BIND: the Biomolecular Interaction Network Database.

The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67

SNPs3D: candidate gene and SNP selection for association studies. BMC Bioinformatics (2006) 21.54

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

The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46

Scansite 2.0: Proteome-wide prediction of cell signaling interactions using short sequence motifs. Nucleic Acids Res (2003) 15.74

IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02

Taverna: a tool for building and running workflows of services. Nucleic Acids Res (2006) 14.90

Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36

The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res (2005) 12.94

STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44

The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19

MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res (2006) 7.75

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res (2009) 7.34

Functional atlas of the integrin adhesome. Nat Cell Biol (2007) 6.89

ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86

Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet (2011) 6.20

iRefIndex: a consolidated protein interaction database with provenance. BMC Bioinformatics (2008) 5.77

Protein networks in disease. Genome Res (2008) 5.65

The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae. J Biol (2006) 5.57

An experimentally derived confidence score for binary protein-protein interactions. Nat Methods (2008) 5.27

Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26

Network-based global inference of human disease genes. Mol Syst Biol (2008) 5.01

Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics (2004) 4.97

RNA interference screen for human genes associated with West Nile virus infection. Nature (2008) 4.93

The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res (2005) 4.90

CORUM: the comprehensive resource of mammalian protein complexes--2009. Nucleic Acids Res (2009) 4.71

Web services at the European bioinformatics institute. Nucleic Acids Res (2007) 4.48

Advancing translational research with the Semantic Web. BMC Bioinformatics (2007) 4.38

Literature-curated protein interaction datasets. Nat Methods (2009) 4.21

A proteome-scale map of the human interactome network. Cell (2014) 3.91

Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79

HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics (2005) 3.75

MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res (2006) 3.68

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res (2007) 3.68

Genomic analysis of the hierarchical structure of regulatory networks. Proc Natl Acad Sci U S A (2006) 3.51

Epstein-Barr virus and virus human protein interaction maps. Proc Natl Acad Sci U S A (2007) 3.50

Stratus not altocumulus: a new view of the yeast protein interaction network. PLoS Biol (2006) 3.44

Genes2Networks: connecting lists of gene symbols using mammalian protein interactions databases. BMC Bioinformatics (2007) 3.44

The aMAZE LightBench: a web interface to a relational database of cellular processes. Nucleic Acids Res (2004) 3.39

L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol (2005) 3.27

CORUM: the comprehensive resource of mammalian protein complexes. Nucleic Acids Res (2007) 3.23

Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol (2009) 3.03

Disease candidate gene identification and prioritization using protein interaction networks. BMC Bioinformatics (2009) 3.03

Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A (2004) 2.93

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers. Mol Syst Biol (2010) 2.92

Hepatitis C virus infection protein network. Mol Syst Biol (2008) 2.91

VisANT: an online visualization and analysis tool for biological interaction data. BMC Bioinformatics (2004) 2.88

VisANT: an integrative framework for networks in systems biology. Brief Bioinform (2008) 2.85

Michigan Molecular Interactions (MiMI): putting the jigsaw puzzle together. Nucleic Acids Res (2006) 2.77

The Rat Genome Database (RGD): developments towards a phenome database. Nucleic Acids Res (2005) 2.77

Mutation of SHOC2 promotes aberrant protein N-myristoylation and causes Noonan-like syndrome with loose anagen hair. Nat Genet (2009) 2.57

Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks. BMC Bioinformatics (2006) 2.57

Improved human disease candidate gene prioritization using mouse phenotype. BMC Bioinformatics (2007) 2.56

Atlas - a data warehouse for integrative bioinformatics. BMC Bioinformatics (2005) 2.51

Regulators of cyclin-dependent kinases are crucial for maintaining genome integrity in S phase. J Cell Biol (2010) 2.43

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43

Global networks of functional coupling in eukaryotes from comprehensive data integration. Genome Res (2009) 2.43

A predicted interactome for Arabidopsis. Plant Physiol (2007) 2.41

Chapter 2: Data-driven view of disease biology. PLoS Comput Biol (2012) 2.40

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto. Bioinformatics (2009) 2.34

Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics (2008) 2.32

Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res (2006) 2.30

HIPPIE: Integrating protein interaction networks with experiment based quality scores. PLoS One (2012) 2.17

Scaffolds: interaction platforms for cellular signalling circuits. Trends Cell Biol (2009) 2.15

Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res (2008) 2.09

The use of edge-betweenness clustering to investigate biological function in protein interaction networks. BMC Bioinformatics (2005) 1.97

Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts. PLoS Comput Biol (2009) 1.90

VirtualPlant: a software platform to support systems biology research. Plant Physiol (2009) 1.88

Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces using PRISM. Nat Protoc (2011) 1.84

Design logic of a cannabinoid receptor signaling network that triggers neurite outgrowth. Science (2008) 1.82

Predicting protein complex membership using probabilistic network reliability. Genome Res (2004) 1.79

Automating document classification for the Immune Epitope Database. BMC Bioinformatics (2007) 1.76

AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology. Nucleic Acids Res (2007) 1.76

Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology. Nucleic Acids Res (2008) 1.65

DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64

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

A map of human protein interactions derived from co-expression of human mRNAs and their orthologs. Mol Syst Biol (2008) 1.53

HitPredict: a database of quality assessed protein-protein interactions in nine species. Nucleic Acids Res (2010) 1.50

PHIDIAS: a pathogen-host interaction data integration and analysis system. Genome Biol (2007) 1.50

A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47

TopNet: a tool for comparing biological sub-networks, correlating protein properties with topological statistics. Nucleic Acids Res (2004) 1.45

SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res (2009) 1.44

Meta-Analysis of Large-Scale Toxicogenomic Data Finds Neuronal Regeneration Related Protein and Cathepsin D to Be Novel Biomarkers of Drug-Induced Toxicity. PLoS One (2015) 1.41

Impact of vitamin D on immune function: lessons learned from genome-wide analysis. Front Physiol (2014) 1.40

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology. Plant Cell (2017) 1.39

In search of the biological significance of modular structures in protein networks. PLoS Comput Biol (2007) 1.38

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

SPIKE--a database, visualization and analysis tool of cellular signaling pathways. BMC Bioinformatics (2008) 1.35

Abnormal expression of FLI1 protein is an adverse prognostic factor in acute myeloid leukemia. Blood (2011) 1.34

The Biomolecular Interaction Network Database in PSI-MI 2.5. Database (Oxford) (2011) 1.34

Lists2Networks: integrated analysis of gene/protein lists. BMC Bioinformatics (2010) 1.33

Design principles of molecular networks revealed by global comparisons and composite motifs. Genome Biol (2006) 1.33

Predicting deleterious nsSNPs: an analysis of sequence and structural attributes. BMC Bioinformatics (2006) 1.32

FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol (2009) 1.32

Visualization and interpretation of protein networks in Mycobacterium tuberculosis based on hierarchical clustering of genome-wide functional linkage maps. Nucleic Acids Res (2003) 1.31

Host pathogen protein interactions predicted by comparative modeling. Protein Sci (2007) 1.29

Modelling protein-protein interaction networks via a stickiness index. J R Soc Interface (2006) 1.29

Dissecting the interface between signaling and transcriptional regulation in human B cells. Pac Symp Biocomput (2009) 1.28

Classifying protein-protein interaction articles using word and syntactic features. BMC Bioinformatics (2011) 1.27

Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66

Entrez: molecular biology database and retrieval system. Methods Enzymol (1996) 30.67

Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science (2001) 24.48

CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res (2002) 18.54

MINT: a Molecular INTeraction database. FEBS Lett (2002) 17.21

DIP, the Database of Interacting Proteins: a research tool for studying cellular networks of protein interactions. Nucleic Acids Res (2002) 15.70

CDART: protein homology by domain architecture. Genome Res (2002) 12.95

Protein modules and signalling networks. Nature (1995) 12.53

The Protein Data Bank: unifying the archive. Nucleic Acids Res (2002) 12.37

BIND--The Biomolecular Interaction Network Database. Nucleic Acids Res (2001) 11.74

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08

MMDB: Entrez's 3D-structure database. Nucleic Acids Res (2002) 4.42

BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways. Bioinformatics (2000) 4.40

SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics (2002) 2.84

Proteomics. Proteomics in genomeland. Science (2001) 2.80

Automatic annotation of BIND molecular interactions from three-dimensional structures. Biopolymers (2002) 2.24

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature (2002) 37.66

An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics (2003) 15.42

A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules. Science (2001) 7.08

Analyzing yeast protein-protein interaction data obtained from different sources. Nat Biotechnol (2002) 7.06

PreBIND and Textomy--mining the biomedical literature for protein-protein interactions using a support vector machine. BMC Bioinformatics (2003) 6.31

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. Genome Biol (2013) 4.67

Genetic dissection of the miR-17~92 cluster of microRNAs in Myc-induced B-cell lymphomas. Genes Dev (2009) 4.43

Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol (2009) 3.66

Characterization of small RNAs in Aplysia reveals a role for miR-124 in constraining synaptic plasticity through CREB. Neuron (2009) 3.27

Widespread regulatory activity of vertebrate microRNA* species. RNA (2010) 2.97

SeqHound: biological sequence and structure database as a platform for bioinformatics research. BMC Bioinformatics (2002) 2.84

Genome-wide identification of microRNA targets in human ES cells reveals a role for miR-302 in modulating BMP response. Genes Dev (2011) 1.55

CO: A chemical ontology for identification of functional groups and semantic comparison of small molecules. FEBS Lett (2005) 1.51

NBLAST: a cluster variant of BLAST for NxN comparisons. BMC Bioinformatics (2002) 1.20

Searching, viewing, and visualizing data in the Biomolecular Interaction Network Database (BIND). Curr Protoc Bioinformatics (2006) 1.16

Genome-wide identification of miRNA targets by PAR-CLIP. Methods (2012) 1.16

The expanding role of miR-302-367 in pluripotency and reprogramming. Cell Cycle (2012) 1.13

Cloning and expression of a novel UDP-GlcNAc:alpha-D-mannoside beta1,2-N-acetylglucosaminyltransferase homologous to UDP-GlcNAc:alpha-3-D-mannoside beta1,2-N-acetylglucosaminyltransferase I. Biochem J (2002) 1.10

Armadillo: domain boundary prediction by amino acid composition. J Mol Biol (2005) 1.09

Probabilistic sampling of protein conformations: new hope for brute force? Proteins (2002) 1.06

Mutation profiling of mismatch repair-deficient colorectal cncers using an in silico genome scan to identify coding microsatellites. Cancer Res (2002) 1.05

Structure-templated predictions of novel protein interactions from sequence information. PLoS Comput Biol (2007) 1.03

Domain-based small molecule binding site annotation. BMC Bioinformatics (2006) 1.01

The other side of staying out of a BIND. Nat Biotechnol (2007) 0.91

Kangaroo--a pattern-matching program for biological sequences. BMC Bioinformatics (2002) 0.91

Neurophysiological defects and neuronal gene deregulation in Drosophila mir-124 mutants. PLoS Genet (2012) 0.87

Hardware-accelerated protein identification for mass spectrometry. Rapid Commun Mass Spectrom (2005) 0.84

A complete small molecule dataset from the protein data bank. FEBS Lett (2006) 0.82

Analysis of domain correlations in yeast protein complexes. Bioinformatics (2004) 0.82

Species-specific protein sequence and fold optimizations. BMC Bioinformatics (2002) 0.80

Protein kinases display minimal interpositional dependence on substrate sequence: potential implications for the evolution of signalling networks. Philos Trans R Soc Lond B Biol Sci (2012) 0.80

Intermediate filament networks: in vitro and in vivo assembly models. C R Biol (2004) 0.78

Near-membrane ensemble elongation in the proline-rich LRP6 intracellular domain may explain the mysterious initiation of the Wnt signaling pathway. BMC Bioinformatics (2011) 0.78

Fluorescence based structural analysis of tryptophan analogue-AMP formation in single tryptophan mutants of Bacillus stearothermophilus tryptophanyl-tRNA synthetase. Biochemistry (2003) 0.75