Genotypic and Functional Impact of HIV-1 Adaptation to Its Host Population during the North American Epidemic

CTL-Mediated Selective Pressure Influences Dynamic Evolution and Pathogenic Functions of HIV-1 Nef

(2014) T. Ueno et al.   JOURNAL OF IMMUNOLOGY

A Molecular Basis for the Control of Preimmune Escape Variants by HIV-Specific CD8+ T Cells

(2013) Kristin Ladell et al.   IMMUNITY

Barriers to a cure for HIV: new ways to target and eradicate HIV-1 reservoirs

(2013) Christine Katlama et al.   LANCET

FUBAR: A Fast, Unconstrained Bayesian AppRoximation for Inferring Selection

(2013) B. Murrell et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ability of HIV-1 Nef to downregulate CD4 and HLA class I differs among viral subtypes

(2013) Jaclyn K Mann et al.   Retrovirology

Attenuation of multiple Nef functions in HIV-1 elite controllers

(2013) Philip Mwimanzi et al.   Retrovirology

Dynamic range of Nef functions in chronic HIV-1 infection

(2013) Philip Mwimanzi et al.   VIROLOGY

Evidence for a Continuous Drift of the HIV-1 Species towards Higher Resistance to Neutralizing Antibodies over the Course of the Epidemic

(2013) Mélanie Bouvin-Pley et al.   PLoS Pathogens

HLA class I sequence-based typing using DNA recovered from frozen plasma

(2012) Laura A. Cotton et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Cytotoxic T-Lymphocyte Escape Mutations Identified by HLA Association Favor Those Which Escape and Revert Rapidly

(2012) Helen R. Fryer et al.   JOURNAL OF VIROLOGY

Significant Reductions in Gag-Protease-Mediated HIV-1 Replication Capacity during the Course of the Epidemic in Japan

(2012) Shigeru Nomura et al.   JOURNAL OF VIROLOGY

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

(2012) J. M. Carlson et al.   JOURNAL OF VIROLOGY

Widespread Impact of HLA Restriction on Immune Control and Escape Pathways of HIV-1

(2012) J. M. Carlson et al.   JOURNAL OF VIROLOGY

CTL Responses of High Functional Avidity and Broad Variant Cross-Reactivity Are Associated with HIV Control

(2012) Beatriz Mothe et al.   PLoS One

Developing strategies for HIV-1 eradication

(2012) Christine M. Durand et al.   TRENDS IN IMMUNOLOGY

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic

(2011) Ingrid M.M. Schellens et al.   AIDS

Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission

(2011) Joshua T. Herbeck et al.   AIDS

Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China

(2011) T. Dong et al.   BLOOD

Prevention of HIV-1 Infection with Early Antiretroviral Therapy

(2011) Myron S. Cohen et al.   NEW ENGLAND JOURNAL OF MEDICINE

Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology

(2010) W. Delport et al.   BIOINFORMATICS

Virus-Specific CD8+ T-Cell Responses Better Define HIV Disease Progression than HLA Genotype

(2010) W. L. Dinges et al.   JOURNAL OF VIROLOGY

Gag-Protease-Mediated Replication Capacity in HIV-1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

(2010) Jaclyn K. Wright et al.   JOURNAL OF VIROLOGY

Early Selection in Gag by Protective HLA Alleles Contributes to Reduced HIV-1 Replication Capacity That May Be Largely Compensated for in Chronic Infection

(2010) M. A. Brockman et al.   JOURNAL OF VIROLOGY

Efficacious Early Antiviral Activity of HIV Gag- and Pol-Specific HLA-B*2705-Restricted CD8+T Cells

(2010) Rebecca P. Payne et al.   JOURNAL OF VIROLOGY

Association of highly active antiretroviral therapy coverage, population viral load, and yearly new HIV diagnoses in British Columbia, Canada: a population-based study

(2010) Julio SG Montaner et al.   LANCET

Adaptation of HIV-1 envelope gp120 to humoral immunity at a population level

(2010) Evelien M Bunnik et al.   NATURE MEDICINE

Preexposure Chemoprophylaxis for HIV Prevention in Men Who Have Sex with Men

(2010) Robert M. Grant et al.   NEW ENGLAND JOURNAL OF MEDICINE

Effectiveness and Safety of Tenofovir Gel, an Antiretroviral Microbicide, for the Prevention of HIV Infection in Women

(2010) Q. Abdool Karim et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Modelling the Evolution and Spread of HIV Immune Escape Mutants

(2010) Helen R. Fryer et al.   PLoS Pathogens

No evidence of a change in HIV-1 virulence since 1996 in France

(2009) Pénélope Troude et al.   AIDS

Multiple transmissions of a stable human leucocyte antigen-B27 cytotoxic T-cell-escape strain of HIV-1 in The Netherlands

(2009) Marion Cornelissen et al.   AIDS

HLA Footprints on Human Immunodeficiency Virus Type 1 Are Associated with Interclade Polymorphisms and Intraclade Phylogenetic Clustering

(2009) P. C. Matthews et al.   JOURNAL OF VIROLOGY

Adaptation of HIV-1 to human leukocyte antigen class I

(2009) Yuka Kawashima et al.   NATURE

Vaccination with ALVAC and AIDSVAX to Prevent HIV-1 Infection in Thailand

(2009) Supachai Rerks-Ngarm et al.   NEW ENGLAND JOURNAL OF MEDICINE

Viral Load Levels Measured at Set-Point Have Risen Over the Last Decade of the HIV Epidemic in the Netherlands

(2009) Luuk Gras et al.   PLoS One

The Challenge of Finding a Cure for HIV Infection

(2009) D. D. Richman et al.   SCIENCE

An Evolutionary Model-Based Algorithm for Accurate Phylogenetic Breakpoint Mapping and Subtype Prediction in HIV-1

(2009) Sergei L. Kosakovsky Pond et al.   PLoS Computational Biology

HLA-Associated Clinical Progression Correlates with Epitope Reversion Rates in Early Human Immunodeficiency Virus Infection

(2008) A. Duda et al.   JOURNAL OF VIROLOGY

Transmission and Long-Term Stability of Compensated CD8 Escape Mutations

(2008) A. Schneidewind et al.   JOURNAL OF VIROLOGY

HLA-Associated Alterations in Replication Capacity of Chimeric NL4-3 Viruses Carrying gag-protease from Elite Controllers of Human Immunodeficiency Virus Type 1

(2008) T. Miura et al.   JOURNAL OF VIROLOGY

Protective HLA Class I Alleles That Restrict Acute-Phase CD8+ T-Cell Responses Are Associated with Viral Escape Mutations Located in Highly Conserved Regions of Human Immunodeficiency Virus Type 1

(2008) Y. E. Wang et al.   JOURNAL OF VIROLOGY

Marked Epitope- and Allele-Specific Differences in Rates of Mutation in Human Immunodeficiency Type 1 (HIV-1) Gag, Pol, and Nef Cytotoxic T-Lymphocyte Epitopes in Acute/Early HIV-1 Infection

(2008) Z. L. Brumme et al.   JOURNAL OF VIROLOGY

Central Role of Reverting Mutations in HLA Associations with Human Immunodeficiency Virus Set Point

(2008) P. C. Matthews et al.   JOURNAL OF VIROLOGY

Lack of Evidence for Changing Virulence of HIV-1 in North America

(2008) Joshua T. Herbeck et al.   PLoS One

Molecular Evolution of Human Immunodeficiency Virus Type 1 upon Transmission between Human Leukocyte Antigen Disparate Donor-Recipient Pairs

(2008) Marjon Navis et al.   PLoS One

HLA-Driven Convergence of HIV-1 Viral Subtypes B and F Toward the Adaptation to Immune Responses in Human Populations

(2008) Dario Alberto Dilernia et al.   PLoS One

Statistical Resolution of Ambiguous HLA Typing Data

(2008) Jennifer Listgarten et al.   PLoS Computational Biology

Frequent Toggling between Alternative Amino Acids Is Driven by Selection in HIV-1

(2008) Wayne Delport et al.   PLoS Pathogens