Published in Bioinformatics on August 04, 2004
An introduction to bioinformatics for glycomics research. PLoS Comput Biol (2008) 1.05
PLecDom: a program for identification and analysis of plant lectin domains. Nucleic Acids Res (2009) 0.83
Functional network of glycan-related molecules: glyco-net in glycoconjugate data bank. BMC Syst Biol (2010) 0.75
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
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
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
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
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
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
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
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
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
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
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
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
Observing metabolic functions at the genome scale. Genome Biol (2007) 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
Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules. Bioinformatics (2006) 1.09
Oligomeric procyanidins in apple polyphenol are main active components for inhibition of pancreatic lipase and triglyceride absorption. J Agric Food Chem (2007) 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
Similarity-based machine learning methods for predicting drug-target interactions: a brief review. Brief Bioinform (2013) 1.08
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
An approximation method for solving the steady-state probability distribution of probabilistic Boolean networks. Bioinformatics (2007) 1.05
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
Long-term effect of efavirenz autoinduction on plasma/peripheral blood mononuclear cell drug exposure and CD4 count is influenced by UGT2B7 and CYP2B6 genotypes among HIV patients. J Antimicrob Chemother (2011) 1.04
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics (2010) 1.04
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. J Biomed Semantics (2010) 1.04
Structural controllability of unidirectional bipartite networks. Sci Rep (2013) 1.04
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
Algorithms for finding small attractors in Boolean networks. EURASIP J Bioinform Syst Biol (2007) 1.00
Treatment with risperidone for 4 weeks increased plasma 3-methoxy-4-hydroxypnenylglycol (MHPG) levels, but did not alter plasma brain-derived neurotrophic factor (BDNF) levels in schizophrenic patients. Prog Neuropsychopharmacol Biol Psychiatry (2007) 1.00
Subcellular location prediction of proteins using support vector machines with alignment of block sequences utilizing amino acid composition. BMC Bioinformatics (2007) 1.00
New amino acid indices based on residue network topology. Genome Inform (2007) 1.00