Inference of Epistatic Effects Leading to Entrenchment and Drug Resistance in HIV-1 Protease

ACE: adaptive cluster expansion for maximum entropy graphical model inference

(2016) J. P. Barton et al.   BIOINFORMATICS

Epistasis and the Dynamics of Reversion in Molecular Evolution

(2016) D. M. McCandlish et al.   GENETICS

Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

(2016) Jeffrey I. Boucher et al.   PROTEIN SCIENCE

Structural propensities of kinase family proteins from a Potts model of residue co-variation

(2016) Allan Haldane et al.   PROTEIN SCIENCE

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

(2016) John P. Barton et al.   Nature Communications

Benchmarking Inverse Statistical Approaches for Protein Structure and Design with Exactly Solvable Models

(2016) Hugo Jacquin et al.   PLoS Computational Biology

Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein

(2016) Aditi Gupta et al.   PLoS Genetics

Experimental Estimation of the Effects of All Amino-Acid Mutations to HIV’s Envelope Protein on Viral Replication in Cell Culture

(2016) Hugh K. Haddox et al.   PLoS Pathogens

Detecting epistasis from an ensemble of adapting populations

(2015) David M. McCandlish et al.   EVOLUTION

Protein structure determination by combining sparse NMR data with evolutionary couplings

(2015) Yuefeng Tang et al.   NATURE METHODS

Contingency and entrenchment in protein evolution under purifying selection

(2015) Premal Shah et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From residue coevolution to protein conformational ensembles and functional dynamics

(2015) Ludovico Sutto et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput identification of protein mutant stability computed from a double mutant fitness landscape

(2015) Nicholas C. Wu et al.   PROTEIN SCIENCE

Deep Sequencing of Protease Inhibitor Resistant HIV Patient Isolates Reveals Patterns of Correlated Mutations in Gag and Protease

(2015) William F. Flynn et al.   PLoS Computational Biology

Persistence of Transmitted HIV-1 Drug Resistance Mutations Associated with Fitness Costs and Viral Genetic Backgrounds

(2015) Wan-Lin Yang et al.   PLoS Pathogens

Strong evidence for protein epistasis, weak evidence against it

(2014) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

(2014) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models

(2013) Magnus Ekeberg et al.   PHYSICAL REVIEW E

Coevolutionary signals across protein lineages help capture multiple protein conformations

(2013) F. Morcos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrophobic Core Flexibility Modulates Enzyme Activity in HIV-1 Protease

(2012) Seema Mittal et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein structure prediction from sequence variation

(2012) Debora S Marks et al.   NATURE BIOTECHNOLOGY

Amino acid coevolution induces an evolutionary Stokes shift

(2012) D. D. Pollock et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics-aided structure prediction

(2012) J. I. Sulkowska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human Immunodeficiency Virus gag and protease: partners in resistance

(2012) Axel Fun et al.   Retrovirology

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease

(2012) Omar Haq et al.   PLoS Computational Biology

Interplay between Single Resistance-Associated Mutations in the HIV-1 Protease and Viral Infectivity, Protease Activity, and Inhibitor Sensitivity

(2011) Gavin J. Henderson et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

A Cleavage Enzyme-Cytometric Bead Array Provides Biochemical Profiling of Resistance Mutations in HIV-1 Gag and Protease

(2011) Sebastian Breuer et al.   BIOCHEMISTRY

PSICOV: precise structural contact prediction using sparse inverse covariance estimation on large multiple sequence alignments

(2011) David T. Jones et al.   BIOINFORMATICS

Accessory Mutations Maintain Stability in Drug-Resistant HIV-1 Protease

(2011) Max W. Chang et al.   JOURNAL OF MOLECULAR BIOLOGY

Dynamics of Preferential Substrate Recognition in HIV-1 Protease: Redefining the Substrate Envelope

(2011) Ayşegül Özen et al.   JOURNAL OF MOLECULAR BIOLOGY

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

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

Inhibition of autoprocessing of natural variants and multidrug resistant mutant precursors of HIV-1 protease by clinical inhibitors

(2011) J. M. Louis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three Residues in HIV-1 Matrix Contribute to Protease Inhibitor Susceptibility and Replication Capacity

(2010) Chris M. Parry et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Learning generative models for protein fold families

(2010) Sivaraman Balakrishnan et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Disentangling Direct from Indirect Co-Evolution of Residues in Protein Alignments

(2010) Lukas Burger et al.   PLoS Computational Biology

Human Immunodeficiency Virus Type 1 Protease-Correlated Cleavage Site Mutations Enhance Inhibitor Resistance

(2009) M. Kolli et al.   JOURNAL OF VIROLOGY

On the accuracy of inferring energetic coupling between distant sites in protein families from evolutionary imprints: Illustrations using lattice model

(2009) Zhenxing Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Emergence of Drug Resistance in HIV Type 1–Infected Patients after Receipt of First‐Line Highly Active Antiretroviral Therapy: A Systematic Review of Clinical Trials

(2008) Ravindra Gupta et al.   CLINICAL INFECTIOUS DISEASES

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

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

Understanding Protein Evolution: From Protein Physics to Darwinian Selection

(2007) Konstantin B. Zeldovich et al.   Annual Review of Physical Chemistry