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Discrete Model-Based Methods for Control of Complex BiologicalSyetems

Research Project

Project/Area Number 22650045
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeSingle-year Grants
Research Field Sensitivity informatics/Soft computing
Research InstitutionKyoto University

Principal Investigator

AKUTSU Tatsuya  京都大学, 化学研究所, 教授 (90261859)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥3,620,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥720,000)
Fiscal Year 2012: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2011: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Fiscal Year 2010: ¥500,000 (Direct Cost: ¥500,000)
Keywords複雑生体ネットワーク / ブーリアンネットワーク / スケールフリーネットワーク / 遺伝子ネットワーク / 代謝ネットワーク / 制御理論 / 構造的可制御性 / 代謝流束解析 / 線形離散時間システム / 確率ブーリアンネットワーク / 制御 / アトラクター / NP完全 / Canalyzing関数
Research Abstract

We performed studies on analysis and control of complex biological networks from various viewpoints. In particular, we developed algorithms for detecting a singleton attractor and a periodic attractor in certain kinds of Boolean networks, clarified the computational hardness of control of probabilistic Boolean networks, developed an approximate method to derive distribution of the number of reactions impacted by knockout of a single reaction, developed a method for network completion using dynamic programming and least-squares fitting, and analyzed structural controllability of complex networks using the concept of the minimum dominating set in graph theory.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (28 results)

All 2012 2011 2010

All Journal Article (12 results) (of which Peer Reviewed: 6 results) Presentation (16 results)

  • [Journal Article] Integer Programming-Based Approach to Attractor Detection and Control of Boolean Networks2012

    • Author(s)
      T. Akutsu, Y. Zhao, M. Hayashida, T.Tamura
    • Journal Title

      IEICE Transactions on Information and Systems

      Volume: E95.D Issue: 12 Pages: 2960-2970

    • DOI

      10.1587/transinf.E95.D.2960

    • NAID

      10031161464

    • ISSN
      0916-8532, 1745-1361
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Network completion using dynamic programming and least-squares fitting2012

    • Author(s)
      N. Nakajima, T. Tamura, Y. Yamanishi, K. Horimoto, T. Akutsu
    • Journal Title

      The Scientific World Journal

      Volume: 2012 Pages: 957620-957620

    • DOI

      10.1100/2012/957620

    • NAID

      120005054551

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Journal Article] Finding a periodic attractor of a Boolean network2012

    • Author(s)
      T. Akutsu, S. Kosub, A. A. Melkman, T.Tamura
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 9 Issue: 5 Pages: 1410-1421

    • DOI

      10.1109/tcbb.2012.87

    • NAID

      120004873985

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Journal Article] Dominating scale-free networks with variable scaling exponent: Heterogeneous networks are notdifficult to control2012

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

      New Journal of Physics

      Volume: 14 Issue: 7 Pages: 73005-73005

    • DOI

      10.1088/1367-2630/14/7/073005

    • NAID

      120004419126

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis of the impact degree distribution in metabolic networks using branching process approximation2012

    • Author(s)
      K. Takemoto, T. Tamura, Y. Cong,W-K. Ching, J-P. Vert, T. Akutsu
    • Journal Title

      Physica A

      Volume: 391 Issue: 1-2 Pages: 379-397

    • DOI

      10.1016/j.physa.2011.08.011

    • NAID

      120003497116

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Journal Article] Singleton and 2-periodic attractors of sign-definite Boolean networks2012

    • Author(s)
      T. Akutsu, A. A. Melkman, T. Tamura
    • Journal Title

      Information Processing Letters

      Volume: 112 Issue: 1-2 Pages: 35-38

    • DOI

      10.1016/j.ipl.2011.10.002

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
  • [Journal Article] An Efficient Method of Computing Impact Degrees for Multiple Reactions in Metabolic Networks with Cycles2011

    • Author(s)
      T. Tamura, Y. Cong, T. Akutsu, W-K. Ching
    • Journal Title

      IEICE Transactions on Information and Systems

      Volume: E94-D Issue: 12 Pages: 2393-2399

    • DOI

      10.1587/transinf.E94.D.2393

    • NAID

      10030538036

    • ISSN
      0916-8532, 1745-1361
    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Determining a singletonattractor of a Boolean network with nested canalyzing functions2011

    • Author(s)
      T. Akutsu, A. A. Melkman, T. Tamura, M. Yamamoto
    • Journal Title

      Journal of Computational Biology

      Volume: 18 Issue: 10 Pages: 1275-1290

    • DOI

      10.1089/cmb.2010.0281

    • NAID

      120003517916

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On the degree distribution of projected networks mappedfrom bipartite networks2011

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

      Physica A

      Volume: 390 Issue: 23-24 Pages: 4636-4651

    • DOI

      10.1016/j.physa.2011.06.073

    • Related Report
      2012 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks2010

    • Author(s)
      T. Tamura and T. Akutsu
    • Journal Title

      IEICE Trans. Fundamentals

      Volume: E93-A Pages: 1497-1507

    • NAID

      10027367933

    • Related Report
      2012 Final Research Report
  • [Journal Article] Determining a singleton attractor of an AND/OR Boolean network in O(1.587^n) time2010

    • Author(s)
      A. A. Melkman, T. Tamura and T. Akutsu
    • Journal Title

      Information Processing Letters

      Volume: 110 Issue: 14-15 Pages: 565-569

    • DOI

      10.1016/j.ipl.2010.05.001

    • Related Report
      2012 Final Research Report 2010 Annual Research Report
  • [Journal Article] Exact algorithms for finding a minimum reaction cut under a Boolean model of metabolic networks2010

    • Author(s)
      T.Tamura, T.Akutsu
    • Journal Title

      IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences

      Volume: E93-A Pages: 1497-1507

    • NAID

      10027367933

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Presentation] ブーリアンネットワークとスケールフリーネットワークの制御2012

    • Author(s)
      阿久津達也
    • Organizer
      計測自動制御学会 関西支部 物理と情報をつなぐ次世代システム制御研究会
    • Place of Presentation
      京都大学
    • Year and Date
      2012-10-13
    • Related Report
      2012 Annual Research Report 2012 Final Research Report
  • [Presentation] 遺伝子ネットワークと代謝ネットワークの離散数理モデルとその制御2012

    • Author(s)
      阿久津達也
    • Organizer
      2012年電子情報通信学会総合大会
    • Place of Presentation
      岡山大学
    • Year and Date
      2012-03-22
    • Related Report
      2012 Final Research Report
  • [Presentation] 遺伝子ネットワークと代謝ネットワークの離散数理モデルとその制御2012

    • Author(s)
      阿久津達也
    • Organizer
      2012年電子情報通信学会総合大会
    • Place of Presentation
      岡山大学(招待講演)
    • Year and Date
      2012-03-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] Analysis on controlling complex networks based on dominating sets2012

    • Author(s)
      Jose C. Nacher, Tatsuya Akutsu
    • Organizer
      International Conference on Mathematical Modeling in Physical Sciences, IC-MSQUARE
    • Place of Presentation
      Budapest, Hungary
    • Related Report
      2012 Annual Research Report
  • [Presentation] Controlling bipartite networks with power-law degree distributions using dominating sets2012

    • Author(s)
      Jose C. Nacher, Tatsuya Akutsu
    • Organizer
      International Conference on Systems Medicine (SYSMED 2012)
    • Place of Presentation
      Carton House Hotel & Conference Centre, Dublin, Ireland
    • Related Report
      2012 Annual Research Report
  • [Presentation] Integer programming method for completing ortholog-based gene-protein-reaction network by gene essentiality2012

    • Author(s)
      Takeyuki Tamura, Tatsuya Akutsu
    • Organizer
      23rd International Conference on Genome Informatics
    • Place of Presentation
      National Cheng Kung University, Tainan, Taiwan
    • Related Report
      2012 Annual Research Report
  • [Presentation] Analyzing metabolic networks using Boolean models2011

    • Author(s)
      T. Akutsu
    • Organizer
      Modeling andAnalysis in the Life Sciences: A ReaDiLab Conference in Tokyo
    • Place of Presentation
      東京大学
    • Year and Date
      2011-11-28
    • Related Report
      2012 Final Research Report
  • [Presentation] Analyzing metabolic networks using Boolean models2011

    • Author(s)
      T.Akutsu
    • Organizer
      Modeling and Analysis in the Life Sciences : A ReaDiLab Conference in Tokyo
    • Place of Presentation
      東京大学大学院数理科学研究科(招待講演)
    • Year and Date
      2011-11-28
    • Related Report
      2011 Annual Research Report
  • [Presentation] Attractor detection and control of Boolean networks2011

    • Author(s)
      T.Akutsu
    • Organizer
      International Symposium on Symbolic Systems Biology
    • Place of Presentation
      湘南国際村センター
    • Year and Date
      2011-11-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] Analyzing metabolic networks using Boolean models2011

    • Author(s)
      T. Akutsu
    • Organizer
      The International Conference on Computational and Systems Biology 2011
    • Place of Presentation
      Great Tang Hotel Shanghai, China
    • Year and Date
      2011-10-15
    • Related Report
      2012 Final Research Report
  • [Presentation] Analyzing metabolic networks using Boolean models2011

    • Author(s)
      T.Akutsu
    • Organizer
      The International Conference on Computational and Systems Biology 2011
    • Place of Presentation
      Great Tang Hotel Shanghai, China(招待講演)
    • Year and Date
      2011-10-15
    • Related Report
      2011 Annual Research Report
  • [Presentation] Finding optimal control policy in probabilistic Boolean networks with hard constraints by using integer programming and dynamic programming2010

    • Author(s)
      X.Chen, T.Akutsu, T.Tamura, T., W-K.Ching
    • Organizer
      IEEE International Conference on Bioinformatics and Biomedicine 2010
    • Place of Presentation
      Hong Kong, China
    • Year and Date
      2010-12-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Control of Boolean networks and probabilistic Boolean networks2010

    • Author(s)
      T. Akutsu
    • Organizer
      2nd Symposium on Systems and Synthetic Biology
    • Place of Presentation
      産業技術総合研究所CBRC, 東京
    • Year and Date
      2010-10-04
    • Related Report
      2012 Final Research Report
  • [Presentation] Control of Boolean networks and probabilistic Boolean networks2010

    • Author(s)
      T.Akutsu
    • Organizer
      2nd Symposium on Systems and Synthetic Biology
    • Place of Presentation
      CBRC, Tokyo, Japan(招待講演)
    • Year and Date
      2010-10-04
    • Related Report
      2010 Annual Research Report
  • [Presentation] Algorithmic aspects of analysis and control of Boolean networks2010

    • Author(s)
      T. Akutsu
    • Organizer
      Every Spring School on Modelling Complex Biological Systems in the Context of Genomics
    • Place of Presentation
      Evry, France
    • Year and Date
      2010-05-04
    • Related Report
      2012 Final Research Report
  • [Presentation] Algorithmic aspects of analysis and control of Boolean networks2010

    • Author(s)
      T.Akutsu
    • Organizer
      Every Spring School on Modelling Complex Biological Systems in the Context of Genomics
    • Place of Presentation
      Evry, France(招待講演)
    • Year and Date
      2010-05-04
    • Related Report
      2010 Annual Research Report

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Published: 2010-08-23   Modified: 2019-07-29  

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