Published in Nucleic Acids Res on November 10, 2006
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Human Protein Reference Database--2009 update. Nucleic Acids Res (2008) 21.25
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Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe (2008) 11.97
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Supergenomic network compression and the discovery of EXP1 as a glutathione transferase inhibited by artesunate. Cell (2014) 1.91
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Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases. Hum Genet (2008) 1.72
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Hubba: hub objects analyzer--a framework of interactome hubs identification for network biology. Nucleic Acids Res (2008) 1.65
HAPPI: an online database of comprehensive human annotated and predicted protein interactions. BMC Genomics (2009) 1.61
Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.61
Finding friends and enemies in an enemies-only network: a graph diffusion kernel for predicting novel genetic interactions and co-complex membership from yeast genetic interactions. Genome Res (2008) 1.61
The binary protein interactome of Treponema pallidum--the syphilis spirochete. PLoS One (2008) 1.59
A computational screen for regulators of oxidative phosphorylation implicates SLIRP in mitochondrial RNA homeostasis. PLoS Genet (2009) 1.56
The Firegoose: two-way integration of diverse data from different bioinformatics web resources with desktop applications. BMC Bioinformatics (2007) 1.51
A survey of available tools and web servers for analysis of protein-protein interactions and interfaces. Brief Bioinform (2009) 1.47
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Arena3D: visualization of biological networks in 3D. BMC Syst Biol (2008) 1.45
Rank-rank hypergeometric overlap: identification of statistically significant overlap between gene-expression signatures. Nucleic Acids Res (2010) 1.45
Update of the G2D tool for prioritization of gene candidates to inherited diseases. Nucleic Acids Res (2007) 1.42
Genome sequence of the pathogenic intestinal spirochete brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS One (2009) 1.41
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol (2009) 1.32
Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice. Plant Physiol (2007) 1.32
The Negatome database: a reference set of non-interacting protein pairs. Nucleic Acids Res (2009) 1.32
Genomic analysis of Campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets. BMC Microbiol (2009) 1.30
Sequence-based feature prediction and annotation of proteins. Genome Biol (2009) 1.28
A network-based integrative approach to prioritize reliable hits from multiple genome-wide RNAi screens in Drosophila. BMC Genomics (2009) 1.27
Universally distributed single-copy genes indicate a constant rate of horizontal transfer. PLoS One (2011) 1.25
Practical and theoretical advances in predicting the function of a protein by its phylogenetic distribution. J R Soc Interface (2008) 1.24
Human papillomavirus type 16 E7 oncoprotein associates with E2F6. J Virol (2008) 1.22
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Candidate gene prioritization by network analysis of differential expression using machine learning approaches. BMC Bioinformatics (2010) 1.21
The Modular Organization of Protein Interactions in Escherichia coli. PLoS Comput Biol (2009) 1.20
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Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat Chem Biol (2009) 1.19
Gene expression profiling for the investigation of soft tissue sarcoma pathogenesis and the identification of diagnostic, prognostic, and predictive biomarkers. Virchows Arch (2009) 1.19
ProdoNet: identification and visualization of prokaryotic gene regulatory and metabolic networks. Nucleic Acids Res (2008) 1.18
Network neighbors of drug targets contribute to drug side-effect similarity. PLoS One (2011) 1.17
Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol Cell Proteomics (2010) 1.16
Chemical databases for environmental health and clinical research. Toxicol Lett (2008) 1.15
Evidence of the role of tick subolesin in gene expression. BMC Genomics (2008) 1.15
Layers of epistasis: genome-wide regulatory networks and network approaches to genome-wide association studies. Wiley Interdiscip Rev Syst Biol Med (2010) 1.15
Network analysis of differential expression for the identification of disease-causing genes. PLoS One (2009) 1.14
Novel protein-protein interactions inferred from literature context. PLoS One (2009) 1.13
Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance. BMC Microbiol (2008) 1.13
Signature genes as a phylogenomic tool. Mol Biol Evol (2008) 1.13
Discovering functional novelty in metagenomes: examples from light-mediated processes. J Bacteriol (2008) 1.06
Length variations amongst protein domain superfamilies and consequences on structure and function. PLoS One (2009) 1.06
Bacteriome.org--an integrated protein interaction database for E. coli. Nucleic Acids Res (2007) 1.06
GTPase-mediated regulation of the unfolded protein response in Caenorhabditis elegans is dependent on the AAA+ ATPase CDC-48. Mol Cell Biol (2008) 1.06
In vivo analysis of proteomes and interactomes using Parallel Affinity Capture (iPAC) coupled to mass spectrometry. Mol Cell Proteomics (2011) 1.05
EcID. A database for the inference of functional interactions in E. coli. Nucleic Acids Res (2008) 1.05
The Escherichia coli K-12 ORFeome: a resource for comparative molecular microbiology. BMC Genomics (2010) 1.05
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 1.04
The COG database: an updated version includes eukaryotes. BMC Bioinformatics (2003) 60.98
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
Comparative metagenomics of microbial communities. Science (2005) 25.88
The Database of Interacting Proteins: 2004 update. Nucleic Acids Res (2004) 23.67
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BioGRID: a general repository for interaction datasets. Nucleic Acids Res (2006) 22.41
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res (2005) 20.05
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MINT: a Molecular INTeraction database. FEBS Lett (2002) 17.21
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
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The use of gene clusters to infer functional coupling. Proc Natl Acad Sci U S A (1999) 16.35
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res (2005) 12.94
Human protein reference database--2006 update. Nucleic Acids Res (2006) 12.16
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
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WormBase: better software, richer content. Nucleic Acids Res (2006) 6.78
STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene. Nucleic Acids Res (2000) 5.68
Genome Snapshot: a new resource at the Saccharomyces Genome Database (SGD) presenting an overview of the Saccharomyces cerevisiae genome. Nucleic Acids Res (2006) 3.59
Computational methods for the prediction of protein interactions. Curr Opin Struct Biol (2002) 3.35
SIMAP: the similarity matrix of proteins. Nucleic Acids Res (2006) 2.26
DILIMOT: discovery of linear motifs in proteins. Nucleic Acids Res (2006) 2.17
Nucleocytoplasmic transport: integrating mRNA production and turnover with export through the nuclear pore. Mol Cell Biol (2004) 1.55
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A method and server for predicting damaging missense mutations. Nat Methods (2010) 78.53
Human non-synonymous SNPs: server and survey. Nucleic Acids Res (2002) 50.45
Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature (2002) 45.19
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Comparative metagenomics of microbial communities. Science (2005) 25.88
InterPro: the integrative protein signature database. Nucleic Acids Res (2008) 25.07
Recent improvements to the SMART domain-based sequence annotation resource. Nucleic Acids Res (2002) 25.06
The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Res (2003) 24.72
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Enterotypes of the human gut microbiome. Nature (2011) 24.36
Comparative assessment of large-scale data sets of protein-protein interactions. Nature (2002) 24.25
Proteome survey reveals modularity of the yeast cell machinery. Nature (2006) 20.77
STRING 8--a global view on proteins and their functional interactions in 630 organisms. Nucleic Acids Res (2008) 20.62
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
SMART 4.0: towards genomic data integration. Nucleic Acids Res (2004) 19.37
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
STRING v9.1: protein-protein interaction networks, with increased coverage and integration. Nucleic Acids Res (2012) 18.26
InterPro, progress and status in 2005. Nucleic Acids Res (2005) 17.53
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08
Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics (2006) 14.96
Toward automatic reconstruction of a highly resolved tree of life. Science (2006) 14.96
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
New developments in the InterPro database. Nucleic Acids Res (2007) 12.49
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res (2011) 10.82
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
SMART 6: recent updates and new developments. Nucleic Acids Res (2008) 9.80
STRING: a database of predicted functional associations between proteins. Nucleic Acids Res (2003) 9.45
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Drug target identification using side-effect similarity. Science (2008) 9.24
SMART 7: recent updates to the protein domain annotation resource. Nucleic Acids Res (2011) 9.15
Bioinformatics in the post-sequence era. Nat Genet (2003) 8.83
mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev (2006) 8.78
Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci Signal (2010) 8.61
PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments. Nucleic Acids Res (2006) 8.36
Literature mining for the biologist: from information retrieval to biological discovery. Nat Rev Genet (2006) 8.23
Protein disorder prediction: implications for structural proteomics. Structure (2003) 7.93
Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58
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Systematic discovery of in vivo phosphorylation networks. Cell (2007) 6.94
Richness of human gut microbiome correlates with metabolic markers. Nature (2013) 6.93
ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res (2003) 6.86
A side effect resource to capture phenotypic effects of drugs. Mol Syst Biol (2010) 6.75
The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69
The ecoresponsive genome of Daphnia pulex. Science (2011) 6.55
The genome of the model beetle and pest Tribolium castaneum. Nature (2008) 6.50
Association of genes to genetically inherited diseases using data mining. Nat Genet (2002) 5.78
Functional and evolutionary insights from the genomes of three parasitoid Nasonia species. Science (2010) 5.56
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
Dynamic complex formation during the yeast cell cycle. Science (2005) 5.11
STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res (2007) 4.88
Genomes in flux: the evolution of archaeal and proteobacterial gene content. Genome Res (2002) 4.85
eggNOG: automated construction and annotation of orthologous groups of genes. Nucleic Acids Res (2007) 4.84
Transcriptome complexity in a genome-reduced bacterium. Science (2009) 4.64
Mining electronic health records: towards better research applications and clinical care. Nat Rev Genet (2012) 4.42
Update on XplorMed: A web server for exploring scientific literature. Nucleic Acids Res (2003) 4.42
Genomic variation landscape of the human gut microbiome. Nature (2012) 4.38
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
A genome-wide survey of human pseudogenes. Genome Res (2003) 4.34
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06
iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci (2008) 4.03
Proteome organization in a genome-reduced bacterium. Science (2009) 3.97
Molecular eco-systems biology: towards an understanding of community function. Nat Rev Microbiol (2008) 3.95
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges. Nucleic Acids Res (2011) 3.94
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SuperTarget and Matador: resources for exploring drug-target relationships. Nucleic Acids Res (2007) 3.82