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List of works by Jesse D. Bloom

A computational-experimental approach identifies mutations that enhance surface expression of an oseltamivir-resistant influenza neuraminidase

scientific article

A diverse family of thermostable cytochrome P450s created by recombination of stabilizing fragments

scientific article

A mutant influenza virus that uses an N1 neuraminidase as the receptor-binding protein

scientific article published on 11 September 2013

A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike

scientific article published in 2023

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

scientific article published in 2022

APOBEC3C Tandem Domain Proteins Create Super Restriction Factors against HIV-1

scientific article published on 28 April 2020

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

scientific article published on 03 June 2016

An antigenic atlas of HIV-1 escape from broadly neutralizing antibodies

article

An experimentally determined evolutionary model dramatically improves phylogenetic fit.

scientific article

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

scientific article

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization

scientific article published on 01 July 2019

Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets ⬇️

scientific article published on October 2, 2003

Attenuated Influenza Virions Expressing the SARS-CoV-2 Receptor-Binding Domain Induce Neutralizing Antibodies in Mice

scientific article published on 05 September 2020

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

scientific article published on 13 August 2020

Bidirectional amyloid fiber growth for a yeast prion determinant.

scientific article

Breaking proteins with mutations: threads and thresholds in evolution

scientific article published on 30 January 2007

Broad protection against influenza infection by vectored immunoprophylaxis in mice

scientific article

Broadly neutralizing antibodies target a haemagglutinin anchor epitope

scientific article published on 23 December 2021

Characterization of Influenza B Virus Variants with Reduced Neuraminidase Inhibitor Susceptibility

scientific article published on 24 October 2018

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

article

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

scientific article published on 10 September 2020

Complete mapping of viral escape from neutralizing antibodies

scientific article

Comprehensive mapping of HIV-1 escape from a broadly neutralizing antibody

article

Comprehensive mapping of adaptation of the avian influenza polymerase protein PB2 to humans

scientific article published on 30 April 2019

Comprehensive mapping of avian influenza polymerase adaptation to the human host

Comprehensive profiling of translation initiation in influenza virus infected cells

Comprehensive profiling of translation initiation in influenza virus infected cells

scientific article published on 23 January 2019

Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site.

scientific article

Consensus protein design without phylogenetic bias

scientific article

Cooperating H3N2 Influenza Virus Variants Are Not Detectable in Primary Clinical Samples

scientific article published on 3 January 2018

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

Cooperation between distinct viral variants promotes growth of H3N2 influenza in cell culture.

scientific article published on 15 March 2016

Deep Mutational Scan of the Highly Conserved Influenza A Virus M1 Matrix Protein Reveals Substantial Intrinsic Mutational Tolerance

scientific article published on 14 June 2019

Deep Mutational Scanning Comprehensively Maps How Zika Envelope Protein Mutations Affect Viral Growth and Antibody Escape

scientific article published on 13 November 2019

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

scientific article

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

scientific article published on 17 June 2020

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

article published in the Proceedings of the National Academy of Sciences of the United States of America

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

Defining the risk of SARS-CoV-2 variants on immune protection

scientific article published on 31 March 2022

Destabilized adaptive influenza variants critical for innate immune system escape are potentiated by host chaperones

scientific article published on 17 September 2018

Determinants of Zika virus host tropism uncovered by deep mutational scanning

scientific article published on 18 March 2019

Different genetic barriers for resistance to HA stem antibodies in influenza H3 and H1 viruses

scientific article published on 01 June 2020

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

scientific article published on 27 November 2020

Enhanced ER proteostasis and temperature differentially impact the mutational tolerance of influenza hemagglutinin

scientific article published on 06 September 2018

Epistatically interacting substitutions are enriched during adaptive protein evolution

scientific article

Estimating the fitness advantage conferred by permissive neuraminidase mutations in recent oseltamivir-resistant A(H1N1)pdm09 influenza viruses

scientific article (publication date: April 2014)

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

article

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

scientific article published in 2018

Evolution favors protein mutational robustness in sufficiently large populations

scientific article

Evolutionary rate depends on number of protein-protein interactions independently of gene expression level: response

scientific article

Evolving strategies for enzyme engineering

scientific article

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

scientific article

Extreme heterogeneity of influenza virus infection in single cells

scientific article published on 16 February 2018

Fitness effects of mutations to SARS-CoV-2 proteins

scientific article published in July 2023

Genetic and structural basis for SARS-CoV-2 variant neutralization by a two-antibody cocktail

scientific article published on 21 September 2021

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

scientific article

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

scientific article published on 21 February 2020

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

scientific article published on 17 January 2017

Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market

scientific article published on 30 December 2023

Improving pandemic influenza risk assessment

scientific article

In the light of directed evolution: pathways of adaptive protein evolution

scientific article

Inferring stabilizing mutations from protein phylogenies: application to influenza hemagglutinin

scientific article

Influenza viruses with receptor-binding N1 neuraminidases occur sporadically in several lineages and show no attenuation in cell culture or mice.

scientific article

Investigate the origins of COVID-19

scientific article

Linking influenza virus evolution within and between human hosts

scientific article published on 01 January 2020

Mapping mutational effects along the evolutionary landscape of HIV envelope

article

Mapping mutational effects along the evolutionary landscape of HIV envelope.

scientific article

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

scientific article published on 27 August 2019

Massively Parallel Profiling of HIV-1 Resistance to the Fusion Inhibitor Enfuvirtide

scientific article published on 15 May 2019

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

article

Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral divergence

scientific article

Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence

article

Mucin biopolymers as broad-spectrum antiviral agents

scientific article published on 21 May 2012

Mutational effects on stability are largely conserved during protein evolution

scientific article published on 09 December 2013

Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution

scientific article

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

scientific article published on 14 August 2020 on medRxiv

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

scientific article published on 21 August 2020 in Journal of Clinical Microbiology

Parallel evolution of influenza across multiple spatiotemporal scales

scientific article

Permissive secondary mutations enable the evolution of influenza oseltamivir resistance

scientific article

Positive Selection in CD8+ T-Cell Epitopes of Influenza Virus Nucleoprotein Revealed by a Comparative Analysis of Human and Swine Viral Lineages

scientific article

Potential antigenic explanation for atypical H1N1 infections among middle-aged adults during the 2013-2014 influenza season

scientific article

Predicting the tolerance of proteins to random amino acid substitution

scientific article

Probing the role of PrP repeats in conformational conversion and amyloid assembly of chimeric yeast prions

scientific article

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

scientific article published on 01 December 2020

Protein stability promotes evolvability

scientific article

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

scientific article published on 24 April 2020

Reconciling disparate estimates of viral genetic diversity during human influenza infections

article

Reconciling disparate estimates of viral genetic diversity during human influenza infections

scientific article published on 01 September 2019

Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic

scientific article published on 14 August 2021

Selection Analysis Identifies Clusters of Unusual Mutational Changes in Omicron Lineage BA.1 That Likely Impact Spike Function

scientific article published on 01 April 2022

Sera from Individuals with Narrowly Focused Influenza Virus Antibodies Rapidly Select Viral Escape Mutations

scientific article published on 12 September 2018

Serological identification of SARS-CoV-2 infections among children visiting a hospital during the initial Seattle outbreak

scientific article published on 01 September 2020

Seroprevalence of SARS-CoV-2 among children visiting a hospital during the initial Seattle outbreak

scientific article published on 28 May 2020

Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity

scientific article published on 28 June 2019

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

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

scientific article

Software for the analysis and visualization of deep mutational scanning data

scientific article

Stability and the evolvability of function in a model protein

scientific article

Stability-mediated epistasis constrains the evolution of an influenza protein

scientific article published in 2013

Structural determinants of the rate of protein evolution in yeast.

scientific article

Structure-guided recombination creates an artificial family of cytochromes P450.

scientific article

The effect of single mutations in Zika virus envelope on escape from broadly neutralizing antibodies

scientific article published on 30 November 2023

The elongation of yeast prion fibers involves separable steps of association and conversion

scholarly article

The global spread of drug-resistant influenza

scientific article

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

scientific article

The interface of protein structure, protein biophysics, and molecular evolution

scientific article

Thermodynamic prediction of protein neutrality

scientific article

Thermodynamics of neutral protein evolution

scientific article

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

scientific article published on 04 May 2020

Why highly expressed proteins evolve slowly

scientific article

Within-Host Evolution of Human Influenza Virus.

scientific article

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

scientific article published on 11 December 2019

dms-viz: Structure-informed visualizations for deep mutational scanning and other mutation-based datasets

scientific article published on 17 July 2024

phydms: Software for phylogenetic analyses informed by deep mutational scanning

scholarly article published 29 March 2017

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