Author: Trevor Bedford

Downloads per author, site-wide

Preprints

Cryptic transmission of SARS-CoV-2 in Washington State

• Downloaded 9,056 times
• Download rankings, all-time:
  • Site-wide: 789
  • In epidemiology: 106
• Year to date:
  • Site-wide: 5,014
• Since beginning of last month:
  • Site-wide: 5,508

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

• Downloaded 6,270 times
• Download rankings, all-time:
  • Site-wide: 1,268
  • In infectious diseases: 327
• Year to date:
  • Site-wide: 20,207
• Since beginning of last month:
  • Site-wide: 16,125

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

• Downloaded 5,819 times
• Download rankings, all-time:
  • Site-wide: 1,404
  • In epidemiology: 165
• Year to date:
  • Site-wide: 21,720
• Since beginning of last month:
  • Site-wide: 17,961

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

• Downloaded 4,632 times
• Download rankings, all-time:
  • Site-wide: 1,928
  • In genomics: 217
• Year to date:
  • Site-wide: 13,210
• Since beginning of last month:
  • Site-wide: 31,367

MERS-CoV spillover at the camel-human interface

• Downloaded 1,747 times
• Download rankings, all-time:
  • Site-wide: 7,991
  • In epidemiology: 585
• Year to date:
  • Site-wide: 40,784
• Since beginning of last month:
  • Site-wide: 55,848

Epidemiological and evolutionary analysis of the 2014 Ebola virus outbreak

• Downloaded 1,717 times
• Download rankings, all-time:
  • Site-wide: 8,206
  • In evolutionary biology: 260
• Year to date:
  • Site-wide: 116,398
• Since beginning of last month:
  • Site-wide: 67,366

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

• Downloaded 1,664 times
• Download rankings, all-time:
  • Site-wide: 8,640
  • In epidemiology: 619
• Year to date:
  • Site-wide: 119,133
• Since beginning of last month:
  • Site-wide: 120,647

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

• Downloaded 1,448 times
• Download rankings, all-time:
  • Site-wide: 10,602
  • In epidemiology: 721
• Year to date:
  • Site-wide: 6,230
• Since beginning of last month:
  • Site-wide: 3,976

Seasonal influenza circulation patterns and projections for 2016-2017

• Downloaded 1,433 times
• Download rankings, all-time:
  • Site-wide: 10,790
  • In evolutionary biology: 378
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: 119,283

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

• Downloaded 1,315 times
• Download rankings, all-time:
  • Site-wide: 12,268
  • In infectious diseases: 1,201
• Year to date:
  • Site-wide: 64,147
• Since beginning of last month:
  • Site-wide: 39,463

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

• Downloaded 1,078 times
• Download rankings, all-time:
  • Site-wide: 16,596
  • In infectious diseases: 1,387
• Year to date:
  • Site-wide: 100,424
• Since beginning of last month:
  • Site-wide: 70,572

Real-time analysis and visualization of pathogen sequence data

• Downloaded 886 times
• Download rankings, all-time:
  • Site-wide: 22,117
  • In microbiology: 1,255
• Year to date:
  • Site-wide: 121,886
• Since beginning of last month:
  • Site-wide: 92,800

Dengue antigenic relationships predict evolutionary dynamics

• Downloaded 886 times
• Download rankings, all-time:
  • Site-wide: 22,124
  • In evolutionary biology: 1,034
• Year to date:
  • Site-wide: 97,994
• Since beginning of last month:
  • Site-wide: 16,460

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

• Downloaded 759 times
• Download rankings, all-time:
  • Site-wide: 27,469
  • In epidemiology: 1,402
• Year to date:
  • Site-wide: 111,641
• Since beginning of last month:
  • Site-wide: 118,204

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

• Downloaded 758 times
• Download rankings, all-time:
  • Site-wide: 27,554
  • In microbiology: 1,618
• Year to date:
  • Site-wide: 46,429
• Since beginning of last month:
  • Site-wide: 67,796

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

• Downloaded 733 times
• Download rankings, all-time:
  • Site-wide: 28,862
  • In evolutionary biology: 1,461
• Year to date:
  • Site-wide: 57,756
• Since beginning of last month:
  • Site-wide: 42,377

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

• Downloaded 717 times
• Download rankings, all-time:
  • Site-wide: 29,742
  • In microbiology: 1,768
• Year to date:
  • Site-wide: 26,730
• Since beginning of last month:
  • Site-wide: 104,704

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

• Downloaded 669 times
• Download rankings, all-time:
  • Site-wide: 32,674
  • In epidemiology: 1,574
• Year to date:
  • Site-wide: 11,901
• Since beginning of last month:
  • Site-wide: 7,049

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

• Downloaded 649 times
• Download rankings, all-time:
  • Site-wide: 34,009
  • In epidemiology: 1,619
• Year to date:
  • Site-wide: 119,742
• Since beginning of last month:
  • Site-wide: 116,222

Comprehensive mapping of avian influenza polymerase adaptation to the human host

• Downloaded 635 times
• Download rankings, all-time:
  • Site-wide: 34,961
  • In microbiology: 2,085
• Year to date:
  • Site-wide: 64,293
• Since beginning of last month:
  • Site-wide: 113,686

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

• Downloaded 624 times
• Download rankings, all-time:
  • Site-wide: 35,778
  • In genomics: 3,116
• Year to date:
  • Site-wide: 83,874
• Since beginning of last month:
  • Site-wide: 80,628

Nextstrain: real-time tracking of pathogen evolution

• Downloaded 520 times
• Download rankings, all-time:
  • Site-wide: 44,914
  • In evolutionary biology: 2,495
• Year to date:
  • Site-wide: 81,513
• Since beginning of last month:
  • Site-wide: 85,934

Early Prediction of Antigenic Transitions for Influenza A H3N2

• Downloaded 510 times
• Download rankings, all-time:
  • Site-wide: 45,919
  • In epidemiology: 2,032
• Year to date:
  • Site-wide: 117,004
• Since beginning of last month:
  • Site-wide: 121,954

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

• Downloaded 496 times
• Download rankings, all-time:
  • Site-wide: 47,435
  • In genomics: 3,813
• Year to date:
  • Site-wide: 55,802
• Since beginning of last month:
  • Site-wide: 106,097

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

• Downloaded 494 times
• Download rankings, all-time:
  • Site-wide: 47,730
  • In evolutionary biology: 2,691
• Year to date:
  • Site-wide: 102,860
• Since beginning of last month:
  • Site-wide: 55,047

Limited predictability of amino acid substitutions in seasonal influenza viruses

• Downloaded 478 times
• Download rankings, all-time:
  • Site-wide: 49,490
  • In evolutionary biology: 2,802
• Year to date:
  • Site-wide: 29,255
• Since beginning of last month:
  • Site-wide: 30,901

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

• Downloaded 471 times
• Download rankings, all-time:
  • Site-wide: 50,395
  • In microbiology: 3,247
• Year to date:
  • Site-wide: 64,275
• Since beginning of last month:
  • Site-wide: 92,007

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

• Downloaded 452 times
• Download rankings, all-time:
  • Site-wide: 52,715
  • In evolutionary biology: 2,980
• Year to date:
  • Site-wide: 104,319
• Since beginning of last month:
  • Site-wide: 102,589

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

• Downloaded 439 times
• Download rankings, all-time:
  • Site-wide: 54,379
  • In evolutionary biology: 3,075
• Year to date:
  • Site-wide: 99,877
• Since beginning of last month:
  • Site-wide: 101,064

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

• Downloaded 366 times
• Download rankings, all-time:
  • Site-wide: 65,024
  • In evolutionary biology: 3,694
• Year to date:
  • Site-wide: 110,227
• Since beginning of last month:
  • Site-wide: 116,634

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

• Downloaded 304 times
• Download rankings, all-time:
  • Site-wide: 75,885
  • In bioinformatics: 7,078
• Year to date:
  • Site-wide: 79,861
• Since beginning of last month:
  • Site-wide: 33,986

Seasonal influenza circulation patterns and projections for 2017-2018

• Downloaded 288 times
• Download rankings, all-time:
  • Site-wide: 79,016
  • In evolutionary biology: 4,436
• Year to date:
  • Site-wide: 82,737
• Since beginning of last month:
  • Site-wide: 119,677

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

• Downloaded 247 times
• Download rankings, all-time:
  • Site-wide: 87,446
  • In evolutionary biology: 4,828
• Year to date:
  • Site-wide: 73,790
• Since beginning of last month:
  • Site-wide: 98,348

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

• Downloaded 216 times
• Download rankings, all-time:
  • Site-wide: 93,962
  • In epidemiology: 3,771
• Year to date:
  • Site-wide: 35,491
• Since beginning of last month:
  • Site-wide: 30,024

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

• Downloaded 176 times
• Download rankings, all-time:
  • Site-wide: 102,317
  • In evolutionary biology: 5,499
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 175 times
• Download rankings, all-time:
  • Site-wide: 102,498
  • In evolutionary biology: 5,511
• Year to date:
  • Site-wide: 101,080
• Since beginning of last month:
  • Site-wide: 113,528

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

• Downloaded 109 times
• Download rankings, all-time:
  • Site-wide: 114,628
  • In microbiology: 8,807
• Year to date:
  • Site-wide: 58,511
• Since beginning of last month:
  • Site-wide: 107,242

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

• Downloaded 57 times
• Download rankings, all-time:
  • Site-wide: 121,979
  • In infectious diseases: 3,881
• Year to date:
  • Site-wide: None
• Since beginning of last month:
  • Site-wide: None

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

• Downloaded 38 times
• Download rankings, all-time:
  • Site-wide: 123,093
  • In microbiology: 9,701
• Year to date:
  • Site-wide: 63,556
• Since beginning of last month:
  • Site-wide: 21,641