Investigating the Consequences of Interference between Multiple CD8+ T Cell Escape Mutations in Early HIV Infection

Structured Observations Reveal Slow HIV-1 CTL Escape

(2015) Hannah E. Roberts et al.   PLoS Genetics

A General Functional Response of Cytotoxic T Lymphocyte-Mediated Killing of Target Cells

(2014) Saikrishna Gadhamsetty et al.   BIOPHYSICAL JOURNAL

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

(2014) Aridaman Pandit et al.   Retrovirology

Loss and Recovery of Genetic Diversity in Adapting Populations of HIV

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

Modeling the within-host dynamics of HIV infection

(2013) Alan S Perelson et al.   BMC BIOLOGY

SHIFTING FITNESS LANDSCAPES IN RESPONSE TO ALTERED ENVIRONMENTS

(2013) Ryan T. Hietpas et al.   EVOLUTION

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

Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses

(2013) Vitaly V Ganusov et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

The quantitative theory of within-host viral evolution

(2013) Igor M Rouzine et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

FFPopSim: an efficient forward simulation package for the evolution of large populations

(2012) Fabio Zanini et al.   BIOINFORMATICS

Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations

(2012) B. H. Good et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Emergent Neutrality in Adaptive Asexual Evolution

(2011) Stephan Schiffels et al.   GENETICS

The Dynamics of HIV-1 Adaptation in Early Infection

(2011) J. da Silva   GENETICS

Timing of the Components of the HIV Life Cycle in Productively Infected CD4+ T Cells in a Population of HIV-Infected Individuals

(2011) J. M. Murray et al.   JOURNAL OF VIROLOGY

Conditional CD8+ T Cell Escape during Acute Simian Immunodeficiency Virus Infection

(2011) S. L. O'Connor et al.   JOURNAL OF VIROLOGY

Fitness Costs and Diversity of the Cytotoxic T Lymphocyte (CTL) Response Determine the Rate of CTL Escape during Acute and Chronic Phases of HIV Infection

(2011) V. V. Ganusov et al.   JOURNAL OF VIROLOGY

Killing of Targets by CD8+ T Cells in the Mouse Spleen Follows the Law of Mass Action

(2011) Vitaly V. Ganusov et al.   PLoS One

The Role of Recombination for the Coevolutionary Dynamics of HIV and the Immune Response

(2011) Rafal Mostowy et al.   PLoS One

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

(2011) Yi Liu et al.   PLoS One

Estimate of effective recombination rate and average selection coefficient for HIV in chronic infection

(2011) R. Batorsky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical genetics and evolution of quantitative traits

(2011) Richard A. Neher et al.   REVIEWS OF MODERN PHYSICS

Effect of Host Species on the Distribution of Mutational Fitness Effects for an RNA Virus

(2011) Jasna Lalić et al.   PLoS Genetics

Viral Evolution and Escape during Acute HIV‐1 Infection

(2010) Christian L. Boutwell et al.   JOURNAL OF INFECTIOUS DISEASES

The Speed of Evolution in Large Asexual Populations

(2010) Su-Chan Park et al.   JOURNAL OF STATISTICAL PHYSICS

Estimation of the Initial Viral Growth Rate and Basic Reproductive Number during Acute HIV-1 Infection

(2010) R. M. Ribeiro et al.   JOURNAL OF VIROLOGY

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

(2010) Will Fischer et al.   PLoS One

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

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

Recombination Rate and Selection Strength in HIV Intra-patient Evolution

(2010) Richard A. Neher et al.   PLoS Computational Biology

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

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

Kinetics of Expansion of Epitope-Specific T Cell Responses during Primary HIV-1 Infection

(2009) E. L. Turnbull et al.   JOURNAL OF IMMUNOLOGY

Modeling sequence evolution in acute HIV-1 infection

(2009) Ha Youn Lee et al.   JOURNAL OF THEORETICAL BIOLOGY

Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted Variants

(2009) M.-R. Abrahams et al.   JOURNAL OF VIROLOGY

P09-19 LB. CTL escape mutations in gag epitopes restricted by protective HLA class I alleles cause substantial reductions in viral replication capacity

(2009) CL Boutwell et al.   Retrovirology

P09-20 LB. Ultra-deep sequencing of full-length HIV-1 genomes identifies rapid viral evolution during acute infection

(2009) MR Henn et al.   Retrovirology

Investigating CTL Mediated Killing with a 3D Cellular Automaton

(2009) Frederik Graw et al.   PLoS Computational Biology

Selection dramatically reduces effective population size in HIV-1 infection

(2008) Yi Liu et al.   BMC EVOLUTIONARY BIOLOGY

Clonal Interference, Multiple Mutations and Adaptation in Large Asexual Populations

(2008) C. A. Fogle et al.   GENETICS

Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae

(2008) Katy C Kao et al.   NATURE GENETICS

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

Dynamics of Immune Escape during HIV/SIV Infection

(2008) Christian L. Althaus et al.   PLoS Computational Biology