Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

How single mutations affect viral escape from broad and narrow antibodies to H1 influenza hemagglutinin

(2018) Michael B. Doud et al.   Nature Communications

Mapping mutational effects along the evolutionary landscape of HIV envelope

(2018) Hugh K Haddox et al.   eLife

Alternative evolutionary histories in the sequence space of an ancient protein

(2017) Tyler N. Starr et al.   NATURE

A structural explanation for the low effectiveness of the seasonal influenza H3N2 vaccine

(2017) Nicholas C. Wu et al.   PLoS Pathogens

Complete mapping of viral escape from neutralizing antibodies

(2017) Michael B. Doud et al.   PLoS Pathogens

Deep mutational scanning identifies sites in influenza nucleoprotein that affect viral inhibition by MxA

(2017) Orr Ashenberg et al.   PLoS Pathogens

phydms: software for phylogenetic analyses informed by deep mutational scanning

(2017) Sarah K. Hilton et al.   PeerJ

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

Epistasis in protein evolution

(2016) Tyler N. Starr et al.   PROTEIN SCIENCE

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

(2016) Michael Doud et al.   Viruses-Basel

Identification of Low- and High-Impact Hemagglutinin Amino Acid Substitutions That Drive Antigenic Drift of Influenza A(H1N1) Viruses

(2016) William T. Harvey et al.   PLoS Pathogens

Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody

(2016) Ning Chai et al.   PLoS Pathogens

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

Selection of antigenically advanced variants of seasonal influenza viruses

(2016) Chengjun Li et al.   Nature Microbiology

nextflu: real-time tracking of seasonal influenza virus evolution in humans

(2015) Richard A. Neher et al.   BIOINFORMATICS

Software for the analysis and visualization of deep mutational scanning data

(2015) Jesse D Bloom   BMC BIOINFORMATICS

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

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

Global circulation patterns of seasonal influenza viruses vary with antigenic drift

(2015) Trevor Bedford et al.   NATURE

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

Structure and receptor binding preferences of recombinant human A(H3N2) virus hemagglutinins

(2015) Hua Yang et al.   VIROLOGY

Identification of Hemagglutinin Residues Responsible for H3N2 Antigenic Drift during the 2014–2015 Influenza Season

(2015) Benjamin S. Chambers et al.   Cell Reports

High-resolution genetic profile of viral genomes: why it matters

(2015) Hangfei Qi et al.   Current Opinion in Virology

The effects of a deleterious mutation load on patterns of influenza A/H3N2's antigenic evolution in humans

(2015) Katia Koelle et al.   eLife

An Experimentally Determined Evolutionary Model Dramatically Improves Phylogenetic Fit

(2014) Jesse D. Bloom   MOLECULAR BIOLOGY AND EVOLUTION

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

(2014) Michael J. Harms et al.   NATURE

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Influenza hemagglutinin stem-fragment immunogen elicits broadly neutralizing antibodies and confers heterologous protection

(2014) V. V. A. Mallajosyula et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Receptor mimicry by antibody F045–092 facilitates universal binding to the H3 subtype of influenza virus

(2014) Peter S. Lee et al.   Nature Communications

High-throughput profiling of influenza A virus hemagglutinin gene at single-nucleotide resolution

(2014) Nicholas C. Wu et al.   Scientific Reports

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

(2014) Bargavi Thyagarajan et al.   eLife

Predicting evolution from the shape of genealogical trees

(2014) Richard A Neher et al.   eLife

Broadly neutralizing antibodies against influenza viruses

(2013) Nick S. Laursen et al.   ANTIVIRAL RESEARCH

Most Influenza A Virions Fail To Express at Least One Essential Viral Protein

(2013) C. B. Brooke et al.   JOURNAL OF VIROLOGY

A Mutant Influenza Virus That Uses an N1 Neuraminidase as the Receptor-Binding Protein

(2013) Kathryn A. Hooper et al.   JOURNAL OF VIROLOGY

Comparison of Mutation Patterns in Full-Genome A/H3N2 Influenza Sequences Obtained Directly from Clinical Samples and the Same Samples after a Single MDCK Passage

(2013) Hong Kai Lee et al.   PLoS One

Maximum Allowed Solvent Accessibilites of Residues in Proteins

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

Genome-wide mutagenesis of influenza virus reveals unique plasticity of the hemagglutinin and NS1 proteins

(2013) N. S. Heaton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epistasis Among Adaptive Mutations in Deer Mouse Hemoglobin

(2013) C. Natarajan et al.   SCIENCE

Substitutions Near the Receptor Binding Site Determine Major Antigenic Change During Influenza Virus Evolution

(2013) B. F. Koel et al.   SCIENCE

Using Sequence Data To Infer the Antigenicity of Influenza Virus

(2013) H. Sun et al.   mBio

Influenza Virus Reassortment Occurs with High Frequency in the Absence of Segment Mismatch

(2013) Nicolle Marshall et al.   PLoS Pathogens

Stability-mediated epistasis constrains the evolution of an influenza protein

(2013) Lizhi Ian Gong et al.   eLife

Clonal Interference in the Evolution of Influenza

(2012) N. Strelkowa et al.   GENETICS

Immunodominance of Antigenic Site B over Site A of Hemagglutinin of Recent H3N2 Influenza Viruses

(2012) Lyubov Popova et al.   PLoS One

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

Strength and tempo of selection revealed in viral gene genealogies

(2011) Trevor Bedford et al.   BMC EVOLUTIONARY BIOLOGY

Upstream start codon in segment 4 of North American H2 avian influenza A viruses

(2011) Geneviève Girard et al.   INFECTION GENETICS AND EVOLUTION

The Genomic Rate of Molecular Adaptation of the Human Influenza A Virus

(2011) Samir Bhatt et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cleavage of Influenza Virus Hemagglutinin by Airway Proteases TMPRSS2 and HAT Differs in Subcellular Localization and Susceptibility to Protease Inhibitors

(2010) E. Bottcher-Friebertshauser et al.   JOURNAL OF VIROLOGY

Modifications to the Hemagglutinin Cleavage Site Control the Virulence of a Neurotropic H1N1 Influenza Virus

(2010) X. Sun et al.   JOURNAL OF VIROLOGY

Permissive Secondary Mutations Enable the Evolution of Influenza Oseltamivir Resistance

(2010) J. D. Bloom et al.   SCIENCE

Quasispecies Theory and the Behavior of RNA Viruses

(2010) Adam S. Lauring et al.   PLoS Pathogens

Recent Human Influenza A/H3N2 Virus Evolution Driven by Novel Selection Factors in Addition to Antigenic Drift

(2009) Matthew J. Memoli et al.   JOURNAL OF INFECTIOUS DISEASES

Homologous Recombination Is Very Rare or Absent in Human Influenza A Virus

(2008) M. F. Boni et al.   JOURNAL OF VIROLOGY