Study of HIV-1 envelop V3 region based on coding theory

• Project/Area Number: 22740071
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: General mathematics (including Probability theory/Statistical mathematics)
• Research Institution: Tokyo University of Science
• Principal Investigator: KEIKO Sato 東京理科大学, 理工学部, 准教授 (30366439)
• Project Period (FY): 2010-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000); Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2012: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000); Fiscal Year 2011: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2010: ¥780,000 (Direct Cost: ¥600,000、Indirect Cost: ¥180,000)
• Keywords: 符号構造 / HIV-1感染症患者 / 病期進行 / 符号理論 / HIV-1env遺伝子 / HIV-lenv遺伝子

Research Abstract

The speed of HIV-1 disease progression varies between HIV-1 infected individuals. We applied artificial codes in coding theory to sequence analysis of the V3 region of HIV-1. In this study, HIV-1 infected patients were classified into groups with rapid progression, slow progression or long-term non progression by the code structure of the V3 region sequences obtained in the early stage of HIV-1 infection. Moreover, we found that the code structure of the V3 sequences obtained longitudinally for the rapid progressors changes around the time of AIDS diagnosis.

Research Products

• [Journal Article] The code structure of the p53 DNA-binding domain and the prognosis of breast cancer patients (2013)
  • Author(s): K.Sato, T.Hara and M.Ohya
  • Journal Title: Bioinformatics Volume: 29(22) Issue: 22 Pages: 2822-2825
  • DOI: 10.1093/bioinformatics/btt497
  • Peer Reviewed
• [Journal Article] Study of HIV-1 Evolution by Coding Theory and Entropic Chaos Degree (2011)
  • Author(s): K. Sato
  • Journal Title: QP-PQ : Quantum Bio-Informatics IV Volume: 28 Pages: 451-460
  • Peer Reviewed
• [Journal Article] angled Effects of Two Consecutive Pairs in Residues and Its Use in Alignn (2011)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Journal Title: QP-PQ : Quantum Bio-Informatics IV Volume: 28 Pages: 129-136
  • Peer Reviewed
• [Journal Article] Study of HIV-1 Evolution by Coding Theory and Entropic Chaos Degre (2011)
  • Author(s): K.Sato
  • Journal Title: QP-PQ : Quantum Bio-Informatics IV Volume: 28 Pages: 451-460
  • Peer Reviewed
• [Journal Article] Evolution of HIV-1 from the viewpoint of Information Theory (2010)
  • Author(s): K. Sato and M. Ohya
  • Journal Title: Proceedings of the International Symposium on Applied Sciences in Biomedical and Communication Technologies Pages: 1-5
  • DOI: 10.1109/isabel.2010.5702806
  • Peer Reviewed
• [Journal Article] How to Classify Influenza A viruses and Understand Their Severity (2010)
  • Author(s): K. Sato, T. Tanabe and M. Ohya
  • Journal Title: Open Systems & Information Dynamics Volume: 17 Pages: 297-310
  • Peer Reviewed
• [Journal Article] MTRAP : Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues (2010)
  • Author(s): T. Hara, K. Sato and M. Ohya
  • Journal Title: BMC BIOINFORMATICS Volume: Vol.11: 235 Issue: 1 Pages: 1-11
  • DOI: 10.1186/1471-2105-11-235
  • Peer Reviewed
• [Journal Article] Significant Improvement of Sequence Alignment can be Done by Considering Transition Probability between Two Consecutive Pairs of Residues (2010)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Journal Title: QP-PQ : Quantum Bio-Informatics III Volume: 26 Pages: 443-452
  • Peer Reviewed
• [Journal Article] MTRAP : Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues (2010)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Journal Title: BMC BIOINFORMATICS Volume: 11
  • Peer Reviewed
• [Presentation] Entangled Sequence Alignment and Its Application for Bio-Sciences (2011)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Organizer: International Conference in Quantum Bio-Informatics Center
  • Place of Presentation: Chiba
  • Year and Date: 2011-03-11
• [Presentation] A treatable interface for MTRAP sequence alignment method (2011)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Organizer: 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies
  • Place of Presentation: Barcelona(招待講演)
• [Presentation] Classification of Influenza A Viruses Based on the Code Structure (2011)
  • Author(s): K.Sato
  • Organizer: 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies
  • Place of Presentation: Barcelona(招待講演)
• [Presentation] New alignment and software package for sequence analysis (2011)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Organizer: 12th International Congress on Amino Acids, Peptides and Proteins
  • Place of Presentation: Beijing
• [Presentation] The Code Structure of the Receptor Binding Domain of Influenza A Viruses (2011)
  • Author(s): K.Sato
  • Organizer: 12th International Congress on Amino Acids, Peptides and Proteins
  • Place of Presentation: Beijing
• [Presentation] Evolution of HIV-1 from the viewpoint of Information Theory (2010)
  • Author(s): Keiko Sato
  • Organizer: 3rd International Symposium on Applied Science in Biomedical and Communication Technologies (ISABEL 2010)
  • Place of Presentation: Roma
  • Year and Date: 2010-11-09
• [Presentation] New Sequence Alignment by a Measure due to Entangled Correlation in two Consecutive Residues (2010)
  • Author(s): T.Hara, K.Sato, M.Ohya
  • Organizer: 3rd International Symposium on Applied Science in Biomedical and Communication Technologies (ISABEL 2010)
  • Place of Presentation: Roma
  • Year and Date: 2010-11-09
• [Presentation] ペア間推移量を用いた配列アライメント法 (2010)
  • Author(s): 原利英, 佐藤圭子, 大矢雅則
  • Organizer: 情報処理学会 第22回バイオ情報学研究会
  • Place of Presentation: 東京
  • Year and Date: 2010-07-28
• [Presentation] The Code Structure of Influenza A Viruses
  • Author(s): K. Sato, T. Hara and M. Ohya
  • Organizer: A Marcus Wallenberg Symposium "Quantum Theory : Advances and Problems" - QTAP, Satellite workshop "Quantum Foundations & Quantum Information"-QF & QI
  • Place of Presentation: Linnaeus University, Sweden
• [Presentation] The Code Structure of the P53 DNA-binding Domain and the Prognosis of Breast Cancer Patients
  • Author(s): K. Sato and T. Hara
  • Organizer: Third QBIC workshop 2013
  • Place of Presentation: Noda Campus of Tokyo University of Science, Japan
• [Presentation] Mathematical formulation of adaptive dynamics and non-Kolmogorov probability theory
  • Author(s): M. Ohya and K. Sato
  • Organizer: QP33 "Quantum Probabilities and Related Fields"
  • Place of Presentation: Centre International de Rencontres Mathématiques, France
• [Presentation] Classification of Influenza A Viruses Based on the Code Structure
  • Author(s): K. Sato
  • Organizer: 4th International Symposium on Applied Sciences in Biomedical and Communication Technologies (ISABEL 2011)
  • Place of Presentation: Spain
• [Presentation] Evolution of HIV-1 from the Viewpoint of Information Theory
  • Author(s): K. Sato and M. Ohya
  • Organizer: 3rd International Symposium on Applied Science in Biomedical and Communication Technologies (ISABEL 2010)
  • Place of Presentation: Center for Ecclesiastical Services, Italy
• [Presentation] The Code Structure of Influenza A viruses
  • Author(s): Keiko Sato, Toshihide Hara and Masanori Ohya
  • Organizer: A Marcus Wallenberg Symposium "Quantum Theory: Advances and Problems" - QTAP, Satellite workshop "Quantum Foundations & Quantum Information"-QF & QI
  • Place of Presentation: Linnaeus University, Sweden
• [Presentation] The Code Structure of the P53 DNA-binding Domain and the Prognosis of Breast Cancer Patients
  • Author(s): Keiko Sato, Toshihide Hara and Masanori Ohya
  • Organizer: Third QBIC Workshop 2013
  • Place of Presentation: Noda Campus of Tokyo University of Science, Japan
• [Presentation] 塩基の挿入欠失を含む進化モデルに基づく系統解析
  • Author(s): 西巻拓真、佐藤圭子
  • Organizer: 生命の起源および進化学会・第３９回学術講演会
  • Place of Presentation: 広島市、広島修道大学
• [Presentation] Mathematical formulation of adaptive dynamics and non-Kolmogorov probability theory
  • Author(s): Masanori Ohya and Keiko Sato
  • Organizer: QP33 "Quantum Probabilities and Related fields"
  • Place of Presentation: Marseille
• [Presentation] Kimuraの2変数法の拡張
  • Author(s): 西巻拓真 佐藤圭子
  • Organizer: 生命の起源および進化学会
  • Place of Presentation: 福岡
• [Presentation] アノテーション情報を考慮したアミノ酸配列アライメント
  • Author(s): 原利英 佐藤圭子
  • Organizer: 生命の起源および進化学会
  • Place of Presentation: 福岡