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Author: Jesse D Bloom

Rankings

  • All-time downloads: 236,912 (rank: 184 )
  • Categories:
    • bioinformatics: 1,609 (rank: 9,113 (tie) )
    • biophysics: 466 (rank: 10,840 (tie) )
    • epidemiology: 78,146 (rank: 168 (tie) )
    • evolutionary biology: 8,247 (rank: 268 )
    • genomics: 1,743 (rank: 13,299 (tie) )
    • immunology: 3,666 (rank: 2,059 (tie) )
    • infectious diseases: 30,175 (rank: 1,542 (tie) )
    • microbiology: 111,640 (rank: 73 )
    • molecular biology: 1,220 (rank: 4,470 (tie) )

Downloads per author, site-wide

Preprints

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

microbiology more details view paper

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

microbiology more details view paper

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Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody

immunology more details view paper

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

epidemiology more details view paper
  • Downloaded 78,146 times
  • Download rankings, all-time:
    • Site-wide: 65
    • In epidemiology: 13
  • Year to date:
    • Site-wide: 102
  • Since beginning of last month:
    • Site-wide: 226

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 52,297 times
  • Download rankings, all-time:
    • Site-wide: 106
    • In microbiology: 9
  • Year to date:
    • Site-wide: 7
  • Since beginning of last month:
    • Site-wide: 72

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 25,524 times
  • Download rankings, all-time:
    • Site-wide: 263
    • In infectious diseases: 98
  • Year to date:
    • Site-wide: 1,620
  • Since beginning of last month:
    • Site-wide: 2,413

A human coronavirus evolves antigenically to escape antibody immunity

microbiology more details view paper
  • Downloaded 13,620 times
  • Download rankings, all-time:
    • Site-wide: 522
    • In microbiology: 60
  • Year to date:
    • Site-wide: 160
  • Since beginning of last month:
    • Site-wide: 514

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

microbiology more details view paper
  • Downloaded 11,263 times
  • Download rankings, all-time:
    • Site-wide: 690
    • In microbiology: 71
  • Year to date:
    • Site-wide: 731
  • Since beginning of last month:
    • Site-wide: 1,025

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

microbiology more details view paper
  • Downloaded 7,854 times
  • Download rankings, all-time:
    • Site-wide: 1,098
    • In microbiology: 102
  • Year to date:
    • Site-wide: 1,632
  • Since beginning of last month:
    • Site-wide: 1,617

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

microbiology more details view paper
  • Downloaded 5,650 times
  • Download rankings, all-time:
    • Site-wide: 1,703
    • In microbiology: 141
  • Year to date:
    • Site-wide: 409
  • Since beginning of last month:
    • Site-wide: 2,152

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

microbiology more details view paper
  • Downloaded 3,945 times
  • Download rankings, all-time:
    • Site-wide: 2,802
    • In microbiology: 200
  • Year to date:
    • Site-wide: 1,313
  • Since beginning of last month:
    • Site-wide: 3,346

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

infectious diseases more details view paper
  • Downloaded 2,844 times
  • Download rankings, all-time:
    • Site-wide: 4,475
    • In infectious diseases: 770
  • Year to date:
    • Site-wide: 21,415
  • Since beginning of last month:
    • Site-wide: 24,572

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

microbiology more details view paper
  • Downloaded 2,367 times
  • Download rankings, all-time:
    • Site-wide: 5,867
    • In microbiology: 339
  • Year to date:
    • Site-wide: 83,694
  • Since beginning of last month:
    • Site-wide: 73,385

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

infectious diseases more details view paper
  • Downloaded 1,807 times
  • Download rankings, all-time:
    • Site-wide: 8,752
    • In infectious diseases: 1,132
  • Year to date:
    • Site-wide: 5,808
  • Since beginning of last month:
    • Site-wide: 9,612

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

microbiology more details view paper
  • Downloaded 1,554 times
  • Download rankings, all-time:
    • Site-wide: 10,948
    • In microbiology: 610
  • Year to date:
    • Site-wide: 674
  • Since beginning of last month:
    • Site-wide: 239

An experimentally determined evolutionary model dramatically improves phylogenetic fit

evolutionary biology more details view paper
  • Downloaded 1,521 times
  • Download rankings, all-time:
    • Site-wide: 11,257
    • In evolutionary biology: 374
  • Year to date:
    • Site-wide: 62,642
  • Since beginning of last month:
    • Site-wide: 87,578

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

evolutionary biology more details view paper
  • Downloaded 1,399 times
  • Download rankings, all-time:
    • Site-wide: 12,780
    • In evolutionary biology: 457
  • Year to date:
    • Site-wide: 82,232
  • Since beginning of last month:
    • Site-wide: 94,754

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

immunology more details view paper
  • Downloaded 1,395 times
  • Download rankings, all-time:
    • Site-wide: 12,846
    • In immunology: 364
  • Year to date:
    • Site-wide: 777
  • Since beginning of last month:
    • Site-wide: 964

Extreme heterogeneity of influenza virus infection in single cells

genomics more details view paper
  • Downloaded 1,354 times
  • Download rankings, all-time:
    • Site-wide: 13,443
    • In genomics: 1,431
  • Year to date:
    • Site-wide: 107,422
  • Since beginning of last month:
    • Site-wide: 96,162

Expanding the Atlas of Functional Missense Variation for Human Genes

molecular biology more details view paper
  • Downloaded 1,220 times
  • Download rankings, all-time:
    • Site-wide: 15,757
    • In molecular biology: 435
  • Year to date:
    • Site-wide: 68,218
  • Since beginning of last month:
    • Site-wide: 78,917

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

microbiology more details view paper
  • Downloaded 1,160 times
  • Download rankings, all-time:
    • Site-wide: 16,982
    • In microbiology: 962
  • Year to date:
    • Site-wide: 968
  • Since beginning of last month:
    • Site-wide: 459

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

microbiology more details view paper
  • Downloaded 1,110 times
  • Download rankings, all-time:
    • Site-wide: 18,083
    • In microbiology: 1,026
  • Year to date:
    • Site-wide: 87,688
  • Since beginning of last month:
    • Site-wide: 107,889

Reconciling disparate estimates of viral genetic diversity during human influenza infections

evolutionary biology more details view paper
  • Downloaded 1,084 times
  • Download rankings, all-time:
    • Site-wide: 18,748
    • In evolutionary biology: 755
  • Year to date:
    • Site-wide: 91,855
  • Since beginning of last month:
    • Site-wide: 105,117

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

evolutionary biology more details view paper
  • Downloaded 1,055 times
  • Download rankings, all-time:
    • Site-wide: 19,510
    • In evolutionary biology: 813
  • Year to date:
    • Site-wide: 116,684
  • Since beginning of last month:
    • Site-wide: 123,184

Comprehensive profiling of translation initiation in influenza virus infected cells

microbiology more details view paper
  • Downloaded 950 times
  • Download rankings, all-time:
    • Site-wide: 22,675
    • In microbiology: 1,301
  • Year to date:
    • Site-wide: 54,552
  • Since beginning of last month:
    • Site-wide: 54,001

Software for the analysis and visualization of deep mutational scanning data

bioinformatics more details view paper
  • Downloaded 905 times
  • Download rankings, all-time:
    • Site-wide: 24,391
    • In bioinformatics: 2,863
  • Year to date:
    • Site-wide: 95,739
  • Since beginning of last month:
    • Site-wide: 103,529

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

microbiology more details view paper
  • Downloaded 870 times
  • Download rankings, all-time:
    • Site-wide: 25,777
    • In microbiology: 1,510
  • Year to date:
    • Site-wide: 26,395
  • Since beginning of last month:
    • Site-wide: 38,067

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

microbiology more details view paper
  • Downloaded 795 times
  • Download rankings, all-time:
    • Site-wide: 29,225
    • In microbiology: 1,716
  • Year to date:
    • Site-wide: 121,863
  • Since beginning of last month:
    • Site-wide: 107,934

Linking influenza virus evolution within and between human hosts

evolutionary biology more details view paper
  • Downloaded 756 times
  • Download rankings, all-time:
    • Site-wide: 31,358
    • In evolutionary biology: 1,524
  • Year to date:
    • Site-wide: 87,283
  • Since beginning of last month:
    • Site-wide: 78,063

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

immunology more details view paper
  • Downloaded 752 times
  • Download rankings, all-time:
    • Site-wide: 31,567
    • In immunology: 904
  • Year to date:
    • Site-wide: 102,584
  • Since beginning of last month:
    • Site-wide: 106,072

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

evolutionary biology more details view paper
  • Downloaded 750 times
  • Download rankings, all-time:
    • Site-wide: 31,740
    • In evolutionary biology: 1,541
  • Year to date:
    • Site-wide: 95,770
  • Since beginning of last month:
    • Site-wide: 74,407

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

evolutionary biology more details view paper
  • Downloaded 733 times
  • Download rankings, all-time:
    • Site-wide: 32,805
    • In evolutionary biology: 1,612
  • Year to date:
    • Site-wide: 99,208
  • Since beginning of last month:
    • Site-wide: 105,366

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

microbiology more details view paper
  • Downloaded 731 times
  • Download rankings, all-time:
    • Site-wide: 32,897
    • In microbiology: 1,955
  • Year to date:
    • Site-wide: 84,743
  • Since beginning of last month:
    • Site-wide: 108,511

Complete mapping of viral escape from neutralizing antibodies

microbiology more details view paper
  • Downloaded 716 times
  • Download rankings, all-time:
    • Site-wide: 33,727
    • In microbiology: 2,016
  • Year to date:
    • Site-wide: 106,274
  • Since beginning of last month:
    • Site-wide: 102,979

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

immunology more details view paper
  • Downloaded 685 times
  • Download rankings, all-time:
    • Site-wide: 35,902
    • In immunology: 1,021
  • Year to date:
    • Site-wide: 52,315
  • Since beginning of last month:
    • Site-wide: 65,076

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 659 times
  • Download rankings, all-time:
    • Site-wide: 37,793
    • In microbiology: 2,265
  • Year to date:
    • Site-wide: 94,953
  • Since beginning of last month:
    • Site-wide: 80,238

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

microbiology more details view paper
  • Downloaded 643 times
  • Download rankings, all-time:
    • Site-wide: 38,989
    • In microbiology: 2,354
  • Year to date:
    • Site-wide: 106,289
  • Since beginning of last month:
    • Site-wide: 88,499

Comprehensive mapping of avian influenza polymerase adaptation to the human host

microbiology more details view paper
  • Downloaded 642 times
  • Download rankings, all-time:
    • Site-wide: 39,024
    • In microbiology: 2,358
  • Year to date:
    • Site-wide: 125,251
  • Since beginning of last month:
    • Site-wide: 128,186

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

microbiology more details view paper
  • Downloaded 605 times
  • Download rankings, all-time:
    • Site-wide: 42,146
    • In microbiology: 2,584
  • Year to date:
    • Site-wide: 127,714
  • Since beginning of last month:
    • Site-wide: 125,745

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

microbiology more details view paper
  • Downloaded 557 times
  • Download rankings, all-time:
    • Site-wide: 46,703
    • In microbiology: 2,914
  • Year to date:
    • Site-wide: 85,082
  • Since beginning of last month:
    • Site-wide: 67,503

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

microbiology more details view paper
  • Downloaded 548 times
  • Download rankings, all-time:
    • Site-wide: 47,639
    • In microbiology: 2,980
  • Year to date:
    • Site-wide: 107,354
  • Since beginning of last month:
    • Site-wide: 95,368

Mapping mutational effects along the evolutionary landscape of HIV envelope

microbiology more details view paper
  • Downloaded 528 times
  • Download rankings, all-time:
    • Site-wide: 49,724
    • In microbiology: 3,140
  • Year to date:
    • Site-wide: 133,519
  • Since beginning of last month:
    • Site-wide: 128,822

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

evolutionary biology more details view paper
  • Downloaded 508 times
  • Download rankings, all-time:
    • Site-wide: 52,070
    • In evolutionary biology: 2,829
  • Year to date:
    • Site-wide: 111,954
  • Since beginning of last month:
    • Site-wide: 117,544

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

immunology more details view paper
  • Downloaded 471 times
  • Download rankings, all-time:
    • Site-wide: 56,756
    • In immunology: 1,588
  • Year to date:
    • Site-wide: 124,730
  • Since beginning of last month:
    • Site-wide: 124,402

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

biophysics more details view paper
  • Downloaded 466 times
  • Download rankings, all-time:
    • Site-wide: 57,422
    • In biophysics: 2,001
  • Year to date:
    • Site-wide: 67,575
  • Since beginning of last month:
    • Site-wide: 100,405

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

microbiology more details view paper
  • Downloaded 449 times
  • Download rankings, all-time:
    • Site-wide: 59,647
    • In microbiology: 3,910
  • Year to date:
    • Site-wide: 58,756
  • Since beginning of last month:
    • Site-wide: 76,564

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

microbiology more details view paper
  • Downloaded 443 times
  • Download rankings, all-time:
    • Site-wide: 60,546
    • In microbiology: 3,975
  • Year to date:
    • Site-wide: 106,297
  • Since beginning of last month:
    • Site-wide: 94,492

phydms: Software for phylogenetic analyses informed by deep mutational scanning

evolutionary biology more details view paper
  • Downloaded 441 times
  • Download rankings, all-time:
    • Site-wide: 60,806
    • In evolutionary biology: 3,322
  • Year to date:
    • Site-wide: 122,458
  • Since beginning of last month:
    • Site-wide: 87,399

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

genomics more details view paper
  • Downloaded 389 times
  • Download rankings, all-time:
    • Site-wide: 68,943
    • In genomics: 4,820
  • Year to date:
    • Site-wide: 123,633
  • Since beginning of last month:
    • Site-wide: 107,854

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

bioinformatics more details view paper
  • Downloaded 374 times
  • Download rankings, all-time:
    • Site-wide: 71,343
    • In bioinformatics: 6,773
  • Year to date:
    • Site-wide: 112,601
  • Since beginning of last month:
    • Site-wide: 112,545

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

microbiology more details view paper
  • Downloaded 366 times
  • Download rankings, all-time:
    • Site-wide: 72,880
    • In microbiology: 4,971
  • Year to date:
    • Site-wide: 131,512
  • Since beginning of last month:
    • Site-wide: 133,390

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

immunology more details view paper
  • Downloaded 363 times
  • Download rankings, all-time:
    • Site-wide: 73,408
    • In immunology: 2,043
  • Year to date:
    • Site-wide: 4,953
  • Since beginning of last month:
    • Site-wide: 2,367

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

bioinformatics more details view paper
  • Downloaded 330 times
  • Download rankings, all-time:
    • Site-wide: 79,438
    • In bioinformatics: 7,298
  • Year to date:
    • Site-wide: 80,422
  • Since beginning of last month:
    • Site-wide: 91,234

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

microbiology more details view paper
  • Downloaded 301 times
  • Download rankings, all-time:
    • Site-wide: 85,369
    • In microbiology: 6,008
  • Year to date:
    • Site-wide: 120,494
  • Since beginning of last month:
    • Site-wide: 105,595

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

microbiology more details view paper
  • Downloaded 242 times
  • Download rankings, all-time:
    • Site-wide: 98,225
    • In microbiology: 7,134
  • Year to date:
    • Site-wide: 88,312
  • Since beginning of last month:
    • Site-wide: 72,013

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 222 times
  • Download rankings, all-time:
    • Site-wide: 102,501
    • In microbiology: 7,539
  • Year to date:
    • Site-wide: 63,593
  • Since beginning of last month:
    • Site-wide: 98,312

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

microbiology more details view paper
  • Downloaded 173 times
  • Download rankings, all-time:
    • Site-wide: 113,563
    • In microbiology: 8,510
  • Year to date:
    • Site-wide: 89,133
  • Since beginning of last month:
    • Site-wide: 82,619

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

microbiology more details view paper
  • Downloaded 172 times
  • Download rankings, all-time:
    • Site-wide: 113,731
    • In microbiology: 8,538
  • Year to date:
    • Site-wide: 121,593
  • Since beginning of last month:
    • Site-wide: 131,732

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

microbiology more details view paper
  • Downloaded 143 times
  • Download rankings, all-time:
    • Site-wide: 119,885
    • In microbiology: 9,079
  • Year to date:
    • Site-wide: 134,020
  • Since beginning of last month:
    • Site-wide: 134,746

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

microbiology more details view paper
  • Downloaded 65 times
  • Download rankings, all-time:
    • Site-wide: 132,907
    • In microbiology: 10,320
  • Year to date:
    • Site-wide: 42,137
  • Since beginning of last month:
    • Site-wide: 16,093

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