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Integrative modeling of genetic interactions based on intertwined multi-level networks

Research Project

Project/Area Number 23710233
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field System genome science
Research InstitutionHokkaido University

Principal Investigator

TAKIGAWA Ichigaku  北海道大学, 創成研究機構, 特任助教 (10374597)

Project Period (FY) 2011 – 2013
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2011: ¥2,080,000 (Direct Cost: ¥1,600,000、Indirect Cost: ¥480,000)
Keywords多階層ネットワーク / 分子間相互作用 / 遺伝子 / 発現制御 / 分子ネットワーク / 遺伝子間相互作用 / グラフマイニング / 分子間ネットワーク / 機械学習 / モデル化
Research Abstract

Genes had been considered to be factors that can be analyzed individually, and their effect on functions and phenotypes can be modeled linearly. However, now they are rather considered as non-linearly interacting entities to other genes and other types of biomolecules whose roles and control would be more complicated and context-dependent than we thought. This research regards genes as building blocks of intertwined multi-level networks of various biomolecules, and develops computational methods for integratively analyzing behaviors thorough the networks and for relating quantitative measurements of individual building blocks to the known structures of corresponding networks. Recent studies are producing large data such as transcriptomes, metabolomes, proteomes, and fluxomes, and many databases on biological networks are being developed. The integrative computational approaches thus need to be established to leverage these rich data on various networks and their constituents.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • 2011 Research-status Report
  • Research Products

    (13 results)

All 2013 2012 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results) Presentation (5 results) (of which Invited: 1 results) Remarks (2 results)

  • [Journal Article] Similarity-based machine learning methods for predicting drug.target interactions : a brief review2013

    • Author(s)
      Ding H, Takigawa I, Mamitsuka H, Zhu S
    • Journal Title

      Briefings in Bioinformatics

      Volume: (印刷中・先行オンライン出版済) Issue: 5 Pages: 737-747

    • DOI

      10.1093/bib/bbt056

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] SIBIC : A Web Server for Generating Gene Set Seiworks Based on Blelusters Obtained by Maximal Frequent Itemsel Mining2013

    • Author(s)
      Keiichio Takahashi. Ichigaku Takigawa and Hiroshi Mamitsuka
    • Journal Title

      PLOS ONE

      Volume: 8(12) Issue: 12 Pages: e82890-e82890

    • DOI

      10.1371/journal.pone.0082890

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] An In Silico Model for Interpreting Polypharmacological Relationships in Drug-Target Networks2013

    • Author(s)
      Ichigaku Takigawa, Koji Tsuda, Hiroshi Mamitsuka
    • Journal Title

      Methods in Molecular Biology (In Silico Models for Drug Discovery)

      Volume: 993 Pages: 67-80

    • DOI

      10.1007/978-1-62703-342-8_5

    • ISBN
      9781627033411, 9781627033428
    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Graph mining: procedure, application to drug discovery and recent advances2013

    • Author(s)
      Ichigaku Takigawa, Hiroshi Mamitsuka
    • Journal Title

      Drug Discovery Today

      Volume: 18: 1-2 Issue: 1-2 Pages: 50-57

    • DOI

      10.1016/j.drudis.2012.07.016

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Identifying Pathways of Coordinated Gene Expression2013

    • Author(s)
      Timothy Hancock, Ichigaku Takigawa, Hiroshi Mamitsuka
    • Journal Title

      Methods in Molecular Biology (Data Mining for Systems Biology)

      Volume: 939 Pages: 69-85

    • DOI

      10.1007/978-1-62703-107-3_7

    • ISBN
      9781627031066, 9781627031073
    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Identifying neighborhoods of coordinated gene expression and metabolite profiles2012

    • Author(s)
      Hancock T, Wicker N, Takigawa I, Mamitsuka, H
    • Journal Title

      PLoS One

      Volume: 7(2) Issue: 2 Pages: e31345-e31345

    • DOI

      10.1371/journal.pone.0031345

    • Related Report
      2013 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Presentation] Finding structural patterns shared among interacting molecules2013

    • Author(s)
      Takigawa I
    • Organizer
      3rd Beilstein Symposium on Glyco-Bioinformatics
    • Place of Presentation
      Potsdam, Germany
    • Related Report
      2013 Final Research Report
  • [Presentation] Identifying paired substructures significantly shared among interacting structure pairs2013

    • Author(s)
      Takigawa I
    • Organizer
      2013 International Workshop on Machine Learning and Applications to Biology (MLAB Sapporo 2013)
    • Place of Presentation
      Sapporo, Japan
    • Related Report
      2013 Final Research Report
  • [Presentation] Finding Structural Patterns Shared Among Interacting Molecules2013

    • Author(s)
      I Takigawa
    • Organizer
      The 3rd Beilstein Symposium on Glyco-Bioinformatics
    • Place of Presentation
      Hotel am Griebnitzsee, Potsdam, Germany
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Identifying Paired Substructures Significantly Shared among Interacting Structure Pairs2013

    • Author(s)
      I Takigawa
    • Organizer
      International Workshop on Machine Learning and Applications to Biology
    • Place of Presentation
      Hokkaido University, Sapporo, Japan
    • Related Report
      2013 Annual Research Report
  • [Presentation] Learning sparse linear models over subgraph indicators2012

    • Author(s)
      Takigawa I
    • Organizer
      2012 Sapporo Workshop on Machine Learning and Applications to Biology (MLAB Sapporo 2012)
    • Place of Presentation
      Sapporo, Japan
    • Related Report
      2013 Final Research Report
  • [Remarks] SiBIC

    • URL

      http://utrecht.kuicr.kyoto-u.ac.jp:8080/miami/faces/index.jsp

    • Related Report
      2013 Final Research Report
  • [Remarks] SiBIC

    • URL

      http://utrecht.kuicr.kyoto-u.ac.jp:8080/miami/faces/index.jsp

    • Related Report
      2013 Annual Research Report

URL: 

Published: 2011-08-05   Modified: 2019-07-29  

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