Analysis of SNPs that induce structural change of RNA secondary structures

• Project/Area Number: 22700305
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Keio University
• Principal Investigator: SATO Kengo 慶應義塾大学, 理工学部, 講師 (20365472)
• Project Period (FY): 2010 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥2,730,000 (Direct Cost: ¥2,100,000、Indirect Cost: ¥630,000); Fiscal Year 2011: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2010: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000)
• Keywords: RNA二次構造 / 一塩基多型 / バイオインフォマティクス

Research Abstract

We developed an efficient algorithm for detecting structural changes of RNA secondary structures induced by SNPs on RNA sequences. Comprehensive analysis on the SNP database using our method revealed statistical significance of structural changes induced by synonymous SNPs on coding regions and SNPs on non-coding regions of mRNAs from clinically associated genes.

Research Products

• [Journal Article] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming (2012)
  • Author(s): Kato, Y., Sato, K., Asai, K., Akutsu, T.
  • Journal Title: Nucleic Acids Res Volume: (in press)
  • Peer Reviewed
• [Journal Article] COPICAT : A software system for predicting interactions between proteins and chemical compounds (2012)
  • Author(s): Sakakibara, Y., Hachiya, T., Uchida, M., Nagamine, N., Sugawara, Y., Yokota, M., Nakamura, M., Poperdorf, K., Komori, T., Sato, K.
  • Journal Title: Bioinformatics Volume: vol.28, no.5 Pages: 745-756
  • Peer Reviewed
• [Journal Article] Improved measurements of RNA structure conservation with generalized centroid estimators (2011)
  • Author(s): Okada, Y., Saito, Y., Sato, K., Sakakibara, Y.
  • Journal Title: Front. Gene Volume: 2 Pages: 54-54
  • Peer Reviewed
• [Journal Article] Using binding profiles to predict binding sites of target RNAs (2011)
  • Author(s): Poolsap, U., Kato, Y., Sato, K., Akutsu, T.
  • Journal Title: J. Bioinform. Comput. Biol Volume: vol.9, no.6 Pages: 697-713
  • Peer Reviewed
• [Journal Article] CentroidHomfold-LAST : Accurate prediction of RNA secondary structure using automatically collected homologous sequences (2011)
  • Author(s): Hamada, M., Yamada, K., Sato, K., Frith, MC., Asai, K.
  • Journal Title: Nucleic Acids Res Volume: vol.39
  • Peer Reviewed
• [Journal Article] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming (2011)
  • Author(s): Sato, K., Kato, Y., Hamada, M., Akutsu, T., Asai, K.
  • Journal Title: Bioinformatics Volume: vol.27, no.13
  • Peer Reviewed
• [Journal Article] Adaptive seeds tame genomic sequence comparison (2011)
  • Author(s): Kielbasa, SM., Wan, R., Sato, K., Horton, P., Frith, MC
  • Journal Title: Genome Res Volume: vol.21, no.3 Pages: 487-493
  • Peer Reviewed
• [Journal Article] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures (2011)
  • Author(s): Saito, Y., Sato, K., Sakakibara, Y.
  • Journal Title: BMC Bioinformatics Volume: 12(Suppl 1)
  • Peer Reviewed
• [Journal Article] Improving the accuracy of predicting secondary structure for aligned RNA sequences (2011)
  • Author(s): Hamada, M., Sato, K., Asai, K.
  • Journal Title: Nucleic Acids Res Volume: vol.39, no.2 Pages: 393-402
  • Peer Reviewed
• [Journal Article] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming (2011)
  • Author(s): K.Sato, Y.Kato, M.Hamada, T.Akutsu, K.Asai
  • Journal Title: Bioinformatics Volume: 27 Issue: 13 Pages: i85-i93
  • DOI: 10.1093/bioinformatics/btr215
  • Peer Reviewed
• [Journal Article] CentroidHomfold-LAST : accurate prediction of RNA secondary structure using automatically collected homologous sequences (2011)
  • Author(s): Michiaki Hamada, Koichiro Yamada, Kengo Sato, Martin C Frith, Kiyoshi Asai
  • Journal Title: Nucleic Acids Res Volume: 39 Issue: suppl_2 Pages: W100-W106
  • DOI: 10.1093/nar/gkr290
  • Peer Reviewed
• [Journal Article] Using binding profiles to predict RNA binding sites of target RNAs (2011)
  • Author(s): U.Poolsap, Y.Kato, K.Sato, T.Akutsu
  • Journal Title: Tournal of Bioinformatics and Computational Biology Volume: 9 Issue: 06 Pages: 697-713
  • DOI: 10.1142/s0219720011005628
  • Peer Reviewed
• [Journal Article] Improved measurements of RNA structure conservation with generalized centroid estimators (2011)
  • Author(s): Yohei Okada
  • Journal Title: Frontiers in Genetics Volume: 2 Pages: 54-54
  • DOI: 10.3389/fgene.2011.00054
  • Peer Reviewed
• [Journal Article] Improving the accuracy of predicting secondary structure for aligned RNA sequences (2011)
  • Author(s): Michiaki Hamada
  • Journal Title: Nucleic Acids Research Volume: 39 Pages: 393-402
  • Peer Reviewed
• [Journal Article] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures (2011)
  • Author(s): Yutaka Saito
  • Journal Title: BMC Bioinformatics Volume: 12
  • Peer Reviewed
• [Journal Article] Prediction of RNA secondary structure by maximizing pseudo-expected accuracy (2010)
  • Author(s): Hamada, M., Sato, K., Asai, K.
  • Journal Title: BMC Bioinformatics Volume: 11 Pages: 586-586
  • Peer Reviewed
• [Journal Article] Robust and accurate prediction of noncoding RNAs from aligned sequences (2010)
  • Author(s): Saito, Y., Sato, K., Sakakibara, Y.
  • Journal Title: BMC Bioinformatics Volume: 11(Suppl 7)
  • Peer Reviewed
• [Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming (2010)
  • Author(s): Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.
  • Journal Title: Bioinformatics Volume: vol.26, no.18
  • Peer Reviewed
• [Journal Article] A non-parametric Bayesian approach for predicting RNA secondary structures (2010)
  • Author(s): Sato, K., Hamada, M., Mituyama, T., Asai, K., Sakakibara, Y.
  • Journal Title: J. Bioinform. Comput. Biol Volume: vol.8, no.4 Pages: 727-742
  • Peer Reviewed
• [Journal Article] A non-parametric Bayesian approach for predicting RNA secondary structures (2010)
  • Author(s): Kengo Sato
  • Journal Title: Journal of Bioinformatics and Computational Biology Volume: 8 Pages: 727-742
  • Peer Reviewed
• [Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming (2010)
  • Author(s): Yuki Kato, Kengo Sato
  • Journal Title: Bioinformatics Volume: 26
  • Peer Reviewed
• [Journal Article] Robust and accurate prediction of noncoding RNAs from aligned sequences (2010)
  • Author(s): Yutaka Saito
  • Journal Title: BMC Bioinformatics Volume: 11
  • Peer Reviewed
• [Journal Article] Prediction of RNA secondary structure by maximizing pseudo-expected accuray (2010)
  • Author(s): Michiaki Hamada
  • Journal Title: BMC Bioinformatics Volume: 11 Pages: 586-586
  • Peer Reviewed
• [Presentation] 双対分解によるRNA構造アラインメント (2012)
  • Author(s): 佐藤健吾, 加藤有己, 浅井潔, 阿久津達也, 榊原康文
  • Organizer: 第28回情報処理学会バイオ情報学研究会
  • Place of Presentation: 仙台
  • Year and Date: 2012-03-28
• [Presentation] 双対分解によるRNA構造アラインメント (2012)
  • Author(s): 佐藤健吾
  • Organizer: 第28回情報処理学会バイオ情報学研究会
  • Place of Presentation: 東北大学
  • Year and Date: 2012-03-28
• [Presentation] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming (2011)
  • Author(s): 佐藤健吾, 加藤有己, 浅井潔, 阿久津達也
  • Organizer: 第34回分子生物学会年会
  • Place of Presentation: 横浜
  • Year and Date: 2011-12-14
• [Presentation] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming (2011)
  • Author(s): 佐藤健吾
  • Organizer: 第34回分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2011-12-14
• [Presentation] Simultaneous aligning and folding RNA sequences by dual decomposition (2011)
  • Author(s): Sato, K., Kato, Y., Akutsu, T., Asai, K., Sakakibara, Y.
  • Organizer: CBI/JSBi 2011合同大会
  • Place of Presentation: 神戸
  • Year and Date: 2011-11-10
• [Presentation] Simultaneous aligning and folding RNA sequences by dual decomposition (2011)
  • Author(s): Kengo Sato
  • Organizer: CBI/JSBi 2011合同大会
  • Place of Presentation: 神戸国際会議場
  • Year and Date: 2011-11-10
• [Presentation] 機能性RNAのクラスタリング:大規模な配列から2次構造ファミリーを発見する (2011)
  • Author(s): 斎藤裕
  • Organizer: 新しいRNA/RNPを見つける会2011
  • Place of Presentation: フェストーネ(沖縄)
  • Year and Date: 2011-09-16
• [Presentation] Rtips : an integrated web server for RNA structure prediction using IP scheme (2011)
  • Author(s): 佐藤健吾
  • Organizer: 新しいRNA/RNPを見つける会2011
  • Place of Presentation: フェストーネ(沖縄)
  • Year and Date: 2011-09-16
• [Presentation] RNA-seqによるメダカ機能性RNAのトランスクリプトーム解析 (2011)
  • Author(s): 阿部雅哉
  • Organizer: 新しいRNA/RNPを見つける会2011
  • Place of Presentation: フェストーネ(沖縄)
  • Year and Date: 2011-09-15
• [Presentation] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming (2011)
  • Author(s): Sato, K., Kato, Y., Hamada, M., Akutsu, T., Asai, K.
  • Organizer: ISMB/ECCB 2011
  • Place of Presentation: ウィーン
  • Year and Date: 2011-07-17
• [Presentation] Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach (2011)
  • Author(s): Masaya Abe
  • Organizer: 16^<th> Annual Meeting of the RNA Society
  • Place of Presentation: 京都国際センター
  • Year and Date: 2011-06-17
• [Presentation] Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach (2011)
  • Author(s): Abe, M., Hase, S., Ogawa, M., Okada, Y., Sato, K., Saito, Y., Sakakibara, Y.
  • Organizer: The 16th Annual Meeting of the RNA society
  • Place of Presentation: 京都
  • Year and Date: 2011-06-15
• [Presentation] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures (2011)
  • Author(s): Saito, Y., Sato, K., Sakakibara, Y.
  • Organizer: The 9th Asia Pacific Bioinformatics Conference(APBC 2011)
  • Place of Presentation: インチョン
  • Year and Date: 2011-01-14
• [Presentation] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming (2010)
  • Author(s): Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.
  • Organizer: The 9th European Conference on Computational Biology(ECCB 2010)
  • Place of Presentation: ゲント
  • Year and Date: 2010-09-27
• [Presentation] Robust and accurate prediction of noncoding RNAs from aligned sequences (2010)
  • Author(s): Saito, Y., Sato, K., Sakakibara, Y.
  • Organizer: The International Conference on Bioinformatics(InCoB 2010)
  • Place of Presentation: 東京
  • Year and Date: 2010-09-26
• [Presentation] 機能性RNAの相同性検索:BLAST-likeなアプローチ (2010)
  • Author(s): 斎藤裕
  • Organizer: 新しいRNA/RNPを見つける会2010
  • Place of Presentation: 弘前大学
  • Year and Date: 2010-09-06
• [Presentation] Fast and accurate RNA structure prediction tools : RactIP for RNA-RNA interaction and IPknot for RNA pseudoknot structure prediction (2010)
  • Author(s): 佐藤健吾
  • Organizer: 新しいRNA/RNPを見つける会2010
  • Place of Presentation: 弘前大学
  • Year and Date: 2010-09-06
• [Presentation] 期待精度最大化に基づくRNAシュードノット予測 (2010)
  • Author(s): 佐藤健吾, 加藤有己, 阿久津達也, 浅井潔
  • Organizer: 第22回情報処理学会バイオ情報学研究会
  • Place of Presentation: 東京
  • Year and Date: 2010-07-29
• [Presentation] 期待精度最大化に基づくRNAジュードノット予測 (2010)
  • Author(s): 加藤有己
  • Organizer: 第22回情報処理学会バイオ情報学研究会
  • Place of Presentation: 産総研臨海副都心センター
  • Year and Date: 2010-07-28
• [Presentation] RNA-RNA interaction prediction using integer programming with threshold cut (2010)
  • Author(s): 加藤有己, 佐藤健吾, 浜田道昭, 浅井潔, 阿久津達也
  • Organizer: 第21回情報処理学会バイオ情報学研究会
  • Place of Presentation: 那覇
  • Year and Date: 2010-06-19
• [Presentation] RNA-RNA interaction prediction using integer programming with threshold cut (2010)
  • Author(s): 加藤有己
  • Organizer: 第21回情報処理学会バイオ情報学研究会
  • Place of Presentation: 琉球大学
  • Year and Date: 2010-06-19
• [Presentation] Improved prediction of transcription binding sites from chromatin modification data (2010)
  • Author(s): Sato, K., Whitington, T., Bailey, T., Horton, P.
  • Organizer: The 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology(CIBCB 2010)
  • Place of Presentation: モントリオール
  • Year and Date: 2010-05-05
• [Remarks] Rtips
  • URL: http://rna.naist.jp/
• [Remarks] DAFS
  • URL: http://www.ncrna.org/software/dafs/
• [Remarks] RactIP
  • URL: http://www.ncrna.org/software/ractip/
• [Remarks] IPknot
  • URL: http://www.ncrna.org/software/ipknot/
• [Remarks] CentroidFold
  • URL: http://www.ncrna.org/software/centroidfold/
• [Remarks] BPLA kernels
  • URL: http://bpla-kernel.dna.bio.keio.ac.jp/