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Author: Trevor Bedford

Rankings

  • All-time downloads: 96,122 (rank: 2,325 (tie) )
  • Categories:
    • bioinformatics: 406 (rank: 39,522 (tie) )
    • epidemiology: 43,371 (rank: 630 )
    • evolutionary biology: 17,556 (rank: 116 )
    • genomics: 6,336 (rank: 4,725 )
    • infectious diseases: 14,070 (rank: 5,557 (tie) )
    • microbiology: 4,468 (rank: 4,906 )
    • molecular biology: 6,512 (rank: 597 (tie) )

Downloads per author, site-wide

Preprints

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

epidemiology more details view paper
  • Downloaded 13,100 times
  • Download rankings, all-time:
    • Site-wide: 966
    • In epidemiology: 147
  • Year to date:
    • Site-wide: 2,404
  • Since beginning of last month:
    • Site-wide: 11,761

Cryptic transmission of SARS-CoV-2 in Washington State

epidemiology more details view paper
  • Downloaded 10,013 times
  • Download rankings, all-time:
    • Site-wide: 1,349
    • In epidemiology: 179
  • Year to date:
    • Site-wide: 28,396
  • Since beginning of last month:
    • Site-wide: 21,433

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

infectious diseases more details view paper
  • Downloaded 7,190 times
  • Download rankings, all-time:
    • Site-wide: 2,090
    • In infectious diseases: 581
  • Year to date:
    • Site-wide: 47,981
  • Since beginning of last month:
    • Site-wide: 16,713

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

molecular biology more details view paper
  • Downloaded 6,624 times
  • Download rankings, all-time:
    • Site-wide: 2,336
    • In molecular biology: 40
  • Year to date:
    • Site-wide: 14,805
  • Since beginning of last month:
    • Site-wide: 11,586

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

epidemiology more details view paper
  • Downloaded 6,289 times
  • Download rankings, all-time:
    • Site-wide: 2,510
    • In epidemiology: 285
  • Year to date:
    • Site-wide: 71,348
  • Since beginning of last month:
    • Site-wide: 108,897

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

genomics more details view paper
  • Downloaded 5,087 times
  • Download rankings, all-time:
    • Site-wide: 3,331
    • In genomics: 289
  • Year to date:
    • Site-wide: 56,753
  • Since beginning of last month:
    • Site-wide: None

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

evolutionary biology more details view paper
  • Downloaded 4,690 times
  • Download rankings, all-time:
    • Site-wide: 3,729
    • In evolutionary biology: 49
  • Year to date:
    • Site-wide: 4,943
  • Since beginning of last month:
    • Site-wide: 95,682

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

epidemiology more details view paper
  • Downloaded 3,590 times
  • Download rankings, all-time:
    • Site-wide: 5,453
    • In epidemiology: 581
  • Year to date:
    • Site-wide: 500
  • Since beginning of last month:
    • Site-wide: 4,023

Associations between SARS-CoV-2 variants and risk of COVID-19 hospitalization among confirmed cases in Washington State: a retrospective cohort study

infectious diseases more details view paper
  • Downloaded 2,630 times
  • Download rankings, all-time:
    • Site-wide: 8,625
    • In infectious diseases: 1,455
  • Year to date:
    • Site-wide: 4,748
  • Since beginning of last month:
    • Site-wide: 58,816

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

evolutionary biology more details view paper
  • Downloaded 2,171 times
  • Download rankings, all-time:
    • Site-wide: 11,539
    • In evolutionary biology: 304
  • Year to date:
    • Site-wide: 36,668
  • Since beginning of last month:
    • Site-wide: 108,313

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

epidemiology more details view paper
  • Downloaded 1,984 times
  • Download rankings, all-time:
    • Site-wide: 13,191
    • In epidemiology: 966
  • Year to date:
    • Site-wide: 79,016
  • Since beginning of last month:
    • Site-wide: 90,709

MERS-CoV spillover at the camel-human interface

epidemiology more details view paper
  • Downloaded 1,925 times
  • Download rankings, all-time:
    • Site-wide: 13,823
    • In epidemiology: 989
  • Year to date:
    • Site-wide: 139,044
  • Since beginning of last month:
    • Site-wide: 46,621

Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak

evolutionary biology more details view paper
  • Downloaded 1,861 times
  • Download rankings, all-time:
    • Site-wide: 14,534
    • In evolutionary biology: 386
  • Year to date:
    • Site-wide: 149,862
  • Since beginning of last month:
    • Site-wide: 152,923

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

epidemiology more details view paper
  • Downloaded 1,842 times
  • Download rankings, all-time:
    • Site-wide: 14,778
    • In epidemiology: 1,039
  • Year to date:
    • Site-wide: 188,482
  • Since beginning of last month:
    • Site-wide: 74,851

Seasonal influenza circulation patterns and projections for 2016-2017

evolutionary biology more details view paper
  • Downloaded 1,529 times
  • Download rankings, all-time:
    • Site-wide: 19,731
    • In evolutionary biology: 568
  • Year to date:
    • Site-wide: 204,598
  • 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 1,512 times
  • Download rankings, all-time:
    • Site-wide: 20,087
    • In infectious diseases: 2,252
  • Year to date:
    • Site-wide: 158,057
  • Since beginning of last month:
    • Site-wide: 162,445

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 1,343 times
  • Download rankings, all-time:
    • Site-wide: 24,284
    • In infectious diseases: 2,495
  • Year to date:
    • Site-wide: 107,362
  • Since beginning of last month:
    • Site-wide: 162,446

Recombination patterns in coronaviruses

evolutionary biology more details view paper
  • Downloaded 1,314 times
  • Download rankings, all-time:
    • Site-wide: 25,118
    • In evolutionary biology: 834
  • Year to date:
    • Site-wide: 19,090
  • 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 1,171 times
  • Download rankings, all-time:
    • Site-wide: 30,175
    • In epidemiology: 1,716
  • Year to date:
    • Site-wide: 77,338
  • Since beginning of last month:
    • Site-wide: 157,634

SARS-CoV-2 variant dynamics across US states show consistent differences in effective reproduction numbers

epidemiology more details view paper
  • Downloaded 1,067 times
  • Download rankings, all-time:
    • Site-wide: 34,820
    • In epidemiology: 2,206
  • Year to date:
    • Site-wide: 4,496
  • Since beginning of last month:
    • Site-wide: None

Dengue antigenic relationships predict evolutionary dynamics

evolutionary biology more details view paper
  • Downloaded 1,037 times
  • Download rankings, all-time:
    • Site-wide: 36,370
    • In evolutionary biology: 1,369
  • Year to date:
    • Site-wide: 144,819
  • Since beginning of last month:
    • Site-wide: 125,326

Real-time analysis and visualization of pathogen sequence data

microbiology more details view paper
  • Downloaded 1,028 times
  • Download rankings, all-time:
    • Site-wide: 36,835
    • In microbiology: 2,088
  • Year to date:
    • Site-wide: 134,123
  • Since beginning of last month:
    • Site-wide: 40,421

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

microbiology more details view paper
  • Downloaded 940 times
  • Download rankings, all-time:
    • Site-wide: 42,268
    • In microbiology: 2,398
  • Year to date:
    • Site-wide: 148,968
  • Since beginning of last month:
    • Site-wide: 165,693

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

epidemiology more details view paper
  • Downloaded 918 times
  • Download rankings, all-time:
    • Site-wide: 43,845
    • In epidemiology: 2,217
  • Year to date:
    • Site-wide: 161,668
  • Since beginning of last month:
    • Site-wide: 75,400

State-dependent evolutionary models reveal modes of solid tumor growth

cancer biology more details view paper
  • Downloaded 895 times
  • Download rankings, all-time:
    • Site-wide: 45,596
    • In cancer biology: None
  • Year to date:
    • Site-wide: 4,116
  • Since beginning of last month:
    • Site-wide: 1,204

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

evolutionary biology more details view paper
  • Downloaded 890 times
  • Download rankings, all-time:
    • Site-wide: 45,907
    • In evolutionary biology: 1,945
  • Year to date:
    • Site-wide: 109,330
  • Since beginning of last month:
    • Site-wide: 12,185

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

microbiology more details view paper
  • Downloaded 885 times
  • Download rankings, all-time:
    • Site-wide: 46,347
    • In microbiology: 2,640
  • Year to date:
    • Site-wide: 139,328
  • Since beginning of last month:
    • Site-wide: 186,573

Comprehensive mapping of avian influenza polymerase adaptation to the human host

microbiology more details view paper
  • Downloaded 750 times
  • Download rankings, all-time:
    • Site-wide: 59,270
    • In microbiology: 3,389
  • Year to date:
    • Site-wide: 198,757
  • Since beginning of last month:
    • Site-wide: 128,942

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

genomics more details view paper
  • Downloaded 749 times
  • Download rankings, all-time:
    • Site-wide: 59,428
    • In genomics: 4,121
  • Year to date:
    • Site-wide: 124,647
  • Since beginning of last month:
    • Site-wide: 62,498

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

epidemiology more details view paper
  • Downloaded 738 times
  • Download rankings, all-time:
    • Site-wide: 60,732
    • In epidemiology: 2,792
  • Year to date:
    • Site-wide: 192,715
  • Since beginning of last month:
    • Site-wide: None

Limited predictability of amino acid substitutions in seasonal influenza viruses

evolutionary biology more details view paper
  • Downloaded 715 times
  • Download rankings, all-time:
    • Site-wide: 63,551
    • In evolutionary biology: 2,810
  • Year to date:
    • Site-wide: 116,226
  • Since beginning of last month:
    • Site-wide: 163,524

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

evolutionary biology more details view paper
  • Downloaded 700 times
  • Download rankings, all-time:
    • Site-wide: 65,539
    • In evolutionary biology: 2,937
  • Year to date:
    • Site-wide: 118,033
  • 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 676 times
  • Download rankings, all-time:
    • Site-wide: 68,775
    • In infectious diseases: 4,325
  • Year to date:
    • Site-wide: 48,686
  • Since beginning of last month:
    • Site-wide: 119,416

Nextstrain: real-time tracking of pathogen evolution

evolutionary biology more details view paper
  • Downloaded 649 times
  • Download rankings, all-time:
    • Site-wide: 72,839
    • In evolutionary biology: 3,241
  • Year to date:
    • Site-wide: 165,821
  • Since beginning of last month:
    • Site-wide: 51,437

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

microbiology more details view paper
  • Downloaded 609 times
  • Download rankings, all-time:
    • Site-wide: 78,927
    • In microbiology: 4,780
  • Year to date:
    • Site-wide: 173,061
  • Since beginning of last month:
    • Site-wide: 131,237

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

infectious diseases more details view paper
  • Downloaded 591 times
  • Download rankings, all-time:
    • Site-wide: 82,094
    • In infectious diseases: 5,198
  • Year to date:
    • Site-wide: 15,288
  • Since beginning of last month:
    • Site-wide: 166,152

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

epidemiology more details view paper
  • Downloaded 586 times
  • Download rankings, all-time:
    • Site-wide: 82,876
    • In epidemiology: 3,651
  • Year to date:
    • Site-wide: 48,510
  • Since beginning of last month:
    • Site-wide: 179,974

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

genomics more details view paper
  • Downloaded 586 times
  • Download rankings, all-time:
    • Site-wide: 83,004
    • In genomics: 5,220
  • Year to date:
    • Site-wide: 196,497
  • Since beginning of last month:
    • Site-wide: 62,002

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

evolutionary biology more details view paper
  • Downloaded 566 times
  • Download rankings, all-time:
    • Site-wide: 86,647
    • In evolutionary biology: 3,893
  • Year to date:
    • Site-wide: 190,139
  • Since beginning of last month:
    • Site-wide: 80,905

Early Prediction of Antigenic Transitions for Influenza A H3N2

epidemiology more details view paper
  • Downloaded 560 times
  • Download rankings, all-time:
    • Site-wide: 87,800
    • In epidemiology: 3,748
  • Year to date:
    • Site-wide: 207,637
  • Since beginning of last month:
    • Site-wide: None

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

evolutionary biology more details view paper
  • Downloaded 512 times
  • Download rankings, all-time:
    • Site-wide: 97,682
    • In evolutionary biology: 4,377
  • Year to date:
    • Site-wide: 208,441
  • Since beginning of last month:
    • Site-wide: None

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

infectious diseases more details view paper
  • Downloaded 477 times
  • Download rankings, all-time:
    • Site-wide: 105,762
    • In infectious diseases: 5,532
  • Year to date:
    • Site-wide: 96,811
  • Since beginning of last month:
    • Site-wide: 144,080

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

evolutionary biology more details view paper
  • Downloaded 459 times
  • Download rankings, all-time:
    • Site-wide: 109,809
    • In evolutionary biology: 4,974
  • Year to date:
    • Site-wide: 201,330
  • Since beginning of last month:
    • Site-wide: 175,332

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

epidemiology more details view paper
  • Downloaded 442 times
  • Download rankings, all-time:
    • Site-wide: 114,080
    • In epidemiology: 4,826
  • Year to date:
    • Site-wide: 128,582
  • Since beginning of last month:
    • Site-wide: 91,949

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

bioinformatics more details view paper
  • Downloaded 423 times
  • Download rankings, all-time:
    • Site-wide: 118,924
    • In bioinformatics: 9,575
  • Year to date:
    • Site-wide: 197,422
  • Since beginning of last month:
    • Site-wide: 185,575

Seasonal influenza circulation patterns and projections for 2017-2018

evolutionary biology more details view paper
  • Downloaded 380 times
  • Download rankings, all-time:
    • Site-wide: 131,004
    • In evolutionary biology: 5,869
  • Year to date:
    • Site-wide: 201,365
  • Since beginning of last month:
    • Site-wide: 129,295

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

evolutionary biology more details view paper
  • Downloaded 313 times
  • Download rankings, all-time:
    • Site-wide: 150,817
    • In evolutionary biology: 6,760
  • Year to date:
    • Site-wide: 204,266
  • Since beginning of last month:
    • Site-wide: 158,113

Mapping the emergence of SARS-CoV-2 Omicron variants on a university campus

epidemiology more details view paper
  • Downloaded 312 times
  • Download rankings, all-time:
    • Site-wide: 151,248
    • In epidemiology: 6,254
  • Year to date:
    • Site-wide: 23,587
  • Since beginning of last month:
    • Site-wide: 138,164

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

evolutionary biology more details view paper
  • Downloaded 265 times
  • Download rankings, all-time:
    • Site-wide: 164,980
    • In evolutionary biology: 7,298
  • Year to date:
    • Site-wide: 203,953
  • Since beginning of last month:
    • Site-wide: 106,989

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

microbiology more details view paper
  • Downloaded 239 times
  • Download rankings, all-time:
    • Site-wide: 172,201
    • In microbiology: 12,381
  • Year to date:
    • Site-wide: 171,016
  • Since beginning of last month:
    • Site-wide: 111,605

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

microbiology more details view paper
  • Downloaded 159 times
  • Download rankings, all-time:
    • Site-wide: 191,057
    • In microbiology: 14,098
  • Year to date:
    • Site-wide: 174,050
  • Since beginning of last month:
    • Site-wide: 180,958

Trends in risk factors and symptoms associated with SARS-CoV-2 and Rhinovirus test positivity in King County, Washington: A Test-Negative Design Study of the Greater Seattle Coronavirus Assessment Network

epidemiology more details view paper
  • Downloaded 141 times
  • Download rankings, all-time:
    • Site-wide: 194,315
    • In epidemiology: None
  • Year to date:
    • Site-wide: 69,499
  • Since beginning of last month:
    • Site-wide: 146,166

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