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2009 Fiscal Year Final Research Report

Development of method for evaluating the consistency between network model in the cell and the molecular measured data

Research Project

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Project/Area Number 19201039
Research Category

Grant-in-Aid for Scientific Research (A)

Allocation TypeSingle-year Grants
Section一般
Research Field 基礎ゲノム科学
Research InstitutionNational Institute of Advanced Industrial Science and Technology

Principal Investigator

HORIMOTO Katsuhisa  National Institute of Advanced Industrial Science and Technology, 生命情報工学研究センター, 研究チーム長 (40238803)

Co-Investigator(Kenkyū-buntansha) ABURATANI Sachiyo  独立行政法人産業技術総合研究所, 生命情報工学研究センター, 研究員 (10361627)
TOMINAGA Daisuke  独立行政法人産業技術総合研究所, 生命情報工学研究センター, 研究員 (20357578)
ANAI Hirokazu  株式会社富士通研究所, Tコア研究所, 研究員 (20417520)
YOSHIDA Hiroshi  九州大学, 数理科学研究院, 特任助教授 (60401262)
Project Period (FY) 2007 – 2009
Keywordsシステム生物学 / ネットワーク解析 / グラフィカル・モデル / 記号計算
Research Abstract

We have developed two methods for evaluating the consistency between the given network structures and the measured data of constituent molecules, based on the statistical and symbolic-numeric approaches. By using these methods, the active networks can be detected under a particular condition, and furthermore, the changes of network structures can be traced, depending on the environmental changes.

  • Research Products

    (43 results)

All 2010 2009 2008 2007 Other

All Journal Article (25 results) (of which Peer Reviewed: 24 results) Presentation (11 results) Book (5 results) Remarks (2 results)

  • [Journal Article] Altered Hepatic Gene Expression Profiles Associated with Myocardial Ischemia.2010

    • Author(s)
      Ootsuji, H., Honda, M., Takamura, M., Usui, S., Okajima, M., D, Okada, H., Sakai, Y., Takamura, T., Horimoto, K., Kaneko, S
    • Journal Title

      Circ Cardiovasc Genet 3

      Pages: 68-77

    • Peer Reviewed
  • [Journal Article] Period-Phase Map: Two-diemsional Selection of Circadian Rhythm-Related Genes.2009

    • Author(s)
      Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H., Horimoto, K
    • Journal Title

      IET Sys. Biol 3

      Pages: 487-495

    • Peer Reviewed
  • [Journal Article] TRAIL inhibited the cyclic AMP responsible element mediated gene expression.2009

    • Author(s)
      Tokumoto, Y., Horimoto, K., Miyake, J
    • Journal Title

      Biochem. Biophys. Res. Commun 381

      Pages: 533-536

    • Peer Reviewed
  • [Journal Article] Differential miRNA expression between hepatitis B and hepatitis C leading disease progression to HCC.2009

    • Author(s)
      Ura, S., Honda, M., Yamashita, T., Ueda, T., Takatori, H., Nishino, R., Sunagozaka, H., Sakai, Y., Horimoto, K., Kaneko, S
    • Journal Title

      Hepatology 49

      Pages: 1098-1112

    • Peer Reviewed
  • [Journal Article] Detection of network structure changes by graphical chain modeling: a case study of hepatitis C virus-related hepatocellular carcinoma.2009

    • Author(s)
      Saito, S., Honda, M., Kaneko, S., Horimoto, K
    • Journal Title

      Proceedings of 48th IEEE Conference on Decision and Control

      Pages: 5624-5630

    • Peer Reviewed
  • [Journal Article] Co-Expressed Gene Assessment Based on the Path Consistency Algorithm: Operon Detention in Escherichia coli. Proceedings of IEEE International Conference on Systems2009

    • Author(s)
      Saito, S., Horimoto, K
    • Journal Title

      Man and Cybernetics

      Pages: 4280-4286

    • Peer Reviewed
  • [Journal Article] Parameter Optimization in the network dynamics including unmeasured variables by the symbolic-numeric approach.2009

    • Author(s)
      Nakatsui, M., Horimoto, K
    • Journal Title

      Proceedings of the Third International Symposium on Optimization and Systems Biology (OSB'09)

      Pages: 245-253

    • Peer Reviewed
  • [Journal Article] Complementing Networks Using Observed Data.2009

    • Author(s)
      Akutsu, T., Tamura, T., Horimoto, K
    • Journal Title

      Lecture Notes in Artificial Intelligence 5809

      Pages: 126-140

    • Peer Reviewed
  • [Journal Article] Inference of Probabilities over a Stochastic IL-System by Quantifier Elimination.2008

    • Author(s)
      Yoshida, H., Horimoto, K., Anai, H
    • Journal Title

      Math. Comput. Sci 1

      Pages: 473-485

    • Peer Reviewed
  • [Journal Article] Identification of novel candidate tumour marker genes for intrahepatic cholangiocarcinoma.2008

    • Author(s)
      Nishino, R., Honda, M., Yamashita, T., Takatori, H., Minato, H., Zen, Y., Sasaki, M., Takamura, H., Horimoto, K., Ohta, T., Nakanuma, Y., Kaneko, S
    • Journal Title

      J. Hepatol 49

      Pages: 207-216

    • Peer Reviewed
  • [Journal Article] Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis.2008

    • Author(s)
      Hayashida, M., Sun, F., Aburatani, S., Horimoto, K., Akutsu, T
    • Journal Title

      Int. J. Bioinformatics Research and Applications 4

      Pages: 385-399

    • Peer Reviewed
  • [Journal Article] Network evaluation from the consistency of the graph structure with the measured data.2008

    • Author(s)
      Saito, S., Aburatani, S., Horimoto, K
    • Journal Title

      BMC Sys. Biol 2

      Pages: 84

    • Peer Reviewed
  • [Journal Article] Analysis of network dynamics including hidden variables by symbolic-numeric approach.2008

    • Author(s)
      Tominaga, D., Tokumoto, Y., Nakatsui, M., Sun, F., Miyake, J., Horimoto, K
    • Journal Title

      Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB'08)

      Pages: 242-248

    • Peer Reviewed
  • [Journal Article] Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus.2008

    • Author(s)
      Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H., Horimoto, K
    • Journal Title

      Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB'08)

      Pages: 109-114

    • Peer Reviewed
  • [Journal Article] An Algebraic-Numeric Algorithm for the Model Selection in Network Motifs in Escherichia coli.2008

    • Author(s)
      Nakatsui, M., Yoshida, H., Horimoto, K
    • Journal Title

      Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB'08)

      Pages: 257-264

    • Peer Reviewed
  • [Journal Article] Time Series Segmentation for Gene Regulatory Process with Time-Window-Extension Technique.2008

    • Author(s)
      Zhang, Z.Y., Horimoto, K., Liu, Z
    • Journal Title

      Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB'08)

      Pages: 198-203

    • Peer Reviewed
  • [Journal Article] Revealing Disease Related Interactions by Correlation Analysis.2008

    • Author(s)
      Wu, Z.K., Zhang, Z.Y., Zhang, L.W., Horimoto, K
    • Journal Title

      Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB'08)

      Pages: 341-349

    • Peer Reviewed
  • [Journal Article] Gene systems network inferred from expression profiles in hepatocellular carcinogenesis by graphical Gaussian model.2007

    • Author(s)
      Aburatani, S., Sun, F., Saito, S., Honda, M., Kaneko, S., Horimoto, K
    • Journal Title

      EURASIP J. Bioinfo. Systems Biol

      Pages: 47214

    • Peer Reviewed
  • [Journal Article] Derivation of rigorous conditions for high cell-type diversity by algebraic approach.2007

    • Author(s)
      Yoshida, H., Anai, H., Horimoto, K
    • Journal Title

      BioSystems 90

      Pages: 486-495

    • Peer Reviewed
  • [Journal Article] Inference of Protein-Protein Interactions by Using Co-evolutionary Information.2007

    • Author(s)
      Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., Toh, H
    • Journal Title

      Algebraic Biology, Lecture Notes in Computer Science(In Anai, H., Horimoto, K. and Kutsia, T. (eds)) 4545

      Pages: 322-333

    • Peer Reviewed
  • [Journal Article] Exact parameter determination for Parkinson's disease diagnosis with PET using an algebraic approach.2007

    • Author(s)
      Yoshida, H., Nakagawa, K., Anai, H., Horimoto, K
    • Journal Title

      Algebraic Biology, Lecture Notes in Computer Science(In Anai, H., Horimoto, K., Kutsia, T. (eds)) 4545

      Pages: 110-124

  • [Journal Article] An Algebraic-Numeric Algorithm for the Model Selection in Kinetic Networks.2007

    • Author(s)
      Yoshida, H., Nakagawa, K., Anai, H., Horimoto, K
    • Journal Title

      Proceedings of 10th CASC, LNCS(Springer, Heidelberg) 4770

      Pages: 433-447

    • Peer Reviewed
  • [Journal Article] Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis.2007

    • Author(s)
      Hayashida, M., Sun, F., Aburatani, S., Horimoto, K., Akutsu, T
    • Journal Title

      Proceedings of 10th OSB, Lecture Notes in Operation Research(Publishing Corporation)

      Pages: 288-301

    • Peer Reviewed
  • [Journal Article] Brute force meets Bruno force in parameter optimization: Introduction of novel constraints for parameter estimation by symbolic computation.

    • Author(s)
      Nakatsu, M., Horimoto, K., Lemaire, F., Urguplu, A., Sedoglavic, A., Boulier, F
    • Journal Title

      IET Sys. Biol (in press)

    • Peer Reviewed
  • [Journal Article] Parameter Optimization by Using Differential Elimination: a General Approach for Introducing Constraints into Objective Function.

    • Author(s)
      Nakatsui, M., Horimoto, K., Okamoto, M., Tokumoto, Y., Miyake, J
    • Journal Title

      BMC Sys. Biol (in press)

    • Peer Reviewed
  • [Presentation] Detection of network structure changes by graphical chain modeling: a case study of hepatitis C virus-related hepatocellular carcinoma.2009

    • Author(s)
      Saito, S., Honda, M., Kaneko, S., Horimoto, K
    • Organizer
      48th IEEE Conference on Decision and Control
    • Place of Presentation
      China
    • Year and Date
      2009-12-17
  • [Presentation] Co-Expressed Gene Assessment Based on the Path Consistency Algorithm: Operon Detention in Escherichia coli.2009

    • Author(s)
      Saito, S., Horimoto, K
    • Organizer
      IEEE International Conference on Systems, Man and Cybernetics
    • Place of Presentation
      USA
    • Year and Date
      2009-10-11
  • [Presentation] Parameter Optimization in the network dynamics including unmeasured variables by the symbolic-numeric approach.2009

    • Author(s)
      Nakatsui, M., Horimoto, K
    • Organizer
      The Third International Symposium on Optimization and Systems Biology (OSB'09)
    • Place of Presentation
      China
    • Year and Date
      2009-09-20
  • [Presentation] Analysis of network dynamics including hidden variables by symbolic-numeric approach.2008

    • Author(s)
      Tominaga, D., Tokumoto, Y., Nakatsui, M., Sun, F., Miyake, J., Horimoto, K
    • Organizer
      The Second International Symposium on Optimization and Systems Biology (OSB'08)
    • Place of Presentation
      China
    • Year and Date
      2008-10-18
  • [Presentation] Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus.2008

    • Author(s)
      Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H., Horimoto, K
    • Organizer
      The Second International Symposium on Optimization and Systems Biology (OSB'08)
    • Place of Presentation
      China
    • Year and Date
      2008-10-18
  • [Presentation] An Algebraic-Numeric Algorithm for the Model Selection in Network Motifs in Escherichia coli.2008

    • Author(s)
      Nakatsui, M., Yoshida, H., Horimoto, K
    • Organizer
      The Second International Symposium on Optimization and Systems Biology (OSB'08)
    • Place of Presentation
      China
    • Year and Date
      2008-10-18
  • [Presentation] Time Series Segmentation for Gene Regulatory Process with Time-Window-Extension Technique.2008

    • Author(s)
      Zhang, Z.Y., Horimoto, K., Liu, Z
    • Organizer
      The Second International Symposium on Optimization and Systems Biology (OSB'08)
    • Place of Presentation
      China
    • Year and Date
      2008-10-18
  • [Presentation] Revealing Disease Related Interactions by Correlation Analysis.2008

    • Author(s)
      Wu, Z.K., Zhang, Z.Y., Zhang, L.W., Horimoto, K
    • Organizer
      The Second International Symposium on Optimization and Systems Biology (OSB'08)
    • Place of Presentation
      China
    • Year and Date
      2008-10-18
  • [Presentation] An Algebraic-Numeric Algorithm for the Model Selection in Kinetic Networks.2007

    • Author(s)
      Yoshida, H., Nakagawa, K., Anai, H., Horimoto, K
    • Organizer
      10th CASC
    • Place of Presentation
      Germany
    • Year and Date
      2007-09-16
  • [Presentation] Inference of Protein-Protein Interactions by Using Co-evolutionary Information2007

    • Author(s)
      Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M., Toh, H
    • Organizer
      Algebraic Biology 2007
    • Place of Presentation
      Austria
    • Year and Date
      2007-07-02
  • [Presentation] Exact parameter determination for Parkinson's disease diagnosis with PET using an algebraic approach2007

    • Author(s)
      Yoshida, H., Nakagawa, K., Anai, H., Horimoto, K
    • Organizer
      Algebraic Biology 2007
    • Place of Presentation
      Austria
    • Year and Date
      2007-07-02
  • [Book] Bioinformatics for Systems Biology: Second Edition, Introduction to Informatics(In Krawetz, S. (ed))2009

    • Author(s)
      Aburatani, S., Saito, S., Horimoto, K
    • Total Pages
      563-577
    • Publisher
      Humana Press
  • [Book] Symbolic Computation in Biology, Math. Comput. Sci2009

    • Author(s)
      Anai, H., Horimoto, K. (eds)
    • Total Pages
      399-556
  • [Book] Algebraic Biology, Lecture Notes in Computer Science2008

    • Author(s)
      Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds)
    • Publisher
      Springer
  • [Book] Algebraic Biology, Lecture Notes in Computer Science2007

    • Author(s)
      Anai, H., Horimoto, K., Kutsia, T. (eds)
    • Publisher
      Springer
  • [Book] Applied statistics for Network Biology: Methods in Systems Biology(F., Dehmer, M., Salvador, A. and Graber, A. (eds))

    • Author(s)
      Saito, S., Horimoto, K. : Network Screening
    • Publisher
      Wiley(in press)
  • [Remarks] ネットワーク推定サーバ"ASIAN"

    • URL

      http://eureka.cbrc.jp/asian/

  • [Remarks] 研究会「生体モデリングの新展開-分子からネットワークへ」開催(産業技術総合研究所臨海別館11F第三会議室、2009年11月26日)発表者:岡本正宏(九大院農学研究科)、Francois Lemaire、Alexandre Sedoglavic (Computer Science Lab., Lille Univ.)、阿久津達也(京大化学研究所)、今田友樹、永持仁(京大院情報学研究科)、堀本勝久(産総研CBRC)

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Published: 2011-06-18   Modified: 2016-04-21  

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