Relative rate and location of intra-host HIV evolution to evade cellular immunity are predictable

Broad CTL response is required to clear latent HIV-1 due to dominance of escape mutations

(2015) Kai Deng et al.   NATURE

Scaling laws describe memories of host–pathogen riposte in the HIV population

(2015) John P. Barton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomics of intrapatient HIV-1 evolution

(2015) Fabio Zanini et al.   eLife

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

Recombination-mediated escape from primary CD8+ T cells in acute HIV-1 infection

(2014) Adam John Ritchie et al.   Retrovirology

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

The Fitness Landscape of HIV-1 Gag: Advanced Modeling Approaches and Validation of Model Predictions by In Vitro Testing

(2014) Jaclyn K. Mann et al.   PLoS Computational Biology

Translating HIV Sequences into Quantitative Fitness Landscapes Predicts Viral Vulnerabilities for Rational Immunogen Design

(2013) Andrew L. Ferguson et al.   IMMUNITY

HLA Class I Alleles Are Associated with Peptide-Binding Repertoires of Different Size, Affinity, and Immunogenicity

(2013) S. Paul et al.   JOURNAL OF IMMUNOLOGY

Ising models for neural activity inferred via selective cluster expansion: structural and coding properties

(2013) John Barton et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Mathematical modeling of escape of HIV from cytotoxic T lymphocyte responses

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

Spin models inferred from patient-derived viral sequence data faithfully describe HIV fitness landscapes

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

HIV and HLA Class I: An Evolving Relationship

(2012) Philip J.R. Goulder et al.   IMMUNITY

Are Biological Systems Poised at Criticality?

(2011) Thierry Mora et al.   JOURNAL OF STATISTICAL PHYSICS

A systems analysis of mutational effects in HIV-1 protease and reverse transcriptase

(2011) Trevor Hinkley et al.   NATURE GENETICS

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data

(2011) S. Cocco et al.   PHYSICAL REVIEW LETTERS

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

Coordinate linkage of HIV evolution reveals regions of immunological vulnerability

(2011) V. Dahirel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Maximum entropy models for antibody diversity

(2010) T. Mora et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Human Immunodeficiency Virus Type 1-Specific CD8+ T-Cell Responses during Primary Infection Are Major Determinants of the Viral Set Point and Loss of CD4+ T Cells

(2009) H. Streeck et al.   JOURNAL OF VIROLOGY

NetMHC-3.0: accurate web accessible predictions of human, mouse and monkey MHC class I affinities for peptides of length 8–11

(2008) Claus Lundegaard et al.   NUCLEIC ACIDS RESEARCH

Identification of direct residue contacts in protein-protein interaction by message passing

(2008) M. Weigt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How the thymus designs antigen-specific and self-tolerant T cell receptor sequences

(2008) A. Kosmrlj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA