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

lavaan: AnRPackage for Structural Equation Modeling

(2015) Yves Rosseel   Journal of Statistical Software

A Comparative Study of HLA Binding Affinity and Ligand Diversity: Implications for Generating Immunodominant CD8+ T Cell Responses

(2014) X. Rao et al.   JOURNAL OF IMMUNOLOGY

Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

(2014) Aridaman Pandit et al.   Retrovirology

Selection bias at the heterosexual HIV-1 transmission bottleneck

(2014) J. M. Carlson et al.   SCIENCE

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

(2014) C. Fraser et al.   SCIENCE

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

(2014) Emma Hodcroft et al.   PLoS Pathogens

Computational Inference Methods for Selective Sweeps Arising in Acute HIV Infection

(2013) S. Leviyang   GENETICS

The Rate of Immune Escape Vanishes When Multiple Immune Responses Control an HIV Infection

(2013) H. W. M. van Deutekom et al.   JOURNAL OF IMMUNOLOGY

Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations

(2013) Gregory I. Lang et al.   NATURE

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

(2013) Samuel Alizon et al.   Retrovirology

Virus-induced target cell activation reconciles set-point viral load heritability and within-host evolution

(2013) Anna Hool et al.   Epidemics

Immune Activation Promotes Evolutionary Conservation of T-Cell Epitopes in HIV-1

(2013) Rafael Sanjuán et al.   PLOS BIOLOGY

Clonal Interference in the Evolution of Influenza

(2012) N. Strelkowa et al.   GENETICS

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

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

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

Role of Transmitted Gag CTL Polymorphisms in Defining Replicative Capacity and Early HIV-1 Pathogenesis

(2012) Jessica L. Prince et al.   PLoS Pathogens

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

Loss of HIV-1-derived cytotoxic T lymphocyte epitopes restricted by protective HLA-B alleles during the HIV-1 epidemic

(2011) Ingrid M.M. Schellens et al.   AIDS

Extensive HLA-driven viral diversity following a narrow-source HIV-1 outbreak in rural China

(2011) T. Dong et al.   BLOOD

HLA class I allele promiscuity revisited

(2011) Xiangyu Rao et al.   IMMUNOGENETICS

A Comparative Analysis of Viral Peptides Presented by Contemporary Human and Chimpanzee MHC Class I Molecules

(2011) H. W. M. van Deutekom et al.   JOURNAL OF IMMUNOLOGY

Dynamics of Viral Evolution and CTL Responses in HIV-1 Infection

(2011) Yi Liu et al.   PLoS One

A Strong Case for Viral Genetic Factors in HIV Virulence

(2011) Viktor Müller et al.   Viruses-Basel

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

Additive Contribution of HLA Class I Alleles in the Immune Control of HIV-1 Infection

(2010) A. Leslie et al.   JOURNAL OF VIROLOGY

Experimental depletion of CD8+ cells in acutely SIVagm-Infected African Green Monkeys results in increased viral replication

(2010) Thaidra Gaufin et al.   Retrovirology

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

(2010)   SCIENCE

Quantifying how MHC polymorphism prevents pathogens from adapting to the antigen presentation pathway

(2010) B.V. Schmid et al.   Epidemics

Quantifying the Impact of Human Immunodeficiency Virus-1 Escape From Cytotoxic T-Lymphocytes

(2010) Ulrich D. Kadolsky et al.   PLoS Computational Biology

Modelling the Evolution and Spread of HIV Immune Escape Mutants

(2010) Helen R. Fryer et al.   PLoS Pathogens

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 first T cell response to transmitted/founder virus contributes to the control of acute viremia in HIV-1 infection

(2009) Nilu Goonetilleke et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Adaptation of HIV-1 to human leukocyte antigen class I

(2009) Yuka Kawashima et al.   NATURE

Common Genetic Variation and the Control of HIV-1 in Humans

(2009) Jacques Fellay et al.   PLoS Genetics

NetMHCpan, a method for MHC class I binding prediction beyond humans

(2008) Ilka Hoof et al.   IMMUNOGENETICS

Transmission of HIV-1 Gag immune escape mutations is associated with reduced viral load in linked recipients

(2008) Paul A. Goepfert et al.   JOURNAL OF EXPERIMENTAL MEDICINE

HIV-1 Transmission, by Stage of Infection

(2008) T. Déirdre Hollingsworth et al.   JOURNAL OF INFECTIOUS DISEASES

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

(2008) Michael Worobey et al.   NATURE

Has HIV evolved to induce immune pathogenesis?

(2008) István Bartha et al.   TRENDS IN IMMUNOLOGY