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Development of theory and procedures for personalized medicine using statistical mechanisms of information processing

Research Project

Project/Area Number 18079012
Research Category

Grant-in-Aid for Scientific Research on Priority Areas

Allocation TypeSingle-year Grants
Review Section Science and Engineering
Research InstitutionWaseda University

Principal Investigator

INOUE Masato  Waseda University, 理工学術院, 准教授 (70376953)

Project Period (FY) 2006 – 2009
Project Status Completed (Fiscal Year 2009)
Budget Amount *help
¥9,700,000 (Direct Cost: ¥9,700,000)
Fiscal Year 2009: ¥2,500,000 (Direct Cost: ¥2,500,000)
Fiscal Year 2008: ¥2,600,000 (Direct Cost: ¥2,600,000)
Fiscal Year 2007: ¥2,600,000 (Direct Cost: ¥2,600,000)
Fiscal Year 2006: ¥2,000,000 (Direct Cost: ¥2,000,000)
Keywords情報統計力学 / 確率的情報処理 / 個別化医療 / haplotype推定 / 遺伝子-疾患関連 / ゲノム多様性 / ゲノム情報処理 / バイオインフォマティクス / 統計的推測 / ゲノムデータベース / 遺伝診断学
Research Abstract

We investigated the haplotype inference method, which is an indispensable information processing technique for personalized medicine providing high quality diagnoses or medical treatments based on individual genetic information. This method involves dividing individual genetic information into two groups, one for paternal origins and the other for maternal origins. Our main achievement is the development of a novel highest quality haplotype inference method. The developed software is available for free through our website. We also developed more powerful but less accurate inference methods by using statistical mechanical techniques.

Report

(6 results)
  • 2009 Annual Research Report   Final Research Report ( PDF )
  • 2008 Annual Research Report   Self-evaluation Report ( PDF )
  • 2007 Annual Research Report
  • 2006 Annual Research Report
  • Research Products

    (47 results)

All 2010 2009 2008 2007 2006 Other

All Journal Article (17 results) (of which Peer Reviewed: 12 results) Presentation (25 results) Book (2 results) Remarks (3 results)

  • [Journal Article] 可変長圧縮基準によるテキストの頻出文字列検出2010

    • Author(s)
      岡本勇人, 井上真郷
    • Journal Title

      電子情報通信学会技術研究報告 109(461)

      Pages: 485-489

    • Related Report
      2009 Annual Research Report
  • [Journal Article] 階層的な記憶パターンを持つ自己相関型連想記憶モデルのPCAによる解析2010

    • Author(s)
      塩塚丁二郎, 永田賢二, 福島孝治, 岡田真人, 井上真郷
    • Journal Title

      電子情報通信学会技術研究報告 109(461)

      Pages: 413-418

    • NAID

      110008004336

    • Related Report
      2009 Annual Research Report
  • [Journal Article] Grouping preprocess for haplotype inference from SNP and CNV data Journal of Physics2009

    • Author(s)
      Hiroyuki Shindo, Hiroshi Chigira, Tomoyo Nagaoka, Naoyuki Kamatani, Masato Inoue
    • Journal Title

      Conference Series 197

      Pages: 12009-12009

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Decoding algorithm of low-density parity-check codes based on Bowman-Levin approximation2009

    • Author(s)
      Ken-ichi Tamura, Miho Komiya, Masato Inoue, Yoshiyuki Kabashima
    • Journal Title

      New Generation Computing 27

      Pages: 347-363

    • Related Report
      2009 Annual Research Report 2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Grouping preprocess for haplotype inference from SNP and CNV data2009

    • Author(s)
      H.Shindo, H.Chigira, T. Nagaoka, N.Kamatani, M.Inoue
    • Journal Title

      Journal of Physics : Conference Series 197

      Pages: 12009-12009

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 2体結合モデルによる統計力学的ハプロタイプ推定2009

    • Author(s)
      千明裕, 進藤裕, 井上真郷
    • Journal Title

      電子情報通信学会技術研究報告 108(480)

      Pages: 405-410

    • NAID

      110007324929

    • Related Report
      2008 Annual Research Report 2008 Self-evaluation Report
  • [Journal Article] Grouping preprocess to accurately extend application of EM algorithm to haplotype inference2008

    • Author(s)
      Hiroyuki Shindo, Hiroshi Chigira, Junji Tanaka, Naoyuki Kamatani, Masato Inoue
    • Journal Title

      Journal of Human Genetics 53(8)

      Pages: 747-756

    • NAID

      10021929160

    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Bayesian-Optimal Image Reconstruction for Translational-Symmetric Filters2008

    • Author(s)
      Satohiro Tajima, Masato Inoue, Masato Okada
    • Journal Title

      Journal of the Physical Society of Japan 77(5)

      Pages: 54803-54803

    • NAID

      110006666017

    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] Bayesian-Optimal Image Reconstruction for Translational-Symmetric Filters2008

    • Author(s)
      Satohiro Tajima, Masato Inoue, Masato Okada
    • Journal Title

      Journal of the Physical Society of Japan 77 (5)

      Pages: 54803-54803

    • NAID

      110006666017

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 適応的自然勾配法の特異モデル学習への適用2008

    • Author(s)
      西村佳也, 井上真郷
    • Journal Title

      電子情報通信学会技術研究報告 108 (101)

      Pages: 69-73

    • NAID

      10031000586

    • Related Report
      2008 Annual Research Report
  • [Journal Article] Grouping preprocess to accurately extend application of EM algorithm to haplotype inference2008

    • Author(s)
      H. Shindo, H. Chigira, J. Tanaka, N. Kamatani, M. Inoue
    • Journal Title

      Journal of Human Genetics 53(8)

      Pages: 747-756

    • NAID

      10021929160

    • Related Report
      2008 Annual Research Report
    • Peer Reviewed
  • [Journal Article] 一次視覚野情報からの画像再構築2008

    • Author(s)
      橋口友美, 井上真郷, 岡田真人
    • Journal Title

      電子情報通信学会技術研究報告 107(542)

      Pages: 55-60

    • NAID

      110006783200

    • Related Report
      2007 Annual Research Report
  • [Journal Article] LDPC decoding dynamics from a PCA viewpoint2007

    • Author(s)
      Shinpei Hara, Yuta Akira, Eisuke Ishii, Masato Inoue, Masato Okada
    • Journal Title

      Interdisciplinary Information Sciences 13(1)

      Pages: 43-48

    • NAID

      110006274938

    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report 2006 Annual Research Report
    • Peer Reviewed
  • [Journal Article] LDPC decoding dynamics from a PCA viewpoint2007

    • Author(s)
      Shinpei Hara, Yuta Akira, Eisuke Ishii, Masato lnoue, Masato Okada
    • Journal Title

      Interdisciplinary Information Sciences 13(1)

      Pages: 43-48

    • Related Report
      2007 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Analysis method combining Monte Carlo simulation and principal component analysis - application to Sourlas code2006

    • Author(s)
      Masato Inoue, Koji Hukushima, Masato Okada
    • Journal Title

      Journal of the Physical Society of Japan 75(8)

      Pages: 84003-84003

    • NAID

      110004799201

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Journal Article] Analysis method combining Monte Carlo simulation and principal component analysis -- application to Sourlas code2006

    • Author(s)
      Masato Inoue, Koji Hukushima, Masato Okada
    • Journal Title

      Journal of the Physical Society of Japan 75(8)

      Pages: 84003-84003

    • NAID

      110004799201

    • Related Report
      2008 Self-evaluation Report
    • Peer Reviewed
  • [Journal Article] A haplotype inference method based on sparsely connected multi-body Ising model Journal of Physics

    • Author(s)
      Masashi Kato, Qian Ji Gao, Hiroshi Chigira, Hiroyuki Shindo, Masato Inoue
    • Journal Title

      Conference Series (in press)

    • Related Report
      2009 Final Research Report
    • Peer Reviewed
  • [Presentation] 可変長圧縮基準によるテキストの頻出文字列検出2010

    • Author(s)
      岡本勇人, 井上真郷
    • Organizer
      電子惰報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-03-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] 混合ベルヌーイ分布を用いたクラスタリングによる連想記憶モデルの解析2010

    • Author(s)
      永田賢二. 福島孝治, 塩塚丁二郎, 井上真郷, 岡田真人
    • Organizer
      電子情報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-03-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] 階層的な記憶パターンを持つ自己相関型連想記憶モデルのPCAによる解析2010

    • Author(s)
      塩塚丁二郎, 永田賢二, 福島孝治, 岡田真人, 井上真郷
    • Organizer
      電子情報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-03-11
    • Related Report
      2009 Annual Research Report
  • [Presentation] A haplotype inference method based on sparsely connected multi-body Ising model2010

    • Author(s)
      Masashi Kato, Qian Ji Gao, Hiroshi Chigira, Hiroyuki Shindo, Masato Inoue
    • Organizer
      nternational Workshop on Statistical- Mechanical Informatics 2010 (IW-SMI2010)
    • Place of Presentation
      Kyoto
    • Year and Date
      2010-03-08
    • Related Report
      2009 Final Research Report
  • [Presentation] A haplotype inference method based on sparsely connected multi-body lsing model2010

    • Author(s)
      M.Kato, Q.J.Gao, H.Chigira, H.Shindo, M.Inoue
    • Organizer
      International Workshop on Statistioal-Meohanioal Informatios 2010(IW-SM12010)
    • Place of Presentation
      Kyota
    • Year and Date
      2010-03-08
    • Related Report
      2009 Annual Research Report
  • [Presentation] 集合演算とEMアルゴリズムによるhaplotype推定2010

    • Author(s)
      井上真郷
    • Organizer
      次世代情報処理における揺らぎと確率
    • Place of Presentation
      埼玉
    • Year and Date
      2010-03-04
    • Related Report
      2009 Annual Research Report
  • [Presentation] Boltzmannマシンによるhaplotype推定2009

    • Author(s)
      千明裕, 加藤真志, 進藤裕之, 井上真郷
    • Organizer
      科研費特定領域研究「情報統計力学の深化と展開」平成21年度チュートリァル
    • Place of Presentation
      東京
    • Year and Date
      2009-12-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] 階層パターンを持つ自己相関型連想記憶モデルのPCAによる解析2009

    • Author(s)
      塩塚丁二郎, 永田賢二, 岡田真人, 井上真郷
    • Organizer
      第12回情報論的学習理論ワークショップ(IBIS 2009)
    • Place of Presentation
      福岡
    • Year and Date
      2009-10-20
    • Related Report
      2009 Final Research Report
  • [Presentation] 階層パターンを持つ自己相関型連想記憶モデルのPCAによる解析2009

    • Author(s)
      塩塚丁二郎, 永田賢二, 岡田真人, 井上真郷
    • Organizer
      第12回情報論的学習理論ワークショップ(IBIS2009)
    • Place of Presentation
      福岡
    • Year and Date
      2009-10-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] 混合Bernoulli分布に基づく変分Bayes法による連想記憶モデルの解析2009

    • Author(s)
      荒木佑季, 永田賢二, 岡田真人, 井上 真郷
    • Organizer
      第12回情報論的学習理論ワークショップ(IBIS 2009)
    • Place of Presentation
      福岡
    • Year and Date
      2009-10-19
    • Related Report
      2009 Final Research Report
  • [Presentation] 混合Bernoulli分布に基づく変分Bayes法による連想記憶モデルの解析2009

    • Author(s)
      荒木佑季, 永田賢二, 岡田真人, 井上真郷
    • Organizer
      第12回情報論的学習理論ワークショップ(IBIS2009)
    • Place of Presentation
      福岡
    • Year and Date
      2009-10-19
    • Related Report
      2009 Annual Research Report
  • [Presentation] Grouping preprocess for haplotype inference from SNP and CNV data2009

    • Author(s)
      Hiroyuki Shindo, Hiroshi Chigira, Tomoyo Nagaoka, Naoyuki Kamatani, Masato Inoue
    • Organizer
      International Workshop on Statistical- Mechanical Informatics 2009 (IW-SMI2009)
    • Place of Presentation
      Kyoto
    • Year and Date
      2009-09-13
    • Related Report
      2009 Final Research Report
  • [Presentation] Grouping preprocess for haplotype inference from SNP and CNV data2009

    • Author(s)
      H.Shindo, H.Chigira, T.Nagaoka, N.Kamatani, M.Inoue
    • Organizer
      International Workshop on Statistical-Mechanical Informatics 2009(IW-SMI2009)
    • Place of Presentation
      Kyoto
    • Year and Date
      2009-09-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] SNP及びCNVデータからのHardy-Weinberg平衡を仮定したhaplotype推定2009

    • Author(s)
      千明裕, 進藤裕之, 長岡萌代, 鎌谷直之, 井上真郷
    • Organizer
      ハイテクリサーチセンター第1回成果報告シンポジウム
    • Place of Presentation
      東京
    • Year and Date
      2009-08-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] Haplotype inference from SNP and CNV data assuming Hardy-Weinberg equilibrium2009

    • Author(s)
      Hiroyuki Shindo, Hiroshi Chigira, Tomoyo Nagaoka, Naoyuki Kamatani, Masato Inoue
    • Organizer
      The 1st International Symposium on Biomedical Science and Engineering
    • Place of Presentation
      Tokyo
    • Year and Date
      2009-07-18
    • Related Report
      2009 Annual Research Report 2009 Final Research Report
  • [Presentation] 2体結合モデルによる統計力学的ハブロタイプ推定2009

    • Author(s)
      千明裕, 進藤裕之, 井上真郷
    • Organizer
      電子情報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      東京
    • Year and Date
      2009-03-13
    • Related Report
      2008 Annual Research Report
  • [Presentation] 2体結合モデルによる統計力学的ハプロタイプ推定2009

    • Author(s)
      千明裕, 進藤裕之, 井上真郷
    • Organizer
      電子情報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      東京
    • Related Report
      2008 Self-evaluation Report
  • [Presentation] 隠れMarkovモデルに基づく交叉率推定2008

    • Author(s)
      千明裕, 進藤裕之, 井上真郷
    • Organizer
      科研費特定領域研究『情報統計力学の深化と展開」平成20年度研究成果発表会
    • Place of Presentation
      仙台
    • Year and Date
      2008-12-17
    • Related Report
      2008 Annual Research Report
  • [Presentation] Bowman-Levin法を用いたLDPC復号2008

    • Author(s)
      田村健一, 小宮美穂, 井上真郷, 樺島 祥介
    • Organizer
      第11回情報論的学習理論ワークショップ(IBIS2008)
    • Place of Presentation
      仙台
    • Year and Date
      2008-10-29
    • Related Report
      2009 Final Research Report 2008 Annual Research Report 2008 Self-evaluation Report
  • [Presentation] 一次視覚野情報からの画像再構築2008

    • Author(s)
      橋口友美, 井上真郷, 岡田真人
    • Organizer
      電子情報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      東京
    • Year and Date
      2008-03-12
    • Related Report
      2007 Annual Research Report
  • [Presentation] Dimension reduction using symmetrical structure-an example of the expectation-maximization (EM) algorithm for haplotype inference2008

    • Author(s)
      INOUE Masato
    • Organizer
      Disordered systems group seminar at King's College London, London University (invited seminar)
    • Place of Presentation
      London
    • Year and Date
      2008-03-05
    • Related Report
      2007 Annual Research Report
  • [Presentation] 適応的自然勾配法の特異モデル学習への適用2008

    • Author(s)
      西村佳也, 井上真郷
    • Organizer
      電子情報通信学会ニューロコンピューティング研究会
    • Place of Presentation
      沖縄
    • Related Report
      2008 Annual Research Report 2008 Self-evaluation Report
  • [Presentation] 情報量に基づいた連鎖不平衡指標2007

    • Author(s)
      千明裕, 進藤裕之, 田中順治, 鎌谷直之, 井上真郷
    • Organizer
      科研費特定領域研究「情報統計力学の深化と展開」平成19年度研究成果発表会
    • Place of Presentation
      京都
    • Year and Date
      2007-12-19
    • Related Report
      2007 Annual Research Report
  • [Presentation] haplotype推定における指数関数的計算量を削減するためのグルーピング前処理2007

    • Author(s)
      進藤裕之, 千明裕, 田中順治, 鎌谷直之, 井上真郷
    • Organizer
      日本人類遺伝学会第52回大会
    • Place of Presentation
      東京
    • Year and Date
      2007-09-14
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report 2007 Annual Research Report
  • [Presentation] 畳み込みフィルタ出力を考慮した画像修復2007

    • Author(s)
      橋口友美, 井上真郷, 岡田真人
    • Organizer
      日本物理学会2007年春季大会
    • Place of Presentation
      鹿児島
    • Year and Date
      2007-03-20
    • Related Report
      2009 Final Research Report 2008 Self-evaluation Report
  • [Book] International Workshop on Statisticalmechanical Informatics 2009(Journal of Physics:Conference Series 197)2009

    • Author(s)
      Masato Inoue, Shin Ishii, Yoshiyuki Kabashima, Masato Okada (editors)
    • Total Pages
      244
    • Publisher
      IW-SMI 2009
    • Related Report
      2009 Final Research Report
  • [Book] lnternational Workshop on Statistical-mechanical Informatics 2009(IW-SMI 2009)2009

    • Author(s)
      Masato Inoue, Shin Ishii, Yoshiyuki Kabashima, Masato Okada(editors)
    • Total Pages
      244
    • Publisher
      IOP Publishing
    • Related Report
      2009 Annual Research Report
  • [Remarks] ソフトウエア公開HaploBorder (SNPデータよりhaplotypeを推定するフリーソフトウエア)

    • URL

      http://www.eb.waseda.ac.jp/m_inoue/downloads/

    • Related Report
      2009 Final Research Report
  • [Remarks] ソフトウエア公開 HaploBorder (SNP データよりhaplotype を推定するソフトウエア)

    • URL

      http://www.eb.waseda.ac.jp/m_inoue/downloads/

    • Related Report
      2008 Self-evaluation Report
  • [Remarks] 作成したフリーソフト

    • URL

      http://www.eb.waseda.ac.jp/m_inoue/downloads/

    • Related Report
      2007 Annual Research Report

URL: 

Published: 2006-04-01   Modified: 2018-03-28  

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