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Methods for controlling biological networks using mathematical models

Research Project

Project/Area Number 16K00391
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Life / Health / Medical informatics
Research InstitutionKyoto University

Principal Investigator

Tamura Takeyuki  京都大学, 化学研究所, 准教授 (00437261)

Project Period (FY) 2016-04-01 – 2020-03-31
Project Status Completed (Fiscal Year 2019)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2018: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2017: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2016: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywords代謝ネットワーク / アルゴリズム / 有用物質生産 / 流束均衡解析モデル / ブーリアンモデル / NP完全問題 / 流束均衡解析 / 数理モデル / 反応削除戦略 / 生育結合 / 線形計画 / ブーリアンネットワーク / 遺伝子制御ネットワーク / NP完全 / 整数計画法 / 定常状態 / unification問題 / 遺伝子ネットワーク / GPRネットワーク / 整数線形計画法 / 細胞の制御 / 制御方法
Outline of Final Research Achievements

More than thousands of chemical reactions occur in the cell at the right time and in the right amount to maintain vital functions. This series of chemical reactions is called metabolism, and the network describing the relationship between each reaction is called the metabolic network. In this study, we developed and implemented an algorithm to (1) rapidly compute the reactions to be removed in order to produce useful materials efficiently, and validated it by computer simulation with flow models. (2) A fast algorithm was developed and implemented to simultaneously compute the reactions to be added and the reactions to be removed so that unnecessary metabolites that would be produced in the original state are no longer produced and necessary metabolites that would not be produced in the original state are produced, and was validated by the 0/1 model.

Academic Significance and Societal Importance of the Research Achievements

微生物等の代謝機能を利用した有用物質の生産は、従来の化石燃料等に基づく物質生産にくらべて環境の負荷が小さく、持続可能性が高い。しかし自然状態のままで微生物が生産できる物質は限定的であり、所望の物質を効率よく生産するためには代謝ネットワークを改めてデザインする必要がある。しかしデザインのための組み合わせの数は膨大であり、すべての場合を試すことは不可能である。そこで代謝ネットワークを適切に効率よくデザインするための手法が必要になる。本研究で開発したアルゴリズムは、元の代謝ネットワークから削除や追加すべき反応を効率よく計算可能であり、物質生産の枠組みを根本的に刷新するための数理的な基盤を提供する。

Report

(5 results)
  • 2019 Annual Research Report   Final Research Report ( PDF )
  • 2018 Research-status Report
  • 2017 Research-status Report
  • 2016 Research-status Report
  • Research Products

    (35 results)

All 2020 2019 2018 2017 2016 Other

All Int'l Joint Research (7 results) Journal Article (6 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 6 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (16 results) (of which Int'l Joint Research: 9 results,  Invited: 3 results) Remarks (6 results)

  • [Int'l Joint Research] ベングリオン大学ネゲブ(イスラエル)

    • Related Report
      2019 Annual Research Report
  • [Int'l Joint Research] Monash University(Australia)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] Xi'an Jiaotong University/Beijing Univ. of Chemical Technology(China)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] The University of Hong Kong(Hong Kong)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] Hughes Hall(United Kingdom)

    • Related Report
      2017 Research-status Report
  • [Int'l Joint Research] 香港大学(香港)

    • Related Report
      2016 Research-status Report
  • [Int'l Joint Research] 国立交通大学(台湾)

    • Related Report
      2016 Research-status Report
  • [Journal Article] Improved Hardness of Maximum Common Subgraph Problems on Labeled Graphs of Bounded Treewidth and Bounded Degree2020

    • Author(s)
      Akutsu Tatsuya、Melkman Avraham A.、Tamura Takeyuki
    • Journal Title

      International Journal of Foundations of Computer Science

      Volume: 31 Issue: 02 Pages: 253-273

    • DOI

      10.1142/s0129054120500069

    • Related Report
      2019 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd2018

    • Author(s)
      Tamura Takeyuki
    • Journal Title

      BMC Bioinformatics

      Volume: 19 Issue: 1 Pages: 325-325

    • DOI

      10.1186/s12859-018-2352-6

    • Related Report
      2018 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Computing Minimum Reaction Modifications in a Boolean Metabolic Network2017

    • Author(s)
      Takeyuki Tamura, Wei Lu, Jiangning Song, Tatsuya Akutsu
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: na Issue: 6 Pages: 1-1

    • DOI

      10.1109/tcbb.2017.2777456

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Discrimination of singleton and periodic attractors in Boolean networks2017

    • Author(s)
      Cheng Xiaoqing、Tamura Takeyuki、Ching Wai-Ki、Akutsu Tatsuya
    • Journal Title

      Automatica

      Volume: 84 Pages: 205-213

    • DOI

      10.1016/j.automatica.2017.07.012

    • NAID

      120006542020

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] On the parameterized complexity of associative and commutative unification2017

    • Author(s)
      T. Akutsu, J. Jansson, A. Takasu, T. Tamura
    • Journal Title

      Theoretical Computer Science

      Volume: 660 Pages: 57-74

    • DOI

      10.1016/j.tcs.2016.11.026

    • NAID

      120006537095

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Finding and analyzing the minimum set of driver nodes in control of Boolean networks2016

    • Author(s)
      Wenpin Hou, Takeyuki Tamura, Wai-Ki. Ching and Tatsuya Akutsu
    • Journal Title

      Advances in Complex Systems

      Volume: 19 Issue: 03 Pages: 1650006-1650006

    • DOI

      10.1142/s0219525916500065

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Presentation] 嫌気条件での出芽酵母を用いた生育結合増産の可能性2019

    • Author(s)
      田村 武幸
    • Organizer
      情報処理学会バイオ情報学研究会
    • Related Report
      2019 Annual Research Report
  • [Presentation] Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions2019

    • Author(s)
      Takeyuki Tamura
    • Organizer
      19th Annual International Workshop on Bioinformatics and Systems Biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions2019

    • Author(s)
      Takeyuki Tamura
    • Organizer
      Intelligent Systems for Molecular Biology 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic conditions2019

    • Author(s)
      Takeyuki Tamura
    • Organizer
      Metabolic Pathway Analysis 2019
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 有用化合物を生産・増産する代謝ネットワークの設計2019

    • Author(s)
      田村 武幸
    • Organizer
      生命医薬情報学連合大会2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic condition2019

    • Author(s)
      田村 武幸
    • Organizer
      生命医薬情報学連合大会2019
    • Related Report
      2019 Annual Research Report
  • [Presentation] Integer linear programming-based methods for controlling Boolean metabolic networks2019

    • Author(s)
      Takeyuki Tamura
    • Organizer
      Qualitative computational modeling for biological networks: A workshop in the 20th international workshop in systems biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Growth-coupled overproduction is theoretically possible for most metabolites in Saccharomyces cerevisiae under anaerobic condition2019

    • Author(s)
      Takeyuki Tamura
    • Organizer
      The 20th international workshop in systems biology
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Algorithms for analyzing and controlling Boolean networks as biological networks2019

    • Author(s)
      Takeyuki Tamura
    • Organizer
      International workshop on Boolean networks
    • Related Report
      2019 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 有用化合物を生産・増産する代謝ネットワークを設計するアルゴリズム2018

    • Author(s)
      田村武幸
    • Organizer
      情報処理学会バイオ情報学研究会
    • Related Report
      2018 Research-status Report
  • [Presentation] 有用物質を生産・増産する準最適な代謝流束均衡モデルのデザイン2018

    • Author(s)
      田村武幸
    • Organizer
      日本生物工学大会
    • Related Report
      2018 Research-status Report
  • [Presentation] Grid-Based Computational Methods for the Design of Constraint-Based Parsimonious Chemical Reaction Networks to Simulate Metabolite Production: Gridprod2018

    • Author(s)
      Takeyuki Tamura
    • Organizer
      COBRA conference 2018
    • Related Report
      2018 Research-status Report
    • Int'l Joint Research
  • [Presentation] Computational methods for design of metabolic networks for production of valuable compounds2018

    • Author(s)
      Takeyuki Tamura
    • Organizer
      生命医薬情報学連合大会2018
    • Related Report
      2018 Research-status Report
  • [Presentation] 有用化合物を生産・増産する代謝ネットワークのデザインの計算2017

    • Author(s)
      田村武幸
    • Organizer
      第117回京都大学化学研究所研究発表会
    • Related Report
      2017 Research-status Report
  • [Presentation] 有用化合物を生産・増産する代謝ネットワークのデザインの計算2017

    • Author(s)
      田村武幸
    • Organizer
      2017年度大腸菌システム生物学研究会
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research
  • [Presentation] Finding influential genes using gene expression data and Boolean models of metabolic networks2016

    • Author(s)
      Takeyuki Tamura
    • Organizer
      IEEE 16th International Conference on Bioinformatics and Bioengineering
    • Place of Presentation
      Taichung, Taiwan
    • Year and Date
      2016-10-31
    • Related Report
      2016 Research-status Report
    • Int'l Joint Research
  • [Remarks] 田村武幸の研究業績リスト

    • URL

      https://sunflower.kuicr.kyoto-u.ac.jp/~tamura/paper-list.html

    • Related Report
      2019 Annual Research Report
  • [Remarks] 京都大学教育研究データベース(田村武幸)

    • URL

      https://kyouindb.iimc.kyoto-u.ac.jp/j/cC7oO

    • Related Report
      2019 Annual Research Report
  • [Remarks] 田村武幸のページ(数理生物情報)

    • URL

      http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/

    • Related Report
      2018 Research-status Report
  • [Remarks] 田村武幸のページ(化学研究所)

    • URL

      http://rdb.kuicr.kyoto-u.ac.jp/researchers/view/tamura+takeyuki

    • Related Report
      2018 Research-status Report
  • [Remarks] 田村武幸のページ

    • URL

      http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/

    • Related Report
      2017 Research-status Report
  • [Remarks] 田村武幸のホームページ

    • URL

      http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/paper-list.html

    • Related Report
      2016 Research-status Report

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Published: 2016-04-21   Modified: 2022-02-22  

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