Research Topics
| S GotoSummaryAffiliation: Kyoto University Country: Japan Publications
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Detail Information
Publications
MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolitesMasaaki Kotera
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
BMC Bioinformatics 12:S1. 2011..However, they are optimized for ligand binding and are not suitable for metabolomic studies...- Evolutionary history and functional implications of protein domains and their combinations in eukaryotesMasumi Itoh
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Biol 8:R121. 2007..To elucidate the characteristics and evolutionary mechanisms that underlie such domain combinations, it is essential to examine the different types of domains and their combinations among different groups of eukaryotes... - Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coliShujiro Okuda
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
BMC Genomics 8:48. 2007..Information about such complicated operons is helpful for predicting and analyzing operon structures, as well as understanding gene functions and transcriptional regulation... - Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approachMasashi Fujita
Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
BMC Bioinformatics 8:225. 2007..A protein-level study will provide independent insight into the novel amino acid... - Regulation of metabolic networks by small molecule metabolitesAlex Gutteridge
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Kyoto, Japan 611 0011
BMC Bioinformatics 8:88. 2007..We look at the network properties of this regulatory system and the relationship between the chemical properties of regulatory molecules... - Extraction of phylogenetic network modules from the metabolic networkTakuji Yamada
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611 0011, Japan
BMC Bioinformatics 7:130. 2006..Although each organism has its individual network, some organisms contain common sub-networks based on function. Given a certain sub-network, the distribution of organisms common to it represents the diversity of its function... 
LIGAND: chemical database for enzyme reactionsS Goto
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Bioinformatics 14:591-9. 1998..LIGAND chemical database is our attempt to solve these problems, at least for enzymatic reactions...- [Mastering Web-based analysis of gene networks]Susumu Goto
Tanpakushitsu Kakusan Koso 47:635-41. 2002 - LIGAND: database of chemical compounds and reactions in biological pathwaysSusumu Goto
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 30:402-4. 2002..genome.ad.jp/ligand/). LIGAND may be also downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/kegg/ligand/)... - LIGAND database for enzymes, compounds and reactionsS Goto
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 27:377-9. 1999..The LIGAND database can be accessed through the WWW (http://www.genome.ad.jp/dbget/ligand.html) or may be downloaded by anonymous FTP (ftp://kegg.genome.ad. jp/molecules/ligand)... - LIGAND: chemical database of enzyme reactionsS Goto
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 28:380-2. 2000..The LIGAND database can be accessed through the WWW (http://www.genome.ad.jp/dbget/ligand.html ) or may be downloaded by anonymous FTP (ftp://kegg.genome.ad.jp/molecules/ligand/ )... - Prediction of glycan structures from gene expression data based on glycosyltransferase reactionsShin Kawano
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
Bioinformatics 21:3976-82. 2005..Using expression profiles from the human carcinoma cell, glycan structures with sialic acid and sialyl Lewis X epitope were predicted, which corresponded well with experimental results... - KEGG for linking genomes to life and the environmentMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
Nucleic Acids Res 36:D480-4. 2008..KEGG DRUG contains all approved drugs in the US and Japan, and KEGG DISEASE is a new database linking disease genes, pathways, drugs and diagnostic markers... - KEGG as a glycome informatics resourceKosuke Hashimoto
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
Glycobiology 16:63R-70R. 2006..In all the KEGG resources, various objects including KEGG pathways, chemical compounds, as well as carbohydrate structures are commonly represented as graphs, which are widely studied and utilized in the computer science field... - SIMCOMP/SUBCOMP: chemical structure search servers for network analysesMasahiro Hattori
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 38:W652-6. 2010..The obtained links to PATHWAY or BRITE databases can be used to interpret as the biological meanings of chemical structures from the viewpoint of the various biological functions including metabolic networks... - Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathwaysMasahiro Hattori
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
J Am Chem Soc 125:11853-65. 2003..Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes... - Analysis of a lipid biosynthesis protein family and phospholipid structural variationsMichihiro Tanaka
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 22:191-201. 2010..These findings may provide clues to understanding structural variations and distributions of glycerophospholipids in different organisms... - KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chainsKiyoko F Aoki
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 32:W267-72. 2004..Analogously to BLAST, users are thus able to compare glycan structures of interest with glycans from different glycan databases using a variety of tree-alignment options. KCaM is currently available at http://glycan.genome.ad.jp... - Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosaYoshihiro Yamanishi
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Japan
FEBS J 274:2262-73. 2007..We observed that the predicted gene products catalyzed the expected reactions; no activity was seen when both gene products were omitted from the reaction... - Characterization and classification of adverse drug interactionsMasataka Takarabe
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 22:167-75. 2010..The merged data of drug interactions indicated drug properties that are related to drug interaction mechanisms or symptoms. We investigated the relationships between the drug groups and drug interaction mechanisms or symptoms... - Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotesMichihiro Tanaka
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 17:230-9. 2006..As a result, we estimated enzymatic reaction contents of 227 common ancestors from 228 extant species, and found that links of several specific metabolites have frequently changed during the course of evolution... - varDB: a pathogen-specific sequence database of protein families involved in antigenic variationC Nelson Hayes
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Bioinformatics 24:2564-5. 2008..AVAILABILITY: varDB is freely accessible at http://www.vardb.org/.. - Tools for investigating mechanisms of antigenic variation: new extensions to varDBC Nelson Hayes
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 23:46-59. 2009..We believe that the new sequence analysis tools will improve the usefulness and range of varDB... - A global representation of the carbohydrate structures: a tool for the analysis of glycanKosuke Hashimoto
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 16:214-22. 2005..These resources are available at http://www.genome.jp/kegg/glycan/... - [Integrated drug information resource]Minoru Kanehisa
Tanpakushitsu Kakusan Koso 52:1486-91. 2007 - KEGG for representation and analysis of molecular networks involving diseases and drugsMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 38:D355-60. 2010..The new disease/drug information resource named KEGG MEDICUS can be used as a reference knowledge base for computational analysis of molecular networks, especially, by integrating large-scale experimental datasets... - E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairsYoshihiro Yamanishi
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
Bioinformatics 25:i179-86. 2009..There are numerous reactions known to be present in various pathways but without any official EC numbers, most of which have no hope to be given ones because of the lack of the published articles on enzyme assays... - KEGG Atlas mapping for global analysis of metabolic pathwaysShujiro Okuda
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 36:W423-6. 2008..Once chemical compounds are converted to the C number identifiers in KEGG, metabolomics data can also be displayed in the global map. KEGG Atlas is available at http://www.genome.jp/kegg/atlas/... - An improved scoring scheme for predicting glycan structures from gene expression dataAkitsugu Suga
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 18:237-46. 2007.... - Network analysis of adverse drug interactionsMasataka Takarabe
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
Genome Inform 20:252-9. 2008..To characterize other interactions without interaction factors, we used the ATC classification system and found an association between interaction mechanisms and pharmacological/chemical subgroups... - Generalized reaction patterns for prediction of unknown enzymatic reactionsYugo Shimizu
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 20:149-58. 2008..Thus we will be able to define the similarity between enzymatic reactions by using this cluster information... - EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragmentsAli Masoudi-Nejad
Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 34:W459-62. 2006..The service provides an excellent bioinformatics tool to research groups in wet-lab as well as an all-in-one-tool for sequence handling to bioinformatics researchers... - The KEGG databases at GenomeNetMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 30:42-6. 2002..The KEGG databases are updated daily and made freely available (http://www.genome.ad.jp/kegg/)... - Structural variety of membrane permeable peptidesShiroh Futaki
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Curr Protein Pept Sci 4:87-96. 2003..In this review, we present the structural variety of membrane permeable peptides and provide a survey of the findings on the translocation of these peptides through the cell membranes... - Membrane permeability commonly shared among arginine-rich peptidesShiroh Futaki
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
J Mol Recognit 16:260-4. 2003..The structural and mechanistic features of the translocation of these membrane-permeable arginine-rich peptides are reviewed... - The KEGG resource for deciphering the genomeMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 32:D277-80. 2004..New efforts are being made to abstract knowledge, both computationally and manually, about ortholog clusters in the KO (KEGG Orthology) database, and to collect and analyze carbohydrate structures in the GLYCAN database... - Fast and accurate database homology search using upper bounds of local alignment scoresMasumi Itoh
Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611 0011, Japan
Bioinformatics 21:912-21. 2005..Results of computational experiments suggest that the method is dozens of times faster than SSEARCH if genome sequence data of closely related species are available... - Heuristics for chemical compound matchingMasahiro Hattori
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 14:144-53. 2003..Finally, we showed the effectiveness of our heuristics for compound pairs along metabolic pathways... - Extraction of phylogenetic network modules from prokayrote metabolic pathwaysTakuji Yamada
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 15:249-58. 2004..The enzymes of these modules are related by evolutionary and functional correlation. Our results give a valuable insight into the evolution of metabolic pathways... - Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coliShujiro Okuda
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 16:116-24. 2005..As a result, we also found that many conserved co-regulated gene pairs share the same functions. These observations would help to predict gene co-regulation and protein functions... - ODB: a database of operons accumulating known operons across multiple genomesShujiro Okuda
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 34:D358-62. 2006..In addition, it provides an operon prediction tool, which make the system useful for both bioinformatics researchers and experimental biologists. Our database is accessible at http://odb.kuicr.kyoto-u.ac.jp/... - From genomics to chemical genomics: new developments in KEGGMinoru Kanehisa
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 34:D354-7. 2006..Additionally, drug information is now stored separately and linked to new KEGG DRUG structure maps... - Comprehensive analysis and prediction of synthetic lethality using subcellular locationsTakuji Yamada
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Genome Inform 16:150-8. 2005..The prediction is based on the hierarchical aspect model (HAM) which learns from a data set of cellular location to estimate a likelihood value indicating the synthetic lethality between genes... - KEGG: kyoto encyclopedia of genes and genomesM Kanehisa
Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 28:27-30. 2000..The KEGG databases are daily updated and made freely available (http://www. genome.ad.jp/kegg/)... - KEGG bioinformatics resource for plant genomics researchAli Masoudi Nejad
Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto, Japan
Methods Mol Biol 406:437-58. 2007..Because all the resources in KEGG follow the same architecture and design, an appraisal of EGENES should give readers an idea of the available information stored in KEGG and how to use them efficiently... 
Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycansKosuke Hashimoto
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Carbohydr Res 344:881-7. 2009..Our findings suggest that universality and diversity of glycans originate from two types of evolution of glycosyltransferase families, namely conserved families with few paralogs and diverged families with many paralogs...- Extraction and analysis of chemical modification patterns in drug developmentDaichi Shigemizu
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
J Chem Inf Model 49:1122-9. 2009..These patterns were further applied to the reconstruction of a new structure map. The approach presented here may be applicable to systematic in silico drug modifications... - Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathwaysMina Oh
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
J Chem Inf Model 47:1702-12. 2007..The xenobiotics biodegradation pathways contained the most distinct RDM patterns, and we developed a scheme for predicting bacterial biodegradation pathways given chemical structures of, for example, environmental compounds... - Extraction of correlated gene clusters by multiple graph comparisonA Nakaya
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Genome Inform 12:44-53. 2001..cerevisiae, and estimated the possibility of utilizing our method for screening the datasets that are likely to contain many false positive relations... - The use of network analyses for elucidating mechanisms in cardiovascular diseaseDiego Diez
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Mol Biosyst 6:289-304. 2010..Lastly, the applications of these methods to cardiovascular disease are discussed with focus on the current limitations and future visions of this emerging field... - EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGGAli Masoudi-Nejad
Laboratory of Bioknowledge Systems, Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
Plant Physiol 144:857-66. 2007..EGENES will be updated at least once a year. EGENES is publicly available and is accessible by the following link or by KEGG's navigation system (http://www.genome.jp/kegg-bin/create_kegg_menu?category=plants_egenes)... - PathPred: an enzyme-catalyzed metabolic pathway prediction serverYuki Moriya
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
Nucleic Acids Res 38:W138-43. 2010..The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph... - varDB: a database of antigenic variant sequences--current status and future prospectsDiego Diez
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto, Japan
Acta Trop 114:144-51. 2010..The varDB project is still in its infancy but is expected to continue to grow with the addition of new organisms and gene families as well as input from the general research community... - The commonality of protein interaction networks determined in neurodegenerative disorders (NDDs)Vachiranee Limviphuvadh
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Bioinformatics 23:2129-38. 2007.... - The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomesKosuke Hashimoto
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
J Lipid Res 49:183-91. 2008..This study provides an example of a potent strategy to bridge the gap from genomic knowledge to chemical knowledge... - Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactionsMasaaki Kotera
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
J Am Chem Soc 126:16487-98. 2004.... - Temperature-sensitive mutations in various genes of Escherichia coli K12 can be suppressed by the ssrA gene for 10Sa RNA (tmRNA)H Nakano
Department of Biophysics, Graduate School of Science, Kyoto University, Japan
Mol Genet Genomics 265:615-21. 2001..Considering the fact that ssrA-suppressible mutants could be isolated as temperature-sensitive mutants with mutations in different genes, it seems evident that trans-translation can occur on mRNA that is not lacking its stop codon... - Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysisTadashi Kadowaki
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
Environ Sci Technol 41:7997-8003. 2007.... - Extraction of leukemia specific glycan motifs in humans by computational glycomicsYoshiyuki Hizukuri
Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
Carbohydr Res 340:2270-8. 2005.... - Genome sequence of the cat pathogen, Chlamydophila felisYoshinao Azuma
Department of Microbiology, Yamaguchi University School of Medicine, Ube, Yamaguchi 755 8505, Japan
DNA Res 13:15-23. 2006..The genomic DNA sequence of C. felis provides information for comprehension of diseases and elucidation of the chlamydial evolution... - Nuclear and chloroplast microsatellite analysis of Abies sachalinensis regeneration on fallen logs in a subboreal forest in Hokkaido, JapanChunlan Lian
Asian Natural Environmental Science Center, University of Tokyo, Midori cho 1 1 8, Nishitokyo shi, Tokyo 188 0002, Japan
Mol Ecol 17:2948-62. 2008..These recruitment characters of A. sachalinensis, with a fallen-log-dependent recruitment process, may result in significant genetic structure in early demographic stages... - Effects of pyridine exposure upon structural lipid metabolism in Swiss Webster miceCraig E Wheelock
Department of Entomology and Cancer Research Center, University of California, Davis, California 95616, USA
Chem Res Toxicol 21:583-90. 2008.... - Single-nucleotide polymorphism analysis by hybridization protection assay on solid supportSusumu Goto
Chugai Diagnostics Science, Tokyo, Japan
Anal Biochem 307:25-32. 2002..It also has advantages in discriminating one-base mismatch in targets. These characteristics make it a good candidate for practical SNP analysis of disease-related genes or drug-metabolizing enzymes in large numbers of samples...