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Model of mRNA transcription and transcriptional factor binding

Research Project

Project/Area Number 25830148
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionInstitute of Physical and Chemical Research

Principal Investigator

NIKAIDO Itoshi  国立研究開発法人理化学研究所, 情報基盤センター, ユニットリーダー (00383290)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2015: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000)
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
Outline of Final Research Achievements

Functions of cell are defined by temporal and special regulations of transcriptional networks in our body. Recently, massively parallel DNA sequencer realizes that we easily measure global gene expressions and binding of transcriptional factors on a genomic DNA. However, researchers had carried out simple integration of mRNA quantity and transcription factor binding to understand a transcriptional regulation. Thus, I study to develop statistical and physical models of mRNA transcription for quantitative description and understanding of transcriptional networks.

Report

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

    (14 results)

All 2016 2015 2014 2013 Other

All Journal Article (1 results) (of which Peer Reviewed: 1 results,  Open Access: 1 results) Presentation (3 results) (of which Invited: 3 results) Book (4 results) Remarks (6 results)

  • [Journal Article] Context-dependent wiring of Sox2 regulatory networks for self-renewal of embryonic and trophoblast stem cells2013

    • Author(s)
      Adachi K, Nikaido I, Ohta H, Ohtsuka S, Ura H, Kadota M, Wakayama T, Ueda HR, Niwa H.
    • Journal Title

      Molecular Cell

      Volume: 52 Issue: 3 Pages: 380-392

    • DOI

      10.1016/j.molcel.2013.09.002

    • Related Report
      2013 Research-status Report
    • Peer Reviewed / Open Access
  • [Presentation] BioDevOpsによる再現性のあるDNAシーケンス解析環境の構築2016

    • Author(s)
      二階堂愛
    • Organizer
      NPO並列生物情報処理イニシアティブシンポジウム
    • Place of Presentation
      東京工業大学 (東京都)
    • Year and Date
      2016-03-11
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 生命科学研究を加速するためのAIを計測と計算の融合から考える2016

    • Author(s)
      二階堂愛
    • Organizer
      第2回 理研・産総研共同シンポジウム
    • Place of Presentation
      産業技術研究所 (茨城県・つくば市)
    • Year and Date
      2016-02-02
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Estimation of transcriptional activity from ChIP-Seq and transcriptome2015

    • Author(s)
      Itoshi Nikaido
    • Organizer
      Computational Science in Epigenetics
    • Place of Presentation
      Kobe, Hyogo, Japan
    • Year and Date
      2015-02-13 – 2015-02-14
    • Related Report
      2014 Research-status Report
    • Invited
  • [Book] 二階堂愛2015

    • Author(s)
      Rによる発現ヒートマップの描画 次世代シークエンサーDRY解析教本
    • Total Pages
      408
    • Publisher
      学研メディカル秀潤社
    • Related Report
      2015 Annual Research Report
  • [Book] 次世代シークエンス解析スタンダード〜NGSのポテンシャルを活かしきるWET&DRY2014

    • Author(s)
      二階堂愛
    • Total Pages
      404
    • Publisher
      羊土社
    • Related Report
      2014 Research-status Report
  • [Book] NGSによる転写制御ネットワークのモデリング. 実験医学2013

    • Author(s)
      二階堂愛
    • Total Pages
      4
    • Publisher
      羊土社
    • Related Report
      2013 Research-status Report
  • [Book] 次世代シーケンサーのその先に -シーケンス技術の現在と未来を考える- 細胞工学2013

    • Author(s)
      二階堂愛
    • Total Pages
      2
    • Publisher
      学研メディカル秀潤社
    • Related Report
      2013 Research-status Report
  • [Remarks] 理化学研究所情報基盤センター バイオインフォマティクス研究開発ユニット

    • URL

      http://bit.riken.jp/

    • Related Report
      2015 Annual Research Report
  • [Remarks] 理化学研究所情報基盤センターバイオインフォマティクス研究開発ユニット

    • URL

      http://bit.accc.riken.jp/

    • Related Report
      2014 Research-status Report
  • [Remarks] Bioinformatics Research Unit

    • URL

      http://bit.accc.riken.jp/

    • Related Report
      2013 Research-status Report
  • [Remarks] 研究紹介: 理化学研究所情報基盤センター バイオインフォマティクス研究開発ユニット

    • URL

      http://www.riken.jp/research/labs/accc/bioinf/

    • Related Report
      2013 Research-status Report
  • [Remarks] Linking theory and experiment with bioinformatics

    • URL

      http://www.riken.jp/en/research/rikenresearch/rikenpeople/7505/

    • Related Report
      2013 Research-status Report
  • [Remarks] Sox2が幹細胞性を維持するメカニズム

    • URL

      http://www.cdb.riken.jp/jp/04_news/articles/13/131107_sox2.html

    • Related Report
      2013 Research-status Report

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

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