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

Modelling tree shape and structure in viral phylodynamics

(2013) S. D. W. Frost et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Characterizing HIV Transmission Networks Across the United States

(2012) Jeannette L. Aldous et al.   CLINICAL INFECTIOUS DISEASES

The Rates of HIV Superinfection and Primary HIV Incidence in a General Population in Rakai, Uganda

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

Inferring Epidemic Contact Structure from Phylogenetic Trees

(2012) Gabriel E. Leventhal et al.   PLoS Computational Biology

Simple Epidemiological Dynamics Explain Phylogenetic Clustering of HIV from Patients with Recent Infection

(2012) Erik M. Volz et al.   PLoS Computational Biology

HIV Treatment as Prevention: Debate and Commentary—Will Early Infection Compromise Treatment-as-Prevention Strategies?

(2012) Myron S. Cohen et al.   PLOS MEDICINE

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

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

Complex Population Dynamics and the Coalescent Under Neutrality

(2011) Erik M. Volz   GENETICS

Transmission Network Parameters Estimated From HIV Sequences for a Nationwide Epidemic

(2011) Andrew J. Leigh Brown et al.   JOURNAL OF INFECTIOUS DISEASES

The role of acute and early HIV infection in the spread of HIV and implications for transmission prevention strategies in Lilongwe, Malawi: a modelling study

(2011) Kimberly A Powers et al.   LANCET

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Acute HIV-1 Infection

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

Prevention of HIV-1 Infection with Early Antiretroviral Therapy

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

Estimated HIV Incidence in the United States, 2006–2009

(2011) Joseph Prejean et al.   PLoS One

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

(2011) David A. Rasmussen et al.   PLoS Computational Biology

National estimate of HIV prevalence in the Netherlands: comparison and applicability of different estimation tools

(2010) Maaike G van Veen et al.   AIDS

Viral phylodynamics and the search for an 'effective number of infections'

(2010) S. D. W. Frost et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Transmission of Single HIV-1 Genomes and Dynamics of Early Immune Escape Revealed by Ultra-Deep Sequencing

(2010) Will Fischer et al.   PLoS One

Flexible epidemiological model for estimates and short-term projections in generalised HIV/AIDS epidemics

(2010) D. R. Hogan et al.   SEXUALLY TRANSMITTED INFECTIONS

27 years of the HIV epidemic amongst men having sex with men in the Netherlands: An in depth mathematical model-based analysis

(2010) Daniela Bezemer et al.   Epidemics

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

(2010) Hui Li et al.   PLoS Pathogens

The impact of transmission clusters on primary drug resistance in newly diagnosed HIV-1 infection

(2009) Sabine Yerly et al.   AIDS

Incidence of Human Immunodeficiency Virus Type 1 Dual Infections in Amsterdam, The Netherlands, during 2003–2007

(2009) Antoinette C. van der Kuyl et al.   CLINICAL INFECTIOUS DISEASES

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

HIV-1 Transmission Cluster With T215D Revertant Mutation Among Newly Diagnosed Patients From the Basque Country, Spain

(2009) Maria Teresa Cuevas et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Drug Resistance Mutations for Surveillance of Transmitted HIV-1 Drug-Resistance: 2009 Update

(2009) Diane E. Bennett et al.   PLoS One

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

Estimating HIV incidence in the United States from HIV/AIDS surveillance data and biomarker HIV test results

(2008) John M. Karon et al.   STATISTICS IN MEDICINE

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

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