Development of method to extract drug effect by state space model

• Project/Area Number: 22700308
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: The University of Tokyo
• Principal Investigator: YAMAGUCHI Rui 東京大学, 医科学研究所, 講師 (90380675)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000); Fiscal Year 2011: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2010: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
• Keywords: 薬剤効果 / 状態空間モデル / 統計的モデリング / システム生物学 / バイオインフォマティクス / データ解析

Research Abstract

We have developed a methodology based on state-space modeling to extract dynamic drug-effect profile on cellular system from time-course gene expression data taken from cells stimulated by a drug.

Research Products

• [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
• [Journal Article] SiGN large-scale gene network estimation environment for high performance computing (2011)
  • Author(s): Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S.
  • Journal Title: Genome Informatics Volume: 25巻 Pages: 40-52
  • NAID: 130004567842
  • URL: http://www.jstage.jst.go.jp/article/gi/25/1/25_1_40/_article
  • Peer Reviewed
• [Journal Article] SiGN : large-scale gene network estimation environment for high performance computing (2011)
  • Author(s): Tamada Y, Shimamura T, Yamaguchi R, Imoto S, Nagasaki M, Miyano S
  • Journal Title: Genome Informatics Volume: 25 Pages: 40-52
  • NAID: 130004567842
  • 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 Pages: 1172-1173
  • Peer Reviewed
• [Presentation] Estimation of dynamic drug effects on gene modules from time-course transcriptome data by using state-space model (2012)
  • Author(s): Rui Yamaguchi, 他
  • Organizer: X-Gen Congress & Expo
  • Place of Presentation: Hilton hotel,米国(San Diego)
  • Year and Date: 2012-03-06
• [Presentation] Estimation of dynamic drug effects on gene modules from time-course transcriptome data by using state-space mode (2012)
  • Author(s): Rui Yamaguchi, Seiya Imoto, Mai Yamauchi, Asuka Nakata, Kunihiko Hinohara, Yoshinori Tamada, Ryo Yoshida, Teppei Shimamura, Masao Nagasaki, Noriko Gotoh, Satoru Miyano
  • Organizer: X-Gen Congress & Expo
  • Place of Presentation: Hilton hotel,米国(San Diego)
  • Year and Date: 2012-03-06
• [Presentation] Identification of dissimilarities in high-dimensional gene regulatory systems by predicted discrepancies from state space model (2011)
  • Author(s): Rui Yamaguchi
  • Organizer: The Joint Meeting of the 2011 Taipei International Statistical Symposium and 7th Conference of the Asian Regional Section of the IASC
  • Place of Presentation: Academia Sinica、台湾
  • Year and Date: 2011-12-17
• [Presentation] Identification of dissimilarities in high-dimensional gene regulatory systems by predicted discrepancies from state space model (2011)
  • Author(s): Rui Yamaguchi
  • Organizer: The Joint Meeting of the 2011 Taipei International Statistical Symposium and 7th Conference of the Asian Regional Section of the IASC
  • Place of Presentation: Academia Sinica,台湾(台北)(招待講演)
  • Year and Date: 2011-12-17
• [Presentation] 動的予測による遺伝子間制御関係の異常探索 (2010)
  • Author(s): 山口類
  • Organizer: 大分統計談話会第42回大会
  • Place of Presentation: 富士通大分ソフトウェアラボラトリ、大分
  • Year and Date: 2010-10-21
• [Presentation] 動的予測による遺伝子間制御関係の異常探索 (2010)
  • Author(s): 山口類
  • Organizer: 大分統計談話会第42回大会
  • Place of Presentation: 富士通大分ソフトウェアラボラトリ 大分
  • Year and Date: 2010-10-21
• [Presentation] 状態空間モデリングによる遺伝子発現制御に関わる動的薬剤効果の推定 (2010)
  • Author(s): 山口類、井元清哉、山内麻衣、島村徹平、後藤典子、宮野悟
  • Organizer: 2010年度統計関連学会連合大会
  • Place of Presentation: 早稲田大学、東京
  • Year and Date: 2010-09-08
• [Presentation] 状態空間モデリングによる遺伝子発現制御に関わる動的薬剤効果の推定 (2010)
  • Author(s): 山口類, 井元清哉, 山内麻衣, 島村徹平, 後藤典子, 宮野悟
  • Organizer: 2010年度統計関連学会連合大会
  • Place of Presentation: 早稲田大学 東京
  • Year and Date: 2010-09-08
• [Presentation] Detection of Systematic Differences in Gene Regulations and Extraction of Gene Signatures by Using State Space Model (2010)
  • Author(s): Rui Yamaguchi
  • Organizer: 2010 NCTS International Conference on Probability and Statistics with Applications in Biology
  • Place of Presentation: National Center for Theoretical Sciences,台湾
  • Year and Date: 2010-07-15
• [Presentation] Detection of Systematic Differences in Gene Regulations and Extraction of Gene Signatures by Using State Space Model (2010)
  • Author(s): Rui Yamaguchi
  • Organizer: 2010 NCTS International Conference on Probability and Statistics with Applications in Biology
  • Place of Presentation: National Center for Theoretical Sciences, Taiwan
  • Year and Date: 2010-07-15