Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe

Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control

(2017) István Bartha et al.   PLoS Computational Biology

Prospective Study of Acute HIV-1 Infection in Adults in East Africa and Thailand

(2016) Merlin L. Robb et al.   NEW ENGLAND JOURNAL OF MEDICINE

Potential Pitfalls in Estimating Viral Load Heritability

(2016) Gabriel E. Leventhal et al.   TRENDS IN MICROBIOLOGY

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

IVA: accuratede novoassembly of RNA virus genomes

(2015) Martin Hunt et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification

(2014) Daniel Struck et al.   NUCLEIC ACIDS RESEARCH

Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence

(2014) Rebecca Payne et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective

(2014) C. Fraser et al.   SCIENCE

A Linear-Time Algorithm for Gaussian and Non-Gaussian Trait Evolution Models

(2014) Lam si Tung Ho et al.   SYSTEMATIC BIOLOGY

Immuno-epidemiological Modeling of HIV-1 Predicts High Heritability of the Set-Point Virus Load, while Selection for CTL Escape Dominates Virulence Evolution

(2014) Christiaan H. van Dorp et al.   PLoS Computational Biology

The Contribution of Viral Genotype to Plasma Viral Set-Point in HIV Infection

(2014) Emma Hodcroft et al.   PLoS Pathogens

Temporal trends in prognostic markers of HIV-1 virulence and transmissibility: an observational cohort study

(2014) Nikos Pantazis et al.   Lancet HIV

Inferring the Source of Transmission with Phylogenetic Data

(2013) Erik M. Volz et al.   PLoS Computational Biology

Partner Characteristics Predicting HIV-1 Set Point in Sexually Acquired HIV-1 Among African Seroconverters

(2012) Jairam R. Lingappa et al.   AIDS RESEARCH AND HUMAN RETROVIRUSES

Universal Amplification, Next-Generation Sequencing, and Assembly of HIV-1 Genomes

(2012) A. Gall et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Correlates of Protective Cellular Immunity Revealed by Analysis of Population-Level Immune Escape Pathways in HIV-1

(2012) J. M. Carlson et al.   JOURNAL OF VIROLOGY

Cumulative Impact of Host and Viral Factors on HIV-1 Viral-Load Control during Early Infection

(2012) L. Yue et al.   JOURNAL OF VIROLOGY

Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission

(2011) Joshua T. Herbeck et al.   AIDS

Transmission Selects for HIV-1 Strains of Intermediate Virulence: A Modelling Approach

(2011) George Shirreff et al.   PLoS Computational Biology

HIV RNA levels in transmission sources only weakly predict plasma viral load in recipients

(2010) Antoinette C van der Kuyl et al.   AIDS

Effect of treating co-infections on HIV-1 viral load: a systematic review

(2010) Kayvon Modjarrad et al.   LANCET INFECTIOUS DISEASES

HIV-1 Transmitting Couples Have Similar Viral Load Set-Points in Rakai, Uganda

(2010) T. Déirdre Hollingsworth et al.   PLoS Pathogens

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

(2010) Samuel Alizon et al.   PLoS Pathogens

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Performance of the New Roche Cobas AmpliPrep-Cobas TaqMan Version 2.0 Human Immunodeficiency Virus Type 1 Assay

(2009) L. Scott et al.   JOURNAL OF CLINICAL MICROBIOLOGY