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2012 Fiscal Year Final Research Report

Development of Gene Regulatory Network Analysis Methods for Revealing Cell Differentiation Processes

Research Project

  • PDF
Project/Area Number 22310125
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field System genome science
Research InstitutionOsaka University

Principal Investigator

MATSUDA Hideo  大阪大学, 情報科学研究科, 教授 (50183950)

Co-Investigator(Kenkyū-buntansha) TAKENAKA Yoichi  大阪大学, 情報科学研究科, 准教授 (00324830)
Project Period (FY) 2010 – 2012
Keywords遺伝子ネットワーク / 細胞分化 / ベイジアンネットワーク
Research Abstract

We constructed a mathematical model for expressing gene regulatory relationships, based on gene regulatory networks, on multiple cell differentiations. We successfully explored several regulatory genes appeared in both of the two cell differentiations of mouse adipocytes and osteoblasts. We developed a parallel processing method on massively parallel servers to reduce a large amount of computational costs of the processing.

  • Research Products

    (13 results)

All 2013 2012 2011 2010

All Journal Article (5 results) (of which Peer Reviewed: 5 results) Presentation (8 results)

  • [Journal Article] An estimation method for a cellular-state-specific gene regulatory network along tree-structured gene expression profiles2013

    • Author(s)
      Ryo Araki, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      Gene

      Volume: Vol.518

    • DOI

      doi:10.1016/j.gene.2012.11.090

    • Peer Reviewed
  • [Journal Article] A method for isoform prediction from RNA-Seq data by iterative mapping2012

    • Author(s)
      Tomoshige Ohno, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      IPSJ Transactions on Bioinformatics

      Volume: Vol.5 Pages: 27-33

    • DOI

      doi:10.2197/ipsjtbio.5.27

    • Peer Reviewed
  • [Journal Article] An estimation method for inference of gene regulatory network using Bayesian network with uniting of partial problems2012

    • Author(s)
      Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      BMC Genomics

      Volume: Vol.13 Pages: S12

    • DOI

      doi:10.1186/1471-2164-13-S1-S12

    • Peer Reviewed
  • [Journal Article] Inference of S-system models of gene regulatory networks using immune algorithm2011

    • Author(s)
      Tomoyoshi Nakayama, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Journal Title

      Journal of Bioinformatics and Computational Biology

      Volume: Vol.9 Pages: 75-86

    • DOI

      doi:10.1142/S0219720011005768

    • Peer Reviewed
  • [Journal Article] 細胞分化クロストークのモデル化と細胞分化クロストーク遺伝子の推定手法2011

    • Author(s)
      吉澤陽志, 瀬尾茂人, 竹中要一, 松田秀雄
    • Journal Title

      情報処理学会論文誌 数理モデル化と応用

      Volume: 4巻 Pages: 59-68

    • Peer Reviewed
  • [Presentation] Estimate Dynamic Gene Regulatory Networks in Adipocyte Differentiation for Detecting Changes of Gene Regulations by Splitting Time Course Data2012

    • Author(s)
      Tomoyoshi Nakayama, Yoshiyuki Kido,Hiromi Daiyasu, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      23rd International Conference on Genome Informatics(GIW2012)
    • Place of Presentation
      National Cheng Kung University, Tainan, Taiwan
    • Year and Date
      2012-12-13
  • [Presentation] Large-Scale Gene Regulatory Network Analysis for Adipocyte Differentiation on High-Performance Computer2012

    • Author(s)
      Hideo Matsuda
    • Organizer
      The 23rd International Conference on Genome Informatics (GIW2012)
    • Place of Presentation
      National Cheng Kung University, Tainan, Taiwan
    • Year and Date
      2012-12-12
  • [Presentation] Direct unique gene regulatory networks along dendrogram of cell differentiation2011

    • Author(s)
      Ryo Araki, Yoichi Takenaka, Tomoshige Ohno, Yukito Watanabe, Shigeto Seno, Hideo Matsuda
    • Organizer
      InCoB/ISCB-Asia Joint Conference 2011
    • Place of Presentation
      Renaissance Hotel, Kuala Lumpur, Malaysia
    • Year and Date
      2011-11-30
  • [Presentation] Network analysis for time-series expression profile using nested effects models2011

    • Author(s)
      Tatsuya Kitaguchi, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 2011 Joint Conference of CBI and JSBi (CBI/JSBi2011)
    • Place of Presentation
      Kobe International Conference Center, Hyogo.
    • Year and Date
      2011-11-08
  • [Presentation] A Directed Graphical Gaussian Model for Inferring Gene Regulatory Networks2011

    • Author(s)
      Tomoshige Ohno, Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
    • Place of Presentation
      Austria Center Vienna, Vienna, Austria
    • Year and Date
      2011-07-19
  • [Presentation] A Method for Inference of Gene Regulatory Network based on Bayesian Network with Uniting of Partial Problems2011

    • Author(s)
      Yukito Watanabe, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 19th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB2011)
    • Place of Presentation
      Austria Center Vienna, Vienna, Austria.
    • Year and Date
      2011-07-18
  • [Presentation] Revealing regulatory relationships of crosstalk with multiple time-series gene expression profiles2010

    • Author(s)
      Kiyoshi Yoshizawa, Shigeto Seno, Yoichi Takenaka, Hideo Matsuda
    • Organizer
      The 2010 Annual Conference of the Japanese Society for Bioinformatics (JSBi2010)
    • Place of Presentation
      Centennial Hall, Kyushu University School of Medicine, Fukuoka.
    • Year and Date
      2010-12-13
  • [Presentation] Reconstruction of Gene Regulatory Networks for Drug Target Discovery2010

    • Author(s)
      Hideo Matsuda
    • Organizer
      The 3rd National Seminar and Workshop on Computer Aided-Drug Design: Virtual Screening (CADD2010)
    • Place of Presentation
      Gurney Hotel, Penang, Malaysia
    • Year and Date
      2010-12-03

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Published: 2014-08-29  

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