Integrated mathematical model and analysis of Boolean biological network

• Project/Area Number: 25730005
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Theory of informatics
• Research Institution: Kyoto University
• Principal Investigator: Tamura Takeyuki 京都大学, 化学研究所, 助教 (00437261)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2016: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2014: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: アルゴリズム / 整数線形計画法 / 遺伝子制御ネットワーク / 代謝ネットワーク / ブーリアンモデル / 定常状態 / 制御 / 固定パラメータ / 整数計画法 / 木幅 / NP完全

Outline of Final Research Achievements

There are many chemical compounds in cells, and biological activities are maintained by many chemical reactions. Such relationships between chemical compounds and reactions are represented by metabolic networks. In Boolean metabolic networks, each node is assigned either 0 or 1. 0 means that the chemical compound is not producible or the chemical reaction does not take place. 1 means that the chemical compound is producible or the chemical reaction takes place. In this research, I mathematically analyzed and developed integer linear programming-based methods for the following problems. (1)the problem to find the minimum number of additional reactions so that the target compounds become producible (2)the problem to find the minimum number of common reactions whose knockouts result that the target compound is not producible in one network but producible in the other network.

Research Products

• [Int'l Joint Research] 香港大学(香港)
• [Int'l Joint Research] モナッシュ大学(オーストラリア)
• [Int'l Joint Research] ハーバード大学(米国)
• [Int'l Joint Research] 国立台湾大学(台湾)
• [Int'l Joint Research] ベングリオン大学ネゲブ(イスラエル)
• [Journal Article] Computational methods for modification of metabolic networks (2015)
  • Author(s): T. Tamura, W. Liu, T. Akutsu
  • Journal Title: Computational and Structural Biotechnology Journal Volume: 12 Pages: 376-381
  • DOI: 10.1016/j.csbj.2015.05.004
  • NAID: 120005712915
  • Peer Reviewed / Open Access
• [Journal Article] Similar subtree search using extended tree inclusion (2015)
  • Author(s): T. Mori, A. Takasu, J. Jansson, J. Hwang, T. Tamura, T. Akutsu
  • Journal Title: IEEE Transactions on Knowledge and Data Engineering Volume: 27 Issue: 12 Pages: 3360-3373
  • DOI: 10.1109/tkde.2015.2457922
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] On the complexity of finding a largest common subtree of bounded degree (2015)
  • Author(s): T. Akutsu, T. Tamura, A.A. Melkman, A. Takasu
  • Journal Title: Theoretical Computer Science Volume: 590 Pages: 2-16
  • DOI: 10.1016/j.tcs.2014.10.012
  • NAID: 120005689204
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Computing smallest intervention strategies for multiple metabolic networks in a boolean model. (2015)
  • Author(s): Lu, W., Tamura, T., Song, J. & Akutsu, T.
  • Journal Title: Journal of computational biology Volume: 22 Issue: 2 Pages: 85-110
  • DOI: 10.1089/cmb.2014.0274
  • NAID: 120005657917
  • Peer Reviewed / Open Access
• [Journal Article] A Fixed-Parameter Algorithm for Detecting a Singleton Attractor in an AND/OR Boolean Network with Bounded Treewidth (2015)
  • Author(s): Chia-Jung Chang, Takeyuki Tamura, Kun-Mao Chao and Tatsuya Akutsu
  • Journal Title: IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences Volume: E98.A Issue: 1 Pages: 384-390
  • DOI: 10.1587/transfun.E98.A.384
  • NAID: 130004770922
  • ISSN: 0916-8508, 1745-1337
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Integer Programming-based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model (2014)
  • Author(s): Wei Lu*, Takeyuki Tamura*, Jiangning Song, Tatsuya Akutsu, (* joint first authors)
  • Journal Title: PLoS ONE Volume: e92637 Issue: 3 Pages: e92637-e92637
  • DOI: 10.1371/journal.pone.0092637
  • Peer Reviewed
• [Presentation] Integer Programming-based Method for Designing Synthetic Metabolic Networks by Minimum Reaction Insertion in a Boolean Model (2015)
  • Author(s): Takeyuki Tamura
  • Organizer: 情報処理学会バイオ情報学研究会
  • Place of Presentation: 横浜
  • Year and Date: 2015-09-12
• [Presentation] Computing Minimum Reaction Modifications in a Boolean Metabolic Network (2015)
  • Author(s): Takeyuki Tamura
  • Organizer: GIW/InCoB2015
  • Place of Presentation: 東京
  • Year and Date: 2015-09-09
  • Int'l Joint Research
• [Presentation] On the parameterized complexity of associative and commutative unification (2014)
  • Author(s): Tatsuya Akutsu, Jesper Jansson, Atsuhiro Takasu, Takeyuki Tamura
  • Organizer: 9th International Symposium on Parameterized and Exact Computation (IPEC 2014)
  • Place of Presentation: ヴロツワフ（ポーランド）
  • Year and Date: 2014-09-08 – 2014-09-12
• [Remarks] 田村武幸のホームページ
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/
• [Remarks] 田村武幸（化学研究所）
  • URL: http://rdb.kuicr.kyoto-u.ac.jp/researchers/view/tamura+takeyuki
• [Remarks] 田村武幸（京都大学教育研究活動データベース）
  • URL: https://kyouindb.iimc.kyoto-u.ac.jp/j/cC7oO
• [Remarks] Paper list of Takeyuki Tamura
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/paper-list.html
• [Remarks] 論文リスト
  • URL: http://sunflower.kuicr.kyoto-u.ac.jp/~tamura/paper-list.html