Shuichi Kawashima

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. 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
  2. pmc The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
    Toshiaki Katayama
    Database Center for Life Science, Research Organization of Information and Systems, 2 11 16 Yayoi, Bunkyo ku, Tokyo, 113 0032, Japan
    J Biomed Semantics 2:4. 2011
  3. pmc The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
    Toshiaki Katayama
    Database Center for Life Science, Research Organization of Information and Systems, 2 11 16 Yayoi, Bunkyo ku, Tokyo, 113 0032, Japan
    J Biomed Semantics 1:8. 2010
  4. 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
  5. ncbi request reprint Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes
    Shuichi Kawashima
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 19:50-60. 2007
  6. pmc AAindex: amino acid index database, progress report 2008
    Shuichi Kawashima
    Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai Minato ku Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D202-5. 2008
  7. 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
  8. 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
  9. 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
  10. ncbi request reprint Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis
    Shinobu Okamoto
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
    Proteomics 7:900-9. 2007

Detail Information

Publications17

  1. 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/)...
  2. pmc The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications
    Toshiaki Katayama
    Database Center for Life Science, Research Organization of Information and Systems, 2 11 16 Yayoi, Bunkyo ku, Tokyo, 113 0032, Japan
    J Biomed Semantics 2:4. 2011
    ..abstract:..
  3. pmc The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*
    Toshiaki Katayama
    Database Center for Life Science, Research Organization of Information and Systems, 2 11 16 Yayoi, Bunkyo ku, Tokyo, 113 0032, Japan
    J Biomed Semantics 1:8. 2010
    ....
  4. 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...
  5. ncbi request reprint Comparative pair-wise domain-combinations for screening the clade specific domain-architectures in metazoan genomes
    Shuichi Kawashima
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 19:50-60. 2007
    ..Such a small number of ecdysozoan-specific domain-combinations is consistent with the extensive gene-losses through the evolution of ecdysozoans...
  6. pmc AAindex: amino acid index database, progress report 2008
    Shuichi Kawashima
    Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokane dai Minato ku Tokyo 108 8639, Japan
    Nucleic Acids Res 36:D202-5. 2008
    ..The database can be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.jp/dbget-bin/www_bfind?aaindex) or downloaded by anonymous FTP (ftp://ftp.genome.jp/pub/db/community/aaindex/)...
  7. 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...
  8. 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...
  9. 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
    ....
  10. ncbi request reprint Prediction of nitrogen metabolism-related genes in Anabaena by kernel-based network analysis
    Shinobu Okamoto
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Japan
    Proteomics 7:900-9. 2007
    ..The prediction of functional relationships between proteins rather than functions of individual proteins will thus assist the discovery from the large-scale datasets...
  11. 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...
  12. 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/...
  13. 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...
  14. ncbi request reprint New amino acid indices based on residue network topology
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
    Genome Inform 18:152-61. 2007
    ..75. It indicates that the network property based amino acid indices can be useful complements to the existing physicochemical property based amino acid indices...
  15. 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...
  16. pmc Update of MAGEST: Maboya Gene Expression patterns and Sequence Tags
    Takeshi Kawashima
    Department of Zoology, Graduate School of Science, Kyoto University, Sakyo ku, Kyoto 606 8502, Japan
    Nucleic Acids Res 30:119-20. 2002
    ..Using this information comprehensively, we should obtain new information on gene functions. The MAGEST database is accessible via the Internet at http://www.genome.ad.jp/magest/...
  17. pmc VisANT 3.0: new modules for pathway visualization, editing, prediction and construction
    Zhenjun Hu
    Center for Advanced Genomic Technology, Boston University, Boston, MA 02215, USA
    Nucleic Acids Res 35:W625-32. 2007
    ..Pathways in the format of VisML can be securely shared within an interested group or published online using a simple Web link. VisANT is freely available at http://visant.bu.edu...