R3603S last accessed: 2022-11-04

entrez_gene
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

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

Other names: Entrez Gene, Gene, entrez_gene, NCBI

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can efficiently retrieve related sequences, structures, and references. It can provide views of gene and protein sequences and chromosome maps.

Webpage:

https://www.ncbi.nlm.nih.gov/search/

Licence:

Name: NCBI - specific / free to use and distribute
URL: https://www.ncbi.nlm.nih.gov/home/about/policies/

Publications:

Publications
More detailed information about this field from each metasource.

Entrez Gene: gene-centered information at NCBI
PMID: 15608257
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

Entrez Gene: gene-centered information at NCBI
PMID: 21115458
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

Entrez Gene: gene-centered information at NCBI
PMID: 17148475
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

Gene: a gene-centered information resource at NCBI
PMID: 25355515
metasource: BiŌkeanós-Medsourcing
version: 0.0.1:2022-11-04T13:34:25.975929

http://dx.doi.org/10.1093/nar/gku1055
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

Entrez Gene: gene-centered information at NCBI PubMed citations: 416.

416 articles citing: Entrez Gene: gene-centered information at NCBI

OBI: A computational tool for the analysis and systematization of the positive selection in proteins. PMID:35910305
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. PMID:35776534
A Hybrid Protocol for Finding Novel Gene Targets for Various Diseases Using Microarray Expression Data Analysis and Text Mining. PMID:35713858
The amniotic fluid proteome changes with gestational age in normal pregnancy: a cross-sectional study. PMID:35022423
Adhesion of Enteropathogenic, Enterotoxigenic, and Commensal Escherichia coli to the Major Zymogen Granule Membrane Glycoprotein 2. PMID:35020452
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Network medicine for disease module identification and drug repurposing with the NeDRex platform. PMID:34824199
Integrative COVID-19 biological network inference with probabilistic core decomposition. PMID:34791019
mapMECFS: a portal to enhance data discovery across biological disciplines and collaborative sites. PMID:34749736
Experiment level curation of transcriptional regulatory interactions in neurodevelopment. PMID:34665801
StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication. PMID:34567086
Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PMID:34395068
Extended many-item similarity indices for sets of nucleotide and protein sequences. PMID:34257841
A novel computational drug repurposing approach for Systemic Lupus Erythematosus (SLE) treatment using Semantic Web technologies. PMID:34220244
Embryonic thermal manipulation impacts the postnatal transcriptome response of heat-challenged Japanese quails. PMID:34193035
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. PMID:34112877
Effects of FUdR on gene expression in the C. elegans bacterial diet OP50. PMID:34103088
Knowledge bases and software support for variant interpretation in precision oncology. PMID:33971666
Transcriptomics-based drug repositioning pipeline identifies therapeutic candidates for COVID-19. PMID:33821262
Functional Signatures in Non-Small-Cell Lung Cancer: A Systematic Review and Meta-Analysis of Sex-Based Differences in Transcriptomic Studies. PMID:33526761
An empirical meta-analysis of the life sciences linked open data on the web. PMID:33479214
Transcriptional Profiling of Immune and Inflammatory Responses in the Context of SARS-CoV-2 Fungal Superinfection in a Human Airway Epithelial Model. PMID:33322535
Preclinical validation of therapeutic targets predicted by tensor factorization on heterogeneous graphs. PMID:33106501
SynergyAge, a curated database for synergistic and antagonistic interactions of longevity-associated genes. PMID:33106474
Differential gene regulatory pattern in the human brain from schizophrenia using transcriptomic-causal network. PMID:33087039
Integration of anatomy ontology data with protein-protein interaction networks improves the candidate gene prediction accuracy for anatomical entities. PMID:33028186
Nuclear and mitochondrial genome sequencing of North-African Leishmania infantum isolates from cured and relapsed visceral leishmaniasis patients reveals variations correlating with geography and phenotype. PMID:32975503
miRTissue ce: extending miRTissue web service with the analysis of ceRNA-ceRNA interactions. PMID:32938402
METATRYP v 2.0: Metaproteomic Least Common Ancestor Analysis for Taxonomic Inference Using Specialized Sequence Assemblies-Standalone Software and Web Servers for Marine Microorganisms and Coronaviruses. PMID:32897080
Phenotypic and molecular spectrum of pyridoxamine-5'-phosphate oxidase deficiency: A scoping review of 87 cases of pyridoxamine-5'-phosphate oxidase deficiency. PMID:32888189
Inducers of the endothelial cell barrier identified through chemogenomic screening in genome-edited hPSC-endothelial cells. PMID:32759214
Study of genetic correlation between children's sleep and obesity. PMID:32555314
GDNF drives rapid tubule morphogenesis in a novel 3D in vitro model for ADPKD. PMID:32513820
Human gene and disease associations for clinical-genomics and precision medicine research. PMID:32508008
Broad-coverage biomedical relation extraction with SemRep. PMID:32410573
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. PMID:32369553
DES-ROD: Exploring Literature to Develop New Links between RNA Oxidation and Human Diseases. PMID:32308806
Network-based identification of signature genes KLF6 and SPOCK1 associated with oral submucous fibrosis. PMID:32190310
FibroAtlas: A Database for the Exploration of Fibrotic Diseases and Their Genes. PMID:32082621
Exploring Metabolic Consequences of CPS1 and CAD Dysregulation in Hepatocellular Carcinoma by Network Reconstruction. PMID:32021853
RHPCG: a database of the Regulation of the Hippo Pathway in Cancer Genome. PMID:31848596
Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. PMID:31725862
Dataset for dose and time-dependent transcriptional response to ionizing radiation exposure. PMID:31692674
Debutant iOS app and gene-disease complexities in clinical genomics and precision medicine. PMID:31586224
Enabling Web-scale data integration in biomedicine through Linked Open Data. PMID:31531395
Mapping anatomical related entities to human body parts based on wikipedia in discharge summaries. PMID:31419946
DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks. PMID:31409281
ARID1A and PI3-kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion. PMID:31391455
OCTANE: Oncology Clinical Trial Annotation Engine. PMID:31265323
Can trophectoderm RNA analysis predict human blastocyst competency? PMID:31244343
The prediction of early preeclampsia: Results from a longitudinal proteomics study. PMID:31163045
The NCATS BioPlanet - An Integrated Platform for Exploring the Universe of Cellular Signaling Pathways for Toxicology, Systems Biology, and Chemical Genomics. PMID:31133849
PathMe: merging and exploring mechanistic pathway knowledge. PMID:31092193
OsteoporosAtlas: a human osteoporosis-related gene database. PMID:31086734
CANCROX: a cross-species cancer therapy database. PMID:31032838
Electrophysiological and transcriptomic correlates of neuropathic pain in human dorsal root ganglion neurons. PMID:30887021
Gene2vec: distributed representation of genes based on co-expression. PMID:30712510
Admixture mapping reveals evidence of differential multiple sclerosis risk by genetic ancestry. PMID:30653506
Variant information systems for precision oncology. PMID:30463544
Drug repositioning using drug-disease vectors based on an integrated network. PMID:30463505
Lamin mutation location predicts cardiac phenotype severity: combined analysis of the published literature. PMID:30402260
Systematic analysis of breast atypical hyperplasia-associated hub genes and pathways based on text mining. PMID:30394935
Combining DNA methylation and RNA sequencing data of cancer for supervised knowledge extraction. PMID:30386434
SEdb: a comprehensive human super-enhancer database. PMID:30371817
LION LBD: a literature-based discovery system for cancer biology. PMID:30304355
Lead Modulates trans- and cis-Expression Quantitative Trait Loci (eQTLs) in Drosophila melanogaster Heads. PMID:30294342
Discovering large conserved functional components in global network alignment by graph matching. PMID:30255780
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
Adhesion of Salmonella to Pancreatic Secretory Granule Membrane Major Glycoprotein GP2 of Human and Porcine Origin Depends on FimH Sequence Variation. PMID:30186250
A network pharmacology approach to explore the mechanisms of Erxian decoction in polycystic ovary syndrome. PMID:30181771
Autosomal single-gene disorders involved in human infertility. PMID:30108436
Elastic Net Constrained Stereotype Logit Model for Ordered Categorical Data. PMID:30058001
HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases. PMID:30053237
FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining. PMID:29954318
AllerGAtlas 1.0: a human allergy-related genes database. PMID:29688358
A systematic and prospectively validated approach for identifying synergistic drug combinations against malaria. PMID:29642892
Massive mining of publicly available RNA-seq data from human and mouse. PMID:29636450
A Genome-Wide Search for Gene-Environment Effects in Isolated Cleft Lip with or without Cleft Palate Triads Points to an Interaction between Maternal Periconceptional Vitamin Use and Variants in ESRRG. PMID:29535761
Systematic target function annotation of human transcription factors. PMID:29325558
Conservation of Specificity in Two Low-Specificity Proteins. PMID:29240404
Generating a Tolerogenic Cell Therapy Knowledge Graph from Literature. PMID:29238346
Entity recognition in the biomedical domain using a hybrid approach. PMID:29122011
Chromosome preference of disease genes and vectorization for the prediction of non-coding disease genes. PMID:29108274
Identification of novel mazEF/pemIK family toxin-antitoxin loci and their distribution in the Staphylococcus genus. PMID:29044211
CODA: Integrating multi-level context-oriented directed associations for analysis of drug effects. PMID:28790372
The prediction of late-onset preeclampsia: Results from a longitudinal proteomics study. PMID:28738067
DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species. PMID:28729549
Assigning factuality values to semantic relations extracted from biomedical research literature. PMID:28678823
Network mirroring for drug repositioning. PMID:28539121
RNA-Seq based genome-wide analysis reveals loss of inter-chromosomal regulation in breast cancer. PMID:28496157
Unified Alignment of Protein-Protein Interaction Networks. PMID:28424527
DES-ncRNA: A knowledgebase for exploring information about human micro and long noncoding RNAs based on literature-mining. PMID:28387604
Origin and Evolutionary Alteration of the Mitochondrial Import System in Eukaryotic Lineages. PMID:28369657
BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. PMID:28365720
ExCAPE-DB: an integrated large scale dataset facilitating Big Data analysis in chemogenomics. PMID:28316655
The maternal plasma proteome changes as a function of gestational age in normal pregnancy: a longitudinal study. PMID:28263753
Molecular features of early onset adult myelodysplastic syndrome. PMID:28255022
Medical Subject Heading (MeSH) annotations illuminate maize genetics and evolution. PMID:28250803
Selection and Prioritization of Candidate Drug Targets for Amyotrophic Lateral Sclerosis Through a Meta-Analysis Approach. PMID:28236105
From comorbidities of chronic obstructive pulmonary disease to identification of shared molecular mechanisms by data integration. PMID:28185567
Protein Bioinformatics Databases and Resources. PMID:28150231
The systematic analysis of coding and long non-coding RNAs in the sub-chronic and chronic stages of spinal cord injury. PMID:28106101
FirebrowseR: an R client to the Broad Institute's Firehose Pipeline. PMID:28062517
Drug-drug interaction discovery and demystification using Semantic Web technologies. PMID:28031284
Interactomic analysis of REST/NRSF and implications of its functional links with the transcription suppressor TRIM28 during neuronal differentiation. PMID:27976729
Transcriptomic Analysis Implicates the p53 Signaling Pathway in the Establishment of HIV-1 Latency in Central Memory CD4 T Cells in an In Vitro Model. PMID:27898737
Combining multiple tools outperforms individual methods in gene set enrichment analyses. PMID:27694195
GeneSCF: a real-time based functional enrichment tool with support for multiple organisms. PMID:27618934
RNALocate: a resource for RNA subcellular localizations. PMID:27543076
A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism. PMID:27467583
A network-driven approach for genome-wide association mapping. PMID:27307613
Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array. PMID:27230772
High-performance web services for querying gene and variant annotation. PMID:27154141
Genome-wide variant analysis of simplex autism families with an integrative clinical-bioinformatics pipeline. PMID:27148569
Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. PMID:27081850
Maternal genome-wide DNA methylation profiling in gestational diabetes shows distinctive disease-associated changes relative to matched healthy pregnancies. PMID:27019060
Extracting genetic alteration information for personalized cancer therapy from ClinicalTrials.gov. PMID:27013523
LowMACA: exploiting protein family analysis for the identification of rare driver mutations in cancer. PMID:26860319
Bridging semantics and syntax with graph algorithms-state-of-the-art of extracting biomedical relations. PMID:26851224
Osteogenic Differentiation of MSC through Calcium Signaling Activation: Transcriptomics and Functional Analysis. PMID:26828589
Prediction of drugs having opposite effects on disease genes in a directed network. PMID:26818006
Medoidshift clustering applied to genomic bulk tumor data. PMID:26817708
Multiple myeloma cell lines and primary tumors proteoma: protein biosynthesis and immune system as potential therapeutic targets. PMID:26807199
Population Genetic Structure and Potential Incursion Pathways of the Bluetongue Virus Vector Culicoides brevitarsis (Diptera: Ceratopogonidae) in Australia. PMID:26771743
HitWalker2: visual analytics for precision medicine and beyond. PMID:26708334
Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond. PMID:26615025
Resource constrained flux balance analysis predicts selective pressure on the global structure of metabolic networks. PMID:26597226
Mapping of genetic loci that modulate differential colonization by Escherichia coli O157:H7 TUV86-2 in advanced recombinant inbred BXD mice. PMID:26573818
Connectivity Homology Enables Inter-Species Network Models of Synthetic Lethality. PMID:26451775
WDR5 Expression Is Prognostic of Breast Cancer Outcome. PMID:26355959
Methylation of HOXA9 and ISL1 Predicts Patient Outcome in High-Grade Non-Invasive Bladder Cancer. PMID:26332997
GESPA: classifying nsSNPs to predict disease association. PMID:26206375
Overview of the Cancer Genetics and Pathway Curation tasks of BioNLP Shared Task 2013. PMID:26202570
Stress-induced DNA damage biomarkers: applications and limitations. PMID:26082923
ComiRNet: a web-based system for the analysis of miRNA-gene regulatory networks. PMID:26051695
Text mining facilitates database curation - extraction of mutation-disease associations from Bio-medical literature. PMID:26047637
SBGNViz: A Tool for Visualization and Complexity Management of SBGN Process Description Maps. PMID:26030594
Network of co-mutations in Ebola virus genome predicts the disease lethality. PMID:25976404
Community challenges in biomedical text mining over 10 years: success, failure and the future. PMID:25935162
The uniform-score gene set analysis for identifying common pathways associated with different diabetes traits. PMID:25898945
ANDSystem: an Associative Network Discovery System for automated literature mining in the field of biology. PMID:25881313
L-GRAAL: Lagrangian graphlet-based network aligner. PMID:25725498
Adapting a natural language processing tool to facilitate clinical trial curation for personalized cancer therapy. PMID:25717412
mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer. PMID:25710561
Large scale aggregate microarray analysis reveals three distinct molecular subclasses of human preeclampsia. PMID:25679511
Learning Graphical Models With Hubs. PMID:25620891
Learning to rank-based gene summary extraction. PMID:25474678
E-cadherin interactome complexity and robustness resolved by quantitative proteomics. PMID:25468996
Analysis of the AHR gene proximal promoter GGGGC-repeat polymorphism in lung, breast, and colon cancer. PMID:25447411
The evolution and adaptive potential of transcriptional variation in sticklebacks--signatures of selection and widespread heritability. PMID:25429004
Cooperation of DLC1 and CDK6 affects breast cancer clinical outcome. PMID:25425654
Tuning of peroxiredoxin catalysis for various physiological roles. PMID:25403613
Development and use of the Cytoscape app GFD-Net for measuring semantic dissimilarity of gene networks. PMID:25400907
PubAngioGen: a database and knowledge for angiogenesis and related diseases. PMID:25392416
A p-Median approach for predicting drug response in tumour cells. PMID:25359173
OvMark: a user-friendly system for the identification of prognostic biomarkers in publically available ovarian cancer gene expression datasets. PMID:25344116
ToxDBScan: Large-scale similarity screening of toxicological databases for drug candidates. PMID:25338045
Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. PMID:25294834
RADB: a database of rheumatoid arthritis-related polymorphisms. PMID:25228593
Multilayered genetic and omics dissection of mitochondrial activity in a mouse reference population. PMID:25215496
SPARQLGraph: a web-based platform for graphically querying biological Semantic Web databases. PMID:25127889
Modeling sequence and function similarity between proteins for protein functional annotation. PMID:25101328
Generalising semantic category disambiguation with large lexical resources for fun and profit. PMID:25093067
Processing biological literature with customizable Web services supporting interoperable formats. PMID:25006225
Augmenting microarray data with literature-based knowledge to enhance gene regulatory network inference. PMID:24921649
Prognostic B-cell signatures using mRNA-seq in patients with subtype-specific breast and ovarian cancer. PMID:24916698
MOPED 2.5--an integrated multi-omics resource: multi-omics profiling expression database now includes transcriptomics data. PMID:24910945
OWL reasoning framework over big biological knowledge network. PMID:24877076
Pancreatic Cancer Database: an integrative resource for pancreatic cancer. PMID:24839966
OncoSearch: cancer gene search engine with literature evidence. PMID:24813447
Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. PMID:24777452
A customized Web portal for the genome of the ctenophore Mnemiopsis leidyi. PMID:24773765
A three step network based approach (TSNBA) to finding disease molecular signature and key regulators: a case study of IL-1 and TNF-alpha stimulated inflammation. PMID:24747419
Comparative analysis of Salmonella genomes identifies a metabolic network for escalating growth in the inflamed gut. PMID:24643865
Angiotensin II-induced cardiovascular load regulates cardiac remodeling and related gene expression in late-gestation fetal sheep. PMID:24614802
geneCommittee: a web-based tool for extensively testing the discriminatory power of biologically relevant gene sets in microarray data classification. PMID:24475928
Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns. PMID:24465517
Reprogramming of lysosomal gene expression by interleukin-4 and Stat6. PMID:24314139
Candidate gene identification for systemic lupus erythematosus using network centrality measures and gene ontology. PMID:24312583
The semantic web in translational medicine: current applications and future directions. PMID:24197933
Dual analysis of the murine cytomegalovirus and host cell transcriptomes reveal new aspects of the virus-host cell interface. PMID:24086132
An immunological fingerprint differentiates muscular lymphatics from arteries and veins. PMID:24044756
BreastMark: an integrated approach to mining publicly available transcriptomic datasets relating to breast cancer outcome. PMID:23820017
Key genes for modulating information flow play a temporal role as breast tumor coexpression networks are dynamically rewired by letrozole. PMID:23819860
ToP: a trend-of-disease-progression procedure works well for identifying cancer genes from multi-state cohort gene expression data for human colorectal cancer. PMID:23799036
PIMiner: a web tool for extraction of protein interactions from biomedical literature. PMID:23798227
Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. PMID:23599415
Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer. PMID:23547718
Application of Top-Down and Bottom-up Systems Approaches in Ruminant Physiology and Metabolism. PMID:23372424
Transcription and redox enzyme activities: comparison of equilibrium and disequilibrium levels in the three-spined stickleback. PMID:23363636
Knowledge Driven Variable Selection (KDVS) - a new approach to enrichment analysis of gene signatures obtained from high-throughput data. PMID:23302187
Identifying the status of genetic lesions in cancer clinical trial documents using machine learning. PMID:23282337
IntPath--an integrated pathway gene relationship database for model organisms and important pathogens. PMID:23282057
Signaling network of Oncostatin M pathway. PMID:23255051
Complex evolutionary relationships among four classes of modular RNA-binding splicing regulators in eukaryotes: the hnRNP, SR, ELAV-like and CELF proteins. PMID:23179353
A multicellular signal transduction network of AGE/RAGE signaling. PMID:23161412
Finding biomedical categories in Medline®. PMID:23046816
Tethering of the conserved piggyBac transposase fusion protein CSB-PGBD3 to chromosomal AP-1 proteins regulates expression of nearby genes in humans. PMID:23028371
Event extraction across multiple levels of biological organization. PMID:22962484
Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. PMID:22909249
Structural requirements for the activity of the MirB ferrisiderophore transporter of Aspergillus fumigatus. PMID:22903978
Using Galaxy to perform large-scale interactive data analyses. PMID:22700312
Relationship of a variant in the NTRK1 gene to white matter microstructure in young adults. PMID:22539856
Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge. PMID:22443377
Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems. PMID:22412335
Single-nucleotide polymorphisms associated with skin naphthyl-keratin adduct levels in workers exposed to naphthalene. PMID:22391508
Ten years of pathway analysis: current approaches and outstanding challenges. PMID:22383865
dbPTB: a database for preterm birth. PMID:22323062
Nearest hyperplane distance neighbor clustering algorithm applied to gene co-expression analysis in Alzheimer's disease. PMID:22255598
Preservation of ranking order in the expression of human Housekeeping genes. PMID:22216246
Comparative analysis of human and bovine protein kinases reveals unique relationship and functional diversity. PMID:22215962
Constructing a semantic predication gold standard from the biomedical literature. PMID:22185221
Overview of biological database mapping services for interoperation between different 'omics' datasets. PMID:22155608
Soft tagging of overlapping high confidence gene mention variants for cross-species full-text gene normalization. PMID:22152021
Cross-species gene normalization by species inference. PMID:22151999
Comparative microbial modules resource: generation and visualization of multi-species biclusters. PMID:22144874
PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. PMID:22070195
gViz, a novel tool for the visualization of co-expression networks. PMID:22032859
SegMine workflows for semantic microarray data analysis in Orange4WS. PMID:22029475
Accelerated recruitment of new brain development genes into the human genome. PMID:22028629
Challenges in the association of human single nucleotide polymorphism mentions with unique database identifiers. PMID:21992066
GO-based functional dissimilarity of gene sets. PMID:21884611
Tissue-specific gene expression templates for accurate molecular characterization of the normal physiological states of multiple human tissues with implication in development and cancer studies. PMID:21880155
Transcriptome analysis of epithelial and stromal contributions to mammogenesis in three week prepartum cows. PMID:21829467
Exome sequencing and analysis of induced pluripotent stem cells identify the cilia-related gene male germ cell-associated kinase (MAK) as a cause of retinitis pigmentosa. PMID:21825139
Disease embryo development network reveals the relationship between disease genes and embryo development genes. PMID:21824480
S3QL: a distributed domain specific language for controlled semantic integration of life sciences data. PMID:21756325
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
Exome-wide DNA capture and next generation sequencing in domestic and wild species. PMID:21729323
Characterization of autosomal copy-number variation in African Americans: the HyperGEN Study. PMID:21673747
Mining the TRAF6/p62 interactome for a selective ubiquitination motif. PMID:21554762
PR-10, defensin and cold dehydrin genes are among those over expressed in Oxytropis (Fabaceae) species adapted to the arctic. PMID:21499864
Genetic and clinical correlates of early-outgrowth colony-forming units. PMID:21493818
Knowledge management for systems biology a general and visually driven framework applied to translational medicine. PMID:21375767
Omics-based molecular target and biomarker identification. PMID:21370102
Identification of Parkinson's disease candidate genes using CAESAR and screening of MAPT and SNCAIP in South African Parkinson's disease patients. PMID:21344240
Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. PMID:21266472
Molecular correlates of experimental cerebral malaria detectable in whole blood. PMID:21149594
Generalized random set framework for functional enrichment analysis using primary genomics datasets. PMID:20971985
PathEx: a novel multi factors based datasets selector web tool. PMID:20969778
Identification of the Rage-dependent gene regulatory network in a mouse model of skin inflammation. PMID:20923549
Homeorhetic adaptation to lactation: comparative transcriptome analysis of mammary, liver, and adipose tissue during the transition from pregnancy to lactation in rats. PMID:20852911
In silico models of cancer. PMID:20836040
Overexpression of the RNA binding protein HuR impairs tumor growth in triple negative breast cancer associated with deficient angiogenesis. PMID:20724828
GPCRs, G-proteins, effectors and their interactions: human-gpDB, a database employing visualization tools and data integration techniques. PMID:20689020
Publishing Chinese medicine knowledge as Linked Data on the Web. PMID:20663193
GeneBrowser 2: an application to explore and identify common biological traits in a set of genes. PMID:20663121
Functional implications of the emergence of alternative splicing in hnRNP A/B transcripts. PMID:20651029
The gene expression profile in the synovium as a predictor of the clinical response to infliximab treatment in rheumatoid arthritis. PMID:20593016
FuncBase: a resource for quantitative gene function annotation. PMID:20495000
MAGIA, a web-based tool for miRNA and Genes Integrated Analysis. PMID:20484379
From IMGT-ONTOLOGY to IMGT/LIGMotif: the IMGT standardized approach for immunoglobulin and T cell receptor gene identification and description in large genomic sequences. PMID:20433708
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer. PMID:20370918
BisoGenet: a new tool for gene network building, visualization and analysis. PMID:20163717
Evolutionary dynamics of U12-type spliceosomal introns. PMID:20163699
Comparison of breast cancer to healthy control tissue discovers novel markers with potential for prognosis and early detection. PMID:20161755
LINNAEUS: a species name identification system for biomedical literature. PMID:20149233
Human cancer protein-protein interaction network: a structural perspective. PMID:20011507
Linking human diseases to animal models using ontology-based phenotype annotation. PMID:19956802
EGAN: exploratory gene association networks. PMID:19933825
Edgetic perturbation models of human inherited disorders. PMID:19888216
A statistical model of protein sequence similarity and function similarity reveals overly-specific function predictions. PMID:19844580
Analysis of blood stem cell activity and cystatin gene expression in a mouse model presenting a chromosomal deletion encompassing Csta and Stfa2l1. PMID:19838297
The stanley neuropathology consortium integrative database: a novel, web-based tool for exploring neuropathological markers in psychiatric disorders and the biological processes associated with abnormalities of those markers. PMID:19829293
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
Transcriptional profiling differences for articular cartilage and repair tissue in equine joint surface lesions. PMID:19751507
Molecular biology, genetics and biochemistry of the repulsive guidance molecule family. PMID:19698085
Effects of atherogenic diet on hepatic gene expression across mouse strains. PMID:19671657
Hmrbase: a database of hormones and their receptors. PMID:19589147
Pleiotropic effects of negative energy balance in the postpartum dairy cow on splenic gene expression: repercussions for innate and adaptive immunity. PMID:19567785
A gene signature for post-infectious chronic fatigue syndrome. PMID:19555476
OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. PMID:19528066
Gendoo: functional profiling of gene and disease features using MeSH vocabulary. PMID:19498079
How do human cells react to the absence of mitochondrial DNA? PMID:19492094
Aberrant gene expression profile in a mouse model of endometriosis mirrors that observed in women. PMID:19473656
Exploratory Visual Analysis of statistical results from microarray experiments comparing high and low grade glioma. PMID:19390666
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. PMID:19374773
SNPit: a federated data integration system for the purpose of functional SNP annotation. PMID:19327864
The effect of trans-10, cis-12 conjugated linoleic acid on gene expression profiles related to lipid metabolism in human intestinal-like Caco-2 cells. PMID:19283423
A bayesian analysis strategy for cross-study translation of gene expression biomarkers. PMID:19222378
MicroRNA transcriptome profiles during swine skeletal muscle development. PMID:19208255
Graded Smad2/3 activation is converted directly into levels of target gene expression in embryonic stem cells. PMID:19172185
Quantification of fibronectin 1 (FN1) splice variants, including two novel ones, and analysis of integrins as candidate FN1 receptors in bovine preimplantation embryos. PMID:19126199
Alterations in cell growth and signaling in ErbB3 binding protein-1 (Ebp1) deficient mice. PMID:19094237
KAGIANA: an excel-based tool for retrieving summary information on Arabidopsis genes. PMID:19043069
A survey of visualization tools for biological network analysis. PMID:19040716
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. PMID:19015123
Differential gene expression associated with postnatal equine articular cartilage maturation. PMID:18986532
Michigan molecular interactions r2: from interacting proteins to pathways. PMID:18978014
IUPHAR-DB: the IUPHAR database of G protein-coupled receptors and ion channels. PMID:18948278
TCMGeneDIT: a database for associated traditional Chinese medicine, gene and disease information using text mining. PMID:18854039
RAPID: Resource of Asian Primary Immunodeficiency Diseases. PMID:18842635
DAVID gene ID conversion tool. PMID:18841237
Gene expression profile in colon cancer cells with respect to XIAP expression status. PMID:18704457
A comparative analysis of retrieval features used in the TREC 2006 Genomics Track passage retrieval task. PMID:18693910
Constructing disease-specific gene networks using pair-wise relevance metric: application to colon cancer identifies interleukin 8, desmin and enolase 1 as the central elements. PMID:18691435
Arabidopsis reactome: a foundation knowledgebase for plant systems biology. PMID:18591350
VisANT: an integrative framework for networks in systems biology. PMID:18463131
Clinical uses of microarrays in cancer research. PMID:18453086
Extraction of semantic biomedical relations from text using conditional random fields. PMID:18433469
Using galaxy to perform large-scale interactive data analyses. PMID:18428782
EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries. PMID:18402700
MultiPriDe: automated batch development of quantitative real-time PCR primers. PMID:18400781
An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence. PMID:18395495
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. PMID:18384671
Large-scale analysis of Macaca fascicularis transcripts and inference of genetic divergence between M. fascicularis and M. mulatta. PMID:18294402
SPIKE--a database, visualization and analysis tool of cellular signaling pathways. PMID:18289391
Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'. PMID:18201381
MeInfoText: associated gene methylation and cancer information from text mining. PMID:18194557
MetaReg: a platform for modeling, analysis and visualization of biological systems using large-scale experimental data. PMID:18171474
PARPs database: a LIMS systems for protein-protein interaction data mining or laboratory information management system. PMID:18093328
Evaluation of resequencing on number of tag SNPs of 13 atherosclerosis-related genes in Thai population. PMID:18043865
Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. PMID:18042645
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. PMID:17980028
From "glycosyltransferase" to "congenital muscular dystrophy": integrating knowledge from NCBI Entrez Gene and the Gene Ontology. PMID:17911917
Microarray analysis reveals potential mechanisms of BRMS1-mediated metastasis suppression. PMID:17896182
Adaptive evolution of conserved noncoding elements in mammals. PMID:17845075
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. PMID:17678529
Distinct gene expression profiles in peripheral blood mononuclear cells from patients infected with vaccinia virus, yellow fever 17D virus, or upper respiratory infections. PMID:17651872
The functional modulation of epigenetic regulators by alternative splicing. PMID:17651478
Manual curation is not sufficient for annotation of genomic databases. PMID:17646325
The need for a multidisciplinary team approach to life science workflows. PMID:17641759
Faster rates of post-puberty kidney deterioration in males is correlated with elevated oxidative stress in males vs females at early puberty. PMID:17620128
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. PMID:17576678
Immediate-early and delayed primary response genes are distinct in function and genomic architecture. PMID:17575275
Identification and expression analysis of genes associated with bovine blastocyst formation. PMID:17559642
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. PMID:17547750
The selection of acceptable protein mutations. PMID:17540730
nuID: a universal naming scheme of oligonucleotides for illumina, affymetrix, and other microarrays. PMID:17540033
bZIPDB: a database of regulatory information for human bZIP transcription factors. PMID:17535445
Prediction of GPCR-G protein coupling specificity using features of sequences and biological functions. PMID:17531799
ESTpass: a web-based server for processing and annotating expressed sequence tag (EST) sequences. PMID:17526512
Interaction of the GraRS two-component system with the VraFG ABC transporter to support vancomycin-intermediate resistance in Staphylococcus aureus. PMID:17502406
Detecting multivariate differentially expressed genes. PMID:17490475
Mutational analysis of EGFR and related signaling pathway genes in lung adenocarcinomas identifies a novel somatic kinase domain mutation in FGFR4. PMID:17487277
A search engine to identify pathway genes from expression data on multiple organisms. PMID:17477880
Power-law-like distributions in biomedical publications and research funding. PMID:17472739
Splicy: a web-based tool for the prediction of possible alternative splicing events from Affymetrix probeset data. PMID:17430561
Statistical analysis of genomic protein family and domain controlled annotations for functional investigation of classified gene lists. PMID:17430558
Reactome: a knowledge base of biologic pathways and processes. PMID:17367534
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis. PMID:17338820
Automatic extraction of protein point mutations using a graph bigram association. PMID:17274683
Global reconstruction of the human metabolic network based on genomic and bibliomic data. PMID:17267599
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes. PMID:17254313
Shape identification within the SPECIALIST textTools. PMID:17238530
SemCat: semantically categorized entities for genomics. PMID:17238442
DiscoverySpace: an interactive data analysis application. PMID:17210078
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. PMID:17204154
The Rat Genome Database, update 2007--easing the path from disease to data and back again. PMID:17151068
TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels. PMID:17135193
Effect of infliximab on mRNA expression profiles in synovial tissue of rheumatoid arthritis patients. PMID:17134501
The mouse Gene Expression Database (GXD): 2007 update. PMID:17130151
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. PMID:17108355
methBLAST and methPrimerDB: web-tools for PCR based methylation analysis. PMID:17094804
Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications. PMID:17085479
EPConDB: a web resource for gene expression related to pancreatic development, beta-cell function and diabetes. PMID:17071715
Babel's tower revisited: a universal resource for cross-referencing across annotation databases. PMID:17068090
PhenomicDB: a new cross-species genotype/phenotype resource. PMID:16982638
EGASP: the human ENCODE Genome Annotation Assessment Project. PMID:16925836
A novel data mining method to identify assay-specific signatures in functional genomic studies. PMID:16907975
UniPep--a database for human N-linked glycosites: a resource for biomarker discovery. PMID:16901351
Gene and protein nomenclature in public databases. PMID:16899134
Challenges and strategies of the Genetics Home Reference. PMID:16888669
Design and implementation of a library-based information service in molecular biology and genetics at the University of Pittsburgh. PMID:16888665
TFBScluster web server for the identification of mammalian composite regulatory elements. PMID:16845063
Machine learning and word sense disambiguation in the biomedical domain: design and evaluation issues. PMID:16822321
The Autoimmune Disease Database: a dynamically compiled literature-derived database. PMID:16803617
Bok, Bcl-2-related Ovarian Killer, Is Cell Cycle-regulated and Sensitizes to Stress-induced Apoptosis. PMID:16772296
Argument-predicate distance as a filter for enhancing precision in extracting predications on the genetic etiology of disease. PMID:16762065
Variants in the GH-IGF axis confer susceptibility to lung cancer. PMID:16741161
Enhancing access to the Bibliome: the TREC 2004 Genomics Track. PMID:16722581
The comparative toxicogenomics database: a cross-species resource for building chemical-gene interaction networks. PMID:16675512
Human SNPs resulting in premature stop codons and protein truncation. PMID:16595072
Comparison of gene coverage of mouse oligonucleotide microarray platforms. PMID:16551360
Amplification of the Gene Ontology annotation of Affymetrix probe sets. PMID:16549014
NovelFam3000--uncharacterized human protein domains conserved across model organisms. PMID:16533400
SNP-RFLPing: restriction enzyme mining for SNPs in genomes. PMID:16503968
A map of recent positive selection in the human genome. PMID:16494531
The chicken immunoregulatory receptor families SIRP, TREM, and CMRF35/CD300L. PMID:16493555
Comparison of human (and other) genome browsers. PMID:16460652
Discovering semantic features in the literature: a foundation for building functional associations. PMID:16438716
Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration. PMID:16426464
RTPrimerDB: the real-time PCR primer and probe database, major update 2006. PMID:16381959
The International Gene Trap Consortium Website: a portal to all publicly available gene trap cell lines in mouse. PMID:16381950
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. PMID:16381948
SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. PMID:16381944
QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL. PMID:16381937
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. PMID:16381929
pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer. PMID:16381926
LMPD: LIPID MAPS proteome database. PMID:16381922
Human protein reference database--2006 update. PMID:16381900
The HUGO Gene Nomenclature Database, 2006 updates. PMID:16381876
LOCATE: a mouse protein subcellular localization database. PMID:16381849
ChimerDB--a knowledgebase for fusion sequences. PMID:16381848
Database resources of the National Center for Biotechnology Information. PMID:16381840
NPInter: the noncoding RNAs and protein related biomacromolecules interaction database. PMID:16381834
TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. PMID:16381825
The Gene Set Builder: collation, curation, and distribution of sets of genes. PMID:16371163
Integrating probe-level expression changes across generations of Affymetrix arrays. PMID:16356924
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention. PMID:16351756
Inherited disorder phenotypes: controlled annotation and statistical analysis for knowledge mining from gene lists. PMID:16351744
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. PMID:16344560
GPX-Macrophage Expression Atlas: a database for expression profiles of macrophages challenged with a variety of pro-inflammatory, anti-inflammatory, benign and pathogen insults. PMID:16343346
ErmineJ: tool for functional analysis of gene expression data sets. PMID:16280084
EXPANDER--an integrative program suite for microarray data analysis. PMID:16176576
Dynamic covariation between gene expression and proteome characteristics. PMID:16131395
Tools and strategies for physiological genomics: the Rat Genome Database. PMID:16106031
Plant genome resources at the national center for biotechnology information. PMID:16010002
Recent additions and improvements to the Onto-Tools. PMID:15980579
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. PMID:15980570
Tools enabling the elucidation of molecular pathways active in human disease: application to Hepatitis C virus infection. PMID:15967031
Exploring relationships and mining data with the UCSC Gene Sorter. PMID:15867434
NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. PMID:15608248
Database resources of the National Center for Biotechnology Information. PMID:15608222
Entrez Gene: gene-centered information at NCBI PubMed citations: 393.

393 articles citing: Entrez Gene: gene-centered information at NCBI

PheNominal: an EHR-integrated web application for structured deep phenotyping at the point of care. PMID:35902925
A Narrative Literature Review of Natural Language Processing Applied to the Occupational Exposome. PMID:35886395
DES-Amyloidoses "Amyloidoses through the looking-glass": A knowledgebase developed for exploring and linking information related to human amyloid-related diseases. PMID:35877764
The heterogeneous pharmacological medical biochemical network PharMeBINet. PMID:35821017
EnhFFL: A database of enhancer mediated feed-forward loops for human and mouse. PMID:35694152
Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases. PMID:35639335
Unraveling T Cell Responses for Long Term Protection of SARS-CoV-2 Infection. PMID:35601483
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. PMID:35562840
A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural Mesothelioma. PMID:35558518
Machine-Learning Analysis of Serum Proteomics in Neuropathic Pain after Nerve Injury in Breast Cancer Surgery Points at Chemokine Signaling via SIRT2 Regulation. PMID:35408848
Genomic Evidence Supports the Recognition of Endometriosis as an Inflammatory Systemic Disease and Reveals Disease-Specific Therapeutic Potentials of Targeting Neutrophil Degranulation. PMID:35401535
Transcriptomic Analysis of Liver Indicates Novel Vaccine to Porcine Reproductive and Respiratory Virus Promotes Homeostasis in T-Cell and Inflammatory Immune Responses Compared to a Commercial Vaccine in Pigs. PMID:35400088
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
TBGA: a large-scale Gene-Disease Association dataset for Biomedical Relation Extraction. PMID:35361129
Genome-wide association studies of metabolites in Finnish men identify disease-relevant loci. PMID:35347128
Impact of 6 month conjugated equine estrogen versus estradiol-treatment on biomarkers and enriched gene sets in healthy mammary tissue of non-human primates. PMID:35298474
Differential expression analyses reveal extensive transcriptional plasticity induced by temperature in New Zealand silver trevally (Pseudocaranx georgianus). PMID:35233245
Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits. PMID:35189878
Endothelial Cell RNA-Seq Data: Differential Expression and Functional Enrichment Analyses to Study Phenotypic Switching. PMID:35099752
The speed of information propagation in the scientific network distorts biomedical research. PMID:35070506
A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments. PMID:35052563
An annotated dataset for extracting gene-melanoma relations from scientific literature. PMID:35045882
Identification of human gene research articles with wrongly identified nucleotide sequences. PMID:35022248
The characteristics of early-stage research into human genes are substantially different from subsequent research. PMID:34990452
Text Mining and Hub Gene Network Analysis of Endometriosis. PMID:34917684
A Standardized Brain Molecular Atlas: A Resource for Systems Modeling and Simulation. PMID:34858137
miRTarBase update 2022: an informative resource for experimentally validated miRNA-target interactions. PMID:34850920
Pairwise Biological Network Alignment Based on Discrete Bat Algorithm. PMID:34777564
RNAInter v4.0: RNA interactome repository with redefined confidence scoring system and improved accessibility. PMID:34718726
Selection on ancestral genetic variation fuels repeated ecotype formation in bottlenose dolphins. PMID:34705499
Music of metagenomics-a review of its applications, analysis pipeline, and associated tools. PMID:34657989
CTR-DB, an omnibus for patient-derived gene expression signatures correlated with cancer drug response. PMID:34570230
Genetic Prioritization, Therapeutic Repositioning and Cross-Disease Comparisons Reveal Inflammatory Targets Tractable for Kidney Stone Disease. PMID:34489936
Whole-Genome Differentially Hydroxymethylated DNA Regions among Twins Discordant for Cardiovascular Death. PMID:34440357
Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review. PMID:34439912
MicroRNA Regulation of Bone Marrow Mesenchymal Stem Cell Chondrogenesis: Toward Articular Cartilage. PMID:34328786
A comprehensive analysis of SNPs and CNVs identifies novel markers associated with disease outcomes in colorectal cancer. PMID:34309201
DES-Tcell is a knowledgebase for exploring immunology-related literature. PMID:34253812
TIDB: a comprehensive database of trained immunity. PMID:34244719
MaxDIA enables library-based and library-free data-independent acquisition proteomics. PMID:34239088
Databases for Protein-Protein Interactions. PMID:34236665
Multifaceted regulation of hepatic lipid metabolism by YY1. PMID:34099540
TRPM2, PDLIM5, BCL3, CD14, GBA Genes as Feasible Markers for Premature Coronary Heart Disease Risk. PMID:34093636
Integrated analysis of methylation-driven genes and pretreatment prognostic factors in patients with hepatocellular carcinoma. PMID:34034705
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. PMID:33929018
Single-cell melanoma transcriptomes depicting functional versatility and clinical implications of STIM1 in the tumor microenvironment. PMID:33859736
A first-generation pediatric cancer dependency map. PMID:33753930
Effects of estrogen inhibition formula herbal mixture for danazol-induced precocious puberty in female rats: an experimental study with network pharmacology. PMID:33665096
TOXPANEL: A Gene-Set Analysis Tool to Assess Liver and Kidney Injuries. PMID:33633572
Tandem Mass Tag-Based Proteomic Analysis of Potential Biomarkers for Hepatocellular Carcinoma Differentiation. PMID:33603407
Gene function finding through cross-organism ensemble learning. PMID:33579334
Orthology-Based Estimate of the Contribution of Horizontal Gene Transfer from Distantly Related Bacteria to the Intraspecific Diversity and Differentiation of Xylella fastidiosa. PMID:33430372
Informatics Inference of Exercise-Induced Modulation of Brain Pathways Based on Cerebrospinal Fluid Micro-RNAs in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome. PMID:33274349
Genetic and non-genetic factors associated with the phenotype of exceptional longevity & normal cognition. PMID:33154391
Predicting candidate genes from phenotypes, functions and anatomical site of expression. PMID:33051643
SC2disease: a manually curated database of single-cell transcriptome for human diseases. PMID:33010177
The 2019 National Natural language processing (NLP) Clinical Challenges (n2c2)/Open Health NLP (OHNLP) shared task on clinical concept normalization for clinical records. PMID:32968800
Unveiling Sex-Based Differences in the Effects of Alcohol Abuse: A Comprehensive Functional Meta-Analysis of Transcriptomic Studies. PMID:32967293
Applications of Genome-Wide Screening and Systems Biology Approaches in Drug Repositioning. PMID:32967266
ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature. PMID:32921303
Gene Expression Clustering and Selected Head and Neck Cancer Gene Signatures Highlight Risk Probability Differences in Oral Premalignant Lesions. PMID:32756466
Computational analysis of microarray data of Arabidopsis thaliana challenged with Alternaria brassicicola for identification of key genes in Brassica. PMID:32607787
Building a PubMed knowledge graph. PMID:32591513
Genome-wide Enrichment of De Novo Coding Mutations in Orofacial Cleft Trios. PMID:32574564
Facial shape and allometry quantitative trait locus intervals in the Diversity Outbred mouse are enriched for known skeletal and facial development genes. PMID:32502155
Evolutionary analyses reveal independent origins of gene repertoires and structural motifs associated to fast inactivation in calcium-selective TRPV channels. PMID:32457384
MyoMiner: explore gene co-expression in normal and pathological muscle. PMID:32393257
Methodological challenges in translational drug response modeling in cancer: A systematic analysis with FORESEE. PMID:32310964
Test of Arabidopsis Space Transcriptome: A Discovery Environment to Explore Multiple Plant Biology Spaceflight Experiments. PMID:32265943
Attractor Concepts to Evaluate the Transcriptome-wide Dynamics Guiding Anaerobic to Aerobic State Transition in Escherichia coli. PMID:32246034
Multiple Pathways Involved in Palmitic Acid-Induced Toxicity: A System Biology Approach. PMID:32076395
Tumor suppressor genes and allele-specific expression: mechanisms and significance. PMID:32064050
RefDNN: a reference drug based neural network for more accurate prediction of anticancer drug resistance. PMID:32024872
Long-term epilepsy-associated tumors: transcriptional signatures reflect clinical course. PMID:31919458
Genetic links between endometriosis and cancers in women. PMID:31879572
The distributions of protein coding genes within chromatin domains in relation to human disease. PMID:31805995
New C-Terminal Conserved Regions of Tafazzin, a Catalyst of Cardiolipin Remodeling. PMID:31781330
Investigating the Systems-Level Effect of Pueraria lobata for Menopause-Related Metabolic Diseases Using an Ovariectomized Rat Model and Network Pharmacological Analysis. PMID:31752216
Complex alternative splicing of human Endonuclease V mRNA, but evidence for only a single protein isoform. PMID:31703097
PlantRegMap: charting functional regulatory maps in plants. PMID:31701126
miRTarBase 2020: updates to the experimentally validated microRNA-target interaction database. PMID:31647101
The role of extracellular matrix in mouse and human corneal neovascularization. PMID:31582785
Activation and In Vivo Evolution of the MAIT Cell Transcriptome in Mice and Humans Reveals Tissue Repair Functionality. PMID:31533045
ABCD: Alzheimer's disease Biomarkers Comprehensive Database. PMID:31501752
Targeting amphiregulin (AREG) derived from senescent stromal cells diminishes cancer resistance and averts programmed cell death 1 ligand (PD-L1)-mediated immunosuppression. PMID:31493351
AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature. PMID:31467448
Integration of curated and high-throughput screening data to elucidate environmental influences on disease pathways. PMID:31453412
Exome-Wide Rare Variant Analysis From the DiscovEHR Study Identifies Novel Candidate Predisposition Genes for Endometrial Cancer. PMID:31338326
Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases. PMID:31323264
Analysis of the equine "cumulome" reveals major metabolic aberrations after maturation in vitro. PMID:31315563
Atlas of Subcellular RNA Localization Revealed by APEX-Seq. PMID:31230715
Literature-Based Enrichment Insights into Redox Control of Vascular Biology. PMID:31223421
Metabolic and Stress Response Changes Precede Disease Onset in the Spinal Cord of Mutant SOD1 ALS Mice. PMID:31213966
Aquatic Adaptation and Depleted Diversity: A Deep Dive into the Genomes of the Sea Otter and Giant Otter. PMID:31212313
Geneshot: search engine for ranking genes from arbitrary text queries. PMID:31114885
A context-based ABC model for literature-based discovery. PMID:31017923
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. PMID:30944313
CSgator: an integrated web platform for compound set analysis. PMID:30830479
Increased TGF-β and BMP Levels and Improved Chondrocyte-Specific Marker Expression In Vitro under Cartilage-Specific Physiological Osmolarity. PMID:30781744
Taxonomical over splitting in the Rhodnius prolixus (Insecta: Hemiptera: Reduviidae) clade: Are R. taquarussuensis (da Rosa et al., 2017) and R. neglectus (Lent, 1954) the same species? PMID:30730919
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. PMID:30576489
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. PMID:30576488
Integrated analysis of microRNA and mRNA expression profiles in splenomegaly induced by non-cirrhotic portal hypertension in rats. PMID:30573742
Proteomics of Bronchoalveolar Lavage Fluid Reveals a Lung Oxidative Stress Response in Murine Herpesvirus-68 Infection. PMID:30486363
Interpretation of an individual functional genomics experiment guided by massive public data. PMID:30478325
Expression of mitochondrial dysfunction-related genes and pathways in paclitaxel-induced peripheral neuropathy in breast cancer survivors. PMID:30426838
Selecting Multiple Biomarker Subsets with Similarly Effective Binary Classification Performances. PMID:30371672
Targeting SPINK1 in the damaged tumour microenvironment alleviates therapeutic resistance. PMID:30333494
IRE1α-XBP1 controls T cell function in ovarian cancer by regulating mitochondrial activity. PMID:30305738
An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations. PMID:30239680
Comprehensive network map of interferon gamma signaling. PMID:30191398
DES-Mutation: System for Exploring Links of Mutations and Diseases. PMID:30190574
FungiDB: An Integrated Bioinformatic Resource for Fungi and Oomycetes. PMID:30152809
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PMID:30142147
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
IsopiRBank: a research resource for tracking piRNA isoforms. PMID:29961820
MGOGP: a gene module-based heuristic algorithm for cancer-related gene prioritization. PMID:29871590
Chemical-Induced Phenotypes at CTD Help Inform the Predisease State and Construct Adverse Outcome Pathways. PMID:29846728
Involvement of β-Carbonic Anhydrase Genes in Bacterial Genomic Islands and Their Horizontal Transfer to Protists. PMID:29802189
Network-Based Disease Module Discovery by a Novel Seed Connector Algorithm with Pathobiological Implications. PMID:29791871
Functional signaling and gene regulatory networks between the oocyte and the surrounding cumulus cells. PMID:29747587
Recent stimulant use and leukocyte gene expression in methamphetamine users with treated HIV infection. PMID:29679637
Evolution of dopamine receptors: phylogenetic evidence suggests a later origin of the DRD2l and DRD4rs dopamine receptor gene lineages. PMID:29666757
Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature. PMID:29650041
SQUID: transcriptomic structural variation detection from RNA-seq. PMID:29650026
AOP-DB: A database resource for the exploration of Adverse Outcome Pathways through integrated association networks. PMID:29454060
Genomic study and Medical Subject Headings enrichment analysis of early pregnancy rate and antral follicle numbers in Nelore heifers. PMID:29293733
HIDEEP: a systems approach to predict hormone impacts on drug efficacy based on effect paths. PMID:29192270
Random walks on mutual microRNA-target gene interaction network improve the prediction of disease-associated microRNAs. PMID:29137601
miRTarBase update 2018: a resource for experimentally validated microRNA-target interactions. PMID:29126174
"Personalized Cancer Therapy": A Publicly Available Precision Oncology Resource. PMID:29092956
Assessment of the significance of patent-derived information for the early identification of compound-target interaction hypotheses. PMID:29086108
LiverWiki: a wiki-based database for human liver. PMID:29029599
Systematic integration of biomedical knowledge prioritizes drugs for repurposing. PMID:28936969
Precision annotation of digital samples in NCBI's gene expression omnibus. PMID:28925997
FANTOM5 CAGE profiles of human and mouse reprocessed for GRCh38 and GRCm38 genome assemblies. PMID:28850105
Genome-wide meta-analysis of copy number variations with alcohol dependence. PMID:28696413
Enriching plausible new hypothesis generation in PubMed. PMID:28678852
Data mining and pathway analysis of glucose-6-phosphate dehydrogenase with natural language processing. PMID:28627690
OncoScore: a novel, Internet-based tool to assess the oncogenic potential of genes. PMID:28387367
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. PMID:28365736
BRIDG: a domain information model for translational and clinical protocol-driven research. PMID:28339791
Genotype-based gene signature of glioma risk. PMID:28339748
Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans. PMID:28333345
GEAR: A database of Genomic Elements Associated with drug Resistance. PMID:28294141
Meta-Analysis of Gene Expression Profiles in Acute Promyelocytic Leukemia Reveals Involved Pathways. PMID:28286608
Using predictive specificity to determine when gene set analysis is biologically meaningful. PMID:28204549
The use of gene interaction networks to improve the identification of cancer driver genes. PMID:28149674
Recruitment of Tiam1 to Semaphorin 4D Activates Rac and Enhances Proliferation, Invasion, and Metastasis in Oral Squamous Cell Carcinoma. PMID:28038319
PCAN: phenotype consensus analysis to support disease-gene association. PMID:27923364
dbDEMC 2.0: updated database of differentially expressed miRNAs in human cancers. PMID:27899556
snpGeneSets: An R Package for Genome-Wide Study Annotation. PMID:27807048
Identification of lncRNA functions in lung cancer based on associated protein-protein interaction modules. PMID:27786280
Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes. PMID:27756223
OAHG: an integrated resource for annotating human genes with multi-level ontologies. PMID:27703231
Identification of novel prognostic indicators for triple-negative breast cancer patients through integrative analysis of cancer genomics data and protein interactome data. PMID:27690302
MiR-139-5p is associated with inflammatory regulation through c-FOS suppression, and contributes to the progression of primary biliary cholangitis. PMID:27668889
Mapping Phenotypic Information in Heterogeneous Textual Sources to a Domain-Specific Terminological Resource. PMID:27643689
Oxidative stress controls the choice of alternative last exons via a Brahma-BRCA1-CstF pathway. PMID:27591253
Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera. PMID:27540087
Signaling network map of the aryl hydrocarbon receptor. PMID:27465749
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
BLAT2DOLite: An Online System for Identifying Significant Relationships between Genetic Sequences and Diseases. PMID:27315278
Characterization of Somatically-Eliminated Genes During Development of the Sea Lamprey (Petromyzon marinus). PMID:27288344
Extracting a low-dimensional description of multiple gene expression datasets reveals a potential driver for tumor-associated stroma in ovarian cancer. PMID:27287041
Galectin-related protein: An integral member of the network of chicken galectins 1. From strong sequence conservation of the gene confined to vertebrates to biochemical characteristics of the chicken protein and its crystal structure. PMID:27268118
Advancing Exposure Science through Chemical Data Curation and Integration in the Comparative Toxicogenomics Database. PMID:27170236
Ferret: a user-friendly Java tool to extract data from the 1000 Genomes Project. PMID:27153588
Identifying Network Perturbation in Cancer. PMID:27145341
An integrated signal transduction network of macrophage migration inhibitory factor. PMID:27139435
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
An inter-species protein-protein interaction network across vast evolutionary distance. PMID:27107014
A new molecular signature method for prediction of driver cancer pathways from transcriptional data. PMID:27098033
Genic insights from integrated human proteomics in GeneCards. PMID:27048349
DNA Damage Response Is Involved in the Developmental Toxicity of Mebendazole in Zebrafish Retina. PMID:27014071
Global Metabolic Reconstruction and Metabolic Gene Evolution in the Cattle Genome. PMID:26992093
Genes with high penetrance for syndromic and non-syndromic autism typically function within the nucleus and regulate gene expression. PMID:26985359
A Human "eFP" Browser for Generating Gene Expression Anatograms. PMID:26954504
Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases. PMID:26950747
Overlapping cell population expression profiling and regulatory inference in C. elegans. PMID:26926147
The Implicitome: A Resource for Rationalizing Gene-Disease Associations. PMID:26919047
Featured Article: Genotation: Actionable knowledge for the scientific reader. PMID:26900164
CSGene: a literature-based database for cell senescence genes and its application to identify critical cell aging pathways and associated diseases. PMID:26775705
Identification of novel genes and pathways in carotid atheroma using integrated bioinformatic methods. PMID:26742467
Fundamentals of protein interaction network mapping. PMID:26681426
pubmed.mineR: an R package with text-mining algorithms to analyse PubMed abstracts. PMID:26564970
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
The Transporter Classification Database (TCDB): recent advances. PMID:26546518
DESM: portal for microbial knowledge exploration systems. PMID:26546514
Classification of Cancer Primary Sites Using Machine Learning and Somatic Mutations. PMID:26539502
An evidence-based knowledgebase of metastasis suppressors to identify key pathways relevant to cancer metastasis. PMID:26486520
dbSUPER: a database of super-enhancers in mouse and human genome. PMID:26438538
Computational Identification of Post Translational Modification Regulated RNA Binding Protein Motifs. PMID:26368004
Systematic Analysis of Endometrial Cancer-Associated Hub Proteins Based on Text Mining. PMID:26366417
Curation of the Mammalian Palmitoylome Indicates a Pivotal Role for Palmitoylation in Diseases and Disorders of the Nervous System and Cancers. PMID:26275289
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder. PMID:26228432
A Methodology for the Development of RESTful Semantic Web Services for Gene Expression Analysis. PMID:26207740
The extracellular matrix: Tools and insights for the "omics" era. PMID:26163349
Mac-1 Regulates IL-13 Activity in Macrophages by Directly Interacting with IL-13Rα1. PMID:26160172
Genome Modeling System: A Knowledge Management Platform for Genomics. PMID:26158448
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. PMID:26100720
dbEMT: an epithelial-mesenchymal transition associated gene resource. PMID:26099468
ZFIN, The zebrafish model organism database: Updates and new directions. PMID:26097180
GeneWeaver: finding consilience in heterogeneous cross-species functional genomics data. PMID:26092690
HCSD: the human cancer secretome database. PMID:26078477
Lysoplex: An efficient toolkit to detect DNA sequence variations in the autophagy-lysosomal pathway. PMID:26075876
A Survival Association Study of 102 Polymorphisms Previously Associated with Survival Outcomes in Colorectal Cancer. PMID:26064972
A survey on the computational approaches to identify drug targets in the postgenomic era. PMID:26060814
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. PMID:25971743
Inference of Evolutionary Forces Acting on Human Biological Pathways. PMID:25971280
Understanding multicellular function and disease with human tissue-specific networks. PMID:25915600
Exploring the genetic signature of body size in Yucatan miniature pig. PMID:25885114
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles. PMID:25861967
Detection of convergent genome-wide signals of adaptation to tropical forests in humans. PMID:25849546
Efficacy of Carboplatin Alone and in Combination with ABT888 in Intracranial Murine Models of BRCA-Mutated and BRCA-Wild-Type Triple-Negative Breast Cancer. PMID:25824335
Transhydrogenase promotes the robustness and evolvability of E. coli deficient in NADPH production. PMID:25715029
Identifying genetic interactions associated with late-onset Alzheimer's disease. PMID:25649863
Genetic redundancy is prevalent within the 6.7 Mb Sinorhizobium meliloti genome. PMID:25638282
Sparse expression bases in cancer reveal tumor drivers. PMID:25583238
Selecting causal genes from genome-wide association studies via functionally coherent subnetworks. PMID:25532137
Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson's disease. PMID:25528190
Molecular profiling of thyroid cancer subtypes using large-scale text mining. PMID:25521965
OntoGene web services for biomedical text mining. PMID:25472638
Expanded microbial genome coverage and improved protein family annotation in the COG database. PMID:25428365
Araport: the Arabidopsis information portal. PMID:25414324
Beyond protein expression, MOPED goes multi-omics. PMID:25404128
Database resources of the National Center for Biotechnology Information. PMID:25398906
Co-expression Network Analysis of Human lncRNAs and Cancer Genes. PMID:25392693
Text mining in cancer gene and pathway prioritization. PMID:25392685
PubAngioGen: a database and knowledge for angiogenesis and related diseases. PMID:25392416
Genenames.org: the HGNC resources in 2015. PMID:25361968
Gene: a gene-centered information resource at NCBI. PMID:25355515
The human DEPhOsphorylation database DEPOD: a 2015 update. PMID:25332398
BCCTBbp: the Breast Cancer Campaign Tissue Bank bioinformatics portal. PMID:25332396
The effect of colonoscopy on whole blood gene expression profile: an experimental investigation for colorectal cancer biomarker discovery. PMID:25306939
CODEX: a next-generation sequencing experiment database for the haematopoietic and embryonic stem cell communities. PMID:25270877
Widespread signals of convergent adaptation to high altitude in Asia and america. PMID:25262650
Integration strategy is a key step in network-based analysis and dramatically affects network topological properties and inferring outcomes. PMID:25243127
circBase: a database for circular RNAs. PMID:25234927
Small RNAs as important regulators for the hybrid vigour of super-hybrid rice. PMID:25129133
Integrative Pathway Analysis Using Graph-Based Learning with Applications to TCGA Colon and Ovarian Data. PMID:25125969
Composition and applications of focus libraries to phenotypic assays. PMID:25104937
DNAVaxDB: the first web-based DNA vaccine database and its data analysis. PMID:25104313
Inferring the perturbed microRNA regulatory networks from gene expression data using a network propagation based method. PMID:25069957
Clinical phenotype-based gene prioritization: an initial study using semantic similarity and the human phenotype ontology. PMID:25047600
Gene network-based analysis identifies two potential subtypes of small intestinal neuroendocrine tumors. PMID:25023465
ShrimpGPAT: a gene and protein annotation tool for knowledge sharing and gene discovery in shrimp. PMID:24952385
Web services-based text-mining demonstrates broad impacts for interoperability and process simplification. PMID:24919658
The molecular mechanisms of Tanshinone IIA on the apoptosis and arrest of human esophageal carcinoma cells. PMID:24829906
ToppMiR: ranking microRNAs and their mRNA targets based on biological functions and context. PMID:24829448
OTX2 duplication is implicated in hemifacial microsomia. PMID:24816892
Transcriptional changes in canine distemper virus-induced demyelinating leukoencephalitis favor a biphasic mode of demyelination. PMID:24755553
Identification of ethnically specific genetic variations in pan-asian ethnos. PMID:24748860
RetrogeneDB--a database of animal retrogenes. PMID:24739306
A functional screen for copper homeostasis genes identifies a pharmacologically tractable cellular system. PMID:24708151
The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. PMID:24705354
GeneSense: a new approach for human gene annotation integrated with protein-protein interaction networks. PMID:24667292
Comparative transcriptional profiling of three super-hybrid rice combinations. PMID:24595241
A network map of the gastrin signaling pathway. PMID:24584707
Computational drug repositioning through heterogeneous network clustering. PMID:24564976
Transcriptomic meta-analysis of multiple sclerosis and its experimental models. PMID:24475162
Composition of seed sequence is a major determinant of microRNA targeting patterns. PMID:24470575
Pathway analysis for drug repositioning based on public database mining. PMID:24460210
DevMouse, the mouse developmental methylome database and analysis tools. PMID:24408217
Genetics of new-onset diabetes after transplantation. PMID:24309190
Plasma Proteome Database as a resource for proteomics research: 2014 update. PMID:24304897
PAV ontology: provenance, authoring and versioning. PMID:24267948
Generic information can retrieve known biological associations: implications for biomedical knowledge discovery. PMID:24260124
Database resources of the National Center for Biotechnology Information. PMID:24259429
The transporter classification database. PMID:24225317
CoMAGC: a corpus with multi-faceted annotations of gene-cancer relations. PMID:24225062
Annotating cancer variants and anti-cancer therapeutics in reactome. PMID:24213504
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. PMID:24174544
The mouse Gene Expression Database (GXD): 2014 update. PMID:24163257
HoPaCI-DB: host-Pseudomonas and Coxiella interaction database. PMID:24137008
Evaluation and cross-comparison of lexical entities of biological interest (LexEBI). PMID:24124474
DGIdb: mining the druggable genome. PMID:24122041
Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources. PMID:24112383
Sensitive detection of viral transcripts in human tumor transcriptomes. PMID:24098097
A systematic approach identifies FOXA1 as a key factor in the loss of epithelial traits during the epithelial-to-mesenchymal transition in lung cancer. PMID:24093963
Guide: a desktop application for analysing gene expression data. PMID:24093424
Complete Genome Sequence of Encapsulated Haemophilus influenzae Type f KR494, an Invasive Isolate That Caused Necrotizing Myositis. PMID:24092777
CoCiter: an efficient tool to infer gene function by assessing the significance of literature co-citation. PMID:24086311
Nicotinic acetylcholine receptors mediate lung cancer growth. PMID:24062692
Role of conserved cis-regulatory elements in the post-transcriptional regulation of the human MECP2 gene involved in autism. PMID:24040966
IQdb: an intelligence quotient score-associated gene resource for human intelligence. PMID:24030781
Learning a Markov Logic network for supervised gene regulatory network inference. PMID:24028533
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses. PMID:23987304
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. PMID:23981286
Defining cell-type specificity at the transcriptional level in human disease. PMID:23950145
HSC-explorer: a curated database for hematopoietic stem cells. PMID:23936191
Accuracy and coverage assessment of Oryctolagus cuniculus (rabbit) genes encoding immunoglobulins in the whole genome sequence assembly (OryCun2.0) and localization of the IGH locus to chromosome 20. PMID:23925440
Human choline dehydrogenase: medical promises and biochemical challenges. PMID:23906661
Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data. PMID:23895370
BGDB: a database of bivalent genes. PMID:23894186
3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data. PMID:23875761
dbNSFP v2.0: a database of human non-synonymous SNVs and their functional predictions and annotations. PMID:23843252
Integrating pathways of Parkinson's disease in a molecular interaction map. PMID:23832570
Robust identification of local adaptation from allele frequencies. PMID:23821598
Distinct microRNAs expression profile in primary biliary cirrhosis and evaluation of miR 505-3p and miR197-3p as novel biomarkers. PMID:23776611
The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes. PMID:23729657
Gene expression analysis of peripheral blood cells reveals Toll-like receptor pathway deregulation in colorectal cancer. PMID:23650534
Chapter 15: disease gene prioritization. PMID:23633938
Origin and evolution of the cystic fibrosis transmembrane regulator protein R domain. PMID:23578801
Where in the genome are we? A cautionary tale of database use in genomics research. PMID:23519237
A pathway approach to investigate the function and regulation of SREBPs. PMID:23516131
An integrated map of corticotropin-releasing hormone signaling pathway. PMID:23504413
Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. PMID:23492669
search GenBank: interactive orchestration and ad-hoc choreography of Web services in the exploration of the biomedical resources of the National Center For Biotechnology Information. PMID:23452691
crcTRP: a translational research platform for colorectal cancer. PMID:23431356
STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation. PMID:23409969
TGF-β/Smad2/3 signaling directly regulates several miRNAs in mouse ES cells and early embryos. PMID:23390484
Novel genes underlying beta cell survival in metabolic stress. PMID:23390342
Whole exome sequencing identifies a mutation for a novel form of corneal intraepithelial dyskeratosis. PMID:23349227
Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective. PMID:23348003
Haptoglobin genotype is a consistent marker of coronary heart disease risk among individuals with elevated glycosylated hemoglobin. PMID:23312704
A vertex similarity-based framework to discover and rank orphan disease-related genes. PMID:23281592
Computational analysis of transcriptome of Indian major carp, Labeo rohita (Hamilton-Buchanan, 1822) for functional annotation. PMID:23275698
Gene family matters: expanding the HGNC resource. PMID:23245209
Identification of 3' gene ends using transcriptional and genomic conservation across vertebrates. PMID:23244605
Contextualization procedure and modeling of monocyte specific TLR signaling. PMID:23236359
CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes. PMID:23228284
CYP1B1, MYOC, and LTBP2 mutations in primary congenital glaucoma patients in the United States. PMID:23218701
Wiki-pi: a web-server of annotated human protein-protein interactions to aid in discovery of protein function. PMID:23209562
PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. PMID:23193289
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. PMID:23193282
The NIH genetic testing registry: a new, centralized database of genetic tests to enable access to comprehensive information and improve transparency. PMID:23193275
Database resources of the National Center for Biotechnology Information. PMID:23193264
Interactogeneous: disease gene prioritization using heterogeneous networks and full topology scores. PMID:23185389
Animal QTLdb: an improved database tool for livestock animal QTL/association data dissemination in the post-genome era. PMID:23180796
Collaborative biocuration--text-mining development task for document prioritization for curation. PMID:23180769
BioGPS and MyGene.info: organizing online, gene-centric information. PMID:23175613
Reconstruction of Danio rerio metabolic model accounting for subcellular compartmentalisation. PMID:23166792
Genenames.org: the HGNC resources in 2013. PMID:23161694
Atlas of genetics and cytogenetics in oncology and haematology in 2013. PMID:23161685
First survey and functional annotation of prohormone and convertase genes in the pig. PMID:23153308
Spliceosome database: a tool for tracking components of the spliceosome. PMID:23118483
IUPHAR-DB: updated database content and new features. PMID:23087376
Microbial virus genome annotation-mustering the troops to fight the sequence onslaught. PMID:23084289
"Orphan" retrogenes in the human genome. PMID:23066043
Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions. PMID:23060433
Development of an undergraduate bioinformatics degree program at a liberal arts college. PMID:23012579
Online tools for bioinformatics analyses in nutrition sciences. PMID:22983844
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
RhesusBase: a knowledgebase for the monkey research community. PMID:22965133
On-line resources for Xenopus. PMID:22956109
Using ProHits to store, annotate, and analyze affinity purification-mass spectrometry (AP-MS) data. PMID:22948730
Large scale of human duplicate genes divergence. PMID:22922908
CDA: combinatorial drug discovery using transcriptional response modules. PMID:22905152
A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. PMID:22901054
Nanoinformatics: a new area of research in nanomedicine. PMID:22866003
TPX: Biomedical literature search made easy. PMID:22829734
CIDeR: multifactorial interaction networks in human diseases. PMID:22809392
Comparative analysis of diguanylate cyclase and phosphodiesterase genes in Klebsiella pneumoniae. PMID:22776320
Concept annotation in the CRAFT corpus. PMID:22776079
Rational drug repositioning guided by an integrated pharmacological network of protein, disease and drug. PMID:22748168
Whole-genome sequencing and analysis of the Malaysian cynomolgus macaque (Macaca fascicularis) genome. PMID:22747675
DEFOG: discrete enrichment of functionally organized genes. PMID:22706384
IMGT-ONTOLOGY 2012. PMID:22654892
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts. PMID:22641850
Analyzing large biological datasets with association networks. PMID:22638576
Relax with CouchDB--into the non-relational DBMS era of bioinformatics. PMID:22609849
3'-Phosphoadenosine 5'-phosphosulfate (PAPS) synthases, naturally fragile enzymes specifically stabilized by nucleotide binding. PMID:22451673
AtPAN: an integrated system for reconstructing transcriptional regulatory networks in Arabidopsis thaliana. PMID:22397531
GrameneMart: the BioMart data portal for the Gramene project. PMID:22374386
CytoSaddleSum: a functional enrichment analysis plugin for Cytoscape based on sum-of-weights scores. PMID:22345616
Identifying gene interaction networks. PMID:22307715
IntegromeDB: an integrated system and biological search engine. PMID:22260095
Human PAPS synthase isoforms are dynamically regulated enzymes with access to nucleus and cytoplasm. PMID:22242175
Guidelines for information about therapy experiments: a proposal on best practice for recording experimental data on cancer therapy. PMID:22226027
Similarity-based disease risk assessment for personal genomes: proof of concept. PMID:22195217
Identification of co-occurring transcription factor binding sites from DNA sequence using clustered position weight matrices. PMID:22187154
Genome-wide transcriptional profiling of peripheral blood leukocytes from cattle infected with Mycobacterium bovis reveals suppression of host immune genes. PMID:22182502
Analysis of cancer metabolism with high-throughput technologies. PMID:22166000
Database resources of the National Center for Biotechnology Information. PMID:22140104
A comprehensive manually curated protein-protein interaction database for the Death Domain superfamily. PMID:22135292
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. PMID:22121212
GONUTS: the Gene Ontology Normal Usage Tracking System. PMID:22110029
WikiPathways: building research communities on biological pathways. PMID:22096230
The forkhead transcription factor FOXK2 promotes AP-1-mediated transcriptional regulation. PMID:22083952
The Gene Wiki in 2011: community intelligence applied to human gene annotation. PMID:22075991
zfishbook: connecting you to a world of zebrafish revertible mutants. PMID:22067444
EcoliWiki: a wiki-based community resource for Escherichia coli. PMID:22064863
The Reactome BioMart. PMID:22012987
pubmed2ensembl: a resource for mining the biological literature on genes. PMID:21980353
The UCSC Genome Browser. PMID:21975940
CpG site degeneration triggered by the loss of functional constraint created a highly polymorphic macaque drug-metabolizing gene, CYP1A2. PMID:21961956
ppiTrim: constructing non-redundant and up-to-date interactomes. PMID:21873645
Reactome pathway analysis to enrich biological discovery in proteomics data sets. PMID:21751369
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. PMID:21697123
Analysis of in vitro bioactivity data extracted from drug discovery literature and patents: Ranking 1654 human protein targets by assayed compounds and molecular scaffolds. PMID:21569515
mirConnX: condition-specific mRNA-microRNA network integrator. PMID:21558324
MAISTAS: a tool for automatic structural evaluation of alternative splicing products. PMID:21498402
Entrez Gene: gene-centered information at NCBI PubMed citations: 280.

280 articles citing: Entrez Gene: gene-centered information at NCBI

Deep neural network prediction of genome-wide transcriptome signatures - beyond the Black-box. PMID:35197482
Prediction of Novel Drug Targets and Vaccine Candidates against Human Lice (Insecta), Acari (Arachnida), and Their Associated Pathogens. PMID:35062669
CellMeSH: Probabilistic Cell-Type Identification Using Indexed Literature. PMID:34893819
An efficient chemical screening method for structure-based inhibitors to nucleic acid enzymes targeting the DNA repair-replication interface and SARS CoV-2. PMID:34776222
The genome of New Zealand trevally (Carangidae: Pseudocaranx georgianus) uncovers a XY sex determination locus. PMID:34727894
Curating COBRA Models of Microbial Metabolism. PMID:34719001
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. PMID:33929018
Differential gene expression data from the human central nervous system across Alzheimer's disease, Lewy body diseases, and the amyotrophic lateral sclerosis and frontotemporal dementia spectrum. PMID:33665258
Biomedical articles share annotations with their citation neighbors. PMID:33637047
Systematic review and meta-analysis of human transcriptomics reveals neuroinflammation, deficient energy metabolism, and proteostasis failure across neurodegeneration. PMID:33347974
PDmethDB: A curated Parkinson's disease associated methylation information database. PMID:33304468
Urinary vitronectin identifies patients with high levels of fibrosis in kidney grafts. PMID:33275196
Araport Lives: An Updated Framework for Arabidopsis Bioinformatics. PMID:32699173
Automated gene data integration with Databio. PMID:32238171
The Role of Secretory Pathways in Candida albicans Pathogenesis. PMID:32102426
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal. PMID:31713622
Dataset of the frequency patterns of publications annotated to human protein-coding genes, their protein products and genetic relevance. PMID:31453287
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. PMID:31317185
Integrating node embeddings and biological annotations for genes to predict disease-gene associations. PMID:30598097
Vesiclepedia 2019: a compendium of RNA, proteins, lipids and metabolites in extracellular vesicles. PMID:30395310
Genomic data integration systematically biases interactome mapping. PMID:30332399
RefEx, a reference gene expression dataset as a web tool for the functional analysis of genes. PMID:28850115
MOBAS: identification of disease-associated protein subnetworks using modularity-based scoring. PMID:28194175
Identifying Functional Cysteine Residues in the Mitochondria. PMID:28157297
Biomarker and competing endogenous RNA potential of tumor-specific long noncoding RNA in chromophobe renal cell carcinoma. PMID:27799788
Morphological and Transcriptomic Analysis of a Beetle Chemosensory System Reveals a Gnathal Olfactory Center. PMID:27751175
Combinatorial identification of DNA methylation patterns over age in the human brain. PMID:27663458
DenHunt - A Comprehensive Database of the Intricate Network of Dengue-Human Interactions. PMID:27618709
Histone Deacetylases and Their Inhibition in Candida Species. PMID:27547205
Gene-Disease Interaction Retrieval from Multiple Sources: A Network Based Method. PMID:27478829
High expression of orphan nuclear receptor NR4A1 in a subset of ovarian tumors with worse outcome. PMID:26946093
Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. PMID:26784240
Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data. PMID:26657508
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
PathwaysWeb: a gene pathways API with directional interactions, expanded gene ontology, and versioning. PMID:26400039
An integrated network platform for contextual prioritization of drugs and pathways. PMID:26315485
kpath: integration of metabolic pathway linked data. PMID:26055101
Identification of genomic features in the classification of loss- and gain-of-function mutation. PMID:26043747
Identification of agonists for a group of human odorant receptors. PMID:25784876
Protein interactome of muscle invasive bladder cancer. PMID:25569276
Immunoglobulins: 25 years of immunoinformatics and IMGT-ONTOLOGY. PMID:25521638
In silico prediction of physical protein interactions and characterization of interactome orphans. PMID:25402006
IMGT®, the international ImMunoGeneTics information system® 25 years on. PMID:25378316
GO2MSIG, an automated GO based multi-species gene set generator for gene set enrichment analysis. PMID:24884810
Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation. PMID:24865352
Pancreatic Cancer Database: an integrative resource for pancreatic cancer. PMID:24839966
Immunoglobulin and T Cell Receptor Genes: IMGT(®) and the Birth and Rise of Immunoinformatics. PMID:24600447
Loss of connectivity in cancer co-expression networks. PMID:24489837
Using semantic predications to uncover drug-drug interactions in clinical data. PMID:24448204
A guide to bioinformatics for immunologists. PMID:24363654
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. PMID:24335146
Exogenous administration of a recombinant variant of TWEAK impairs healing after myocardial infarction by aggravation of inflammation. PMID:24244389
Prediction of oncogenic interactions and cancer-related signaling networks based on network topology. PMID:24204854
PhenoTimer: software for the visual mapping of time-resolved phenotypic landscapes. PMID:23951317
An informatics approach to integrating genetic and neurological data in speech and language neuroscience. PMID:23949335
Systematic identification of DNA variants associated with ultraviolet radiation using a novel Geographic-Wide Association Study (GeoWAS). PMID:23786662
Information exploration system for sickle cell disease and repurposing of hydroxyfasudil. PMID:23762313
Cataloging the biomedical world of pain through semi-automated curation of molecular interactions. PMID:23707966
SSX2IP promotes metastasis and chemotherapeutic resistance of hepatocellular carcinoma. PMID:23452395
Gene selection and cancer type classification of diffuse large-B-cell lymphoma using a bivariate mixture model for two-species data. PMID:23289441
Vesiclepedia: a compendium for extracellular vesicles with continuous community annotation. PMID:23271954
Identifying stage-specific protein subnetworks for colorectal cancer. PMID:23173715
Using rule-based natural language processing to improve disease normalization in biomedical text. PMID:23043124
Detection of biomarkers for hepatocellular carcinoma using a hybrid univariate gene selection methods. PMID:22867264
HINT: High-quality protein interactomes and their applications in understanding human disease. PMID:22846459
A smoking-associated 7-gene signature for lung cancer diagnosis and prognosis. PMID:22825454
SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research. PMID:22807998
SigCS base: an integrated genetic information resource for human cerebral stroke. PMID:22784567
A simple method for analyzing exome sequencing data shows distinct levels of nonsynonymous variation for human immune and nervous system genes. PMID:22701602
The barley EST DNA Replication and Repair Database (bEST-DRRD) as a tool for the identification of the genes involved in DNA replication and repair. PMID:22697361
What Can Domesticated Genes Tell Us about the Intron Gain in Mammals? PMID:22693680
Biomine: predicting links between biological entities using network models of heterogeneous databases. PMID:22672646
IMGT-ONTOLOGY 2012. PMID:22654892
Context-specific protein network miner--an online system for exploring context-specific protein interaction networks from the literature. PMID:22493694
The transcription factor encyclopedia. PMID:22458515
Reducing false-positive prediction of minimotifs with a genetic interaction filter. PMID:22403687
Maximizing biomarker discovery by minimizing gene signatures. PMID:22369133
Identification of novel androgen-regulated pathways and mRNA isoforms through genome-wide exon-specific profiling of the LNCaP transcriptome. PMID:22194994
GenSensor Suite: A Web-Based Tool for the Analysis of Gene and Protein Interactions, Pathways, and Regulation. PMID:22194743
Assessment of NER solutions against the first and second CALBC Silver Standard Corpus. PMID:22166494
Extensive intron gain in the ancestor of placental mammals. PMID:22112745
Immune response and mitochondrial metabolism are commonly deregulated in DMD and aging skeletal muscle. PMID:22096509
PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update. PMID:22086960
Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks. PMID:22035267
Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles. PMID:22032172
Snat: a SNP annotation tool for bovine by integrating various sources of genomic information. PMID:21982513
Silencing of p130cas in ovarian carcinoma: a novel mechanism for tumor cell death. PMID:21957230
The UlaG protein family defines novel structural and functional motifs grafted on an ancient RNase fold. PMID:21943130
Bioinformatics and systems biology of the lipidome. PMID:21939287
In Silico discovery of transcription factors as potential diagnostic biomarkers of ovarian cancer. PMID:21923952
Immunome database for marsupials and monotremes. PMID:21854560
Domain-domain interactions underlying herpesvirus-human protein-protein interaction networks. PMID:21760902
Integrated bio-entity network: a system for biological knowledge discovery. PMID:21738677
The Strategies WDK: a graphical search interface and web development kit for functional genomics databases. PMID:21705364
DADA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization. PMID:21699738
Identification of robust hypoxia biomarker candidates from fin of medaka (Oryzias latipes). PMID:21664487
A compendium of canine normal tissue gene expression. PMID:21655323
Evolutionary plasticity of segmentation clock networks. PMID:21652651
Impact of exercise training on endothelial transcriptional profiles in healthy swine: a genome-wide microarray analysis. PMID:21622830
Transcriptional double-autorepression feedforward circuits act for multicellularity and nervous system development. PMID:21569329
TRAM (Transcriptome Mapper): database-driven creation and analysis of transcriptome maps from multiple sources. PMID:21333005
Annotating genes and genomes with DNA sequences extracted from biomedical articles. PMID:21325301
Dr. PIAS: an integrative system for assessing the druggability of protein-protein interactions. PMID:21303559
An ancient family of SelB elongation factor-like proteins with a broad but disjunct distribution across archaea. PMID:21255425
Thymic stromal lymphopoietin (TSLP) is associated with allergic rhinitis in children with asthma. PMID:21244681
A novel isoform of the 8p22 tumor suppressor gene DLC1 suppresses tumor growth and is frequently silenced in multiple common tumors. PMID:21217778
A machine learning approach for genome-wide prediction of morbid and druggable human genes based on systems-level data. PMID:21210975
The utility of mass spectrometry-based proteomic data for validation of novel alternative splice forms reconstructed from RNA-Seq data: a preliminary assessment. PMID:21172049
Cholera- and anthrax-like toxins are among several new ADP-ribosyltransferases. PMID:21170356
Genes and biological processes commonly disrupted in rare and heterogeneous developmental delay syndromes. PMID:21147756
Gerontome: a web-based database server for aging-related genes and analysis pipelines. PMID:21143804
Investigation gene and microRNA expression in glioblastoma. PMID:21143783
Integrated analysis of mutations, miRNA and mRNA expression in glioblastoma. PMID:21114830
Database resources of the National Center for Biotechnology Information. PMID:21097890
SPIKE: a database of highly curated human signaling pathways. PMID:21097778
Variants of the adenosine A(2A) receptor gene are protective against proliferative diabetic retinopathy in patients with type 1 diabetes. PMID:21088442
Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. PMID:21085120
Patterns of human gene expression variance show strong associations with signaling network hierarchy. PMID:21073694
miRTarBase: a database curates experimentally validated microRNA-target interactions. PMID:21071411
The mouse Gene Expression Database (GXD): 2011 update. PMID:21062809
Inference of surface membrane factors of HIV-1 infection through functional interaction networks. PMID:20967291
A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1. PMID:20959003
A computational tool for identifying minimotifs in protein-protein interactions and improving the accuracy of minimotif predictions. PMID:20938975
genenames.org: the HGNC resources in 2011. PMID:20929869
Finding new genes for non-syndromic hearing loss through an in silico prioritization study. PMID:20927407
DAnCER: disease-annotated chromatin epigenetics resource. PMID:20876685
Visual presentation as a welcome alternative to textual presentation of gene annotation information. PMID:20865558
TRIP Database: a manually curated database of protein-protein interactions for mammalian TRP channels. PMID:20851834
Use of data-biased random walks on graphs for the retrieval of context-specific networks from genomic data. PMID:20808879
Comparison study of microarray meta-analysis methods. PMID:20678237
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs. PMID:20624716
USP32 is an active, membrane-bound ubiquitin protease overexpressed in breast cancers. PMID:20549504
PhenoHM: human-mouse comparative phenome-genome server. PMID:20507906
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model. PMID:20487560
Screensaver: an open source lab information management system (LIMS) for high throughput screening facilities. PMID:20482787
A Large-scale genetic association study of esophageal adenocarcinoma risk. PMID:20453000
Detection of gene orthology from gene co-expression and protein interaction networks. PMID:20438654
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. PMID:20426874
Comprehensive mapping of the human kinome to epidermal growth factor receptor signaling. PMID:20421302
Systems pharmacology of arrhythmias. PMID:20407125
A common neuronal response to alphaherpesvirus infection. PMID:20401540
Signal pathways JNK and NF-kappaB, identified by global gene expression profiling, are involved in regulation of TNFalpha-induced mPGES-1 and COX-2 expression in gingival fibroblasts. PMID:20398340
Unconstrained mining of transcript data reveals increased alternative splicing complexity in the human transcriptome. PMID:20385588
Using pre-existing microarray datasets to increase experimental power: application to insulin resistance. PMID:20361040
Building and analyzing protein interactome networks by cross-species comparisons. PMID:20353594
Moara: a Java library for extracting and normalizing gene and protein mentions. PMID:20346105
Analytical approaches to RNA profiling data for the identification of genes enriched in specific cells. PMID:20308160
miRSel: automated extraction of associations between microRNAs and genes from the biomedical literature. PMID:20233441
A MOD(ern) perspective on literature curation. PMID:20221640
Detection and correction of false segmental duplications caused by genome mis-assembly. PMID:20219098
Genome-based expression profiling study of Hunner's ulcer type interstitial cystitis: an array of 40-gene model. PMID:20204322
Pathway Palette: a rich internet application for peptide-, protein- and network-oriented analysis of MS data. PMID:20198642
Post-transcriptional regulation of androgen receptor mRNA by an ErbB3 binding protein 1 in prostate cancer. PMID:20159994
The Homeodomain Resource: a comprehensive collection of sequence, structure, interaction, genomic and functional information on the homeodomain protein family. PMID:20157477
Automatic assignment of EC numbers. PMID:20126531
A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins. PMID:20047656
The aldehyde dehydrogenase gene superfamily resource center. PMID:20038501
PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium. PMID:20015972
Gevab: a prototype genome variation analysis browsing server. PMID:19958513
Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted. PMID:19948035
H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. PMID:19933760
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources. PMID:19919682
MeMotif: a database of linear motifs in alpha-helical transmembrane proteins. PMID:19910368
Database resources of the National Center for Biotechnology Information. PMID:19910364
Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes. PMID:19906700
IMGT/3Dstructure-DB and IMGT/DomainGapAlign: a database and a tool for immunoglobulins or antibodies, T cell receptors, MHC, IgSF and MhcSF. PMID:19900967
HHMD: the human histone modification database. PMID:19892823
UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. PMID:19880380
Automation of cDNA synthesis and labelling improves reproducibility. PMID:19841682
Proteomics analysis of A33 immunoaffinity-purified exosomes released from the human colon tumor cell line LIM1215 reveals a tissue-specific protein signature. PMID:19837982
STARNET 2: a web-based tool for accelerating discovery of gene regulatory networks using microarray co-expression data. PMID:19828039
BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum. PMID:19820115
Using a seed-network to query multiple large-scale gene expression datasets from the developing retina in order to identify and prioritize experimental targets. PMID:19812791
Enhancing navigation in biomedical databases by community voting and database-driven text classification. PMID:19799796
An editor for pathway drawing and data visualization in the Biopathways Workbench. PMID:19799790
Collection of Macaca fascicularis cDNAs derived from bone marrow, kidney, liver, pancreas, spleen, and thymus. PMID:19785770
EMAGE mouse embryo spatial gene expression database: 2010 update. PMID:19767607
Discovering cancer genes by integrating network and functional properties. PMID:19765316
Genome-based expression profiles study for the pathogenesis of pelvic organ prolapse: an array of 33 genes model. PMID:19756343
The Gene Wiki: community intelligence applied to human gene annotation. PMID:19755503
Evolutionary history of selenocysteine incorporation from the perspective of SECIS binding proteins. PMID:19744324
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. PMID:19728866
Assessing the druggability of protein-protein interactions by a supervised machine-learning method. PMID:19703312
Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PMID:19649302
Pathway databases and tools for their exploitation: benefits, current limitations and challenges. PMID:19638971
Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PMID:19557189
Forging links between human mental retardation-associated CNVs and mouse gene knockout models. PMID:19557186
Network Features and Pathway Analyses of a Signal Transduction Cascade. PMID:19543432
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. PMID:19498102
Gendoo: functional profiling of gene and disease features using MeSH vocabulary. PMID:19498079
VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology. PMID:19465394
Public databases and software for the pathway analysis of cancer genomes. PMID:19455256
Characterization of the prohormone complement in cattle using genomic libraries and cleavage prediction approaches. PMID:19445702
BioBIKE: a Web-based, programmable, integrated biological knowledge base. PMID:19433511
PAT proteins, an ancient family of lipid droplet proteins that regulate cellular lipid stores. PMID:19375517
The Human Gene Mutation Database: 2008 update. PMID:19348700
Homology modelling: a review about the method on hand of the diabetic antigen GAD 65 structure prediction. PMID:19343288
Comparison of gene expression profile in embryonic mesencephalon and neuronal primary cultures. PMID:19305503
Reconstruction of metabolic pathways for the cattle genome. PMID:19284618
Gene targeting in mouse embryonic stem cells. PMID:19266325
Identifying hypothetical genetic influences on complex disease phenotypes. PMID:19208188
Integrative disease classification based on cross-platform microarray data. PMID:19208125
Global versus local centrality in evolution of yeast protein network. PMID:19142681
Reconstruction of biochemical networks in microorganisms. PMID:19116616
Gene expression levels are a target of recent natural selection in the human genome. PMID:19091723
Identification and characterization of 3-iodothyronamine intracellular transport. PMID:19074582
Human Gene and Protein Database (HGPD): a novel database presenting a large quantity of experiment-based results in human proteomics. PMID:19073703
GeneDistiller--distilling candidate genes from linkage intervals. PMID:19057649
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. PMID:19033363
Cataloguing the HIV type 1 human protein interaction network. PMID:19025396
Identifying differential correlation in gene/pathway combinations. PMID:19017408
AS-ALPS: a database for analyzing the effects of alternative splicing on protein structure, interaction and network in human and mouse. PMID:19015123
A fast document classification algorithm for gene symbol disambiguation in the BITOLA literature-based discovery support system. PMID:18998999
G2Cdb: the Genes to Cognition database. PMID:18984621
IMGT, the international ImMunoGeneTics information system. PMID:18978023
Matching curated genome databases: a non trivial task. PMID:18950477
MDPD: an integrated genetic information resource for Parkinson's disease. PMID:18948286
RTPrimerDB: the portal for real-time PCR primers and probes. PMID:18948285
ConsensusPathDB--a database for integrating human functional interaction networks. PMID:18940869
Database resources of the National Center for Biotechnology Information. PMID:18940862
Evading the annotation bottleneck: using sequence similarity to search non-sequence gene data. PMID:18928517
NCBI Reference Sequences: current status, policy and new initiatives. PMID:18927115
BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. PMID:18925949
RAPID: Resource of Asian Primary Immunodeficiency Diseases. PMID:18842635
tRNADB-CE: tRNA gene database curated manually by experts. PMID:18842632
Concept recognition for extracting protein interaction relations from biomedical text. PMID:18834500
PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood. PMID:18832367
Modeling gene-by-environment interaction in comorbid depression with alcohol use disorders via an integrated bioinformatics approach. PMID:18822146
PharmGKB: an integrated resource of pharmacogenomic data and knowledge. PMID:18819074
Advanced genomic data mining. PMID:18818719
Database for exploration of functional context of genes implicated in ovarian cancer. PMID:18790805
Genome-wide linkage of cotinine pharmacokinetics suggests candidate regions on chromosomes 9 and 11. PMID:18785207
Translational integrity and continuity: personalized biomedical data integration. PMID:18760382
Duffy (Fy), DARC, and neutropenia among women from the United States, Europe and the Caribbean. PMID:18710383
Computational analysis of the human HSPH/HSPA/DNAJ family and cloning of a human HSPH/HSPA/DNAJ expression library. PMID:18686016
Meta-analysis of gene expression profiles in breast cancer: toward a unified understanding of breast cancer subtyping and prognosis signatures. PMID:18662380
Transmembrane protein oxygen content and compartmentalization of cells. PMID:18628944
T2D-Db: an integrated platform to study the molecular basis of Type 2 diabetes. PMID:18605991
TargetRNA: a tool for predicting targets of small RNA action in bacteria. PMID:18477632
IMGT, the International ImMunoGeneTics Information System for Immunoinformatics : methods for querying IMGT databases, tools, and web resources in the context of immunoinformatics. PMID:18463990
What everybody should know about the rat genome and its online resources. PMID:18443589
miRDB: a microRNA target prediction and functional annotation database with a wiki interface. PMID:18426918
Regulation of glycan structures in animal tissues: transcript profiling of glycan-related genes. PMID:18411279
Walking the interactome for prioritization of candidate disease genes. PMID:18371930
Prediction of human disease genes by human-mouse conserved coexpression analysis. PMID:18369433
A visual data mining tool that facilitates reconstruction of transcription regulatory networks. PMID:18320038
An open-source framework for large-scale, flexible evaluation of biomedical text mining systems. PMID:18230184
The strength of co-authorship in gene name disambiguation. PMID:18230174
RGST - Rat Gene Symbol Tracker, a database for defining official rat gene symbols. PMID:18215257
Gene characterization index: assessing the depth of gene annotation. PMID:18213364
Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity. PMID:18208606
Admixture mapping of white cell count: genetic locus responsible for lower white blood cell count in the Health ABC and Jackson Heart studies. PMID:18179887
Extending pathways based on gene lists using InterPro domain signatures. PMID:18177498
WHO-IUIS Nomenclature Subcommittee for immunoglobulins and T cell receptors report. PMID:18046549
Database resources of the National Center for Biotechnology Information. PMID:18045790
SIMAP--structuring the network of protein similarities. PMID:18037617
Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome. PMID:18021451
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. PMID:18006571
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes. PMID:17991680
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update. PMID:17986454
Xenbase: a Xenopus biology and genomics resource. PMID:17984085
The HGNC Database in 2008: a resource for the human genome. PMID:17984084
IDBD: infectious disease biomarker database. PMID:17982173
The full-ORF clone resource of the German cDNA Consortium. PMID:17974005
The Molecule Pages database. PMID:17965093
ChemBank: a small-molecule screening and cheminformatics resource database. PMID:17947324
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. PMID:17933782
MUGEN mouse database; animal models of human immunological diseases. PMID:17932065
Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata. PMID:17932051
Linking microarray reporters with protein functions. PMID:17897448
Bidirectional transcription of a novel chimeric gene mapping to mouse chromosome Yq. PMID:17892569
The Edinburgh human metabolic network reconstruction and its functional analysis. PMID:17882155
Organismal complexity, cell differentiation and gene expression: human over mouse. PMID:17881362
A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis. PMID:17709344
Inflammation and breast cancer. Inflammatory component of mammary carcinogenesis in ErbB2 transgenic mice. PMID:17705881
PepBank--a database of peptides based on sequence text mining and public peptide data sources. PMID:17678535
Histone deacetylases 1 and 2 redundantly regulate cardiac morphogenesis, growth, and contractility. PMID:17639084
ImmTree: database of evolutionary relationships of genes and proteins in the human immune system. PMID:17376226
Database resources of the National Center for Biotechnology Information. PMID:17170002
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. PMID:17130148
Gene: a gene-centered information resource at NCBI PubMed citations: 256.

256 articles citing: Gene: a gene-centered information resource at NCBI

Mechanosensitive Piezo channels mediate the physiological and pathophysiological changes in the respiratory system. PMID:35906615
GeneToList: A Web Application to Assist with Gene Identifiers for the Non-Bioinformatics-Savvy Scientist. PMID:35892968
Helicobacter pylori serology is associated with worse overall survival in patients with melanoma treated with immune checkpoint inhibitors. PMID:35832043
RPpocket: An RNA-Protein Intuitive Database with RNA Pocket Topology Resources. PMID:35805909
Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H2O2) Under Abiotic Stress Condition. PMID:35783965
RegEl corpus: identifying DNA regulatory elements in the scientific literature. PMID:35758881
Exploring automatic inconsistency detection for literature-based gene ontology annotation. PMID:35758780
TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer. PMID:35743803
Solute carrier family 2 members 1 and 2 as prognostic biomarkers in hepatocellular carcinoma associated with immune infiltration. PMID:35665115
A Network Pharmacology Analysis of Cytotoxic Triterpenes Isolated from Euphorbia abyssinica Latex Supported by Drug-likeness and ADMET Studies. PMID:35664578
Mechanism of Peitu Shengjin Formula Shenlingbaizhu Powder in Treating Bronchial Asthma and Allergic Colitis through Different Diseases with Simultaneous Treatment Based on Network Pharmacology and Molecular Docking. PMID:35586697
SigCom LINCS: data and metadata search engine for a million gene expression signatures. PMID:35524556
Inflammation-Related Genes Serve as Prognostic Biomarkers and Involve in Immunosuppressive Microenvironment to Promote Gastric Cancer Progression. PMID:35372408
Uncovering the Pharmacological Mechanisms of Gexia-Zhuyu Formula (GXZY) in Treating Liver Cirrhosis by an Integrative Pharmacology Strategy. PMID:35330838
Positively selected genes in the hoary bat (Lasiurus cinereus) lineage: prominence of thymus expression, immune and metabolic function, and regions of ancient synteny. PMID:35317076
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer. PMID:35303059
Biological mechanisms of aging predict age-related disease co-occurrence in patients. PMID:35259281
Multimodal reasoning based on knowledge graph embedding for specific diseases. PMID:35150235
Genome Nexus: A Comprehensive Resource for the Annotation and Interpretation of Genomic Variants in Cancer. PMID:35148171
A network pharmacology approach to predict potential targets and mechanisms of "Ramulus Cinnamomi (cassiae) - Paeonia lactiflora" herb pair in the treatment of chronic pain with comorbid anxiety and depression. PMID:35098831
Transmembrane Helices Are an Over-Presented and Evolutionarily Conserved Source of Major Histocompatibility Complex Class I and II Epitopes. PMID:35087515
Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT. PMID:34983371
Two-Component System Genes in Sorghum bicolor: Genome-Wide Identification and Expression Profiling in Response to Environmental Stresses. PMID:34899869
Improving QSAR Modeling for Predictive Toxicology using Publicly Aggregated Semantic Graph Data and Graph Neural Networks. PMID:34890148
RefSeq Functional Elements as experimentally assayed nongenic reference standards and functional interactions in human and mouse. PMID:34876495
Weighted Cox regression for the prediction of heterogeneous patient subgroups. PMID:34876106
Author-sourced capture of pathway knowledge in computable form using Biofactoid. PMID:34860157
The cytosolic iron-sulfur cluster assembly (CIA) pathway is required for replication stress tolerance of cancer cells to Chk1 and ATR inhibitors. PMID:34857765
The Aliment to Bodily Condition knowledgebase (ABCkb): a database connecting plants and human health. PMID:34838100
Epione application: An integrated web‑toolkit of clinical genomics and personalized medicine in systemic lupus erythematosus. PMID:34791504
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
Revelation of Pivotal Genes Pertinent to Alzheimer's Pathogenesis: A Methodical Evaluation of 32 GEO Datasets. PMID:34668150
Genetically altered animal models for ATP1A3-related disorders. PMID:34612482
CovPDB: a high-resolution coverage of the covalent protein-ligand interactome. PMID:34581813
RNALocate v2.0: an updated resource for RNA subcellular localization with increased coverage and annotation. PMID:34551440
ViMIC: a database of human disease-related virus mutations, integration sites and cis-effects. PMID:34500462
The Ascidia Ciona robusta Provides Novel Insights on the Evolution of the AP-1 Transcriptional Complex. PMID:34414189
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PMID:34395068
NetControl4BioMed: A web-based platform for controllability analysis of protein-protein interaction networks. PMID:34352070
Early-life social experience affects offspring DNA methylation and later life stress phenotype. PMID:34285226
The tweety Gene Family: From Embryo to Disease. PMID:34262434
Cell Proliferation and Apoptosis-Related Genes Affect the Development of Human Nasopharyngeal Carcinoma Through PI3K/AKT Signaling Pathway. PMID:34236626
Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry. PMID:34201152
A computational workflow for the detection of candidate diagnostic biomarkers of Kawasaki disease using time-series gene expression data. PMID:34136104
Revealing the Modular Similarities and Differences Among Alzheimer's Disease, Vascular Dementia, and Parkinson's Disease in Genomic Networks. PMID:34117614
Predicting anticancer hyperfoods with graph convolutional networks. PMID:34099048
Identification and Functional Annotation of Genes Related to Bone Stability in Laying Hens Using Random Forests. PMID:34066823
Investigation of the Multi-Target Mechanism of Guanxin-Shutong Capsule in Cerebrovascular Diseases: A Systems Pharmacology and Experimental Assessment. PMID:34054530
An Integrated Analysis of Network Pharmacology, Molecular Docking, and Experiment Validation to Explore the New Candidate Active Component and Mechanism of Cuscutae Semen-Mori Fructus Coupled-Herbs in Treating Oligoasthenozoospermia. PMID:34040346
Characterization and comparison of gene-centered human interactomes. PMID:34010955
PD-L1 Blockade During Allergen Sensitization Inhibits the Synthesis of Specific Antibodies and Decreases Mast Cell Activation in a Murine Model of Active Cutaneous Anaphylaxis. PMID:33968057
Updates to HCOP: the HGNC comparison of orthology predictions tool. PMID:33959747
Transcriptome Based Estrogen Related Genes Biomarkers for Diagnosis and Prognosis in Non-small Cell Lung Cancer. PMID:33936178
Demetra Application: An integrated genotype analysis web server for clinical genomics in endometriosis. PMID:33907838
Pathway analysis for genome-wide genetic variation data: Analytic principles, latest developments, and new opportunities. PMID:33896739
Proteomics of protein trafficking by in vivo tissue-specific labeling. PMID:33888706
GPCards: An integrated database of genotype-phenotype correlations in human genetic diseases. PMID:33868597
Easy Synthesis of Complex Biomolecular Assemblies: Wheat Germ Cell-Free Protein Expression in Structural Biology. PMID:33842544
Identification of MiR-93-5p Targeted Pathogenic Markers in Acute Myeloid Leukemia through Integrative Bioinformatics Analysis and Clinical Validation. PMID:33828590
A Network Pharmacology-Based Approach to Investigating the Mechanisms of Fushen Granule Effects on Intestinal Barrier Injury in Chronic Renal Failure. PMID:33747100
Exploration of natural red-shifted rhodopsins using a machine learning-based Bayesian experimental design. PMID:33742139
Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. PMID:33741065
Decoding the Mechanism of Huanglian Jiedu Decoction in Treating Pneumonia Based on Network Pharmacology and Molecular Docking. PMID:33681222
Prognostic Effect of Inflammatory Genes on Stage I-III Colorectal Cancer-Integrative Analysis of TCGA Data. PMID:33670198
Recent Advanced Technologies for the Characterization of Xenobiotic-Degrading Microorganisms and Microbial Communities. PMID:33644024
Network pharmacology integrated molecular docking reveals the bioactive components and potential targets of Morinda officinalis-Lycium barbarum coupled-herbs against oligoasthenozoospermia. PMID:33500463
A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses. PMID:33482803
Transcriptomic biomarkers for predicting response to neoadjuvant treatment in oesophageal cancer. PMID:33442473
Network machine learning maps phytochemically rich "Hyperfoods" to fight COVID-19. PMID:33386081
Exposure to extracellular vesicles from Pseudomonas aeruginosa result in loss of DNA methylation at enhancer and DNase hypersensitive site regions in lung macrophages. PMID:33380271
An Educational Bioinformatics Project to Improve Genome Annotation. PMID:33365016
Essential interpretations of bioinformatics in COVID-19 pandemic. PMID:33349792
Integration of the Drug-Gene Interaction Database (DGIdb 4.0) with open crowdsource efforts. PMID:33237278
Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung. PMID:33187194
Genenames.org: the HGNC and VGNC resources in 2021. PMID:33152070
Determination and Dissection of DNA-Binding Specificity for the Thermus thermophilus HB8 Transcriptional Regulator TTHB099. PMID:33114549
A Network Pharmacology Technique to Investigate the Synergistic Mechanisms of Salvia miltiorrhiza and Radix puerariae in Treatment of Cardio-Cerebral Vascular Diseases. PMID:33082828
A flexible, interpretable, and accurate approach for imputing the expression of unmeasured genes. PMID:33074331
The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals. PMID:33037820
Supplementation with Combined Lactobacillus helveticus R0052 and Bifidobacterium longum R0175 Across Development Reveals Sex Differences in Physiological and Behavioural Effects of Western Diet in Long-Evans Rats. PMID:33027912
StoneMod: a database for kidney stone modulatory proteins with experimental evidence. PMID:32934277
The Role of Chromosome X in Intraocular Pressure Variation and Sex-Specific Effects. PMID:32926103
PCOSKBR2: a database of genes, diseases, pathways, and networks associated with polycystic ovary syndrome. PMID:32895427
Development of Multiscale Transcriptional Regulatory Network in Esophageal Cancer Based on Integrated Analysis. PMID:32851080
Identification of DNA methylation patterns and biomarkers for clear-cell renal cell carcinoma by multi-omics data analysis. PMID:32832275
Sex-Specific Transcriptome Differences in Human Adipose Mesenchymal Stem Cells. PMID:32784482
Gliome database: a comprehensive web-based tool to access and analyze glia secretome data. PMID:32743661
Overview of PAX gene family: analysis of human tissue-specific variant expression and involvement in human disease. PMID:32728807
Comparative transcriptomics of primary cells in vertebrates. PMID:32718981
Leveraging the Comparative Toxicogenomics Database to Fill in Knowledge Gaps for Environmental Health: A Test Case for Air Pollution-induced Cardiovascular Disease. PMID:32663284
Underlying Mechanism of Insulin Resistance: A Bioinformatics Analysis Based on Validated Related-Genes from Public Disease Databases. PMID:32651353
GTDB: an integrated resource for glycosyltransferase sequences and annotations. PMID:32542364
Gene Ontology Curation of Neuroinflammation Biology Improves the Interpretation of Alzheimer's Disease Gene Expression Data. PMID:32417785
Bioinformatics Resources for Plant Abiotic Stress Responses: State of the Art and Opportunities in the Fast Evolving -Omics Era. PMID:32384671
The negative regulator SMAX1 controls mycorrhizal symbiosis and strigolactone biosynthesis in rice. PMID:32355217
The Predicted Key Molecules, Functions, and Pathways That Bridge Mild Cognitive Impairment (MCI) and Alzheimer's Disease (AD). PMID:32308643
Novel application of normalized pointwise mutual information (NPMI) to mine biomedical literature for gene sets associated with disease: use case in breast carcinogenesis. PMID:32274464
Transformation Foci in IDH1-mutated Gliomas Show STAT3 Phosphorylation and Downregulate the Metabolic Enzyme ETNPPL, a Negative Regulator of Glioma Growth. PMID:32218467
Predictive in silico binding algorithms reveal HLA specificities and autoallergen peptides associated with atopic dermatitis. PMID:32152724
Supervised learning is an accurate method for network-based gene classification. PMID:32129827
Nc2Eye: A Curated ncRNAomics Knowledgebase for Bridging Basic and Clinical Research in Eye Diseases. PMID:32117995
Predicting lncRNA-Protein Interactions With miRNAs as Mediators in a Heterogeneous Network Model. PMID:32038709
Comparison of the Transcriptome Response within the Swine Tracheobronchial Lymphnode Following Infection with PRRSV, PCV-2 or IAV-S. PMID:32033425
Identification of Platform-Independent Diagnostic Biomarker Panel for Hepatocellular Carcinoma Using Large-Scale Transcriptomics Data. PMID:31998366
Compartment and hub definitions tune metabolic networks for metabolomic interpretations. PMID:31972021
RNAInter in 2020: RNA interactome repository with increased coverage and annotation. PMID:31906603
A network pharmacology approach to reveal the protective mechanism of Salvia miltiorrhiza-Dalbergia odorifera coupled-herbs on coronary heart disease. PMID:31852981
The JAX Synteny Browser for mouse-human comparative genomics. PMID:31776723
PMBD: a Comprehensive Plastics Microbial Biodegradation Database. PMID:31738435
PCOSBase: a manually curated database of polycystic ovarian syndrome. PMID:31725861
A network pharmacology approach to explore active compounds and pharmacological mechanisms of epimedium for treatment of premature ovarian insufficiency. PMID:31692519
Gene4Denovo: an integrated database and analytic platform for de novo mutations in humans. PMID:31642496
Universal concept signature analysis: genome-wide quantification of new biological and pathological functions of genes and pathways. PMID:31631213
Hemimethylation Patterns in Breast Cancer Cell Lines. PMID:31496635
Progress in data interoperability to support computational toxicology and chemical safety evaluation. PMID:31404555
Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements. PMID:31379925
Network-Based Integrative Analysis of Genomics, Epigenomics and Transcriptomics in Autism Spectrum Disorders. PMID:31323926
Computational Drug Screening Identifies Compounds Targeting Renal Age-associated Molecular Profiles. PMID:31316728
Genome Sequences of Three Cluster C Mycobacteriophages, Bipolarisk, Bread, and FudgeTart. PMID:31296672
HyperFoods: Machine intelligent mapping of cancer-beating molecules in foods. PMID:31270435
Analysis of Genes Involved in Ulcerative Colitis Activity and Tumorigenesis Through Systematic Mining of Gene Co-expression Networks. PMID:31214045
Cancer adjuvant chemotherapy prediction model for non-small cell lung cancer. PMID:31170692
Investigating the dysfunctional pathogenesis of Wilms' tumor through a multidimensional integration strategy. PMID:31157257
HNCDB: An Integrated Gene and Drug Database for Head and Neck Cancer. PMID:31139565
The Plasmodium falciparum MESA erythrocyte cytoskeleton-binding (MEC) motif binds to erythrocyte ankyrin. PMID:31125575
BEERE: a web server for biomedical entity expansion, ranking and explorations. PMID:31114876
Genotify: Fast, lightweight gene lookup and summarization. PMID:31080942
A Network-guided Association Mapping Approach from DNA Methylation to Disease. PMID:30944378
Autophagy accounts for approximately one-third of mitochondrial protein turnover and is protein selective. PMID:30865561
A hybrid approach for automated mutation annotation of the extended human mutation landscape in scientific literature. PMID:30815103
SuCComBase: a manually curated repository of plant sulfur-containing compounds. PMID:30793170
A Network Pharmacology Approach for the Identification of Common Mechanisms of Drug-Induced Peripheral Neuropathy. PMID:30762308
A genome-wide association study identifies single nucleotide polymorphisms associated with time-to-metastasis in colorectal cancer. PMID:30738427
CircFunBase: a database for functional circular RNAs. PMID:30715276
NeuroMuscleDB: a Database of Genes Associated with Muscle Development, Neuromuscular Diseases, Ageing, and Neurodegeneration. PMID:30684219
Biological Interpretation of Complex Genomic Data. PMID:30649721
Computational characterization of the peptidome in transporter associated with antigen processing (TAP)-deficient cells. PMID:30645615
Cell Wall Synthesis, Development of Hyphae and Metabolic Pathways Are Processes Potentially Regulated by MicroRNAs Produced Between the Morphological Stages of Paracoccidioides brasiliensis. PMID:30619144
Abscopal Effect in Non-injected Tumors Achieved with Cytokine-Armed Oncolytic Adenovirus. PMID:30569015
Large-scale genome-wide meta-analysis of polycystic ovary syndrome suggests shared genetic architecture for different diagnosis criteria. PMID:30566500
Embracing the Dark Side: Computational Approaches to Unveil the Functionality of Genes Lacking Biological Annotation in Drug-Induced Liver Injury. PMID:30515189
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer's Disease Data. PMID:30501127
SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping. PMID:30380087
PubChem 2019 update: improved access to chemical data. PMID:30371825
3D Network exploration and visualisation for lifespan data. PMID:30352578
PopHumanScan: the online catalog of human genome adaptation. PMID:30335169
IRS-1 genetic polymorphism (r.2963G>A) in type 2 diabetes mellitus patients associated with insulin resistance. PMID:30319284
Genenames.org: the HGNC and VGNC resources in 2019. PMID:30304474
Integrated systems analysis reveals conserved gene networks underlying response to spinal cord injury. PMID:30277459
Glucocerebrosidase deficiency promotes protein aggregation through dysregulation of extracellular vesicles. PMID:30256786
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. PMID:30239666
coTRaCTE predicts co-occurring transcription factors within cell-type specific enhancers. PMID:30142147
The impact of genome-wide association studies on biomedical research publications. PMID:30103832
A network map of netrin receptor UNC5B-mediated signaling. PMID:30084000
MiRNA-BD: an evidence-based bioinformatics model and software tool for microRNA biomarker discovery. PMID:30081733
Reconstructing phosphorylation signalling networks from quantitative phosphoproteomic data. PMID:30072490
ADReCS-Target: target profiles for aiding drug safety research and application. PMID:30053268
CIGene: a literature-based online resource for cancer initiation genes. PMID:30045691
A Computational Systems Pharmacology Approach to Investigate Molecular Mechanisms of Herbal Formula Tian-Ma-Gou-Teng-Yin for Treatment of Alzheimer's Disease. PMID:29997503
LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs. PMID:29961817
Associations of single nucleotide polymorphisms with mucinous colorectal cancer: genome-wide common variant and gene-based rare variant analyses. PMID:29942513
Bacterial Diversity and Nitrogen Utilization Strategies in the Upper Layer of the Northwestern Pacific Ocean. PMID:29922238
iMusta4SLC: Database for the structural property and variations of solute carrier transporters. PMID:29892515
Expanding the horizons of microRNA bioinformatics. PMID:29871895
Sex-Specific Transcriptome Differences in Substantia Nigra Tissue: A Meta-Analysis of Parkinson's Disease Data. PMID:29799491
Systematic interrogation of diverse Omic data reveals interpretable, robust, and generalizable transcriptomic features of clinically successful therapeutic targets. PMID:29782487
TelNet - a database for human and yeast genes involved in telomere maintenance. PMID:29776332
Thymoquinone increases the expression of neuroprotective proteins while decreasing the expression of pro-inflammatory cytokines and the gene expression NFκB pathway signaling targets in LPS/IFNγ -activated BV-2 microglia cells. PMID:29759145
Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PMID:29590108
A multi-trait Bayesian method for mapping QTL and genomic prediction. PMID:29571285
Spatiotemporal compartmentalization of hepatic NADH and NADPH metabolism. PMID:29514978
Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen. PMID:29491419
Improving Interpretation of Cardiac Phenotypes and Enhancing Discovery With Expanded Knowledge in the Gene Ontology. PMID:29440116
A Genome-Wide Association Study and Complex Network Identify Four Core Hub Genes in Bipolar Disorder. PMID:29257106
Coalitional game theory as a promising approach to identify candidate autism genes. PMID:29218903
ATTED-II in 2018: A Plant Coexpression Database Based on Investigation of the Statistical Property of the Mutual Rank Index. PMID:29216398
DGIdb 3.0: a redesign and expansion of the drug-gene interaction database. PMID:29156001
VarCards: an integrated genetic and clinical database for coding variants in the human genome. PMID:29112736
PI3K and Inhibitor of Apoptosis Proteins Modulate Gentamicin- Induced Hair Cell Death in the Zebrafish Lateral Line. PMID:29093665
Network Diffusion-Based Prioritization of Autism Risk Genes Identifies Significantly Connected Gene Modules. PMID:28993790
AAgMarker 1.0: a resource of serological autoantigen biomarkers for clinical diagnosis and prognosis of various human diseases. PMID:28977551
dbCoRC: a database of core transcriptional regulatory circuitries modeled by H3K27ac ChIP-seq signals. PMID:28977473
SWI/SNF Infobase-An exclusive information portal for SWI/SNF remodeling complex subunits. PMID:28961249
An integrated expression atlas of miRNAs and their promoters in human and mouse. PMID:28829439
Root-Knot and Cyst Nematodes Activate Procambium-Associated Genes in Arabidopsis Roots. PMID:28747918
Knowledge base and mini-expert platform for the diagnosis of inborn errors of metabolism. PMID:28726811
MINERVA-a platform for visualization and curation of molecular interaction networks. PMID:28725475
CrossCheck: an open-source web tool for high-throughput screen data analysis. PMID:28724888
Transcriptome of interstitial cells of Cajal reveals unique and selective gene signatures. PMID:28426719
The elusive MAESTRO gene: Its human reproductive tissue-specific expression pattern. PMID:28406912
A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data. PMID:28321234
GEAR: A database of Genomic Elements Associated with drug Resistance. PMID:28294141
HRGFish: A database of hypoxia responsive genes in fishes. PMID:28205556
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. PMID:28025337
PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. PMID:27924042
AAgAtlas 1.0: a human autoantigen database. PMID:27924021
KBG syndrome involving a single-nucleotide duplication in ANKRD11. PMID:27900361
SCN8A mutation in a child presenting with seizures and developmental delays. PMID:27900360
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs. PMID:27899580
A scored human protein-protein interaction network to catalyze genomic interpretation. PMID:27892958
A New Chicken Genome Assembly Provides Insight into Avian Genome Structure. PMID:27852011
Genenames.org: the HGNC and VGNC resources in 2017. PMID:27799471
Systems genetics analysis of pharmacogenomics variation during antidepressant treatment. PMID:27752142
Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules. PMID:27731320
Meta-Analysis of Parkinson's Disease Transcriptome Data Using TRAM Software: Whole Substantia Nigra Tissue and Single Dopamine Neuron Differential Gene Expression. PMID:27611585
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). PMID:27554092
Family-based exome-wide assessment of maternal genetic effects on susceptibility to childhood B-cell acute lymphoblastic leukemia in hispanics. PMID:27529658
DTMiner: identification of potential disease targets through biomedical literature mining. PMID:27506226
A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes. PMID:27477450
Subfunctionalization of peroxisome proliferator response elements accounts for retention of duplicated fabp1 genes in zebrafish. PMID:27421266
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia. PMID:27355630
QuIN: A Web Server for Querying and Visualizing Chromatin Interaction Networks. PMID:27336171
Molecular and genetic inflammation networks in major human diseases. PMID:27303926
Bioinformatics resources for pollen. PMID:27271281
Systematic analysis of the molecular mechanism underlying atherosclerosis using a text mining approach. PMID:27251057
Generating Gene Ontology-Disease Inferences to Explore Mechanisms of Human Disease at the Comparative Toxicogenomics Database. PMID:27171405
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. PMID:27161010
Synteny Portal: a web-based application portal for synteny block analysis. PMID:27154270
High-performance web services for querying gene and variant annotation. PMID:27154141
Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. PMID:27141961
GCGene: a gene resource for gastric cancer with literature evidence. PMID:27127885
g:Profiler-a web server for functional interpretation of gene lists (2016 update). PMID:27098042
Whole-exome sequencing in obsessive-compulsive disorder identifies rare mutations in immunological and neurodevelopmental pathways. PMID:27023170
REGene: a literature-based knowledgebase of animal regeneration that bridge tissue regeneration and cancer. PMID:26975833
Copy Number Variants Associated with 14 Cases of Self-Injurious Behavior. PMID:26933844
Cell type-specific properties and environment shape tissue specificity of cancer genes. PMID:26856619
The clinical trial landscape in oncology and connectivity of somatic mutational profiles to targeted therapies. PMID:26772741
Integrating 400 million variants from 80,000 human samples with extensive annotations: towards a knowledge base to analyze disease cohorts. PMID:26746786
Derivation of consensus inactivation status for X-linked genes from genome-wide studies. PMID:26719789
ECGene: A Literature-Based Knowledgebase of Endometrial Cancer Genes. PMID:26699919
Human RNase L tunes gene expression by selectively destabilizing the microRNA-regulated transcriptome. PMID:26668391
Database resources of the National Center for Biotechnology Information. PMID:26615191
Lynx: a knowledge base and an analytical workbench for integrative medicine. PMID:26590263
Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank. PMID:26581719
SEA: a super-enhancer archive. PMID:26578594
PCOSKB: A KnowledgeBase on genes, diseases, ontology terms and biochemical pathways associated with PolyCystic Ovary Syndrome. PMID:26578565
Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine. PMID:26578564
GEneSTATION 1.0: a synthetic resource of diverse evolutionary and functional genomic data for studying the evolution of pregnancy-associated tissues and phenotypes. PMID:26567549
Next-generation diagnostics and disease-gene discovery with the Exomiser. PMID:26562621
PharmDB-K: Integrated Bio-Pharmacological Network Database for Traditional Korean Medicine. PMID:26555441
The Degradome database: expanding roles of mammalian proteases in life and disease. PMID:26553809
ATTED-II in 2016: A Plant Coexpression Database Towards Lineage-Specific Coexpression. PMID:26546318
DGIdb 2.0: mining clinically relevant drug-gene interactions. PMID:26531824
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
CauloBrowser: A systems biology resource for Caulobacter crescentus. PMID:26476443
MitoCarta2.0: an updated inventory of mammalian mitochondrial proteins. PMID:26450961
Distilling a Visual Network of Retinitis Pigmentosa Gene-Protein Interactions to Uncover New Disease Candidates. PMID:26267445
Systematic Analysis of the Molecular Mechanism Underlying Decidualization Using a Text Mining Approach. PMID:26222155
Mouse genome annotation by the RefSeq project. PMID:26215545
A unified gene catalog for the laboratory mouse reference genome. PMID:26084703
PAGER: constructing PAGs and new PAG-PAG relationships for network biology. PMID:26072489
Database resources of the National Center for Biotechnology Information. PMID:25398906
HIV-1, human interaction database: current status and new features. PMID:25378338
http://dx.doi.org/10.1093/nar/gku1055

Tags:

Tags
More detailed information about this field from each metasource.

chromosome
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

dna sequence data
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

deoxyribonucleic acid
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene expression
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

gene expression data
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

genome
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

homologous
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

molecular structure
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

organelle
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

phenotype
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

plasmid
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

protein
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

structure
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

transcript
metasource: Fairsharing.org
version: FAIRsharing.org: NCBI Gene; NCBI Gene; DOI: https://doi.org/10.25504/FAIRsharing.5h3maw; Last edited: March 1, 2021, 4:56 p.m.; Last accessed: Jan 03 2022 7:06 p.m.

nucleotide sequence databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

coding and non-coding dna
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657

dna
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

rna
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

bacteria
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

genes
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

genetics
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

genomics
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

proteins
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

sequence analysis
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

taxonomy
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

viruses
metasource: re3data.org
version: re3data.org: NCBI Gene; editing status 2021-12-20; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3603S last accessed: 2022-11-04

molecular interactions, pathways and networks
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

model organisms
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

gene transcripts
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

mapping
metasource: bio.tools
version: extracted_at: 2022-11-04T11:27:06.364802

chromosome dna sequences dna gene gene expression gene expression genome homologous molecular structure organelle phenotype plasmid protein structure transcript nucleic acid sequence coding and non-coding dna dna rna bacteria gene genetics genomics proteins sequence analysis taxonomy viruses molecular interactions, pathways and networks model organisms gene transcripts mapping

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