Published in J Am Chem Soc on October 01, 2003
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
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
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
Prediction of drug-target interactions and drug repositioning via network-based inference. PLoS Comput Biol (2012) 2.63
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
Supervised prediction of drug-target interactions using bipartite local models. Bioinformatics (2009) 2.20
Drug-target interaction prediction from chemical, genomic and pharmacological data in an integrated framework. Bioinformatics (2010) 2.14
Small Molecule Subgraph Detector (SMSD) toolkit. J Cheminform (2009) 1.94
ChemMine tools: an online service for analyzing and clustering small molecules. Nucleic Acids Res (2011) 1.56
PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res (2010) 1.49
Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities. PLoS One (2012) 1.43
Semi-supervised drug-protein interaction prediction from heterogeneous biological spaces. BMC Syst Biol (2010) 1.36
SubMAP: aligning metabolic pathways with subnetwork mappings. J Comput Biol (2011) 1.24
Extraction of phylogenetic network modules from the metabolic network. BMC Bioinformatics (2006) 1.23
SIMCOMP/SUBCOMP: chemical structure search servers for network analyses. Nucleic Acids Res (2010) 1.16
Predicting Drug-Target Interactions for New Drug Compounds Using a Weighted Nearest Neighbor Profile. PLoS One (2013) 1.09
Application of 3D Zernike descriptors to shape-based ligand similarity searching. J Cheminform (2009) 1.08
Structural analyses of a hypothetical minimal metabolism. Philos Trans R Soc Lond B Biol Sci (2007) 1.01
Automatic assignment of EC numbers. PLoS Comput Biol (2010) 0.99
Drug-target interaction prediction through domain-tuned network-based inference. Bioinformatics (2013) 0.99
Retrieval, alignment, and clustering of computational models based on semantic annotations. Mol Syst Biol (2011) 0.99
DINIES: drug-target interaction network inference engine based on supervised analysis. Nucleic Acids Res (2014) 0.96
Bioinformatics and molecular modeling in glycobiology. Cell Mol Life Sci (2010) 0.95
Physiochemical property space distribution among human metabolites, drugs and toxins. BMC Bioinformatics (2009) 0.95
Prediction of disease-related interactions between microRNAs and environmental factors based on a semi-supervised classifier. PLoS One (2012) 0.94
Regulation of metabolic networks by small molecule metabolites. BMC Bioinformatics (2007) 0.94
Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol (2009) 0.93
Toward more realistic drug-target interaction predictions. Brief Bioinform (2014) 0.92
An efficient algorithm for de novo predictions of biochemical pathways between chemical compounds. BMC Bioinformatics (2012) 0.92
Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition. BMC Bioinformatics (2010) 0.91
Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways. Nucleic Acids Res (2013) 0.90
Functional group and substructure searching as a tool in metabolomics. PLoS One (2008) 0.89
Discovering the targets of drugs via computational systems biology. J Biol Chem (2011) 0.86
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol (2013) 0.86
A semi-supervised method for drug-target interaction prediction with consistency in networks. PLoS One (2013) 0.85
NLLSS: Predicting Synergistic Drug Combinations Based on Semi-supervised Learning. PLoS Comput Biol (2016) 0.85
Metabolite and reaction inference based on enzyme specificities. Bioinformatics (2009) 0.84
Identification of Conserved Moieties in Metabolic Networks by Graph Theoretical Analysis of Atom Transition Networks. PLoS Comput Biol (2016) 0.84
GlycoPattern: a web platform for glycan array mining. Bioinformatics (2014) 0.84
Comparison and enumeration of chemical graphs. Comput Struct Biotechnol J (2013) 0.83
Machine learning based analyses on metabolic networks supports high-throughput knockout screens. BMC Syst Biol (2008) 0.83
Large-scale binding ligand prediction by improved patch-based method Patch-Surfer2.0. Bioinformatics (2014) 0.83
MP-Align: alignment of metabolic pathways. BMC Syst Biol (2014) 0.82
Neighborhood Regularized Logistic Matrix Factorization for Drug-Target Interaction Prediction. PLoS Comput Biol (2016) 0.81
A systematic investigation of computation models for predicting Adverse Drug Reactions (ADRs). PLoS One (2014) 0.81
Three-dimensional compound comparison methods and their application in drug discovery. Molecules (2015) 0.81
A weighted q-gram method for glycan structure classification. BMC Bioinformatics (2010) 0.80
Metabolome-scale de novo pathway reconstruction using regioisomer-sensitive graph alignments. Bioinformatics (2015) 0.79
3-D clustering: a tool for high throughput docking. J Mol Model (2008) 0.79
Improved prediction of drug-target interactions using regularized least squares integrating with kernel fusion technique. Anal Chim Acta (2016) 0.79
DASPfind: new efficient method to predict drug-target interactions. J Cheminform (2016) 0.79
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites. BMC Bioinformatics (2011) 0.78
Propagating semantic information in biochemical network models. BMC Bioinformatics (2012) 0.78
A similarity search using molecular topological graphs. J Biomed Biotechnol (2009) 0.78
CMPF: class-switching minimized pathfinding in metabolic networks. BMC Bioinformatics (2012) 0.78
Assignment of EC numbers to enzymatic reactions with reaction difference fingerprints. PLoS One (2012) 0.77
PatchSurfers: Two methods for local molecular property-based binding ligand prediction. Methods (2015) 0.77
PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation. J Chem Inf Model (2016) 0.76
Simultaneous prediction of enzyme orthologs from chemical transformation patterns for de novo metabolic pathway reconstruction. Bioinformatics (2016) 0.76
Predicting Drug-Target Interactions via Within-Score and Between-Score. Biomed Res Int (2015) 0.76
Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat Methods (2016) 0.76
A multiple kernel learning algorithm for drug-target interaction prediction. BMC Bioinformatics (2016) 0.76
Boolean network model for GPR142 against Type 2 diabetes and relative dynamic change ratio analysis using systems and biological circuits approach. Syst Synth Biol (2015) 0.76
Prediction of compound-target interactions of natural products using large-scale drug and protein information. BMC Bioinformatics (2016) 0.75
Inferring novel indications of approved drugs via a learning method with local and global consistency. PLoS One (2014) 0.75
Extracting glycan motifs using a biochemicallyweighted kernel. Bioinformation (2011) 0.75
Determining similarity of scientific entities in annotation datasets. Database (Oxford) (2015) 0.75
Predicting drug-target interactions by dual-network integrated logistic matrix factorization. Sci Rep (2017) 0.75
SELF-BLM: Prediction of drug-target interactions via self-training SVM. PLoS One (2017) 0.75
Aligning Metabolic Pathways Exploiting Binary Relation of Reactions. PLoS One (2016) 0.75
Predicting existing targets for new drugs base on strategies for missing interactions. BMC Bioinformatics (2016) 0.75
PROXIMAL: a method for Prediction of Xenobiotic Metabolism. BMC Syst Biol (2015) 0.75
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. BMC Bioinformatics (2016) 0.75
Metabolomics analysis: Finding out metabolic building blocks. PLoS One (2017) 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
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
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
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
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
MicroRNA-338-3p and microRNA-451 contribute to the formation of basolateral polarity in epithelial cells. Nucleic Acids Res (2009) 1.23
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
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
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
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
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