Epistasis and entrenchment of drug resistance in HIV-1 subtype B

Constrained Mutational Sampling of Amino Acids in HIV-1 Protease Evolution

(2019) Jeffrey I Boucher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Learning protein constitutive motifs from sequence data

(2019) Jérôme Tubiana et al.   eLife

Coevolutionary Landscape of Kinase Family Proteins: Sequence Probabilities and Functional Motifs

(2018) Allan Haldane et al.   BIOPHYSICAL JOURNAL

Structure of the peptidoglycan polymerase RodA resolved by evolutionary coupling analysis

(2018) Megan Sjodt et al.   NATURE

Fitness landscape of the human immunodeficiency virus envelope protein that is targeted by antibodies

(2018) Raymond H. Y. Louie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The impact of HIV-1 within-host evolution on transmission dynamics

(2018) Kristof Theys et al.   Current Opinion in Virology

Mapping mutational effects along the evolutionary landscape of HIV envelope

(2018) Hugh K Haddox et al.   eLife

Elucidating the Interdependence of Drug Resistance from Combinations of Mutations

(2017) Debra A. Ragland et al.   Journal of Chemical Theory and Computation

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

(2017) William F. Flynn et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutation effects predicted from sequence co-variation

(2017) Thomas A Hopf et al.   NATURE BIOTECHNOLOGY

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

Locally weighted histogram analysis and stochastic solution for large-scale multi-state free energy estimation

(2016) Zhiqiang Tan et al.   JOURNAL OF CHEMICAL PHYSICS

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

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1

(2015) Matteo Figliuzzi et al.   MOLECULAR BIOLOGY AND EVOLUTION

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

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

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

Current Perspectives on HIV-1 Antiretroviral Drug Resistance

(2014) Pinar Iyidogan et al.   Viruses-Basel

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

Impact of Primary Elvitegravir Resistance-Associated Mutations in HIV-1 Integrase on Drug Susceptibility and Viral Replication Fitness

(2013) Michael E. Abram et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

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

A sensitive real-time PCR based assay to estimate the impact of amino acid substitutions on the competitive replication fitness of human immunodeficiency virus type 1 in cell culture

(2012) Yi Liu et al.   JOURNAL OF VIROLOGICAL METHODS

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

Correlated Electrostatic Mutations Provide a Reservoir of Stability in HIV Protease

(2012) Omar Haq et al.   PLoS Computational Biology

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

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

Fitness Epistasis and Constraints on Adaptation in a Human Immunodeficiency Virus Type 1 Protein Region

(2010) J. da Silva et al.   GENETICS

Effect of Raltegravir Resistance Mutations in HIV-1 Integrase on Viral Fitness

(2010) Zixin Hu et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Learning generative models for protein fold families

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

Primary mutations selected in vitro with raltegravir confer large fold changes in susceptibility to first-generation integrase inhibitors, but minor fold changes to inhibitors with second-generation resistance profiles

(2010) Olivia Goethals et al.   VIROLOGY

Constraint satisfaction problems and neural networks: A statistical physics perspective

(2009) Marc Mézard et al.   JOURNAL OF PHYSIOLOGY-PARIS

Loss of Raltegravir Susceptibility by Human Immunodeficiency Virus Type 1 Is Conferred via Multiple Nonoverlapping Genetic Pathways

(2009) S. Fransen et al.   JOURNAL OF VIROLOGY

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

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

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

Structure and Function of HIV-1 Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition

(2008) Stefan G. Sarafianos et al.   JOURNAL OF MOLECULAR BIOLOGY

Resistance Mutations in Human Immunodeficiency Virus Type 1 Integrase Selected with Elvitegravir Confer Reduced Susceptibility to a Wide Range of Integrase Inhibitors

(2008) O. Goethals et al.   JOURNAL OF VIROLOGY

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