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Author: Trevor Bedford

Rankings

  • All-time downloads: 72,663 (rank: 2,142 )
  • Categories:
    • bioinformatics: 355 (rank: 32,719 (tie) )
    • epidemiology: 35,183 (rank: 497 )
    • evolutionary biology: 11,191 (rank: 164 )
    • genomics: 5,991 (rank: 3,998 )
    • infectious diseases: 10,157 (rank: 5,123 (tie) )
    • microbiology: 3,873 (rank: 4,070 (tie) )
    • molecular biology: 5,913 (rank: 507 (tie) )

Downloads per author, site-wide

Preprints

Rapid and parallel adaptive mutations in spike S1 drive clade success in SARS-CoV-2

evolutionary biology more details view paper

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Emergence and Expansion of the SARS-CoV-2 Variant B.1.526 Identified in New York

epidemiology more details view paper
  • Downloaded 10,863 times
  • Download rankings, all-time:
    • Site-wide: 854
    • In epidemiology: 120
  • Year to date:
    • Site-wide: 171
  • Since beginning of last month:
    • Site-wide: 2,591

Cryptic transmission of SARS-CoV-2 in Washington State

epidemiology more details view paper
  • Downloaded 9,523 times
  • Download rankings, all-time:
    • Site-wide: 1,006
    • In epidemiology: 132
  • Year to date:
    • Site-wide: 8,262
  • Since beginning of last month:
    • Site-wide: 32,731

A Genomic Survey of SARS-CoV-2 Reveals Multiple Introductions into Northern California without a Predominant Lineage

infectious diseases more details view paper
  • Downloaded 6,829 times
  • Download rankings, all-time:
    • Site-wide: 1,523
    • In infectious diseases: 415
  • Year to date:
    • Site-wide: 6,956
  • Since beginning of last month:
    • Site-wide: 45,764

Effects of weather-related social distancing on city-scale transmission of respiratory viruses

epidemiology more details view paper
  • Downloaded 6,003 times
  • Download rankings, all-time:
    • Site-wide: 1,839
    • In epidemiology: 217
  • Year to date:
    • Site-wide: 30,455
  • Since beginning of last month:
    • Site-wide: 107,467

SwabExpress: An end-to-end protocol for extraction-free COVID-19 testing

molecular biology more details view paper
  • Downloaded 5,913 times
  • Download rankings, all-time:
    • Site-wide: 1,871
    • In molecular biology: 36
  • Year to date:
    • Site-wide: 6,321
  • Since beginning of last month:
    • Site-wide: 67,535

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

genomics more details view paper
  • Downloaded 4,832 times
  • Download rankings, all-time:
    • Site-wide: 2,472
    • In genomics: 242
  • Year to date:
    • Site-wide: 26,521
  • Since beginning of last month:
    • Site-wide: 25,099

MERS-CoV spillover at the camel-human interface

epidemiology more details view paper
  • Downloaded 1,815 times
  • Download rankings, all-time:
    • Site-wide: 10,107
    • In epidemiology: 767
  • Year to date:
    • Site-wide: 79,185
  • Since beginning of last month:
    • Site-wide: 75,120

Evidence for adaptive evolution in the receptor-binding domain of seasonal coronaviruses OC43 and 229E

evolutionary biology more details view paper
  • Downloaded 1,788 times
  • Download rankings, all-time:
    • Site-wide: 10,337
    • In evolutionary biology: 298
  • Year to date:
    • Site-wide: 2,655
  • Since beginning of last month:
    • Site-wide: 113,636

Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak

evolutionary biology more details view paper
  • Downloaded 1,757 times
  • Download rankings, all-time:
    • Site-wide: 10,595
    • In evolutionary biology: 313
  • Year to date:
    • Site-wide: 119,074
  • Since beginning of last month:
    • Site-wide: None

Multiple introductions of Zika virus into the United States revealed through genomic epidemiology

epidemiology more details view paper
  • Downloaded 1,728 times
  • Download rankings, all-time:
    • Site-wide: 10,847
    • In epidemiology: 801
  • Year to date:
    • Site-wide: 90,558
  • Since beginning of last month:
    • Site-wide: None

Viral genome sequencing places White House COVID-19 outbreak into phylogenetic context

epidemiology more details view paper
  • Downloaded 1,719 times
  • Download rankings, all-time:
    • Site-wide: 10,952
    • In epidemiology: 805
  • Year to date:
    • Site-wide: 17,070
  • Since beginning of last month:
    • Site-wide: 44,734

Seasonal influenza circulation patterns and projections for 2016-2017

evolutionary biology more details view paper
  • Downloaded 1,459 times
  • Download rankings, all-time:
    • Site-wide: 13,922
    • In evolutionary biology: 462
  • Year to date:
    • Site-wide: 141,104
  • Since beginning of last month:
    • Site-wide: None

The Seattle Flu Study: a multi-arm community-based prospective study protocol for assessing influenza prevalence, transmission, and genomic epidemiology

infectious diseases more details view paper
  • Downloaded 1,404 times
  • Download rankings, all-time:
    • Site-wide: 14,756
    • In infectious diseases: 1,642
  • Year to date:
    • Site-wide: 67,175
  • Since beginning of last month:
    • Site-wide: 107,372

Seattle Flu Study - Swab and Send: Study Protocol for At-Home Surveillance Methods to Estimate the Burden of Respiratory Pathogens on a City-Wide Scale

infectious diseases more details view paper
  • Downloaded 1,169 times
  • Download rankings, all-time:
    • Site-wide: 19,397
    • In infectious diseases: 1,871
  • Year to date:
    • Site-wide: 67,394
  • Since beginning of last month:
    • Site-wide: 46,165

Dengue antigenic relationships predict evolutionary dynamics

evolutionary biology more details view paper
  • Downloaded 925 times
  • Download rankings, all-time:
    • Site-wide: 27,332
    • In evolutionary biology: 1,171
  • Year to date:
    • Site-wide: 117,650
  • Since beginning of last month:
    • Site-wide: None

Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State

epidemiology more details view paper
  • Downloaded 925 times
  • Download rankings, all-time:
    • Site-wide: 27,316
    • In epidemiology: 1,521
  • Year to date:
    • Site-wide: 19,603
  • Since beginning of last month:
    • Site-wide: 28,165

Real-time analysis and visualization of pathogen sequence data

microbiology more details view paper
  • Downloaded 921 times
  • Download rankings, all-time:
    • Site-wide: 27,470
    • In microbiology: 1,640
  • Year to date:
    • Site-wide: 128,031
  • Since beginning of last month:
    • Site-wide: 70,716

High-resolution influenza mapping of a city reveals socioeconomic determinants of transmission within and between urban quarters

microbiology more details view paper
  • Downloaded 814 times
  • Download rankings, all-time:
    • Site-wide: 32,682
    • In microbiology: 1,975
  • Year to date:
    • Site-wide: 91,016
  • Since beginning of last month:
    • Site-wide: 40,447

Genetic characterization of the Zika virus epidemic in the US Virgin Islands

epidemiology more details view paper
  • Downloaded 797 times
  • Download rankings, all-time:
    • Site-wide: 33,642
    • In epidemiology: 1,739
  • Year to date:
    • Site-wide: 121,499
  • Since beginning of last month:
    • Site-wide: 82,355

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

evolutionary biology more details view paper
  • Downloaded 774 times
  • Download rankings, all-time:
    • Site-wide: 35,085
    • In evolutionary biology: 1,612
  • Year to date:
    • Site-wide: 110,748
  • Since beginning of last month:
    • Site-wide: 78,052

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

microbiology more details view paper
  • Downloaded 759 times
  • Download rankings, all-time:
    • Site-wide: 36,035
    • In microbiology: 2,199
  • Year to date:
    • Site-wide: 100,363
  • Since beginning of last month:
    • Site-wide: 41,584

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

epidemiology more details view paper
  • Downloaded 682 times
  • Download rankings, all-time:
    • Site-wide: 41,647
    • In epidemiology: 2,048
  • Year to date:
    • Site-wide: 130,436
  • Since beginning of last month:
    • Site-wide: None

Comprehensive mapping of avian influenza polymerase adaptation to the human host

microbiology more details view paper
  • Downloaded 655 times
  • Download rankings, all-time:
    • Site-wide: 43,940
    • In microbiology: 2,715
  • Year to date:
    • Site-wide: 141,737
  • Since beginning of last month:
    • Site-wide: 64,464

Recombination patterns in coronaviruses

evolutionary biology more details view paper
  • Downloaded 654 times
  • Download rankings, all-time:
    • Site-wide: 44,020
    • In evolutionary biology: 2,127
  • Year to date:
    • Site-wide: 5,767
  • Since beginning of last month:
    • Site-wide: 36,609

Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia

genomics more details view paper
  • Downloaded 649 times
  • Download rankings, all-time:
    • Site-wide: 44,396
    • In genomics: 3,544
  • Year to date:
    • Site-wide: 136,432
  • Since beginning of last month:
    • Site-wide: None

Nextstrain: real-time tracking of pathogen evolution

evolutionary biology more details view paper
  • Downloaded 579 times
  • Download rankings, all-time:
    • Site-wide: 51,331
    • In evolutionary biology: 2,594
  • Year to date:
    • Site-wide: 91,929
  • Since beginning of last month:
    • Site-wide: 78,195

Limited predictability of amino acid substitutions in seasonal influenza viruses

evolutionary biology more details view paper
  • Downloaded 577 times
  • Download rankings, all-time:
    • Site-wide: 51,605
    • In evolutionary biology: 2,602
  • Year to date:
    • Site-wide: 57,364
  • Since beginning of last month:
    • Site-wide: 115,284

Seasonal influenza circulation patterns and projections for September 2019 to September 2020

evolutionary biology more details view paper
  • Downloaded 555 times
  • Download rankings, all-time:
    • Site-wide: 54,024
    • In evolutionary biology: 2,764
  • Year to date:
    • Site-wide: 91,486
  • Since beginning of last month:
    • Site-wide: None

Early Prediction of Antigenic Transitions for Influenza A H3N2

epidemiology more details view paper
  • Downloaded 522 times
  • Download rankings, all-time:
    • Site-wide: 58,171
    • In epidemiology: 2,615
  • Year to date:
    • Site-wide: 151,629
  • Since beginning of last month:
    • Site-wide: None

Evolution and rapid spread of a reassortant A(H3N2) virus that predominated the 2017-2018 influenza season

genomics more details view paper
  • Downloaded 510 times
  • Download rankings, all-time:
    • Site-wide: 59,799
    • In genomics: 4,369
  • Year to date:
    • Site-wide: 147,638
  • Since beginning of last month:
    • Site-wide: 83,380

Quantifying within-host diversity of H5N1 influenza viruses in humans and poultry in Cambodia

microbiology more details view paper
  • Downloaded 509 times
  • Download rankings, all-time:
    • Site-wide: 59,821
    • In microbiology: 3,873
  • Year to date:
    • Site-wide: 116,107
  • Since beginning of last month:
    • Site-wide: None

Seasonal influenza circulation patterns and projections for Feb 2018 to Feb 2019

evolutionary biology more details view paper
  • Downloaded 482 times
  • Download rankings, all-time:
    • Site-wide: 63,511
    • In evolutionary biology: 3,306
  • Year to date:
    • Site-wide: 132,026
  • Since beginning of last month:
    • Site-wide: 57,571

Modern-Day SIV viral diversity generated by extensive recombination and cross-species transmission

evolutionary biology more details view paper
  • Downloaded 467 times
  • Download rankings, all-time:
    • Site-wide: 65,856
    • In evolutionary biology: 3,437
  • Year to date:
    • Site-wide: 134,429
  • Since beginning of last month:
    • Site-wide: 78,306

Seasonal influenza circulation patterns and projections for Sep 2017 to Sep 2018

evolutionary biology more details view paper
  • Downloaded 383 times
  • Download rankings, all-time:
    • Site-wide: 80,034
    • In evolutionary biology: 4,185
  • Year to date:
    • Site-wide: 149,609
  • Since beginning of last month:
    • Site-wide: None

Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State

infectious diseases more details view paper
  • Downloaded 366 times
  • Download rankings, all-time:
    • Site-wide: 83,391
    • In infectious diseases: 3,859
  • Year to date:
    • Site-wide: 13,352
  • Since beginning of last month:
    • Site-wide: 49,698

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

bioinformatics more details view paper
  • Downloaded 355 times
  • Download rankings, all-time:
    • Site-wide: 85,666
    • In bioinformatics: 7,724
  • Year to date:
    • Site-wide: 100,812
  • Since beginning of last month:
    • Site-wide: 69,703

Seasonal influenza circulation patterns and projections for 2017-2018

evolutionary biology more details view paper
  • Downloaded 314 times
  • Download rankings, all-time:
    • Site-wide: 94,432
    • In evolutionary biology: 4,871
  • Year to date:
    • Site-wide: 134,415
  • Since beginning of last month:
    • Site-wide: None

Operationalizing genomic epidemiology during the Nord-Kivu Ebola outbreak, Democratic Republic of the Congo.

epidemiology more details view paper
  • Downloaded 303 times
  • Download rankings, all-time:
    • Site-wide: 96,873
    • In epidemiology: 4,076
  • Year to date:
    • Site-wide: 65,243
  • Since beginning of last month:
    • Site-wide: 108,435

SARS-CoV-2 Epidemiology on a Public University Campus in Washington State

epidemiology more details view paper
  • Downloaded 303 times
  • Download rankings, all-time:
    • Site-wide: 96,943
    • In epidemiology: 4,081
  • Year to date:
    • Site-wide: 17,572
  • Since beginning of last month:
    • Site-wide: 99,201

Repeated introductions and intensive community transmission fueled a mumps virus outbreak in Washington State

infectious diseases more details view paper
  • Downloaded 275 times
  • Download rankings, all-time:
    • Site-wide: 103,543
    • In infectious diseases: 4,397
  • Year to date:
    • Site-wide: 29,065
  • Since beginning of last month:
    • Site-wide: 34,141

Characterising the epidemic spread of Influenza A/H3N2 within a city through phylogenetics

evolutionary biology more details view paper
  • Downloaded 266 times
  • Download rankings, all-time:
    • Site-wide: 105,639
    • In evolutionary biology: 5,377
  • Year to date:
    • Site-wide: 143,874
  • Since beginning of last month:
    • Site-wide: 98,619

Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution

evolutionary biology more details view paper
  • Downloaded 211 times
  • Download rankings, all-time:
    • Site-wide: 119,328
    • In evolutionary biology: 5,998
  • Year to date:
    • Site-wide: 122,765
  • Since beginning of last month:
    • Site-wide: None

Helicobacter pylori diversification during chronic infection within a single host generates sub-populations with distinct phenotypes

microbiology more details view paper
  • Downloaded 150 times
  • Download rankings, all-time:
    • Site-wide: 133,584
    • In microbiology: 10,156
  • Year to date:
    • Site-wide: 110,311
  • Since beginning of last month:
    • Site-wide: 8,902

A Remote Household-Based Approach to Influenza Self-Testing and Antiviral Treatment

infectious diseases more details view paper
  • Downloaded 114 times
  • Download rankings, all-time:
    • Site-wide: 141,278
    • In infectious diseases: 5,502
  • Year to date:
    • Site-wide: 56,175
  • Since beginning of last month:
    • Site-wide: None

Evaluating Specimen Quality and Results from a Community-Wide, Home-Based Respiratory Surveillance Study

microbiology more details view paper
  • Downloaded 65 times
  • Download rankings, all-time:
    • Site-wide: 148,766
    • In microbiology: 11,580
  • Year to date:
    • Site-wide: 131,025
  • Since beginning of last month:
    • Site-wide: None

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