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Design and Analysis for Dynamical Genetic Circuits based on various Mathematical Models

Planned Research

Project AreaSynthetic biology for the comprehension of biomolecular networks
Project/Area Number 23119008
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Complex systems
Research InstitutionTokyo Institute of Technology

Principal Investigator

YAMAMURA Masayuki  東京工業大学, 総合理工学研究科, 教授 (00220442)

Co-Investigator(Renkei-kenkyūsha) KONAGAYA Akihiko  東京工業大学, 総合理工学研究科, 教授 (00301200)
SUZUKI Yasuhiro  名古屋大学, 情報科学研究科, 准教授 (50292983)
KOBAYASHI Tetsuya  東京大学, 生産技術研究所, 准教授 (90513359)
MOCHIZUKI Atsushi  理化学研究所, 望月理論生物学研究室, 主任研究員 (10304726)
TAKAYASU Misako  東京工業大学, 総合理工学研究科, 准教授 (20296776)
ONO Isao  東京工業大学, 総合理工学研究科, 准教授 (20078166)
ITO Hiroshi  九州大学, 芸術工学研究院, 助教 (20512627)
SEKINE Ryoji  理化学研究所, 生命システム研究センター, 研究員 (70730232)
Project Period (FY) 2011-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥41,340,000 (Direct Cost: ¥31,800,000、Indirect Cost: ¥9,540,000)
Fiscal Year 2015: ¥8,970,000 (Direct Cost: ¥6,900,000、Indirect Cost: ¥2,070,000)
Fiscal Year 2014: ¥8,840,000 (Direct Cost: ¥6,800,000、Indirect Cost: ¥2,040,000)
Fiscal Year 2013: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2012: ¥9,230,000 (Direct Cost: ¥7,100,000、Indirect Cost: ¥2,130,000)
Fiscal Year 2011: ¥4,940,000 (Direct Cost: ¥3,800,000、Indirect Cost: ¥1,140,000)
Keywords人工遺伝子回路 / 非線形動力学 / 確率過程 / 複雑ネットワーク / 並列シミュレーション / 並列シュミレーション / 合成生物学 / 遺伝子回路 / 代謝経路 / 非線形システム
Outline of Final Research Achievements

The research plan is devided into following five subgoals. (1) We achieved to model fundamental processes such as gene regulation and inter cellular communication, collaborating with Kiga-project. (2) We achieved to design oscillating artificial genetic circuits by using genetic algorithms with frequency characteristics as the fitness evaluation. (3) We analized cascading two artificial genetic circuit from the viewpoint of impedance matching. (4) We proposed a multicellular developement model for multi layered bacterial sheet in hot fountain. (5) In order to build common modeling bench for Synthetic Biology, we collect necessary mathematical methodology such as non-linear differencial equation system, stochastic process system, cellular automata system, and so on.

Report

(6 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (31 results)

All 2015 2014 2013 2012 2011

All Journal Article (30 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 23 results,  Open Access: 5 results,  Acknowledgement Compliant: 2 results) Book (1 results)

  • [Journal Article] Genetic PEGylation with different lengths on one polypeptide backbone2015

    • Author(s)
      Qingmin Zang, Seiichi Tada, Takanori Uzawa, Daisuke Kiga, Masayuki Yamamura, and *Yoshihiro Ito
    • Journal Title

      Chemical Communications

      Volume: 51 Issue: 76 Pages: 14385-14388

    • DOI

      10.1039/c5cc04486c

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] In vitro selection of a photoresponsive peptide aptamer to glutathione-immobilized microbeads2015

    • Author(s)
      Seiichi Tada, Qingmin Zang, Wei Wang, Masuki Kawamoto, Mingzhe Liu, Michiru Iwashita, Takanori Uzawa, Daisuke Kiga, Masayuki Yamamura, and Yoshihiro Ito
    • Journal Title

      J. Biosci. Bioeng.

      Volume: 119 Issue: 2 Pages: 137-139

    • DOI

      10.1016/j.jbiosc.2014.06.018

    • NAID

      110009922573

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Effects of downstream genes on synthetic genetic circuits2014

    • Author(s)
      Takefumi Moriya, Masayuki Yamamura, Daisuke Kiga
    • Journal Title

      BMC Systems Biology

      Volume: 8(suppl 4) Issue: S4 Pages: 1-10

    • DOI

      10.1186/1752-0509-8-s4-s4

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Cluster Newton Method for Sampling Multiple Solutions of Underdetermined Inverse Problems: Application to a Parameter Identification Problem in Pharmacokinetics2014

    • Author(s)
      Yasunori Aoki
    • Journal Title

      SIAM J. Scientific Computing

      Volume: 36 Issue: 1 Pages: 122-141

    • DOI

      10.1137/120885462

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Generalised Central Limit Theorems for Growth Rate2014

    • Author(s)
      Misako Takayasu
    • Journal Title

      Journal of Statistical Physics

      Volume: 155 Issue: 1 Pages: 47-71

    • DOI

      10.1007/s10955-014-0956-4

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Design and Control of Synthetic Biological Systems2013

    • Author(s)
      Ryoji Sekine
    • Journal Title

      Natural Computing and Beyond

      Volume: 6 Pages: 104-114

    • DOI

      10.1007/978-4-431-54394-7_9

    • ISBN
      9784431543930, 9784431543947
    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 周波数特性を用いた振動する人工遺伝子回路の自動設計2013

    • Author(s)
      林孝文
    • Journal Title

      計測自動制御学会第40回知能システムシンポジウム資料集

      Volume: - Pages: 211-216

    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
  • [Journal Article] General applicability of synthetic gene-overexpression for cell-type ratio control via reprogramming2013

    • Author(s)
      K. Ishimatsu
    • Journal Title

      ACS Synthetic Biology

      Volume: - Issue: 9 Pages: 638-644

    • DOI

      10.1021/sb400102w

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Estimation of feasible solution space using Cluster Newton Method : application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models.2013

    • Author(s)
      Yoshida K, Maeda K, Kusuhara H, Konagaya A.
    • Journal Title

      BMC Syst Biol.

      Volume: S3 Issue: S3

    • DOI

      10.1186/1752-0509-7-s3-s3

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Modeling “info-chemical” Mediated Ecological System by using Multi Agent System2013

    • Author(s)
      Yasuhiro Suzuki
    • Journal Title

      ICAART

      Volume: - Pages: 318-323

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Harness the Nature for Computation2013

    • Author(s)
      Yasuhiro Suzuki
    • Journal Title

      Proceedings in Information and Communications Technology

      Volume: 6 Pages: 49-70

    • DOI

      10.1007/978-4-431-54394-7_5

    • ISBN
      9784431543930, 9784431543947
    • Related Report
      2013 Annual Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Single Cell Visualization of Yeast Gene Expression Shows Correlation of Epigenetic Switching Between Multiple Heterochromatic Regions Through Multiple Generations2013

    • Author(s)
      Yasunobu Mano, Tetsuya J. Kobayashi, Jun-ichi Nakayama, Hiroyuki Uchida, Masaya Oki
    • Journal Title

      Plos Biology

      Volume: 11 Issue: 7 Pages: e1001601-e1001601

    • DOI

      10.1371/journal.pbio.1001601

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 定量データが切り開く生命科学2013

    • Author(s)
      小林徹也
    • Journal Title

      実験医学

      Volume: 31 Pages: 1202-1208

    • Related Report
      2013 Annual Research Report
  • [Journal Article] Dynamics and control at feedback vertex sets. I: Informative and determining nodes in regulatory networks2013

    • Author(s)
      Fiedler B.
    • Journal Title

      J. Dyn. Differ. Eqns.

      Volume: 25 Issue: 3 Pages: 563-604

    • DOI

      10.1007/s10884-013-9312-7

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics and control at feedback vertex sets. II: A faithful monitor to determine the diversity of molecular activities in regulatory networks2013

    • Author(s)
      Mochizuki A.
    • Journal Title

      J. Theor. Biol.

      Volume: 335 Pages: 130-146

    • DOI

      10.1016/j.jtbi.2013.06.009

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Relations between allometric scalings and fluctuations in complex systems: The case of Japanese firms2013

    • Author(s)
      Hayafumi Watanabe
    • Journal Title

      Physica A

      Volume: 392 Issue: 4 Pages: 741-756

    • DOI

      10.1016/j.physa.2012.10.020

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dynamics and control at feedback vertex sets. I: Informative and determining nodes in regulatory networks2013

    • Author(s)
      Fiedler B.
    • Journal Title

      J. Dyn. Differ. Equ.

      Volume: -

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Empirical analysis of collective human behavior for extraordinary events in the blogosphere2013

    • Author(s)
      Yukie Sano
    • Journal Title

      Physical Review E

      Volume: - Issue: 1

    • DOI

      10.1103/physreve.87.012805

    • Related Report
      2012 Annual Research Report
  • [Journal Article] Design strategy for an initial state-independent diversity generator2012

    • Author(s)
      Ryoji Sekine
    • Journal Title

      Chem-Bio Informatics Journal

      Volume: vol. 12 Pages: 39-49

    • NAID

      130004138125

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Behaviors of Chemical Reactions with Small Number of Molecules2012

    • Author(s)
      Y. Suzuki
    • Journal Title

      Lecture Notes in Computer Science

      Volume: vol. 5777 Pages: 394-401

    • DOI

      10.1007/978-3-642-21283-3_49

    • ISBN
      9783642212826, 9783642212833
    • Related Report
      2012 Annual Research Report
  • [Journal Article] Theoretical aspect of cellular decision-making and information processing2012

    • Author(s)
      Tetsuya J. Kobayashi
    • Journal Title

      Advances in Experimental Medicine and Biology

      Volume: vol. 736 Pages: 275-291

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fluid flow and interlinked feedback loops establish left-right asymmetric decay of Cerl2 mRNA in the mouse embryo2012

    • Author(s)
      Nakamura, T., Saito, D., Kawasumi, A., Shinohara, K., Asai, Y., Takaoka, K., Dong, F., Takamatsu, A., Belo, J.A., Mochizuki, A., and Hamada, H.
    • Journal Title

      Nat.Communic

      Volume: 3 Issue: 1 Pages: 1322-1322

    • DOI

      10.1038/ncomms2319

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Effect of coagulation of nodes in an evolving complex network2012

    • Author(s)
      Wataru Miura, Hideki Takayasu, and Misako Takayasu
    • Journal Title

      Physical Review Letters

      Volume: 108 Issue: 16 Pages: 168701-168701

    • DOI

      10.1103/physrevlett.108.168701

    • NAID

      120006582180

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Efficient numerical optimization algorithm based on new real-coded genetic algorithm, AREX + JGG and application to the inverse problem in systems biology2012

    • Author(s)
      Asako Komori, Yukihiro Maki, Masahiko Nakatsui, Isao Ono, and Masahiro Okamoto
    • Journal Title

      Applied Mathematis

      Volume: 3 Issue: 10 Pages: 1463-1470

    • DOI

      10.4236/am.2012.330205

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 被覆度を考慮したマルチスタート法による多目的連続関数最適化:Adaptive Weighted Aggregation2012

    • Author(s)
      濱田直希
    • Journal Title

      進化計算学会論文誌

      Volume: vol. 3 Pages: 31-46

    • Related Report
      2012 Annual Research Report
  • [Journal Article] A Multiphysics Model of In Vitro Transcription Coupling Enzymatic Reaction and Precipitation Formation.2012

    • Author(s)
      Akama, S., Yamamura, M., and Kigawa, T.
    • Journal Title

      Biophys

      Volume: J. 102 Issue: 2 Pages: 221-230

    • DOI

      10.1016/j.bpj.2011.12.014

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 進化型計算のDNA実装とその応用2012

    • Author(s)
      山村雅幸
    • Journal Title

      電気学会誌

      Volume: 132 Pages: 221-224

    • NAID

      10030521789

    • Related Report
      2011 Annual Research Report
  • [Journal Article] Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling2011

    • Author(s)
      Sekine, R., Yamamura, M., Ayukawa, S., Ishimatsu, K., Akama, S., Takinoue, M., Hagiya, M., Kiga, D.
    • Journal Title

      Proc.Natl.Acad.Sci.U.S.A.

      Volume: 108 Issue: 44 Pages: 17969-17973

    • DOI

      10.1073/pnas.1105901108

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Tunable synthetic phenotypic diversification on Waddington's landscape through autonomous signaling2011

    • Author(s)
      Ryoji Sekine, Masayuki Yamamura, 5名略, Daisuke Kiga
    • Journal Title

      Proceedings of the National Academy of Sciences

      Volume: 108 Pages: 17969-17973

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Multi-objective robust optimization for in vitro RNA synthesis2011

    • Author(s)
      Satoru Akama, Masayuki Yamamura, Takanori Kigawa
    • Journal Title

      The Sixth IASTED International Conference on Computational Intelligence and Bioinformatics (CIB 2011)

      Pages: 74-80

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Book] 自然計算へのいざない 第2章合成生物学 (ナチュラルコンピューティングシリーズ第0巻 小林聡、萩谷昌己、横森貴編)2015

    • Author(s)
      山村雅幸、木賀大介
    • Total Pages
      27
    • Publisher
      近代科学社
    • Related Report
      2015 Annual Research Report

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Published: 2011-08-01   Modified: 2019-07-29  

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