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Author: Jesse D. Bloom

Rankings

  • All-time downloads: 114,800 (rank: 729 )
  • Categories:
    • bioinformatics: 1,552 (rank: 8,632 (tie) )
    • biophysics: 435 (rank: 10,428 (tie) )
    • evolutionary biology: 8,077 (rank: 256 )
    • genomics: 1,716 (rank: 12,527 (tie) )
    • immunology: 1,841 (rank: 3,699 )
    • infectious diseases: 29,112 (rank: 1,373 (tie) )
    • microbiology: 70,882 (rank: 166 )
    • molecular biology: 1,185 (rank: 4,107 (tie) )

Downloads per author, site-wide

Preprints

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

infectious diseases more details view paper
  • Downloaded 24,871 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 22,942 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 10,103 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 9,497 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 7,193 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 4,089 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 3,282 times
  • Download rankings, all-time:
    • 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

infectious diseases more details view paper
  • Downloaded 2,733 times
  • Download rankings, all-time:
    • Site-wide: 4,114
    • In infectious diseases: 652
  • Year to date:
    • Site-wide: 26,579
  • Since beginning of last month:
    • Site-wide: 17,502

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

microbiology more details view paper
  • Downloaded 2,344 times
  • Download rankings, all-time:
    • 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

infectious diseases more details view paper
  • Downloaded 1,508 times
  • Download rankings, all-time:
    • 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

evolutionary biology more details view paper
  • Downloaded 1,488 times
  • Download rankings, all-time:
    • 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

evolutionary biology more details view paper
  • Downloaded 1,374 times
  • Download rankings, all-time:
    • 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

genomics more details view paper
  • Downloaded 1,340 times
  • Download rankings, all-time:
    • 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

molecular biology more details view paper
  • Downloaded 1,185 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • Downloaded 1,087 times
  • Download rankings, all-time:
    • 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

evolutionary biology more details view paper
  • Downloaded 1,065 times
  • Download rankings, all-time:
    • 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

evolutionary biology more details view paper
  • Downloaded 1,043 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • 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

bioinformatics more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

immunology more details view paper
  • 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

evolutionary biology more details view paper
  • 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

evolutionary biology more details view paper
  • 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

microbiology more details view paper
  • 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

evolutionary biology more details view paper
  • 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

microbiology more details view paper
  • 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

immunology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

evolutionary biology more details view paper
  • 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

immunology more details view paper
  • 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

biophysics more details view paper
  • 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

evolutionary biology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

genomics more details view paper
  • 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

microbiology more details view paper
  • 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

bioinformatics more details view paper
  • 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

bioinformatics more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • Downloaded 222 times
  • Download rankings, all-time:
    • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

microbiology more details view paper
  • 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

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