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Author: Andrew Rambaut

Rankings

  • All-time downloads: 145,960 (rank: 744 )
  • Categories:
    • bioinformatics: 1,599 (rank: 10,624 (tie) )
    • epidemiology: 20,024 (rank: 933 )
    • evolutionary biology: 23,793 (rank: 67 )
    • genetic and genomic medicine: 735 (rank: 5,342 (tie) )
    • genetics: 29,363 (rank: 230 )
    • genomics: 5,242 (rank: 5,004 )
    • infectious diseases: 41,438 (rank: 1,400 )
    • microbiology: 23,766 (rank: 764 )

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Preprints

Making Genomic Surveillance Deliver: A Lineage Classification and Nomenclature System to Inform Rabies Virus Elimination

genomics more details view paper

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The emergence of SARS-CoV-2 in Europe and the US

genetics more details view paper
  • Downloaded 27,066 times
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    • Site-wide: 308
    • In genetics: 3
  • Year to date:
    • Site-wide: 1,996
  • Since beginning of last month:
    • Site-wide: 2,853

Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data

infectious diseases more details view paper
  • Downloaded 17,647 times
  • Download rankings, all-time:
    • Site-wide: 503
    • In infectious diseases: 177
  • Year to date:
    • Site-wide: 142
  • Since beginning of last month:
    • Site-wide: 1,077

Evolutionary origins of the SARS-CoV-2 sarbecovirus lineage responsible for the COVID-19 pandemic

evolutionary biology more details view paper
  • Downloaded 17,112 times
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    • Site-wide: 519
    • In evolutionary biology: 8
  • Year to date:
    • Site-wide: 2,692
  • Since beginning of last month:
    • Site-wide: 7,214

The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity

microbiology more details view paper
  • Downloaded 14,573 times
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    • Site-wide: 638
    • In microbiology: 74
  • Year to date:
    • Site-wide: 768
  • Since beginning of last month:
    • Site-wide: 9,973

Genomic epidemiology of SARS-CoV-2 spread in Scotland highlights the role of European travel in COVID-19 emergence

infectious diseases more details view paper
  • Downloaded 8,795 times
  • Download rankings, all-time:
    • Site-wide: 1,209
    • In infectious diseases: 365
  • Year to date:
    • Site-wide: 14,626
  • Since beginning of last month:
    • Site-wide: 15,426

A dynamic nomenclature proposal for SARS-CoV-2 to assist genomic epidemiology

microbiology more details view paper
  • Downloaded 8,550 times
  • Download rankings, all-time:
    • Site-wide: 1,273
    • In microbiology: 120
  • Year to date:
    • Site-wide: 1,225
  • Since beginning of last month:
    • Site-wide: 3,033

Evolution and epidemic spread of SARS-CoV-2 in Brazil

infectious diseases more details view paper
  • Downloaded 6,068 times
  • Download rankings, all-time:
    • Site-wide: 1,975
    • In infectious diseases: 525
  • Year to date:
    • Site-wide: 24,745
  • Since beginning of last month:
    • Site-wide: 45,849

Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity

epidemiology more details view paper
  • Downloaded 5,864 times
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    • Site-wide: 2,061
    • In epidemiology: 247
  • Year to date:
    • Site-wide: 6,289
  • Since beginning of last month:
    • Site-wide: 9,019

Rapid SARS-CoV-2 whole genome sequencing for informed public health decision making in the Netherlands

genomics more details view paper
  • Downloaded 4,782 times
  • Download rankings, all-time:
    • Site-wide: 2,722
    • In genomics: 261
  • Year to date:
    • Site-wide: 17,841
  • Since beginning of last month:
    • Site-wide: 52,419

Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil

epidemiology more details view paper
  • Downloaded 4,353 times
  • Download rankings, all-time:
    • Site-wide: 3,105
    • In epidemiology: 332
  • Year to date:
    • Site-wide: 635
  • Since beginning of last month:
    • Site-wide: 4,139

Genomic epidemiology of SARS-CoV-2 in Guangdong Province, China

infectious diseases more details view paper
  • Downloaded 4,149 times
  • Download rankings, all-time:
    • Site-wide: 3,318
    • In infectious diseases: 726
  • Year to date:
    • Site-wide: 5,436
  • Since beginning of last month:
    • Site-wide: 3,905

A SARS-CoV-2 lineage A variant (A.23.1) with altered spike has emerged and is dominating the current Uganda epidemic

infectious diseases more details view paper
  • Downloaded 3,086 times
  • Download rankings, all-time:
    • Site-wide: 5,017
    • In infectious diseases: 952
  • Year to date:
    • Site-wide: 961
  • Since beginning of last month:
    • Site-wide: 3,974

Virus genomes reveal the factors that spread and sustained the West African Ebola epidemic.

epidemiology more details view paper
  • Downloaded 2,518 times
  • Download rankings, all-time:
    • Site-wide: 6,753
    • In epidemiology: 580
  • Year to date:
    • Site-wide: 70,920
  • Since beginning of last month:
    • Site-wide: 64,712

MERS-CoV recombination: implications about the reservoir and potential for adaptation

evolutionary biology more details view paper
  • Downloaded 2,502 times
  • Download rankings, all-time:
    • Site-wide: 6,818
    • In evolutionary biology: 152
  • Year to date:
    • Site-wide: 83,629
  • Since beginning of last month:
    • Site-wide: 121,248

Identification of a common deletion in the spike protein of SARS-CoV-2

genetics more details view paper
  • Downloaded 1,915 times
  • Download rankings, all-time:
    • Site-wide: 10,056
    • In genetics: 423
  • Year to date:
    • Site-wide: 50,076
  • Since beginning of last month:
    • Site-wide: 65,487

Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

epidemiology more details view paper
  • Downloaded 1,828 times
  • Download rankings, all-time:
    • Site-wide: 10,785
    • In epidemiology: 814
  • Year to date:
    • Site-wide: 8,596
  • Since beginning of last month:
    • Site-wide: 27,285

MERS-CoV spillover at the camel-human interface

epidemiology more details view paper
  • Downloaded 1,827 times
  • Download rankings, all-time:
    • Site-wide: 10,799
    • In epidemiology: 816
  • Year to date:
    • Site-wide: 95,843
  • Since beginning of last month:
    • Site-wide: 141,389

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

epidemiology more details view paper
  • Downloaded 1,762 times
  • Download rankings, all-time:
    • Site-wide: 11,399
    • In epidemiology: 856
  • Year to date:
    • Site-wide: 88,750
  • Since beginning of last month:
    • Site-wide: 104,178

Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study.

evolutionary biology more details view paper
  • Downloaded 1,649 times
  • Download rankings, all-time:
    • Site-wide: 12,534
    • In evolutionary biology: 380
  • Year to date:
    • Site-wide: 44,777
  • Since beginning of last month:
    • Site-wide: 52,883

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

evolutionary biology more details view paper
  • Downloaded 1,395 times
  • Download rankings, all-time:
    • Site-wide: 16,175
    • In evolutionary biology: 539
  • Year to date:
    • Site-wide: 60,950
  • Since beginning of last month:
    • Site-wide: 125,060

MAJORA: Continuous integration supporting decentralised sequencing for SARS-CoV-2 genomic surveillance

bioinformatics more details view paper
  • Downloaded 1,214 times
  • Download rankings, all-time:
    • Site-wide: 19,863
    • In bioinformatics: 2,264
  • Year to date:
    • Site-wide: 7,467
  • Since beginning of last month:
    • Site-wide: 25,914

Temporal signal and the phylodynamic threshold of SARS-CoV-2

evolutionary biology more details view paper
  • Downloaded 1,135 times
  • Download rankings, all-time:
    • Site-wide: 21,974
    • In evolutionary biology: 837
  • Year to date:
    • Site-wide: 44,788
  • Since beginning of last month:
    • Site-wide: 114,175

Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak

epidemiology more details view paper
  • Downloaded 1,080 times
  • Download rankings, all-time:
    • Site-wide: 23,614
    • In epidemiology: 1,418
  • Year to date:
    • Site-wide: 134,959
  • Since beginning of last month:
    • Site-wide: 124,030

COVID-19 in healthcare workers in three hospitals in the South of the Netherlands, March 2020

infectious diseases more details view paper
  • Downloaded 940 times
  • Download rankings, all-time:
    • Site-wide: 29,019
    • In infectious diseases: 2,431
  • Year to date:
    • Site-wide: 82,372
  • Since beginning of last month:
    • Site-wide: 97,355

Epidemic waves of COVID-19 in Scotland: a genomic perspective on the impact of the introduction and relaxation of lockdown on SARS-CoV-2

epidemiology more details view paper
  • Downloaded 792 times
  • Download rankings, all-time:
    • Site-wide: 36,969
    • In epidemiology: 1,923
  • Year to date:
    • Site-wide: 6,209
  • Since beginning of last month:
    • Site-wide: 44,656

Generation and transmission of inter-lineage recombinants in the SARS-CoV-2 pandemic

infectious diseases more details view paper
  • Downloaded 753 times
  • Download rankings, all-time:
    • Site-wide: 39,725
    • In infectious diseases: 2,873
  • Year to date:
    • Site-wide: 6,699
  • Since beginning of last month:
    • Site-wide: 22,106

Genomic Sequencing of SARS-COV-2 in Rwanda: evolution and regional dynamics

genetic and genomic medicine more details view paper
  • Downloaded 735 times
  • Download rankings, all-time:
    • Site-wide: 41,001
    • In genetic and genomic medicine: 176
  • Year to date:
    • Site-wide: 6,936
  • Since beginning of last month:
    • Site-wide: 7,182

Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

microbiology more details view paper
  • Downloaded 643 times
  • Download rankings, all-time:
    • Site-wide: 49,081
    • In microbiology: 3,013
  • Year to date:
    • Site-wide: 47,801
  • Since beginning of last month:
    • Site-wide: 96,780

Pango lineage designation and assignment using SARS-CoV-2 spike gene nucleotide sequences

genomics more details view paper
  • Downloaded 460 times
  • Download rankings, all-time:
    • Site-wide: 73,155
    • In genomics: 4,983
  • Year to date:
    • Site-wide: 13,967
  • Since beginning of last month:
    • Site-wide: 2,358

SANTA-SIM: Simulating Viral Sequence Evolution Dynamics Under Selection and Recombination

bioinformatics more details view paper
  • Downloaded 385 times
  • Download rankings, all-time:
    • Site-wide: 87,085
    • In bioinformatics: 7,787
  • Year to date:
    • Site-wide: 138,661
  • Since beginning of last month:
    • Site-wide: 142,756

Methylation-Based Age Estimation in a Wild Mouse

genetics more details view paper
  • Downloaded 382 times
  • Download rankings, all-time:
    • Site-wide: 87,799
    • In genetics: 3,748
  • Year to date:
    • Site-wide: 40,602
  • Since beginning of last month:
    • Site-wide: 30,407

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