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Design automation of multi-element gene circuits

Planned Research

Project AreaSynthetic biology for the comprehension of biomolecular networks
Project/Area Number 23119009
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 InstitutionThe University of Tokyo

Principal Investigator

Iba Hitoshi  東京大学, 情報理工学(系)研究科, 教授 (40302773)

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: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000)
Fiscal Year 2014: ¥9,100,000 (Direct Cost: ¥7,000,000、Indirect Cost: ¥2,100,000)
Fiscal Year 2013: ¥8,450,000 (Direct Cost: ¥6,500,000、Indirect Cost: ¥1,950,000)
Fiscal Year 2012: ¥8,060,000 (Direct Cost: ¥6,200,000、Indirect Cost: ¥1,860,000)
Fiscal Year 2011: ¥7,280,000 (Direct Cost: ¥5,600,000、Indirect Cost: ¥1,680,000)
Keywords遺伝子ネットワーク / 進化計算 / DNAツールボックス / ラボラトリーオートメーション / 遺伝的アルゴリズム / 遺伝的プログラミング / 人工遺伝子回路 / ラボラトリオートメーション / 合成生物学 / バイオ・ケミカル・ネットワーク / 反応化学系 / 共進化 / 発振回路 / 生化学ネットワーク / 遺伝子制御ネットワーク
Outline of Final Research Achievements

The design of genetic networks has been studied for implementing desired biological systems, and in particular, some researchers have proposed automatic design methods using optimization techniques. However, it is difficult to implement genetic networks designed by previous methods due to overly simplified model descriptions whose parameters are infeasible in the real world. Additionally, the methods do not ensure robustness against parameter perturbation. In this project, we have proposed an effective design method and a fitness function evaluating robustness to create genetic networks which can be implemented experimentally. Further, we suggest the knowledge about robust network structures from results of optimization.

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

    (42 results)

All 2015 2014 2013 2012 Other

All Journal Article (13 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 13 results,  Open Access: 3 results,  Acknowledgement Compliant: 3 results) Presentation (20 results) (of which Int'l Joint Research: 3 results) Book (6 results) Remarks (3 results)

  • [Journal Article] Evolving Robust Gene Regulatory Networks2015

    • Author(s)
      Noman,N., Monjo,T., Moscato,P., Iba,H.
    • Journal Title

      PLoS ONE

      Volume: 10 Issue: 1 Pages: 1-21

    • DOI

      10.1371/journal.pone.0116258

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Improved sampling using loopy belief propagation for probabilistic model building genetic programming2015

    • Author(s)
      Sato,H., Hasegawa,Y., Bollegala,D., Iba,H.
    • Journal Title

      Swarm and Evolutionary Computation

      Volume: 23 Pages: 1-10

    • DOI

      10.1016/j.swevo.2015.02.002

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems2015

    • Author(s)
      Dinh,H., Aubert,N., Noman,N., Fujii,T., Rondelez,Y., Iba,H.
    • Journal Title

      IEEE Transactions on Evolutionary Computation

      Volume: 19 Issue: 3 Pages: 374-386

    • DOI

      10.1109/tevc.2014.2326863

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] An Effective Method for Evolving Reaction Networks in Synthetic Biochemical Systems2015

    • Author(s)
      Dinh,H., Noman,N. Fujii,T. Rondelez,Y., Iba,H.
    • Journal Title

      IEEE Transactions on Evolutionary Computation

      Volume: PP Pages: 1-1

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Oscillatory synthetic biological system construction using interactive evolutionary computations2014

    • Author(s)
      Dinh,H., Noman,N., Iba,H.
    • Journal Title

      Journal of Computer Science

      Volume: 10 Pages: 2640-2652

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reverse Engineering of Gene Regulatory Networks Using Dissipative Particle Swarm Optimization2013

    • Author(s)
      Palafox,L., Noman,N., Iba,H.
    • Journal Title

      IEEE Transactions on Evolutionary Computation

      Volume: 17 Issue: 4 Pages: 557-587

    • DOI

      10.1109/tevc.2012.2218610

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Evolving Genetic Networks for Synthetic Biology2013

    • Author(s)
      Noman,N., Palafox,L., Iba,H.
    • Journal Title

      New Generation Computing

      Volume: 31 Pages: 93-103

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 対話的パラメータ最適化のための集団探索打ち切り型探索アルゴリズムの提案2012

    • Author(s)
      渡辺晃生, 伊庭斉志
    • Journal Title

      進化計算学会論文誌

      Volume: 2 Pages: 47-62

    • NAID

      130004965143

    • Related Report
      2012 Annual Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 遺伝的プログラミングの理論的展開2012

    • Author(s)
      伊庭斉志
    • Journal Title

      情報処理

      Volume: 53 Pages: 938-941

    • NAID

      10028090019

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On Model Selection Criteria in Reverse Engineering Gene Networks Using RNN Model2012

    • Author(s)
      Noman,N., Palafox,L., Iba,H.,
    • Journal Title

      Convergence and Hybrid Information Technology, Lecture Notes in Computer Science

      Volume: vol.7425 Pages: 155-164

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reverse Engineering of Gene Regulatory Networks using Dissipative Particle Swarm Optimization2012

    • Author(s)
      Palafox,L., Nasimul,N.,Iba,H
    • Journal Title

      IEEE Transactions on Evolutionary Computation

      Volume: vol.99 Pages: 1-1

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reconstruction of Gene Regulatory Networks from Gene Expression Data Using Decoupled Recurrent Neural Network Model2012

    • Author(s)
      Noman,N., Palafox,L., Iba,H.,
    • Journal Title

      Natural Computing and Beyond Y. Suzuki and T. Nakagaki (Eds.)

      Volume: PICT6 Pages: 93-103

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Study on the Use of Evolutionary Techniques for Inference in Gene Regulatory Networks2012

    • Author(s)
      Palafox,L., Nasimul,N.,Iba,H
    • Journal Title

      Natural Computing and Beyond Y. Suzuki and T. Nakagaki (Eds.)

      Volume: PICT6

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] Feature selection and classification using ensembles of genetic programs and within-class and between-class permutations2015

    • Author(s)
      Ivert,A., Aranha,C., Iba,H.
    • Organizer
      2015 IEEE Congress on Evolutionary Computation (CEC)
    • Place of Presentation
      仙台国際センター(宮城県,仙台市)
    • Year and Date
      2015-05-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Evolutionary design of oscillatory genetic networks in silico2015

    • Author(s)
      Naruse,Y., Hamada,H., Hanai,T., Iba,H.
    • Organizer
      2015 IEEE Congress on Evolutionary Computation (CEC)
    • Place of Presentation
      仙台国際センター(宮城県,仙台市)
    • Year and Date
      2015-05-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] A double swarm methodology for parameter estimation in oscillating Gene Regulatory Networks2015

    • Author(s)
      Nobile,M.S., Iba,H.
    • Organizer
      2015 IEEE Congress on Evolutionary Computation (CEC)
    • Place of Presentation
      仙台国際センター(宮城県,仙台市)
    • Year and Date
      2015-05-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Nonlinear protein degradation for temperature compensation2014

    • Author(s)
      Peng,Y., Hasegawa,Y., Noman,N., Iba,H.
    • Organizer
      GIW / ISCB-Asia 2014
    • Place of Presentation
      東京国際交流館、東京都
    • Year and Date
      2014-12-15 – 2014-12-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] Evolutionary construction of dynamic biochemical systems performing mathematical calculations2014

    • Author(s)
      Dinh,H. Iba,H., Rondelez,Y.
    • Organizer
      DNA20 (DNA Computing and Molecular Programming)
    • Place of Presentation
      京都大学、京都府
    • Year and Date
      2014-09-22 – 2014-09-26
    • Related Report
      2014 Annual Research Report
  • [Presentation] Designing Robust Network Topology with Surrogate Assisted Genetic Algorithm2014

    • Author(s)
      Noman,N., Iba,H., Pablo,M.
    • Organizer
      The 15th International Conference on Systems Biology (ICSB)
    • Place of Presentation
      メルボルン、オーストラリア
    • Year and Date
      2014-09-14 – 2014-09-18
    • Related Report
      2014 Annual Research Report
  • [Presentation] Nonlinear Protein Degradation for Temperature Compensation2014

    • Author(s)
      Peng,Y., Hasegawa,Y., Noman,N., Iba,H.
    • Organizer
      International conference on computer science and manufacturing technologies (CMST-2014)
    • Place of Presentation
      バリ、インドネシア
    • Year and Date
      2014-08-02 – 2014-08-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] Constrained Group Counseling Optimization2014

    • Author(s)
      Eita,M., Shoukry,A., Iba,H.
    • Organizer
      Alife’14, The Fourteenth International Conference On The Synthesis and Simulation Of Living Systems
    • Place of Presentation
      ニューヨーク、アメリカ
    • Year and Date
      2014-07-31 – 2014-08-02
    • Related Report
      2014 Annual Research Report
  • [Presentation] Extending Population Based Incremental Learning using Dirichlet Processes2013

    • Author(s)
      Palafox,L., Noman,N., Iba,H.
    • Organizer
      IEEE Congress on Evolutionary Computation 2013 (CEC2013)
    • Place of Presentation
      メキシコ、カンクン
    • Related Report
      2013 Annual Research Report
  • [Presentation] Learning non-linear ranking functions for web search using probabilistic model building GP2013

    • Author(s)
      Hettiarachchi,D.S, Noman,N., Iba,H.
    • Organizer
      IEEE Congress on Evolutionary Computation 2013 (CEC2013)
    • Place of Presentation
      メキシコ、カンクン
    • Related Report
      2013 Annual Research Report
  • [Presentation] Evolution of Cheating DNA-based Agents Playing the Game of Rock-Paper-Scissors2013

    • Author(s)
      Aubert,N., Dinh,Q.H., Hagiya,M., Iba.H., Fujii,T., Bredeche,N., Rondelez,Y.
    • Organizer
      The Twelfth European Conference on the Synthesis and Simulation of Living Systems, Advances in Artificial Life (ECAL2013)
    • Place of Presentation
      イタリア、タオルミーナ
    • Related Report
      2013 Annual Research Report
  • [Presentation] Your Own Facial Parameter Generation for a 3D Avatar Interface Using an MRI Medical Image2013

    • Author(s)
      Dohi,H., Iba,H., Ishizuka,M.
    • Organizer
      The 15th International Conference on Human-Computer Interaction (HCI2013)
    • Place of Presentation
      アメリカ、ラスベガス
    • Related Report
      2013 Annual Research Report
  • [Presentation] Gene regulatory network reverse engineering using population based incremental learning and K-means2012

    • Author(s)
      Palafox,L., Iba,H.
    • Organizer
      The Genetic and Evolutionary Computation Conference (GECCO2012)
    • Place of Presentation
      Philadelphia, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] The search for robust topologies of oscillatory gene regulatory networks by evolutionary computation2012

    • Author(s)
      Komiya,K., Noman,N., Iba,H.
    • Organizer
      The Genetic and Evolutionary Computation Conference (GECCO2012)
    • Place of Presentation
      Philadelphia, USA
    • Related Report
      2012 Annual Research Report
  • [Presentation] Probabilistic model building GP with Belief propagation2012

    • Author(s)
      Sato,H., Hasegawa,Y., Bollegala,D., Iba,H.
    • Organizer
      IEEE Congress on Evolutionary Computation 2012 (CEC2012)
    • Place of Presentation
      Brisbane, Australia
    • Related Report
      2012 Annual Research Report
  • [Presentation] On the use of Population Based Incremental Learning to do Reverse Engineering on Gene Regulatory Networks2012

    • Author(s)
      Palafox,L., Iba,H.
    • Organizer
      IEEE Congress on Evolutionary Computation 2012 (CEC2012)
    • Place of Presentation
      Brisbane, Australia
    • Related Report
      2012 Annual Research Report
  • [Presentation] Multi-objective portfolio optimization and rebalancing using genetic algorithms with local search2012

    • Author(s)
      Soam,V., Palafox,L., Iba,H.
    • Organizer
      IEEE Congress on Evolutionary Computation 2012 (CEC2012)
    • Place of Presentation
      Brisbane, Australia
    • Related Report
      2012 Annual Research Report
  • [Presentation] On the use of Population Based Incremental Learning to do Reverse Engineering on Gene Regulatory Networks2012

    • Author(s)
      Palafox,L., Iba,H.
    • Organizer
      Proceedings of IEEE Congress on Evolutionary Computation 2012 (CEC2012)
    • Place of Presentation
      Australia, Brisbane
    • Related Report
      2011 Annual Research Report
  • [Presentation] Probabilistic model building GP with Belief propagation2012

    • Author(s)
      Sato,H., Hasegawa,Y., Bollegala,D., Iba.H.
    • Organizer
      Proceedings of IEEE Congress on Evolutionary Computation 2012 (CEC2012)
    • Place of Presentation
      Australia, Brisbane
    • Related Report
      2011 Annual Research Report
  • [Presentation] On Model Selection Criteria in Reverse Engineering Gene Networks Using RNN Model2012

    • Author(s)
      Noman,N., Palafox,L., Iba,H.
    • Organizer
      Proceedings of Convergence and Hybrid Information Technology - 6th International Conference, (ICHIT2012)
    • Place of Presentation
      Korea, Daejeon
    • Related Report
      2011 Annual Research Report
  • [Book] Weiley2015

    • Author(s)
      Iba,H., Noman,N., (eds.)
    • Total Pages
      464
    • Publisher
      Evolutionary Computation in Gene Regulatory Network Research (Wiley Series in Bioinformatics)
    • Related Report
      2015 Annual Research Report
  • [Book] 進化計算と深層学習―創発する知能―2015

    • Author(s)
      伊庭斉志
    • Total Pages
      182
    • Publisher
      オーム社
    • Related Report
      2015 Annual Research Report
  • [Book] 人工知能の方法2014

    • Author(s)
      伊庭斉志
    • Total Pages
      253
    • Publisher
      コロナ社
    • Related Report
      2014 Annual Research Report
  • [Book] Inferring Genetic Networks with a Recurrent Neural Network Model Using Differential Evolution, in Handbook of Bio-/Neuro-Informatics, Kasabov,Nikola K.(ed.)2013

    • Author(s)
      Noman,N., Palafox,L., Iba,H.
    • Publisher
      Springer
    • Related Report
      2013 Annual Research Report
  • [Book] 人工知能と人工生命の基礎2013

    • Author(s)
      伊庭斉志
    • Total Pages
      253
    • Publisher
      オーム社
    • Related Report
      2013 Annual Research Report
  • [Book] Chapman and Hall/CRC, ISBN-10:146656234X2013

    • Author(s)
      Iba, H.
    • Total Pages
      296
    • Publisher
      Agent-Based Modeling and Simulation with Swarm
    • Related Report
      2013 Annual Research Report
  • [Remarks] 東京大学・伊庭研究室

    • URL

      http://www.iba.t.u-tokyo.ac.jp/

    • Related Report
      2015 Annual Research Report
  • [Remarks] 東京大学大学院 情報理工学系研究科 電子情報学専攻 伊庭研究室

    • URL

      http://www.iba.t.u-tokyo.ac.jp/

    • Related Report
      2013 Annual Research Report
  • [Remarks] 東京大学大学院 情報理工学系研究科 電子情報学専攻 伊庭研究室

    • URL

      http://www.iba.t.u-tokyo.ac.jp/

    • Related Report
      2012 Annual Research Report

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

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