Shujiro Okuda

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. pmc KAAS: an automatic genome annotation and pathway reconstruction server
    Yuki Moriya
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 35:W182-5. 2007

Detail Information

Publications16

  1. 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...
  2. 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/...
  3. 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...
  4. 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...
  5. 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/...
  6. 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...
  7. 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...
  8. 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...
  9. 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...
  10. pmc KAAS: an automatic genome annotation and pathway reconstruction server
    Yuki Moriya
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Nucleic Acids Res 35:W182-5. 2007
    ..The method is based on sequence similarities, bi-directional best hit information and some heuristics, and has achieved a high degree of accuracy when compared with the manually curated KEGG GENES database...
  11. doi request reprint Identification of Enzyme Genes Using Chemical Structure Alignments of Substrate-Product Pairs
    Yuki Moriya
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    J Chem Inf Model 56:510-6. 2016
    ..We believe that this approach will facilitate experimental identification of genes for orphan enzymes. ..
  12. 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...
  13. ncbi request reprint [Integrated drug information resource]
    Minoru Kanehisa
    Tanpakushitsu Kakusan Koso 52:1486-91. 2007
  14. pmc GlycoRDF: an ontology to standardize glycomics data in RDF
    René Ranzinger
    Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA, Research Center for Medical Glycoscience, National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan, Faculty of Engineering, Soka University, Tokyo, Japan, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia, Database Center for Life Science, Research Organization of Information and Systems, Chiba, Japan, Institute of Veterinary Physiology and Biochemistry, Justus Liebig University Giessen, Giessen, Germany, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan, N D Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia and Laboratory of Glyco organic Chemistry, The Noguchi Institute, Tokyo, Japan
    Bioinformatics 31:919-25. 2015
    ..Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information...
  15. ncbi request reprint Extracting sequence motifs and the phylogenetic features of SNARE-dependent membrane traffic
    Akiyasu C Yoshizawa
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611 0011, Japan
    Traffic 7:1104-18. 2006
    ....
  16. pmc Electrophoretic mobility of Bacillus subtilis knockout mutants with and without flagella
    Shujiro Okuda
    Faculty of Science and Engineering, Ritsumeikan University, Kusatsu 525 8577, Japan
    J Bacteriol 185:3711-7. 2003
    ..These results indicate that the flagella are a key factor influencing cell surface properties...