Structural topology defines protective CD8+ T cell epitopes in the HIV proteome

An optimal distance cutoff for contact-based Protein Structure Networks using side-chain centers of mass

(2017) Juan Salamanca Viloria et al.   Scientific Reports

HIV-1 epitopes presented by MHC class I types associated with superior immune containment of viremia have highly constrained fitness landscapes

(2017) Aleksandr M. Gorin et al.   PLoS Pathogens

Molecular Determinants of Mutant Phenotypes, Inferred from Saturation Mutagenesis Data

(2016) Arti Tripathi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cryo-EM structure of a CD4-bound open HIV-1 envelope trimer reveals structural rearrangements of the gp120 V1V2 loop

(2016) Haoqing Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Systematic Mutant Analyses Elucidate General and Client-Specific Aspects of Hsp90 Function

(2016) Parul Mishra et al.   Cell Reports

Differences in the Selection Bottleneck between Modes of Sexual Transmission Influence the Genetic Composition of the HIV-1 Founder Virus

(2016) Damien C. Tully et al.   PLoS Pathogens

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into the trimeric HIV-1 envelope glycoprotein structure

(2015) Andrew B. Ward et al.   TRENDS IN BIOCHEMICAL SCIENCES

Systematic Mapping of Protein Mutational Space by Prolonged Drift Reveals the Deleterious Effects of Seemingly Neutral Mutations

(2015) Liat Rockah-Shmuel et al.   PLoS Computational Biology

CD8+ T-cell Cytotoxic Capacity Associated with Human Immunodeficiency Virus-1 Control Can Be Mediated through Various Epitopes and Human Leukocyte Antigen Types

(2015) Stephen A. Migueles et al.   EBioMedicine

A Comprehensive Biophysical Description of Pairwise Epistasis throughout an Entire Protein Domain

(2014) C. Anders Olson et al.   CURRENT BIOLOGY

The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development

(2014) Robert J O’Connell et al.   Expert Review of Vaccines

HIV Control Is Mediated in Part by CD8+ T-Cell Targeting of Specific Epitopes

(2014) F. Pereyra et al.   JOURNAL OF VIROLOGY

Comprehensive mutational scanning of a kinasein vivoreveals substrate-dependent fitness landscapes

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

A Quantitative High-Resolution Genetic Profile Rapidly Identifies Sequence Determinants of Hepatitis C Viral Fitness and Drug Sensitivity

(2014) Hangfei Qi et al.   PLoS Pathogens

HIV escape mutations occur preferentially at HLA-binding sites of CD8 T-cell epitopes

(2013) Corine Bronke et al.   AIDS

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

(2013) Andrew L. Ferguson et al.   IMMUNITY

Analyses of the Effects of All Ubiquitin Point Mutants on Yeast Growth Rate

(2013) Benjamin P. Roscoe et al.   JOURNAL OF MOLECULAR BIOLOGY

HIV-1 Conserved-Element Vaccines: Relationship between Sequence Conservation and Replicative Capacity

(2013) M. Rolland et al.   JOURNAL OF VIROLOGY

Fitness Costs of Mutations at the HIV-1 Capsid Hexamerization Interface

(2013) Siriphan Manocheewa et al.   PLoS One

Maximum Allowed Solvent Accessibilites of Residues in Proteins

(2013) Matthew Z. Tien et al.   PLoS One

Extreme Genetic Fragility of the HIV-1 Capsid

(2013) Suzannah J. Rihn et al.   PLoS Pathogens

High-dimensional immunomonitoring models of HIV-1-specific CD8 T-cell responses accurately identify subjects achieving spontaneous viral control

(2012) Z. M. Ndhlovu et al.   BLOOD

De novo assembly of highly diverse viral populations

(2012) Xiao Yang et al.   BMC GENOMICS

Degenerate T-cell Recognition of Peptides on MHC Molecules Creates Large Holes in the T-cell Repertoire

(2012) Jorg J. A. Calis et al.   PLoS Computational Biology

Whole Genome Deep Sequencing of HIV-1 Reveals the Impact of Early Minor Variants Upon Immune Recognition During Acute Infection

(2012) Matthew R. Henn et al.   PLoS Pathogens

RING: networking interacting residues, evolutionary information and energetics in protein structures

(2011) A. J. M. Martin et al.   BIOINFORMATICS

Atomic-level modelling of the HIV capsid

(2011) Owen Pornillos et al.   NATURE

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

Salt bridges: Geometrically specific, designable interactions

(2010) Jason E. Donald et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Major Genetic Determinants of HIV-1 Control Affect HLA Class I Peptide Presentation

(2010)   SCIENCE

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

Lytic Granule Loading of CD8+ T Cells Is Required for HIV-Infected Cell Elimination Associated with Immune Control

(2008) Stephen A. Migueles et al.   IMMUNITY

Satisfaction of hydrogen-bonding potential influences the conservation of polar sidechains

(2008) Catherine L. Worth et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS