The Genealogical Population Dynamics of HIV-1 in a Large Transmission Chain: Bridging within and among Host Evolutionary Rates

Sexually-Transmitted/Founder HIV-1 Cannot Be Directly Predicted from Plasma or PBMC-Derived Viral Quasispecies in the Transmitting Partner

(2013) Pierre Frange et al.   PLoS One

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

Within-host and between-host evolutionary rates across the HIV-1 genome

(2013) Samuel Alizon et al.   Retrovirology

A counting renaissance: combining stochastic mapping and empirical Bayes to quickly detect amino acid sites under positive selection

(2012) Philippe Lemey et al.   BIOINFORMATICS

Previously Transmitted HIV-1 Strains Are Preferentially Selected During Subsequent Sexual Transmissions

(2012) Andrew D. Redd et al.   JOURNAL OF INFECTIOUS DISEASES

Accurate Model Selection of Relaxed Molecular Clocks in Bayesian Phylogenetics

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improving the Accuracy of Demographic and Molecular Clock Model Comparison While Accommodating Phylogenetic Uncertainty

(2012) Guy Baele et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

New insights into the evolutionary rate of HIV-1 at the within-host and epidemiological levels

(2012) K. A. Lythgoe et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Assessment of phylogenetic sensitivity for reconstructing HIV-1 epidemiological relationships

(2012) Apostolos Beloukas et al.   VIRUS RESEARCH

Time-measured phylogenies of gag, pol and env sequence data reveal the direction and time interval of HIV-1 transmission

(2011) Andrea Rachinger et al.   AIDS

Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data

(2011) Art F.Y. Poon et al.   AIDS

Ancient Hybridization and an Irish Origin for the Modern Polar Bear Matriline

(2011) Ceiridwen J. Edwards et al.   CURRENT BIOLOGY

Demographic Processes Affect HIV-1 Evolution in Primary Infection before the Onset of Selective Processes

(2011) J. T. Herbeck et al.   JOURNAL OF VIROLOGY

Science in court: the myth of HIV fingerprinting

(2011) Ana B Abecasis et al.   LANCET INFECTIOUS DISEASES

Inconsistencies in Estimating the Age of HIV-1 Subtypes Due to Heterotachy

(2011) J. O. Wertheim et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

(2011) José M. Cuevas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Rapid Escape from Preserved Cross-Reactive Neutralizing Humoral Immunity without Loss of Viral Fitness in HIV-1-Infected Progressors and Long-Term Nonprogressors

(2010) M. J. van Gils et al.   JOURNAL OF VIROLOGY

Impact of CCR5delta32 Host Genetic Background and Disease Progression on HIV-1 Intrahost Evolutionary Processes: Efficient Hypothesis Testing through Hierarchical Phylogenetic Models

(2010) D. Edo-Matas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences

(2010) D. I. Scaduto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving Marginal Likelihood Estimation for Bayesian Phylogenetic Model Selection

(2010) Wangang Xie et al.   SYSTEMATIC BIOLOGY

Genetic composition of replication competent clonal HIV-1 variants isolated from peripheral blood mononuclear cells (PBMC), HIV-1 proviral DNA from PBMC and HIV-1 RNA in serum in the course of HIV-1 infection

(2010) Diana Edo-Matas et al.   VIROLOGY

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

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary analysis of the dynamics of viral infectious disease

(2009) Oliver G. Pybus et al.   NATURE REVIEWS GENETICS

Bayesian Phylogeography Finds Its Roots

(2009) Philippe Lemey et al.   PLoS Computational Biology

Smooth Skyride through a Rough Skyline: Bayesian Coalescent-Based Inference of Population Dynamics

(2008) V. N. Minin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960

(2008) Michael Worobey 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