Published in J Am Chem Soc on December 22, 2004
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
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
Systems chemical biology. Nat Chem Biol (2007) 2.35
GLIDA: GPCR--ligand database for chemical genomics drug discovery--database and tools update. Nucleic Acids Res (2007) 2.22
GLIDA: GPCR-ligand database for chemical genomic drug discovery. Nucleic Acids Res (2006) 2.21
PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways. Nucleic Acids Res (2005) 2.12
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49
Non-homologous isofunctional enzymes: a systematic analysis of alternative solutions in enzyme evolution. Biol Direct (2010) 1.35
Critical assessment of human metabolic pathway databases: a stepping stone for future integration. BMC Syst Biol (2011) 1.10
New metrics for comparative genomics. Curr Opin Biotechnol (2006) 1.08
EC-BLAST: a tool to automatically search and compare enzyme reactions. Nat Methods (2014) 1.06
Using reaction mechanism to measure enzyme similarity. J Mol Biol (2007) 1.04
The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles. BMC Syst Biol (2008) 1.02
Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context. BMC Bioinformatics (2007) 1.00
Quantitative comparison of catalytic mechanisms and overall reactions in convergently evolved enzymes: implications for classification of enzyme function. PLoS Comput Biol (2010) 1.00
Automatic assignment of EC numbers. PLoS Comput Biol (2010) 0.99
Evolutionarily conserved substrate substructures for automated annotation of enzyme superfamilies. PLoS Comput Biol (2008) 0.98
AnEnPi: identification and annotation of analogous enzymes. BMC Bioinformatics (2008) 0.95
GENIES: gene network inference engine based on supervised analysis. Nucleic Acids Res (2012) 0.95
Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets. Bioinformatics (2013) 0.90
Functional group and substructure searching as a tool in metabolomics. PLoS One (2008) 0.89
Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst Biol (2012) 0.87
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol (2013) 0.86
Current understanding of the formation and adaptation of metabolic systems based on network theory. Metabolites (2012) 0.86
The genome of the Tiger Milk mushroom, Lignosus rhinocerotis, provides insights into the genetic basis of its medicinal properties. BMC Genomics (2014) 0.84
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PLoS Comput Biol (2016) 0.84
Comparison of RNA expression profiles on generations of Porphyra yezoensis (Rhodophyta), based on suppression subtractive hybridization (SSH). BMC Res Notes (2011) 0.83
Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2. J Cheminform (2014) 0.81
XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Res (2014) 0.81
Metabolome-scale prediction of intermediate compounds in multistep metabolic pathways with a recursive supervised approach. Bioinformatics (2014) 0.81
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. BMC Bioinformatics (2011) 0.78
Difference in the distribution pattern of substrate enzymes in the metabolic network of Escherichia coli, according to chaperonin requirement. BMC Syst Biol (2011) 0.78
Reaction graph kernels predict EC numbers of unknown enzymatic reactions in plant secondary metabolism. BMC Bioinformatics (2010) 0.78
Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints. PLoS One (2012) 0.77
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. Bioinformatics (2016) 0.76
Atom mapping with constraint programming. Algorithms Mol Biol (2014) 0.76
A new network representation of the metabolism to detect chemical transformation modules. BMC Bioinformatics (2015) 0.76
Characterising Complex Enzyme Reaction Data. PLoS One (2016) 0.76
Generation, analysis and functional annotation of expressed sequence tags from the sheepshead minnow (Cyprinodon variegatus). BMC Genomics (2010) 0.76
Enzyme reaction annotation using cloud techniques. Biomed Res Int (2013) 0.75
Exploring functionally related enzymes using radially distributed properties of active sites around the reacting points of bound ligands. BMC Struct Biol (2012) 0.75
Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis. Biophys Physicobiol (2016) 0.75
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
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
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
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
Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol (2007) 6.59
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
AAindex: amino acid index database, progress report 2008. Nucleic Acids Res (2007) 4.21
KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
iPath: interactive exploration of biochemical pathways and networks. Trends Biochem Sci (2008) 4.03
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
Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics (2008) 2.96
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
iPath2.0: interactive pathway explorer. Nucleic Acids Res (2011) 2.50
Prediction of protein subcellular locations by support vector machines using compositions of amino acids and amino acid pairs. Bioinformatics (2003) 2.45
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
Towards zoomable multidimensional maps of the cell. Nat Biotechnol (2007) 2.20
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
Identification of a new cryptochrome class. Structure, function, and evolution. Mol Cell (2003) 2.11
Gene annotation and pathway mapping in KEGG. Methods Mol Biol (2007) 2.09
Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol (2005) 1.80
EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res (2006) 1.75
The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics (2005) 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
DNA microarray analysis of redox-responsive genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803. J Bacteriol (2003) 1.46
Histamine synthesis is required for granule maturation in murine mast cells. Eur J Immunol (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
Positive regulation of sugar catabolic pathways in the cyanobacterium Synechocystis sp. PCC 6803 by the group 2 sigma factor sigE. J Biol Chem (2005) 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
Extracting active pathways from gene expression data. Bioinformatics (2003) 1.31
Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics (2005) 1.28
Drug target prediction using adverse event report systems: a pharmacogenomic approach. Bioinformatics (2012) 1.27
Using the KEGG database resource. Curr Protoc Bioinformatics (2005) 1.25
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
Using the KEGG database resource. Curr Protoc Bioinformatics (2012) 1.19
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
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics (2006) 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