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Development of machine learning methods to comprehensively predict drug targets from omics data

Research Project

Project/Area Number 25700029
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Life / Health / Medical informatics
Research InstitutionKyushu University

Principal Investigator

Yamanishi Yoshihiro  九州大学, 高等研究院, 准教授 (60437267)

Project Period (FY) 2013-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥24,050,000 (Direct Cost: ¥18,500,000、Indirect Cost: ¥5,550,000)
Fiscal Year 2015: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000)
Fiscal Year 2014: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
Fiscal Year 2013: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000)
Keywords機械学習 / インシリコ創薬 / 標的分子 / 相互作用予測 / 薬物
Outline of Final Research Achievements

The identification of interactions between drugs and target proteins is a key area in genomic drug discovery. Various high-throughput experimental projects enable us to analyze the genome, transcriptome, proteome. At the same time, the high-throughput screening of large-scale chemical compound libraries with various biological assays produce chemical and phenotypic data on drugs and bioactive compounds. In this project, we develop machine learning methods to infer unknown drug-target interactions by integrating various large-scale omics data.

Report

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

    (44 results)

All 2016 2015 2014 2013 Other

All Journal Article (10 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 10 results,  Open Access: 2 results,  Acknowledgement Compliant: 4 results) Presentation (33 results) (of which Int'l Joint Research: 4 results,  Invited: 21 results) Remarks (1 results)

  • [Journal Article] Predicting target proteins for drug candidate compounds based on drug-induced gene expression data in a chemical structure-independent manner2015

    • Author(s)
      Hizukuri, Y., Sawada, R., and Yamanishi, Y.
    • Journal Title

      BMC Medical Genomics

      Volume: 8 Issue: 1 Pages: 82-82

    • DOI

      10.1186/s12920-015-0158-1

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Target-based drug repositioning using large-scale chemical-protein interactome data2015

    • Author(s)
      Sawada, R., Iwata, H., Mizutani, S., and Yamanishi, Y.
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 55 Issue: 12 Pages: 2717-2730

    • DOI

      10.1021/acs.jcim.5b00330

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Mining discriminative patterns from graph data with multiple labels and its application to QSAR2015

    • Author(s)
      Shao, Z., Hirayama, Y., Yamanishi, Y., Saigo, H.
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 55 Issue: 12 Pages: 2519-2527

    • DOI

      10.1021/acs.jcim.5b00376

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Large-scale prediction of beneficial drug combinations using drug efficacy and target profiles2015

    • Author(s)
      Iwata, H., Sawada, R., Mizutani, S., Kotera, M., and Yamanishi, Y.
    • Journal Title

      Journal of Chemical Information and Modeling

      Volume: 55 Issue: 12 Pages: 2705-2716

    • DOI

      10.1021/acs.jcim.5b00444

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] DINIES: drug-target interaction network inference engine based on supervised analysis2014

    • Author(s)
      Yoshihiro Yamanishi, Masaaki Kotera, Yuki Moriya, Ryusuke Sawada, Minoru Kanehisa, Susumu Goto
    • Journal Title

      Nucleic Acids Research

      Volume: 42 Issue: W1 Pages: W39-W45

    • DOI

      10.1093/nar/gku337

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Benchmarking a wide range of chemical descriptors for drug-target interaction prediction using a chemogenomic approach2014

    • Author(s)
      Ryusuke Sawada, Masaaki Kotera, and Yoshihiro Yamanishi
    • Journal Title

      Molecular Informatics

      Volume: 33 Issue: 11-12 Pages: 719-731

    • DOI

      10.1002/minf.201400066

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Journal Article] KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics2013

    • Author(s)
      Masaaki Kotera, Yasuo Tabei, Yoshihiro Yamanishi, Yuki Moriya, Toshiaki Tokimatsu, Minoru Kanehisa and Susumu Goto.
    • Journal Title

      BMC Systems Biology

      Volume: 7 Issue: S6

    • DOI

      10.1186/1752-0509-7-s6-s2

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Scalable prediction of compound-protein interactions using minwise hashing2013

    • Author(s)
      Y.Tabei and Y.Yamanishi
    • Journal Title

      BMC Systems Biology

      Volume: 7 Issue: Suppl 6 Pages: S3-S3

    • DOI

      10.1186/1752-0509-7-s6-s3

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring protein domains associated with drug side effects based on drug-target interaction network2013

    • Author(s)
      Iwata, H., Mizutani, S., Tabei, Y., Kotera, M., Goto, S., and Yamanishi, Y.
    • Journal Title

      BMC Systems Biology

      Volume: 7(Suppl 6) Issue: S6

    • DOI

      10.1186/1752-0509-7-s6-s18

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Inferring chemogenomic features from drug-target interaction networks2013

    • Author(s)
      Yamanishi, Y.
    • Journal Title

      Molecular Informatics

      Volume: 32 Issue: 11-12 Pages: 991-999

    • DOI

      10.1002/minf.201300079

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Presentation] Computational drug repositioning using medical big data2016

    • Author(s)
      Yamanishi, Y.
    • Organizer
      The 6th French-Japanese Workshop on Computational Methods in Chemistry
    • Place of Presentation
      Kyoto
    • Year and Date
      2016-03-16
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 医薬ビッグデータと機械学習によるインシリコ創薬2015

    • Author(s)
      山西芳裕
    • Organizer
      新生命科学分野開拓とスーパーコンピュータ「京」
    • Place of Presentation
      福岡
    • Year and Date
      2015-12-17
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 化合物応答遺伝子発現プロファイルの大規模解析による生理活性化合物の作用機序推定と創薬への応用2015

    • Author(s)
      岩田通夫, 澤田隆介, 山西芳裕
    • Organizer
      BMB2015(第38回分子生物学会・第88回生化学会合同大会)
    • Place of Presentation
      神戸
    • Year and Date
      2015-12-01
    • Related Report
      2015 Annual Research Report
  • [Presentation] 医薬ビッグデータと機械学習によるインシリコ創薬2015

    • Author(s)
      山西芳裕
    • Organizer
      日本計算機統計学会 第29回シンポジウム
    • Place of Presentation
      釧路
    • Year and Date
      2015-11-27
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] Systematic drug repositioning via omics data analysis with machine learning methods2015

    • Author(s)
      Yamanishi, Y.
    • Organizer
      Autumn School of Chemoinformatics in Tokyo
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-11-25
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Systematic drug repositioning for a wide range of diseases with machine learning methods2015

    • Author(s)
      Yamanishi, Y.
    • Organizer
      Study Sessions on Bioinformatics and Related Topics
    • Place of Presentation
      Osaka
    • Year and Date
      2015-11-04
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 医薬ビッグデータと機械学習によるインシリコ創薬2015

    • Author(s)
      山西芳裕
    • Organizer
      第19回バイオメディカル研究会「人工知能のバイオメディカル応用」
    • Place of Presentation
      大阪
    • Year and Date
      2015-10-30
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 化合物摂動と遺伝子摂動の遺伝子発現プロファイルを用いた医薬品候補化合物の標的タンパク質予測2015

    • Author(s)
      澤田隆介, 岩田通夫, 山西芳裕
    • Organizer
      第4回生命医薬情報学連合大会
    • Place of Presentation
      宇治
    • Year and Date
      2015-10-29
    • Related Report
      2015 Annual Research Report
  • [Presentation] 化合物・タンパク質間インターラクトーム情報とオミックスデータに基づくドラッグリポジショニング2015

    • Author(s)
      澤田隆介, 岩田通夫, 山西芳裕
    • Organizer
      情報計算化学生物学会2015年大会
    • Place of Presentation
      東京
    • Year and Date
      2015-10-27
    • Related Report
      2015 Annual Research Report
  • [Presentation] 医薬ビッグデータ解析に基づくインシリコ創薬2015

    • Author(s)
      山西芳裕
    • Organizer
      HPCIセミナー「予測する生命科学・医療および創薬基盤」
    • Place of Presentation
      東京
    • Year and Date
      2015-10-23
    • Related Report
      2015 Annual Research Report
    • Invited
  • [Presentation] 医療ビッグデータの創薬応用のための機械学習法2015

    • Author(s)
      山西芳裕
    • Organizer
      第31回大規模データ科学に関する研究会
    • Place of Presentation
      札幌
    • Year and Date
      2015-08-24
    • Related Report
      2015 Annual Research Report
  • [Presentation] Systematic drug repositioning for a wide range of diseases with computational approaches2015

    • Author(s)
      Yamanishi, Y.
    • Organizer
      JCUP VI
    • Place of Presentation
      Tokyo
    • Year and Date
      2015-06-04
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] DINIES: A web-based application for predicting drug-target interaction networks2015

    • Author(s)
      Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M., and Goto, S.
    • Organizer
      The Thirteenth Asia Pacific Bioinformatics Conference
    • Place of Presentation
      HsinChu
    • Year and Date
      2015-01-21 – 2015-01-23
    • Related Report
      2014 Annual Research Report
  • [Presentation] オミックスデータ解析と機械学習によるインシリコ創薬2014

    • Author(s)
      山西芳裕
    • Organizer
      平成26年度九州大学高等研究院-公益財団法人九州先端科学技術研究所 研究交流会
    • Place of Presentation
      福岡
    • Year and Date
      2014-12-01
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] 薬物の潜在標的分子と新規効能のインシリコ予測2014

    • Author(s)
      山西芳裕
    • Organizer
      日本化学会情報化学部会主催 第二回若手の会
    • Place of Presentation
      東京
    • Year and Date
      2014-11-29
    • Related Report
      2014 Annual Research Report
  • [Presentation] オミックスデータ解析と機械学習によるインシリコ創薬2014

    • Author(s)
      山西芳裕
    • Organizer
      第23回BMIRC研究会
    • Place of Presentation
      飯塚
    • Year and Date
      2014-10-08
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] オミックスデータに基づく分子間相互作用ネットワークの予測と創薬への応用2014

    • Author(s)
      山西芳裕
    • Organizer
      第3回生命医薬情報学連合大会
    • Place of Presentation
      仙台
    • Year and Date
      2014-10-02 – 2014-10-04
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Analysis and inference of drug-target interaction networks2014

    • Author(s)
      Yamanishi, Y.
    • Organizer
      International Symposium on Bioinformatics and its Application
    • Place of Presentation
      Tokyo
    • Year and Date
      2014-09-30
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] ケモゲノミクスや薬理ゲノミクスに基づくインシリコ創薬2014

    • Author(s)
      山西芳裕
    • Organizer
      天然薬物研究方法論アカデミー第17回シンポジウム
    • Place of Presentation
      富山
    • Year and Date
      2014-07-26 – 2014-07-27
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] DINIES: A web-based application for predicting drug-target interaction networks2014

    • Author(s)
      Yamanishi, Y., Kotera, M., Moriya, Y., Sawada, R., Kanehisa, M., and Goto, S.
    • Organizer
      The 22nd International Conference on Intelligent Systems for Molecular Biology
    • Place of Presentation
      Boston
    • Year and Date
      2014-07-11 – 2014-07-15
    • Related Report
      2014 Annual Research Report
  • [Presentation] Analysis and inference of drug-target interaction networks2014

    • Author(s)
      Yamanishi, Y.
    • Organizer
      The 5th French-Japanese Workshop on Computational Methods in Chemistry
    • Place of Presentation
      Strasbourg
    • Year and Date
      2014-06-30 – 2014-07-01
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] In silico methods for predicting drug targets and new drug indications2014

    • Author(s)
      Yamanishi, Y.
    • Organizer
      The 9th International Symposium of the Institute Network
    • Place of Presentation
      Osaka
    • Year and Date
      2014-06-19 – 2014-06-20
    • Related Report
      2014 Annual Research Report
  • [Presentation] ネットワーク解析に基づくドラッグリポジショニング2014

    • Author(s)
      山西芳裕
    • Organizer
      日本薬剤学会第29年会
    • Place of Presentation
      さいたま
    • Year and Date
      2014-05-20 – 2014-05-22
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Predicting drug-target interaction networks from the integration of chemical, genomic, and pharmacological spaces2014

    • Author(s)
      Yamanishi, Y.
    • Organizer
      International Symposium on Tumor Biology in Kanazawa & Academic Drug Discovery Symposium
    • Place of Presentation
      Kanazawa, Japan
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 薬物の潜在標的分子と新規効能のインシリコ予測2014

    • Author(s)
      山西芳裕
    • Organizer
      共進化社会システム創成拠点フォーラム
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ドラッグ・リポジショニングのためのイン・シリコ手法2014

    • Author(s)
      山西芳裕
    • Organizer
      千里ライフサイエンス振興財団専門実務セミナー
    • Place of Presentation
      大阪
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] オミックスデータから薬物標的分子を網羅的に予測するためのバイオインフォマティクス2013

    • Author(s)
      山西芳裕
    • Organizer
      第3回NGS現場の会
    • Place of Presentation
      神戸
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ゲノム情報、ケミカル情報、薬理情報から薬物標的分子を予測する統計手法2013

    • Author(s)
      山西芳裕
    • Organizer
      2013年度統計関連学会連合大会
    • Place of Presentation
      大阪
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] ケモゲノミクスや薬理ゲノミクスの手法による薬物・標的タンパク質間相互作用ネットワークの予測2013

    • Author(s)
      山西芳裕
    • Organizer
      第2回生命システム理論研究会
    • Place of Presentation
      東京
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 機械学習による薬物の標的分子や副作用の網羅的予測2013

    • Author(s)
      山西芳裕
    • Organizer
      第41回構造活性相関シンポジウム
    • Place of Presentation
      西宮
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] KCF-S: KEGG Chemical Function and Substructure for improved interpretability and prediction in chemical bioinformatics2013

    • Author(s)
      Kotera, M., Tabei, Y., Yamanishi, Y., Moriya, Y., Tokimatsu, T., Kanehisa, M., and Goto, S.
    • Organizer
      The 24th International Conference on Genome Informatics (GIW2013)
    • Place of Presentation
      Singapore, Singapore
    • Related Report
      2013 Annual Research Report
  • [Presentation] Scalable prediction of compound-protein interactions using minwise hashing2013

    • Author(s)
      Tabei, Y. and Yamanishi, Y.
    • Organizer
      The 24th International Conference on Genome Informatics (GIW2013)
    • Place of Presentation
      Singapore, Singapore
    • Related Report
      2013 Annual Research Report
  • [Presentation] Inferring protein domains associated with drug side effects based on drug-target interaction network2013

    • Author(s)
      Iwata, H., Mizutani, S., Tabei, Y., Kotera, M., Goto, S., and Yamanishi, Y.
    • Organizer
      The 24th International Conference on Genome Informatics (GIW2013)
    • Place of Presentation
      Singapore, Singapore
    • Related Report
      2013 Annual Research Report
  • [Remarks] DINIES

    • URL

      http://www.genome.jp/tools/dinies/

    • Related Report
      2015 Annual Research Report 2014 Annual Research Report

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Published: 2013-05-21   Modified: 2019-07-29  

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