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

ACE: adaptive cluster expansion for maximum entropy graphical model inference

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

Inferring interaction partners from protein sequences

(2016) Anne-Florence Bitbol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal immunization cocktails can promote induction of broadly neutralizing Abs against highly mutable pathogens

(2016) J. Scott Shaffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis

(2016) Thomas Gueudré et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses

(2016) Richard A. Neher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enhanced clearance of HIV-1-infected cells by broadly neutralizing antibodies against HIV-1 in vivo

(2016) C.-L. Lu et al.   SCIENCE

Accurate Measurement of the Effects of All Amino-Acid Mutations on Influenza Hemagglutinin

(2016) Michael Doud et al.   Viruses-Basel

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

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

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

Fusarium: Molecular Diversity and Intrinsic Drug Resistance

(2016) Abdullah M. S. Al-Hatmi et al.   PLoS Pathogens

Manipulating the Selection Forces during Affinity Maturation to Generate Cross-Reactive HIV Antibodies

(2015) Shenshen Wang et al.   CELL

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

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

CATNAP: a tool to compile, analyze and tally neutralizing antibody panels

(2015) Hyejin Yoon et al.   NUCLEIC ACIDS RESEARCH

Competitive exclusion by autologous antibodies can prevent broad HIV-1 antibodies from arising

(2015) Shishi Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Functional Constraint Profiling of a Viral Protein Reveals Discordance of Evolutionary Conservation and Functionality

(2015) Nicholas C. Wu et al.   PLoS Genetics

Broad and potent HIV-1 neutralization by a human antibody that binds the gp41–gp120 interface

(2014) Jinghe Huang et al.   NATURE

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

Multimeric Scaffolds Displaying the HIV-1 Envelope MPER Induce MPER-Specific Antibodies and Cross-Neutralizing Antibodies when Co-Immunized with gp160 DNA

(2014) Shelly J. Krebs et al.   PLoS One

A critical question for HIV vaccine development: Which antibodies to induce?

(2014) S. Zolla-Pazner   SCIENCE

Autoreactivity in HIV-1 broadly neutralizing antibodies

(2014) Laurent Verkoczy et al.   Current Opinion in HIV and AIDS

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

Quantitative analysis of mammalian GIRK2 channel regulation by G proteins, the signaling lipid PIP2 and Na+ in a reconstituted system

(2014) Weiwei Wang et al.   eLife

Somatic Mutations of the Immunoglobulin Framework Are Generally Required for Broad and Potent HIV-1 Neutralization

(2013) Florian Klein et al.   CELL

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

(2013) Andrew L. Ferguson et al.   IMMUNITY

HIV-1 neutralizing antibodies: understanding nature's pathways

(2013) John R. Mascola et al.   IMMUNOLOGICAL REVIEWS

Induction of HIV-1 Broad Neutralizing Antibodies in 2F5 Knock-in Mice: Selection against Membrane Proximal External Region-Associated Autoreactivity Limits T-Dependent Responses

(2013) L. Verkoczy 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

Antibody-mediated immunotherapy of macaques chronically infected with SHIV suppresses viraemia

(2013) Masashi Shingai et al.   NATURE

Therapeutic efficacy of potent neutralizing HIV-1-specific monoclonal antibodies in SHIV-infected rhesus monkeys

(2013) Dan H. Barouch et al.   NATURE

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

(2013) Karthik Shekhar et al.   PHYSICAL REVIEW E

Crystal Structure of a Soluble Cleaved HIV-1 Envelope Trimer

(2013) J.-P. Julien et al.   SCIENCE

The Antibody Response against HIV-1

(2013) J. Overbaugh et al.   Cold Spring Harbor Perspectives in Medicine

A Blueprint for HIV Vaccine Discovery

(2012) Dennis R. Burton et al.   Cell Host & Microbe

Broad neutralization by a combination of antibodies recognizing the CD4 binding site and a new conformational epitope on the HIV-1 envelope protein

(2012) Florian Klein et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

HIV therapy by a combination of broadly neutralizing antibodies in humanized mice

(2012) Florian Klein et al.   NATURE

Mechanism of Neutralization by the Broadly Neutralizing HIV-1 Monoclonal Antibody VRC01

(2011) Y. Li et al.   JOURNAL OF VIROLOGY

Profound early control of highly pathogenic SIV by an effector memory T-cell vaccine

(2011) Scott G. Hansen et al.   NATURE

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

Relationship between Functional Profile of HIV-1 Specific CD8 T Cells and Epitope Variability with the Selection of Escape Mutants in Acute HIV-1 Infection

(2011) Guido Ferrari et al.   PLoS Pathogens

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

(2010) J. da Silva et al.   GENETICS

Maximum entropy models for antibody diversity

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

Identification of a Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Variant Resistant to Cold Inactivation

(2009) A. Kassa et al.   JOURNAL OF VIROLOGY

Effector memory T cell responses are associated with protection of rhesus monkeys from mucosal simian immunodeficiency virus challenge

(2009) Scott G Hansen et al.   NATURE MEDICINE

Structure of HIV-1 gp120 with gp41-interactive region reveals layered envelope architecture and basis of conformational mobility

(2009) M. Pancera et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

HIV-1 Broadly Neutralizing Antibody Extracts Its Epitope from a Kinked gp41 Ectodomain Region on the Viral Membrane

(2008) Zhen-Yu J. Sun et al.   IMMUNITY

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