Timing and Order of Transmission Events Is Not Directly Reflected in a Pathogen Phylogeny

The undiagnosed HIV epidemic in France and its implications for HIV screening strategies

(2014) Virginie Supervie et al.   AIDS

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV

(2014) Pleuni S. Pennings et al.   PLoS Genetics

Towards Estimation of HIV-1 Date of Infection: A Time-Continuous IgG-Model Shows That Seroconversion Does Not Occur at the Midpoint between Negative and Positive Tests

(2013) Helena Skar et al.   PLoS One

HIV-1 Transmission during Early Infection in Men Who Have Sex with Men: A Phylodynamic Analysis

(2013) Erik M. Volz et al.   PLOS MEDICINE

Estimating the Strength of Selective Sweeps from Deep Population Diversity Data

(2012) P. W. Messer et al.   GENETICS

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

Low Prevalence of Transmitted Drug Resistance in Patients Newly Diagnosed with HIV-1 Infection in Sweden 2003–2010

(2012) Annika Karlsson et al.   PLoS One

Agent-based and phylogenetic analyses reveal how HIV-1 moves between risk groups: Injecting drug users sustain the heterosexual epidemic in Latvia

(2012) Frederik Graw et al.   Epidemics

Ambiguous Nucleotide Calls From Population-based Sequencing of HIV-1 are a Marker for Viral Diversity and the Age of Infection

(2011) Roger D. Kouyos et al.   CLINICAL INFECTIOUS DISEASES

Determination of Mean Recency Period for Estimation of HIV Type 1 Incidence with the BED-Capture EIA in Persons Infected with Diverse Subtypes

(2010) Bharat S. Parekh et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Treatment to Prevent Transmission of HIV‐1

(2010) Myron S. Cohen et al.   CLINICAL INFECTIOUS DISEASES

Molecular Epidemiology Reveals Long‐Term Changes in HIV Type 1 Subtype B Transmission in Switzerland

(2010) Roger D. Kouyos et al.   JOURNAL OF INFECTIOUS DISEASES

HIV-2 Genetic Evolution in Patients with Advanced Disease Is Faster than That in Matched HIV-1 Patients

(2010) H. Skar et al.   JOURNAL OF VIROLOGY

Dynamics of Two Separate but Linked HIV-1 CRF01_AE Outbreaks among Injection Drug Users in Stockholm, Sweden, and Helsinki, Finland

(2010) H. Skar et al.   JOURNAL OF VIROLOGY

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

Phylogenetic Approach Reveals That Virus Genotype Largely Determines HIV Set-Point Viral Load

(2010) Samuel Alizon et al.   PLoS Pathogens

Prevalence of drug resistance and importance of viral load measurements in Honduran HIV-infected patients failing antiretroviral treatment

(2009) W Murillo et al.   HIV 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

Evolutionary analysis of the dynamics of viral infectious disease

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

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

Discordance of Species Trees with Their Most Likely Gene Trees: The Case of Five Taxa

(2008) Noah A. Rosenberg et al.   SYSTEMATIC BIOLOGY

Dynamic Correlation between Intrahost HIV-1 Quasispecies Evolution and Disease Progression

(2008) Ha Youn Lee et al.   PLoS Computational Biology