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Author: Timothy G. Vaughan

Rankings

  • All-time downloads: 100,954 (rank: 2,127 )
  • Categories:
    • bioinformatics: 1,413 (rank: 15,216 (tie) )
    • ecology: 264 (rank: 22,832 (tie) )
    • epidemiology: 88,695 (rank: 273 )
    • evolutionary biology: 7,464 (rank: 673 )
    • infectious diseases: 2,110 (rank: 23,458 (tie) )

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Preprints

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

epidemiology more details view paper
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    • Site-wide: 99
    • In epidemiology: 23
  • Year to date:
    • Site-wide: 956
  • Since beginning of last month:
    • Site-wide: 1,770

The origin and early spread of SARS-CoV-2 in Europe

infectious diseases more details view paper
  • Downloaded 2,138 times
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    • Site-wide: 11,818
    • In infectious diseases: 1,714
  • Year to date:
    • Site-wide: 114,401
  • Since beginning of last month:
    • Site-wide: 113,778

Novel Integrative Modeling of Molecules and Morphology across Evolutionary Timescales

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  • Downloaded 1,563 times
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    • Site-wide: 19,045
    • In evolutionary biology: 558
  • Year to date:
    • Site-wide: 112,676
  • Since beginning of last month:
    • Site-wide: 51,506

BEAST 2.5: An Advanced Software Platform for Bayesian Evolutionary Analysis

evolutionary biology more details view paper
  • Downloaded 1,515 times
  • Download rankings, all-time:
    • Site-wide: 20,011
    • In evolutionary biology: 594
  • Year to date:
    • Site-wide: 101,951
  • Since beginning of last month:
    • Site-wide: 100,950

Estimating epidemic incidence and prevalence from genomic data

epidemiology more details view paper
  • Downloaded 1,511 times
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    • Site-wide: 20,100
    • In epidemiology: 1,294
  • Year to date:
    • Site-wide: 133,964
  • Since beginning of last month:
    • Site-wide: 80,078

Infectious disease phylodynamics with occurrence data

evolutionary biology more details view paper
  • Downloaded 1,011 times
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    • Site-wide: 37,831
    • In evolutionary biology: 1,443
  • Year to date:
    • Site-wide: 106,247
  • Since beginning of last month:
    • Site-wide: None

A Multi-State Birth-Death model for Bayesian inference of lineage-specific birth and death rates

evolutionary biology more details view paper
  • Downloaded 943 times
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    • Site-wide: 42,087
    • In evolutionary biology: 1,671
  • Year to date:
    • Site-wide: 133,749
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    • Site-wide: 74,789

Improved multi-type birth-death phylodynamic inference in BEAST 2

evolutionary biology more details view paper
  • Downloaded 879 times
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    • Site-wide: 46,852
    • In evolutionary biology: 1,897
  • Year to date:
    • Site-wide: 68,449
  • Since beginning of last month:
    • Site-wide: 158,738

IcyTree: Rapid browser-based visualization for phylogenetic trees and networks

bioinformatics more details view paper
  • Downloaded 785 times
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    • Site-wide: 55,462
    • In bioinformatics: 5,322
  • Year to date:
    • Site-wide: 179,548
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    • Site-wide: 62,167

Estimates of outbreak-specific SARS-CoV-2 epidemiological parameters from genomic data

epidemiology more details view paper
  • Downloaded 744 times
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    • Site-wide: 60,093
    • In epidemiology: 2,946
  • Year to date:
    • Site-wide: 71,152
  • Since beginning of last month:
    • Site-wide: 143,925

Bayesian inference of ancestral recombination graphs for bacterial populations

evolutionary biology more details view paper
  • Downloaded 674 times
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    • Site-wide: 69,136
    • In evolutionary biology: 3,018
  • Year to date:
    • Site-wide: 175,636
  • Since beginning of last month:
    • Site-wide: 129,242

Bayesian inference of reassortment networks reveals fitness benefits of reassortment in human influenza viruses

evolutionary biology more details view paper
  • Downloaded 619 times
  • Download rankings, all-time:
    • Site-wide: 77,480
    • In evolutionary biology: 3,408
  • Year to date:
    • Site-wide: 161,959
  • Since beginning of last month:
    • Site-wide: 84,449

Swiss public health measures associated with reduced SARS-CoV-2 transmission using genome data

epidemiology more details view paper
  • Downloaded 488 times
  • Download rankings, all-time:
    • Site-wide: 103,149
    • In epidemiology: 4,983
  • Year to date:
    • Site-wide: 48,516
  • Since beginning of last month:
    • Site-wide: None

TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses

bioinformatics more details view paper
  • Downloaded 430 times
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    • Site-wide: 117,149
    • In bioinformatics: 9,875
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    • Site-wide: 16,517
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    • Site-wide: 168,991

Investigation of the validity of two Bayesian ancestral state reconstruction models for estimating Salmonella transmission during outbreaks

epidemiology more details view paper
  • Downloaded 327 times
  • Download rankings, all-time:
    • Site-wide: 146,601
    • In epidemiology: 5,979
  • Year to date:
    • Site-wide: 195,256
  • Since beginning of last month:
    • Site-wide: 76,047

Joint inference of migration and reassortment patterns for viruses with segment genomes

evolutionary biology more details view paper
  • Downloaded 312 times
  • Download rankings, all-time:
    • Site-wide: 151,151
    • In evolutionary biology: 6,786
  • Year to date:
    • Site-wide: 163,628
  • Since beginning of last month:
    • Site-wide: 135,847

The effect of sequencing and assembly on the inference of horizontal gene transfer on chromosomal and plasmid phylogenies

bioinformatics more details view paper
  • Downloaded 292 times
  • Download rankings, all-time:
    • Site-wide: 156,949
    • In bioinformatics: 12,017
  • Year to date:
    • Site-wide: 73,893
  • Since beginning of last month:
    • Site-wide: 117,805

Disentangling the role of poultry farms and wild birds in the spread of highly pathogenic avian influenza virus H5N8 in Europe

ecology more details view paper
  • Downloaded 284 times
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    • Site-wide: 159,565
    • In ecology: 4,946
  • Year to date:
    • Site-wide: 62,472
  • Since beginning of last month:
    • Site-wide: 97,417

Robust phylodynamic analysis of genetic sequencing data from structured populations

evolutionary biology more details view paper
  • Downloaded 108 times
  • Download rankings, all-time:
    • Site-wide: 200,002
    • In evolutionary biology: 8,592
  • Year to date:
    • Site-wide: 89,342
  • Since beginning of last month:
    • Site-wide: 173,552

Assessing the effects of date and sequence data in phylodynamics

evolutionary biology more details view paper
  • Downloaded 79 times
  • Download rankings, all-time:
    • Site-wide: 204,446
    • In evolutionary biology: 8,752
  • Year to date:
    • Site-wide: 117,362
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