S Goto

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. pmc SIMCOMP/SUBCOMP: chemical structure search servers for network analyses
    Masahiro Hattori
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 38:W652-6. 2010
  2. pmc GENIES: gene network inference engine based on supervised analysis
    Masaaki Kotera
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 40:W162-7. 2012
  3. pmc KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters
    Akihiro Nakaya
    Center for Transdisciplinary Research, Niigata University, 1 757 Asahimachi dori, Chuo Ku, Niigata 951 8585, Japan
    Nucleic Acids Res 41:D353-7. 2013
  4. pmc Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
    Masaaki Kotera
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Bioinformatics 29:i135-44. 2013
  5. pmc Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics
    Diego Diez
    Laboratory of Bioinformatics and Genomics, World Premier International Immunology Frontier Research Center, Osaka University, Osaka 565 0871, Japan
    BMC Med Genomics 5:27. 2012
  6. pmc Evaluation method for the potential functionome harbored in the genome and metagenome
    Hideto Takami
    Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima, Yokosuka, 237 0061, Japan
    BMC Genomics 13:699. 2012
  7. pmc MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites
    Masaaki Kotera
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 12:S1. 2011
  8. pmc Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
    Masumi Itoh
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Genome Biol 8:R121. 2007
  9. pmc Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli
    Shujiro Okuda
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    BMC Genomics 8:48. 2007
  10. pmc Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
    Masashi Fujita
    Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, Japan
    BMC Bioinformatics 8:225. 2007

Detail Information

Publications68

  1. pmc SIMCOMP/SUBCOMP: chemical structure search servers for network analyses
    Masahiro 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...
  2. pmc GENIES: gene network inference engine based on supervised analysis
    Masaaki Kotera
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 40:W162-7. 2012
    ..GENIES (http://www.genome.jp/tools/genies/) is publicly available as one of the genome analysis tools in GenomeNet...
  3. pmc KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters
    Akihiro Nakaya
    Center for Transdisciplinary Research, Niigata University, 1 757 Asahimachi dori, Chuo Ku, Niigata 951 8585, Japan
    Nucleic Acids Res 41:D353-7. 2013
    ..The KEGG OC resources are accessible via OC Viewer that provides an interactive visualization of OCs at different taxonomic levels...
  4. pmc Supervised de novo reconstruction of metabolic pathways from metabolome-scale compound sets
    Masaaki Kotera
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Bioinformatics 29:i135-44. 2013
    ..Therefore, the most important challenge in metabolomics is the automated de novo reconstruction of metabolic pathways, which includes the elucidation of previously unknown reactions to bridge the metabolic gaps...
  5. pmc Network analysis identifies a putative role for the PPAR and type 1 interferon pathways in glucocorticoid actions in asthmatics
    Diego Diez
    Laboratory of Bioinformatics and Genomics, World Premier International Immunology Frontier Research Center, Osaka University, Osaka 565 0871, Japan
    BMC Med Genomics 5:27. 2012
    ..While the role of GCs in disease management is well understood, few studies have examined the holistic effects on the airway epithelium...
  6. pmc Evaluation method for the potential functionome harbored in the genome and metagenome
    Hideto Takami
    Microbial Genome Research Group, Japan Agency for Marine Earth Science and Technology JAMSTEC, 2 15 Natsushima, Yokosuka, 237 0061, Japan
    BMC Genomics 13:699. 2012
    ..We have developed a new evaluation method for the potential functionome, based on the completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG) functional modules...
  7. pmc MUCHA: multiple chemical alignment algorithm to identify building block substructures of orphan secondary metabolites
    Masaaki 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...
  8. pmc Evolutionary history and functional implications of protein domains and their combinations in eukaryotes
    Masumi 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...
  9. pmc Characterization of relationships between transcriptional units and operon structures in Bacillus subtilis and Escherichia coli
    Shujiro 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...
  10. pmc Mining prokaryotic genomes for unknown amino acids: a stop-codon-based approach
    Masashi 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...
  11. pmc Regulation of metabolic networks by small molecule metabolites
    Alex 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...
  12. pmc Extraction of phylogenetic network modules from the metabolic network
    Takuji 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...
  13. ncbi request reprint LIGAND: chemical database for enzyme reactions
    S 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...
  14. pmc LIGAND: database of chemical compounds and reactions in biological pathways
    Susumu 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/)...
  15. ncbi request reprint [Mastering Web-based analysis of gene networks]
    Susumu Goto
    Tanpakushitsu Kakusan Koso 47:635-41. 2002
  16. pmc LIGAND database for enzymes, compounds and reactions
    S 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)...
  17. pmc LIGAND: chemical database of enzyme reactions
    S 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/ )...
  18. ncbi request reprint Prediction of glycan structures from gene expression data based on glycosyltransferase reactions
    Shin 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...
  19. pmc KEGG for linking genomes to life and the environment
    Minoru 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...
  20. ncbi request reprint Extraction of correlated gene clusters by multiple graph comparison
    A 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...
  21. ncbi request reprint Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways
    Masahiro 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...
  22. ncbi request reprint KEGG as a glycome informatics resource
    Kosuke 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...
  23. pmc KEGG: kyoto encyclopedia of genes and genomes
    M 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/)...
  24. pmc E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs
    Yoshihiro 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...
  25. ncbi request reprint Analysis of a lipid biosynthesis protein family and phospholipid structural variations
    Michihiro 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...
  26. ncbi request reprint Characterization and classification of adverse drug interactions
    Masataka 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...
  27. ncbi request reprint [Integrated drug information resource]
    Minoru Kanehisa
    Tanpakushitsu Kakusan Koso 52:1486-91. 2007
  28. pmc KEGG for representation and analysis of molecular networks involving diseases and drugs
    Minoru 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...
  29. ncbi request reprint Generalized reaction patterns for prediction of unknown enzymatic reactions
    Yugo 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...
  30. pmc KEGG Atlas mapping for global analysis of metabolic pathways
    Shujiro 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/...
  31. ncbi request reprint An improved scoring scheme for predicting glycan structures from gene expression data
    Akitsugu Suga
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Genome Inform 18:237-46. 2007
    ....
  32. pmc varDB: a pathogen-specific sequence database of protein families involved in antigenic variation
    C Nelson Hayes
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Bioinformatics 24:2564-5. 2008
    ..This resource will enable researchers to compare antigenic variation within and across taxa with the goal of identifying common mechanisms of pathogenicity to assist in the fight against a range of devastating diseases...
  33. ncbi request reprint Network analysis of adverse drug interactions
    Masataka 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...
  34. ncbi request reprint Tools for investigating mechanisms of antigenic variation: new extensions to varDB
    C 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...
  35. ncbi request reprint Analysis of the differences in metabolic network expansion between prokaryotes and eukaryotes
    Michihiro 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...
  36. ncbi request reprint Comprehensive analysis and prediction of synthetic lethality using subcellular locations
    Takuji 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...
  37. ncbi request reprint Conservation of gene co-regulation between two prokaryotes: Bacillus subtilis and Escherichia coli
    Shujiro 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...
  38. ncbi request reprint A global representation of the carbohydrate structures: a tool for the analysis of glycan
    Kosuke 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/...
  39. pmc From genomics to chemical genomics: new developments in KEGG
    Minoru 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...
  40. ncbi request reprint Extraction of phylogenetic network modules from prokayrote metabolic pathways
    Takuji 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...
  41. pmc ODB: a database of operons accumulating known operons across multiple genomes
    Shujiro 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/...
  42. ncbi request reprint Heuristics for chemical compound matching
    Masahiro 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...
  43. ncbi request reprint Fast and accurate database homology search using upper bounds of local alignment scores
    Masumi Itoh
    Bioinformatics Center, Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611 0011, Japan
    Bioinformatics 21:912-21. 2005
    ..However, recent growth of sequence database size makes homolog detection difficult, and rapid and accurate methods are required...
  44. pmc KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains
    Kiyoko 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...
  45. pmc The KEGG resource for deciphering the genome
    Minoru 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...
  46. pmc EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments
    Ali 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...
  47. ncbi request reprint Membrane permeability commonly shared among arginine-rich peptides
    Shiroh 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...
  48. ncbi request reprint Prediction of missing enzyme genes in a bacterial metabolic network. Reconstruction of the lysine-degradation pathway of Pseudomonas aeruginosa
    Yoshihiro 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...
  49. ncbi request reprint Structural variety of membrane permeable peptides
    Shiroh 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...
  50. pmc The KEGG databases at GenomeNet
    Minoru 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/)...
  51. ncbi request reprint Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways
    Mina 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...
  52. doi request reprint Extraction and analysis of chemical modification patterns in drug development
    Daichi 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...
  53. doi request reprint Comprehensive analysis of glycosyltransferases in eukaryotic genomes for structural and functional characterization of glycans
    Kosuke 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...
  54. ncbi request reprint KEGG bioinformatics resource for plant genomics research
    Ali 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...
  55. ncbi request reprint The repertoire of desaturases and elongases reveals fatty acid variations in 56 eukaryotic genomes
    Kosuke 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...
  56. ncbi request reprint Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions
    Masaaki Kotera
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    J Am Chem Soc 126:16487-98. 2004
    ....
  57. doi request reprint The use of network analyses for elucidating mechanisms in cardiovascular disease
    Diego 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...
  58. pmc EGENES: transcriptome-based plant database of genes with metabolic pathway information and expressed sequence tag indices in KEGG
    Ali 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)...
  59. doi request reprint varDB: a database of antigenic variant sequences--current status and future prospects
    Diego 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...
  60. ncbi request reprint 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
    ....
  61. pmc PathPred: an enzyme-catalyzed metabolic pathway prediction server
    Yuki 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...
  62. ncbi request reprint 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...
  63. ncbi request reprint Identification of endocrine disruptor biodegradation by integration of structure-activity relationship with pathway analysis
    Tadashi Kadowaki
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Environ Sci Technol 41:7997-8003. 2007
    ....
  64. ncbi request reprint Extraction of leukemia specific glycan motifs in humans by computational glycomics
    Yoshiyuki Hizukuri
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Carbohydr Res 340:2270-8. 2005
    ....
  65. ncbi request reprint Genome sequence of the cat pathogen, Chlamydophila felis
    Yoshinao 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...
  66. ncbi request reprint Nuclear and chloroplast microsatellite analysis of Abies sachalinensis regeneration on fallen logs in a subboreal forest in Hokkaido, Japan
    Chunlan 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...
  67. ncbi request reprint Single-nucleotide polymorphism analysis by hybridization protection assay on solid support
    Susumu 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...
  68. doi request reprint Effects of pyridine exposure upon structural lipid metabolism in Swiss Webster mice
    Craig E Wheelock
    Department of Entomology and Cancer Research Center, University of California, Davis, California 95616, USA
    Chem Res Toxicol 21:583-90. 2008
    ....