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

A benchmark study on error-correction by read-pairing and tag-clustering in amplicon-based deep sequencing

(2016) Tian-Hao Zhang et al.   BMC GENOMICS

Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B, and G

(2016) Guillaume B.E. Stewart-Jones et al.   CELL

A Prominent Site of Antibody Vulnerability on HIV Envelope Incorporates a Motif Associated with CCR5 Binding and Its Camouflaging Glycans

(2016) Devin Sok et al.   IMMUNITY

HIV Vaccine Design to Target Germline Precursors of Glycan-Dependent Broadly Neutralizing Antibodies

(2016) Jon M. Steichen et al.   IMMUNITY

Buffering deleterious polymorphisms in highly constrained parts of HIV-1 envelope by flexible regions

(2016) Romain Gasser et al.   Retrovirology

HIV-1 broadly neutralizing antibody precursor B cells revealed by germline-targeting immunogen

(2016) J. G. Jardine et al.   SCIENCE

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

(2016) Michael Doud et al.   Viruses-Basel

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

(2016) Parul Mishra et al.   Cell Reports

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting

(2016) David Mavor et al.   eLife

Software for the analysis and visualization of deep mutational scanning data

(2015) Jesse D Bloom   BMC BIOINFORMATICS

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

(2015) Michael A. Stiffler et al.   CELL

Immunogenicity of Stabilized HIV-1 Envelope Trimers with Reduced Exposure of Non-neutralizing Epitopes

(2015) Steven W. de Taeye et al.   CELL

Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors

(2015) Tongqing Zhou et al.   CELL

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

The utility of protein structure as a predictor of site-wise dN/dSvaries widely among HIV-1 proteins

(2015) Austin G. Meyer et al.   Journal of the Royal Society Interface

HIV-1 Fitness Cost Associated with Escape from the VRC01 Class of CD4 Binding Site Neutralizing Antibodies

(2015) Rebecca M. Lynch et al.   JOURNAL OF VIROLOGY

Site-Specific Amino Acid Preferences Are Mostly Conserved in Two Closely Related Protein Homologs

(2015) Michael B. Doud et al.   MOLECULAR BIOLOGY AND EVOLUTION

Massively parallel single-amino-acid mutagenesis

(2015) Jacob O Kitzman et al.   NATURE METHODS

Antibody potency relates to the ability to recognize the closed, pre-fusion form of HIV Env

(2015) Miklos Guttman et al.   Nature Communications

Extremely High Mutation Rate of HIV-1 In Vivo

(2015) José M. Cuevas et al.   PLOS BIOLOGY

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

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

Population genomics of intrapatient HIV-1 evolution

(2015) Fabio Zanini et al.   eLife

Massively Parallel Functional Analysis of BRCA1 RING Domain Variants

(2015) Lea M. Starita et al.   GENETICS

Pyvolve: A Flexible Python Module for Simulating Sequences along Phylogenies

(2015) Stephanie J. Spielman et al.   PLoS One

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

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

Viewing Protein Fitness Landscapes Through a Next-Gen Lens

(2014) J. I. Boucher et al.   GENETICS

Broadly Neutralizing HIV Antibodies Define a Glycan-Dependent Epitope on the Prefusion Conformation of gp41 on Cleaved Envelope Trimers

(2014) Emilia Falkowska et al.   IMMUNITY

Structural Delineation of a Quaternary, Cleavage-Dependent Epitope at the gp41-gp120 Interface on Intact HIV-1 Env Trimers

(2014) Claudia Blattner et al.   IMMUNITY

An Experimentally Informed Evolutionary Model Improves Phylogenetic Fit to Divergent Lactamase Homologs

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) Jinghe Huang et al.   NATURE

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

(2014) Marie Pancera et al.   NATURE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

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

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

High-throughput profiling of point mutations across the HIV-1 genome

(2014) Laith Q Al-Mawsawi et al.   Retrovirology

Antibody 8ANC195 Reveals a Site of Broad Vulnerability on the HIV-1 Envelope Spike

(2014) Louise Scharf et al.   Cell Reports

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

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan 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

Replication-Competent Noninduced Proviruses in the Latent Reservoir Increase Barrier to HIV-1 Cure

(2013) Ya-Chi Ho et al.   CELL

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

Quantifying Selection against Synonymous Mutations in HIV-1 env Evolution

(2013) F. Zanini et al.   JOURNAL OF VIROLOGY

Maximum Allowed Solvent Accessibilites of Residues in Proteins

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

A systematic study of the N-glycosylation sites of HIV-1 envelope protein on infectivity and antibody-mediated neutralization

(2013) Wenbo Wang et al.   Retrovirology

The Antibody Response against HIV-1

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

A serine sensor for multicellularity in a bacterium

(2013) Arvind R Subramaniam et al.   eLife

The spatial architecture of protein function and adaptation

(2012) Richard N. McLaughlin Jr et al.   NATURE

Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution

(2012) K. E. Langergraber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The HIV-1 Rev response element

(2012) Jason Fernandes et al.   RNA Biology

Exploring the Complexity of the HIV-1 Fitness Landscape

(2012) Roger D. Kouyos et al.   PLoS Genetics

The Relationship Between Relative Solvent Accessibility and Evolutionary Rate in Protein Evolution

(2011) Duncan C. Ramsey et al.   GENETICS

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

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

The Fitness Effects of Synonymous Mutations in DNA and RNA Viruses

(2011) José M. Cuevas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde 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

The role of unintegrated DNA in HIV infection

(2011) Richard D Sloan et al.   Retrovirology

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

(2010) J. da Silva et al.   GENETICS

Nature, Position, and Frequency of Mutations Made in a Single Cycle of HIV-1 Replication

(2010) M. E. Abram et al.   JOURNAL OF VIROLOGY

Parallel, tag-directed assembly of locally derived short sequence reads

(2010) Joseph B Hiatt et al.   NATURE METHODS

High-resolution mapping of protein sequence-function relationships

(2010) Douglas M Fowler et al.   NATURE METHODS

Quantitative profiling of the full APOBEC3 mRNA repertoire in lymphocytes and tissues: implications for HIV-1 restriction

(2010) Eric W. Refsland et al.   NUCLEIC ACIDS RESEARCH

Structural Basis for Broad and Potent Neutralization of HIV-1 by Antibody VRC01

(2010) T. Zhou et al.   SCIENCE

Architecture and secondary structure of an entire HIV-1 RNA genome

(2009) Joseph M. Watts et al.   NATURE

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

Specificity of the autologous neutralizing antibody response

(2009) Penny L Moore et al.   Current Opinion in HIV and AIDS

Only Five of 10 Strictly Conserved Disulfide Bonds Are Essential for Folding and Eight for Function of the HIV-1 Envelope Glycoprotein

(2008) Eelco van Anken et al.   MOLECULAR BIOLOGY OF THE CELL