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2011 Fiscal Year Final Research Report

Analysis of SNPs that induce structural change of RNA secondary structures

Research Project

  • PDF
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
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.

  • Research Products

    (30 results)

All 2012 2011 2010 Other

All Journal Article (13 results) (of which Peer Reviewed: 13 results) Presentation (11 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)

    • 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

    • 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

    • 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

    • 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 Pages: W100-106

    • 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 Pages: i85-i93

    • 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

    • 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) Pages: S48

    • 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

    • 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

    • 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) Pages: S3

    • 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 Pages: i460-i466

    • 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

    • 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] 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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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
  • [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] 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
  • [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
  • [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/

URL: 

Published: 2013-07-31  

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