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A population genetics analysis of RNA secondary structures

Research Project

Project/Area Number 25870190
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Life / Health / Medical informatics
System genome science
Research InstitutionThe University of Tokyo

Principal Investigator

Kiryu Hisanori  東京大学, 大学院新領域創成科学研究科, 准教授 (80415778)

Research Collaborator ASAI Kiyoshi  
HAMADA Michiaki  
SATO Kengo  
KATO Yuki  
IWASAKI Wataru  
ONO Yukiteru  
TERAI Goro  
OZAKI Haruka  
MATSUMOTO Hirotaka  
FUKUNAGA Tsukasa  
MORI Ryota  
KASHIHARA Yuki  
KAWAGUCHI Risa  
Project Period (FY) 2013-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000)
Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsバイオインフォマティクス / RNA / RNA二次構造 / アルゴリズム / RNA結合タンパク質 / 文脈自由文法 / RNA進化 / 進化 / 構造進化 / RNA構造進化 / 数理モデル / 確率文脈自由文法 / 集団遺伝学 / 合祖理論 / 二次構造
Outline of Final Research Achievements

RNA molecules in a cell play very important roles so that genetic information encoded in the genome is instantiated as proteins and exerts actual functions. Three dimensional structure of an RNA is understood by its arrangement of stem structures, and it is important to investigate the properties of this secondary structure to understand the functions of RNAs. In this study, we have succeeded in developing an algorithm (ParasoR) for computing several properties of RNA secondary structures of very long RNAs such as messenger RNAs and long non-coding RNAs for the first time. We have also succeeded in developing an algorithm (CapR) for computing secondary structural context around the binding regions of RNA binding proteins.

Report

(5 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • 2013 Research-status Report
  • Research Products

    (17 results)

All 2016 2015 2014 2013 Other

All Journal Article (4 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 4 results,  Open Access: 4 results,  Acknowledgement Compliant: 3 results) Presentation (11 results) (of which Int'l Joint Research: 1 results,  Invited: 3 results) Book (1 results) Remarks (1 results)

  • [Journal Article] SCOUP: a probabilistic model based on the Ornstein-Uhlenbeck process to analyze single-cell expression data during differentiation2016

    • Author(s)
      Hirotaka Matsumoto and Hisanori Kiryu
    • Journal Title

      BMC Bioinformatics

      Volume: 17 Issue: 1 Pages: 232-232

    • DOI

      10.1186/s12859-016-1109-3

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Parallel computation of genome-scale RNA secondary structure to detect structural constraints on human genome.2016

    • Author(s)
      Risa Kawaguchi and Hisanori Kiryu.
    • Journal Title

      BMC Bioinformatics

      Volume: 17 Issue: 1 Pages: 203-203

    • DOI

      10.1186/s12859-016-1067-9

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Rtools: a web server for various secondary structural analyses on single RNA sequences2016

    • 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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] CapR : revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data2014

    • Author(s)
      Tsukasa Fukunaga, Haruka Ozaki, Goro Terai, Kiyoshi Asai, Wataru Iwasaki and Hisanori Kiryu
    • Journal Title

      Genome Biology

      Volume: 15 Issue: 1

    • DOI

      10.1186/gb-2014-15-1-r16

    • Related Report
      2014 Research-status Report 2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] ParasoR:ゲノムワイド局所的二次構造解析によるイントロン領域の塩基対の安定化傾向2015

    • Author(s)
      河口 理紗
    • Organizer
      生命情報科学若手の回第7回研究会
    • Place of Presentation
      慶應義塾大学鶴岡タウンキャンパス
    • Year and Date
      2015-10-01
    • Related Report
      2015 Research-status Report
  • [Presentation] RBP結合領域におけるRNAの構造モチーフ探索アルゴリズム2015

    • Author(s)
      三宅 博史
    • Organizer
      生命情報科学若手の会 第7回研究会
    • Place of Presentation
      慶應義塾大学鶴岡タウンキャンパス
    • Year and Date
      2015-10-01
    • Related Report
      2015 Research-status Report
  • [Presentation] ParasoR: Genome-wide computational analysis of local RNA secondary structures2015

    • Author(s)
      Risa Kawaguchi
    • Organizer
      Computational Analysis of RNA Structure and Function
    • Place of Presentation
      Spain, Benasque
    • Year and Date
      2015-07-20
    • Related Report
      2015 Research-status Report
    • Int'l Joint Research
  • [Presentation] ゲノムワイド局所RNA二次構造予測による転写領域の構造的性質の解析2015

    • Author(s)
      河口 理紗
    • Organizer
      NGS現場の会第4回研究会
    • Place of Presentation
      つくば国際会議場
    • Year and Date
      2015-07-01
    • Related Report
      2015 Research-status Report
  • [Presentation] ゲノムワイドRNA二次構造解析を利用したSNVによる構造変化の網羅的解析2014

    • Author(s)
      河口理紗
    • Organizer
      第5回生物情報若手の会
    • Place of Presentation
      検見川セミナーハウス、千葉市
    • Related Report
      2013 Research-status Report
  • [Presentation] An Algorithm for Evolutionary Analysis about the Influence of Single Nucleotide Variants on RNA secondary structure landscape2013

    • Author(s)
      河口理紗
    • Organizer
      7th Asian Young Researchers Conference on Computational and Omics Biology
    • Place of Presentation
      産総研臨海副都心センター、東京
    • Related Report
      2013 Research-status Report
  • [Presentation] A comprehensive analysis of RNA secondary structure with deletion, insertion and mutation2013

    • Author(s)
      河口理紗
    • Organizer
      RiboClub meeting
    • Place of Presentation
      ケベック、カナダ
    • Related Report
      2013 Research-status Report
  • [Presentation] The Algorithm for Evolutionary Analyses about the Influence of Single Nucleotide Variants on RNA Secondary Structure Landscape & Genome Wide Analyses of RNA Secondary Structure Using Scalable Inside Outside Algorithm2013

    • Author(s)
      河口理紗
    • Organizer
      RNAアルゴリズム研究会
    • Place of Presentation
      産総研臨海副都心センター、東京
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] ゲノムスケールのRNA配列解析2013

    • Author(s)
      木立 尚孝
    • Organizer
      RNAアルゴリズム研究会
    • Place of Presentation
      産総研臨海副都心センター、東京
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Ribonomic analysis reveals structural specificities of RNA-binding protein target recognition2013

    • Author(s)
      福永 津嵩
    • Organizer
      RNAアルゴリズム研究会
    • Place of Presentation
      産総研臨海副都心センター、東京
    • Related Report
      2013 Research-status Report
    • Invited
  • [Presentation] Ribonomic analysis reveals structural specificities of RNA-binding protein target recognition2013

    • Author(s)
      福永 津嵩
    • Organizer
      th Asian Young Researchers Conference on Computational and Omics Biology
    • Place of Presentation
      産総研臨海副都心センター、東京
    • Related Report
      2013 Research-status Report
  • [Book] RNA-Seq実験ハンドブック2016

    • Author(s)
      鈴木穣 編集
    • Total Pages
      282
    • Publisher
      羊土社
    • Related Report
      2015 Research-status Report
  • [Remarks] CapR

    • URL

      https://sites.google.com/site/fukunagatsu/software/capr

    • Related Report
      2013 Research-status Report

URL: 

Published: 2014-07-25   Modified: 2019-07-29  

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