Author: Jesse D. Bloom

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Preprints

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

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  • Site-wide: 234
  • In infectious diseases: 91
• Year to date:
  • Site-wide: 1,005
• Since beginning of last month:
  • Site-wide: 779

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

• Downloaded 22,942 times
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  • Site-wide: 257
  • In microbiology: 28
• Year to date:
  • Site-wide: 3
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 10,103 times
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  • Site-wide: 688
  • In microbiology: 73
• Year to date:
  • Site-wide: 389
• Since beginning of last month:
  • Site-wide: 819

A human coronavirus evolves antigenically to escape antibody immunity

• Downloaded 9,497 times
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  • Site-wide: 744
  • In microbiology: 76
• Year to date:
  • Site-wide: 104
• Since beginning of last month:
  • Site-wide: 19

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

• Downloaded 7,193 times
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  • Site-wide: 1,073
  • In microbiology: 99
• Year to date:
  • Site-wide: 1,115
• Since beginning of last month:
  • Site-wide: 2,127

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

• Downloaded 4,089 times
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  • Site-wide: 2,306
  • In microbiology: 163
• Year to date:
  • Site-wide: 126
• Since beginning of last month:
  • Site-wide: 64

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

• Downloaded 3,282 times
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  • Site-wide: 3,197
  • In microbiology: 208
• Year to date:
  • Site-wide: 479
• Since beginning of last month:
  • Site-wide: 1,490

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

• Downloaded 2,733 times
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  • Site-wide: 4,114
  • In infectious diseases: 652
• Year to date:
  • Site-wide: 26,579
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  • Site-wide: 17,502

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

• Downloaded 2,344 times
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  • Site-wide: 5,209
  • In microbiology: 301
• Year to date:
  • Site-wide: 67,901
• Since beginning of last month:
  • Site-wide: 45,403

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

• Downloaded 1,508 times
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  • Site-wide: 10,001
  • In infectious diseases: 1,092
• Year to date:
  • Site-wide: 8,854
• Since beginning of last month:
  • Site-wide: 4,236

An experimentally determined evolutionary model dramatically improves phylogenetic fit

• Downloaded 1,488 times
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  • Site-wide: 10,194
  • In evolutionary biology: 351
• Year to date:
  • Site-wide: 47,446
• Since beginning of last month:
  • Site-wide: 76,589

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

• Downloaded 1,374 times
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  • Site-wide: 11,503
  • In evolutionary biology: 422
• Year to date:
  • Site-wide: 75,989
• Since beginning of last month:
  • Site-wide: 99,535

Extreme heterogeneity of influenza virus infection in single cells

• Downloaded 1,340 times
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  • Site-wide: 11,938
  • In genomics: 1,337
• Year to date:
  • Site-wide: 81,051
• Since beginning of last month:
  • Site-wide: 94,463

Expanding the Atlas of Functional Missense Variation for Human Genes

• Downloaded 1,185 times
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  • Site-wide: 14,358
  • In molecular biology: 401
• Year to date:
  • Site-wide: 103,505
• Since beginning of last month:
  • Site-wide: 70,940

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

• Downloaded 1,087 times
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  • Site-wide: 16,375
  • In microbiology: 918
• Year to date:
  • Site-wide: 96,278
• Since beginning of last month:
  • Site-wide: 87,743

Reconciling disparate estimates of viral genetic diversity during human influenza infections

• Downloaded 1,065 times
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  • Site-wide: 16,877
  • In evolutionary biology: 717
• Year to date:
  • Site-wide: 66,817
• Since beginning of last month:
  • Site-wide: 91,155

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

• Downloaded 1,043 times
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  • Site-wide: 17,378
  • In evolutionary biology: 744
• Year to date:
  • Site-wide: 91,652
• Since beginning of last month:
  • Site-wide: 120,838

Comprehensive profiling of translation initiation in influenza virus infected cells

• Downloaded 913 times
• Download rankings, all-time:
  • Site-wide: 21,147
  • In microbiology: 1,198
• Year to date:
  • Site-wide: 30,416
• Since beginning of last month:
  • Site-wide: 46,736

Software for the analysis and visualization of deep mutational scanning data

• Downloaded 887 times
• Download rankings, all-time:
  • Site-wide: 22,095
  • In bioinformatics: 2,694
• Year to date:
  • Site-wide: 69,356
• Since beginning of last month:
  • Site-wide: 102,633

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

• Downloaded 798 times
• Download rankings, all-time:
  • Site-wide: 25,640
  • In microbiology: 1,495
• Year to date:
  • Site-wide: 8,263
• Since beginning of last month:
  • Site-wide: 20,658

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

• Downloaded 783 times
• Download rankings, all-time:
  • Site-wide: 26,297
  • In microbiology: 1,535
• Year to date:
  • Site-wide: 116,346
• Since beginning of last month:
  • Site-wide: 67,287

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

• Downloaded 736 times
• Download rankings, all-time:
  • Site-wide: 28,692
  • In immunology: 765
• Year to date:
  • Site-wide: 78,400
• Since beginning of last month:
  • Site-wide: 101,018

Linking influenza virus evolution within and between human hosts

• Downloaded 735 times
• Download rankings, all-time:
  • Site-wide: 28,774
  • In evolutionary biology: 1,451
• Year to date:
  • Site-wide: 67,955
• Since beginning of last month:
  • Site-wide: 73,064

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

• Downloaded 733 times
• Download rankings, all-time:
  • Site-wide: 28,861
  • In evolutionary biology: 1,457
• Year to date:
  • Site-wide: 54,877
• Since beginning of last month:
  • Site-wide: 42,377

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

• Downloaded 717 times
• Download rankings, all-time:
  • Site-wide: 29,740
  • In microbiology: 1,768
• Year to date:
  • Site-wide: 26,034
• Since beginning of last month:
  • Site-wide: 104,704

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

• Downloaded 715 times
• Download rankings, all-time:
  • Site-wide: 29,871
  • In evolutionary biology: 1,526
• Year to date:
  • Site-wide: 87,848
• Since beginning of last month:
  • Site-wide: 95,752

Complete mapping of viral escape from neutralizing antibodies

• Downloaded 700 times
• Download rankings, all-time:
  • Site-wide: 30,714
  • In microbiology: 1,820
• Year to date:
  • Site-wide: 93,193
• Since beginning of last month:
  • Site-wide: 88,488

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

• Downloaded 644 times
• Download rankings, all-time:
  • Site-wide: 34,372
  • In immunology: 909
• Year to date:
  • Site-wide: 36,207
• Since beginning of last month:
  • Site-wide: 64,844

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

• Downloaded 637 times
• Download rankings, all-time:
  • Site-wide: 34,883
  • In microbiology: 2,075
• Year to date:
  • Site-wide: 110,346
• Since beginning of last month:
  • Site-wide: 76,585

Comprehensive mapping of avian influenza polymerase adaptation to the human host

• Downloaded 635 times
• Download rankings, all-time:
  • Site-wide: 34,960
  • In microbiology: 2,085
• Year to date:
  • Site-wide: 66,101
• Since beginning of last month:
  • Site-wide: 113,686

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

• Downloaded 628 times
• Download rankings, all-time:
  • Site-wide: 35,531
  • In microbiology: 2,132
• Year to date:
  • Site-wide: 76,401
• Since beginning of last month:
  • Site-wide: 78,250

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

• Downloaded 595 times
• Download rankings, all-time:
  • Site-wide: 37,990
  • In microbiology: 2,317
• Year to date:
  • Site-wide: 110,972
• Since beginning of last month:
  • Site-wide: 92,047

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

• Downloaded 533 times
• Download rankings, all-time:
  • Site-wide: 43,640
  • In microbiology: 2,710
• Year to date:
  • Site-wide: 90,520
• Since beginning of last month:
  • Site-wide: 51,148

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

• Downloaded 532 times
• Download rankings, all-time:
  • Site-wide: 43,715
  • In microbiology: 2,721
• Year to date:
  • Site-wide: 108,861
• Since beginning of last month:
  • Site-wide: 74,742

Mapping mutational effects along the evolutionary landscape of HIV envelope

• Downloaded 523 times
• Download rankings, all-time:
  • Site-wide: 44,627
  • In microbiology: 2,799
• Year to date:
  • Site-wide: 102,958
• Since beginning of last month:
  • Site-wide: 101,532

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

• Downloaded 494 times
• Download rankings, all-time:
  • Site-wide: 47,690
  • In evolutionary biology: 2,689
• Year to date:
  • Site-wide: 87,398
• Since beginning of last month:
  • Site-wide: 114,483

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

• Downloaded 461 times
• Download rankings, all-time:
  • Site-wide: 51,558
  • In immunology: 1,365
• Year to date:
  • Site-wide: 106,499
• Since beginning of last month:
  • Site-wide: 116,318

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

• Downloaded 435 times
• Download rankings, all-time:
  • Site-wide: 54,962
  • In biophysics: 1,947
• Year to date:
  • Site-wide: 59,295
• Since beginning of last month:
  • Site-wide: 89,489

phydms: Software for phylogenetic analyses informed by deep mutational scanning

• Downloaded 430 times
• Download rankings, all-time:
  • Site-wide: 55,627
  • In evolutionary biology: 3,153
• Year to date:
  • Site-wide: 106,644
• Since beginning of last month:
  • Site-wide: 121,849

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

• Downloaded 426 times
• Download rankings, all-time:
  • Site-wide: 56,065
  • In microbiology: 3,712
• Year to date:
  • Site-wide: 103,054
• Since beginning of last month:
  • Site-wide: 118,030

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

• Downloaded 411 times
• Download rankings, all-time:
  • Site-wide: 58,251
  • In microbiology: 3,882
• Year to date:
  • Site-wide: 60,945
• Since beginning of last month:
  • Site-wide: 47,378

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

• Downloaded 376 times
• Download rankings, all-time:
  • Site-wide: 63,507
  • In genomics: 4,576
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 103,665

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

• Downloaded 361 times
• Download rankings, all-time:
  • Site-wide: 65,969
  • In microbiology: 4,489
• Year to date:
  • Site-wide: 75,900
• Since beginning of last month:
  • Site-wide: 90,826

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

• Downloaded 361 times
• Download rankings, all-time:
  • Site-wide: 65,860
  • In bioinformatics: 6,445
• Year to date:
  • Site-wide: 90,071
• Since beginning of last month:
  • Site-wide: 120,487

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

• Downloaded 304 times
• Download rankings, all-time:
  • Site-wide: 75,884
  • In bioinformatics: 7,080
• Year to date:
  • Site-wide: 79,425
• Since beginning of last month:
  • Site-wide: 33,986

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

• Downloaded 290 times
• Download rankings, all-time:
  • Site-wide: 78,613
  • In microbiology: 5,555
• Year to date:
  • Site-wide: 87,451
• Since beginning of last month:
  • Site-wide: 96,562

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

• Downloaded 222 times
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  • Site-wide: 92,653
  • In microbiology: 6,791
• Year to date:
  • Site-wide: 60,126
• Since beginning of last month:
  • Site-wide: 91,045

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

• Downloaded 190 times
• Download rankings, all-time:
  • Site-wide: 99,537
  • In microbiology: 7,461
• Year to date:
  • Site-wide: 46,376
• Since beginning of last month:
  • Site-wide: 36,461

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

• Downloaded 164 times
• Download rankings, all-time:
  • Site-wide: 104,634
  • In microbiology: 7,904
• Year to date:
  • Site-wide: 71,115
• Since beginning of last month:
  • Site-wide: 106,423

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

• Downloaded 149 times
• Download rankings, all-time:
  • Site-wide: 107,515
  • In microbiology: 8,174
• Year to date:
  • Site-wide: 118,431
• Since beginning of last month:
  • Site-wide: 74,827

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

• Downloaded 138 times
• Download rankings, all-time:
  • Site-wide: 109,452
  • In microbiology: 8,342
• Year to date:
  • Site-wide: 99,866
• Since beginning of last month:
  • Site-wide: 110,897