The Gene Ontology (GO) project in 2006.

The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol (2007) 35.41

The human disease network. Proc Natl Acad Sci U S A (2007) 19.58

IntAct--open source resource for molecular interaction data. Nucleic Acids Res (2006) 13.82

The UCSC genome browser database: update 2007. Nucleic Acids Res (2006) 13.04

The Gene Ontology project in 2008. Nucleic Acids Res (2007) 11.71

SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80

Gene Ontology annotations at SGD: new data sources and annotation methods. Nucleic Acids Res (2007) 9.03

PANTHER version 6: protein sequence and function evolution data with expanded representation of biological pathways. Nucleic Acids Res (2006) 6.20

Gene--environment-wide association studies: emerging approaches. Nat Rev Genet (2010) 6.10

Bio-ontologies: current trends and future directions. Brief Bioinform (2006) 5.96

Framework for a protein ontology. BMC Bioinformatics (2007) 5.24

ChemBank: a small-molecule screening and cheminformatics resource database. Nucleic Acids Res (2007) 5.10

miRGen: a database for the study of animal microRNA genomic organization and function. Nucleic Acids Res (2006) 4.91

Gramene: a growing plant comparative genomics resource. Nucleic Acids Res (2007) 4.59

The mouse genome database (MGD): new features facilitating a model system. Nucleic Acids Res (2006) 4.52

SUBA: the Arabidopsis Subcellular Database. Nucleic Acids Res (2006) 3.63

The mouse Gene Expression Database (GXD): 2007 update. Nucleic Acids Res (2006) 3.30

T1DBase: integration and presentation of complex data for type 1 diabetes research. Nucleic Acids Res (2006) 3.25

BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res (2007) 2.94

AgBase: a unified resource for functional analysis in agriculture. Nucleic Acids Res (2006) 2.92

Gene Ontology annotations: what they mean and where they come from. BMC Bioinformatics (2008) 2.84

The TIGR Plant Transcript Assemblies database. Nucleic Acids Res (2006) 2.62

COPI complex is a regulator of lipid homeostasis. PLoS Biol (2008) 2.47

Epigenetic activation of a subset of mRNAs by eIF4E explains its effects on cell proliferation. PLoS One (2007) 2.35

Molecular clustering identifies complement and endothelin induction as early events in a mouse model of glaucoma. J Clin Invest (2011) 2.25

Computational approaches for detecting protein complexes from protein interaction networks: a survey. BMC Genomics (2010) 2.19

modMine: flexible access to modENCODE data. Nucleic Acids Res (2011) 2.18

Genome-wide mapping and analysis of active promoters in mouse embryonic stem cells and adult organs. Genome Res (2007) 2.16

The plant structure ontology, a unified vocabulary of anatomy and morphology of a flowering plant. Plant Physiol (2006) 2.03

The Molecular Biology Database Collection: 2007 update. Nucleic Acids Res (2006) 2.03

GO PaD: the Gene Ontology Partition Database. Nucleic Acids Res (2006) 1.98

GeneTools--application for functional annotation and statistical hypothesis testing. BMC Bioinformatics (2006) 1.96

Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. Mol Cell (2008) 1.93

Unraveling protein networks with power graph analysis. PLoS Comput Biol (2008) 1.77

MINT and IntAct contribute to the Second BioCreative challenge: serving the text-mining community with high quality molecular interaction data. Genome Biol (2008) 1.76

FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res (2007) 1.75

Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol (2007) 1.69

ButterflyBase: a platform for lepidopteran genomics. Nucleic Acids Res (2007) 1.65

Network analysis of FDA approved drugs and their targets. Mt Sinai J Med (2007) 1.65

PhenomicDB: a new cross-species genotype/phenotype resource. Nucleic Acids Res (2006) 1.65

SLiMDisc: short, linear motif discovery, correcting for common evolutionary descent. Nucleic Acids Res (2006) 1.61

Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res (2009) 1.60

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57

An improved ontological representation of dendritic cells as a paradigm for all cell types. BMC Bioinformatics (2009) 1.56

Large-scale analysis of yeast filamentous growth by systematic gene disruption and overexpression. Mol Biol Cell (2007) 1.55

Identifying disease-specific genes based on their topological significance in protein networks. BMC Syst Biol (2009) 1.54

A realism-based approach to the evolution of biomedical ontologies. AMIA Annu Symp Proc (2006) 1.53

MetaCrop: a detailed database of crop plant metabolism. Nucleic Acids Res (2007) 1.53

3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res (2008) 1.51

SSWAP: A Simple Semantic Web Architecture and Protocol for semantic web services. BMC Bioinformatics (2009) 1.49

SPODOBASE: an EST database for the lepidopteran crop pest Spodoptera. BMC Bioinformatics (2006) 1.48

Mice expressing BMPR2R899X transgene in smooth muscle develop pulmonary vascular lesions. Am J Physiol Lung Cell Mol Physiol (2008) 1.47

Inter- and intra-combinatorial regulation by transcription factors and microRNAs. BMC Genomics (2007) 1.45

Mapping proteins to disease terminologies: from UniProt to MeSH. BMC Bioinformatics (2008) 1.45

Radiation treatment inhibits monocyte entry into the optic nerve head and prevents neuronal damage in a mouse model of glaucoma. J Clin Invest (2012) 1.44

Semantic integration to identify overlapping functional modules in protein interaction networks. BMC Bioinformatics (2007) 1.43

What we can learn about Escherichia coli through application of Gene Ontology. Trends Microbiol (2009) 1.40

Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae. BMC Microbiol (2009) 1.39

Essential role of pre-B-cell colony enhancing factor in ventilator-induced lung injury. Am J Respir Crit Care Med (2008) 1.38

Gene expression in BMPR2 mutation carriers with and without evidence of pulmonary arterial hypertension suggests pathways relevant to disease penetrance. BMC Med Genomics (2008) 1.37

Integrating protein-protein interactions and text mining for protein function prediction. BMC Bioinformatics (2008) 1.36

Automated recognition of malignancy mentions in biomedical literature. BMC Bioinformatics (2006) 1.36

A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies. Proc Natl Acad Sci U S A (2007) 1.34

Functional protein divergence in the evolution of Homo sapiens. Genome Biol (2008) 1.32

An anatomy ontology to represent biological knowledge in Dictyostelium discoideum. BMC Genomics (2008) 1.32

Gene expression in the prefrontal cortex during adolescence: implications for the onset of schizophrenia. BMC Med Genomics (2009) 1.31

Fibrotic myofibroblasts manifest genome-wide derangements of translational control. PLoS One (2008) 1.30

A transversal approach to predict gene product networks from ontology-based similarity. BMC Bioinformatics (2007) 1.29

An annotated cDNA library and microarray for large-scale gene-expression studies in the ant Solenopsis invicta. Genome Biol (2007) 1.22

Onset of lactation in the bovine mammary gland: gene expression profiling indicates a strong inhibition of gene expression in cell proliferation. Funct Integr Genomics (2008) 1.21

Computational analysis of biological functions and pathways collectively targeted by co-expressed microRNAs in cancer. BMC Bioinformatics (2007) 1.21

Selective sweeps reveal candidate genes for adaptation to drought and salt tolerance in common sunflower, Helianthus annuus. Genetics (2007) 1.21

WildSilkbase: an EST database of wild silkmoths. BMC Genomics (2008) 1.21

Global profiling of co- and post-translationally N-myristoylated proteomes in human cells. Nat Commun (2014) 1.19

Non-muscle myosin light chain kinase isoform is a viable molecular target in acute inflammatory lung injury. Am J Respir Cell Mol Biol (2010) 1.19

Ontological evaluation of transcriptional differences between sperm of infertile males and fertile donors using microarray analysis. J Assist Reprod Genet (2010) 1.18

Cloud-based uniform ChIP-Seq processing tools for modENCODE and ENCODE. BMC Genomics (2013) 1.18

Automated discovery of functional generality of human gene expression programs. PLoS Comput Biol (2007) 1.18

Applying negative rule mining to improve genome annotation. BMC Bioinformatics (2007) 1.18

A predictive model of the oxygen and heme regulatory network in yeast. PLoS Comput Biol (2008) 1.18

The SLiMDisc server: short, linear motif discovery in proteins. Nucleic Acids Res (2007) 1.16

BioPortal as a Dataset of Linked Biomedical Ontologies and Terminologies in RDF. Semant Web (2013) 1.16

The Pathway Less Traveled: Moving from Candidate Genes to Candidate Pathways in the Analysis of Genome-Wide Data from Large Scale Pharmacogenetic Association Studies. Curr Pharmacogenomics Person Med (2008) 1.16

Preparation and analysis of an expressed sequence tag library from the toxic dinoflagellate Alexandrium catenella. Mar Biotechnol (NY) (2008) 1.13

Gene expression profiles of the NCI-60 human tumor cell lines define molecular interaction networks governing cell migration processes. PLoS One (2012) 1.13

A Large-scale genetic association study of esophageal adenocarcinoma risk. Carcinogenesis (2010) 1.12

The Innate Immune Database (IIDB). BMC Immunol (2008) 1.11

A systematic search for positive selection in higher plants (Embryophytes). BMC Plant Biol (2006) 1.10

Comparative transcriptome analysis of Arabidopsis thaliana infested by diamond back moth (Plutella xylostella) larvae reveals signatures of stress response, secondary metabolism, and signalling. BMC Genomics (2008) 1.10

Murine lung responses to ambient particulate matter: genomic analysis and influence on airway hyperresponsiveness. Environ Health Perspect (2008) 1.09

Signal transduction-related responses to phytohormones and environmental challenges in sugarcane. BMC Genomics (2007) 1.09

Murine pulmonary response to chronic hypoxia is strain specific. Exp Lung Res (2008) 1.09

Immunological profiles of Bos taurus and Bos indicus cattle infested with the cattle tick, Rhipicephalus (Boophilus) microplus. Clin Vaccine Immunol (2009) 1.09

Identification of novel regulatory modules in dicotyledonous plants using expression data and comparative genomics. Genome Biol (2006) 1.08

RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics (2011) 1.08

New metrics for comparative genomics. Curr Opin Biotechnol (2006) 1.08

TomatEST database: in silico exploitation of EST data to explore expression patterns in tomato species. Nucleic Acids Res (2006) 1.07

GeneSpeed: protein domain organization of the transcriptome. Nucleic Acids Res (2006) 1.07

Common genetic variation in the sex hormone metabolic pathway and endometrial cancer risk: pathway-based evaluation of candidate genes. Carcinogenesis (2010) 1.07

Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res (2007) 1.06

Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet (2000) 336.52

Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19

Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73

The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37

The Unified Medical Language System (UMLS): integrating biomedical terminology. Nucleic Acids Res (2004) 25.99

GoMiner: a resource for biological interpretation of genomic and proteomic data. Genome Biol (2003) 22.63

Ontological analysis of gene expression data: current tools, limitations, and open problems. Bioinformatics (2005) 22.22

Relations in biomedical ontologies. Genome Biol (2005) 22.07

Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05

GenBank. Nucleic Acids Res (2005) 19.25

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res (2004) 18.75

The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol (2005) 18.20

Textpresso: an ontology-based information retrieval and extraction system for biological literature. PLoS Biol (2004) 15.72

Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC Bioinformatics (2005) 14.50

High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics (2005) 14.02

Ontology-based knowledge representation for bioinformatics. Brief Bioinform (2000) 11.63

A methodology to migrate the gene ontology to a description logic environment using DAML+OIL. Pac Symp Biocomput (2003) 7.04

An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics (2005) 6.58

Association of genes to genetically inherited diseases using data mining. Nat Genet (2002) 5.78

Obol: integrating language and meaning in bio-ontologies. Comp Funct Genomics (2004) 5.53

Knowledge acquisition, consistency checking and concurrency control for Gene Ontology (GO). Bioinformatics (2003) 3.97

Predicting gene function from patterns of annotation. Genome Res (2003) 3.55

Ontologies for molecular biology and bioinformatics. In Silico Biol (2002) 2.93

Gene Ontology: looking backwards and forwards. Genome Biol (2004) 2.83

Sequence ontology annotation guide. Comp Funct Genomics (2004) 2.77

An ontology for collaborative construction and analysis of cellular pathways. Bioinformatics (2004) 2.66

A procedure for assessing GO annotation consistency. Bioinformatics (2005) 2.11

The MGED ontology: a framework for describing functional genomics experiments. Comp Funct Genomics (2003) 1.92

Mapping the gene ontology into the unified medical language system. Comp Funct Genomics (2004) 1.68

Bringing ontology to the gene ontology. Comp Funct Genomics (2003) 1.57

Building ontologies in DAML + OIL. Comp Funct Genomics (2003) 1.25

Creating the gene ontology resource: design and implementation. Genome Res (2001) 55.73

The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res (2004) 54.37

The Gene Ontology project in 2008. Nucleic Acids Res (2007) 11.71

The Gene Ontology in 2010: extensions and refinements. Nucleic Acids Res (2009) 11.49

Gene Ontology Consortium: going forward. Nucleic Acids Res (2014) 7.76

Gene Ontology annotations and resources. Nucleic Acids Res (2012) 6.13

The Gene Ontology: enhancements for 2011. Nucleic Acids Res (2011) 5.82

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol (2012) 1.65