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Author: Jesse D Bloom

Rankings

  • All-time downloads: 339,096 (rank: 98 )
  • Categories:
    • bioinformatics: 1,722 (rank: 10,403 (tie) )
    • biophysics: 536 (rank: 13,021 (tie) )
    • epidemiology: 83,573 (rank: 216 (tie) )
    • evolutionary biology: 75,957 (rank: 27 )
    • genomics: 1,862 (rank: 14,725 (tie) )
    • immunology: 8,117 (rank: 1,310 )
    • infectious diseases: 33,308 (rank: 1,894 )
    • microbiology: 131,260 (rank: 85 )
    • molecular biology: 1,345 (rank: 5,337 (tie) )
    • synthetic biology: 1,416 (rank: 1,666 (tie) )

Downloads per author, site-wide

Preprints

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

epidemiology more details view paper
  • Downloaded 83,573 times
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    • Site-wide: 82
    • In epidemiology: 17
  • Year to date:
    • Site-wide: 219
  • Since beginning of last month:
    • Site-wide: 533

Recovery of deleted deep sequencing data sheds more light on the early Wuhan SARS-CoV-2 epidemic

evolutionary biology more details view paper
  • Downloaded 65,776 times
  • Download rankings, all-time:
    • Site-wide: 111
    • In evolutionary biology: 3
  • Year to date:
    • Site-wide: 31
  • Since beginning of last month:
    • Site-wide: 253

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 56,948 times
  • Download rankings, all-time:
    • Site-wide: 132
    • In microbiology: 10
  • Year to date:
    • Site-wide: 38
  • Since beginning of last month:
    • Site-wide: 1,273

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 27,209 times
  • Download rankings, all-time:
    • Site-wide: 319
    • In infectious diseases: 118
  • Year to date:
    • Site-wide: 1,501
  • Since beginning of last month:
    • Site-wide: 2,561

A human coronavirus evolves antigenically to escape antibody immunity

microbiology more details view paper
  • Downloaded 15,006 times
  • Download rankings, all-time:
    • Site-wide: 635
    • In microbiology: 72
  • Year to date:
    • Site-wide: 481
  • Since beginning of last month:
    • Site-wide: 8,904

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

microbiology more details view paper
  • Downloaded 11,920 times
  • Download rankings, all-time:
    • Site-wide: 864
    • In microbiology: 89
  • Year to date:
    • Site-wide: 1,848
  • Since beginning of last month:
    • Site-wide: 27,289

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

microbiology more details view paper
  • Downloaded 8,672 times
  • Download rankings, all-time:
    • Site-wide: 1,301
    • In microbiology: 122
  • Year to date:
    • Site-wide: 2,690
  • Since beginning of last month:
    • Site-wide: 33,609

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

microbiology more details view paper
  • Downloaded 6,397 times
  • Download rankings, all-time:
    • Site-wide: 1,910
    • In microbiology: 156
  • Year to date:
    • Site-wide: 1,113
  • Since beginning of last month:
    • Site-wide: 15,844

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

microbiology more details view paper
  • Downloaded 4,450 times
  • Download rankings, all-time:
    • Site-wide: 3,156
    • In microbiology: 225
  • Year to date:
    • Site-wide: 3,254
  • Since beginning of last month:
    • Site-wide: 33,563

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

infectious diseases more details view paper
  • Downloaded 3,113 times
  • Download rankings, all-time:
    • Site-wide: 5,208
    • In infectious diseases: 996
  • Year to date:
    • Site-wide: 23,278
  • Since beginning of last month:
    • Site-wide: 48,018

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

immunology more details view paper
  • Downloaded 2,921 times
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    • Site-wide: 5,738
    • In immunology: 213
  • Year to date:
    • Site-wide: 1,215
  • Since beginning of last month:
    • Site-wide: 1,981

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 2,776 times
  • Download rankings, all-time:
    • Site-wide: 6,156
    • In microbiology: 388
  • Year to date:
    • Site-wide: 1,300
  • Since beginning of last month:
    • Site-wide: 10,741

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
  • Downloaded 2,772 times
  • Download rankings, all-time:
    • Site-wide: 6,168
    • In microbiology: 389
  • Year to date:
    • Site-wide: 1,302
  • Since beginning of last month:
    • Site-wide: 1,630

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

infectious diseases more details view paper
  • Downloaded 2,569 times
  • Download rankings, all-time:
    • Site-wide: 6,911
    • In infectious diseases: 1,180
  • Year to date:
    • Site-wide: 4,749
  • Since beginning of last month:
    • Site-wide: 10,139

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

microbiology more details view paper
  • Downloaded 2,467 times
  • Download rankings, all-time:
    • Site-wide: 7,334
    • In microbiology: 437
  • Year to date:
    • Site-wide: 1,511
  • Since beginning of last month:
    • Site-wide: 8,428

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

microbiology more details view paper
  • Downloaded 2,435 times
  • Download rankings, all-time:
    • Site-wide: 7,468
    • In microbiology: 446
  • Year to date:
    • Site-wide: 118,315
  • Since beginning of last month:
    • Site-wide: 158,421

Structural basis for broad sarbecovirus neutralization by a human monoclonal antibody

immunology more details view paper
  • Downloaded 2,033 times
  • Download rankings, all-time:
    • Site-wide: 9,735
    • In immunology: 342
  • Year to date:
    • Site-wide: 1,931
  • Since beginning of last month:
    • Site-wide: 8,980

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 1,607 times
  • Download rankings, all-time:
    • Site-wide: 13,836
    • In microbiology: 803
  • Year to date:
    • Site-wide: 2,698
  • Since beginning of last month:
    • Site-wide: 34,834

An experimentally determined evolutionary model dramatically improves phylogenetic fit

evolutionary biology more details view paper
  • Downloaded 1,553 times
  • Download rankings, all-time:
    • Site-wide: 14,606
    • In evolutionary biology: 457
  • Year to date:
    • Site-wide: 138,806
  • Since beginning of last month:
    • Site-wide: 147,089

ACE2 binding is an ancestral and evolvable trait of sarbecoviruses

evolutionary biology more details view paper
  • Downloaded 1,505 times
  • Download rankings, all-time:
    • Site-wide: 15,393
    • In evolutionary biology: 491
  • Year to date:
    • Site-wide: 2,985
  • Since beginning of last month:
    • Site-wide: 3,140

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

evolutionary biology more details view paper
  • Downloaded 1,449 times
  • Download rankings, all-time:
    • Site-wide: 16,309
    • In evolutionary biology: 525
  • Year to date:
    • Site-wide: 133,739
  • Since beginning of last month:
    • Site-wide: 146,329

Extreme heterogeneity of influenza virus infection in single cells

genomics more details view paper
  • Downloaded 1,443 times
  • Download rankings, all-time:
    • Site-wide: 16,408
    • In genomics: 1,580
  • Year to date:
    • Site-wide: 109,123
  • Since beginning of last month:
    • Site-wide: 51,724

Multivalent designed proteins protect against SARS-CoV-2 variants of concern

synthetic biology more details view paper
  • Downloaded 1,416 times
  • Download rankings, all-time:
    • Site-wide: 16,902
    • In synthetic biology: 199
  • Year to date:
    • Site-wide: 3,250
  • Since beginning of last month:
    • Site-wide: 4,541

Expanding the Atlas of Functional Missense Variation for Human Genes

molecular biology more details view paper
  • Downloaded 1,345 times
  • Download rankings, all-time:
    • Site-wide: 18,264
    • In molecular biology: 491
  • Year to date:
    • Site-wide: 74,159
  • Since beginning of last month:
    • Site-wide: 39,077

The inherent mutational tolerance and antigenic evolvability of influenza hemagglutinin

microbiology more details view paper
  • Downloaded 1,178 times
  • Download rankings, all-time:
    • Site-wide: 22,316
    • In microbiology: 1,296
  • Year to date:
    • Site-wide: 120,459
  • Since beginning of last month:
    • Site-wide: 68,866

Reconciling disparate estimates of viral genetic diversity during human influenza infections

evolutionary biology more details view paper
  • Downloaded 1,153 times
  • Download rankings, all-time:
    • Site-wide: 23,041
    • In evolutionary biology: 867
  • Year to date:
    • Site-wide: 120,679
  • Since beginning of last month:
    • Site-wide: 92,885

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

evolutionary biology more details view paper
  • Downloaded 1,086 times
  • Download rankings, all-time:
    • Site-wide: 25,290
    • In evolutionary biology: 996
  • Year to date:
    • Site-wide: 157,707
  • Since beginning of last month:
    • Site-wide: 150,068

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

microbiology more details view paper
  • Downloaded 1,050 times
  • Download rankings, all-time:
    • Site-wide: 26,610
    • In microbiology: 1,554
  • Year to date:
    • Site-wide: 37,352
  • Since beginning of last month:
    • Site-wide: 33,654

Comprehensive profiling of translation initiation in influenza virus infected cells

microbiology more details view paper
  • Downloaded 1,021 times
  • Download rankings, all-time:
    • Site-wide: 27,746
    • In microbiology: 1,613
  • Year to date:
    • Site-wide: 100,049
  • Since beginning of last month:
    • Site-wide: 144,452

Stabilization of the SARS-CoV-2 Spike receptor-binding domain using deep mutational scanning and structure-based design

microbiology more details view paper
  • Downloaded 945 times
  • Download rankings, all-time:
    • Site-wide: 31,049
    • In microbiology: 1,825
  • Year to date:
    • Site-wide: 5,907
  • Since beginning of last month:
    • Site-wide: 2,811

Software for the analysis and visualization of deep mutational scanning data

bioinformatics more details view paper
  • Downloaded 938 times
  • Download rankings, all-time:
    • Site-wide: 31,406
    • In bioinformatics: 3,445
  • Year to date:
    • Site-wide: 151,699
  • Since beginning of last month:
    • Site-wide: 145,745

Linking influenza virus evolution within and between human hosts

evolutionary biology more details view paper
  • Downloaded 845 times
  • Download rankings, all-time:
    • Site-wide: 36,557
    • In evolutionary biology: 1,597
  • Year to date:
    • Site-wide: 102,772
  • Since beginning of last month:
    • Site-wide: 53,387

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

microbiology more details view paper
  • Downloaded 824 times
  • Download rankings, all-time:
    • Site-wide: 37,962
    • In microbiology: 2,269
  • Year to date:
    • Site-wide: 159,699
  • Since beginning of last month:
    • Site-wide: 146,645

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

microbiology more details view paper
  • Downloaded 811 times
  • Download rankings, all-time:
    • Site-wide: 38,809
    • In microbiology: 2,319
  • Year to date:
    • Site-wide: 109,185
  • Since beginning of last month:
    • Site-wide: 72,548

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

evolutionary biology more details view paper
  • Downloaded 802 times
  • Download rankings, all-time:
    • Site-wide: 39,461
    • In evolutionary biology: 1,758
  • Year to date:
    • Site-wide: 137,075
  • Since beginning of last month:
    • Site-wide: 145,624

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

immunology more details view paper
  • Downloaded 794 times
  • Download rankings, all-time:
    • Site-wide: 39,957
    • In immunology: 1,289
  • Year to date:
    • Site-wide: 147,957
  • Since beginning of last month:
    • Site-wide: 150,334

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

immunology more details view paper
  • Downloaded 782 times
  • Download rankings, all-time:
    • Site-wide: 40,897
    • In immunology: 1,317
  • Year to date:
    • Site-wide: 81,526
  • Since beginning of last month:
    • Site-wide: 47,978

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

evolutionary biology more details view paper
  • Downloaded 767 times
  • Download rankings, all-time:
    • Site-wide: 42,042
    • In evolutionary biology: 1,904
  • Year to date:
    • Site-wide: 152,732
  • Since beginning of last month:
    • Site-wide: 155,297

A SARS-CoV-2 variant elicits an antibody response with a shifted immunodominance hierarchy

microbiology more details view paper
  • Downloaded 767 times
  • Download rankings, all-time:
    • Site-wide: 42,121
    • In microbiology: 2,518
  • Year to date:
    • Site-wide: 8,208
  • Since beginning of last month:
    • Site-wide: 625

Complete mapping of viral escape from neutralizing antibodies

microbiology more details view paper
  • Downloaded 755 times
  • Download rankings, all-time:
    • Site-wide: 42,995
    • In microbiology: 2,579
  • Year to date:
    • Site-wide: 150,770
  • Since beginning of last month:
    • Site-wide: 143,879

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

immunology more details view paper
  • Downloaded 724 times
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    • Site-wide: 45,647
    • In immunology: 1,447
  • Year to date:
    • Site-wide: 8,996
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    • Site-wide: 7,342

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 724 times
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    • Site-wide: 45,679
    • In microbiology: 2,742
  • Year to date:
    • Site-wide: 125,731
  • Since beginning of last month:
    • Site-wide: 144,052

Comprehensive mapping of avian influenza polymerase adaptation to the human host

microbiology more details view paper
  • Downloaded 712 times
  • Download rankings, all-time:
    • Site-wide: 46,722
    • In microbiology: 2,823
  • Year to date:
    • Site-wide: 130,834
  • Since beginning of last month:
    • Site-wide: 59,434

Structure, receptor recognition and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein

microbiology more details view paper
  • Downloaded 684 times
  • Download rankings, all-time:
    • Site-wide: 49,389
    • In microbiology: 2,993
  • Year to date:
    • Site-wide: 9,830
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    • Site-wide: 742

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

microbiology more details view paper
  • Downloaded 681 times
  • Download rankings, all-time:
    • Site-wide: 49,692
    • In microbiology: 3,020
  • Year to date:
    • Site-wide: 150,970
  • Since beginning of last month:
    • Site-wide: 162,061

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

microbiology more details view paper
  • Downloaded 654 times
  • Download rankings, all-time:
    • Site-wide: 52,508
    • In microbiology: 3,228
  • Year to date:
    • Site-wide: 149,166
  • Since beginning of last month:
    • Site-wide: 147,081

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

microbiology more details view paper
  • Downloaded 619 times
  • Download rankings, all-time:
    • Site-wide: 56,512
    • In microbiology: 3,510
  • Year to date:
    • Site-wide: 124,490
  • Since beginning of last month:
    • Site-wide: 158,789

Mapping mutational effects along the evolutionary landscape of HIV envelope

microbiology more details view paper
  • Downloaded 595 times
  • Download rankings, all-time:
    • Site-wide: 59,427
    • In microbiology: 3,710
  • Year to date:
    • Site-wide: 137,714
  • Since beginning of last month:
    • Site-wide: 59,488

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

microbiology more details view paper
  • Downloaded 580 times
  • Download rankings, all-time:
    • Site-wide: 61,387
    • In microbiology: 3,843
  • Year to date:
    • Site-wide: 155,654
  • Since beginning of last month:
    • Site-wide: 157,547

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

microbiology more details view paper
  • Downloaded 575 times
  • Download rankings, all-time:
    • Site-wide: 62,045
    • In microbiology: 3,891
  • Year to date:
    • Site-wide: 70,629
  • Since beginning of last month:
    • Site-wide: 118,414

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

evolutionary biology more details view paper
  • Downloaded 540 times
  • Download rankings, all-time:
    • Site-wide: 66,951
    • In evolutionary biology: 3,310
  • Year to date:
    • Site-wide: 156,038
  • Since beginning of last month:
    • Site-wide: 147,654

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

biophysics more details view paper
  • Downloaded 536 times
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    • Site-wide: 67,626
    • In biophysics: 2,362
  • Year to date:
    • Site-wide: 109,475
  • Since beginning of last month:
    • Site-wide: 135,824

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

immunology more details view paper
  • Downloaded 495 times
  • Download rankings, all-time:
    • Site-wide: 74,136
    • In immunology: 2,248
  • Year to date:
    • Site-wide: 162,801
  • Since beginning of last month:
    • Site-wide: 153,423

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

microbiology more details view paper
  • Downloaded 485 times
  • Download rankings, all-time:
    • Site-wide: 75,746
    • In microbiology: 5,012
  • Year to date:
    • Site-wide: 148,437
  • Since beginning of last month:
    • Site-wide: 143,431

phydms: Software for phylogenetic analyses informed by deep mutational scanning

evolutionary biology more details view paper
  • Downloaded 481 times
  • Download rankings, all-time:
    • Site-wide: 76,546
    • In evolutionary biology: 3,839
  • Year to date:
    • Site-wide: 153,493
  • Since beginning of last month:
    • Site-wide: 136,623

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

microbiology more details view paper
  • Downloaded 430 times
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    • Site-wide: 86,230
    • In microbiology: 5,772
  • Year to date:
    • Site-wide: 138,823
  • Since beginning of last month:
    • Site-wide: 62,273

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

genomics more details view paper
  • Downloaded 419 times
  • Download rankings, all-time:
    • Site-wide: 88,359
    • In genomics: 5,618
  • Year to date:
    • Site-wide: 159,413
  • Since beginning of last month:
    • Site-wide: 160,928

Humoral immunogenicity of the seasonal influenza vaccine before and after CAR-T-cell therapy

infectious diseases more details view paper
  • Downloaded 417 times
  • Download rankings, all-time:
    • Site-wide: 88,864
    • In infectious diseases: 4,414
  • Year to date:
    • Site-wide: 21,333
  • Since beginning of last month:
    • Site-wide: 21,858

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

bioinformatics more details view paper
  • Downloaded 398 times
  • Download rankings, all-time:
    • Site-wide: 92,940
    • In bioinformatics: 8,137
  • Year to date:
    • Site-wide: 160,774
  • Since beginning of last month:
    • Site-wide: 152,540

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

bioinformatics more details view paper
  • Downloaded 386 times
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    • Site-wide: 95,616
    • In bioinformatics: 8,324
  • Year to date:
    • Site-wide: 127,480
  • Since beginning of last month:
    • Site-wide: 143,259

Antibody-mediated broad sarbecovirus neutralization through ACE2 molecular mimicry

immunology more details view paper
  • Downloaded 368 times
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    • Site-wide: 99,846
    • In immunology: 2,997
  • Year to date:
    • Site-wide: 25,765
  • Since beginning of last month:
    • Site-wide: 1,956

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

microbiology more details view paper
  • Downloaded 334 times
  • Download rankings, all-time:
    • Site-wide: 108,001
    • In microbiology: 7,573
  • Year to date:
    • Site-wide: 156,957
  • Since beginning of last month:
    • Site-wide: 158,894

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 297 times
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    • Site-wide: 117,409
    • In microbiology: 8,380
  • Year to date:
    • Site-wide: 102,757
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    • Site-wide: 108,698

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

microbiology more details view paper
  • Downloaded 278 times
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    • Site-wide: 122,405
    • In microbiology: 8,832
  • Year to date:
    • Site-wide: 147,621
  • Since beginning of last month:
    • Site-wide: 155,114

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

microbiology more details view paper
  • Downloaded 230 times
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    • Site-wide: 135,100
    • In microbiology: 9,963
  • Year to date:
    • Site-wide: 130,454
  • Since beginning of last month:
    • Site-wide: 130,778

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

microbiology more details view paper
  • Downloaded 207 times
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    • Site-wide: 140,810
    • In microbiology: 10,455
  • Year to date:
    • Site-wide: 56,199
  • Since beginning of last month:
    • Site-wide: 24,915

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

microbiology more details view paper
  • Downloaded 206 times
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    • Site-wide: 141,019
    • In microbiology: 10,472
  • Year to date:
    • Site-wide: 157,416
  • Since beginning of last month:
    • Site-wide: 157,358

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

microbiology more details view paper
  • Downloaded 168 times
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    • Site-wide: 149,620
    • In microbiology: 11,281
  • Year to date:
    • Site-wide: 164,113
  • Since beginning of last month:
    • Site-wide: 152,155

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