Persistent HIV-1 replication maintains the tissue reservoir during therapy

Eight challenges in phylodynamic inference

(2015) Simon D.W. Frost et al.   Epidemics

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Persistent HIV-1 replication is associated with lower antiretroviral drug concentrations in lymphatic tissues

(2014) Courtney V. Fletcher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Specific HIV integration sites are linked to clonal expansion and persistence of infected cells

(2014) F. Maldarelli et al.   SCIENCE

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Quantifying the Turnover of Transcriptional Subclasses of HIV-1-Infected Cells

(2014) Christian L. Althaus et al.   PLoS Computational Biology

Lack of Detectable HIV-1 Molecular Evolution during Suppressive Antiretroviral Therapy

(2014) Mary F. Kearney et al.   PLoS Pathogens

Human APOBEC3 Induced Mutation of Human Immunodeficiency Virus Type-1 Contributes to Adaptation and Evolution in Natural Infection

(2014) Eun-Young Kim et al.   PLoS Pathogens

The Distribution of HIV DNA and RNA in Cell Subsets Differs in Gut and Blood of HIV-Positive Patients on ART: Implications for Viral Persistence

(2013) Steven A. Yukl et al.   JOURNAL OF INFECTIOUS DISEASES

Why Time Matters: Codon Evolution and the Temporal Dynamics of dN/dS

(2013) Carina F. Mugal et al.   MOLECULAR BIOLOGY AND EVOLUTION

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data

(2011) Mattia C. F. Prosperi et al.   BIOINFORMATICS

Clonal Sequences Recovered from Plasma from Patients with Residual HIV-1 Viremia and on Intensified Antiretroviral Therapy Are Identical to Replicating Viral RNAs Recovered from Circulating Resting CD4+ T Cells

(2011) J. A. Anderson et al.   JOURNAL OF VIROLOGY

A Random Effects Branch-Site Model for Detecting Episodic Diversifying Selection

(2011) Sergei L. Kosakovsky Pond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Majority of CD4+ T cells from peripheral blood of HIV-1-infected individuals contain only one HIV DNA molecule

(2011) L. Josefsson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid Emergence of Protease Inhibitor Resistance in Hepatitis C Virus

(2010) L. Rong et al.   Science Translational Medicine

HIV reservoir size and persistence are driven by T cell survival and homeostatic proliferation

(2009) Nicolas Chomont et al.   NATURE MEDICINE

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Viral reservoirs, residual viremia, and the potential of highly active antiretroviral therapy to eradicate HIV infection

(2008) Lin Shen et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics