Published in Genome Inform on January 01, 2003
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
A Markov chain model for N-linked protein glycosylation - towards a low-parameter tool for model-driven glycoengineering. Metab Eng (2015) 0.82
A weighted q-gram method for glycan structure classification. BMC Bioinformatics (2010) 0.80
GS-align for glycan structure alignment and similarity measurement. Bioinformatics (2015) 0.78
The KEGG resource for deciphering the genome. Nucleic Acids Res (2004) 53.05
KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res (2007) 29.46
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
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
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
Protein homology detection using string alignment kernels. Bioinformatics (2004) 2.13
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
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics (2011) 1.59
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
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
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics (2013) 1.44
Effects of paroxetine or milnacipran on serum brain-derived neurotrophic factor in depressed patients. Prog Neuropsychopharmacol Biol Psychiatry (2007) 1.44
KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. Nucleic Acids Res (2004) 1.43
Reduction of brain gamma-aminobutyric acid (GABA) concentrations in early-stage schizophrenia patients: 3T Proton MRS study. Schizophr Res (2009) 1.41
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
A novel representation of protein sequences for prediction of subcellular location using support vector machines. Protein Sci (2005) 1.38
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters. Nucleic Acids Res (2012) 1.36
Graph kernels for molecular structure-activity relationship analysis with support vector machines. J Chem Inf Model (2005) 1.35
Cascleave: towards more accurate prediction of caspase substrate cleavage sites. Bioinformatics (2010) 1.34
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
Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinformatics (2009) 1.33
Extracting active pathways from gene expression data. Bioinformatics (2003) 1.31
PROSPER: an integrated feature-based tool for predicting protease substrate cleavage sites. PLoS One (2012) 1.28
Supervised enzyme network inference from the integration of genomic data and chemical information. Bioinformatics (2005) 1.28
Toward more accurate pan-specific MHC-peptide binding prediction: a review of current methods and tools. Brief Bioinform (2011) 1.26
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
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
TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules. PLoS One (2012) 1.18
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
Enumerating treelike chemical graphs with given path frequency. J Chem Inf Model (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
Pharmacogenetic & pharmacokinetic biomarker for efavirenz based ARV and rifampicin based anti-TB drug induced liver injury in TB-HIV infected patients. PLoS One (2011) 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
Allie: a database and a search service of abbreviations and long forms. Database (Oxford) (2011) 1.12
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
Observing metabolic functions at the genome scale. Genome Biol (2007) 1.10
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
Enumerating tree-like chemical graphs with given upper and lower bounds on path frequencies. BMC Bioinformatics (2011) 1.10
MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics (2006) 1.09
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
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics (2006) 1.09