:35150235
Machine learning prediction and tau-based screening identifies potential Alzheimer's disease genes relevant to immunity. PMID:35149761
Identification of recurrent genetic patterns from targeted sequencing panels with advanced data science: a case-study on sporadic and genetic neurodegenerative diseases. PMID:35144616
blitzGSEA: Efficient computation of Gene Set Enrichment Analysis through Gamma distribution approximation. PMID:35143610
The Mechanism Study of Common Flavonoids on Antiglioma Based on Network Pharmacology and Molecular Docking. PMID:35140796
The DOMINO web-server for active module identification analysis. PMID:35139202
Evolutionary rewiring of regulatory networks contributes to phenotypic differences between human and mouse orthologous genes. PMID:35137181
Sperm acquire epididymis-derived proteins through epididymosomes. PMID:35137089
The genome of the Paleogene relic tree Bretschneidera sinensis: insights into trade-offs in gene family evolution, demographic history, and adaptive SNPs. PMID:35137004
PlantGF: an analysis and annotation platform for plant gene families. PMID:35134149
In silico prediction of HIV-1-host molecular interactions and their directionality. PMID:35134057
Role of mitochondrial genetic interactions in determining adaptation to high altitude human population. PMID:35132109
Common DNA methylation changes in biliary tract cancers identify subtypes with different immune characteristics and clinical outcomes. PMID:35130881
Shared Genetic Architecture and Causal Relationship Between Asthma and Cardiovascular Diseases: A Large-Scale Cross-Trait Analysis. PMID:35126453
Identification and validation of an autophagy-related gene signature for predicting prognosis in patients with esophageal squamous cell carcinoma. PMID:35121801
Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow. PMID:35119923
Identification of biomarkers for the diagnosis and treatment of primary colorectal cancer based on microarray technology. PMID:35117711
Comparison of confound adjustment methods in the construction of gene co-expression networks. PMID:35115012
Deep learning program to predict protein functions based on sequence information. PMID:35111575
Neuropeptidergic regulation of compulsive ethanol seeking in C. elegans. PMID:35110557
An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection. PMID:35102208
Potential Clinical Value of Biomarker-Guided Emergency Triage for Thoracic Aortic Dissection. PMID:35096998
Making sense of the linear genome, gene function and TADs. PMID:35090532
A novel variant in SMG9 causes intellectual disability, confirming a role for nonsense-mediated decay components in neurocognitive development. PMID:35087184
Bioactive peptides from broccoli stems strongly enhance regenerative keratinocytes by stimulating controlled proliferation. PMID:35086428
Proteomic screen reveals diverse protein transport between connected neurons in the visual system. PMID:35081342
Haploidy in somatic cells is induced by mature oocytes in mice. PMID:35079104
NonLoss: a novel analytical method for differential biological module identification from single-cell transcriptome. PMID:35071482
A comprehensive characterization of the transcriptome in enzalutamide resistance prostate cancer. PMID:35071476
Cross-talk of pyroptosis and tumor immune landscape in lung adenocarcinoma. PMID:35070752
Comparison between Heat-Clearing Medicine and Antirheumatic Medicine in Treatment of Gastric Cancer Based on Network Pharmacology, Molecular Docking, and Tumor Immune Infiltration Analysis. PMID:35069767
Utilizing network pharmacology and experimental validation to explore the potential molecular mechanisms of BanXia-YiYiRen in treating insomnia. PMID:35067174
Tissue-specific multi-omics analysis of atrial fibrillation. PMID:35064145
Tumor microenvironment-related multigene prognostic prediction model for breast cancer. PMID:35060926
ICEO, a biological ontology for representing and analyzing bacterial integrative and conjugative elements. PMID:35058462
A novel gene functional similarity calculation model by utilizing the specificity of terms and relationships in gene ontology. PMID:35057740
Biallelic Variants in PYROXD2 Cause a Severe Infantile Metabolic Disorder Affecting Mitochondrial Function. PMID:35055180
Single-Cell Analysis of Aneurysmal Aortic Tissue in Patients with Marfan Syndrome Reveals Dysfunctional TGF-β Signaling. PMID:35052435
Capturing SNP Association across the NK Receptor and HLA Gene Regions in Multiple Sclerosis by Targeted Penalised Regression Models. PMID:35052430
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome. PMID:35044719
Signatures of natural selection in a foundation tree along Mediterranean climatic gradients. PMID:35038378
The initial expression alterations occurring to transcription factors during the formation of breast cancer: Evidence from bioinformatics. PMID:35037412
Schisandrin B suppresses osteosarcoma lung metastasis in vivo by inhibiting the activation of the Wnt/β‑catenin and PI3K/Akt signaling pathways. PMID:35029287
Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. PMID:35024099
RNAseq reveals extensive metabolic disruptions in the sensitive SF-295 cell line treated with schweinfurthins. PMID:35013404
Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets. PMID:35013229
Titanium with nanotopography attenuates the osteoclast-induced disruption of osteoblast differentiation by regulating histone methylation. PMID:35012895
Altered White Matter and microRNA Expression in a Murine Model Related to Williams Syndrome Suggests That miR-34b/c Affects Brain Development via Ptpru and Dcx Modulation. PMID:35011720
Searching beyond the streetlight: Neonicotinoid exposure alters the neurogenomic state of worker honey bees. PMID:35003705
Identification of the molecular subgroups in asthma by gene expression profiles: airway inflammation implications. PMID:35000593
Deep learning-based brain transcriptomic signatures associated with the neuropathological and clinical severity of Alzheimer's disease. PMID:34993477
HESML: a real-time semantic measures library for the biomedical domain with a reproducible survey. PMID:34991460
HMDB 5.0: the Human Metabolome Database for 2022. PMID:34986597
Prediction of lncRNA-disease association based on a Laplace normalized random walk with restart algorithm on heterogeneous networks. PMID:34983367
Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19. PMID:34981034
Structure-function relationships of the disease-linked A218T oxytocin receptor variant. PMID:34980886
Ultradian rhythms of AKT phosphorylation and gene expression emerge in the absence of the circadian clock components Per1 and Per2. PMID:34968386
Dichotomous Responses to Chronic Fetal Hypoxia Lead to a Predetermined Aging Phenotype. PMID:34958949
Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin. PMID:34956303
DeepSVP: Integration of genotype and phenotype for structural variant prioritization using deep learning. PMID:34951628
Immunosenescence in Choroidal Neovascularization (CNV)-Transcriptional Profiling of Naïve and CNV-Associated Retinal Myeloid Cells during Aging. PMID:34948115
MicroRNA Analysis of Human Stroke Brain Tissue Resected during Decompressive Craniectomy/Stroke-Ectomy Surgery. PMID:34946809
8-Hydroxydaidzein Downregulates JAK/STAT, MMP, Oxidative Phosphorylation, and PI3K/AKT Pathways in K562 Cells. PMID:34944720
Transcriptomic Profiles Reveal Downregulation of Low-Density Lipoprotein Particle Receptor Pathway Activity in Patients Surviving Severe COVID-19. PMID:34944005
Transcriptome Analysis of Induced Pluripotent Stem Cells and Neuronal Progenitor Cells, Derived from Discordant Monozygotic Twins with Parkinson's Disease. PMID:34943986
Genome-Wide RNAi Screening Identifies Novel Pathways/Genes Involved in Oxidative Stress and Repurposable Drugs to Preserve Cystic Fibrosis Airway Epithelial Cell Integrity. PMID:34943039
Co-existing TP53 and ARID1A mutations promote aggressive endometrial tumorigenesis. PMID:34941867
Proteomic profiling reveals engineered chitosan nanoparticles mediated cellular crosstalk and immunomodulation for therapeutic application in apical periodontitis. PMID:34938914
Extensive mitochondrial proteome disturbance occurs during the early stages of acute myocardial ischemia. PMID:34938367
Biosafety and Proteome Profiles of Different Heat Inactivation Methods for Mycobacterium tuberculosis. PMID:34937194
Druggable genetic targets in endometrial cancer✰,✰✰. PMID:34933203
Type I CRISPR-Cas provides robust immunity but incomplete attenuation of phage-induced cellular stress. PMID:34928385
exoRBase 2.0: an atlas of mRNA, lncRNA and circRNA in extracellular vesicles from human biofluids. PMID:34918744
GENPPI: standalone software for creating protein interaction networks from genomes. PMID:34915867
Identification of Potential circRNA-microRNA-mRNA Regulatory Network in Skeletal Muscle. PMID:34912845
Metabolic drug survey highlights cancer cell dependencies and vulnerabilities. PMID:34907165
Whole-transcriptome analysis of aluminum-exposed rat hippocampus and identification of ceRNA networks to investigate neurotoxicity of Al. PMID:34900398
A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data. PMID:34900140
Gene Ontology Enrichment Analysis of Renal Agenesis: Improving Prenatal Molecular Diagnosis. PMID:34899145
New data and collaborations at the Saccharomyces Genome Database: updated reference genome, alleles, and the Alliance of Genome Resources. PMID:34897464
Integrated Analysis of Angiogenesis-Mediated Tumor Immune Microenvironment Pattern in Hepatocellular Carcinoma (HCC) and a Novel Prognostic Model Construction to Predict Patient Outcome. PMID:34897268
Integrative analysis of immune-related multi-omics profiles identifies distinct prognosis and tumor microenvironment patterns in osteosarcoma. PMID:34894177
Integrated genome and tissue engineering enables screening of cancer vulnerabilities in physiologically relevant perfusable ex vivo cultures. PMID:34890975
Meta-analyses identify DNA methylation associated with kidney function and damage. PMID:34887417
Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus. PMID:34887389
Splice-Variant Knock-Out of TGFβ Receptors Perturbates the Proteome of Ovarian Carcinoma Cells. PMID:34884451
The Power of Universal Contextualized Protein Embeddings in Cross-species Protein Function Prediction. PMID:34880594
Identifying the temporal electrophysiological and molecular changes that contribute to TSC-associated epileptogenesis. PMID:34877936
RYR2 mutation in non-small cell lung cancer prolongs survival via down-regulation of DKK1 and up-regulation of GS1-115G20.1: A weighted gene Co-expression network analysis and risk prognostic models. PMID:34877784
Identification and validation of cellular senescence patterns to predict clinical outcomes and immunotherapeutic responses in lung adenocarcinoma. PMID:34872577
Identification of Galectin-3 as Potential Biomarkers for Renal Fibrosis by RNA-Sequencing and Clinicopathologic Findings of Kidney Biopsy. PMID:34869439
Comprehensive Analysis Uncovers Prognostic and Immunogenic Characteristics of Cellular Senescence for Lung Adenocarcinoma. PMID:34869385
Multifaceted pathomolecular mechanism of a VWF large deletion involved in the pathogenesis of severe VWD. PMID:34861678
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
Multiscale interactome analysis coupled with off-target drug predictions reveals drug repurposing candidates for human coronavirus disease. PMID:34857794
Identification of the Active Constituents and Significant Pathways of Shen-qi-Yi-zhu Decoction on Antigastric Cancer: A Network Pharmacology Research and Experimental Validation. PMID:34853601
Transcriptomic dataset for Sardina pilchardus: Assembly, annotation, and expression of nine tissues. PMID:34849383
Toll-Like Receptor (TLR) Signaling Enables Cyclic GMP-AMP Synthase (cGAS) Sensing of HIV-1 Infection in Macrophages. PMID:34844429
Knowledge-guided artificial intelligence technologies for decoding complex multiomics interactions in cells. PMID:34844399
Identification of copy number variation-driven molecular subtypes informative for prognosis and treatment in pancreatic adenocarcinoma of a Chinese cohort. PMID:34839264
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
Transcriptome Analysis of Lolium temulentum Exposed to a Combination of Drought and Heat Stress. PMID:34834610
Multi-Omics Analysis Reveals Anti-Staphylococcus aureus Activity of Actinomycin D Originating from Streptomyces parvulus. PMID:34830114
Identification of Disease-Related Genes That Are Common between Alzheimer's and Cardiovascular Disease Using Blood Genome-Wide Transcriptome Analysis. PMID:34829754
Proteomics Profiling with SWATH-MS Quantitative Analysis of Changes in the Human Brain with HIV Infection Reveals a Differential Impact on the Frontal and Temporal Lobes. PMID:34827437
Single-cell analysis identifies dynamic gene expression networks that govern B cell development and transformation. PMID:34824268
A ROS-responsive, self-immolative and self-reporting hydrogen sulfide donor with multiple biological activities for the treatment of myocardial infarction. PMID:34820564
Quantitative dissection of multilocus pathogenic variation in an Egyptian infant with severe neurodevelopmental disorder resulting from multiple molecular diagnoses. PMID:34816580
Multiple regression analysis of a comprehensive transcriptomic data assembly elucidates mechanically- and biochemically-driven responses to focused ultrasound blood-brain barrier disruption. PMID:34815790
A Novel Autophagy-Related Long Non-Coding RNA Signature to Predict Prognosis and Therapeutic Response in Esophageal Squamous Cell Carcinoma. PMID:34815705
p300 or CBP is required for insulin-stimulated glucose uptake in skeletal muscle and adipocytes. PMID:34813504
Delayed DNA replication in haploid human embryonic stem cells. PMID:34810218
Hsa-mir-3163 and CCNB1 may be potential biomarkers and therapeutic targets for androgen receptor positive triple-negative breast cancer. PMID:34797837
Follicular T cells are clonally and transcriptionally distinct in B cell-driven mouse autoimmune disease. PMID:34795279
Altered cell and RNA isoform diversity in aging Down syndrome brains. PMID:34795060
APOBEC Mutagenesis Inhibits Breast Cancer Growth through Induction of T cell-Mediated Antitumor Immune Responses. PMID:34795033
Inferred expression regulator activities suggest genes mediating cardiometabolic genetic signals. PMID:34793442
The disease-associated proteins Drosophila Nab2 and Ataxin-2 interact with shared RNAs and coregulate neuronal morphology. PMID:34791182
Identification of Hub Genes and Potential ceRNA Networks of Diabetic Nephropathy by Weighted Gene Co-Expression Network Analysis. PMID:34790229
Dynamic Urinary Proteome Changes in Ovalbumin-Induced Asthma Mouse Model Using Data-Independent Acquisition Proteomics. PMID:34785909
The differentiation state of the Schwann cell progenitor drives phenotypic variation between two contagious cancers. PMID:34780568
Identification of discriminative gene-level and protein-level features associated with pathogenic gain-of-function and loss-of-function variants. PMID:34762822
Microarray profiling predicts early neurological and immune phenotypic traits in advance of CNS disease during disease progression in Trypanosoma. b. brucei infected CD1 mouse brains. PMID:34762691
Binge Ethanol Exposure in Mice Represses Expression of Genes Involved in Osteoblast Function and Induces Expression of Genes Involved in Osteoclast Differentiation Independently of Endogenous Catalase. PMID:34755883
BRAD V3.0: an upgraded Brassicaceae database. PMID:34755871
T2-DAG: a powerful test for differentially expressed gene pathways via graph-informed structural equation modeling. PMID:34755844
Regulatory network of miRNA, lncRNA, transcription factor and target immune response genes in bovine mastitis. PMID:34753991
Co-evolution based machine-learning for predicting functional interactions between human genes. PMID:34753957
The human telomeric proteome during telomere replication. PMID:34747482
International Prognostic Index-Based Immune Prognostic Model for Diffuse Large B-Cell Lymphoma. PMID:34745101
BCG vaccination and the risk of COVID 19: A possible correlation. PMID:34742127
Fibromine is a multi-omics database and mining tool for target discovery in pulmonary fibrosis. PMID:34741074
Prognostic and Immune-Infiltrate Significance of miR-222-3p and Its Target Genes in Thyroid Cancer. PMID:34737762
Cross-platform transcriptomic profiling of the response to recombinant human erythropoietin. PMID:34737331
Dysregulated expression levels of APH1B in peripheral blood are associated with brain atrophy and amyloid-β deposition in Alzheimer's disease. PMID:34732252
Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PMID:34731163
Comparison of critical biomarkers in 2 erectile dysfunction models based on GEO and NOS-cGMP-PDE5 pathway. PMID:34731136
MCDB: A comprehensive curated mitotic catastrophe database for retrieval, protein sequence alignment, and target prediction. PMID:34729303
Weighted gene co-expression network analysis to identify key modules and hub genes associated with paucigranulocytic asthma. PMID:34727921
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. PMID:34725363
VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. PMID:34718728
Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture. PMID:34716321
A human iPSC-astroglia neurodevelopmental model reveals divergent transcriptomic patterns in schizophrenia. PMID:34716291
Nanoencapsulation of sulforaphane in broccoli membrane vesicles and their in vitro antiproliferative activity. PMID:34714214
Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform. PMID:34712617
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PMID:34710081
Identification of lncRNA-associated competing endogenous RNA networks for occurrence and prognosis of gastric carcinoma. PMID:34704289
Whole-exome analysis in Tunisian Imazighen and Arabs shows the impact of demography in functional variation. PMID:34702931
Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci. PMID:34699533
Mouse Genome Informatics (MGI): latest news from MGD and GXD. PMID:34698891
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. PMID:34697638
Elucidate multidimensionality of type 1 diabetes mellitus heterogeneity by multifaceted information. PMID:34697343
Genome-Wide Association Studies for Growth Curves in Meat Rabbits Through the Single-Step Nonlinear Mixed Model. PMID:34691158
Recent innovations and in-depth aspects of post-genome wide association study (Post-GWAS) to understand the genetic basis of complex phenotypes. PMID:34689168
TAGOPSIN: collating taxa-specific gene and protein functional and structural information. PMID:34688246
Adaptive translational pausing is a hallmark of the cellular response to severe environmental stress. PMID:34686314
Microarray profile analysis identifies ETS1 as potential biomarker regulated by miR-23b and modulates TCF4 in gastric cancer. PMID:34686186
Investigations on the Degradation of the Bile Salt Cholate via the 9,10-Seco-Pathway Reveals the Formation of a Novel Recalcitrant Steroid Compound by a Side Reaction in Sphingobium sp. Strain Chol11. PMID:34683472
Entropy-Based Graph Clustering of PPI Networks for Predicting Overlapping Functional Modules of Proteins. PMID:34681995
Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships. PMID:34679164
Platelet proteome dynamics in hibernating 13-lined ground squirrels. PMID:34677084
Mechanisms of Rhizoma Coptidis against type 2 diabetes mellitus explored by network pharmacology combined with molecular docking and experimental validation. PMID:34675276
Lung proteomic biomarkers associated with chronic obstructive pulmonary disease. PMID:34668408
Screening of anti-chronic nonbacterial prostatitis activity of different extractions of the aerial part of Glycyrrhiza uralensis, and network pharmacology research. PMID:34667596
Antibiotics accelerate growth at the expense of immunity. PMID:34666517
Co-evolutionary Signals Identify Burkholderia pseudomallei Survival Strategies in a Hostile Environment. PMID:34662416
Pan-Genome of the Genus Streptomyces and Prioritization of Biosynthetic Gene Clusters With Potential to Produce Antibiotic Compounds. PMID:34659136
Comprehensive landscape and interference of clonal haematopoiesis mutations for liquid biopsy: A Chinese pan-cancer cohort. PMID:34658138
Combinatorial patterns of gene expression changes contribute to variable expressivity of the developmental delay-associated 16p12.1 deletion. PMID:34657631
Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. PMID:34656098
Analyzing the whole-transcriptome profiles of ncRNAs and predicting the competing endogenous RNA networks in cervical cancer cell lines with cisplatin resistance. PMID:34641878
Three chromosome-level duck genome assemblies provide insights into genomic variation during domestication. PMID:34635656
Disulfiram Alone Functions as a Radiosensitizer for Pancreatic Cancer Both In Vitro and In Vivo. PMID:34631519
Clustering Spatial Transcriptomics Data. PMID:34623423
A Taxon-Wise Insight Into Rock Weathering and Nitrogen Fixation Functional Profiles of Proglacial Systems. PMID:34621246
Phenotyping stomatal closure by thermal imaging for GWAS and TWAS of water use efficiency-related genes. PMID:34618072
Neuronal activity regulates the nuclear proteome to promote activity-dependent transcription. PMID:34617965
Host genetic factors associated with the range limit of a European hantavirus. PMID:34614264
A metric for evaluating biological information in gene sets and its application to identify co-expressed gene clusters in PBMC. PMID:34613979
An updated SYSCILIA gold standard (SCGSv2) of known ciliary genes, revealing the vast progress that has been made in the cilia research field. PMID:34613793
Genome-wide associations for immune traits in two maternal pig lines. PMID:34610786
High Throughput Transcriptome Data Analysis and Computational Verification Reveal Immunotherapy Biomarkers of Compound Kushen Injection for Treating Triple-Negative Breast Cancer. PMID:34604090
Bioinformatics and system biology approaches to identify pathophysiological impact of COVID-19 to the progression and severity of neurological diseases. PMID:34601390
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale. PMID:34597405
Dramatic transcriptomic differences in Macaca mulatta and Macaca fascicularis with Plasmodium knowlesi infections. PMID:34593836
Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19. PMID:34592166
Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels. PMID:34591957
Divergent patterns of selection on metabolite levels and gene expression. PMID:34587900
Identical twins carry a persistent epigenetic signature of early genome programming. PMID:34584077
Integrative proteome analysis implicates aberrant RNA splicing in impaired developmental potential of aged mouse oocytes. PMID:34582091
Predicting metabolic pathway membership with deep neural networks by integrating sequential and ontology information. PMID:34579673
Quantitative Proteomics and Phosphoproteomics Reveal TNF-α-Mediated Protein Functions in Hepatocytes. PMID:34576943
Isolation and Characterization of Outer Membrane Vesicles of Pectobacterium brasiliense 1692. PMID:34576813
Antioxidant and Antiproliferative Activity of Finasteride against Glioblastoma Cells. PMID:34575486
Comparative Transcriptome Analysis of the Expression of Antioxidant and Immunity Genes in the Spleen of a Cyanidin 3-O-Glucoside-Treated Alzheimer's Mouse Model. PMID:34573067
Promoter Hypermethylation Promotes the Binding of Transcription Factor NFATc1, Triggering Oncogenic Gene Activation in Pancreatic Cancer. PMID:34572796
Position Specific Alternative Splicing and Gene Expression Profiles Along the Tonotopic Axis of Chick Cochlea. PMID:34568429
Immune Mechanism, Gene Module, and Molecular Subtype Identification of Astragalus Membranaceus in the Treatment of Dilated Cardiomyopathy: An Integrated Bioinformatics Study. PMID:34567206
Viral suppressor of RNA silencing in vascular plants also interferes with the development of the bryophyte Physcomitrella patens. PMID:34564869
Challenges and opportunities in the study of extracellular vesicles: Global institutional context and national state of the art. PMID:34559503
clusterProfiler 4.0: A universal enrichment tool for interpreting omics data. PMID:34557778
COVID19db: a comprehensive database platform to discover potential drugs and targets of COVID-19 at whole transcriptomic scale. PMID:34554255
Examination of Gene Loss in the DNA Mismatch Repair Pathway and Its Mutational Consequences in a Fungal Phylum. PMID:34554246
The role of metadata in reproducible computational research. PMID:34553169
A novel lncRNA Discn fine-tunes replication protein A (RPA) availability to promote genomic stability. PMID:34552092
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. PMID:34551440
Novel insights into the molecular mechanisms underlying risk of colorectal cancer from smoking and red/processed meat carcinogens by modeling exposure in normal colon organoids. PMID:34548904
Using informative features in machine learning based method for COVID-19 drug repurposing. PMID:34544500
Long Noncoding RNA AC007639.1 Promotes the Pathogenesis and Progression of Hepatocellular Carcinoma Through Inhibiting Apoptosis and Stimulating Chemotherapeutic Resistance. PMID:34540685
Genomic comparison of non-photosynthetic plants from the family Balanophoraceae with their photosynthetic relatives. PMID:34540375
KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases. PMID:34537014
Transcriptome analysis reveals the mechanism of stromal cell-derived factor-1 and exendin-4 synergistically promoted periodontal ligament stem cells osteogenic differentiation. PMID:34532163
Identification of key genes and immune infiltration modulated by CPAP in obstructive sleep apnea by integrated bioinformatics analysis. PMID:34529670
Bioinformatic analysis for potential biological processes and key targets of heart failure-related stroke. PMID:34514752
Identifying Protein Complexes With Clear Module Structure Using Pairwise Constraints in Protein Interaction Networks. PMID:34512712
Chromosomal neighbourhoods allow identification of organ specific changes in gene expression. PMID:34506480
The Cancer Epitope Database and Analysis Resource: A Blueprint for the Establishment of a New Bioinformatics Resource for Use by the Cancer Immunology Community. PMID:34504503
Comprehensive Analysis of YTH Domain Family in Lung Adenocarcinoma: Expression Profile, Association with Prognostic Value, and Immune Infiltration. PMID:34497675
Single-cell analysis of a tumor-derived exosome signature correlates with prognosis and immunotherapy response. PMID:34496872
Vision, challenges and opportunities for a Plant Cell Atlas. PMID:34491200
Modelling the impact of decidual senescence on embryo implantation in human endometrial assembloids. PMID:34487490
Identification and Validation of a PPP1R12A-Related Five-Gene Signature Associated With Metabolism to Predict the Prognosis of Patients With Prostate Cancer. PMID:34484299
Effects of NaCl Concentrations on Growth Patterns, Phenotypes Associated With Virulence, and Energy Metabolism in Escherichia coli BW25113. PMID:34484145
Identification of anti-horn fly vaccine antigen candidates using a reverse vaccinology approach. PMID:34479607
The association of immunosurveillance and distant metastases in colorectal cancer. PMID:34476575
INHBA is a novel mediator regulating cellular senescence and immune evasion in colorectal cancer. PMID:34476008
Release of Notch activity coordinated by IL-1β signalling confers differentiation plasticity of airway progenitors via Fosl2 during alveolar regeneration. PMID:34475534
Human genetic analyses of organelles highlight the nucleus in age-related trait heritability. PMID:34467851
A novel missense variant in ACAA1 contributes to early-onset Alzheimer's disease, impairs lysosomal function, and facilitates amyloid-β pathology and cognitive decline. PMID:34465723
Predictability of polygenic risk score for progression to dementia and its interaction with APOE ε4 in mild cognitive impairment. PMID:34465370
Multitrait GWAS to connect disease variants and biological mechanisms. PMID:34460823
Comprehensive Analysis of the Systemic Transcriptomic Alternations and Inflammatory Response during the Occurrence and Progress of COVID-19. PMID:34457122
The blood transcriptome prior to ovarian cancer diagnosis: A case-control study in the NOWAC postgenome cohort. PMID:34449791
Identification of key proteins in the signaling crossroads between wound healing and cancer hallmark phenotypes. PMID:34446793
Pan-cancer analysis of longitudinal metastatic tumors reveals genomic alterations and immune landscape dynamics associated with pembrolizumab sensitivity. PMID:34446728
Promising Anticancer Activity of [Bis(1,8-quinolato)palladium (II)] Alone and in Combination. PMID:34445176
CANVS: an easy-to-use application for the analysis and visualization of mass spectrometry-based protein-protein interaction/association data. PMID:34432510
Depletion of TAX1BP1 Amplifies Innate Immune Responses during Respiratory Syncytial Virus Infection. PMID:34431698
Bacterial surface properties influence the activity of the TAT-RasGAP317-326 antimicrobial peptide. PMID:34430812
Transcriptional Analysis of Liver Tissue Identifies Distinct Phenotypes of Indeterminate Pediatric Acute Liver Failure. PMID:34430782
CeTF: an R/Bioconductor package for transcription factor co-expression networks using regulatory impact factors (RIF) and partial correlation and information (PCIT) analysis. PMID:34416858
Cadherin and Wnt signaling pathways as key regulators in diabetic nephropathy. PMID:34411124
Screening differentially expressed genes between endometriosis and ovarian cancer to find new biomarkers for endometriosis. PMID:34409913
Interferon stimulated binding of ISRE is cell type specific and is predicted by homeostatic chromatin state. PMID:34409284
Modeling the effects of EMT-immune dynamics on carcinoma disease progression. PMID:34408236
PhenoDB, GeneMatcher and VariantMatcher, tools for analysis and sharing of sequence data. PMID:34407837
A primary cell wall cellulose-dependent defense mechanism against vascular pathogens revealed by time-resolved dual transcriptomics. PMID:34404410
The Role of Long Noncoding RNA AL161431.1 in the Development and Progression of Pancreatic Cancer. PMID:34395245
Compressing deep graph convolution network with multi-staged knowledge distillation. PMID:34388224
Cortical Networks of Creative Ability Trace Gene Expression Profiles of Synaptic Plasticity in the Human Brain. PMID:34381343
Diffusion enables integration of heterogeneous data and user-driven learning in a desktop knowledge-base. PMID:34379637
Tumor microenvironment evaluation promotes precise checkpoint immunotherapy of advanced gastric cancer. PMID:34376552
From a genome assembly to full regulatory network prediction: the case study of Rhodotorula toruloides putative Haa1-regulon. PMID:34376148
Identification of m6A-Related Biomarkers Associated with Prognosis of Colorectal Cancer. PMID:34373442
Toward a systematic conflict resolution framework for ontologies. PMID:34372934
IRF7-Associated Immunophenotypes Have Dichotomous Responses to Virus/Allergen Coexposure and OM-85-Induced Reprogramming. PMID:34367159
Hanseniaspora smithiae sp. nov., a Novel Apiculate Yeast Species From Patagonian Forests That Lacks the Typical Genomic Domestication Signatures for Fermentative Environments. PMID:34367085
An Ontology-Based Framework for Psychological Monitoring in Education During the COVID-19 Pandemic. PMID:34366992
Collagen fiber orientation disorder from H&E images is prognostic for early stage breast cancer: clinical trial validation. PMID:34362928
Investigation of RNA metabolism through large-scale genetic interaction profiling in yeast. PMID:34358317
"Guilt by association" is not competitive with genetic association for identifying autism risk genes. PMID:34354131
Evaluating whole-genome expression differences in idiopathic and diabetic adhesive capsulitis. PMID:34352401
The 5-formyl-tetrahydrofolate proteome links folates with C/N metabolism and reveals feedback regulation of folate biosynthesis. PMID:34352110
Characterization of Five Transmembrane Proteins: With Focus on the Tweety, Sideroflexin, and YIP1 Domain Families. PMID:34350187
Myeloid-resident neuropilin-1 influences brown adipose tissue in obesity. PMID:34344941
Comprehensive Strain-Level Analysis of the Gut Microbe Faecalibacterium prausnitzii in Patients with Liver Cirrhosis. PMID:34342541
A systems-level study reveals host-targeted repurposable drugs against SARS-CoV-2 infection. PMID:34339582
Developmental lineage of human pluripotent stem cell-derived cardiac fibroblasts affects their functional phenotype. PMID:34339055
Computational identification of repurposed drugs against viruses causing epidemics and pandemics via drug-target network analysis. PMID:34332351
Epigenetic Analysis of the Chromatin Landscape Identifies a Repertoire of Murine Eosinophil-Specific PU.1-Bound Enhancers. PMID:34330753
Topological network based drug repurposing for coronavirus 2019. PMID:34324563
Proteomic analysis reveals dexamethasone rescues matrix breakdown but not anabolic dysregulation in a cartilage injury model. PMID:34322675
Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin. PMID:34322205
Gene expression profile of the murine ischemic retina and its response to Aflibercept (VEGF-Trap). PMID:34321516
Planarian Anatomy Ontology: a resource to connect data within and across experimental platforms. PMID:34318308
Characterization of a RAD51C-silenced high-grade serous ovarian cancer model during development of PARP inhibitor resistance. PMID:34316715
Mechanistic models of signaling pathways deconvolute the glioblastoma single-cell functional landscape. PMID:34316686
Recent ultra-rare inherited variants implicate new autism candidate risk genes. PMID:34312540
Host preference and invasiveness of commensal bacteria in the Lotus and Arabidopsis root microbiota. PMID:34312531
A new strategy to uncover fragile X proteomic biomarkers using the nascent proteome of peripheral blood mononuclear cells (PBMCs). PMID:34312401
Genomic signatures of the unjamming transition in compressed human bronchial epithelial cells. PMID:34301595
Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae. PMID:34301255
Long-range linkage disequilibrium in French beef cattle breeds. PMID:34301193
Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease. PMID:34297416
Characterizing the Metabolic and Immune Landscape of Non-small Cell Lung Cancer Reveals Prognostic Biomarkers Through Omics Data Integration. PMID:34295900
Highly accurate protein structure prediction for the human proteome. PMID:34293799
Single-cell transcriptomic profile of human pulmonary artery endothelial cells in health and pulmonary arterial hypertension. PMID:34282213
Development of a Novel Immune Infiltration-Related ceRNA Network and Prognostic Model for Sarcoma. PMID:34277600
The Infectious Disease Ontology in the age of COVID-19. PMID:34275487
FOXC2 controls adult lymphatic endothelial specialization, function, and gut lymphatic barrier preventing multiorgan failure. PMID:34272244
Oxidation of Hemoglobin Drives a Proatherogenic Polarization of Macrophages in Human Atherosclerosis. PMID:34269613
Distinct mechanisms mediate X chromosome dosage compensation in Anopheles and Drosophila. PMID:34266874
Multimarker profiling identifies protective and harmful immune processes in heart failure: findings from BIOSTAT-CHF. PMID:34264317
A network-biology approach for identification of key genes and pathways involved in malignant peritoneal mesothelioma. PMID:34261301
Genome sequence of Apostasia ramifera provides insights into the adaptive evolution in orchids. PMID:34256691
Using Cell Type-Specific Genes to Identify Cell-Type Transitions Between Different in vitro Culture Conditions. PMID:34249906
IL-17 signaling pathway plays a key role in laryngeal squamous cell carcinoma with ethnic specificity. PMID:34249422
Stress Granules and Neurodegenerative Disorders: A Scoping Review. PMID:34248597
ANANSE: an enhancer network-based computational approach for predicting key transcription factors in cell fate determination. PMID:34244796
TIDB: a comprehensive database of trained immunity. PMID:34244719
Proteomic signatures for perioperative oxygen delivery in skin after major elective surgery: mechanistic sub-study of a randomised controlled trial. PMID:34238546
Whole-exome imputation within UK Biobank powers rare coding variant association and fine-mapping analyses. PMID:34226706
Coordinated changes in gene expression kinetics underlie both mouse and human erythroid maturation. PMID:34225769
ReporterSeq reveals genome-wide dynamic modulators of the heat shock response across diverse stressors. PMID:34223816
Resident Kupffer cells and neutrophils drive liver toxicity in cancer immunotherapy. PMID:34215680
Fundamental limits on the rate of bacterial growth and their influence on proteomic composition. PMID:34214468
Machine Learning-Based Approach Highlights the Use of a Genomic Variant Profile for Precision Medicine in Ovarian Failure. PMID:34199109
Towards a global investigation of transcriptomic signatures through co-expression networks and pathway knowledge for the identification of disease mechanisms. PMID:34197603
A prognostic nomogram based on competing endogenous RNA network for clear-cell renal cell carcinoma. PMID:34196116
Extracellular matrix remodeling associated with bleomycin-induced lung injury supports pericyte-to-myofibroblast transition. PMID:34195593
Altered hypothalamic DNA methylation and stress-induced hyperactivity following early life stress. PMID:34193254
Epigenetic effects of parasites and pesticides on captive and wild nestling birds. PMID:34188846
Evolution of fibroblasts in the lung metastatic microenvironment is driven by stage-specific transcriptional plasticity. PMID:34169837
Long non-coding RNA ELFN1-AS1 in the pathogenesis of pancreatic cancer. PMID:34164511
Environmental enrichment preserves a young DNA methylation landscape in the aged mouse hippocampus. PMID:34162876
The brain transcriptome of the wolf spider, Schizocosa ocreata. PMID:34162407
Identification of Somatic Gene Signatures in Circulating Cell-Free DNA Associated with Disease Progression in Metastatic Prostate Cancer by a Novel Machine Learning Platform. PMID:34157173
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. PMID:34156446
A small RNA regulates pprM, a modulator of pleiotropic proteins promoting DNA repair, in Deinococcus radiodurans under ionizing radiation. PMID:34155239
ALKBH1-8 and FTO: Potential Therapeutic Targets and Prognostic Biomarkers in Lung Adenocarcinoma Pathogenesis. PMID:34150745
Effect of the Expression of ELOVL5 and IGFBP6 Genes on the Metastatic Potential of Breast Cancer Cells. PMID:34149804
Damage-Net: A program for DNA repair meta-analysis identifies a network of novel repair genes that facilitate cancer evolution. PMID:34147942
Systematic analysis of exonic germline and postzygotic de novo mutations in bipolar disorder. PMID:34145229
RNA sequencing of long-term label-retaining colon cancer stem cells identifies novel regulators of quiescence. PMID:34142064
Evolving Up-regulation of Biliary Fibrosis-Related Extracellular Matrix Molecules After Successful Portoenterostomy. PMID:34141988
Genotype-by-environment interactions for reproduction, body composition, and growth traits in maternal-line pigs based on single-step genomic reaction norms. PMID:34139991
Transcriptomic analyses of gastrulation-stage mouse embryos with differential susceptibility to alcohol. PMID:34137816
Genome-scale mechanistic modeling of signaling pathways made easy: A bioconductor/cytoscape/web server framework for the analysis of omic data. PMID:34136096
Transcriptomic Signature Differences Between SARS-CoV-2 and Influenza Virus Infected Patients. PMID:34135895
Transcriptomics of type 2 diabetic and healthy human neutrophils. PMID:34134627
Microglia RAGE exacerbates the progression of neurodegeneration within the SOD1G93A murine model of amyotrophic lateral sclerosis in a sex-dependent manner. PMID:34130712
Inter-individual body mass variations relate to fractionated functional brain hierarchies. PMID:34127795
A genetic interaction of NRXN2 with GABRE, SYT1 and CASK in migraine patients: a case-control study. PMID:34126933
Investigation of the Mechanism of Complement System in Diabetic Nephropathy via Bioinformatics Analysis. PMID:34124269
FGGA-lnc: automatic gene ontology annotation of lncRNA sequences based on secondary structures. PMID:34123354
Integrated Analyses Reveal the Multi-Omics and Prognostic Characteristics of ATP5B in Breast Cancer. PMID:34122507
Novel deep learning-based transcriptome data analysis for drug-drug interaction prediction with an application in diabetes. PMID:34116627
Integrating protein networks and machine learning for disease stratification in the Hereditary Spastic Paraplegias. PMID:34113825
Characterization of the small RNA transcriptomes of cell protrusions and cell bodies of highly metastatic hepatocellular carcinoma cells via RNA sequencing. PMID:34113396
Essential function and targets of BMP signaling during midbrain neural crest delamination. PMID:34102166
IL10RB as a key regulator of COVID-19 host susceptibility and severity. PMID:34100031
Transcriptome Analysis Reveals Differentially Expressed Genes and Long Non-coding RNAs Associated With Fecundity in Sheep Hypothalamus With Different FecB Genotypes. PMID:34095109
Differential expression of striatal proteins in a mouse model of DOPA-responsive dystonia reveals shared mechanisms among dystonic disorders. PMID:34092491
Chamber-enriched gene expression profiles in failing human hearts with reduced ejection fraction. PMID:34088950
Transmembrane adaptor protein PAG is a mediator of PD-1 inhibitory signaling in human T cells. PMID:34083754
Axonopathy precedes cell death in ocular damage mediated by blast exposure. PMID:34083587
A combination of Class-I fumarases and metabolites (α-ketoglutarate and fumarate) signal the DNA damage response in Escherichia coli. PMID:34083440
Patterns of recent natural selection on genetic loci associated with sexually differentiated human body size and shape phenotypes. PMID:34081690
Critical COVID-19 is associated with distinct leukocyte phenotypes and transcriptome patterns. PMID:34080738
Pan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli. PMID:34067383
Oncogenic Potential of the Dual-Function Protein MEX3A. PMID:34067172
Host Response of Atlantic Salmon (Salmo salar) Re-Inoculated with Paramoeba perurans. PMID:34062978
An in vitro model of tumor heterogeneity resolves genetic, epigenetic, and stochastic sources of cell state variability. PMID:34061819
The liver-clock coordinates rhythmicity of peripheral tissues in response to feeding. PMID:34059820
Model-based analysis uncovers mutations altering autophagy selectivity in human cancer. PMID:34059679
MicroRNA panel in serum reveals novel diagnostic biomarkers for prostate cancer. PMID:34055487
Identifying Subgroups of Patients With Autism by Gene Expression Profiles Using Machine Learning Algorithms. PMID:34054599
Multi-Omics Approach in the Identification of Potential Therapeutic Biomolecule for COVID-19. PMID:34054532
Synaptic proteins associated with cognitive performance and neuropathology in older humans revealed by multiplexed fractionated proteomics. PMID:34052751
Rapid evolution of mammalian APLP1 as a synaptic adhesion molecule. PMID:34050225
Proteotyping of knockout mouse strains reveals sex- and strain-specific signatures in blood plasma. PMID:34050187
Mergeomics 2.0: a web server for multi-omics data integration to elucidate disease networks and predict therapeutics. PMID:34048577
emiRIT: a text-mining-based resource for microRNA information. PMID:34048547
Transcriptomic analysis of atopic dermatitis in African Americans is characterized by Th2/Th17-centered cutaneous immune activation. PMID:34045476
Context-Dependent miR-21 Regulation of TLR7-Mediated Autoimmune and Foreign Antigen-Driven Antibody-Forming Cell and Germinal Center Responses. PMID:34039637
Adaptation to mitochondrial stress requires CHOP-directed tuning of ISR. PMID:34039602
Coordination of microbe-host homeostasis by crosstalk with plant innate immunity. PMID:34031541
Transcriptomic response of brain tissue to focused ultrasound-mediated blood-brain barrier disruption depends strongly on anesthesia. PMID:34027087
DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks. PMID:34025035
MyCLADE: a multi-source domain annotation server for sequence functional exploration. PMID:34023906
Gene expression of intracortical bone demonstrates loading-induced increases in Wnt1 and Ngf and inhibition of bone remodeling processes. PMID:34023542
Chromatin-associated MRN complex protects highly transcribing genes from genomic instability. PMID:34020942
Genome-wide analysis identifies a novel LINC-PINT splice variant associated with vascular amyloid pathology in Alzheimer's disease. PMID:34020725
Defining the role of the polyasparagine repeat domain of the S. cerevisiae transcription factor Azf1p. PMID:34019539
A computational approach for detecting physiological homogeneity in the midst of genetic heterogeneity. PMID:34015270
Platelets orchestrate the resolution of pulmonary inflammation in mice by T reg cell repositioning and macrophage education. PMID:34014253
Characterization and comparison of gene-centered human interactomes. PMID:34010955
Chromosomal instability by mutations in the novel minor spliceosome component CENATAC. PMID:34009673
Activated mast cells in skeletal muscle can be a potential mediator for cancer-associated cachexia. PMID:34008339
Differential host circRNA expression profiles in human lung epithelial cells infected with SARS-CoV-2. PMID:34004360
Genome-wide bioinformatic analyses predict key host and viral factors in SARS-CoV-2 pathogenesis. PMID:34002013
A miR-375/YAP axis regulates neuroendocrine differentiation and tumorigenesis in lung carcinoid cells. PMID:34001972
The nuclear receptor HNF4 drives a brush border gene program conserved across murine intestine, kidney, and embryonic yolk sac. PMID:34001900
Primordial super-enhancers: heat shock-induced chromatin organization in yeast. PMID:34001402
Mutant PRPF8 Causes Widespread Splicing Changes in Spliceosome Components in Retinitis Pigmentosa Patient iPSC-Derived RPE Cells. PMID:33994920
Multimodality assessment of heart failure with preserved ejection fraction skeletal muscle reveals differences in the machinery of energy fuel metabolism. PMID:33991175
Functional dynamic genetic effects on gene regulation are specific to particular cell types and environmental conditions. PMID:33988505
Mining TCGA database for gene expression in ovarian serous cystadenocarcinoma microenvironment. PMID:33987033
Identification of a five-gene signature in association with overall survival for hepatocellular carcinoma. PMID:33986994
ARTEMIS: A Novel Mass-Spec Platform for HLA-Restricted Self and Disease-Associated Peptide Discovery. PMID:33986749
IDSM ChemWebRDF: SPARQLing small-molecule datasets. PMID:33980298
Comparative Genome Analyses Highlight Transposon-Mediated Genome Expansion and the Evolutionary Architecture of 3D Genomic Folding in Cotton. PMID:33973633
Genoppi is an open-source software for robust and standardized integration of proteomic and genetic data. PMID:33972534
Collagen fiber regulation in human pediatric aortic valve development and disease. PMID:33963260
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Common genetic associations between age-related diseases. PMID:33959723
Identification of seven tumor-educated platelets RNAs for cancer diagnosis. PMID:33955587
Protective effects of Lycium barbarum polysaccharide on ovariectomy‑induced cognition reduction in aging mice. PMID:33955518
Evidence for phloem loading via the abaxial bundle sheath cells in maize leaves. PMID:33955497
Use of Network Pharmacology to Explore the Mechanism of Gegen (Puerariae lobatae Radix) in the Treatment of Type 2 Diabetes Mellitus Associated with Hyperlipidemia. PMID:33953784
Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. PMID:33953401
Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3. PMID:33951478
Characterization of Extracellular Vesicles Secreted in Lentiviral Producing HEK293SF Cell Cultures. PMID:33946875
Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3. PMID:33944776
Protein structure-based gene expression signatures. PMID:33941686
Bioinformatic identification of hub genes and related transcription factors in low shear stress treated endothelial cells. PMID:33941187
Experimental and natural evidence of SARS-CoV-2-infection-induced activation of type I interferon responses. PMID:33937724
A SARS-CoV-2 (COVID-19) biological network to find targets for drug repurposing. PMID:33931664
A clinical transcriptome approach to patient stratification and therapy selection in acute myeloid leukemia. PMID:33931648
Isolation and Characterization of Human Colon Adenocarcinoma Stem-Like Cells Based on the Endogenous Expression of the Stem Markers. PMID:33925224
Assessing Various Control Samples for Microarray Gene Expression Profiling of Laryngeal Squamous Cell Carcinoma. PMID:33923685
Characterization of the Survival Influential Genes in Carcinogenesis. PMID:33922264
Investigation of the Initial Host Response of Naïve Atlantic Salmon (Salmo salar) Inoculated with Paramoeba perurans. PMID:33918228
Altered microRNA Transcriptome in Cultured Human Liver Cells upon Infection with Ebola Virus. PMID:33917562
Single-Cell Atlas Reveals Fatty Acid Metabolites Regulate the Functional Heterogeneity of Mesenchymal Stem Cells. PMID:33912565
Reproductive Proteins Evolve Faster Than Non-reproductive Proteins Among Solanum Species. PMID:33912206
5-hydroxymethylcytosine is dynamically regulated during forebrain organoid development and aberrantly altered in Alzheimer's disease. PMID:33910000
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. PMID:33904398
The microRNA analysis portal is a next-generation tool for exploring and analyzing miRNA-focused data in the literature. PMID:33903708
Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities. PMID:33896739
The VRNetzer platform enables interactive network analysis in Virtual Reality. PMID:33893283
Network-Based Analysis of Fatal Comorbidities of COVID-19 and Potential Therapeutics. PMID:33891554
System-Level Analysis of Alzheimer's Disease Prioritizes Candidate Genes for Neurodegeneration. PMID:33889174
Transcriptomic alterations in malignant pleural mesothelioma cells in response to long‑term treatment with bullfrog sialic acid‑binding lectin. PMID:33880588
An EPIC predictor of gestational age and its application to newborns conceived by assisted reproductive technologies. PMID:33875015
Ontology-Based Graphs of Research Communities: A Tool for Understanding Threat Reduction Networks. PMID:33870041
Population-scale tissue transcriptomics maps long non-coding RNAs to complex disease. PMID:33864768
Conserved long-range base pairings are associated with pre-mRNA processing of human genes. PMID:33863890
Silencing SHMT2 inhibits the progression of tongue squamous cell carcinoma through cell cycle regulation. PMID:33863325
Disparate Interferon Signaling and Shared Aberrant Basaloid Cells in Single-Cell Profiling of Idiopathic Pulmonary Fibrosis and Systemic Sclerosis-Associated Interstitial Lung Disease. PMID:33859634
Multi-omic profiling of pituitary thyrotropic cells and progenitors. PMID:33858413
Interacting impact of maternal inflammatory response and stress on the amygdala transcriptome of pigs. PMID:33856433
Functional annotation of lung cancer‒associated genetic variants by cell type‒specific epigenome and long-range chromatin interactome. PMID:33840167
Dual-process brain mitochondria isolation preserves function and clarifies protein composition. PMID:33836587
MendelVar: gene prioritization at GWAS loci using phenotypic enrichment of Mendelian disease genes. PMID:33836063
MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data. PMID:33830183
Gene expression evaluation of antioxidant enzymes in patients with hepatocellular carcinoma: RT-qPCR and bioinformatic analyses. PMID:33821873
Age-dependent pathogenic characteristics of SARS-CoV-2 infection in ferrets. PMID:33821260
Differential MicroRNA Expression Involved in Endometrial Receptivity of Goats. PMID:33810054
Distinct miRNA Signatures and Networks Discern Fetal from Adult Erythroid Differentiation and Primary from Immortalized Erythroid Cells. PMID:33807258
Chronic Alcohol Use Induces Molecular Genetic Changes in the Dorsomedial Thalamus of People with Alcohol-Related Disorders. PMID:33805312
Selective Activation of CNS and Reference PPARGC1A Promoters Is Associated with Distinct Gene Programs Relevant for Neurodegenerative Diseases. PMID:33804860
A Streamlined Approach to Pathway Analysis from RNA-Sequencing Data. PMID:33802642
Candidate Genes for the High-Altitude Adaptations of Two Mountain Pine Taxa. PMID:33801727
Transcriptional Regulatory Networks Associate with Early Stages of Potato Virus X Infection of Solanum tuberosum. PMID:33799566
Volume-constrained microcontainers enable myoepithelial functional differentiation in highly parallel mammary organoid culture. PMID:33796842
Building blocks and blueprints for bacterial autolysins. PMID:33793553
Investigations of Kidney Dysfunction-Related Gene Variants in Sickle Cell Disease Patients in Cameroon (Sub-Saharan Africa). PMID:33790942
Trans-acting genetic variation affects the expression of adjacent genes. PMID:33789351
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. PMID:33787872
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature. PMID:33787871
An expanding manifold in transmodal regions characterizes adolescent reconfiguration of structural connectome organization. PMID:33787489
USP42 protects ZNRF3/RNF43 from R-spondin-dependent clearance and inhibits Wnt signalling. PMID:33786993
Gene Set Knowledge Discovery with Enrichr. PMID:33780170
Gene Expression Analysis Suggests Immunological Changes of Peripheral Blood Monocytes in the Progression of Patients With Coronary Artery Disease. PMID:33777109
Regulatory Function of Sympathetic Innervation on the Endo/Lysosomal Trafficking of Acetylcholine Receptor. PMID:33776791
The deubiquitinase Usp9x regulates PRC2-mediated chromatin reprogramming during mouse development. PMID:33767158
In-Depth Analysis of the Hidradenitis Suppurativa Serum Proteome Identifies Distinct Inflammatory Subtypes. PMID:33766512
Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids. PMID:33760032
SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks. PMID:33758926
G-quadruplexes originating from evolutionary conserved L1 elements interfere with neuronal gene expression in Alzheimer's disease. PMID:33758195
Novel ultra-rare exonic variants identified in a founder population implicate cadherins in schizophrenia. PMID:33756103
Cell-autonomous immune gene expression is repressed in pulmonary neuroendocrine cells and small cell lung cancer. PMID:33750914
Appyters: Turning Jupyter Notebooks into data-driven web apps. PMID:33748796
Noise regularization removes correlation artifacts in single-cell RNA-seq data preprocessing. PMID:33748795
Benchmark and Best Practices for Biomedical Knowledge Graph Embeddings. PMID:33746351
Expression and molecular profiles of the AlkB family in ovarian serous carcinoma. PMID:33744868
Identification of disease treatment mechanisms through the multiscale interactome. PMID:33741907
Differential microRNAs expression profiles in liver from three different lifestyle modification mice models. PMID:33740891
Natural variation in the regulation of neurodevelopmental genes modifies flight performance in Drosophila. PMID:33735180
Aberrant proteins expressed in skin fibroblasts of Parkinson's disease patients carrying heterozygous variants of glucocerebrosidase and parkin genes. PMID:33732455
Ultrafast functional profiling of RNA-seq data for nonmodel organisms. PMID:33731361
Chronic villitis of unknown etiology: Investigations into viral pathogenesis. PMID:33730616
A KDM5-Prospero transcriptional axis functions during early neurodevelopment to regulate mushroom body formation. PMID:33729157
Pathway size matters: the influence of pathway granularity on over-representation (enrichment analysis) statistics. PMID:33726670
COVID-19 patient transcriptomic and genomic profiling reveals comorbidity interactions with psychiatric disorders. PMID:33723208
Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast. PMID:33720010
Transcriptional analysis of islets of Langerhans from organ donors of different ages. PMID:33711030
Maternal Iron Deficiency Modulates Placental Transcriptome and Proteome in Mid-Gestation of Mouse Pregnancy. PMID:33693820
Copper Availability Influences the Transcriptomic Response of Candida albicans to Fluconazole Stress. PMID:33693623
Integrative network analyses of transcriptomics data reveal potential drug targets for acute radiation syndrome. PMID:33692493
Changes in protein expression due to metformin treatment and hyperinsulinemia in a human endometrial cancer cell line. PMID:33690729
Biodegradation of lignin monomers and bioconversion of ferulic acid to vanillic acid by Paraburkholderia aromaticivorans AR20-38 isolated from Alpine forest soil. PMID:33687503
Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain. PMID:33686078
Medication for Acromegaly Reduces Expression of MUC16, MACC1 and GRHL2 in Pituitary Neuroendocrine Tumour Tissue. PMID:33680922
Giant ankyrin-G regulates cardiac function. PMID:33675749
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:33674719
Mitochondrial arginase-2 is essential for IL-10 metabolic reprogramming of inflammatory macrophages. PMID:33674584
Unique Human and Mouse β-Cell Senescence-Associated Secretory Phenotype (SASP) Reveal Conserved Signaling Pathways and Heterogeneous Factors. PMID:33674410
Next-Generation Sequencing in the Field of Primary Immunodeficiencies: Current Yield, Challenges, and Future Perspectives. PMID:33666867
The Changes of Leukocytes in Brain and Blood After Intracerebral Hemorrhage. PMID:33659003
RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats. PMID:33653002
Dual DNA and protein tagging of open chromatin unveils dynamics of epigenomic landscapes in leukemia. PMID:33649590
Genomically Complex Human Angiosarcoma and Canine Hemangiosarcoma Establish Convergent Angiogenic Transcriptional Programs Driven by Novel Gene Fusions. PMID:33649193
Comprehensive analysis of cancer breakpoints reveals signatures of genetic and epigenetic contribution to cancer genome rearrangements. PMID:33647036
An update of KAIKObase, the silkworm genome database. PMID:33645624
Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer. PMID:33637530
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. PMID:33633572
RDmap: a map for exploring rare diseases. PMID:33632281
Genomic insight into diet adaptation in the biological control agent Cryptolaemus montrouzieri. PMID:33632122
Five key aspects of metaproteomics as a tool to understand functional interactions in host-associated microbiomes. PMID:33630960
Based on Network Pharmacology Tools to Investigate the Molecular Mechanism of Cordyceps sinensis on the Treatment of Diabetic Nephropathy. PMID:33628839
Automating parameter selection to avoid implausible biological pathway models. PMID:33623016
Hybrid semantic recommender system for chemical compounds in large-scale datasets. PMID:33622374
Discovery of molecular features underlying the morphological landscape by integrating spatial transcriptomic data with deep features of tissue images. PMID:33619564
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions. PMID:33616531
Identification of biomarkers and pathways for the SARS-CoV-2 infections that make complexities in pulmonary arterial hypertension patients. PMID:33611340
Zinc transporter ZIP7 is a novel determinant of ferroptosis. PMID:33608508
A Functional Taxonomy of Tumor Suppression in Oncogenic KRAS-Driven Lung Cancer. PMID:33608386
Local adaptation contributes to gene expression divergence in maize. PMID:33604670
Curation of over 10 000 transcriptomic studies to enable data reuse. PMID:33599246
Comparative transcriptomics of spotted seatrout (Cynoscion nebulosus) populations to cold and heat stress. PMID:33598136
Limited effects of long-term daily cranberry consumption on the gut microbiome in a placebo-controlled study of women with recurrent urinary tract infections. PMID:33596852
Role of opiorphin genes in prostate cancer growth and progression. PMID:33593085
Converting disease maps into heavyweight ontologies: general methodology and application to Alzheimer's disease. PMID:33590873
Tonic Immobility Is Influenced by Starvation, Life Stage, and Body Mass in Ixodid Ticks. PMID:33590870
Cold Adaptation Mechanisms of a Snow Alga Chlamydomonas nivalis During Temperature Fluctuations. PMID:33584575
Identification of key biomarkers and functional pathways in osteosarcomas with lung metastasis: Evidence from bioinformatics analysis. PMID:33578541
Integration of single-cell datasets reveals novel transcriptomic signatures of β-cells in human type 2 diabetes. PMID:33575641
Family-specific analysis of variant pathogenicity prediction tools. PMID:33575576
Potential Drug Prediction of Glioblastoma Based on Drug Perturbation-Induced Gene Expression Signatures. PMID:33575336
A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. PMID:33575256
Transcriptomic and proteomic analysis of Hemidactylus frenatus during initial stages of tail regeneration. PMID:33574494
Human myelomeningocele risk and ultra-rare deleterious variants in genes associated with cilium, WNT-signaling, ECM, cytoskeleton and cell migration. PMID:33574475
Gene expression and epigenetics reveal species-specific mechanisms acting upon common molecular pathways in the evolution of task division in bees. PMID:33574391
A Molecular network approach reveals shared cellular and molecular signatures between chronic fatigue syndrome and other fatiguing illnesses. PMID:33564792
RIP-seq reveals LINE-1 ORF1p association with p-body enriched mRNAs. PMID:33563338
Modular Reorganization of Signaling Networks during the Development of Colon Adenoma and Carcinoma. PMID:33562960
Phosphoproteomic Landscape of AML Cells Treated with the ATP-Competitive CK2 Inhibitor CX-4945. PMID:33562780
Characterization of the Rhipicephalus (Boophilus) microplus Sialotranscriptome Profile in Response to Theileria equi Infection. PMID:33557100
Integrative Identification of Hub Genes Associated With Immune Cells in Atrial Fibrillation Using Weighted Gene Correlation Network Analysis. PMID:33553270
The functional analysis of ABCG transporters in the adaptation of pigeon pea (Cajanus cajan) to abiotic stresses. PMID:33552725
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. PMID:33547799
Multiomics-Identified Intervention to Restore Ethanol-Induced Dysregulated Proteostasis and Secondary Sarcopenia in Alcoholic Liver Disease. PMID:33543862
BSGatlas: a unified Bacillus subtilis genome and transcriptome annotation atlas with enhanced information access. PMID:33539279
Long non‑coding RNA LINC00491 promotes proliferation and inhibits apoptosis in esophageal squamous cell carcinoma. PMID:33537830
GEOlimma: differential expression analysis and feature selection using pre-existing microarray data. PMID:33535967
Independent component analysis recovers consistent regulatory signals from disparate datasets. PMID:33529205
Human keratinocyte-derived extracellular vesicles activate the MAPKinase pathway and promote cell migration and proliferation in vitro. PMID:33526070
Systematic Analysis of Functionally Related Gene Clusters in the Opportunistic Pathogen, Candida albicans. PMID:33525750
DeCompress: tissue compartment deconvolution of targeted mRNA expression panels using compressed sensing. PMID:33524140
From fuzziness to precision medicine: on the rapidly evolving proteomics with implications in mitochondrial connectivity to rare human disease. PMID:33521598
American lobster postlarvae alter gene regulation in response to ocean warming and acidification. PMID:33520168
An In-Silico Study on the Most Effective Growth Factors in Retinal Regeneration Utilizing Tissue Engineering Concepts. PMID:33520128
Identifying RBM47, HCK, CD53, TYROBP, and HAVCR2 as Hub Genes in Advanced Atherosclerotic Plaques by Network-Based Analysis and Validation. PMID:33519905
Computational resources for identifying and describing proteins driving liquid-liquid phase separation. PMID:33517364
Lipids, lysosomes and mitochondria: insights into Lewy body formation from rare monogenic disorders. PMID:33515275
Amynthas corticis genome reveals molecular mechanisms behind global distribution. PMID:33514865
The role of gene to gene interaction in the breast's genomic signature of pregnancy. PMID:33514799
Reporting on the Role of miRNAs and Affected Pathways on the Molecular Backbone of Ovarian Insufficiency: A Systematic Review and Critical Analysis Mapping of Future Research. PMID:33511114
Gene signature of children with severe respiratory syncytial virus infection. PMID:33510411
The Epstein-Barr virus deubiquitinase BPLF1 targets SQSTM1/p62 to inhibit selective autophagy. PMID:33509017
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. PMID:33507271
Genome-Wide Identification and Analysis of Chitinase GH18 Gene Family in Mycogone perniciosa. PMID:33505368
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. PMID:33494105
Short hairpin RNA attenuates liver fibrosis by regulating the PPAR‑γ and NF‑κB pathways in HBV‑induced liver fibrosis in mice. PMID:33491741
Inference of Intercellular Communications and Multilayer Gene-Regulations of Epithelial-Mesenchymal Transition From Single-Cell Transcriptomic Data. PMID:33488673
HELQ and EGR3 expression correlate with IGHV mutation status and prognosis in chronic lymphocytic leukemia. PMID:33485349
Integrative computational approach identifies drug targets in CD4+ T-cell-mediated immune disorders. PMID:33483502
Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways. PMID:33480182
Potential interactions between the TBX4-FGF10 and SHH-FOXF1 signaling during human lung development revealed using ChIP-seq. PMID:33478486
Effect of Aging on Homeostasis in the Soft Tissue of the Periodontium: A Narrative Review. PMID:33477537
DOMINO: a network-based active module identification algorithm with reduced rate of false calls. PMID:33471440
Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming. PMID:33469464
Comprehensive computational target fishing approach to identify Xanthorrhizol putative targets. PMID:33452398
A systems-level gene regulatory network model for Plasmodium falciparum. PMID:33450011
A genome-wide strategy to identify causes and consequences of retrotransposon expression finds activation by BRCA1 in ovarian cancer. PMID:33447827
Late p65 nuclear translocation in glioblastoma cells indicates non-canonical TLR4 signaling and activation of DNA repair genes. PMID:33446690
An Integrative Transcriptomic Analysis of Systemic Juvenile Idiopathic Arthritis for Identifying Potential Genetic Markers and Drug Candidates. PMID:33445803
Knowledge Network Embedding of Transcriptomic Data from Spaceflown Mice Uncovers Signs and Symptoms Associated with Terrestrial Diseases. PMID:33445483
Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB. PMID:33445429
Genome-wide identification, characterization and transcriptional profiling of NHX-type (Na+/H+) antiporters under salinity stress in soybean. PMID:33442515
Embeddings from deep learning transfer GO annotations beyond homology. PMID:33441905
Signatures of conserved and unique molecular features in Afrotheria. PMID:33441654
Blood-derived mitochondrial DNA copy number is associated with gene expression across multiple tissues and is predictive for incident neurodegenerative disease. PMID:33441415
Ceruloplasmin Deamidation in Neurodegeneration: From Loss to Gain of Function. PMID:33440850
A modular master regulator landscape controls cancer transcriptional identity. PMID:33434495
Transcriptome profiling of insulin sensitive tissues from GH deficient mice following GH treatment. PMID:33433889
Ascending dorsal column sensory neurons respond to spinal cord injury and downregulate genes related to lipid metabolism. PMID:33431991
Absence of NLRP3 Inflammasome in Hematopoietic Cells Reduces Adverse Remodeling After Experimental Myocardial Infarction. PMID:33426377
The iPPI-DB initiative: A Community-centered database of Protein-Protein Interaction modulators. PMID:33416858
Plasma membrane vesicles from cauliflower meristematic tissue and their role in water passage. PMID:33413105
Evaluation of the potential of Pap test fluid and cervical swabs to serve as clinical diagnostic biospecimens for the detection of ovarian cancer by mass spectrometry-based proteomics. PMID:33413078
Shared Blood Transcriptomic Signatures between Alzheimer's Disease and Diabetes Mellitus. PMID:33406707
Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis. PMID:33398403
Computationally predicted SARS-COV-2 encoded microRNAs target NFKB, JAK/STAT and TGFB signaling pathways. PMID:33398248
Spatiotemporal profiling of cytosolic signaling complexes in living cells by selective proximity proteomics. PMID:33397984
The Interactome of Cancer-Related Lysyl Oxidase and Lysyl Oxidase-Like Proteins. PMID:33383846
Effect of let-7c on the PI3K/Akt/FoxO signaling pathway in hepatocellular carcinoma. PMID:33376529
The m6A RNA Demethylase ALKBH5 Promotes Radioresistance and Invasion Capability of Glioma Stem Cells. PMID:33375621
Inflammatory Proteins HMGA2 and PRTN3 as Drivers of Vulvar Squamous Cell Carcinoma Progression. PMID:33374674
FIGNL1 promotes non‑small cell lung cancer cell proliferation. PMID:33367932
Comprehensive Profiling of Gene Expression in the Cerebral Cortex and Striatum of BTBRTF/ArtRbrc Mice Compared to C57BL/6J Mice. PMID:33362469
Salmonella enterica Serovars Dublin and Enteritidis Comparative Proteomics Reveals Differential Expression of Proteins Involved in Stress Resistance, Virulence, and Anaerobic Metabolism. PMID:33361201
A primer for generating and using transcriptome data and gene sets. PMID:33361089
Generation of an Interactome for the Tetratricopeptide Repeat Domain of O-GlcNAc Transferase Indicates a Role for the Enzyme in Intellectual Disability. PMID:33356293
Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. PMID:33347974
A Novel Family of Acinetobacter Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes. PMID:33343549
Episodic Decrease in Temperature Increases mcy Gene Transcription and Cellular Microcystin in Continuous Cultures of Microcystis aeruginosa PCC 7806. PMID:33343544
Transcriptional profiles of human islet and exocrine endothelial cells in subjects with or without impaired glucose metabolism. PMID:33339897
Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells. PMID:33338397
Modeling the human aging transcriptome across tissues, health status, and sex. PMID:33336875
Distinct Signatures in the Receptor Repertoire Discriminate CD56bright and CD56dim Natural Killer Cells. PMID:33335526
Upregulation of 5'-terminal oligopyrimidine mRNA translation upon loss of the ARF tumor suppressor. PMID:33335292
Cerina: systematic circRNA functional annotation based on integrative analysis of ceRNA interactions. PMID:33335165
Biological and physical approaches on the role of piplartine (piperlongumine) in cancer. PMID:33335138
The identification of co-expressed gene modules in Streptococcus pneumonia from colonization to infection to predict novel potential virulence genes. PMID:33334315
Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease. PMID:33333559
A Machine Learning Approach for Tracing Tumor Original Sites With Gene Expression Profiles. PMID:33330438
Comprehensive Transcriptomic Analysis Reveals Dysregulated Competing Endogenous RNA Network in Endocrine Resistant Breast Cancer Cells. PMID:33324567
Genetic Determinants of Gating Functions: Do We Get Closer to Understanding Schizophrenia Etiopathogenesis? PMID:33324248
PEREGRINE: A genome-wide prediction of enhancer to gene relationships supported by experimental evidence. PMID:33320871
Analysis of readability and structural accuracy in SNOMED CT. PMID:33319711
Quality assurance and enrichment of biological and biomedical ontologies and terminologies. PMID:33319696
Genome-wide correlation analysis to identify amplitude regulators of circadian transcriptome output. PMID:33318596
Hearing impairment due to Mir183/96/182 mutations suggests both loss and gain of function effects. PMID:33318051
Expression of PAWR predicts prognosis of ovarian cancer. PMID:33317551
Exostosin1 as a novel prognostic and predictive biomarker for squamous cell lung carcinoma: A study based on bioinformatics analysis. PMID:33314711
Hierarchical Canonical Correlation Analysis Reveals Phenotype, Genotype, and Geoclimate Associations in Plants. PMID:33313545
Comparative proteomic analysis highlights metabolic dysfunction in α-synucleinopathy. PMID:33311497
Transcriptomic Profiling of Human Pluripotent Stem Cell-derived Retinal Pigment Epithelium over Time. PMID:33307245
Applying graph database technology for analyzing perturbed co-expression networks in cancer. PMID:33306799
A Multi-Network Comparative Analysis of Transcriptome and Translatome Identifies Novel Hub Genes in Cardiac Remodeling. PMID:33304386
tRNA-Derived Fragments (tRFs) in Bladder Cancer: Increased 5'-tRF-LysCTT Results in Disease Early Progression and Patients' Poor Treatment Outcome. PMID:33291319
PANTHER version 16: a revised family classification, tree-based classification tool, enhancer regions and extensive API. PMID:33290554
The Gene Ontology resource: enriching a GOld mine. PMID:33290552
Identification of Dysregulated Genes for Late-Onset Alzheimer's Disease Using Gene Expression Data in Brain. PMID:33282526
Network Pharmacology Identifies the Mechanisms of Action of Tongxie Anchang Decoction in the Treatment of Irritable Bowel Syndrome with Diarrhea Predominant. PMID:33281910
Machine Learning Based Network Analysis Determined Clinically Relevant miRNAs in Breast Cancer. PMID:33281885
A Novel Proximity Biotinylation Assay Based on the Self-Associating Split GFP1-10/11. PMID:33276494
Urinary vitronectin identifies patients with high levels of fibrosis in kidney grafts. PMID:33275196
CovMulNet19, Integrating Proteins, Diseases, Drugs, and Symptoms: A Network Medicine Approach to COVID-19. PMID:33274348
Reprogramming to recover youthful epigenetic information and restore vision. PMID:33268865
Humoral immune responses mediate the development of a restrictive phenotype of chronic lung allograft dysfunction. PMID:33268593
Comparative Analysis of the Global Transcriptomic Response to Oxidative Stress of Bacillus anthracis htrA-Disrupted and Parental Wild Type Strains. PMID:33265965
HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. PMID:33264402
Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. PMID:33262328
Adaptation Strategies of Halophytic Barley Hordeum marinum ssp. marinum to High Salinity and Osmotic Stress. PMID:33260985
Regulators of TNFα mediated insulin resistance elucidated by quantitative proteomics. PMID:33257747
MiR-215-5p Reduces Liver Metastasis in an Experimental Model of Colorectal Cancer through Regulation of ECM-Receptor Interactions and Focal Adhesion. PMID:33255928
TET2/IDH1/2/WT1 and NPM1 Mutations Influence the RUNX1 Expression Correlations in Acute Myeloid Leukemia. PMID:33255417
Essential gene prediction using limited gene essentiality information-An integrative semi-supervised machine learning strategy. PMID:33253254
Identifying longevity associated genes by integrating gene expression and curated annotations. PMID:33253142
Frequent Assembly of Chimeric Complexes in the Protein Interaction Network of an Interspecies Yeast Hybrid. PMID:33252673
Evolved bacterial resistance against fluoropyrimidines can lower chemotherapy impact in the Caenorhabditis elegans host. PMID:33252330
Spatial Proteomic Approach to Characterize Skeletal Muscle Myofibers. PMID:33251806
The Draft Genome of Red Lechwe, Kobus leche leche. PMID:33250921
A New Catalog of Structural Variants in 1,301 A. thaliana Lines from Africa, Eurasia, and North America Reveals a Signature of Balancing Selection at Defense Response Genes. PMID:33247723
Transcriptome and proteome profiling reveal complementary scavenger and immune features of rat liver sinusoidal endothelial cells and liver macrophages. PMID:33246411
In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. PMID:33243861
Multiparametric Profiling of Engineered Nanomaterials: Unmasking the Surface Coating Effect. PMID:33240770
MutRank: an R shiny web-application for exploratory targeted mutual rank-based coexpression analyses integrated with user-provided supporting information. PMID:33240618
Identifying transcriptomic correlates of histology using deep learning. PMID:33237966
The STRING database in 2021: customizable protein-protein networks, and functional characterization of user-uploaded gene/measurement sets. PMID:33237311
UniProt: the universal protein knowledgebase in 2021. PMID:33237286
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. PMID:33237278
Reduced lipolysis in lipoma phenocopies lipid accumulation in obesity. PMID:33235355
Is the Proteome of Bronchoalveolar Lavage Extracellular Vesicles a Marker of Advanced Lung Cancer? PMID:33233545
Physiological Changes in Barley mlo-11 Powdery Mildew Resistance Conditioned by Tandem Repeat Copy Number. PMID:33233522
Identification and analysis of immune-related subtypes of hepatocellular carcinoma. PMID:33231514
Phylostratic Shift of Whole-Genome Duplications in Normal Mammalian Tissues towards Unicellularity Is Driven by Developmental Bivalent Genes and Reveals a Link to Cancer. PMID:33228223
LnCeCell: a comprehensive database of predicted lncRNA-associated ceRNA networks at single-cell resolution. PMID:33219686
FlyBase: updates to the Drosophila melanogaster knowledge base. PMID:33219682
MolluscDB: an integrated functional and evolutionary genomics database for the hyper-diverse animal phylum Mollusca. PMID:33219670
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. PMID:33211854
DEEPScreen: high performance drug-target interaction prediction with convolutional neural networks using 2-D structural compound representations. PMID:33209251
Whole exome sequencing and trio analysis to broaden the variant spectrum of genes in idiopathic hypogonadotropic hypogonadism. PMID:33208564
8-Hydroxydaidzein, an Isoflavone from Fermented Soybean, Induces Autophagy, Apoptosis, Differentiation, and Degradation of Oncoprotein BCR-ABL in K562 Cells. PMID:33207739
DeepPheno: Predicting single gene loss-of-function phenotypes using an ontology-aware hierarchical classifier. PMID:33206638
The Ontologies Community of Practice: A CGIAR Initiative for Big Data in Agrifood Systems. PMID:33205138
Epigenetic profiling of Italian patients identified methylation sites associated with hereditary transthyretin amyloidosis. PMID:33203445
Genome-Wide Functional Screen for Calcium Transients in Escherichia coli Identifies Increased Membrane Potential Adaptation to Persistent DNA Damage. PMID:33199283
OrthoDB in 2020: evolutionary and functional annotations of orthologs. PMID:33196836
RBP2GO: a comprehensive pan-species database on RNA-binding proteins, their interactions and functions. PMID:33196814
NONCODEV6: an updated database dedicated to long non-coding RNA annotation in both animals and plants. PMID:33196801
KG-COVID-19: A Framework to Produce Customized Knowledge Graphs for COVID-19 Response. PMID:33196056
Integrated transcriptome meta-analysis of pancreatic ductal adenocarcinoma and matched adjacent pancreatic tissues. PMID:33194391
MaizeMine: A Data Mining Warehouse for the Maize Genetics and Genomics Database. PMID:33193550
Gene Expression Signatures in AML-12 Hepatocyte Cells upon Dengue virus Infection and Acetaminophen Treatment. PMID:33182673
FunRes: resolving tissue-specific functional cell states based on a cell-cell communication network model. PMID:33179736
Mesenchymal stem cells negatively regulate CD4<sup>+</sup> T cell activation in patients with primary Sjögren syndrome through the miRNA‑125b and miRNA‑155 TCR pathway. PMID:33179091
Prolonged Targeted Cardiovascular Epidural Stimulation Improves Immunological Molecular Profile: A Case Report in Chronic Severe Spinal Cord Injury. PMID:33177997
High SEMA4C expression promotes the epithelial-mesenchymal transition and predicts poor prognosis in colorectal carcinoma. PMID:33177246
PLK1 and NOTCH Positively Correlate in Melanoma and Their Combined Inhibition Results in Synergistic Modulations of Key Melanoma Pathways. PMID:33177155
Avian Immunome DB: an example of a user-friendly interface for extracting genetic information. PMID:33176685
Insulin-promoted mobilization of GLUT4 from a perinuclear storage site requires RAB10. PMID:33175605
Anti‑inflammatory mechanism of berberine on lipopolysaccharide‑induced IEC‑18 models based on comparative transcriptomics. PMID:33174609
MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. PMID:33174596
Gene expression profile of lipopolysaccharide‑induced apoptosis of nucleus pulposus cells reversed by syringic acid. PMID:33174055
Identification of inflammation‑associated circulating long non‑coding RNAs and genes in intracranial aneurysm rupture‑induced subarachnoid hemorrhage. PMID:33174039
Using mRNA deep sequencing to analyze differentially expressed genes during Panax notoginseng saponin treatment of ischemic stroke. PMID:33173991
Integrated microarray analysis of key genes and a miRNA‑mRNA regulatory network of early‑onset preeclampsia. PMID:33173953
A compound downregulation of SRRM2 and miR-27a-3p with upregulation of miR-27b-3p in PBMCs of Parkinson's patients is associated with the early stage onset of disease. PMID:33171483
Survey of metaproteomics software tools for functional microbiome analysis. PMID:33170893
Genome Variation Map: a worldwide collection of genome variations across multiple species. PMID:33170268
The Zebrafish Information Network: major gene page and home page updates. PMID:33170210
LegumeIP V3: from models to crops-an integrative gene discovery platform for translational genomics in legumes. PMID:33166388
CSF1R inhibition depletes tumor-associated macrophages and attenuates tumor progression in a mouse sonic Hedgehog-Medulloblastoma model. PMID:33159168
CLAVATA Signaling Ensures Reproductive Development in Plants across Thermal Environments. PMID:33157018
Lipopolysaccharide triggers different transcriptional signatures in taurine and indicine cattle macrophages: Reactive oxygen species and potential outcomes to the development of immune response to infections. PMID:33156842
The InterPro protein families and domains database: 20 years on. PMID:33156333
Deep learning approach for predicting functional Z-DNA regions using omics data. PMID:33154517
DNMSO; an ontology for representing de novo sequencing results from Tandem-MS data. PMID:33150092
Constitution of a comprehensive phytochemical profile and network pharmacology based investigation to decipher molecular mechanisms of Teucrium polium L. in the treatment of type 2 diabetes mellitus. PMID:33150068
Loss of PHF6 leads to aberrant development of human neuron-like cells. PMID:33149206
Integrated Bioinformatics Analysis of Hub Genes and Pathways Associated with a Compression Model of Spinal Cord Injury in Rats. PMID:33149108
Dissecting Herpes Simplex Virus 1-Induced Host Shutoff at the RNA Level. PMID:33148793
Blocking IL1 Beta Promotes Tumor Regression and Remodeling of the Myeloid Compartment in a Renal Cell Carcinoma Model: Multidimensional Analyses. PMID:33148676
The Role of Salmonella Genomic Island 4 in Metal Tolerance of Salmonella enterica Serovar I 4,[5],12:i:- Pork Outbreak Isolate USDA15WA-1. PMID:33142960
Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. PMID:33140449
Bacterial-fungal interactions revealed by genome-wide analysis of bacterial mutant fitness. PMID:33139882
Ensembl 2021. PMID:33137190
Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors. PMID:33137164
Differential transcript usage in the Parkinson's disease brain. PMID:33137089
Many, but not all, lineage-specific genes can be explained by homology detection failure. PMID:33137085
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
Plasma Proteomics Identify Biomarkers and Pathogenesis of COVID-19. PMID:33128875
Higher miR-543 levels correlate with lower STK31 expression and longer pancreatic cancer survival. PMID:33128354
Bufalin exerts antitumor effects in neuroblastoma via the induction of reactive oxygen species‑mediated apoptosis by targeting the electron transport chain. PMID:33125107
Paternal reprogramming-escape histone H3K4me3 marks located within promoters of RNA splicing genes. PMID:33119058
Common Adaptive Strategies Underlie Within-Host Evolution of Bacterial Pathogens. PMID:33118035
Murine interfollicular epidermal differentiation is gradualistic with GRHL3 controlling progression from stem to transition cell states. PMID:33116143
Analysing the meta-interaction between pathways by gene set topological impact analysis. PMID:33109101
Systematic Investigation of Resistance Evolution to Common Antibiotics Reveals Conserved Collateral Responses across Common Human Pathogens. PMID:33106260
Soluble Compounds Released by Hypoxic Stroma Confer Invasive Properties to Pancreatic Ductal Adenocarcinoma. PMID:33105540
PhycoCosm, a comparative algal genomics resource. PMID:33104790
The mouse Gene Expression Database (GXD): 2021 update. PMID:33104772
Genomic and transcriptomic landscapes and evolutionary dynamics of molluscan glycoside hydrolase families with implications for algae-feeding biology. PMID:33101612
DEG 15, an update of the Database of Essential Genes that includes built-in analysis tools. PMID:33095861
The efficacy of chemotherapeutic drug combinations may be predicted by concordance of gene response to the single agents. PMID:33093925
Maximized quantitative phosphoproteomics allows high confidence dissection of the DNA damage signaling network. PMID:33093574
Transcriptome analysis of Actinoplanes utahensis reveals molecular signature of saccharide impact on acarbose biosynthesis. PMID:33088668
Comprehensive Analysis of Differentially Expressed Circular RNAs in Patients with Senile Osteoporotic Vertebral Compression Fracture. PMID:33083467
Network-Based Coexpression Analysis Identifies Functional and Prognostic Long Noncoding RNAs in Hepatocellular Carcinoma. PMID:33083449
Transcriptome Analysis Identifies Novel Prognostic Genes in Osteosarcoma. PMID:33082842
Mitochondrial-Y chromosome epistasis in Drosophila melanogaster. PMID:33081607
Quantifying the distribution of protein oligomerization degree reflects cellular information capacity. PMID:33077848
Predicted functional interactome of Caenorhabditis elegans and a web tool for the functional interpretation of differentially expressed genes. PMID:33076954
Exploration of the sputum methylome and omics deconvolution by quadratic programming in molecular profiling of asthma and COPD: the road to sputum omics 2.0. PMID:33076907
SWI/SNF inactivation in the endometrial epithelium leads to loss of epithelial integrity. PMID:33075803
Differential Transcription and Alternative Splicing in Cotton Underly Specialized Defense Responses Against Pests. PMID:33072149
No Assembly Required: Using BTyper3 to Assess the Congruency of a Proposed Taxonomic Framework for the Bacillus cereus Group With Historical Typing Methods. PMID:33072050
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell. PMID:33067542
Increased RNA editing in maternal immune activation model of neurodevelopmental disease. PMID:33067431
Divergent Resistance Mechanisms to Immunotherapy Explain Responses in Different Skin Cancers. PMID:33065980
ScatLay: utilizing transcriptome-wide noise for identifying and visualizing differentially expressed genes. PMID:33060728
Biomarker exploration of microRNA-203 as a promising substrate for predicting poor survival outcome in colorectal cancer. PMID:33059609
During bacteremia, Pseudomonas aeruginosa PAO1 adapts by altering the expression of numerous virulence genes including those involved in quorum sensing. PMID:33057423
smORFunction: a tool for predicting functions of small open reading frames and microproteins. PMID:33054771
Monosomy X in Female Mice Influences the Regional Formation and Augments the Severity of Angiotensin II-Induced Aortopathies. PMID:33054396
IurV, Encoded by ORF VCA0231, Is Involved in the Regulation of Iron Uptake Genes in Vibrio cholerae. PMID:33053678
A high-throughput CRISPR interference screen for dissecting functional regulators of GPCR/cAMP signaling. PMID:33052901
Semantic similarity and machine learning with ontologies. PMID:33049044
Maximizing cohesion and separation for detecting protein functional modules in protein-protein interaction networks. PMID:33048996
Electricity from lignocellulosic substrates by thermophilic Geobacillus species. PMID:33046790
Protein ontology on the semantic web for knowledge discovery. PMID:33046717
Transcriptome analysis revealed misregulated gene expression in blastoderms of interspecific chicken and Japanese quail F1 hybrids. PMID:33044996
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
In vivo mRNA display enables large-scale proteomics by next generation sequencing. PMID:33037152
Mitochondria under the spotlight: On the implications of mitochondrial dysfunction and its connectivity to neuropsychiatric disorders. PMID:33033576
A realism-based approach to an ontological representation of symbiotic interactions. PMID:33032576
Data mining of human plasma proteins generates a multitude of highly predictive aging clocks that reflect different aspects of aging. PMID:33031577
Graph-based exploitation of gene ontology using GOxploreR for scrutinizing biological significance. PMID:33028846
Root-Secreted Coumarins and the Microbiota Interact to Improve Iron Nutrition in Arabidopsis. PMID:33027611
Compartment-specific transcriptomics of ozone-exposed murine lungs reveals sex- and cell type-associated perturbations relevant to mucoinflammatory lung diseases. PMID:33026818
Development of a Cardiac Sarcomere Functional Genomics Platform to Enable Scalable Interrogation of Human TNNT2 Variants. PMID:33025817
A Novel Proteomic Method Reveals NLS Tagging of T-DM1 Contravenes Classical Nuclear Transport in a Model of HER2-Positive Breast Cancer. PMID:33024794
Transcript Isoforms of SLC7A11-AS1 Are Associated With Varicocele-Related Male Infertility. PMID:33024440
Long-Term m5C Methylome Dynamics Parallel Phenotypic Adaptation in the Cyanobacterium Trichodesmium. PMID:33022053
lncRNAKB, a knowledgebase of tissue-specific functional annotation and trait association of long noncoding RNA. PMID:33020484
Pseudo2GO: A Graph-Based Deep Learning Method for Pseudogene Function Prediction by Borrowing Information From Coding Genes. PMID:33014009
Human Pluripotent Stem Cell-Derived Neural Cells and Brain Organoids Reveal SARS-CoV-2 Neurotropism Predominates in Choroid Plexus Epithelium. PMID:33010822
Identification of NUF2 and FAM83D as potential biomarkers in triple-negative breast cancer. PMID:33005492
Transcriptomic signatures of cold adaptation and heat stress in the winter ant (Prenolepis imparis). PMID:33002025
Phenotype-genotype comorbidity analysis of patients with rare disorders provides insight into their pathological and molecular bases. PMID:33001999
Knockdown of SERPINE1 reverses resistance of triple‑negative breast cancer to paclitaxel via suppression of VEGFA. PMID:33000256
Uncovering potential differentially expressed miRNAs and targeted mRNAs in myocardial infarction based on integrating analysis. PMID:33000230
Implication of ZNF217 in Accelerating Tumor Development and Therapeutically Targeting ZNF217-Induced PI3K-AKT Signaling for the Treatment of Metastatic Osteosarcoma. PMID:32999043
SlFERL Interacts with S-Adenosylmethionine Synthetase to Regulate Fruit Ripening. PMID:32999005
Efficient Propagation of Circulating Tumor Cells: A First Step for Probing Tumor Metastasis. PMID:32998338
Identification of the significant pathways of Banxia Houpu decoction in the treatment of depression based on network pharmacology. PMID:32997725
Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction. PMID:32992050
Functional signatures of evolutionarily young CTCF binding sites. PMID:32988407
Cancer-associated fibroblasts of the prostate promote a compliant and more invasive phenotype in benign prostate epithelial cells. PMID:32984808
Pharmacological and phosphoproteomic approaches to roles of protein kinase C in kappa opioid receptor-mediated effects in mice. PMID:32976891
TREND-DB-a transcriptome-wide atlas of the dynamic landscape of alternative polyadenylation. PMID:32976578
Burden of rare deleterious variants in WNT signaling genes among 511 myelomeningocele patients. PMID:32970752
Aldh inhibitor restores auditory function in a mouse model of human deafness. PMID:32970669
Thyroid hormone receptor α in skeletal muscle is essential for T3-mediated increase in energy expenditure. PMID:32969079
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
Circular RNAs associated with a mouse model of concanavalin A-induced autoimmune hepatitis: preliminary screening and comprehensive functional analysis. PMID:32965791
Review on the Computational Genome Annotation of Sequences Obtained by Next-Generation Sequencing. PMID:32962098
Identification of hub genes in colon cancer via bioinformatics analysis. PMID:32961078
Identification of novel candidate risk genes for myelomeningocele within the glucose homeostasis/oxidative stress and folate/one-carbon metabolism networks. PMID:32960507
Localized inhibition in the Drosophila mushroom body. PMID:32955437
Designing custom CRISPR libraries for hypothesis-driven drug target discovery. PMID:32952937
Knockdown of SAR1B suppresses proliferation and induces apoptosis of RKO colorectal cancer cells. PMID:32952655
An unanticipated tumor-suppressive role of the SUMO pathway in the intestine unveiled by Ubc9 haploinsufficiency. PMID:32948837
Bioinformatics Data Mining Repurposes the JAK2 (Janus Kinase 2) Inhibitor Fedratinib for Treating Pancreatic Ductal Adenocarcinoma by Reversing the KRAS (Kirsten Rat Sarcoma 2 Viral Oncogene Homolog)-Driven Gene Signature. PMID:32947833
Multi-layered Spatial Transcriptomics Identify Secretory Factors Promoting Human Hematopoietic Stem Cell Development. PMID:32946788
miR‑592 acts as an oncogene and promotes medullary thyroid cancer tumorigenesis by targeting cyclin‑dependent kinase 8. PMID:32945439
Small RNA deep sequencing reveals novel miRNAs in peripheral blood mononuclear cells from patients with IgA nephropathy. PMID:32945407
A clinical and multi‑omics study of Van der Woude syndrome in three generations of a Chinese family. PMID:32945398
Resveratrol modulates the apoptosis and autophagic death of human lung adenocarcinoma A549 cells via a p53‑dependent pathway: Integrated bioinformatics analysis and experimental validation. PMID:32945383
Enzyme-Constrained Models and Omics Analysis of Streptomyces coelicolor Reveal Metabolic Changes that Enhance Heterologous Production. PMID:32942174
IDDB: a comprehensive resource featuring genes, variants and characteristics associated with infertility. PMID:32941628
Chitinase 3-Like 1 Contributes to Food Allergy via M2 Macrophage Polarization. PMID:32935492
Cellular expression profiles of Epstein-Barr virus-transformed B-lymphoblastoid cell lines. PMID:32934816
TMEM206 is a potential prognostic marker of hepatocellular carcinoma. PMID:32934741
Immunotyping of tumor-infiltrating lymphocytes in triple-negative breast cancer and genetic characterization. PMID:32934708
Drosophila Voltage-Gated Sodium Channels Are Only Expressed in Active Neurons and Are Localized to Distal Axonal Initial Segment-like Domains. PMID:32928889
Deciphering the Plasma Proteome of Type 2 Diabetes. PMID:32928870
A Pilot Study on MicroRNA Profile in Tear Fluid to Predict Response to Anti-VEGF Treatments for Diabetic Macular Edema. PMID:32927780
Characterization and functional prediction of the microRNAs differentially expressed in a mouse model of concanavalin A-induced autoimmune hepatitis. PMID:32922197
Expression Profiles of Long Non-coding RNA and Messenger RNA in Human Traumatic Brain Injury. PMID:32919233
Comprehensive Characterization of Prognostic Long Noncoding RNAs in Osteosarcoma. PMID:32908905
Identification of Biomarkers to Construct a Competing Endogenous RNA Network and Establishment of a Genomic-Clinicopathologic Nomogram to Predict Survival for Children with Rhabdoid Tumors of the Kidney. PMID:32908900
Network Pharmacology to Uncover the Biological Basis of Spleen Qi Deficiency Syndrome and Herbal Treatment. PMID:32908629
ReactomeGSA - Efficient Multi-Omics Comparative Pathway Analysis. PMID:32907876
Differentially expressed genes on the growth of mouse Leydig cells treated with standardised Eurycoma longifolia extract. PMID:32901880
De novo transcriptome sequencing of Paecilomyces tenuipes revealed genes involved in adenosine biosynthesis. PMID:32901833
High-Resolution Mass Spectrometry-Based Approaches for the Detection and Quantification of Peptidase Activity in Plasma. PMID:32899982
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age. PMID:32898168
Understanding microcephaly through the study of centrosome regulation in Drosophila neural stem cells. PMID:32897294
A long non-coding RNA (Lrap) modulates brain gene expression and levels of alcohol consumption in rats. PMID:32893479
Functional, Morphological, and Evolutionary Characterization of Hearing in Subterranean, Eusocial African Mole-Rats. PMID:32888484
Osteopontin Expression Identifies a Subset of Recruited Macrophages Distinct from Kupffer Cells in the Fatty Liver. PMID:32888418
Secretome Proteomic Approaches for Biomarker Discovery: An Update on Colorectal Cancer. PMID:32878319
Changes in MicroRNA Expression during Rabbit Hemorrhagic Disease Virus (RHDV) Infection. PMID:32878241
Term Matrix: a novel Gene Ontology annotation quality control system based on ontology term co-annotation patterns. PMID:32875947
Differential contribution of bone marrow-derived infiltrating monocytes and resident macrophages to persistent lung inflammation in chronic air pollution exposure. PMID:32873817
Dissecting Transcription Factor-Target Interaction in Bovine Coronavirus Infection. PMID:32872640
Proteomics and Metabolomics Approaches towards a Functional Insight onto AUTISM Spectrum Disorders: Phenotype Stratification and Biomarker Discovery. PMID:32872562
Computational Methods and Software Tools for Functional Analysis of miRNA Data. PMID:32872205
Inference and multiscale model of epithelial-to-mesenchymal transition via single-cell transcriptomic data. PMID:32870263
Elucidation of remdesivir cytotoxicity pathways through genome-wide CRISPR-Cas9 screening and transcriptomics. PMID:32869031
Single-cell RNA expression profiling of SARS-CoV-2-related ACE2 and TMPRSS2 in human trophectoderm and placenta. PMID:32851697
Screening and Identification of Therapeutic Targets for Pulmonary Arterial Hypertension Through Microarray Technology. PMID:32849793
Newly identified Gon4l/Udu-interacting proteins implicate novel functions. PMID:32848183
Experimental Evolution of Bacillus subtilis Reveals the Evolutionary Dynamics of Horizontal Gene Transfer and Suggests Adaptive and Neutral Effects. PMID:32847815
KG-COVID-19: a framework to produce customized knowledge graphs for COVID-19 response. PMID:32839776
Differential processing and localization of human Nocturnin controls metabolism of mRNA and nicotinamide adenine dinucleotide cofactors. PMID:32839274
Identification and classification of differentially expressed genes reveal potential molecular signature associated with SARS-CoV-2 infection in lung adenocarcinomal cells. PMID:32835074
Innate immune response in neuronopathic forms of Gaucher disease confers resistance against viral-induced encephalitis. PMID:32831144
Risuteganib Protects against Hydroquinone-induced Injury in Human RPE Cells. PMID:32818234
Experimental and Biological Insights from Proteomic Analyses of Extracellular Vesicle Cargos in Normalcy and Disease. PMID:32815324
Grad-seq shines light on unrecognized RNA and protein complexes in the model bacterium Escherichia coli. PMID:32813020
The current landscape of coronavirus-host protein-protein interactions. PMID:32811513
Extreme Phenotype Approach Suggests Taste Transduction Pathway for Carotid Plaque in a Multi-Ethnic Cohort. PMID:32811377
Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment. PMID:32810438
CRISPR interference of nucleotide biosynthesis improves production of a single-domain antibody in Escherichia coli. PMID:32808670
Microarray-based transcriptional profiling of a mouse model of autoimmune hepatitis. PMID:32808463
Optic nerve coloboma as extension of the phenotype of 22q11.23 duplication syndrome: a case report. PMID:32807111
Integrated Framework of the Immune-Defense Transcriptional Signatures in the Arabidopsis Shoot Apical Meristem. PMID:32796535
IFN signaling and neutrophil degranulation transcriptional signatures are induced during SARS-CoV-2 infection. PMID:32793903
Discovery of small molecules that normalize the transcriptome and enhance cysteine cathepsin activity in progranulin-deficient microglia. PMID:32792571
An autophagy-related model of 4 key genes for predicting prognosis of patients with laryngeal cancer. PMID:32791689
Genetic Mutations That Drive Evolutionary Rescue to Lethal Temperature in Escherichia coli. PMID:32785667
Genomic Analysis of Localized High-Risk Prostate Cancer Circulating Tumor Cells at the Single-Cell Level. PMID:32784507
Mechanistic studies of cytotoxic activity of the mesoionic compound MIH 2.4Bl in MCF-7 breast cancer cells. PMID:32782546
Dissecting diagnostic heterogeneity in depression by integrating neuroimaging and genetics. PMID:32781460
Lack of TLR4 modifies the miRNAs profile and attenuates inflammatory signaling pathways. PMID:32780740
SOX10-regulated promoter use defines isoform-specific gene expression in Schwann cells. PMID:32770939
Mutant p53 induces Golgi tubulo-vesiculation driving a prometastatic secretome. PMID:32770028
Transcriptomic analysis reveals differential gene expression, alternative splicing, and novel exons during mouse trophoblast stem cell differentiation. PMID:32762732
FLUTE: Fast and reliable knowledge retrieval from biomedical literature. PMID:32761077
The effect of Jiedu Huoxue decoction on rat model of experimental nonbacterial prostatitis via regulation of miRNAs. PMID:32758035
Glycosaminoglycan-Protein Interactions: The First Draft of the Glycosaminoglycan Interactome. PMID:32757871
Circuits Regulating Superoxide and Nitric Oxide Production and Neutralization in Different Cell Types: Expression of Participating Genes and Changes Induced by Ionizing Radiation. PMID:32756515
Bioinformatics analysis of microRNA profiles and identification of microRNA-mRNA network and biological markers in intracranial aneurysm. PMID:32756097
COVID-19-Related Coagulopathy-Is Transferrin a Missing Link? PMID:32751741
iPS-Derived Early Oligodendrocyte Progenitor Cells from SPMS Patients Reveal Deficient In Vitro Cell Migration Stimulation. PMID:32751289
Metastasis of Uveal Melanoma with Monosomy-3 Is Associated with a Less Glycogenetic Gene Expression Profile and the Dysregulation of Glycogen Storage. PMID:32751097
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation. PMID:32749457
Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder. PMID:32744794
A human ESC-based screen identifies a role for the translated lncRNA LINC00261 in pancreatic endocrine differentiation. PMID:32744504
Single molecule poly(A) tail-seq shows LARP4 opposes deadenylation throughout mRNA lifespan with most impact on short tails. PMID:32744499
An Activity-Guided Map of Electrophile-Cysteine Interactions in Primary Human T Cells. PMID:32730809
Breed Differences in Dog Cognition Associated with Brain-Expressed Genes and Neurological Functions. PMID:32726413
GGCT promotes colorectal cancer migration and invasion via epithelial-mesenchymal transition. PMID:32724344
Single-cell transcriptome profiling reveals neutrophil heterogeneity in homeostasis and infection. PMID:32719519
A Coordinated Approach by Public Domain Bioinformatics Resources to Aid the Fight Against Alzheimer's Disease Through Expert Curation of Key Protein Targets. PMID:32716361
Causal mutations from adaptive laboratory evolution are outlined by multiple scales of genome annotations and condition-specificity. PMID:32711472
A Genome-Wide View of Transcriptional Responses during Aphis glycines Infestation in Soybean. PMID:32707968
Genome‑wide analysis of DNA methylation and gene expression changes in an ovalbumin‑induced asthma mouse model. PMID:32705270
Downregulation of miR‑193a‑3p via targeting cyclin D1 in thyroid cancer. PMID:32705210
Expression profiling of circular RNAs and their potential role in early‑stage diabetic cardiomyopathy. PMID:32705182
Expanded Phenotypic Definition Identifies Hundreds of Potential Causative Genes for Leukodystrophies and Leukoencephalopathies. PMID:32704519
A substrate-based ontology for human solute carriers. PMID:32697042
Meta-analysis of gene expression profiles of lean and obese PCOS to identify differentially regulated pathways and risk of comorbidities. PMID:32695266
DAZL mediates a broad translational program regulating expansion and differentiation of spermatogonial progenitors. PMID:32686646
Inhibition of the catalytic subunit of DNA-dependent protein kinase (DNA-PKcs) stimulates osteoblastogenesis by potentiating bone morphogenetic protein 2 (BMP2) responses. PMID:32686190
The power and limitations of gene expression pathway analyses toward predicting population response to environmental stressors. PMID:32684953
Development and validation of an integrative methylation signature and nomogram for predicting survival in clear cell renal cell carcinoma. PMID:32676392
RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. PMID:32673562
Black Soldier Fly Larvae Adapt to Different Food Substrates through Morphological and Functional Responses of the Midgut. PMID:32668813
Unified inference of missense variant effects and gene constraints in the human genome. PMID:32667917
Nonsense-Mediated RNA Decay Factor UPF1 Is Critical for Posttranscriptional and Translational Gene Regulation in Arabidopsis. PMID:32665305
Investigating higher-order interactions in single-cell data with scHOT. PMID:32661426
Sex- and Region-Specific Differences in the Transcriptomes of Rat Microglia from the Brainstem and Cervical Spinal Cord. PMID:32661056
A Bioinformatics Crash Course for Interpreting Genomics Data. PMID:32658646
Benchmarking gene ontology function predictions using negative annotations. PMID:32657372
Transcriptomic Analysis of Extracellular RNA Governed by the Endocytic Adaptor Protein Cin1 of Cryptococcus deneoformans. PMID:32656093
Transcriptomic and Ultrastructural Signatures of K+-Induced Aggregation in Phytophthora parasitica Zoospores. PMID:32645882
The Lyme disease bacterium, Borrelia burgdorferi, stimulates an inflammatory response in human choroid plexus epithelial cells. PMID:32645014
Protein-Protein Interactions Efficiently Modeled by Residue Cluster Classes. PMID:32640745
Phosphoproteomic quantitation and causal analysis reveal pathways in GPVI/ITAM-mediated platelet activation programs. PMID:32640021
The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST). PMID:32637990
A Comprehensive Coexpression Network Analysis in Vibrio cholerae. PMID:32636337
Low Oxygen Stress During Early Development Influences Regulation of Hypoxia-Response Genes in Farmed Atlantic Salmon (Salmo salar). PMID:32636218
Retinal pigment epithelium transcriptome analysis in chronic smoking reveals a suppressed innate immune response and activation of differentiation pathways. PMID:32634473
Transcriptome Analyses of Candida albicans Biofilms, Exposed to Arachidonic Acid and Fluconazole, Indicates Potential Drug Targets. PMID:32631950
Integrated microarray analysis to identify potential biomarkers and therapeutic targets in dilated cardiomyopathy. PMID:32626989
Placental exosomes isolated from urine of patients with gestational diabetes exhibit a differential profile expression of microRNAs across gestation. PMID:32626972
Transcriptome analysis of testis reveals the effects of developmental exposure to bisphenol a or 17α-ethinylestradiol in medaka (Oryzias latipes). PMID:32622090
Draft Genome Sequence of the Bacterium Paraburkholderia aromaticivorans AR20-38, a Gram-Negative, Cold-Adapted Degrader of Aromatic Compounds. PMID:32616634
Association study based on topological constraints of protein-protein interaction networks. PMID:32612246
Differences in Gene Expression Profile of Primary Tumors in Metastatic and Non-Metastatic Papillary Thyroid Carcinoma-Do They Exist? PMID:32610693
Mechanistic Models of Signaling Pathways Reveal the Drug Action Mechanisms behind Gender-Specific Gene Expression for Cancer Treatments. PMID:32610626
Cardiac Transcriptome Analysis Reveals Nr4a1 Mediated Glucose Metabolism Dysregulation in Response to High-Fat Diet. PMID:32610475
Identification of Novel microRNA Profiles Dysregulated in Plasma and Tissue of Abdominal Aortic Aneurysm Patients. PMID:32605321
Genetic relationship between Hashimoto`s thyroiditis and papillary thyroid carcinoma with coexisting Hashimoto`s thyroiditis. PMID:32603365
Characterizing the dynamic and functional DNA methylation landscape in the developing human cortex. PMID:32602773
Chronic Hypersensitivity Pneumonitis, an Interstitial Lung Disease with Distinct Molecular Signatures. PMID:32602730
Experimentally Determined Long Intrinsically Disordered Protein Regions Are Now Abundant in the Protein Data Bank. PMID:32599863
Fulvic acid increases forage legume growth inducing preferential up-regulation of nodulation and signalling-related genes. PMID:32599619
Transcriptogram analysis reveals relationship between viral titer and gene sets responses during Corona-virus infection. PMID:32587961
Transcriptomic microRNA Profiling of Dendritic Cells in Response to Gut Microbiota-Secreted Vesicles. PMID:32585977
Phenotypic Responses to and Genetic Architecture of Sterility Following Exposure to Sub-Lethal Temperature During Development. PMID:32582294
Transcriptome Analysis of Wounding in the Model Grass Lolium temulentum. PMID:32580425
Identification of Conserved Proteomic Networks in Neurodegenerative Dementia. PMID:32579933
Drosophila models of pathogenic copy-number variant genes show global and non-neuronal defects during development. PMID:32579612
Predicting Functions of Uncharacterized Human Proteins: From Canonical to Proteoforms. PMID:32575886
A Knowledge-Based Machine Learning Approach to Gene Prioritisation in Amyotrophic Lateral Sclerosis. PMID:32575372
Skd3 (human ClpB) is a potent mitochondrial protein disaggregase that is inactivated by 3-methylglutaconic aciduria-linked mutations. PMID:32573439
Manumycin polyketides act as molecular glues between UBR7 and P53. PMID:32572277
TERT Promoter Mutations and Their Impact on Gene Expression Profile in Papillary Thyroid Carcinoma. PMID:32560331
Automated generation of gene summaries at the Alliance of Genome Resources. PMID:32559296
Transcriptome-Wide Regulation of Key Developmental Pathways in the Mouse Neural Tube by Prenatal Alcohol Exposure. PMID:32557641
Sequencing of RNA in single cells reveals a distinct transcriptome signature of hematopoiesis in GATA2 deficiency. PMID:32556286
The evolution of sex-biased gene expression in the Drosophila brain. PMID:32554780
Macrophage correlates with immunophenotype and predicts anti-PD-L1 response of urothelial cancer. PMID:32550918
An age-independent gene signature for monitoring acute rejection in kidney transplantation. PMID:32550916
RNA Binding Proteins as Drivers and Therapeutic Target Candidates in Pancreatic Ductal Adenocarcinoma. PMID:32545414
Expression of SARS-CoV-2 receptor ACE2 and coincident host response signature varies by asthma inflammatory phenotype. PMID:32531372
Pituispheres Contain Genetic Variants Characteristic to Pituitary Adenoma Tumor Tissue. PMID:32528411
PINOT: an intuitive resource for integrating protein-protein interactions. PMID:32527260
A selective inference approach for false discovery rate control using multiomics covariates yields insights into disease risk. PMID:32522875
A Photo-clickable ATP-Mimetic Reveals Nucleotide Interactors in the Membrane Proteome. PMID:32521230
PSIONplusm Server for Accurate Multi-Label Prediction of Ion Channels and Their Types. PMID:32517331
The core SWI/SNF catalytic subunit Brg1 regulates nephron progenitor cell proliferation and differentiation. PMID:32504627
Comparative Target Analysis of Chlorinated Biphenyl Antimicrobials Highlights MenG as a Molecular Target of Triclocarban. PMID:32503913
Identifying genetic variants and pathways associated with extreme levels of fetal hemoglobin in sickle cell disease in Tanzania. PMID:32503527
GC-AG Introns Features in Long Non-coding and Protein-Coding Genes Suggest Their Role in Gene Expression Regulation. PMID:32499820
Identification of prognostic gene biomarkers for metastatic skin cancer using data mining. PMID:32494360
A tissue level atlas of the healthy human virome. PMID:32493363
Biomarker roles identification of miR-106 family for predicting the risk and poor survival of colorectal cancer. PMID:32493303
A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. PMID:32490206
Ebstein anomaly associated with cri du chat (cat's cry) syndrome and 20q duplication. PMID:32487530
Urban air particulate matter induces mitochondrial dysfunction in human olfactory mucosal cells. PMID:32487172
Using Reactome to build an autophagy mechanism knowledgebase. PMID:32486891
Cadmium, Smoking, and Human Blood DNA Methylation Profiles in Adults from the Strong Heart Study. PMID:32484362
A-kinase-anchoring protein 1 (dAKAP1)-based signaling complexes coordinate local protein synthesis at the mitochondrial surface. PMID:32482893
dbPSP 2.0, an updated database of protein phosphorylation sites in prokaryotes. PMID:32472030
Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. PMID:32471448
BEAVR: a browser-based tool for the exploration and visualization of RNA-seq data. PMID:32471392
Drug screening and identification of key candidate genes and pathways of rheumatoid arthritis. PMID:32468016
Regulatory Potential of bHLH-Type Transcription Factors on the Road to Rubber Biosynthesis in Hevea brasiliensis. PMID:32466493
A memory of eS25 loss drives resistance phenotypes. PMID:32463448
Itch attenuates CD4 T-cell proliferation in mice by limiting WBP2 protein stability. PMID:32459862
Inferring Virus-Host relationship between HPV and its host Homo sapiens using protein interaction network. PMID:32457456
Tumor Cell Associated Hyaluronan-CD44 Signaling Promotes Pro-Tumor Inflammation in Breast Cancer. PMID:32455980
Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago. PMID:32453742
Multipathway synergy promotes testicular transition from growth to spermatogenesis in early-puberty goats. PMID:32450814
Systematic identification of chicken type I, II and III interferon-stimulated genes. PMID:32448397
Discrete populations of isotype-switched memory B lymphocytes are maintained in murine spleen and bone marrow. PMID:32444631
Maternal Protein Restriction in Rats Alters the Expression of Genes Involved in Mitochondrial Metabolism and Epitranscriptomics in Fetal Hypothalamus. PMID:32438566
ThETA: transcriptome-driven efficacy estimates for gene-based TArget discovery. PMID:32437556
Effect of aging on the transcriptomic changes associated with the expression of the HERV-K (HML-2) provirus at 1q22. PMID:32435269
Bioinformatics Analysis Identifies the Estrogen Receptor 1 (ESR1) Gene and hsa-miR-26a-5p as Potential Prognostic Biomarkers in Patients with Intrahepatic Cholangiocarcinoma. PMID:32435051
Translational control of one-carbon metabolism underpins ribosomal protein phenotypes in cell division and longevity. PMID:32432546
A Single-Cell Transcriptional Roadmap of the Mouse and Human Lymph Node Lymphatic Vasculature. PMID:32426372
Tradeoff between metabolic i-proteasome addiction and immune evasion in triple-negative breast cancer. PMID:32423906
Molecular Signatures of Placentation and Secretion Uncovered in Poeciliopsis Maternal Follicles. PMID:32421768
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. PMID:32417785
Large-scale network analysis captures biological features of bacterial plasmids. PMID:32415210
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma. PMID:32415191
3'-UTR Shortening Contributes to Subtype-Specific Cancer Growth by Breaking Stable ceRNA Crosstalk of Housekeeping Genes. PMID:32411683
Alternative splicing of LSD1+8a in neuroendocrine prostate cancer is mediated by SRRM4. PMID:32403054
Integrated urine proteomics and renal single-cell genomics identify an IFN-γ response gradient in lupus nephritis. PMID:32396533
Lower oxygen consumption and Complex I activity in mitochondria isolated from skeletal muscle of fetal sheep with intrauterine growth restriction. PMID:32396498
CoCoCoNet: conserved and comparative co-expression across a diverse set of species. PMID:32392296
CK14 Expression Identifies a Basal/Squamous-Like Type of Papillary Non-Muscle-Invasive Upper Tract Urothelial Carcinoma. PMID:32391279
Shared Regulatory Pathways Reveal Novel Genetic Correlations Between Grip Strength and Neuromuscular Disorders. PMID:32391060
Functional genomics analysis of human colon organoids identifies key transcription factors. PMID:32390556
Targeting PHGDH Upregulation Reduces Glutathione Levels and Resensitizes Resistant NRAS-Mutant Melanoma to MAPK Kinase Inhibition. PMID:32389536
Applying knowledge-driven mechanistic inference to toxicogenomics. PMID:32387679
Tomato Atypical Receptor Kinase1 Is Involved in the Regulation of Preinvasion Defense. PMID:32385090
The 15q11.2 BP1-BP2 Microdeletion (Burnside-Butler) Syndrome: In Silico Analyses of the Four Coding Genes Reveal Functional Associations with Neurodevelopmental Phenotypes. PMID:32384786
Proteomic Profiling of Small Extracellular Vesicles Secreted by Human Pancreatic Cancer Cells Implicated in Cellular Transformation. PMID:32382024
GeneTrail 3: advanced high-throughput enrichment analysis. PMID:32379325
Polygenic risk scores indicates genetic overlap between peripheral pain syndromes and chronic postsurgical pain. PMID:32377986
miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems. PMID:32374865
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
Blast2Fish: a reference-based annotation web tool for transcriptome analysis of non-model teleost fish. PMID:32366294
In Vitro Evaluation of the Effects of Commercial Prebiotic GOS and FOS Products on Human Colonic Caco-2 Cells. PMID:32366023
Population-Specific Genetic and Expression Differentiation in Europeans. PMID:32365201
Genome-wide association study of MRI markers of cerebral small vessel disease in 42,310 participants. PMID:32358547
Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications. PMID:32353878
Comprehensive Immunoprofiling of Pediatric Zika Reveals Key Role for Monocytes in the Acute Phase and No Effect of Prior Dengue Virus Infection. PMID:32348760
Contribution of common and rare damaging variants in familial forms of bipolar disorder and phenotypic outcome. PMID:32345981
The phylogenetic landscape and nosocomial spread of the multidrug-resistant opportunist Stenotrophomonas maltophilia. PMID:32341346
Shared genetic architecture and casual relationship between leptin levels and type 2 diabetes: large-scale cross-trait meta-analysis and Mendelian randomization analysis. PMID:32341051
ABC Efflux Transporters and the Circuitry of miRNAs: Kinetics of Expression in Cancer Drug Resistance. PMID:32340269
Identification of Novel Targets of RBM5 in the Healthy and Injured Brain. PMID:32335213
Novel Apoptotic Mediators Identified by Conservation of Vertebrate Caspase Targets. PMID:32326640
Protein Synthesis by Day 16 Bovine Conceptuses during the Time of Maternal Recognition of Pregnancy. PMID:32325999
STAT3-dependent analysis reveals PDK4 as independent predictor of recurrence in prostate cancer. PMID:32323921
WIPI2 depletion inhibits the growth of hepatocellular carcinoma cells through the AMPK signaling pathway. PMID:32323845
Patient‑derived orthotopic xenograft glioma models fail to replicate the magnetic resonance imaging features of the original patient tumor. PMID:32323818
Application of weighted gene co‑expression network analysis to explore the potential diagnostic biomarkers for colorectal cancer. PMID:32323816
A novel plasma lncRNA ENST00000416361 is upregulated in coronary artery disease and is related to inflammation and lipid metabolism. PMID:32323776
Abnormal DNA methylation patterns in patients with infection‑caused leukocytopenia based on methylation microarrays. PMID:32323775
Pilot study and bioinformatics analysis of differentially expressed genes in adipose tissues of rats with excess dietary intake. PMID:32323762
CRISPR-mediated gene targeting of CK1δ/ε leads to enhanced understanding of their role in endocytosis via phosphoregulation of GAPVD1. PMID:32321936
ORF Ι of Mycovirus SsNSRV-1 is Associated with Debilitating Symptoms of Sclerotinia sclerotiorum. PMID:32316519
Setting the basis of best practices and standards for curation and annotation of logical models in biology-highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop. PMID:32313939
RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis. PMID:32311035
Pleiotropy-Based Decomposition of Genetic Risk Scores: Association and Interaction Analysis for Type 2 Diabetes and CAD. PMID:32302534
A Five-Genes-Based Prognostic Signature for Cervical Cancer Overall Survival Prediction. PMID:32300605
Transcriptomic diversity in seedling roots of European flint maize in response to cold. PMID:32293268
Stress-mediated convergence of splicing landscapes in male and female rock doves. PMID:32293250
Sporadic activation of an oxidative stress-dependent NRF2-p53 signaling network in breast epithelial spheroids and premalignancies. PMID:32291314
Cellular origins and genetic landscape of cutaneous gamma delta T cell lymphomas. PMID:32286303
Structured reviews for data and knowledge-driven research. PMID:32283553
Development of IFN-Stimulated Gene Expression from Embryogenesis through Adulthood, with and without Constitutive MDA5 Pathway Activation. PMID:32277054
Genome-Wide Analysis Reveals Mucociliary Remodeling of the Nasal Airway Epithelium Induced by Urban PM2.5. PMID:32275839
Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures. PMID:32275708
GOMCL: a toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. PMID:32272889
Diversity of peripheral blood human NK cells identified by single-cell RNA sequencing. PMID:32271902
Loci associated with conception rate in crossbred beef heifers. PMID:32271764
In Silico Discovery of Candidate Drugs against Covid-19. PMID:32268515
Experimentally-driven protein structure modeling. PMID:32268219
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis. PMID:32259549
Expression profile analysis identifies key genes as prognostic markers for metastasis of osteosarcoma. PMID:32256213
Bayesian integrative analysis of epigenomic and transcriptomic data identifies Alzheimer's disease candidate genes and networks. PMID:32255787
Cell type-specific transcriptomics of esophageal adenocarcinoma as a scalable alternative for single cell transcriptomics. PMID:32255255
Cardiac miRNA Expression and their mRNA Targets in a Rat Model of Prediabetes. PMID:32244869
Adaptive Shifts in Gene Regulation Underlie a Developmental Delay in Thermogenesis in High-Altitude Deer Mice. PMID:32243546
Altered expression of glycoprotein non‑metastatic melanoma protein B in the distal sciatic nerve following injury. PMID:32236569
Uncovering Prognosis-Related Genes and Pathways by Multi-Omics Analysis in Lung Cancer. PMID:32235589
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for phylogenomic dataset assembly. PMID:32228442
Effect of Ionizing Radiation on Transcriptome during Neural Differentiation of Human Embryonic Stem Cells. PMID:32216708
Chronic Ethanol Feeding in Mice Decreases Expression of Genes for Major Structural Bone Proteins in a Nox4-Independent Manner. PMID:32213546
Testing Proximity of Genomic Regions to Transcription Start Sites and Enhancers Complements Gene Set Enrichment Testing. PMID:32211031
Pharmacological target-focused transcriptomic analysis of native vs cultured human and mouse dorsal root ganglia. PMID:32197039
Portal of Juglandaceae: A comprehensive platform for Juglandaceae study. PMID:32194971
Identification of potential key genes in gastric cancer using bioinformatics analysis. PMID:32190306
PDGFD induces ibrutinib resistance of diffuse large B‑cell lymphoma through activation of EGFR. PMID:32186759
Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift. PMID:32184324
AllEnricher: a comprehensive gene set function enrichment tool for both model and non-model species. PMID:32183716
Genomic Landscape and Mutational Spectrum of ADAMTS Family Genes in Mendelian Disorders Based on Gene Evidence Review for Variant Interpretation. PMID:32183147
Identification of key genes and pathways of diagnosis and prognosis in cervical cancer by bioinformatics analysis. PMID:32181600
Integrated miRNA/mRNA Counter-Expression Analysis Highlights Oxidative Stress-Related Genes CCR7 and FOXO1 as Blood Markers of Coronary Arterial Disease. PMID:32178422
Systematical Analysis of the Cancer Genome Atlas Database Reveals EMCN/MUC15 Combination as a Prognostic Signature for Gastric Cancer. PMID:32175327
C-terminal binding proteins 1 and 2 in traumatic brain injury-induced inflammation and their inhibition as an approach for anti-inflammatory treatment. PMID:32174788
Global profile changes in transcripts induced with a phosphate analogue: implications for gene regulation. PMID:32172469
Enabling reusability of plant phenomic datasets with MIAPPE 1.1. PMID:32171029
Investigating global gene expression changes in a murine model of cherubism. PMID:32165349
Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast. PMID:32152323
Temporal changes in the gene expression heterogeneity during brain development and aging. PMID:32139741
A pathway coordinated by DELE1 relays mitochondrial stress to the cytosol. PMID:32132706
Comparative genomic analysis reveals high intra-serovar plasticity within Salmonella Napoli isolated in 2005-2017. PMID:32131727
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. PMID:32128557
Comparative proteomics analysis of Tibetan hull-less barley under osmotic stress via data-independent acquisition mass spectrometry. PMID:32126136
MicroRNA‑449a regulates the progression of brain aging by targeting SCN2B in SAMP8 mice. PMID:32124967
The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. PMID:32122962
Alveolar Macrophage Chromatin Is Modified to Orchestrate Host Response to Mycobacterium bovis Infection. PMID:32117424
An Anti-inflammatory microRNA Signature Distinguishes Group 3 Innate Lymphoid Cells From Natural Killer Cells in Human Decidua. PMID:32117280
Genetic Modifiers and Rare Mendelian Disease. PMID:32106447
Integrative module analysis of HCC gene expression landscapes. PMID:32104233
Predicted Drosophila Interactome Resource and web tool for functional interpretation of differentially expressed genes. PMID:32103267
Data libraries - the missing element for modeling biological systems. PMID:32100391
Integrated characterization and validation of the prognostic significance of microRNA-200s in colorectal cancer. PMID:32099529
Detection and characterization of microRNA expression profiling and its target genes in response to canine parvovirus in Crandell Reese Feline Kidney cells. PMID:32095352
Toxicological response of the model fungus Saccharomyces cerevisiae to different concentrations of commercial graphene nanoplatelets. PMID:32094381
Imipridone Anticancer Compounds Ectopically Activate the ClpP Protease and Represent a New Scaffold for Antibiotic Development. PMID:32094149
Adaptation to Photooxidative Stress: Common and Special Strategies of the Alphaproteobacteria Rhodobacter sphaeroides and Rhodobacter capsulatus. PMID:32093084
In Vitro Zika Virus Infection of Human Neural Progenitor Cells: Meta-Analysis of RNA-Seq Assays. PMID:32079323
Endogenous Retrovirus Activation as a Key Mechanism of Anti-Tumor Immune Response in Radiotherapy. PMID:32074012
The MYCL and MXD1 transcription factors regulate the fitness of murine dendritic cells. PMID:32071205
Whole-exome sequencing of 81 individuals from 27 multiply affected bipolar disorder families. PMID:32066727
SSIF: Subsumption-based Sub-term Inference Framework to audit Gene Ontology. PMID:32065617
A systems approach to infectious disease. PMID:32060427
High-throughput quantification of protein structural change reveals potential mechanisms of temperature adaptation in Mytilus mussels. PMID:32054457
NCBP2 modulates neurodevelopmental defects of the 3q29 deletion in Drosophila and Xenopus laevis models. PMID:32053595
SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates. PMID:32053146
Pilocytic astrocytoma demethylation and transcriptional landscapes link bZIP transcription factors to immune response. PMID:32052037
Probing Carbon Utilization of Cordyceps militaris by Sugar Transportome and Protein Structural Analysis. PMID:32050592
Selection in Australian Thoroughbred horses acts on a locus associated with early two-year old speed. PMID:32049967
Gene expression in immortalized versus primary isolated cardiac endothelial cells. PMID:32042042
Classification of Trispanins: A Diverse Group of Proteins That Function in Membrane Synthesis and Transport Mechanisms. PMID:32039202
Transcriptional and Functional Programming of Decidual Innate Lymphoid Cells. PMID:32038619
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes. PMID:32034905
Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides. PMID:32032360
iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis. PMID:32030085
A rare subpopulation of melanoma cells with low expression of metastasis suppressor NME1 is highly metastatic in vivo. PMID:32029850
PANEV: an R package for a pathway-based network visualization. PMID:32028885
APOE genotype regulates pathology and disease progression in synucleinopathy. PMID:32024799
Establishment and Characterisation by Expression Microarray of Patient-Derived Xenograft Panel of Human Pancreatic Adenocarcinoma Patients. PMID:32024004
The IUPHAR Guide to Immunopharmacology: connecting immunology and pharmacology. PMID:32020584
Astrocyte-Derived Exosomal microRNA miR-200a-3p Prevents MPP+-Induced Apoptotic Cell Death Through Down-Regulation of MKK4. PMID:32016794
Quantitative analysis of protein crotonylation identifies its association with immunoglobulin A nephropathy. PMID:32016442
Proteomic Analysis of Brain Region and Sex-Specific Synaptic Protein Expression in the Adult Mouse Brain. PMID:32012899
BHi-Cect: a top-down algorithm for identifying the multi-scale hierarchical structure of chromosomes. PMID:32009153
Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription. PMID:32006464
miRgo: integrating various off-the-shelf tools for identification of microRNA-target interactions by heterogeneous features and a novel evaluation indicator. PMID:32001758
Highly multiplexed proteomic assessment of human bone marrow in acute myeloid leukemia. PMID:31985806
Biobtree: A tool to search, map and visualize bioinformatics identifiers and special keywords. PMID:31984130
Imputation of Gene Expression Data in Blood Cancer and Its Significance in Inferring Biological Pathways. PMID:31970084
Survival-Associated Metabolic Genes in Human Papillomavirus-Positive Head and Neck Cancers. PMID:31968678
A Similar Genetic Architecture Underlies the Convergent Evolution of the Selfing Syndrome in Capsella. PMID:31964802
The Developmental Transcriptome of Aedes albopictus, a Major Worldwide Human Disease Vector. PMID:31964684
Incorporating biological structure into machine learning models in biomedicine. PMID:31962244
Building a pipeline to solicit expert knowledge from the community to aid gene summary curation. PMID:31960022
A human ciliopathy reveals essential functions for NEK10 in airway mucociliary clearance. PMID:31959991
A Protein Interaction Information-based Generative Model for Enhancing Gene Clustering. PMID:31959782
Transcriptome signature of ventricular arrhythmia in dilated cardiomyopathy reveals increased fibrosis and activated TP53. PMID:31958463
Open Data for Differential Network Analysis in Glioma. PMID:31952211
The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences. PMID:31950984
Role of Secreted Frizzled-Related Protein 1 in Early Mammary Gland Tumorigenesis and Its Regulation in Breast Microenvironment. PMID:31947616
Combined network pharmacology and virtual reverse pharmacology approaches for identification of potential targets to treat vascular dementia. PMID:31937840
Parallel evolutionary paths to produce more than one Pseudomonas aeruginosa biofilm phenotype. PMID:31934344
The DNA polymerases of Drosophila melanogaster. PMID:31933406
Clonal kinetics and single-cell transcriptional profiling of CAR-T cells in patients undergoing CD19 CAR-T immunotherapy. PMID:31924795
Gambogenic acid exerts anticancer effects in cisplatin‑resistant non‑small cell lung cancer cells. PMID:31922223
The transcriptional correlates of divergent electric organ discharges in Paramormyrops electric fish. PMID:31918666
Analysis of HrpG regulons and HrpG-interacting proteins by ChIP-seq and affinity proteomics in Xanthomonas campestris. PMID:31916392
Mechanistic insights into transcription factor cooperativity and its impact on protein-phenotype interactions. PMID:31913281
Integrative network analysis identifies cell-specific trans regulators of m6A. PMID:31912146
Differential Expression in Testis and Liver Transcriptomes from Four Species of Peromyscus (Rodentia: Cricetidae). PMID:31909812
Comparative and Functional Genomic Resource for Mechanistic Studies of Human Blood Pressure-Associated Single Nucleotide Polymorphisms. PMID:31902252
Mechanistic Dissection of RNA-Binding Proteins in Regulated Gene Expression at Chromatin Levels. PMID:31900328
Weighted gene co‑expression network analysis to identify key modules and hub genes associated with atrial fibrillation. PMID:31894294
Cyberinfrastructure and resources to enable an integrative approach to studying forest trees. PMID:31892954
Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework. PMID:31892348
The Acute Phase Response Is a Prominent Renal Proteome Change in Sepsis in Mice. PMID:31892161
The essentiality landscape of cell cycle related genes in human pluripotent and cancer cells. PMID:31889988
Enhancer jungles establish robust tissue-specific regulatory control in the human genome. PMID:31887344
The Use of Whole Exome Sequencing in a Cohort of Transgender Individuals to Identify Rare Genetic Variants. PMID:31882810
Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast. PMID:31881824
Single Nucleotide Polymorphism rs6942067 Is a Risk Factor in Young and in Non-Smoking Patients with HPV Negative Head and Neck Squamous Cell Carcinoma. PMID:31878157
The dynamics of DNA methylation during epigenetic reprogramming of primordial germ cells in medaka (Oryzias latipes). PMID:31851575
Multi-omics analysis of multiple missions to space reveal a theme of lipid dysregulation in mouse liver. PMID:31844325
dictyBase and the Dicty Stock Center (version 2.0) - a progress report. PMID:31840793
Predicting associations among drugs, targets and diseases by tensor decomposition for drug repositioning. PMID:31839008
Profiles of Long Non-Coding RNAs and mRNA Expression in Human Macrophages Regulated by Interleukin-27. PMID:31835347
TRANSNAP: a web database providing comprehensive information on Japanese pear transcriptome. PMID:31831861
Whole-Transcriptome Analysis of Dermal Fibroblasts, Derived from Three Pairs of Monozygotic Twins, Discordant for Parkinson's Disease. PMID:31823283
On the possible origin of protein homochirality, structure, and biochemical function. PMID:31822617
GenoSurf: metadata driven semantic search system for integrated genomic datasets. PMID:31820804
WormCat: An Online Tool for Annotation and Visualization of Caenorhabditis elegans Genome-Scale Data. PMID:31810987
Association between breast cancer cell migration and radiosensitivity in vitro. PMID:31807191
The distributions of protein coding genes within chromatin domains in relation to human disease. PMID:31805995
Reactome and ORCID-fine-grained credit attribution for community curation. PMID:31802127
Integrative Omics Approach to Identifying Genes Associated With Atrial Fibrillation. PMID:31801406
Network-Based Selection of Candidate Markers and Assays to Assess the Impact of Oral Immune Interventions on Gut Functions. PMID:31798593
Lithium alters expression of RNAs in a type-specific manner in differentiated human neuroblastoma neuronal cultures, including specific genes involved in Alzheimer's disease. PMID:31797941
Exploring Relationships between the Density of Charged Tracts within Disordered Regions and Phase Separation. PMID:31797598
The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases. PMID:31796553
Identification of hub genes and key pathways associated with the progression of gynecological cancer. PMID:31788113
Comparative analysis of functional assay evidence use by ClinGen Variant Curation Expert Panels. PMID:31783775
The JAX Synteny Browser for mouse-human comparative genomics. PMID:31776723
Evolution of placental invasion and cancer metastasis are causally linked. PMID:31768023
High content phenotypic screening identifies serotonin receptor modulators with selective activity upon breast cancer cell cycle and cytokine signaling pathways. PMID:31757681
LncRNA ROR1‑AS1 high expression and its prognostic significance in liver cancer. PMID:31746401
The Cyclic AMP Receptor Protein Regulates Quorum Sensing and Global Gene Expression in Yersinia pestis during Planktonic Growth and Growth in Biofilms. PMID:31744922
Genome-Scale Metabolic Networks Shed Light on the Carotenoid Biosynthesis Pathway in the Brown Algae Saccharina japonica and Cladosiphon okamuranus. PMID:31744163
Is MYND Domain-Mediated Assembly of SMYD3 Complexes Involved in Calcium Dependent Signaling? PMID:31737645
The neXtProt knowledgebase in 2020: data, tools and usability improvements. PMID:31724716
Mapping the perturbome network of cellular perturbations. PMID:31723137
The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. PMID:31713623
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
The Cytoscape BioGateway App: explorative network building from the BioGateway triple store. PMID:31710663
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species. PMID:31701156
Hemagglutinin Stability Regulates H1N1 Influenza Virus Replication and Pathogenicity in Mice by Modulating Type I Interferon Responses in Dendritic Cells. PMID:31694942
The IUPHAR/BPS Guide to PHARMACOLOGY in 2020: extending immunopharmacology content and introducing the IUPHAR/MMV Guide to MALARIA PHARMACOLOGY. PMID:31691834
DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes. PMID:31691822
miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database. PMID:31691816
The reactome pathway knowledgebase. PMID:31691815
Enzyme annotation in UniProtKB using Rhea. PMID:31688925
Sequence and Structure Properties Uncover the Natural Classification of Protein Complexes Formed by Intrinsically Disordered Proteins via Mutual Synergistic Folding. PMID:31683980
Expression of Protein-Coding Gene Orthologs in Zebrafish and Mouse Inner Ear Non-sensory Supporting Cells. PMID:31680844
Immune Suppressive Extracellular Vesicle Proteins of Leptopilina heterotoma Are Encoded in the Wasp Genome. PMID:31676506
Phenome-wide association study of TTR and RBP4 genes in 361,194 individuals reveals novel insights in the genetics of hereditary and wildtype transthyretin amyloidoses. PMID:31659433
Chlamydia psittaci-Infected Dendritic Cells Communicate with NK Cells via Exosomes To Activate Antibacterial Immunity. PMID:31658957
Exploring lithium's transcriptional mechanisms of action in bipolar disorder: a multi-step study. PMID:31652432
Bovine Genome Database: new annotation tools for a new reference genome. PMID:31647100
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
SilkDB 3.0: visualizing and exploring multiple levels of data for silkworm. PMID:31642484
Fermentation innovation through complex hybridization of wild and domesticated yeasts. PMID:31636426
GENAVi: a shiny web application for gene expression normalization, analysis and visualization. PMID:31619158
Challenges in the annotation of pseudoenzymes in databases: the UniProtKB approach. PMID:31618524
LnCeVar: a comprehensive database of genomic variations that disturb ceRNA network regulation. PMID:31617563
Biological Network Approaches and Applications in Rare Disease Studies. PMID:31614842
PhaSePro: the database of proteins driving liquid-liquid phase separation. PMID:31612960
DNAproDB: an expanded database and web-based tool for structural analysis of DNA-protein complexes. PMID:31612957
Transcriptome visualization and data availability at the Saccharomyces Genome Database. PMID:31612944
Exosome complex genes mediate RNA degradation and predict survival in mantle cell lymphoma. PMID:31612023
Four targeted genes for predicting the prognosis of colorectal cancer: A bioinformatics analysis case. PMID:31612015
Myo-REG: A Portal for Signaling Interactions in Muscle Regeneration. PMID:31611808
Loss of methionine sulfoxide reductases increases resistance to oxidative stress. PMID:31606431
KnockTF: a comprehensive human gene expression profile database with knockdown/knockout of transcription factors. PMID:31598675
Stereotyped transcriptomic transformation of somatosensory neurons in response to injury. PMID:31592768
YEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts. PMID:31586406
CAGEfightR: analysis of 5'-end data using R/Bioconductor. PMID:31585526
The sugarcane mitochondrial genome: assembly, phylogenetics and transcriptomics. PMID:31579570
Binding to medium and long chain fatty acyls is a common property of HEAT and ARM repeat modules. PMID:31578417
S‑allyl‑cysteine sulfoxide (alliin) alleviates myocardial infarction by modulating cardiomyocyte necroptosis and autophagy. PMID:31573046
Diesel exhaust particles dysregulate multiple immunological pathways in murine macrophages: Lessons from microarray and scRNA-seq technologies. PMID:31568751
Signatures of cell death and proliferation in perturbation transcriptomics data-from confounding factor to effective prediction. PMID:31552418
Alliance of Genome Resources Portal: unified model organism research platform. PMID:31552413
Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. PMID:31548717
Reconstruction and analysis of competitive endogenous RNA network reveals regulatory role of long non‑coding RNAs in hepatic fibrosis. PMID:31545470
Comprehensive expression profiles and bioinformatics analysis reveal special circular RNA expression and potential predictability in the peripheral blood of humans with idiopathic membranous nephropathy. PMID:31545426
Druggable Transcriptional Networks in the Human Neurogenic Epigenome. PMID:31530573
Molecular Profiling of the Drosophila Antenna Reveals Conserved Genes Underlying Olfaction in Insects. PMID:31527046
Using MARRVEL v1.2 for Bioinformatics Analysis of Human Genes and Variant Pathogenicity. PMID:31524990
miRDB: an online database for prediction of functional microRNA targets. PMID:31504780
Migratory Neural Crest Cells Phagocytose Dead Cells in the Developing Nervous System. PMID:31495570
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice. PMID:31489782
Signaling pathways and gene co-expression modules associated with cytoskeleton and axon morphology in breast cancer survivors with chronic paclitaxel-induced peripheral neuropathy. PMID:31486345
A pooled single-cell genetic screen identifies regulatory checkpoints in the continuum of the epithelial-to-mesenchymal transition. PMID:31477929
Navigating MARRVEL, a Web-Based Tool that Integrates Human Genomics and Model Organism Genetics Information. PMID:31475990
Identification of modules and functional analysis in CRC subtypes by integrated bioinformatics analysis. PMID:31469863
A human endogenous retrovirus encoded protease potentially cleaves numerous cellular proteins. PMID:31462935
Identification of microRNA-181 as a promising biomarker for predicting the poor survival in colorectal cancer. PMID:31448575
Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds. PMID:31443466
Randomized trial of weight loss in primary breast cancer: Impact on body composition, circulating biomarkers and tumor characteristics. PMID:31442303
Synergistic Genetic Interactions between Pkhd1 and Pkd1 Result in an ARPKD-Like Phenotype in Murine Models. PMID:31427367
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
Phellem Cell-Wall Components Are Discriminants of Cork Quality in Quercus suber. PMID:31417580
A network-based analysis for mining the risk pathways in glioblastoma. PMID:31402957
Omics Driven Understanding of the Intestines of Parasitic Nematodes. PMID:31402928
MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells. PMID:31399133
Integrated mRNA and miRNA profiling in NIH/3T3 cells in response to bovine papillomavirus E6 gene expression. PMID:31396463
Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins. PMID:31390792
Genetically diverse Pseudomonas aeruginosa populations display similar transcriptomic profiles in a cystic fibrosis explanted lung. PMID:31363089
Differential gene expression and gene ontologies associated with increasing water-stress in leaf and root transcriptomes of perennial ryegrass (Lolium perenne). PMID:31361773
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. PMID:31353404
Integrated identification of key genes and pathways in Alzheimer's disease via comprehensive bioinformatical analyses. PMID:31346329
Identification of differentially expressed genes in small and non-small cell lung cancer based on meta-analysis of mRNA. PMID:31338439
A step-by-step guide to analyzing CAGE data using R/Bioconductor. PMID:31327999
Estimating dispensable content in the human interactome. PMID:31324802
Identification and characterization of sexual dimorphism‑linked gene expression profile in hepatocellular carcinoma. PMID:31322260
Ligand Binding Site Structure Shapes Folding, Assembly and Degradation of Homomeric Protein Complexes. PMID:31306664
Comprehensive in vivo identification of the c-Myc mRNA protein interactome using HyPR-MS. PMID:31296583
Prediction of disease-associated mutations in the transmembrane regions of proteins with known 3D structure. PMID:31291347
A Cyclin A-Myb-MuvB-Aurora B network regulates the choice between mitotic cycles and polyploid endoreplication cycles. PMID:31291240
Cloudy with a Chance of Insights: Context Dependent Gene Regulation and Implications for Evolutionary Studies. PMID:31261769
PropaNet: Time-Varying Condition-Specific Transcriptional Network Construction by Network Propagation. PMID:31258543
Isatin inhibits the invasion of human neuroblastoma SH‑SY5Y cells, based on microarray analysis. PMID:31257543
Analysis of potential functional significance of microRNA‑3613‑3p in human umbilical vein endothelial cells affected by heat stress. PMID:31257536
Identification of key pathways and genes in different types of chronic kidney disease based on WGCNA. PMID:31257514
RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast. PMID:31235518
Protein interactions and consensus clustering analysis uncover insights into herpesvirus virion structure and function relationships. PMID:31199794
Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. PMID:31188086
Bioinformatics analysis of the regulatory lncRNA‑miRNA‑mRNA network and drug prediction in patients with hypertrophic cardiomyopathy. PMID:31180540
Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation. PMID:31174599
Screening key genes and signaling pathways in colorectal cancer by integrated bioinformatics analysis. PMID:31173250
Identification of diagnostic long non‑coding RNA biomarkers in patients with hepatocellular carcinoma. PMID:31173205
SynGO: An Evidence-Based, Expert-Curated Knowledge Base for the Synapse. PMID:31171447
NetR and AttR, Two New Bioinformatic Tools to Integrate Diverse Datasets into Cytoscape Network and Attribute Files. PMID:31159440
LnCompare: gene set feature analysis for human long non-coding RNAs. PMID:31147707
Human pancreatic cancer cell exosomes, but not human normal cell exosomes, act as an initiator in cell transformation. PMID:31134894
INGA 2.0: improving protein function prediction for the dark proteome. PMID:31073595
Comparative transcriptome analysis of trout skin pigment cells. PMID:31072301
Ten quick tips for biocuration. PMID:31048830
A Multigene Assay Determines Risk of Recurrence in Patients with Triple-Negative Breast Cancer. PMID:31048497
Promiscuous Targeting of Cellular Proteins by Vpr Drives Systems-Level Proteomic Remodeling in HIV-1 Infection. PMID:31042482
The Promoter Regions of Intellectual Disability-Associated Genes Are Uniquely Enriched in LTR Sequences of the MER41 Primate-Specific Endogenous Retrovirus: An Evolutionary Connection Between Immunity and Cognition. PMID:31031802
The challenges of big data biology. PMID:30950793
Mutational spectrum and associations with clinical features in patients with acute myeloid leukaemia based on next‑generation sequencing. PMID:30942411
Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation. PMID:30899329
Early Transcriptional Response to DNA Virus Infection in Sclerotinia sclerotiorum. PMID:30893849
Systematic analysis reveals the prevalence and principles of bypassable gene essentiality. PMID:30824696
Identification of Potential Genes Responsible for Thermotolerance in Wheat under High Temperature Stress. PMID:30823586
Integration of macromolecular complex data into the Saccharomyces Genome Database. PMID:30715277
Annotation of gene product function from high-throughput studies using the Gene Ontology. PMID:30715275
Mouse Genome Database (MGD) 2019. PMID:30407599
Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes. PMID:30357405
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More detailed information about this field from each metasource.
animal organ development
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
cellular component
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
function analysis
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
functional association
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene ontology enrichment
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene feature
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene functional annotation
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
molecular function
metasource: Fairsharing.org
version: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
Tags
More detailed information about this field from each metasource.
animal organ development
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
cellular component
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
function analysis
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
functional association
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene ontology enrichment
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene expression data
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene feature
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
gene functional annotation
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
molecular function
metasource: Fairsharing.orgversion: FAIRsharing.org: GAF 2.1; Gene Ontology (GO) Gene Association File Format 2.1; DOI: https://doi.org/10.25504/FAIRsharing.FGJ2T8; Last edited: Sept. 20, 2019, 11:52 a.m.; Last accessed: Jan 03 2022 7:11 p.m.
animal organ development cellular component function analysis functional association gene gene ontology enrichment gene expression gene expression gene feature gene functional annotation molecular function
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