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

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

(2013) Andrew L. Ferguson et al.   IMMUNITY

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

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

Adaptive Cluster Expansion for the Inverse Ising Problem: Convergence, Algorithm and Tests

(2012) S. Cocco et al.   JOURNAL OF STATISTICAL PHYSICS

Impact of HLA-B*81-Associated Mutations in HIV-1 Gag on Viral Replication Capacity

(2012) J. K. Wright et al.   JOURNAL OF VIROLOGY

Immune-mediated attenuation of HIV-1

(2011) Denis R Chopera et al.   Future Virology

Are Biological Systems Poised at Criticality?

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

Adaptive Cluster Expansion for Inferring Boltzmann Machines with Noisy Data

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

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

(2011) F. Morcos 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

Induction of Immunity to Human Immunodeficiency Virus Type-1 by Vaccination

(2010) M. Juliana McElrath et al.   IMMUNITY

Gag-Protease-Mediated Replication Capacity in HIV-1 Subtype C Chronic Infection: Associations with HLA Type and Clinical Parameters

(2010) Jaclyn K. Wright et al.   JOURNAL OF VIROLOGY

Protein Sectors: Evolutionary Units of Three-Dimensional Structure

(2009) Najeeb Halabi et al.   CELL

Ising model for neural data: Model quality and approximate methods for extracting functional connectivity

(2009) Yasser Roudi et al.   PHYSICAL REVIEW E

HLA-Associated Immune Escape Pathways in HIV-1 Subtype B Gag, Pol and Nef Proteins

(2009) Zabrina L. Brumme et al.   PLoS One

Statistical physics of pairwise probability models

(2009) Yasser Roudi   Frontiers in Computational Neuroscience

Variable Fitness Impact of HIV-1 Escape Mutations to Cytotoxic T Lymphocyte (CTL) Response

(2009) Ryan M. Troyer et al.   PLoS Pathogens

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

Crippling HIV one mutation at a time

(2008) Todd M. Allen et al.   JOURNAL OF EXPERIMENTAL MEDICINE

An HIV Vaccine — Challenges and Prospects

(2008) Margaret I. Johnston et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

Toward an AIDS Vaccine

(2008) B. D. Walker et al.   SCIENCE