Published in Bioinformatics on August 15, 2008
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KEGG Atlas mapping for global analysis of metabolic pathways. Nucleic Acids Res (2008) 4.14
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Prediction of drug-target interaction networks from the integration of chemical and genomic spaces. Bioinformatics (2008) 2.96
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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
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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
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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
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Enhancing MEDLINE document clustering by incorporating MeSH semantic similarity. Bioinformatics (2009) 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
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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
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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
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
A probabilistic model for mining implicit 'chemical compound-gene' relations from literature. Bioinformatics (2005) 1.11
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
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics (2006) 1.09
Evolutionary history and functional implications of protein domains and their combinations in eukaryotes. Genome Biol (2007) 1.09
Heuristics for chemical compound matching. Genome Inform (2003) 1.09
Calpain cleavage prediction using multiple kernel learning. PLoS One (2011) 1.09
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Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization. Photosynth Res (2007) 1.08
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Response to oxidative stress involves a novel peroxiredoxin gene in the unicellular cyanobacterium Synechocystis sp. PCC 6803. Plant Cell Physiol (2004) 1.06
A hidden Markov model-based approach for identifying timing differences in gene expression under different experimental factors. Bioinformatics (2007) 1.05
Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli. BMC Genomics (2007) 1.05
PURE: a PubMed article recommendation system based on content-based filtering. Genome Inform (2007) 1.03
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
CaMPDB: a resource for calpain and modulatory proteolysis. Genome Inform (2010) 1.01
New amino acid indices based on residue network topology. Genome Inform (2007) 1.00
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ProfilePSTMM: capturing tree-structure motifs in carbohydrate sugar chains. Bioinformatics (2006) 0.97
Screening for the target gene of cyanobacterial cAMP receptor protein SYCRP1. Mol Microbiol (2002) 0.97
Extraction of phylogenetic network modules from prokayrote metabolic pathways. Genome Inform (2004) 0.97
Efficient tree-matching methods for accurate carbohydrate database queries. Genome Inform (2003) 0.97
Systematic survey for novel types of prokaryotic retroelements based on gene neighborhood and protein architecture. Mol Biol Evol (2008) 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 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
Evaluation method for the potential functionome harbored in the genome and metagenome. BMC Genomics (2012) 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
Annotating gene function by combining expression data with a modular gene network. Bioinformatics (2007) 0.93
Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic. Traffic (2006) 0.92
Clustering of database sequences for fast homology search using upper bounds on alignment score. Genome Inform (2004) 0.91
A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes. Bioinformatics (2005) 0.91
Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags. Nucleic Acids Res (2002) 0.90
Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints. IEEE Trans Cybern (2013) 0.88