Use of average mutual information for studying changes in HIV populations

Khalid Sayood, Federico Hoffman, Charles Wood

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

Average mutual information (AMI) has been used in a number of applications in bioinformatics. In this paper we present its use to study genetic changes in populations; in particular populations of HIV viruses. Disease progression of HIV-1 infection in infants can be rapid resulting in death within the the first year, or slow, allowing the infant to survive beyond the first year. We study the development of rapid and slow progressing HIV population using AMI charts based on average mutual information among amino acids in the env gene from a population of 1142 clones derived from seven infants with slow progressing HIV-1 infection and four infants with rapidly progressing HIV-1 infection. The AMI charts indicate the relative homogeneity of the rapid progressor populations and the much greater heterogeneity of the slow progressor population, especially in later samples. The charts also show the distinct regions of covariation between residues without the need for aligning the sequences. By examining the changes in AMI between populations we can distinguish between clones obtained from rapid progressor and slow progressor. A measure of this change can be used to enhance prediction of disease progression.

Original languageEnglish (US)
Title of host publicationProceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Subtitle of host publicationEngineering the Future of Biomedicine, EMBC 2009
PublisherIEEE Computer Society
Pages3861-3864
Number of pages4
ISBN (Print)9781424432967
DOIs
StatePublished - Jan 1 2009
Event31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009 - Minneapolis, MN, United States
Duration: Sep 2 2009Sep 6 2009

Publication series

NameProceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009

Conference

Conference31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009
CountryUnited States
CityMinneapolis, MN
Period9/2/099/6/09

Fingerprint

HIV
Bioinformatics
Viruses
Population
Amino acids
HIV Infections
Genes
HIV-1
Disease Progression
Clone Cells
env Genes
Computational Biology
Amino Acids

ASJC Scopus subject areas

  • Cell Biology
  • Developmental Biology
  • Biomedical Engineering
  • Medicine(all)

Cite this

Sayood, K., Hoffman, F., & Wood, C. (2009). Use of average mutual information for studying changes in HIV populations. In Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009 (pp. 3861-3864). [5332579] (Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009). IEEE Computer Society. https://doi.org/10.1109/IEMBS.2009.5332579

Use of average mutual information for studying changes in HIV populations. / Sayood, Khalid; Hoffman, Federico; Wood, Charles.

Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society, 2009. p. 3861-3864 5332579 (Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sayood, K, Hoffman, F & Wood, C 2009, Use of average mutual information for studying changes in HIV populations. in Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009., 5332579, Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, IEEE Computer Society, pp. 3861-3864, 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009, Minneapolis, MN, United States, 9/2/09. https://doi.org/10.1109/IEMBS.2009.5332579
Sayood K, Hoffman F, Wood C. Use of average mutual information for studying changes in HIV populations. In Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society. 2009. p. 3861-3864. 5332579. (Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009). https://doi.org/10.1109/IEMBS.2009.5332579
Sayood, Khalid ; Hoffman, Federico ; Wood, Charles. / Use of average mutual information for studying changes in HIV populations. Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009. IEEE Computer Society, 2009. pp. 3861-3864 (Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society: Engineering the Future of Biomedicine, EMBC 2009).
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