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Research Article

Phylogenetic Dependency Networks: Inferring Patterns of CTL Escape and Codon Covariation in HIV-1 Gag

  • Jonathan M. Carlson mail,

    carlson@microsoft.com (JMC); heckerma@microsoft.com (DH)

    Affiliations: eScience Group, Microsoft Research, Redmond, Washington, United States of America, Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America

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  • Zabrina L. Brumme,

    Affiliation: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America

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  • Christine M. Rousseau,

    Affiliation: Department of Microbiology, University of Washington, Seattle, Washington, United States of America

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  • Chanson J. Brumme,

    Affiliation: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America

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  • Philippa Matthews,

    Affiliation: Department of Paediatrics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom

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  • Carl Kadie,

    Affiliation: eScience Group, Microsoft Research, Redmond, Washington, United States of America

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  • James I. Mullins,

    Affiliations: Department of Microbiology, University of Washington, Seattle, Washington, United States of America, Department of Medicine, University of Washington, Seattle, Washington, United States of America

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  • Bruce D. Walker,

    Affiliations: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America

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  • P. Richard Harrigan,

    Affiliations: B.C. Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada

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  • Philip J. R. Goulder,

    Affiliations: Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America, Department of Paediatrics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom, HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa

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  • David Heckerman mail

    carlson@microsoft.com (JMC); heckerma@microsoft.com (DH)

    Affiliation: eScience Group, Microsoft Research, Redmond, Washington, United States of America

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  • Published: November 21, 2008
  • DOI: 10.1371/journal.pcbi.1000225

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