Published in Nucleic Acids Res on January 01, 2004
A core gut microbiome in obese and lean twins. Nature (2008) 52.30
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63
Metagenomic analysis of the human distal gut microbiome. Science (2006) 29.76
The human microbiome project. Nature (2007) 28.53
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
Linking long-term dietary patterns with gut microbial enterotypes. Science (2011) 17.30
SMART 5: domains in the context of genomes and networks. Nucleic Acids Res (2006) 17.13
The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med (2009) 16.02
DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res (2006) 15.19
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
HMDB: the Human Metabolome Database. Nucleic Acids Res (2007) 13.38
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res (2005) 12.88
MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res (2006) 12.48
Network-based classification of breast cancer metastasis. Mol Syst Biol (2007) 12.18
Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe (2008) 11.97
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
The National Microbial Pathogen Database Resource (NMPDR): a genomics platform based on subsystem annotation. Nucleic Acids Res (2006) 11.15
The UCSC Genome Browser Database: update 2006. Nucleic Acids Res (2006) 11.05
Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia (2007) 10.74
STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res (2005) 10.44
AGMIAL: implementing an annotation strategy for prokaryote genomes as a distributed system. Nucleic Acids Res (2006) 10.39
Toward the automated generation of genome-scale metabolic networks in the SEED. BMC Bioinformatics (2007) 9.45
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
GFINDer: genetic disease and phenotype location statistical analysis and mining of dynamically annotated gene lists. Nucleic Acids Res (2005) 9.05
The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell (2009) 7.88
Genome sequence and analysis of the tuber crop potato. Nature (2011) 7.77
MPact: the MIPS protein interaction resource on yeast. Nucleic Acids Res (2006) 7.75
The integrated microbial genomes (IMG) system. Nucleic Acids Res (2006) 7.34
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res (2007) 7.18
Expansion of the BioCyc collection of pathway/genome databases to 160 genomes. Nucleic Acids Res (2005) 7.13
Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins. Proc Natl Acad Sci U S A (2010) 7.09
(V600E)BRAF is associated with disabled feedback inhibition of RAF-MEK signaling and elevated transcriptional output of the pathway. Proc Natl Acad Sci U S A (2009) 6.78
GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists. Genome Biol (2007) 6.11
Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes. Am J Hum Genet (2006) 6.10
SCAN: SNP and copy number annotation. Bioinformatics (2009) 5.96
Evolution of symbiotic bacteria in the distal human intestine. PLoS Biol (2007) 5.79
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol (2010) 5.75
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc (2011) 5.71
The importance of bottlenecks in protein networks: correlation with gene essentiality and expression dynamics. PLoS Comput Biol (2007) 5.63
CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res (2005) 5.25
De novo characterization of a whitefly transcriptome and analysis of its gene expression during development. BMC Genomics (2010) 5.17
High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology (2009) 5.08
The European Bioinformatics Institute's data resources: towards systems biology. Nucleic Acids Res (2005) 4.90
An overview of the PubChem BioAssay resource. Nucleic Acids Res (2009) 4.75
A human functional protein interaction network and its application to cancer data analysis. Genome Biol (2010) 4.73
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res (2005) 4.72
The MicrobesOnline Web site for comparative genomics. Genome Res (2005) 4.48
Complete genome sequence of the probiotic lactic acid bacterium Lactobacillus acidophilus NCFM. Proc Natl Acad Sci U S A (2005) 4.46
Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A (2005) 4.40
MicrobesOnline: an integrated portal for comparative and functional genomics. Nucleic Acids Res (2009) 4.32
The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLoS Biol (2005) 4.28
E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res (2005) 4.25
Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica. Proc Natl Acad Sci U S A (2007) 4.04
Evaluation of genetic variation contributing to differences in gene expression between populations. Am J Hum Genet (2008) 4.01
Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics (2010) 3.99
Structural classification of bacterial response regulators: diversity of output domains and domain combinations. J Bacteriol (2006) 3.86
Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol (2005) 3.79
Decoding signalling networks by mass spectrometry-based proteomics. Nat Rev Mol Cell Biol (2010) 3.78
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
BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res (2006) 3.62
The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol (2007) 3.59
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
Systems approach to refining genome annotation. Proc Natl Acad Sci U S A (2006) 3.58
Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res (2005) 3.56
A census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial IQ, extroverts and introverts. BMC Microbiol (2005) 3.38
A primary xenograft model of small-cell lung cancer reveals irreversible changes in gene expression imposed by culture in vitro. Cancer Res (2009) 3.38
ORENZA: a web resource for studying ORphan ENZyme activities. BMC Bioinformatics (2006) 3.26
From genes to functional classes in the study of biological systems. BMC Bioinformatics (2007) 3.09
Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia (2007) 3.06
Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol Syst Biol (2009) 2.98
Optimizing de novo transcriptome assembly from short-read RNA-Seq data: a comparative study. BMC Bioinformatics (2011) 2.88
Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics (2011) 2.84
OptStrain: a computational framework for redesign of microbial production systems. Genome Res (2004) 2.80
cisRED: a database system for genome-scale computational discovery of regulatory elements. Nucleic Acids Res (2006) 2.75
An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res (2009) 2.69
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
The Molecular Biology Database Collection: 2006 update. Nucleic Acids Res (2006) 2.61
Pseudomonas aeruginosa Genome Database and PseudoCAP: facilitating community-based, continually updated, genome annotation. Nucleic Acids Res (2005) 2.61
miRGator: an integrated system for functional annotation of microRNAs. Nucleic Acids Res (2007) 2.59
Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math Biosci (2009) 2.58
Finished genome of the fungal wheat pathogen Mycosphaerella graminicola reveals dispensome structure, chromosome plasticity, and stealth pathogenesis. PLoS Genet (2011) 2.58
TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res (2006) 2.55
Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics (2011) 2.53
The University of Minnesota Biocatalysis/Biodegradation Database: the first decade. Nucleic Acids Res (2006) 2.52
Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol (2012) 2.45
The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res (2006) 2.45
Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol (2010) 2.44
The partitioned Rhizobium etli genome: genetic and metabolic redundancy in seven interacting replicons. Proc Natl Acad Sci U S A (2006) 2.44
Classification of microarray data using gene networks. BMC Bioinformatics (2007) 2.44
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network. Genome Biol (2009) 2.43
Metagenomics - a guide from sampling to data analysis. Microb Inform Exp (2012) 2.42
GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. PLoS Comput Biol (2009) 2.41
PDTD: a web-accessible protein database for drug target identification. BMC Bioinformatics (2008) 2.35
Deep and highly sensitive proteome coverage by LC-MS/MS without prefractionation. Mol Cell Proteomics (2011) 2.33
MSEA: a web-based tool to identify biologically meaningful patterns in quantitative metabolomic data. Nucleic Acids Res (2010) 2.32
Analysis of protein sequence and interaction data for candidate disease gene prediction. Nucleic Acids Res (2006) 2.30
Gene3D: modelling protein structure, function and evolution. Nucleic Acids Res (2006) 2.30
KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res (2000) 117.00
The KEGG databases at GenomeNet. Nucleic Acids Res (2002) 33.68
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc (2003) 15.30
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
The Complex Carbohydrate Structure Database. Trends Biochem Sci (1989) 9.00
Bioinformatics in the post-sequence era. Nat Genet (2003) 8.83
KEGG for linking genomes to life and the environment. Nucleic Acids Res (2007) 49.37
From genomics to chemical genomics: new developments in KEGG. Nucleic Acids Res (2006) 44.35
The KEGG databases at GenomeNet. Nucleic Acids Res (2002) 33.68
KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res (2011) 30.20
KEGG for representation and analysis of molecular networks involving diseases and drugs. Nucleic Acids Res (2009) 28.60
Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J Am Chem Soc (2003) 15.30
Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res (2013) 15.13
LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res (2002) 13.61
Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J Am Chem Soc (2004) 11.50
KEGG as a glycome informatics resource. Glycobiology (2005) 11.05
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Network-based analysis and characterization of adverse drug-drug interactions. J Chem Inf Model (2011) 7.92
Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model (2007) 7.70
Prediction of glycan structures from gene expression data based on glycosyltransferase reactions. Bioinformatics (2005) 5.76
The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs). Bioinformatics (2007) 5.63
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J Chem Inf Model (2013) 3.58
Mice genetically deficient in vasopressin V1a and V1b receptors are resistant to jet lag. Science (2013) 3.51
Identification of novel microRNA targets based on microRNA signatures in bladder cancer. Int J Cancer (2009) 3.15
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics (2009) 2.88
The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes. J Lipid Res (2007) 2.65
Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans. Carbohydr Res (2009) 2.40
Salt-sensitive hypertension in circadian clock-deficient Cry-null mice involves dysregulated adrenal Hsd3b6. Nat Med (2009) 2.30
Extraction and analysis of chemical modification patterns in drug development. J Chem Inf Model (2009) 2.28
VisANT 3.0: new modules for pathway visualization, editing, prediction and construction. Nucleic Acids Res (2007) 2.17
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics (2010) 2.14
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res (2006) 1.75
Alteration of gene expression in human hepatocellular carcinoma with integrated hepatitis B virus DNA. Clin Cancer Res (2005) 1.64
Germinal center marker GL7 probes activation-dependent repression of N-glycolylneuraminic acid, a sialic acid species involved in the negative modulation of B-cell activation. Mol Cell Biol (2007) 1.63
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
Data mining of the public version of the FDA Adverse Event Reporting System. Int J Med Sci (2013) 1.56
Genome sequence of the cat pathogen, Chlamydophila felis. DNA Res (2006) 1.50
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49
Histamine synthesis is required for granule maturation in murine mast cells. Eur J Immunol (2013) 1.44
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
Proportion of de novo cancers among colorectal cancers in Japan. Gastroenterology (2006) 1.43
The genome of the heartworm, Dirofilaria immitis, reveals drug and vaccine targets. FASEB J (2012) 1.40
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res (2012) 1.36
The KEGG databases and tools facilitating omics analysis: latest developments involving human diseases and pharmaceuticals. Methods Mol Biol (2012) 1.33
MicroRNA: biogenetic and functional mechanisms and involvements in cell differentiation and cancer. J Pharmacol Sci (2006) 1.33
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009. Nucleic Acids Res (2008) 1.32
Drug target prediction using adverse event report systems: a pharmacogenomic approach. Bioinformatics (2012) 1.27
Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines. J Hum Genet (2008) 1.23
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells. Nucleic Acids Res (2009) 1.23
Analysis of multiple compound-protein interactions reveals novel bioactive molecules. Mol Syst Biol (2011) 1.19
Secreted CXCL1 is a potential mediator and marker of the tumor invasion of bladder cancer. Clin Cancer Res (2008) 1.18
Domain shuffling and the evolution of vertebrates. Genome Res (2009) 1.18
Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydr Res (2005) 1.17
Statin-associated muscular and renal adverse events: data mining of the public version of the FDA adverse event reporting system. PLoS One (2011) 1.17
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res (2010) 1.16
Systems biology approaches and pathway tools for investigating cardiovascular disease. Mol Biosyst (2009) 1.15
Hypersensitivity reactions to anticancer agents: data mining of the public version of the FDA adverse event reporting system, AERS. J Exp Clin Cancer Res (2011) 1.15
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. J Biomed Semantics (2014) 1.12
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. Bioinformatics (2005) 1.11
Omeprazole- and esomeprazole-associated hypomagnesaemia: data mining of the public version of the FDA Adverse Event Reporting System. Int J Med Sci (2012) 1.11
A novel chemogenomics analysis of G protein-coupled receptors (GPCRs) and their ligands: a potential strategy for receptor de-orphanization. BMC Bioinformatics (2010) 1.11
Platinum agent-induced hypersensitivity reactions: data mining of the public version of the FDA adverse event reporting system, AERS. Int J Med Sci (2011) 1.10
Relating drug-protein interaction network with drug side effects. Bioinformatics (2012) 1.10
Adverse event profiles of platinum agents: data mining of the public version of the FDA adverse event reporting system, AERS, and reproducibility of clinical observations. Int J Med Sci (2011) 1.09
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol (2007) 1.09
Heuristics for chemical compound matching. Genome Inform (2003) 1.09
Identification of EP4 as a potential target for the treatment of castration-resistant prostate cancer using a novel xenograft model. Cancer Res (2010) 1.08
Inhibition of protein kinase CK2 prevents the progression of glomerulonephritis. Proc Natl Acad Sci U S A (2005) 1.06
The use of network analyses for elucidating mechanisms in cardiovascular disease. Mol Biosyst (2009) 1.06
Adverse event profiles of 5-fluorouracil and capecitabine: data mining of the public version of the FDA Adverse Event Reporting System, AERS, and reproducibility of clinical observations. Int J Med Sci (2011) 1.05
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 1.04
Adverse event profile of tigecycline: data mining of the public version of the U.S. Food and Drug Administration adverse event reporting system. Biol Pharm Bull (2012) 1.02
New amino acid indices based on residue network topology. Genome Inform (2007) 1.00
Mating system, pollen and propagule dispersal, and spatial genetic structure in a high-density population of the mangrove tree Kandelia candel. Mol Ecol (2008) 0.99
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics (2011) 0.99
KEGG bioinformatics resource for plant genomics research. Methods Mol Biol (2007) 0.98
Membrane permeability commonly shared among arginine-rich peptides. J Mol Recognit (2003) 0.98
Identification of genomic biomarkers for concurrent diagnosis of drug-induced renal tubular injury using a large-scale toxicogenomics database. Toxicology (2009) 0.97
Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Inform (2004) 0.97