Published in Genome Inform on January 01, 2005
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
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
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
ODB: a database of operons accumulating known operons across multiple genomes. Nucleic Acids Res (2006) 1.58
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
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
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
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
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
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
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
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
Observing metabolic functions at the genome scale. Genome Biol (2007) 1.10
MIMOX: a web tool for phage display based epitope mapping. BMC Bioinformatics (2006) 1.09
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
t4 workshop report: Pathways of Toxicity. ALTEX (2013) 1.06
Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol (2004) 1.06
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
Partial correlation coefficient between distance matrices as a new indicator of protein-protein interactions. Bioinformatics (2006) 1.03
A two-component Mn2+-sensing system negatively regulates expression of the mntCAB operon in Synechocystis. Plant Cell (2002) 1.03
New amino acid indices based on residue network topology. Genome Inform (2007) 1.00
KEGG bioinformatics resource for plant genomics research. Methods Mol Biol (2007) 0.98
Screening for the target gene of cyanobacterial cAMP receptor protein SYCRP1. Mol Microbiol (2002) 0.97
ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics (2006) 0.97
Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform (2003) 0.97
Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Inform (2004) 0.97
Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. Mol Biol Evol (2008) 0.96
Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics (2012) 0.96
A score matrix to reveal the hidden links in glycans. Bioinformatics (2004) 0.96
Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa. FEBS J (2007) 0.96
KaPPA-View4: a metabolic pathway database for representation and analysis of correlation networks of gene co-expression and metabolite co-accumulation and omics data. Nucleic Acids Res (2010) 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
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
The evolutionary repertoires of the eukaryotic-type ABC transporters in terms of the phylogeny of ATP-binding domains in eukaryotes and prokaryotes. Mol Biol Evol (2004) 0.94
Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic (2006) 0.92
A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics (2005) 0.91
Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Inform (2004) 0.91
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res (2002) 0.90
Analysis of common substructures of metabolic compounds within the different organism groups. Genome Inform (2007) 0.87
An improved scoring scheme for predicting glycan structures from gene expression data. Genome Inform (2007) 0.87
Mining significant tree patterns in carbohydrate sugar chains. Bioinformatics (2008) 0.87
Clustering under the line graph transformation: application to reaction network. BMC Bioinformatics (2004) 0.86
KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics. BMC Syst Biol (2013) 0.86
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
Extraction of species-specific glycan substructures. Genome Inform (2004) 0.83
varDB: a pathogen-specific sequence database of protein families involved in antigenic variation. Bioinformatics (2008) 0.83
Predicting B cell epitope residues with network topology based amino acid indices. Genome Inform (2007) 0.83
Characterization and evolutionary landscape of AmnSINE1 in Amniota genomes. Gene (2008) 0.83
Bioinformatics approaches in glycomics and drug discovery. Curr Opin Mol Ther (2006) 0.82
Using protein motif combinations to update KEGG pathway maps and orthologue tables. Genome Inform (2004) 0.82
Integer programming-based method for completing signaling pathways and its application to analysis of colorectal cancer. Genome Inform (2010) 0.81
Application of a new probabilistic model for recognizing complex patterns in glycans. Bioinformatics (2004) 0.81
PIERO ontology for analysis of biochemical transformations: effective implementation of reaction information in the IUBMB enzyme list. J Bioinform Comput Biol (2014) 0.80
Analysis of a lipid biosynthesis protein family and phospholipid structural variations. Genome Inform (2010) 0.80
Extraction of organism groups from phylogenetic profiles using independent component analysis. Genome Inform (2002) 0.79
MRP1 mutated in the L0 region transports SN-38 but not leukotriene C4 or estradiol-17 (beta-D-glucuronate). Biochem Pharmacol (2005) 0.79
Utilizing evolutionary information and gene expression data for estimating gene networks with bayesian network models. J Bioinform Comput Biol (2005) 0.79