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Mathematical modeling of transcriptional regulatory networks based on bipartite graphs.

Research Project

Project/Area Number 21700327
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionFuture University-Hakodate

Principal Investigator

JOSE Nacher  Future University-Hakodate, システム情報科学部, 准教授 (60452984)

Project Period (FY) 2009 – 2010
Project Status Completed (Fiscal Year 2010)
Budget Amount *help
¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2009: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000)
Keywords生体生命システム情報学 / 複雑ネットワーク科学 / 数理モデル / データ分析 / 転写調節ネットワーク
Research Abstract

We construct the ncRNA-protein interaction network and analyze its large-scale organization as well as the local interaction structure. In addition, an evolutionary model for bipartite graphs that includes several biological mechanisms is presented. We also investigate the distribution of molecular functionalities in these networks by using optimization algorithms. Our findings show that both transcriptional and ncRNA-interactions exhibit characteristic couplings between network and functionality that deviate from random expectations, supporting growing evidences for a ncRNA regulatory capability.

Report

(3 results)
  • 2010 Annual Research Report   Final Research Report ( PDF )
  • 2009 Annual Research Report
  • Research Products

    (7 results)

All 2011 2010

All Journal Article (4 results) (of which Peer Reviewed: 4 results) Presentation (3 results)

  • [Journal Article] Structural characterization and modeling of ncRNA-proten interactions2010

    • Author(s)
      J.C.Nacher, N.Araki
    • Journal Title

      BioSystems Elsevier 101

      Pages: 10-19

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The role of internal duplication in the evolution of multi-domain proteins2010

    • Author(s)
      J.C.Nacher, M.Hayashida, T.Akutsu
    • Journal Title

      BioSystems Elsevier 101

      Pages: 127-135

    • Related Report
      2010 Final Research Report
    • Peer Reviewed
  • [Journal Article] The role of internal duplication in the evolution of multi-domain proteins2010

    • Author(s)
      J.C.Nacher, M.Hayashida, T.Akutsu
    • Journal Title

      BioSystems Elsevier

      Volume: 101 Pages: 127-135

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural characterization and modeling of ncRNA-protein interactions2010

    • Author(s)
      J.C.Nacher, N.Araki
    • Journal Title

      Biosystems Elsevier (印刷中)

    • NAID

      10026760625

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] On the relation between structure and biological function in transcriptional networks and ncRNA-mediated interactions2011

    • Author(s)
      J.C.Nacher, N.Araki
    • Organizer
      2011 IEEE International Conference on Bioscience, Biochemistry and Bioinformatics, pp.348-352
    • Place of Presentation
      Peninsula Excelsior Hotel (Singapore)
    • Year and Date
      2011-02-28
    • Related Report
      2010 Annual Research Report
  • [Presentation] Identifying genes induced by different pathogen-associated molecular patterns2011

    • Author(s)
      J.C.Nacher, V.B.Ryabov
    • Organizer
      2011 Annual International Conference on Bioinformatics and Computational Biology, pp.25-30
    • Place of Presentation
      Hotel Fort Canning (Singapore)
    • Year and Date
      2011-02-28
    • Related Report
      2010 Annual Research Report
  • [Presentation] On the relation between structure and biological function in transcriptional networks and ncRNA-mediated interactions2011

    • Author(s)
      J.C.Nacher, N.Araki
    • Organizer
      In Proc.of 2011 IEEE International Conference on Bioscience, Biochemistry and Bioinformatics pp.348-352
    • Place of Presentation
      Singapore
    • Related Report
      2010 Final Research Report

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Published: 2009-04-01   Modified: 2016-04-21  

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