Author: Jesse D Bloom

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Preprints

Antibodies to the SARS-CoV-2 receptor-binding domain that maximize breadth and resistance to viral escape

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The SARS-CoV-2 mRNA-1273 vaccine elicits more RBD-focused neutralization, but with broader antibody binding within the RBD

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Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody

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Emergence and spread of a SARS-CoV-2 variant through Europe in the summer of 2020

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Comprehensive mapping of mutations to the SARS-CoV-2 receptor-binding domain that affect recognition by polyclonal human serum antibodies

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Neutralizing antibodies correlate with protection from SARS-CoV-2 in humans during a fishery vessel outbreak with high attack rate

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A human coronavirus evolves antigenically to escape antibody immunity

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Deep mutational scanning of SARS-CoV-2 receptor binding domain reveals constraints on folding and ACE2 binding

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Protocol and reagents for pseudotyping lentiviral particles with SARS-CoV-2 Spike protein for neutralization assays

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Prospective mapping of viral mutations that escape antibodies used to treat COVID-19

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Complete mapping of mutations to the SARS-CoV-2 spike receptor-binding domain that escape antibody recognition

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  • Site-wide: 2,802
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  • Site-wide: 1,313
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Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak

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Single-cell virus sequencing of influenza infections that trigger innate immunity

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Dynamics of neutralizing antibody titers in the months after SARS-CoV-2 infection

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Mutational escape from the polyclonal antibody response to SARS-CoV-2 infection is largely shaped by a single class of antibodies

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An experimentally determined evolutionary model dramatically improves phylogenetic fit

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Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models

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Genetic and structural basis for recognition of SARS-CoV-2 spike protein by a two-antibody cocktail

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Extreme heterogeneity of influenza virus infection in single cells

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Expanding the Atlas of Functional Missense Variation for Human Genes

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Complete map of SARS-CoV-2 RBD mutations that escape the monoclonal antibody LY-CoV555 and its cocktail with LY-CoV016

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The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

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Reconciling disparate estimates of viral genetic diversity during human influenza infections

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An experimentally informed evolutionary model improves phylogenetic fit to divergent lactamase homologs

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Comprehensive profiling of translation initiation in influenza virus infected cells

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Software for the analysis and visualization of deep mutational scanning data

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Attenuated influenza virions expressing the SARS-CoV-2 receptor-binding domain induce neutralizing antibodies in mice

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Experimental estimation of the effects of all amino-acid mutations to HIV Env

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Linking influenza virus evolution within and between human hosts

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  • Site-wide: 87,283
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An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies

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  • Site-wide: 31,567
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  • Site-wide: 102,584
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Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants

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Site-specific amino-acid preferences are mostly conserved in two closely related protein homologs

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Mapping person-to-person variation in viral mutations that escape polyclonal serum targeting influenza hemagglutinin

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  • Site-wide: 32,897
  • In microbiology: 1,955
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  • Site-wide: 108,511

Complete mapping of viral escape from neutralizing antibodies

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  • Site-wide: 33,727
  • In microbiology: 2,016
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  • Site-wide: 102,979

Phage-DMS: a comprehensive method for fine mapping of antibody epitopes

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Quantifying the effects of single mutations on viral escape from broad and narrow antibodies to an H1 influenza hemagglutinin

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  • Site-wide: 37,793
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Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody

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  • Site-wide: 38,989
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  • Site-wide: 88,499

Comprehensive mapping of avian influenza polymerase adaptation to the human host

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

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Deep mutational scanning comprehensively maps how Zika envelope protein mutations affect viral growth and antibody escape

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Accurate measurement of the effects of all amino-acid mutations to influenza hemagglutinin

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Mapping mutational effects along the evolutionary landscape of HIV envelope

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  • Site-wide: 49,724
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Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence

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Complete functional mapping of infection- and vaccine-elicited antibodies against the fusion peptide of HIV

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When two are better than one: Modeling the mechanisms of antibody mixtures

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Influenza H3 and H1 hemagglutinins have different genetic barriers for resistance to broadly neutralizing stem antibodies

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Identification of antibodies targeting the H3N2 hemagglutinin receptor binding site following vaccination of humans

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phydms: Software for phylogenetic analyses informed by deep mutational scanning

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Estimating the frequency of multiplets in single-cell RNA sequencing from cell-mixing experiments

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alignparse: A Python package for parsing complex features from high-throughput long-read sequencing

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Cooperating H3N2 influenza virus variants are not detectable in primary clinical samples

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A public broadly neutralizing antibody class targets a membrane-proximal anchor epitope of influenza virus hemagglutinin

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dms-view: Interactive visualization tool for deep mutational scanning data

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Sera from individuals with narrowly focused influenza virus antibodies rapidly select viral escape mutations in ovo

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Massively parallel profiling of HIV-1 resistance to the fusion inhibitor enfuvirtide

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High-resolution mapping of the neutralizing and binding specificities of polyclonal rabbit serum elicited by HIV Env trimer immunization

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Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding

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Identification of HIV-1 Envelope Mutations that Enhance Entry Using Macaque CD4 and CCR5

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APOBEC3C tandem domain proteins create super restriction factors against HIV-1

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Functional development of a V3-specific broadly neutralizing antibody isolated from a case of HIV superinfection

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