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

2013 Fiscal Year Final Research Report

• 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
• Keywords: 符号構造 / HIV-1感染症患者 / 病期進行 / 符号理論

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) 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] 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 Pages: 1-11
  • DOI: 10.1186/1471-2105-11-235
  • Peer Reviewed
• [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