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Author: Jesse D. Bloom

Rankings

  • All-time downloads: 131,921 (rank: 578 )
  • Categories:
    • bioinformatics: 1,552 (rank: 8,661 (tie) )
    • biophysics: 435 (rank: 10,513 (tie) )
    • evolutionary biology: 8,077 (rank: 257 )
    • genomics: 1,718 (rank: 12,536 (tie) )
    • immunology: 1,844 (rank: 3,726 )
    • infectious diseases: 29,182 (rank: 1,393 (tie) )
    • microbiology: 87,928 (rank: 131 )
    • molecular biology: 1,185 (rank: 4,125 (tie) )

Downloads per author, site-wide

Preprints

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 38,127 times
  • Download rankings, all-time:
    • Site-wide: 135
    • In microbiology: 12
  • Year to date:
    • Site-wide: 3
  • Since beginning of last month:
    • Site-wide: None

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: 239
    • In infectious diseases: 93
  • Year to date:
    • Site-wide: 1,797
  • Since beginning of last month:
    • Site-wide: 784

A human coronavirus evolves antigenically to escape antibody immunity

microbiology more details view paper
  • Downloaded 11,342 times
  • Download rankings, all-time:
    • Site-wide: 588
    • In microbiology: 61
  • Year to date:
    • Site-wide: 44
  • Since beginning of last month:
    • Site-wide: 19

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: 690
    • In microbiology: 74
  • Year to date:
    • Site-wide: 682
  • Since beginning of last month:
    • Site-wide: 824

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: 1,081
    • In microbiology: 100
  • Year to date:
    • Site-wide: 1,996
  • Since beginning of last month:
    • Site-wide: 2,135

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: 2,324
    • In microbiology: 163
  • Year to date:
    • Site-wide: 197
  • 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: 3,229
    • In microbiology: 209
  • Year to date:
    • Site-wide: 854
  • 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 2,740 times
  • Download rankings, all-time:
    • Site-wide: 4,135
    • In infectious diseases: 659
  • Year to date:
    • Site-wide: 20,362
  • Since beginning of last month:
    • Site-wide: 17,529

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: 5,248
    • In microbiology: 304
  • Year to date:
    • Site-wide: 83,146
  • Since beginning of last month:
    • Site-wide: 46,046

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

infectious diseases more details view paper
  • Downloaded 1,571 times
  • Download rankings, all-time:
    • Site-wide: 9,510
    • In infectious diseases: 1,082
  • Year to date:
    • Site-wide: 3,270
  • Since beginning of last month:
    • Site-wide: 4,260

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: 10,279
    • In evolutionary biology: 354
  • Year to date:
    • Site-wide: 54,534
  • Since beginning of last month:
    • Site-wide: 76,662

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: 11,582
    • In evolutionary biology: 423
  • Year to date:
    • Site-wide: 85,010
  • Since beginning of last month:
    • Site-wide: 100,547

Extreme heterogeneity of influenza virus infection in single cells

genomics more details view paper
  • Downloaded 1,340 times
  • Download rankings, all-time:
    • Site-wide: 12,026
    • In genomics: 1,339
  • Year to date:
    • Site-wide: 89,265
  • Since beginning of last month:
    • Site-wide: 94,422

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: 14,448
    • In molecular biology: 403
  • Year to date:
    • Site-wide: 111,756
  • Since beginning of last month:
    • Site-wide: 73,120

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: 16,525
    • In microbiology: 926
  • Year to date:
    • Site-wide: 97,012
  • Since beginning of last month:
    • Site-wide: 87,881

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: 17,012
    • In evolutionary biology: 719
  • Year to date:
    • Site-wide: 82,238
  • Since beginning of last month:
    • Site-wide: 93,590

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: 17,539
    • In evolutionary biology: 747
  • Year to date:
    • Site-wide: 94,128
  • Since beginning of last month:
    • Site-wide: 120,930

Comprehensive profiling of translation initiation in influenza virus infected cells

microbiology more details view paper
  • Downloaded 913 times
  • Download rankings, all-time:
    • Site-wide: 21,340
    • In microbiology: 1,205
  • Year to date:
    • Site-wide: 41,177
  • Since beginning of last month:
    • Site-wide: 46,650

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: 22,291
    • In bioinformatics: 2,700
  • Year to date:
    • Site-wide: 74,371
  • Since beginning of last month:
    • Site-wide: 104,898

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: 25,803
    • In microbiology: 1,508
  • Year to date:
    • Site-wide: 12,578
  • Since beginning of last month:
    • Site-wide: 20,754

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: 26,511
    • In microbiology: 1,544
  • Year to date:
    • Site-wide: 119,017
  • Since beginning of last month:
    • Site-wide: 65,921

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

immunology more details view paper
  • Downloaded 739 times
  • Download rankings, all-time:
    • Site-wide: 28,742
    • In immunology: 764
  • Year to date:
    • Site-wide: 60,460
  • Since beginning of last month:
    • Site-wide: 101,901

Linking influenza virus evolution within and between human hosts

evolutionary biology more details view paper
  • Downloaded 735 times
  • Download rankings, all-time:
    • Site-wide: 28,939
    • In evolutionary biology: 1,454
  • Year to date:
    • Site-wide: 83,397
  • Since beginning of last month:
    • Site-wide: 71,439

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: 29,045
    • In evolutionary biology: 1,462
  • Year to date:
    • Site-wide: 72,880
  • Since beginning of last month:
    • Site-wide: 42,548

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: 29,907
    • In microbiology: 1,778
  • Year to date:
    • Site-wide: 33,768
  • Since beginning of last month:
    • Site-wide: 105,218

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: 30,048
    • In evolutionary biology: 1,528
  • Year to date:
    • Site-wide: 100,595
  • Since beginning of last month:
    • Site-wide: 96,045

Complete mapping of viral escape from neutralizing antibodies

microbiology more details view paper
  • Downloaded 700 times
  • Download rankings, all-time:
    • Site-wide: 30,962
    • In microbiology: 1,830
  • Year to date:
    • Site-wide: 95,230
  • Since beginning of last month:
    • Site-wide: 90,517

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: 34,576
    • In immunology: 915
  • Year to date:
    • Site-wide: 45,927
  • Since beginning of last month:
    • Site-wide: 64,900

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: 35,083
    • In microbiology: 2,080
  • Year to date:
    • Site-wide: 119,857
  • Since beginning of last month:
    • Site-wide: 76,652

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: 35,272
    • In microbiology: 2,094
  • Year to date:
    • Site-wide: 79,843
  • Since beginning of last month:
    • Site-wide: 111,988

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

microbiology more details view paper
  • Downloaded 631 times
  • Download rankings, all-time:
    • Site-wide: 35,542
    • In microbiology: 2,127
  • Year to date:
    • Site-wide: 59,231
  • Since beginning of last month:
    • Site-wide: 77,419

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

microbiology more details view paper
  • Downloaded 598 times
  • Download rankings, all-time:
    • Site-wide: 38,008
    • In microbiology: 2,315
  • Year to date:
    • Site-wide: 88,190
  • Since beginning of last month:
    • Site-wide: 92,099

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: 43,912
    • In microbiology: 2,723
  • Year to date:
    • Site-wide: 101,944
  • Since beginning of last month:
    • Site-wide: 52,542

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: 44,015
    • In microbiology: 2,731
  • Year to date:
    • Site-wide: 106,542
  • Since beginning of last month:
    • Site-wide: 74,503

Mapping mutational effects along the evolutionary landscape of HIV envelope

microbiology more details view paper
  • Downloaded 523 times
  • Download rankings, all-time:
    • Site-wide: 44,947
    • In microbiology: 2,805
  • Year to date:
    • Site-wide: 112,899
  • Since beginning of last month:
    • Site-wide: 100,268

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: 48,036
    • In evolutionary biology: 2,698
  • Year to date:
    • Site-wide: 103,381
  • Since beginning of last month:
    • Site-wide: 114,827

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: 51,984
    • In immunology: 1,373
  • Year to date:
    • Site-wide: 107,996
  • Since beginning of last month:
    • Site-wide: 114,395

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: 55,278
    • In biophysics: 1,961
  • Year to date:
    • Site-wide: 66,363
  • Since beginning of last month:
    • Site-wide: 88,189

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: 56,002
    • In evolutionary biology: 3,164
  • Year to date:
    • Site-wide: 106,910
  • Since beginning of last month:
    • Site-wide: 121,985

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: 56,537
    • In microbiology: 3,731
  • Year to date:
    • Site-wide: 111,629
  • Since beginning of last month:
    • Site-wide: 118,561

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

microbiology more details view paper
  • Downloaded 420 times
  • Download rankings, all-time:
    • Site-wide: 57,262
    • In microbiology: 3,792
  • Year to date:
    • Site-wide: 28,392
  • Since beginning of last month:
    • Site-wide: 47,572

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

genomics more details view paper
  • Downloaded 378 times
  • Download rankings, all-time:
    • Site-wide: 63,643
    • In genomics: 4,586
  • Year to date:
    • Site-wide: 107,771
  • Since beginning of last month:
    • Site-wide: 103,902

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

microbiology more details view paper
  • Downloaded 362 times
  • Download rankings, all-time:
    • Site-wide: 66,186
    • In microbiology: 4,499
  • Year to date:
    • Site-wide: 82,671
  • Since beginning of last month:
    • Site-wide: 93,257

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: 66,387
    • In bioinformatics: 6,448
  • Year to date:
    • Site-wide: 100,243
  • Since beginning of last month:
    • Site-wide: 120,584

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

bioinformatics more details view paper
  • Downloaded 304 times
  • Download rankings, all-time:
    • Site-wide: 76,478
    • In bioinformatics: 7,100
  • Year to date:
    • Site-wide: 84,296
  • Since beginning of last month:
    • Site-wide: 33,999

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: 79,199
    • In microbiology: 5,574
  • Year to date:
    • Site-wide: 104,357
  • Since beginning of last month:
    • Site-wide: 95,524

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: 93,487
    • In microbiology: 6,843
  • Year to date:
    • Site-wide: 69,400
  • Since beginning of last month:
    • Site-wide: 91,265

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: 100,234
    • In microbiology: 7,481
  • Year to date:
    • Site-wide: 52,467
  • Since beginning of last month:
    • Site-wide: 36,927

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: 105,435
    • In microbiology: 7,946
  • Year to date:
    • Site-wide: 77,317
  • Since beginning of last month:
    • Site-wide: 107,461

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: 108,246
    • In microbiology: 8,214
  • Year to date:
    • Site-wide: 117,043
  • Since beginning of last month:
    • Site-wide: 75,829

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: 110,278
    • In microbiology: 8,372
  • Year to date:
    • Site-wide: 111,251
  • Since beginning of last month:
    • Site-wide: 110,076

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