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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

About the Authors

Jonathan M. Carlson, Carl Kadie, David Heckerman
eScience Group, Microsoft Research, Redmond, Washington, United States of America
Jonathan M. Carlson
Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America
Zabrina L. Brumme, Chanson J. Brumme, Bruce D. Walker, Philip J. R. Goulder
Partners AIDS Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
Christine M. Rousseau, James I. Mullins
Department of Microbiology, University of Washington, Seattle, Washington, United States of America
Philippa Matthews, Philip J. R. Goulder
Department of Paediatrics, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
James I. Mullins
Department of Medicine, University of Washington, Seattle, Washington, United States of America
Bruce D. Walker
Howard Hughes Medical Institute, Chevy Chase, Maryland, United States of America
P. Richard Harrigan
B.C. Centre for Excellence in HIV/AIDS, Vancouver, British Columbia, Canada
P. Richard Harrigan
Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
Philip J. R. Goulder
HIV Pathogenesis Programme, The Doris Duke Medical Research Institute, University of KwaZulu-Natal, Durban, South Africa

Corresponding Authors

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: JMC ZLB PRH DH. Performed the experiments: JMC. Analyzed the data: JMC ZLB CJB DH. Contributed reagents/materials/analysis tools: JMC ZLB CMR PM CK JIM BDW PRH PJRG DH. Wrote the paper: JMC ZLB DH.