Published in Nucleic Acids Res on October 30, 2009
Structure, function and diversity of the healthy human microbiome. Nature (2012) 30.40
KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res (2011) 30.20
The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored. Nucleic Acids Res (2010) 18.73
DrugBank 3.0: a comprehensive resource for 'omics' research on drugs. Nucleic Acids Res (2010) 13.68
InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res (2011) 13.45
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
IMG: the Integrated Microbial Genomes database and comparative analysis system. Nucleic Acids Res (2012) 12.03
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
A tissue-specific atlas of mouse protein phosphorylation and expression. Cell (2010) 8.65
Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods (2012) 8.37
Statistical analysis strategies for association studies involving rare variants. Nat Rev Genet (2010) 6.79
Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet (2011) 6.43
Metabolic reconstruction for metagenomic data and its application to the human microbiome. PLoS Comput Biol (2012) 6.27
Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol Cell Proteomics (2012) 5.95
Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol (2012) 5.66
Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples. Genome Biol (2012) 4.68
BioCatalogue: a universal catalogue of web services for the life sciences. Nucleic Acids Res (2010) 4.67
International Cancer Genome Consortium Data Portal--a one-stop shop for cancer genomics data. Database (Oxford) (2011) 4.53
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Res (2011) 4.44
Community cyberinfrastructure for Advanced Microbial Ecology Research and Analysis: the CAMERA resource. Nucleic Acids Res (2010) 4.39
The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med (2011) 4.24
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011. Mol Syst Biol (2011) 4.03
Accessing the SEED genome databases via Web services API: tools for programmers. BMC Bioinformatics (2010) 3.99
g:Profiler--a web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res (2011) 3.94
Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci Rep (2013) 3.92
BRENDA, the enzyme information system in 2011. Nucleic Acids Res (2010) 3.83
Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52
Tissue of origin dictates branched-chain amino acid metabolism in mutant Kras-driven cancers. Science (2016) 3.45
PubChem as a public resource for drug discovery. Drug Discov Today (2010) 3.40
A protein complex network of Drosophila melanogaster. Cell (2011) 3.31
Experimental and analytical tools for studying the human microbiome. Nat Rev Genet (2011) 3.30
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
Rhea--a manually curated resource of biochemical reactions. Nucleic Acids Res (2011) 2.87
ConsensusPathDB: toward a more complete picture of cell biology. Nucleic Acids Res (2010) 2.79
The Notch signalling system: recent insights into the complexity of a conserved pathway. Nat Rev Genet (2012) 2.77
IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res (2011) 2.76
Partial genome assembly for a candidate division OP11 single cell from an anoxic spring (Zodletone Spring, Oklahoma). Appl Environ Microbiol (2011) 2.61
INRICH: interval-based enrichment analysis for genome-wide association studies. Bioinformatics (2012) 2.57
iPath2.0: interactive pathway explorer. Nucleic Acids Res (2011) 2.50
clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS (2012) 2.46
UniPathway: a resource for the exploration and annotation of metabolic pathways. Nucleic Acids Res (2011) 2.45
Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches. PLoS Genet (2011) 2.38
Annotating cancer variants and anti-cancer therapeutics in reactome. Cancers (Basel) (2012) 2.35
Chipster: user-friendly analysis software for microarray and other high-throughput data. BMC Genomics (2011) 2.31
PINA v2.0: mining interactome modules. Nucleic Acids Res (2011) 2.23
Coordination of the transcriptome and metabolome by the circadian clock. Proc Natl Acad Sci U S A (2012) 2.22
The genome sequence of the leaf-cutter ant Atta cephalotes reveals insights into its obligate symbiotic lifestyle. PLoS Genet (2011) 2.16
SVA: software for annotating and visualizing sequenced human genomes. Bioinformatics (2011) 2.11
STITCH 3: zooming in on protein-chemical interactions. Nucleic Acids Res (2011) 2.05
Genomic approaches to studying the human microbiota. Nature (2012) 2.00
1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data. BMC Bioinformatics (2012) 1.99
Phosphorylation in protein-protein binding: effect on stability and function. Structure (2011) 1.96
Heterogeneity of tumor-induced gene expression changes in the human metabolic network. Nat Biotechnol (2013) 1.91
The intestinal microbiome in early life: health and disease. Front Immunol (2014) 1.90
Prognostic gene-expression signature of carcinoma-associated fibroblasts in non-small cell lung cancer. Proc Natl Acad Sci U S A (2011) 1.88
Intestinal microbiome analyses identify melanoma patients at risk for checkpoint-blockade-induced colitis. Nat Commun (2016) 1.84
MatrixDB, the extracellular matrix interaction database. Nucleic Acids Res (2010) 1.79
MOPED: Model Organism Protein Expression Database. Nucleic Acids Res (2011) 1.79
GPCRDB: information system for G protein-coupled receptors. Nucleic Acids Res (2010) 1.77
Editing, validating and translating of SBGN maps. Bioinformatics (2010) 1.71
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res (2010) 1.71
The impact of multifunctional genes on "guilt by association" analysis. PLoS One (2011) 1.69
Network-based relating pharmacological and genomic spaces for drug target identification. PLoS One (2010) 1.68
Interpretation of genomic variants using a unified biological network approach. PLoS Comput Biol (2013) 1.67
MACiE: exploring the diversity of biochemical reactions. Nucleic Acids Res (2011) 1.67
Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol (2010) 1.67
DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci U S A (2012) 1.65
In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics (2011) 1.64
Assessing the human gut microbiota in metabolic diseases. Diabetes (2013) 1.64
Structural diversity of bacterial flagellar motors. EMBO J (2011) 1.63
A metabolomics approach using juvenile cystic mice to identify urinary biomarkers and altered pathways in polycystic kidney disease. Am J Physiol Renal Physiol (2010) 1.63
Circadian patterns of gene expression in the human brain and disruption in major depressive disorder. Proc Natl Acad Sci U S A (2013) 1.63
SABIO-RK--database for biochemical reaction kinetics. Nucleic Acids Res (2011) 1.63
One carbon metabolism in SAR11 pelagic marine bacteria. PLoS One (2011) 1.62
Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet (2014) 1.60
NOA: a novel Network Ontology Analysis method. Nucleic Acids Res (2011) 1.60
AutismKB: an evidence-based knowledgebase of autism genetics. Nucleic Acids Res (2011) 1.59
Selective extracellular vesicle-mediated export of an overlapping set of microRNAs from multiple cell types. BMC Genomics (2012) 1.58
Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics. J Pathol Inform (2012) 1.58
Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol Cell Proteomics (2012) 1.55
SNP discovery and development of a high-density genotyping array for sunflower. PLoS One (2012) 1.54
Yeast 5 - an expanded reconstruction of the Saccharomyces cerevisiae metabolic network. BMC Syst Biol (2012) 1.53
Computer-aided drug design platform using PyMOL. J Comput Aided Mol Des (2010) 1.53
DIANA-microT Web server upgrade supports Fly and Worm miRNA target prediction and bibliographic miRNA to disease association. Nucleic Acids Res (2011) 1.51
Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comput Biol (2011) 1.51
Genomewide pharmacogenetics of bisphosphonate-induced osteonecrosis of the jaw: the role of RBMS3. Oncologist (2012) 1.50
COXPRESdb: a database to compare gene coexpression in seven model animals. Nucleic Acids Res (2010) 1.50
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49
Discovery of molecular mechanisms of traditional Chinese medicinal formula Si-Wu-Tang using gene expression microarray and connectivity map. PLoS One (2011) 1.49
The complete genome sequence of Fibrobacter succinogenes S85 reveals a cellulolytic and metabolic specialist. PLoS One (2011) 1.48
YMDB: the Yeast Metabolome Database. Nucleic Acids Res (2011) 1.48
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Nucleic Acids Res (2010) 1.47
Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Mol Syst Biol (2011) 1.46
PathScan: a tool for discerning mutational significance in groups of putative cancer genes. Bioinformatics (2011) 1.46
A computational tool to detect and avoid redundancy in selected reaction monitoring. Mol Cell Proteomics (2012) 1.46
Comparative transcriptome analysis of two oysters, Crassostrea gigas and Crassostrea hongkongensis provides insights into adaptation to hypo-osmotic conditions. PLoS One (2014) 1.46
Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle. Nat Genet (2013) 1.45
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP). PLoS One (2012) 1.44
Chapter 12: Human microbiome analysis. PLoS Comput Biol (2012) 1.44
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
The International HapMap Project. Nature (2003) 73.65
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
Genome-wide association studies for common diseases and complex traits. Nat Rev Genet (2005) 33.96
A database for post-genome analysis. Trends Genet (1997) 32.07
NCBI Reference Sequences: current status, policy and new initiatives. Nucleic Acids Res (2008) 26.04
Linking databases and organisms: GenomeNet resources in Japan. Trends Biochem Sci (1997) 25.00
The cancer genome. Nature (2009) 23.13
The Universal Protein Resource (UniProt) 2009. Nucleic Acids Res (2008) 14.82
McKusick's Online Mendelian Inheritance in Man (OMIM). Nucleic Acids Res (2008) 12.83
Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model (2007) 7.70
E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics (2009) 2.88
BNDB - the Biochemical Network Database. BMC Bioinformatics (2007) 2.75
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
Extraction and analysis of chemical modification patterns in drug development. J Chem Inf Model (2009) 2.28
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
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
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
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
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
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
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
Extraction and analysis of chemical modification patterns in drug development. J Chem Inf Model (2009) 2.28
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics (2010) 2.14
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res (2006) 1.75
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
Enzymatic production of RNAi libraries from cDNAs. Nat Genet (2004) 1.54
Possible involvement of SINEs in mammalian-specific brain formation. Proc Natl Acad Sci U S A (2008) 1.54
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
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 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
Drug target prediction using adverse event report systems: a pharmacogenomic approach. Bioinformatics (2012) 1.27
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
Extraction of leukemia specific glycan motifs in humans by computational glycomics. Carbohydr Res (2005) 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
Relating drug-protein interaction network with drug side effects. Bioinformatics (2012) 1.10
Heuristics for chemical compound matching. Genome Inform (2003) 1.09
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol (2007) 1.09
Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. Photosynth Res (2007) 1.08
The use of network analyses for elucidating mechanisms in cardiovascular disease. Mol Biosyst (2009) 1.06
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
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
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
Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Inform (2004) 0.97
Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa. FEBS J (2007) 0.96
Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics (2012) 0.96
A global representation of the carbohydrate structures: a tool for the analysis of glycan. Genome Inform (2005) 0.95
GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res (2012) 0.95
Representation and analysis of molecular networks involving diseases and drugs. Genome Inform (2009) 0.95
Regulation of metabolic networks by small molecule metabolites. BMC Bioinformatics (2007) 0.94
Network analysis of adverse drug interactions. Genome Inform (2008) 0.94
EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG. Plant Physiol (2007) 0.94
A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PLoS One (2011) 0.93
Structural variety of membrane permeable peptides. Curr Protein Pept Sci (2003) 0.91
Bioinformatics strategies for the analysis of lipids. Methods Mol Biol (2009) 0.90
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. Bioinformatics (2013) 0.90
GeneRegionScan: a Bioconductor package for probe-level analysis of specific, small regions of the genome. Bioinformatics (2009) 0.89
An improved scoring scheme for predicting glycan structures from gene expression data. Genome Inform (2007) 0.87
Clofibrate-induced changes in the liver, heart, brain and white adipose lipid metabolome of Swiss-Webster mice. Metabolomics (2007) 0.86
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol (2013) 0.86
Nuclear and chloroplast microsatellite analysis of Abies sachalinensis regeneration on fallen logs in a subboreal forest in Hokkaido, Japan. Mol Ecol (2008) 0.86
Building multivariate systems biology models. Anal Chem (2012) 0.85
Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach. BMC Bioinformatics (2007) 0.85
Characterization and classification of adverse drug interactions. Genome Inform (2010) 0.84
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics (2008) 0.83
Intracellular delivery of glutathione S-transferase into mammalian cells. Biochem Biophys Res Commun (2003) 0.83
A SINE-derived element constitutes a unique modular enhancer for mammalian diencephalic Fgf8. PLoS One (2012) 0.82
Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Inform (2010) 0.81
Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics. BMC Med Genomics (2012) 0.81
Analysis of a lipid biosynthesis protein family and phospholipid structural variations. Genome Inform (2010) 0.80
PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list. J Bioinform Comput Biol (2014) 0.80
MRP1 mutated in the L0 region transports SN-38 but not leukotriene C4 or estradiol-17 (beta-D-glucuronate). Biochem Pharmacol (2005) 0.79
Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics (2006) 0.79
Prediction of CTL epitope, in silico modeling and functional analysis of cytolethal distending toxin (CDT) protein of Campylobacter jejuni. BMC Res Notes (2014) 0.78
Comprehensive genomic analysis of sulfur-relay pathway genes. Genome Inform (2010) 0.78
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. BMC Bioinformatics (2011) 0.78
Inferring protein domains associated with drug side effects based on drug-target interaction network. BMC Syst Biol (2013) 0.78
Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli. Genome Inform (2005) 0.78
Neutrophil/Lymphocyte Ratio in Patients with Rheumatoid Arthritis Treated with Biological Agents. J Nippon Med Sch (2016) 0.77
Genome-wide analysis of plant UGT family based on sequence and substrate information. Genome Inform (2010) 0.77
Fast and accurate database homology search using upper bounds of local alignment scores. Bioinformatics (2004) 0.77
Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes. Genome Inform (2006) 0.76
Generalized reaction patterns for prediction of unknown enzymatic reactions. Genome Inform (2008) 0.76
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