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Analysis of SNPs that induce structural change of RNA secondary structures

Research Project

Project/Area Number 22700305
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeSingle-year Grants
Research Field Bioinformatics/Life informatics
Research InstitutionKeio 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 *help
¥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)
KeywordsRNA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.

Report

(3 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • Research Products

    (51 results)

All 2012 2011 2010 Other

All Journal Article (23 results) (of which Peer Reviewed: 23 results) Presentation (22 results) Remarks (6 results)

  • [Journal Article] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming2012

    • Author(s)
      Kato, Y., Sato, K., Asai, K., Akutsu, T.
    • Journal Title

      Nucleic Acids Res

      Volume: (in press)

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] COPICAT : A software system for predicting interactions between proteins and chemical compounds2012

    • 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

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Improved measurements of RNA structure conservation with generalized centroid estimators2011

    • Author(s)
      Okada, Y., Saito, Y., Sato, K., Sakakibara, Y.
    • Journal Title

      Front. Gene

      Volume: 2 Pages: 54-54

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Using binding profiles to predict binding sites of target RNAs2011

    • Author(s)
      Poolsap, U., Kato, Y., Sato, K., Akutsu, T.
    • Journal Title

      J. Bioinform. Comput. Biol

      Volume: vol.9, no.6 Pages: 697-713

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] CentroidHomfold-LAST : Accurate prediction of RNA secondary structure using automatically collected homologous sequences2011

    • Author(s)
      Hamada, M., Yamada, K., Sato, K., Frith, MC., Asai, K.
    • Journal Title

      Nucleic Acids Res

      Volume: vol.39

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming2011

    • Author(s)
      Sato, K., Kato, Y., Hamada, M., Akutsu, T., Asai, K.
    • Journal Title

      Bioinformatics

      Volume: vol.27, no.13

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Adaptive seeds tame genomic sequence comparison2011

    • Author(s)
      Kielbasa, SM., Wan, R., Sato, K., Horton, P., Frith, MC
    • Journal Title

      Genome Res

      Volume: vol.21, no.3 Pages: 487-493

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures2011

    • Author(s)
      Saito, Y., Sato, K., Sakakibara, Y.
    • Journal Title

      BMC Bioinformatics

      Volume: 12(Suppl 1)

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Improving the accuracy of predicting secondary structure for aligned RNA sequences2011

    • Author(s)
      Hamada, M., Sato, K., Asai, K.
    • Journal Title

      Nucleic Acids Res

      Volume: vol.39, no.2 Pages: 393-402

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming2011

    • 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

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] CentroidHomfold-LAST : accurate prediction of RNA secondary structure using automatically collected homologous sequences2011

    • 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

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Using binding profiles to predict RNA binding sites of target RNAs2011

    • 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

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Improved measurements of RNA structure conservation with generalized centroid estimators2011

    • Author(s)
      Yohei Okada
    • Journal Title

      Frontiers in Genetics

      Volume: 2 Pages: 54-54

    • DOI

      10.3389/fgene.2011.00054

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Improving the accuracy of predicting secondary structure for aligned RNA sequences2011

    • Author(s)
      Michiaki Hamada
    • Journal Title

      Nucleic Acids Research

      Volume: 39 Pages: 393-402

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures2011

    • Author(s)
      Yutaka Saito
    • Journal Title

      BMC Bioinformatics

      Volume: 12

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of RNA secondary structure by maximizing pseudo-expected accuracy2010

    • Author(s)
      Hamada, M., Sato, K., Asai, K.
    • Journal Title

      BMC Bioinformatics

      Volume: 11 Pages: 586-586

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Robust and accurate prediction of noncoding RNAs from aligned sequences2010

    • Author(s)
      Saito, Y., Sato, K., Sakakibara, Y.
    • Journal Title

      BMC Bioinformatics

      Volume: 11(Suppl 7)

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming2010

    • Author(s)
      Kato, Y., Sato, K., Hamada, M., Watanabe, Y., Asai, K., Akutsu, T.
    • Journal Title

      Bioinformatics

      Volume: vol.26, no.18

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] A non-parametric Bayesian approach for predicting RNA secondary structures2010

    • 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

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] A non-parametric Bayesian approach for predicting RNA secondary structures2010

    • Author(s)
      Kengo Sato
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: 8 Pages: 727-742

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming2010

    • Author(s)
      Yuki Kato, Kengo Sato
    • Journal Title

      Bioinformatics

      Volume: 26

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Robust and accurate prediction of noncoding RNAs from aligned sequences2010

    • Author(s)
      Yutaka Saito
    • Journal Title

      BMC Bioinformatics

      Volume: 11

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Prediction of RNA secondary structure by maximizing pseudo-expected accuray2010

    • Author(s)
      Michiaki Hamada
    • Journal Title

      BMC Bioinformatics

      Volume: 11 Pages: 586-586

    • Related Report
      2010 Annual Research Report
    • 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
    • Related Report
      2011 Final Research Report
  • [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
    • Related Report
      2011 Annual Research Report
  • [Presentation] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming2011

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] Rtips : fast and accurate tools for RNA 2D structure prediction using integer programming2011

    • 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
    • Related Report
      2011 Annual Research Report
  • [Presentation] Simultaneous aligning and folding RNA sequences by dual decomposition2011

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] Simultaneous aligning and folding RNA sequences by dual decomposition2011

    • 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
    • Related Report
      2011 Annual Research Report
  • [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
    • Related Report
      2011 Annual Research Report
  • [Presentation] Rtips : an integrated web server for RNA structure prediction using IP scheme2011

    • 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
    • Related Report
      2011 Annual Research Report
  • [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
    • Related Report
      2011 Annual Research Report
  • [Presentation] IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming2011

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach2011

    • 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
    • Related Report
      2011 Annual Research Report
  • [Presentation] Comprehensive analysis of small non-coding RNAs in medaka transcriptome by deep RNA-seq approach2011

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] Fast and accurate clustering of noncoding RNAs using ensembles of sequence alignments and secondary structures2011

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] RactIP : fast and accurate prediction of RNA-RNA interaction using integer programming2010

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] Robust and accurate prediction of noncoding RNAs from aligned sequences2010

    • 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
    • Related Report
      2011 Final Research Report
  • [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
    • Related Report
      2010 Annual Research Report
  • [Presentation] Fast and accurate RNA structure prediction tools : RactIP for RNA-RNA interaction and IPknot for RNA pseudoknot structure prediction2010

    • 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
    • Related Report
      2010 Annual Research Report
  • [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
    • Related Report
      2011 Final Research Report
  • [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
    • Related Report
      2010 Annual Research Report
  • [Presentation] RNA-RNA interaction prediction using integer programming with threshold cut2010

    • 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
    • Related Report
      2011 Final Research Report
  • [Presentation] RNA-RNA interaction prediction using integer programming with threshold cut2010

    • 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
    • Related Report
      2010 Annual Research Report
  • [Presentation] Improved prediction of transcription binding sites from chromatin modification data2010

    • 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
    • Related Report
      2011 Final Research Report
  • [Remarks] Rtips

    • URL

      http://rna.naist.jp/

    • Related Report
      2011 Final Research Report
  • [Remarks] DAFS

    • URL

      http://www.ncrna.org/software/dafs/

    • Related Report
      2011 Final Research Report
  • [Remarks] RactIP

    • URL

      http://www.ncrna.org/software/ractip/

    • Related Report
      2011 Final Research Report
  • [Remarks] IPknot

    • URL

      http://www.ncrna.org/software/ipknot/

    • Related Report
      2011 Final Research Report
  • [Remarks] CentroidFold

    • URL

      http://www.ncrna.org/software/centroidfold/

    • Related Report
      2011 Final Research Report
  • [Remarks] BPLA kernels

    • URL

      http://bpla-kernel.dna.bio.keio.ac.jp/

    • Related Report
      2011 Final Research Report

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Published: 2010-08-23   Modified: 2016-04-21  

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