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Statistical biomodeling for advanced transcriptome research

Research Project

Project/Area Number 23700346
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Statistical science
Research InstitutionThe Institute of Statistical Mathematics

Principal Investigator

YOSHIDA Ryo  統計数理研究所, モデリング研究系, 准教授 (70401263)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000)
Fiscal Year 2012: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2011: ¥2,210,000 (Direct Cost: ¥1,700,000、Indirect Cost: ¥510,000)
Keywordsベイズ統計学 / 状態空間モデル / システム生物学 / 生体生命情報 / トランスクリプトーム / オミックスデータ
Research Abstract

This research has established statistical methods for making a range of biochemical reaction simulators. The developed methods can be utilized in the applied studies on synthetic biology and metabolic engineering. We also conducted the development of gene regulation simulators for predicting drug responses of drug tolerant lung tumors.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (30 results)

All 2013 2012 2011

All Journal Article (4 results) (of which Peer Reviewed: 4 results) Presentation (24 results) (of which Invited: 3 results) Book (2 results)

  • [Journal Article] Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma2012

    • Author(s)
      Yamauchi, M., Yamaguchi, R., Nakata, A., Kohno, T., Nagasaki, M., Shimamura T., Imoto, S., Saito, A., Ueno, K., Hatanaka, Y., Yoshida, R., Higuchi, T. Nomura, M., Beer, D., Yokota, J., Miyano, S., Gotoh, N.
    • Journal Title

      PLoS One

      Volume: 7(9)

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Identifying gene pathways associated with cancer characteristics via sparse statistical methods2012

    • Author(s)
      Kawano, S., Shimamura, T., Niida, A., Imoto, S., Yamaguchi, R., Nagasaki, M., Yoshida, R., Print, C., Miyano, S.
    • Journal Title

      IEEE/ACM Transactions on Computational Biology and Bioinformatics

      Volume: 9(4) Pages: 966-972

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma2012

    • Author(s)
      Yamauchi, M
    • Journal Title

      PLoS One

      Volume: 7(9)

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] SiGN-SSM : open source parallel software for estimating gene networks with state space models2011

    • Author(s)
      Tamada Y, Yamaguchi R, Imoto S, Hirose O, Yoshida R, Nagasaki M, Miyano S
    • Journal Title

      Bioinformatics

      Volume: 27(8) Issue: 8 Pages: 1172-1173

    • DOI

      10.1093/bioinformatics/btr078

    • Related Report
      2012 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Presentation] ベイズ統計学に基づく医薬品化合物/生化学反応システムの設計2013

    • Author(s)
      吉田亮
    • Organizer
      設計情報学研究会
    • Place of Presentation
      京都
    • Related Report
      2012 Final Research Report
  • [Presentation] ベイズ統計学に基づく医薬品化合物/生化学反応システムの設計2013

    • Author(s)
      吉田亮
    • Organizer
      設計情報学研究会
    • Place of Presentation
      京都白河院
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Bayesian Robust Networking2012

    • Author(s)
      Yoshida, R.
    • Organizer
      Bayesian Inference and Stochastic Computation 2012 workshop
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] Preimage analysis of chemical structures2012

    • Author(s)
      Yamashita, H., Yoshida, R., Iba, Y.
    • Organizer
      Bayesian Inference and Stochastic Computation 2012 workshop
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] Bayesian sparsereconstruction: Latent factoranalysis of gene regulatory programs2012

    • Author(s)
      Yoshida, R.
    • Organizer
      ISBA2012 World Meeting
    • Place of Presentation
      京都
    • Related Report
      2012 Final Research Report
  • [Presentation] ベイジアン・コンピューティングとDNA配列からのプロモータ部位の予測2012

    • Author(s)
      池端久貴,吉田亮
    • Organizer
      2012年度統計関連学会連合大会
    • Place of Presentation
      北海道
    • Related Report
      2012 Final Research Report
  • [Presentation] 分子設計のカーネル逆像問題について:医薬品開発への応用2012

    • Author(s)
      吉田亮,山下博史,伊庭幸人
    • Organizer
      2012年度統計関連学会連合大会
    • Place of Presentation
      北海道
    • Related Report
      2012 Final Research Report
  • [Presentation] データ同化法にもとつくデータ統合・生体シミュレーション技術2012

    • Author(s)
      吉田亮
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Final Research Report
  • [Presentation] 創薬を支援するデータ駆動型化合物設計2012

    • Author(s)
      山下博史,吉田亮,伊庭幸人,樋口知之
    • Organizer
      第15回情報論的学習理論ワークショップ(IBIS2012)
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] タスク分割型ベイジアンモデリングに基づくDNAモチーフ配列の探索2012

    • Author(s)
      池端久貴,吉田亮
    • Organizer
      第15回情報論的学習理論ワークショップ(IBIS2012)
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] 大規模化合物データに基づく創薬情報学の新しいかたち2012

    • Author(s)
      吉田亮
    • Organizer
      情報・システム研究機構シンポジウム2012生命科学のビッグデータ革命-仮想から現実へ
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] ビッグデータ時代のバイオサイエンスと機械学習,ビッグデータとスマートな社会2012

    • Author(s)
      吉田亮
    • Organizer
      第5回ビッグデータに立ち向かう機械学習
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] Bayesian methods for making systems, molecules and others2012

    • Author(s)
      Yoshida, R.
    • Organizer
      Workshop on Applied Physics and Statistics for Quantitative Biology
    • Place of Presentation
      東京
    • Related Report
      2012 Final Research Report
  • [Presentation] Bayesian statistical modeling and computational technologies in systems biology and chemoinformatics2012

    • Author(s)
      Yoshida, R.
    • Organizer
      理化学研究所ゲノム医科学研究センターRCAI Seminar Series 2012
    • Place of Presentation
      横浜
    • Related Report
      2012 Final Research Report
  • [Presentation] Bayesian Robust Networking2012

    • Author(s)
      Yoshida, R.
    • Organizer
      Bayesian Inference and Stochastic Computation 2012 workshop
    • Place of Presentation
      統計数理研究所
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Bayesian sparse reconstruction: Latent factor analysis of gene regulatory programs2012

    • Author(s)
      Yoshida, R
    • Organizer
      ISBA2012 World Meeting
    • Place of Presentation
      京都テルサ
    • Related Report
      2012 Annual Research Report
  • [Presentation] ベイジアン・コンピューティングとDNA配列からのプロモータ部位の予測2012

    • Author(s)
      池端久貴
    • Organizer
      2012年度統計関連学会連合大会
    • Place of Presentation
      北海道大学
    • Related Report
      2012 Annual Research Report
  • [Presentation] データ同化法にもとづくデータ統合・生体シミュレーション技術2012

    • Author(s)
      吉田亮
    • Organizer
      第50回日本生物物理学会年会
    • Place of Presentation
      名古屋大学
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 組織的メタ遺伝子解析の多重検定問題2011

    • Author(s)
      吉田亮
    • Organizer
      2011年度統計関連学会連合大会
    • Place of Presentation
      福岡
    • Related Report
      2012 Final Research Report
  • [Presentation] Bayesian supercomputing tackles cancers2011

    • Author(s)
      Yoshida, R.
    • Organizer
      Joint Meeting of The 2011 Taipei International Statistical Symposium and 7th Conference of The Asian Regional Section of the IASC
    • Place of Presentation
      Taipei, Taiwan
    • Related Report
      2012 Final Research Report
  • [Presentation] Dynamic Bayesian modelling of biological pathways and decoupling of hidden regulatory signals using nonlinear state space models2011

    • Author(s)
      Yoshida, R., Nagao, H., Saito, M.M., Higuchi, T.
    • Organizer
      Yeditepe International Research Conference on Bayesian Learning (YIRCoBL 2011)
    • Place of Presentation
      Istanbul, Turky
    • Related Report
      2012 Final Research Report
  • [Presentation] Hybrid Bayesian filter algorithm for multivariate time-series modellings on cloud computing systems2011

    • Author(s)
      Nagao, H., Yoshida, R., Higuchi, T.
    • Organizer
      Yeditepe International Research Conference on Bayesian Learning (YIRCoBL 2011)
    • Place of Presentation
      Istanbul, Turky
    • Related Report
      2012 Final Research Report
  • [Presentation] Bayesian supercomputing tackles cancers2011

    • Author(s)
      Ryo Yoshida
    • Organizer
      Joint Meeting of The 2011 Taipei International Statistical Symposium and 7th Conference of The Asian Regional Section of the IASC(招待講演)
    • Place of Presentation
      台北
    • Related Report
      2011 Research-status Report
  • [Presentation] Bayesian modelling of biological pathways and decoupling of hidden regulatory signals using nonlinear state space models2011

    • Author(s)
      Ryo Yoshida, Hiromichi Nagao, Masaya M. Saito, Tomoyuki Higuchi
    • Organizer
      Yeditepe International Research Conference on Bayesian Learning (YIRCoBL 2011)(招待講演)
    • Place of Presentation
      トルコ共和国
    • Related Report
      2011 Research-status Report
  • [Book] データ同化入門2011

    • Author(s)
      樋口知之
    • Publisher
      朝倉書店(分担執筆「遺伝子発現調節モデルのデータ同化」)
    • Related Report
      2012 Final Research Report
  • [Book] データ同化入門2011

    • Author(s)
      樋口知之、上野玄太、中村和幸、中野慎也、吉田亮
    • Total Pages
      256
    • Publisher
      朝倉書店
    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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