Research on structure predictions of RNA with modified nucleotieds

• Project/Area Number: 24680031
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Bioinformatics/Life informatics
• Research Institution: Waseda University (2014-2015); The University of Tokyo (2012-2013)
• Principal Investigator: Hamada Michiaki 早稲田大学, 理工学術院, 准教授 (00596538)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥14,300,000 (Direct Cost: ¥11,000,000、Indirect Cost: ¥3,300,000); Fiscal Year 2014: ¥5,460,000 (Direct Cost: ¥4,200,000、Indirect Cost: ¥1,260,000); Fiscal Year 2013: ¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000); Fiscal Year 2012: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
• Keywords: RNA / ２次構造予測 / 修飾塩基 / 学習モデル / 確率モデル / 半教師有り学習 / ２次構造 / 半教師有学習 / 2次構造予測 / lncRNA / 機能性RNA / 分子シミュレーション / 2次構造 / 機械学習

Outline of Final Research Achievements

We have developed bioinformatic methods for predicting secondary structures including modified bases. Due to the limitation of the known structures with modified bases, we employed a semi-supervised learning approach for predicting RNA secondary structures using RNA sequences with and without secondary structures. Moreover, we have developed an integrated web server, Rtools, for performing various analyses based on RNA secondary structures.

Research Products

• [Journal Article] Rtools: a web server for various secondary structural analyses on single RNA sequences (2016)
  • Author(s): Hamada Michiaki, Ono Yukiteru, Kiryu Hisanori, Sato Kengo, Kato Yuki, Fukunaga Tsukasa, Mori Ryota, Asai Kiyosh
  • Journal Title: Nucleic Acids Research Volume: 44 Issue: W1 Pages: W302-W307
  • DOI: 10.1093/nar/gkw337
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Comprehensive prediction of lncRNA–RNA interactions in human transcriptome (2016)
  • Author(s): Goro Terai#, Junichi Iwakiri#, Tomoshi Kameda, Michiaki Hamada*, Kiyoshi Asai*
  • Journal Title: BMC Genomics Volume: 17 Issue: S1 Pages: 12-12
  • DOI: 10.1186/s12864-015-2307-5
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] 長鎖ノンコーディングRNAのためのバイオインフォマティクス (2016)
  • Author(s): 岩切淳一、浜田道昭
  • Journal Title: 生物物理 Volume: 未定
  • NAID: 130005165637
  • Peer Reviewed
• [Journal Article] Bioinformatics tools for lncRNA research. (2015)
  • Author(s): Junichi Iwakiri, Michiaki Hamada, Kiyoshi Asai
  • Journal Title: Biochimica et biophysica acta (BBA) Gene Regulatory Mechanisms Volume: 1859(1) Issue: 1 Pages: 23-30
  • DOI: 10.1016/j.bbagrm.2015.07.014
  • Peer Reviewed / Open Access
• [Journal Article] A semi-supervised learning approach for RNA secondary structure prediction (2015)
  • Author(s): Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: Computational Biology and Chemistry Volume: 未定 Pages: 72-79
  • DOI: 10.1016/j.compbiolchem.2015.02.002
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Learning chromatin states with factorized information criteria (2015)
  • Author(s): Michiaki Hamada, Yukiteru Ono, Ryohei Fujimaki, Kiyoshi Asai
  • Journal Title: Bioinformatics Volume: 未定 Issue: 15 Pages: 2426-2433
  • DOI: 10.1093/bioinformatics/btv163
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Fighting against uncertainty: An essential issue in bioinformatics (2014)
  • Author(s): Michiaki Hamada
  • Journal Title: Briefings in Bionformatics Volume: 未定
  • Peer Reviewed
• [Journal Article] CentroidAlign-Web : A Fast and Accurate Multiple Aligner for Long Non-Coding RNAs (2013)
  • Author(s): Haruka Yonemoto, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: International journal of molecular sciences Volume: 14 Issue: 3 Pages: 6144-6156
  • DOI: 10.3390/ijms14036144
  • Peer Reviewed
• [Journal Article] Analysis of base-pairing probabilities of RNA molecules involved in protein-RNA interactions (2013)
  • Author(s): Junichi Iwakiri, Tomoshi Kameda, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: Bioinformatics Volume: 29 Issue: 20 Pages: 2524-2528
  • DOI: 10.1093/bioinformatics/btt453
  • Peer Reviewed
• [Journal Article] PBSIM: PacBio reads simulator--toward accurate genome assembly (2013)
  • Author(s): Yukiteru Ono, Kiyoshi Asai, Michiaki Hamada
  • Journal Title: Bioinformatics Volume: 29 Pages: 119-121
  • Peer Reviewed
• [Journal Article] Direct updating of an RNA base-pairing probability matrix with marginal probability constraints (2012)
  • Author(s): Michiaki Hamada
  • Journal Title: Journal of Computational Biology Volume: 19 Pages: 1265-1276
  • Peer Reviewed
• [Presentation] Comprehensive prediction of lncRNA–RNA interactions in human transcriptome (2016)
  • Author(s): Michiaki Hamada
  • Organizer: APBC2016
  • Place of Presentation: サンフランシスコ
  • Year and Date: 2016-01-12
  • Int'l Joint Research
• [Presentation] A semi-supervised learning approach for RNA secondary structure prediction (2015)
  • Author(s): 浜田道昭
  • Organizer: The 13-th Asia Pacific Bioinformatics Conference (APBC2015)
  • Place of Presentation: 台湾
  • Year and Date: 2015-01-21
• [Presentation] 2 次構造情報を基盤とした RNA バイオインフォマティクス技 術・ツールの最近の進展 (2013)
  • Author(s): 浜田道昭
  • Organizer: 第15回日本RNA学会
  • Place of Presentation: 愛媛県、ひめぎんホール
• [Presentation] 次世代バイオインフォマティクス技術の研究開発 (2013)
  • Author(s): 浜田道昭
  • Organizer: 医薬会セミナー
  • Place of Presentation: 東京都、国立国際医療研究センター
  • Invited
• [Presentation] Direct updating of an RNA base-pairing probability matrix with marginal Probability constraints (2012)
  • Author(s): Michiaki Hamada
  • Organizer: BIW02012
  • Place of Presentation: 産総研臨海副都心センター(東京都)
  • Year and Date: 2012-11-01
• [Book] 生命情報処理における機械学習 (2016)
  • Author(s): 瀬々潤、浜田道昭
  • Total Pages: 130
  • Publisher: 講談社