Statistical biomodeling for advanced transcriptome research

• Project/Area Number: 23700346
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Statistical science
• Research Institution: The 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: ¥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.

Research Products

• [Journal Article] Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma (2012)
  • 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)
  • Peer Reviewed
• [Journal Article] Identifying gene pathways associated with cancer characteristics via sparse statistical methods (2012)
  • 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
  • Peer Reviewed
• [Journal Article] Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma (2012)
  • Author(s): Yamauchi, M
  • Journal Title: PLoS One Volume: 7(9)
  • Peer Reviewed
• [Journal Article] SiGN-SSM : open source parallel software for estimating gene networks with state space models (2011)
  • 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
  • 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
• [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
  • Invited
• [Presentation] Bayesian Robust Networking (2012)
  • Author(s): Yoshida, R.
  • Organizer: Bayesian Inference and Stochastic Computation 2012 workshop
  • Place of Presentation: 東京
• [Presentation] Preimage analysis of chemical structures (2012)
  • Author(s): Yamashita, H., Yoshida, R., Iba, Y.
  • Organizer: Bayesian Inference and Stochastic Computation 2012 workshop
  • Place of Presentation: 東京
• [Presentation] Bayesian sparsereconstruction: Latent factoranalysis of gene regulatory programs (2012)
  • Author(s): Yoshida, R.
  • Organizer: ISBA2012 World Meeting
  • Place of Presentation: 京都
• [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
• [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
• [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
• [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
• [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
• [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
• [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
• [Presentation] Bayesian methods for making systems, molecules and others (2012)
  • Author(s): Yoshida, R.
  • Organizer: Workshop on Applied Physics and Statistics for Quantitative Biology
  • Place of Presentation: 東京
• [Presentation] Bayesian statistical modeling and computational technologies in systems biology and chemoinformatics (2012)
  • 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
• [Presentation] Bayesian Robust Networking (2012)
  • Author(s): Yoshida, R.
  • Organizer: Bayesian Inference and Stochastic Computation 2012 workshop
  • Place of Presentation: 統計数理研究所
  • Invited
• [Presentation] Bayesian sparse reconstruction: Latent factor analysis of gene regulatory programs (2012)
  • Author(s): Yoshida, R
  • Organizer: ISBA2012 World Meeting
  • Place of Presentation: 京都テルサ
• [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
• [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
  • 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
• [Presentation] Bayesian supercomputing tackles cancers (2011)
  • 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
• [Presentation] Dynamic Bayesian modelling of biological pathways and decoupling of hidden regulatory signals using nonlinear state space models (2011)
  • 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
• [Presentation] Hybrid Bayesian filter algorithm for multivariate time-series modellings on cloud computing systems (2011)
  • Author(s): Nagao, H., Yoshida, R., Higuchi, T.
  • Organizer: Yeditepe International Research Conference on Bayesian Learning (YIRCoBL 2011)
  • Place of Presentation: Istanbul, Turky
• [Presentation] Bayesian supercomputing tackles cancers (2011)
  • 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
• [Presentation] Bayesian modelling of biological pathways and decoupling of hidden regulatory signals using nonlinear state space models (2011)
  • 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
• [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」)
• [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