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Author: Richard A Neher

Rankings

  • All-time downloads: 162,727 (rank: 919 )
  • Categories:
    • bioinformatics: 1,661 (rank: 12,816 (tie) )
    • epidemiology: 121,511 (rank: 202 )
    • evolutionary biology: 12,482 (rank: 213 )
    • genomics: 566 (rank: 43,444 (tie) )
    • infectious diseases: 5,621 (rank: 11,865 )
    • microbiology: 8,068 (rank: 2,778 )
    • public and global health: 8,416 (rank: 767 (tie) )

Downloads per author, site-wide

Preprints

Evolution of the SARS-CoV-2 mutational spectrum

evolutionary biology more details view paper

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

epidemiology more details view paper
  • Downloaded 86,252 times
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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

Impact of seasonal forcing on a potential SARS-CoV-2 pandemic

epidemiology more details view paper
  • Downloaded 18,185 times
  • Download rankings, all-time:
    • Site-wide: 634
    • In epidemiology: 100
  • Year to date:
    • Site-wide: 4,587
  • Since beginning of last month:
    • Site-wide: 2,644

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

Coast-to-coast spread of SARS-CoV-2 in the United States revealed by genomic epidemiology

public and global health more details view paper
  • Downloaded 8,502 times
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    • Site-wide: 1,670
    • In public and global health: 65
  • Year to date:
    • Site-wide: 35,334
  • Since beginning of last month:
    • Site-wide: 28,838

PCR assay to enhance global surveillance for SARS-CoV-2 variants of concern

infectious diseases more details view paper
  • Downloaded 4,408 times
  • Download rankings, all-time:
    • Site-wide: 4,036
    • In infectious diseases: 917
  • Year to date:
    • Site-wide: 3,793
  • Since beginning of last month:
    • Site-wide: 53,624

Estimation and worldwide monitoring of the effective reproductive number of SARS-CoV-2

epidemiology more details view paper
  • Downloaded 3,850 times
  • Download rankings, all-time:
    • Site-wide: 4,938
    • In epidemiology: 475
  • Year to date:
    • Site-wide: 6,996
  • Since beginning of last month:
    • Site-wide: 35,349

panX: pan-genome analysis and exploration

evolutionary biology more details view paper
  • Downloaded 1,959 times
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    • Site-wide: 13,460
    • In evolutionary biology: 343
  • Year to date:
    • Site-wide: 122,849
  • Since beginning of last month:
    • Site-wide: 39,444

COVID-19 Scenarios: an interactive tool to explore the spread and associated morbidity and mortality of SARS-CoV-2

epidemiology more details view paper
  • Downloaded 1,929 times
  • Download rankings, all-time:
    • Site-wide: 13,785
    • In epidemiology: 1,010
  • Year to date:
    • Site-wide: 45,996
  • Since beginning of last month:
    • Site-wide: 41,210

TreeTime: maximum likelihood phylodynamic analysis

evolutionary biology more details view paper
  • Downloaded 1,610 times
  • Download rankings, all-time:
    • Site-wide: 18,192
    • In evolutionary biology: 522
  • Year to date:
    • Site-wide: 87,826
  • Since beginning of last month:
    • Site-wide: 73,092

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

Interactions between seasonal human coronaviruses and implications for the SARS-CoV-2 pandemic: A retrospective study in Stockholm, Sweden, 2009-2020

infectious diseases more details view paper
  • Downloaded 1,526 times
  • Download rankings, all-time:
    • Site-wide: 19,774
    • In infectious diseases: 2,343
  • Year to date:
    • Site-wide: 13,082
  • Since beginning of last month:
    • Site-wide: 111,747

Stability of association between Arabidopsis thaliana and Pseudomonas pathogens over evolutionary time scales

microbiology more details view paper
  • Downloaded 1,459 times
  • Download rankings, all-time:
    • Site-wide: 21,289
    • In microbiology: 1,187
  • Year to date:
    • Site-wide: 144,090
  • Since beginning of last month:
    • Site-wide: 78,766

Resolving structural diversity of Carbapenemase-producing gram-negative bacteria using single molecule sequencing

microbiology more details view paper
  • Downloaded 1,244 times
  • Download rankings, all-time:
    • Site-wide: 27,430
    • In microbiology: 1,542
  • Year to date:
    • Site-wide: 116,553
  • Since beginning of last month:
    • Site-wide: 175,455

Quantifying SARS-CoV-2 spread in Switzerland based on genomic sequencing data

epidemiology more details view paper
  • Downloaded 1,232 times
  • Download rankings, all-time:
    • Site-wide: 27,841
    • In epidemiology: 1,623
  • Year to date:
    • Site-wide: 72,827
  • Since beginning of last month:
    • Site-wide: 41,922

Rapid and consistent evolution of colistin resistance in Pseudomonas aeruginosa during morbidostat culture

microbiology more details view paper
  • Downloaded 1,123 times
  • Download rankings, all-time:
    • Site-wide: 32,195
    • In microbiology: 1,859
  • Year to date:
    • Site-wide: 106,146
  • Since beginning of last month:
    • Site-wide: 45,706

A pseudovirus system enables deep mutational scanning of the full SARS-CoV-2 spike

microbiology more details view paper
  • Downloaded 1,112 times
  • Download rankings, all-time:
    • Site-wide: 32,674
    • In microbiology: None
  • Year to date:
    • Site-wide: 2,931
  • Since beginning of last month:
    • Site-wide: 302

PanGraph: scalable bacterial pan-genome graph construction

bioinformatics more details view paper
  • Downloaded 1,038 times
  • Download rankings, all-time:
    • Site-wide: 36,284
    • In bioinformatics: 4,271
  • Year to date:
    • Site-wide: 3,244
  • Since beginning of last month:
    • Site-wide: 171,864

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

In-vivo mutation rates and fitness landscape of HIV-1

evolutionary biology more details view paper
  • Downloaded 968 times
  • Download rankings, all-time:
    • Site-wide: 40,433
    • In evolutionary biology: 1,548
  • Year to date:
    • Site-wide: 195,053
  • Since beginning of last month:
    • Site-wide: 62,289

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

Contributions of adaptation and purifying selection to SARS-CoV-2 evolution

evolutionary biology more details view paper
  • Downloaded 903 times
  • Download rankings, all-time:
    • Site-wide: 44,883
    • In evolutionary biology: None
  • Year to date:
    • Site-wide: 4,067
  • Since beginning of last month:
    • Site-wide: 912

Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing

microbiology more details view paper
  • Downloaded 855 times
  • Download rankings, all-time:
    • Site-wide: 48,841
    • In microbiology: 2,830
  • Year to date:
    • Site-wide: 148,012
  • Since beginning of last month:
    • Site-wide: 81,759

Evolution, geographic spreading, and demographic distribution of Enterovirus D68

microbiology more details view paper
  • Downloaded 839 times
  • Download rankings, all-time:
    • Site-wide: 50,312
    • In microbiology: 2,882
  • Year to date:
    • Site-wide: 84,194
  • Since beginning of last month:
    • Site-wide: 139,266

Establishment and stability of the latent HIV-1 DNA reservoir

microbiology more details view paper
  • Downloaded 799 times
  • Download rankings, all-time:
    • Site-wide: 54,132
    • In microbiology: 3,090
  • Year to date:
    • Site-wide: 193,015
  • Since beginning of last month:
    • Site-wide: 186,687

Asynchrony between virus diversity and antibody selection limits influenza virus evolution

evolutionary biology more details view paper
  • Downloaded 717 times
  • Download rankings, all-time:
    • Site-wide: 63,304
    • In evolutionary biology: 2,744
  • Year to date:
    • Site-wide: 125,677
  • Since beginning of last month:
    • Site-wide: 65,886

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

Estimating Time Of HIV-1 Infection From Next-Generation Sequence Diversity

epidemiology more details view paper
  • Downloaded 701 times
  • Download rankings, all-time:
    • Site-wide: 65,464
    • In epidemiology: 3,011
  • Year to date:
    • Site-wide: 176,832
  • Since beginning of last month:
    • Site-wide: 80,107

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

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

Efficient estimation of evolutionary rates by covariance aware regression

evolutionary biology more details view paper
  • Downloaded 608 times
  • Download rankings, all-time:
    • Site-wide: 79,128
    • In evolutionary biology: 3,623
  • Year to date:
    • Site-wide: 149,395
  • Since beginning of last month:
    • Site-wide: 49,046

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

Phylodynamics of rapidly adapting pathogens: extinction and speciation of a Red Queen

evolutionary biology more details view paper
  • Downloaded 495 times
  • Download rankings, all-time:
    • Site-wide: 101,385
    • In evolutionary biology: 4,636
  • Year to date:
    • Site-wide: 166,668
  • Since beginning of last month:
    • Site-wide: 62,447

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

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

Efficient inference, potential, and limitations of site-specific substitution model

evolutionary biology more details view paper
  • Downloaded 431 times
  • Download rankings, all-time:
    • Site-wide: 116,769
    • In evolutionary biology: 5,299
  • Year to date:
    • Site-wide: 205,966
  • Since beginning of last month:
    • Site-wide: 139,269

TreeKnit: Inferring Ancestral Reassortment Graphs of influenza viruses

bioinformatics more details view paper
  • Downloaded 430 times
  • Download rankings, all-time:
    • Site-wide: 117,149
    • In bioinformatics: 9,875
  • Year to date:
    • Site-wide: 16,517
  • Since beginning of last month:
    • Site-wide: 168,991

Incomplete inhibition of HIV infection results in more HIV infected lymph node cells by reducing cell death

bioinformatics more details view paper
  • Downloaded 382 times
  • Download rankings, all-time:
    • Site-wide: 130,538
    • In bioinformatics: 10,308
  • Year to date:
    • Site-wide: 186,978
  • Since beginning of last month:
    • Site-wide: 127,431

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

Reversions to consensus are positively selected in HIV-1 and bias substitution rate estimates

evolutionary biology more details view paper
  • Downloaded 315 times
  • Download rankings, all-time:
    • Site-wide: 150,393
    • In evolutionary biology: 6,897
  • Year to date:
    • Site-wide: 23,210
  • Since beginning of last month:
    • Site-wide: 97,860

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

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

Complementation can maintain a quasispecies of drug sensitive and resistant HIV

evolutionary biology more details view paper
  • Downloaded 224 times
  • Download rankings, all-time:
    • Site-wide: 176,220
    • In evolutionary biology: 7,758
  • Year to date:
    • Site-wide: 181,050
  • Since beginning of last month:
    • Site-wide: 158,088

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