Resistance to type 1 interferons is a major determinant of HIV-1 transmission fitness

Stan: A Probabilistic Programming Language

(2017) Bob Carpenter et al.   Journal of Statistical Software

HIV-Host Interactions: Implications for Vaccine Design

(2016) Barton F. Haynes et al.   Cell Host & Microbe

Resistance of Transmitted Founder HIV-1 to IFITM-Mediated Restriction

(2016) Toshana L. Foster et al.   Cell Host & Microbe

Interferon Alpha Subtype-Specific Suppression of HIV-1 InfectionIn Vivo

(2016) Kerry J. Lavender et al.   JOURNAL OF VIROLOGY

Prevention of SHIV transmission by topical IFN-β treatment

(2016) R S Veazey et al.   Mucosal Immunology

Receptor usage dictates HIV-1 restriction by human TRIM5α in dendritic cell subsets

(2016) Carla M. S. Ribeiro et al.   NATURE

Tracing HIV-1 transmission: envelope traits of HIV-1 transmitter and recipient pairs

(2016) Corinna S. Oberle et al.   Retrovirology

Vpu-Mediated Counteraction of Tetherin Is a Major Determinant of HIV-1 Interferon Resistance

(2016) Dorota Kmiec et al.   mBio

Genital inflammation, immune activation and risk of sexual HIV acquisition

(2016) Jo-Ann S. Passmore et al.   Current Opinion in HIV and AIDS

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

(2016) Damien C. Tully et al.   PLoS Pathogens

Transmission of Multiple HIV-1 Subtype C Transmitted/founder Viruses into the Same Recipients Was not Determined by Modest Phenotypic Differences

(2016) Hongshuo Song et al.   Scientific Reports

HIV and mucosal barrier interactions: consequences for transmission and pathogenesis

(2015) Adam Burgener et al.   CURRENT OPINION IN IMMUNOLOGY

HIV-1 Fitness Cost Associated with Escape from the VRC01 Class of CD4 Binding Site Neutralizing Antibodies

(2015) Rebecca M. Lynch et al.   JOURNAL OF VIROLOGY

Innate immunity against HIV-1 infection

(2015) Marcus Altfeld et al.   NATURE IMMUNOLOGY

Bottlenecks in HIV-1 transmission: insights from the study of founder viruses

(2015) Sarah B. Joseph et al.   NATURE REVIEWS MICROBIOLOGY

HIV-1 and interferons: who's interfering with whom?

(2015) Tomas Doyle et al.   NATURE REVIEWS MICROBIOLOGY

The molecular basis for functional plasticity in type I interferon signaling

(2015) Gideon Schreiber et al.   TRENDS IN IMMUNOLOGY

Transmitted Virus Fitness and Host T Cell Responses Collectively Define Divergent Infection Outcomes in Two HIV-1 Recipients

(2015) Ling Yue et al.   PLoS Pathogens

Heterosexual Transmission of Subtype C HIV-1 Selects Consensus-Like Variants without Increased Replicative Capacity or Interferon-α Resistance

(2015) Martin J. Deymier et al.   PLoS Pathogens

Interferon-α Subtypes in an Ex Vivo Model of Acute HIV-1 Infection: Expression, Potency and Effector Mechanisms

(2015) Michael S. Harper et al.   PLoS Pathogens

Ongoing HIV Transmission and the HIV Care Continuum in North Carolina

(2015) Anna B. Cope et al.   PLoS One

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Interactions between HIV-1 and the Cell-Autonomous Innate Immune System

(2014) Greg J. Towers et al.   Cell Host & Microbe

Characteristics and Quantities of HIV Host Cells in Human Genital Tract Secretions

(2014) J. A. Politch et al.   JOURNAL OF INFECTIOUS DISEASES

Activities of Transmitted/Founder and Chronic Clade B HIV-1 Vpu and a C-Terminal Polymorphism Specifically Affecting Virion Release

(2014) M. Jafari et al.   JOURNAL OF VIROLOGY

Type I interferon responses in rhesus macaques prevent SIV infection and slow disease progression

(2014) Netanya G. Sandler et al.   NATURE

Characterization of HIV-1 envelopes in acutely and chronically infected injection drug users

(2014) Behzad Etemad et al.   Retrovirology

Selection bias at the heterosexual HIV-1 transmission bottleneck

(2014) J. M. Carlson et al.   SCIENCE

Interferon-stimulated genes: roles in viral pathogenesis

(2014) John W Schoggins   Current Opinion in Virology

The Interferon-Inducible MxB Protein Inhibits HIV-1 Infection

(2013) Zhenlong Liu et al.   Cell Host & Microbe

Comparison of Viral Env Proteins from Acute and Chronic Infections with Subtype C Human Immunodeficiency Virus Type 1 Identifies Differences in Glycosylation and CCR5 Utilization and Suggests a New Strategy for Immunogen Design

(2013) L.-H. Ping et al.   JOURNAL OF VIROLOGY

Human MX2 is an interferon-induced post-entry inhibitor of HIV-1 infection

(2013) Caroline Goujon et al.   NATURE

Structural basis of a unique interferon-β signaling axis mediated via the receptor IFNAR1

(2013) Nicole A de Weerd et al.   NATURE IMMUNOLOGY

Phenotypic properties of transmitted founder HIV-1

(2013) N. F. Parrish et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Relative resistance of HIV-1 founder viruses to control by interferon-alpha

(2013) Angharad E Fenton-May et al.   Retrovirology

HIV Transmission

(2013) G. M. Shaw et al.   Cold Spring Harbor Perspectives in Medicine

IFN-α subtypes: distinct biological activities in anti-viral therapy

(2012) K Gibbert et al.   BRITISH JOURNAL OF PHARMACOLOGY

Broadly Neutralizing Antibodies Developed by an HIV-Positive Elite Neutralizer Exact a Replication Fitness Cost on the Contemporaneous Virus

(2012) D. N. Sather et al.   JOURNAL OF VIROLOGY

Transmitted/Founder and Chronic HIV-1 Envelope Proteins Are Distinguished by Differential Utilization of CCR5

(2012) Z. F. Parker et al.   JOURNAL OF VIROLOGY

Codon-usage-based inhibition of HIV protein synthesis by human schlafen 11

(2012) Manqing Li et al.   NATURE

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Impact of immune escape mutations on HIV-1 fitness in the context of the cognate transmitted/founder genome

(2012) Hongshuo Song et al.   Retrovirology

Transmitted/Founder and Chronic Subtype C HIV-1 Use CD4 and CCR5 Receptors with Equal Efficiency and Are Not Inhibited by Blocking the Integrin α4β7

(2012) Nicholas F. Parrish et al.   PLoS Pathogens

Early Low-Titer Neutralizing Antibodies Impede HIV-1 Replication and Select for Virus Escape

(2012) Katharine J. Bar et al.   PLoS Pathogens

Barriers to mucosal transmission of immunodeficiency viruses

(2011) B. F. Keele et al.   BLOOD

pROC: an open-source package for R and S+ to analyze and compare ROC curves

(2011) Xavier Robin et al.   BMC BIOINFORMATICS

Binding and activity of all human alpha interferon subtypes

(2011) Thomas B. Lavoie et al.   CYTOKINE

Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection

(2011) V. V. Ganusov et al.   JOURNAL OF VIROLOGY

Phenotypic and Immunologic Comparison of Clade B Transmitted/Founder and Chronic HIV-1 Envelope Glycoproteins

(2011) C. B. Wilen et al.   JOURNAL OF VIROLOGY

Generation of Transmitted/Founder HIV-1 Infectious Molecular Clones and Characterization of Their Replication Capacity in CD4 T Lymphocytes and Monocyte-Derived Macrophages

(2011) C. Ochsenbauer et al.   JOURNAL OF VIROLOGY

SAMHD1 is the dendritic- and myeloid-cell-specific HIV-1 restriction factor counteracted by Vpx

(2011) Nadine Laguette et al.   NATURE

Vpx relieves inhibition of HIV-1 infection of macrophages mediated by the SAMHD1 protein

(2011) Kasia Hrecka et al.   NATURE

Role of donor genital tract HIV-1 diversity in the transmission bottleneck

(2011) D. I. Boeras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Recurrent Signature Patterns in HIV-1 B Clade Envelope Glycoproteins Associated with either Early or Chronic Infections

(2011) S. Gnanakaran et al.   PLoS Pathogens

Estimation of the Initial Viral Growth Rate and Basic Reproductive Number during Acute HIV-1 Infection

(2010) R. M. Ribeiro et al.   JOURNAL OF VIROLOGY

Wide Variation in the Multiplicity of HIV-1 Infection among Injection Drug Users

(2010) K. J. Bar et al.   JOURNAL OF VIROLOGY

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men

(2010) Hui Li et al.   PLoS Pathogens

Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703–positive individuals and their transmission recipients

(2009) Hayley Crawford et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection

(2009) Jesus F. Salazar-Gonzalez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Induction of a Striking Systemic Cytokine Cascade prior to Peak Viremia in Acute Human Immunodeficiency Virus Type 1 Infection, in Contrast to More Modest and Delayed Responses in Acute Hepatitis B and C Virus Infections

(2009) A. R. Stacey et al.   JOURNAL OF VIROLOGY

Heterosexual Transmission of Human Immunodeficiency Virus Type 1 Subtype C: Macrophage Tropism, Alternative Coreceptor Use, and the Molecular Anatomy of CCR5 Utilization

(2009) J. Isaacman-Beck et al.   JOURNAL OF VIROLOGY

Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

(2009) M.-R. Abrahams et al.   JOURNAL OF VIROLOGY

Inflammatory Genital Infections Mitigate a Severe Genetic Bottleneck in Heterosexual Transmission of Subtype A and C HIV-1

(2009) Richard E. Haaland et al.   PLoS Pathogens

The Interferon-Induced Protein BST-2 Restricts HIV-1 Release and Is Downregulated from the Cell Surface by the Viral Vpu Protein

(2008) Nanette Van Damme et al.   Cell Host & Microbe

A GENEALOGICAL APPROACH TO QUANTIFYING LINEAGE DIVERGENCE

(2008) Michael P. Cummings et al.   EVOLUTION

Deciphering Human Immunodeficiency Virus Type 1 Transmission and Early Envelope Diversification by Single-Genome Amplification and Sequencing

(2008) J. F. Salazar-Gonzalez et al.   JOURNAL OF VIROLOGY

Tetherin inhibits retrovirus release and is antagonized by HIV-1 Vpu

(2008) Stuart J. D. Neil et al.   NATURE

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection

(2008) B. F. Keele et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA