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Development of static analysis methods for neuronal signal transduction

Research Project

Project/Area Number 20700272
Research Category

Grant-in-Aid for Young Scientists (B)

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

Principal Investigator

KIKUCHI Shinichi  Keio University, 環境情報学部, 専任講師 (50348851)

Project Period (FY) 2008 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2009: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
Fiscal Year 2008: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywords生体生命システム情報学 / シグナル伝達 / マイクロアレイ / 神経細胞 / 海馬 / 静的解析ネットワーク / ネットワーク / システム生物学 / バイオインフォマティクス
Research Abstract

Dynamic models of signal transduction involve a combinatorial explosion problem in their kinetic parameters modeled. A methodology proposed was a kind of static modeling. An algebraic method showed a reaction participation and pathway ength of extreme pathways which span the kernel of the stoichiometric matrix. Also, a discrete analysis revealed the distribution of k-shortest pathways of a weighted, directed graph. These calculations were possible alternatives for a schematic representation of signal transduction.

Report

(3 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • Research Products

    (21 results)

All 2009 2008 Other

All Journal Article (7 results) (of which Peer Reviewed: 7 results) Presentation (12 results) Remarks (2 results)

  • [Journal Article] Network features and pathway analyses in signal transduction cascade2009

    • Author(s)
      R. Yanashima, N. Kitagawa, Y. Matsubara, R. Weatheritt, K. Oka, S. Kikuchi, M. Tomita, S. Ishizaki.
    • Journal Title

      3

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Network features and pathway analyses in signal transduction cascade2009

    • Author(s)
      R.Yanashima, et al.
    • Journal Title

      Frontiers in Neuroscience 3

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Network features and pathway analyses in signal transduction cascade2009

    • Author(s)
      R. Yanashima
    • Journal Title

      Frontiers in Neuroscience (in press)

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Algebraic method for the analysis of signaling crosstal2008

    • Author(s)
      Y. Matsubara, S. Kikuchi, M. Sugimoto, K. Oka, M. Tomita.
    • Journal Title

      Artificial Life 14(1)

      Pages: 81-94

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Comparison of metabolite production capability indices generated by network analysis methods2008

    • Author(s)
      K. Ishii, S. Nakamura, M. Morohashi, M. Sugimoto, Y. Ohashi, S. Kikuchi, M. Tomita.
    • Journal Title

      Biosystems 91(1)

      Pages: 166-170

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Algebraic method for the analysis of signaling crosstalk2008

    • Author(s)
      Y. Matsubara
    • Journal Title

      Artificial Life 14(1)

      Pages: 81-94

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Comparison of metabolite production capability indices generated by net work analysis methods2008

    • Author(s)
      K. Ishii
    • Journal Title

      Biosystems 91(1)

      Pages: 166-170

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Presentation] 哺乳類海馬CA1部位シグナル伝達経路の主経路抽出法2009

    • Author(s)
      簗島亮次
    • Organizer
      日本神経回路学会全国大会(JNNS)
    • Place of Presentation
      東北大学(宮城県仙台市)
    • Year and Date
      2009-09-25
    • Related Report
      2009 Annual Research Report
  • [Presentation] 哺乳類海馬CA1部位シグナル伝達経路の主経路抽出法2009

    • Author(s)
      簗島亮次, 菊地進一, 石崎俊
    • Organizer
      日本神経回路学会全国大会
    • Place of Presentation
      東北大学
    • Year and Date
      2009-08-15
    • Related Report
      2009 Final Research Report
  • [Presentation] Robustness and differentiation of signal transduction networks(招待講演)2009

    • Author(s)
      S.Kikuchi
    • Organizer
      Intl Workshop on Logical Aspects of Fault Tolerance( LAFT)
    • Place of Presentation
      UCLA(アメリカ合衆国ロサンゼルス市)
    • Year and Date
      2009-08-15
    • Related Report
      2009 Annual Research Report
  • [Presentation] Temporal-specific optimization of k-shortest paths and network motifs in neuronal signaling cascades2009

    • Author(s)
      S. Kikuchi, Y. Matsubara, K. Ishii, M. Sugimoto, K. Oka, M. Tomita
    • Organizer
      INCF Congress of Neuroinformatics
    • Place of Presentation
      Stockholm.
    • Related Report
      2009 Final Research Report
  • [Presentation] アルツハイマー病における海馬シグナル伝達経路のネットワーク解析2008

    • Author(s)
      簗島亮次, 北川統之, 菊地進一, 石崎俊
    • Organizer
      日本神経回路学会大会
    • Place of Presentation
      産業技術総合研究所(つくば市).
    • Related Report
      2009 Final Research Report
  • [Presentation] Significance for hippocampal memory of context-like information generated in hippocampal CA3c2008

    • Author(s)
      T. Samura, M. Hattori, S. Kikuchi, S. Ishizaki.
    • Organizer
      Proc. Intl Conf on Neural Information Processing (ICONIP)
    • Place of Presentation
      Auckland.
    • Related Report
      2009 Final Research Report
  • [Presentation] 海馬CA3の空間・時間選択性の相互作用によるT字迷路課題を想定したループ時系列の曖昧性解消2008

    • Author(s)
      佐村俊和, 服部元信, 菊地進一, 石崎俊
    • Organizer
      情報科学技術フォーラム(FIT)
    • Place of Presentation
      慶應義塾大学(藤沢市)
    • Related Report
      2009 Final Research Report
  • [Presentation] 海馬CA3の空間・時間選択性の相互作用による丁字迷路課題を想定したループ時系列の曖昧性解消2008

    • Author(s)
      佐村俊和
    • Organizer
      情報科学技術フォーラム(FIT)
    • Place of Presentation
      慶應義塾大学(藤沢市)
    • Related Report
      2008 Annual Research Report
  • [Presentation] Temporal-specific optimization of k-shortest paths and network motifs in neuronal signaling cascades2008

    • Author(s)
      S. Kikuchi
    • Organizer
      INCF Congress of Neuroinformatics
    • Place of Presentation
      Stockholm, Sweaden
    • Related Report
      2008 Annual Research Report
  • [Presentation] アルツハイマー病における海馬シグナル伝達経路のネットワーク解析2008

    • Author(s)
      簗島亮次
    • Organizer
      日本神経回路学会大会
    • Place of Presentation
      産業技術総合研究所(つくば市)
    • Related Report
      2008 Annual Research Report
  • [Presentation] Significance for Hippocampal Memory of Context-like Information Gener ated in Hinnoesmnal CA3c2008

    • Author(s)
      Samura, T.
    • Organizer
      nternational Conference on Neural Information ProcessinE (ICONIP)
    • Place of Presentation
      Auckland, New Zealand
    • Related Report
      2008 Annual Research Report
  • [Presentation] Robustness and differentiation of signal transduction networks

    • Author(s)
      S. Kikuchi
    • Organizer
      Intl Workshop on Logical Aspects of Fault Tolerance (LAFT)
    • Place of Presentation
      UCLA(サンフランシスコ)(Invited talk)
    • Related Report
      2009 Final Research Report
  • [Remarks]

    • URL

      http://web.sfc.keio.ac.jp/~kikuchi/

    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://web.sfc.keio.ac.jp/~kikuchi/

    • Related Report
      2008 Annual Research Report

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Published: 2008-04-01   Modified: 2016-04-21  

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