Bioinformatics for Evolutionary Analysis of Complex and Abundant Biological Data

• Project/Area Number: 21810005
• Research Category: Grant-in-Aid for Research Activity Start-up
• Allocation Type: Single-year Grants
• Research Field: ゲノム情報科学
• Research Institution: The University of Tokyo
• Principal Investigator: IWASAKI Wataru The University of Tokyo, 大学院新領域創成科学研究科, 助教 (50545019)
• Project Period (FY): 2009 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥2,756,000 (Direct Cost: ¥2,120,000、Indirect Cost: ¥636,000); Fiscal Year 2010: ¥1,313,000 (Direct Cost: ¥1,010,000、Indirect Cost: ¥303,000); Fiscal Year 2009: ¥1,443,000 (Direct Cost: ¥1,110,000、Indirect Cost: ¥333,000)
• Keywords: 車輪樹法 / 系統樹 / 進化 / NaviCluster / 可視化 / グラフクラスタリング / ネットワーク / 文献情報処理 / バイオインフォマティクス / 進化・系統 / ネットワーク生物学 / データ可視化 / 巡回セールスマン問題 / セントロイド / テキストマイニング

Research Abstract

Abundant and complex biological data represented in graphs or natural languages are rapidly accumulating. In this research, we developed bioinformatics technologies to analyze those data while considering phylogenetic relationships. These technologies are the wheel tree method, a phylogenetic relationship representation method considering vague phylogenetic topologies ; NaviCluster, a tool for interactively investigating complex and large biological networks ; and a database for comprehensively connecting genes and phenotypes.

Research Products

• [Journal Article] Interactive, Multi-Scale Navigation of Large and Complicated Biological Networks. (2011)
  • Author(s): Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki
  • Journal Title: Bioinformatics 27 Pages: 1121-1127
  • NAID: 110007990852
  • Peer Reviewed
• [Journal Article] Generalized Centroid Estimators in Bioinformatics. (2011)
  • Author(s): Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai.
  • Journal Title: PLoS ONE 6
  • Peer Reviewed
• [Journal Article] Generalized Centroid Estimators in Bioinformatics. (2011)
  • Author(s): Michiaki Hamada, Hisanori Kiryu, Wataru Iwasaki, Kiyoshi Asai.
  • Journal Title: PLoS ONE Volume: 6
  • Peer Reviewed
• [Journal Article] Interactive, Multi-Scale Navigation of Large and Complicated Biological Networks. (2011)
  • Author(s): Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki.
  • Journal Title: Bioinformatics Volume: 27 Pages: 1121-1127
  • NAID: 110007990852
  • Peer Reviewed
• [Journal Article] TogoDoc Server/Client System : Smart Recommendation and Efficient Management of Life Science Literature. (2010)
  • Author(s): Wataru Iwasaki, Yasunori Yamamoto, Toshihisa Takagi
  • Journal Title: PLoS ONE 5
  • Peer Reviewed
• [Journal Article] An Intuitive, Informative, and Most Balanced Representation of Phylogenetic Topologies. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Journal Title: Systematic Biology 59 Pages: 584-593
  • Peer Reviewed
• [Journal Article] An Intuitive, Informative, and Most Balanced Representation of Phylogenetic Topologies. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi.
  • Journal Title: Systematic Biology Volume: 59 Pages: 584-593
  • Peer Reviewed
• [Journal Article] TogoDoc Server/Client System : Smart Recommendation and Efficient Management of Life Science Literature. (2010)
  • Author(s): Wataru Iwasaki, Yasunori Yamamoto, Toshihisa Takagi.
  • Journal Title: PLoS ONE Volume: 5
  • Peer Reviewed
• [Journal Article] An Intuitive, Informative, and Most Balanced Representation of Phylogenetic Topologies. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Journal Title: Systematic Biology 1((印刷中)掲載確定)
  • Peer Reviewed
• [Presentation] 誰もが分子進化解析をする時代のための系統関係表現 (2010)
  • Author(s): 岩崎渉,高木利久
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会 合同大会(BMB2010)
  • Place of Presentation: ポートアイランド,神戸
  • Year and Date: 2010-12-07
• [Presentation] 誰もが分子進化解析をする時代のための系統関係表現 (2010)
  • Author(s): 岩崎渉, 高木利久
  • Organizer: 第33回日本分子生物学会年会・第83回日本生化学会大会合同大会(BMB2010)
  • Place of Presentation: ポートアイランド,神戸
  • Year and Date: 2010-12-07
• [Presentation] A Travelling Salesman Approach to Phylogenetic Trees. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Organizer: 4th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB), Biopolis, Singapore
  • Place of Presentation: Singapore.
  • Year and Date: 2010-12-02
• [Presentation] A Travelling Salesman Approach to Phylogenetic Trees. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi.
  • Organizer: 4th Asian Young Researchers Conference on Computational and Omics Biology (AYRCOB)
  • Place of Presentation: Biopolis, Singapore, Singapore
  • Year and Date: 2010-12-02
• [Presentation] Interactive, Multi-Scale Navigation of Large and Complicated Biological Networks. (2010)
  • Author(s): Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki
  • Organizer: 生命情報科学若手の会第2回研究会
  • Place of Presentation: 国立遺伝学研究所,三島
  • Year and Date: 2010-10-10
• [Presentation] 車輪樹法:系統樹を超えて (2010)
  • Author(s): 岩崎渉
  • Organizer: 生命情報科学若手の会第2回研究会
  • Place of Presentation: 国立遺伝学研究所,三島
  • Year and Date: 2010-10-10
• [Presentation] 車輸樹法:系統樹を超えて (2010)
  • Author(s): 岩崎渉
  • Organizer: 生命情報科学若手の会第2回研究会
  • Place of Presentation: 国立遺伝学研究所,三島
  • Year and Date: 2010-10-10
• [Presentation] Interactive, Multi-Scale Navigation of Large and Complicated Biological Networks (2010)
  • Author(s): Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki.
  • Organizer: 生命情報科学若手の会第2回研究会
  • Place of Presentation: 国立遺伝学研究所,三島
  • Year and Date: 2010-10-10
• [Presentation] 系統推定結果の表現と認識 (2010)
  • Author(s): 岩崎渉
  • Organizer: 第147回農林交流センターワークショップ,
  • Place of Presentation: 農林水産省農林水産技術会議事務局筑波事務所,つくば
  • Year and Date: 2010-08-24
• [Presentation] 系統推定結果の表現と認識 (2010)
  • Author(s): 岩崎渉
  • Organizer: 第147回農林交流センターワークショップ
  • Place of Presentation: 農林水産省農林水産技術会議事務局筑波事務所,つくば
  • Year and Date: 2010-08-24
• [Presentation] 車輪樹法:曖昧な進化系統解析結果をどう認識するか (2010)
  • Author(s): 岩崎渉
  • Organizer: 日本進化学会 第12回 東京大会,
  • Place of Presentation: 東京工業大学大岡山キャンパス,東京
  • Year and Date: 2010-08-04
• [Presentation] 車輪樹法:曖昧な進化系統解析結果をどう認識するか (2010)
  • Author(s): 岩崎渉
  • Organizer: 日本進化学会第12回東京大会
  • Place of Presentation: 東京工業大学大岡山キャンパス,東京
  • Year and Date: 2010-08-04
• [Presentation] 膨大な細菌ゲノム情報が可能にする代謝ネットワーク進化の俯瞰的解析 (2010)
  • Author(s): 岩崎渉
  • Organizer: 第83回日本細菌学会総会
  • Place of Presentation: パシフィコ横浜,横浜
  • Year and Date: 2010-03-28
• [Presentation] 1000ゲノム時代に進化を読み解く:分子系統樹では物足りないときどうするか (2010)
  • Author(s): 岩崎渉
  • Organizer: 第37回駒場進化セミナー
  • Place of Presentation: 東京大学駒場キャンパス,東京
  • Year and Date: 2010-03-08
• [Presentation] Wheel Tree : Overlooked Information in Phylogenetic Analysis. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Kyushu University School of Medicine, Fukuoka, Japan
• [Presentation] Interactive, Multi-Scale Navigation of Large and Complicated Biological Networks. (2010)
  • Author(s): Thanet Praneenararat, Wataru Iwasaki, Toshihisa Takagi
  • Organizer: The Annual CBRC Open House Workshop (CBRC2010) on Bioinformatics,
  • Place of Presentation: AIST Tokyo Waterfront, Tokyo, Japan
• [Presentation] Centroid Representation of Phylogenetic Trees Solved as a Travelling Salesman Problem. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Organizer: The Annual CBRC Open House Workshop (CBRC2010) on Bioinformatics,
  • Place of Presentation: AIST Tokyo Waterfront, Tokyo, Japan.
• [Presentation] Effective Multi-Scale Graph Navigation System Powered by Fast and Biologically Meaningful Hierarchical Clustering. (2010)
  • Author(s): Thanet Praneenararat, Wataru Iwasaki, Toshihisa Takagi
  • Organizer: 3rd Asian Young Researchers Conference for Computational and Omics Biology
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan.
• [Presentation] Updated Phylogenetic Tree for the Era of 1000 Genomes. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Organizer: 3rd Asian Young Researchers Conference for Computational and Omics Biology
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan.
• [Presentation] 生命科学研究者のための統合文献情報管理システム/研究者の論文フォルダには何が埋もれているか. (2010)
  • Author(s): 岩崎渉,山本泰智,高木利久
  • Organizer: 第43回人工知能学会 分子生物情報研究会(SIG-MBI)/第13回オープンバイオ研究会
  • Place of Presentation: 北陸先端科学技術大学院大学,能美
• [Presentation] Centroid Representation of Phylogenetic Trees Solved as a Travelling Salesman Problem. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi.
  • Organizer: The Annual CBRC Open House Workshop (CBRC2010) on Bioinformatics
  • Place of Presentation: 産総研臨海副都心センター,東京
• [Presentation] Interactive, Multi-Scale Navigation of Large and Complicated Biological Networks. (2010)
  • Author(s): Thanet Praneenararat, Wataru Iwasaki, Toshihisa Takagi
  • Organizer: The Annual CBRC Open House Workshop (CBRC2010) on Bioinformatics
  • Place of Presentation: 産総研臨海副都心センター,東京
• [Presentation] Wheel Tree : Overlooked Information in Phylogenetic Analysis. (2010)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi.
  • Organizer: The 2010 Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Kyushu University School of Medicine, Fukuoka
• [Presentation] 生命科学研究者のための統合文献情報管理システム/研究者の論文フォルダには何が埋もれているか (2010)
  • Author(s): 岩崎渉, 山本泰智, 高木利久
  • Organizer: 第43回 人工知能学会 分子生物情報研究会(SIG-MBI)/第13回オープンバイオ研究会
  • Place of Presentation: 北陸先端科学技術大学院大学,能美
• [Presentation] Effective Multi-Scale Graph Navigation System Powered by Fast and Biologically Meaningful Hierarchical Clustering (2010)
  • Author(s): Thanet Prancenararat, 岩崎渉, 高木利久
  • Organizer: 3rd Asian Young Researchers Conference for Computational and Omics Biology
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan
• [Presentation] Updated Phylogenetic Tree for the Era of 1000 Genomes (2010)
  • Author(s): 岩崎渉, 高木利久
  • Organizer: 3rd Asian Young Researchers Conference for Computational and Omics Biology
  • Place of Presentation: National Cheng Kung University, Tainan, Taiwan
• [Presentation] 生命科学研究者のための統合文献情報管理システム (2009)
  • Author(s): 岩崎渉,山本泰智,高木利久
  • Organizer: 第32回日本分子生物学会
  • Place of Presentation: パシフィコ横浜,横浜
  • Year and Date: 2009-12-10
• [Presentation] 生命科学研究者のための統合文献情報管理システム (2009)
  • Author(s): 岩崎渉, 山本泰智, 高木利久
  • Organizer: 第32回日本分子生物学会
  • Place of Presentation: パシフィコ横浜, 横浜
  • Year and Date: 2009-12-10
• [Presentation] 複数遺伝子を必要とするシステムの獲得はどのようにして可能になったのか (2009)
  • Author(s): 岩崎渉
  • Organizer: 情報生命科学若手の会第1回研究会
  • Place of Presentation: 国立遺伝学研究所,三島
  • Year and Date: 2009-04-25
• [Presentation] Effective Multi-Scale Graph Navigation System Powered by Fast and Biologically Meaningful Hierarchical Clustering. (2009)
  • Author(s): Thanet Praneenararat, Wataru Iwasaki, Toshihisa Takagi
  • Organizer: The 20th International Conference on Genome Informatics
  • Place of Presentation: Pacifico Yokohama, Yokohama, Japan
• [Presentation] Large-scale genome evolution analysis across the tree of life. (2009)
  • Author(s): Wataru Iwasaki, Toshihisa Takagi
  • Organizer: Global COE Workshop on Bioinformatics in the Era of Genome Information Big Bang
  • Place of Presentation: BGI-Shenzhen, Shenzhen, China.
• [Presentation] Large-scale genome evolution analysis across the tree of life (2009)
  • Author(s): 岩崎渉, 高木利久
  • Organizer: Global COE Workshop on Bioinformatics in the Era of Genome Information Big Bang
  • Place of Presentation: BGI-Shenzhen, Shenzhen, China
• [Presentation] Effective Multi-Scale Graph Navigation System Powered by Fast and Biologically Meaningful Hierarchical Clustering (2009)
  • Author(s): Thanet Prancenararat, 岩崎渉, 高木利久
  • Organizer: The 20th International Conference on Genome Informatics
  • Place of Presentation: Pacifico Yokohama, Yokohama, Japan
• [Remarks] 系統関係可視化のための車輪樹法公開ウェブサイト
  • URL: http://cwt.cb.k.u-tokyo.ac.jp/
• [Remarks] 生命ネットワークナビゲーションのためのNaviCluster公開ウェブサイト
  • URL: http://navicluster.cb.k.u-tokyo.ac.jp/
• [Remarks] 文献管理・推薦システムTogoDoc Client公開ウェブサイト
  • URL: http://tdc.cb.k.u-tokyo.ac.jp/
• [Remarks] 車輪樹法ソフトウェア配布ページ
  • URL: http://cwt.cb.k.u-tokyo.ac.jp/