Kengo Kinoshita

Summary

Affiliation: University of Tokyo
Country: Japan

Publications

  1. ncbi Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
    Kengo Kinoshita
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 25:2677-84. 2009
  2. ncbi Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    DNA Res 16:249-60. 2009
  3. ncbi ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
  4. ncbi Ligand-binding site prediction of proteins based on known fragment-fragment interactions
    Kota Kasahara
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8568, Japan
    Bioinformatics 26:1493-9. 2010
  5. ncbi A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human
    Yosuke Hatanaka
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 20:212-21. 2008
  6. ncbi Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials
    Matsuyuki Shirota
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Protein Sci 18:1906-15. 2009
  7. ncbi Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks
    Ashwini Patil
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    BMC Genomics 12:S19. 2011
  8. ncbi PiSite: a database of protein interaction sites using multiple binding states in the PDB
    Miho Higurashi
    Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D360-4. 2009
  9. ncbi Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network
    Ashwini Patil
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Protein Sci 19:1461-8. 2010
  10. ncbi Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction
    Yuko Tsuchiya
    Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Adv Appl Bioinform Chem 2:79-100. 2009

Detail Information

Publications14

  1. ncbi Multi-dimensional correlations for gene coexpression and application to the large-scale data of Arabidopsis
    Kengo Kinoshita
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Bioinformatics 25:2677-84. 2009
    ..We observed the correlation changes when the first ten principal components were subtracted step-by-step in large-scale Arabidopsis expression data...
  2. ncbi Rank of correlation coefficient as a comparable measure for biological significance of gene coexpression
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, Minato ku, Tokyo, Japan
    DNA Res 16:249-60. 2009
    ..This observation was evaluated by large-scale gene expression data for four species: Arabidopsis, human, mouse and rat...
  3. ncbi ATTED-II provides coexpressed gene networks for Arabidopsis
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D987-91. 2009
    ..With these enhanced functions for gene network representation, ATTED-II can help researchers to clarify the functional and regulatory networks of genes in Arabidopsis...
  4. ncbi Ligand-binding site prediction of proteins based on known fragment-fragment interactions
    Kota Kasahara
    Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8568, Japan
    Bioinformatics 26:1493-9. 2010
    ..Approaches using binding motif information are particularly effective. However, they can only be applied to well-known ligands that frequently appear in the structure databases...
  5. ncbi A novel strategy to search conserved transcription factor binding sites among coexpressing genes in human
    Yosuke Hatanaka
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1, Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 20:212-21. 2008
    ..We also applied basket method analysis for seeking combinatorial activities of those conserved TFBSs...
  6. ncbi Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials
    Matsuyuki Shirota
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Protein Sci 18:1906-15. 2009
    ..These results indicated that the performances of the potentials were more strongly influenced by their characteristics than by the accuracy of the definitions of the reference states...
  7. ncbi Assessing the utility of gene co-expression stability in combination with correlation in the analysis of protein-protein interaction networks
    Ashwini Patil
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    BMC Genomics 12:S19. 2011
    ..We assess the utility of gene co-expression stability as an additional measure to support the co-expression correlation in the analysis of protein-protein interaction networks...
  8. ncbi PiSite: a database of protein interaction sites using multiple binding states in the PDB
    Miho Higurashi
    Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Nucleic Acids Res 37:D360-4. 2009
    ..In addition, PiSite provides a list of proteins with multiple binding partners and multiple binding states, as well as up-to-date statistics of protein-protein interfaces. PiSite is available at http://pisite.hgc.jp...
  9. ncbi Domain distribution and intrinsic disorder in hubs in the human protein-protein interaction network
    Ashwini Patil
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo 108 8639, Japan
    Protein Sci 19:1461-8. 2010
    ..Further, hubs with fewer domains use greater levels of intrinsic disorder to facilitate interaction promiscuity with the prevalence of disorder decreasing with increasing number of ordered domains...
  10. ncbi Classification of heterodimer interfaces using docking models and construction of scoring functions for the complex structure prediction
    Yuko Tsuchiya
    Institute of Medical Science, University of Tokyo, Tokyo, Japan
    Adv Appl Bioinform Chem 2:79-100. 2009
    ..Consequently, we found four heterodimer clusters, and then constructed the multiple scoring functions, each of which was optimized for each cluster. Our multiple scoring functions were applied to the predictions in the unbound docking...
  11. ncbi Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs
    Hirokazu Chiba
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    BMC Genomics 9:152. 2008
    ..A number of studies have compared protein sequences or promoter sequences between mammals, which provided many insights into genomics. However, the correlation between protein conservation and promoter conservation remains controversial...
  12. ncbi Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression
    Matsuyuki Shirota
    Human Genome Center, Institute of Medical Science, University of Tokyo, 4 6 1 Shirokanedai, Minato ku, Tokyo 108 8639, Japan
    Genome Inform 23:149-58. 2009
    ..The meta-score could be also used as the absolute quality of the structures. Our study suggests the benefit of combining several different scoring functions for model evaluation...
  13. ncbi Discrimination between biological interfaces and crystal-packing contacts
    Yuko Tsuchiya
    Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokanedai, Minatoku, Tokyo, 108 8639, Japan
    Adv Appl Bioinform Chem 1:99-113. 2008
    ..Thus, the COMP discriminator can also be used as an indicator of the "biological-ness" of protein-protein interfaces...
  14. ncbi COXPRESdb: a database of coexpressed gene networks in mammals
    Takeshi Obayashi
    Human Genome Center, Institute of Medical Science, The University of Tokyo, 4 6 1 Shirokane dai, Minato ku, Tokyo, Japan
    Nucleic Acids Res 36:D77-82. 2008
    ..COXPRESdb also provides a view to compare the human and mouse coexpression patterns to estimate the conservation between the two species...