Published in Genome Inform on January 01, 2003
Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev (2008) 1.97
ChemMine tools: an online service for analyzing and clustering small molecules. Nucleic Acids Res (2011) 1.56
FINDSITE: a threading-based approach to ligand homology modeling. PLoS Comput Biol (2009) 1.38
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res (2010) 1.16
Q-Dock(LHM): Low-resolution refinement for ligand comparative modeling. J Comput Chem (2010) 0.99
A weighted q-gram method for glycan structure classification. BMC Bioinformatics (2010) 0.80
A similarity search using molecular topological graphs. J Biomed Biotechnol (2009) 0.78
The utility of geometrical and chemical restraint information extracted from predicted ligand-binding sites in protein structure refinement. J Struct Biol (2010) 0.78
Atom mapping with constraint programming. Algorithms Mol Biol (2014) 0.76
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
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
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
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
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
Global correlation analysis for micro-RNA and mRNA expression profiles in human cell lines. J Hum Genet (2008) 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
Using the KEGG database resource. Curr Protoc Bioinformatics (2012) 1.19
Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis. BMC Bioinformatics (2006) 1.18
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