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Comparative analysis of large scale genome data and knowledge discovery

Research Project

Project/Area Number 17018021
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionKyoto University

Principal Investigator

YADA Tetsushi  Kyoto University, 大学院・情報学研究科, 准教授 (10322728)

Co-Investigator(Kenkyū-buntansha) 野口 秀樹 (野口 英樹)  東京大学, 大学院新領域創成科学研究科, 研究拠点形成特任研究員 (50333349)
Project Period (FY) 2005 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥69,600,000 (Direct Cost: ¥69,600,000)
Fiscal Year 2009: ¥13,500,000 (Direct Cost: ¥13,500,000)
Fiscal Year 2008: ¥13,500,000 (Direct Cost: ¥13,500,000)
Fiscal Year 2007: ¥13,800,000 (Direct Cost: ¥13,800,000)
Fiscal Year 2006: ¥13,800,000 (Direct Cost: ¥13,800,000)
Fiscal Year 2005: ¥15,000,000 (Direct Cost: ¥15,000,000)
Keywordsバイオインフォマティックス / ゲノム情報処理 / ゲノム生物学 / バイオインフォマティクス / 配列解析 / プロモーター / miRNA / バイオィンフォマティクス / アラインメント / プロファイル / 遺伝子発見 / アノテーション
Research Abstract

We have accumulated a large amount of knowledge concerning with molecular biology by comparing biological sequences, such as DNA, RNA and amino acid sequences. On the other hand, rapid progress of sequencing technology have brought accumulation of a large amount of sequence data. Then, its quantity is now exceeding the upper limit of application of existing sequence comparison methods. Here, we have developed methods which are capable of comparing such a large amount of sequence data with high accuracy, and have tackled the challenge to biological knowledge discovery by applying the methods. As a result, we have revealed molecular mechanism of transcriptional regulation of microRNA function.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • 2005 Annual Research Report
  • Research Products

    (21 results)

All 2010 2009 2008 2007 2006 2005 Other

All Journal Article (10 results) (of which Peer Reviewed: 2 results) Presentation (7 results) Book (4 results)

  • [Journal Article] Positional effects of polymorphisms in probe-target sequences on genoplot images of oligonucleotide microarrays2010

    • Author(s)
      T.L. Cui, H. Nakaoka, K. Akiyama, H. Kamura, K. Hosomichi, J. Bae, H. Cheong, H. Shin, T. Yada, I. Inoue
    • Journal Title

      Genet. Mol. Res. 23

      Pages: 524-31

    • Related Report
      2009 Final Research Report
  • [Journal Article] Probabilistic Graphical Modeling for Large-scale Combinatorial Regulation of Transcription Factors2008

    • Author(s)
      S.J. Park, N. Ichinose, T. Yada
    • Journal Title

      In the Proc. of Workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI-08)

      Pages: 72-86

    • Related Report
      2009 Final Research Report
  • [Journal Article] Reconstruction of transcription-translation dynamics with a model of gene networks2008

    • Author(s)
      N. Ichinose, T. Yada, O. Gotoh, K. Aihara
    • Journal Title

      J. Theor. Biol. 255

      Pages: 378-86

    • Related Report
      2009 Final Research Report
  • [Journal Article] Probabilistic Graphical Modeling for Large-scale Combinatorial Regulation of Transcription Factors2008

    • Author(s)
      S. J. Park, N. Ichinose and T. Yada
    • Journal Title

      Proc. of the workshop on Knowledge, Language, and Learning in Bioinformatics (KLLBI)

      Pages: 72-86

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Reconstruction of transcription-translation dynamics with a model of gene networks2008

    • Author(s)
      N. Ichinose, T. Yada, O. Gotoh and K. Aihara
    • Journal Title

      Journal of Theoretical Biology 255(4)

      Pages: 378-386

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 遺伝子発見2008

    • Author(s)
      矢田 哲士
    • Journal Title

      実験医学増刊 26

      Pages: 1050-1055

    • Related Report
      2007 Annual Research Report
  • [Journal Article] ゲノム比較時代の配列比較技術2007

    • Author(s)
      矢田 哲士, 後藤 修
    • Journal Title

      細胞工学別冊

      Pages: 21-27

    • Related Report
      2007 Annual Research Report
  • [Journal Article] A motif-based framework for constructing promoter models2006

    • Author(s)
      Yada, T
    • Journal Title

      In proc.of EABS & BSJ 2006

    • Related Report
      2006 Annual Research Report
  • [Journal Article] Chapter 3 : Multiple Sequence Alignment2006

    • Author(s)
      Gotoh, O., Yamada, S., Yada, T.
    • Journal Title

      Handbook of Computational Molecular Biology, (Srinivas Aluru (ed.))(Chapman & Hall/CRC)

    • Related Report
      2005 Annual Research Report
  • [Journal Article] Inferring Probabilistic Conditional Independency from Large-scale Combinatorial Regulation of Transcription Factors

    • Author(s)
      S.J. Park, N. Ichinose, T. Yada
    • Journal Title

      J. Software (in press)

    • Related Report
      2009 Final Research Report
  • [Presentation] A novel method for miRNA target prediction: miRNAs and their targets are frequently coregulated by common transcription factors2009

    • Author(s)
      Yada, T.
    • Organizer
      The 4th Global COR International Symposium 2009 joint with the 19th Hot Spring Harbor Symposium
    • Place of Presentation
      Fukuoka
    • Related Report
      2009 Final Research Report
  • [Presentation] A novel method for miRNA target prediction : miRNAs and their targets are frequently coregulated by common transcription factors2009

    • Author(s)
      Yada, T.
    • Organizer
      The 4th Global COE International Symposium 2009 joint with the 19th Hot Spring Harbor Symposium
    • Place of Presentation
      Fukuoka
    • Related Report
      2009 Annual Research Report
  • [Presentation] A Novel Point of View on MicroRNA Target Prediction2008

    • Author(s)
      Yada, T., Fujiwara, T., Terai, G., Gotoh, O.
    • Organizer
      Proc. of the 2008 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      Osaka
    • Related Report
      2009 Final Research Report
  • [Presentation] Comprehensive Modeling for the Combinatorial Regulation of Transcription Factors2008

    • Author(s)
      S.J. Park, N. Ichinose, T. Yada.
    • Organizer
      Proc. of the 2008 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      Osaka
    • Related Report
      2009 Final Research Report
  • [Presentation] A Novel Point of View on MicroRNA Target Prediction2008

    • Author(s)
      T. Yada, T. Fujiwara, G. Terai, and O. Gotoh
    • Organizer
      日本バイオインフォマティクス学会
    • Place of Presentation
      大阪
    • Related Report
      2008 Annual Research Report
  • [Presentation] Fast Motif Extraction Tool from a Large Number of DNA Sequences2007

    • Author(s)
      N. Ichinose, T. Yada, O. Gotoh
    • Organizer
      Proc. of the 2007 Annual Conference of Japanese Society for Bioinformatics
    • Place of Presentation
      Tokyo
    • Related Report
      2009 Final Research Report
  • [Presentation] A motif-based framework for constructing promoter models2006

    • Author(s)
      Yada, T.
    • Organizer
      The Fifth East Asian Biophysics Symposium & Forty-Fourth Annual Meeting ofthe Biophysical Society of Japan
    • Place of Presentation
      Okinawa
    • Related Report
      2009 Final Research Report
  • [Book] (森下真一、阿久津達也編集, 遺伝子発見, 生命研究への応用と開発が進むバイオデータベースとソフトウェア最前線,実験医学増刊, 26(7))2008

    • Author(s)
      矢田哲士
    • Related Report
      2009 Final Research Report
  • [Book] 財棒工学増刊(藤山秋佐夫監修, ゲノム比較時代の配列比較技術, 比較ゲノム学から読み解く生命システム)2007

    • Author(s)
      矢田哲士, 後藤修
    • Related Report
      2009 Final Research Report
  • [Book] Computer and Information Science Series(Aluru, S. ed., Multiple Sequence Alignment, Handbook of Computational Molecular Biology)2006

    • Author(s)
      O. Gotoh, S. Yamada, T. Yada
    • Publisher
      Chapman & Hall/CRC
    • Related Report
      2009 Final Research Report
  • [Book] 蛋白質核酸酵素増刊(小原・菅野・小笠原・高木・藤山・辻編集, ヒトゲノムのアノテーションデータベース, ゲノムから生命システムへ 50(16))2005

    • Author(s)
      矢田哲士
    • Related Report
      2009 Final Research Report

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Published: 2005-04-01   Modified: 2018-03-28  

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