A spatially varying two-sample recombinant coalescent, with applications to HIV escape response

Alexander Braunstein, Zhi Wei, Shane T. Jensen, Jon D. McAuliffe

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

Abstract

Statistical evolutionary models provide an important mechanism for describing and understanding the escape response of a viral population under a particular therapy. We present a new hierarchical model that incorporates spatially varying mutation and recombination rates at the nucleotide level. It also maintains separate parameters for treatment and control groups, which allows us to estimate treatment effects explicitly. We use the model to investigate the sequence evolution of HIV populations exposed to a recently developed antisense gene therapy, as well as a more conventional drug therapy. The detection of biologically relevant and plausible signals in both therapy studies demonstrates the effectiveness of the method.

Original languageEnglish (US)
Title of host publicationAdvances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference
Pages193-200
Number of pages8
StatePublished - Dec 1 2009
Externally publishedYes
Event22nd Annual Conference on Neural Information Processing Systems, NIPS 2008 - Vancouver, BC, Canada
Duration: Dec 8 2008Dec 11 2008

Publication series

NameAdvances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference

Other

Other22nd Annual Conference on Neural Information Processing Systems, NIPS 2008
CountryCanada
CityVancouver, BC
Period12/8/0812/11/08

All Science Journal Classification (ASJC) codes

  • Information Systems

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