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2008 Fiscal Year Final Research Report

Dynamic simulation and system analysis for gene regulatory networks

Research Project

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Project/Area Number 18300098
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Bioinformatics/Life informatics
Research InstitutionKyushu Institute of Technology

Principal Investigator

KURATA Hiroyuki  Kyushu Institute of Technology, 大学院・情報工学研究院, 教授 (90251371)

Co-Investigator(Kenkyū-buntansha) SHIMIZU Kazuyuki  九州工業大学, 大学院・情報工学研究院, 教授 (00150318)
Project Period (FY) 2006 – 2008
Keywordsシミュレーション工学 / 生体生命情報学 / ゲノム / 微生物 / ロバストネス
Research Abstract

大腸菌アンモニア同化システムの動的モデルをシステム解析することにより環境中のアンモニア濃度の変化に対してシステムがヒステリシスを示すことを予測して, 生物実験を用いて証明した。ヒステリシスがポジティブフィードバック制御に起因することを、理論解析により明らかにした。また、システムのロバストネス解析によって, 窒素同化システムは、ロバストな部分とファインチューンの部分明確に分かれていることわかった.

  • Research Products

    (16 results)

All 2009 2008 2007 2006

All Journal Article (8 results) (of which Peer Reviewed: 6 results) Presentation (8 results)

  • [Journal Article] A gradual update method for simulating the steady-state solution of stiff differential equations in metabolic circuits2009

    • Author(s)
      Emi Shiraishi Kazuhiro Maeda Hiroyuki Kurata
    • Journal Title

      Bioprocess Biosyst. Eng 32

      Pages: 283-288

    • Peer Reviewed
  • [Journal Article] Visualizing Global Properties of Large Complex Networks2008

    • Author(s)
      Li W., Kurata H.
    • Journal Title

      PLoS ONE 3

      Pages: e2541

    • Peer Reviewed
  • [Journal Article] Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli2008

    • Author(s)
      Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata
    • Journal Title

      Molecular Systems Biology 4

      Pages: 160

    • Peer Reviewed
  • [Journal Article] Extended CADLIVE : a novel graphical notation for designing a biochemical network map that enables computational pathway analysis2007

    • Author(s)
      Hiroyuki Kurata, Kentaro Inoue, Kazuhiro Maeda, Koichi Masaki, Yuki Shimokawa, Quanyu Zhao
    • Journal Title

      Nucleic Acids Res 35

      Pages: e134

    • Peer Reviewed
  • [Journal Article] Mathematical identification of critical reactions in the interlocked feedback model2007

    • Author(s)
      H. Kurata, T. Tanaka, F. Ohnishi
    • Journal Title

      PLoS One 2

      Pages: e1103

    • Peer Reviewed
  • [Journal Article] A simple model of positive feedback of the nitrogen assimilation system in E. coli2007

    • Author(s)
      Kouichi Masaki, Hiroyuki Kurata
    • Journal Title

      IPSJ Transactions on Mathematical Modeling and Its Applications 48

      Pages: 104-109

    • Peer Reviewed
  • [Journal Article] Module-Based Analysis of Robustness Tradeoffs in the Heat Shock Response System2006

    • Author(s)
      H. Kurata, H. El Samad, R. Iwasaki, H. Othake, J.C. Doyle, I. Grigorova, C. Gross, and M. Khammash
    • Journal Title

      PLoS Computational Biology 2

      Pages: e59

  • [Journal Article] Effective and fast optimization for a dynamic model of the Drosophila circadian oscillator2006

    • Author(s)
      Shin Tanaka, Hiroyuki Kurata, Takeshi Ohashi
    • Journal Title

      IEEE International Conference on Systems, Man, and Cybernetics(Taipei, Taiwan)

      Pages: 3596-3601

  • [Presentation] Extended CADLIVE : Computer-aided rational design of living systems(S02-1-2)2008

    • Author(s)
      Kentaro Inoue, Tetsuya Shimabara, Toshikazu Onaka, Erika Fujiura, Hiroyuki Kurata
    • Organizer
      The proceedings of the 2th annual conference of the Japanese Society for Bioinformatics
    • Place of Presentation
      Osaka
    • Year and Date
      20081215-16
  • [Presentation] Searching multiple sets of kinetic parameters values reproducing target experimental data in dynamic biochemical models(S063-1-2)2008

    • Author(s)
      Kazuhiro Maeda, Hiroyuki Kurata
    • Organizer
      The proceedings of the 2008th annual conference of the Japanese Society for Bioinformatics
    • Place of Presentation
      Osaka
    • Year and Date
      20081215-16
  • [Presentation] CADLIVE : Computer aided design of biochemical systems(Oral Presentation)2008

    • Author(s)
      Hiroyuki Kurata
    • Organizer
      Supplement of Journal of Biotechnology : 13 th International Biotechnology Symposium and Exhibition (IBS2008)
    • Place of Presentation
      Dailen, China
    • Year and Date
      20081012-17
  • [Presentation] Prediction of flux distribution of mutants by enzyme control fluxes with maximum entropy principal(Oral Presentation)2008

    • Author(s)
      Quanyu Zhao, Hiroyuki Kurata
    • Organizer
      Supplement of Journal of Biotechnology : 13 th International Biotechnology Symposium and Exhibition (IBS2008)
    • Place of Presentation
      Dailen, China
    • Year and Date
      20081012-17
  • [Presentation] Computer-aided rational design of the phosphotransferase system for enhanced glucose uptake in Escherichia coli(Oral Presentation)2008

    • Author(s)
      Yousuke Nishio, Yoshihiro Usuda, Kazuhiko Matsui, Hiroyuki Kurata
    • Organizer
      Supplement of Journal of Biotechnology : 13 th International Biotechnology Symposium and Exhibition (IBS2008)
    • Place of Presentation
      Dailen, China
    • Year and Date
      20081012-17
  • [Presentation] CADLIVE for Construction and Dynamic Simulation of Biochemical Networks2007

    • Author(s)
      Kazuhiro Maeda, Hiroyuki Kurata
    • Organizer
      Proceedings of Asia Pacific Biochemical Engineering Conference
    • Place of Presentation
      Taipei
    • Year and Date
      20071104-07
  • [Presentation] Sensitivity analysis for the E. coli nitrogen assimilation system(16 : P010-1-2)2006

    • Author(s)
      Koichi Masaki, Hiroyuki Kurata
    • Organizer
      The 16th International Conference on Genome Informatics
    • Place of Presentation
      Yokohama
    • Year and Date
      20061218-20
  • [Presentation] 大腸菌窒素同化システムのポジティブフィードバック制御シンプルモデル2006

    • Author(s)
      真崎浩一, 倉田博之
    • Organizer
      数理モデル化と問題解決研究報告
    • Place of Presentation
      名古屋大学(MPS-59 : 61-64)
    • Year and Date
      20060526-26

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Published: 2010-06-10   Modified: 2016-04-21  

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