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Author: Samuel Alizon

Rankings

  • All-time downloads: 25,379 (rank: 7,450 )
  • Categories:
    • bioinformatics: 1,662 (rank: 9,658 (tie) )
    • ecology: 302 (rank: 14,478 (tie) )
    • epidemiology: 12,595 (rank: 1,184 )
    • evolutionary biology: 4,424 (rank: 772 )
    • geriatric medicine: 518 (rank: 223 (tie) )
    • infectious diseases: 5,605 (rank: 7,977 )
    • systems biology: 273 (rank: 12,420 (tie) )

Downloads per author, site-wide

Preprints

Optimal COVID-19 epidemic control until vaccine deployment

infectious diseases more details view paper
  • Downloaded 4,313 times
  • Download rankings, all-time:
    • Site-wide: 2,847
    • In infectious diseases: 615
  • Year to date:
    • Site-wide: 5,404
  • Since beginning of last month:
    • Site-wide: 11,339

Rapid spread of the SARS-CoV-2 δ variant in French regions in June 2021

epidemiology more details view paper
  • Downloaded 2,331 times
  • Download rankings, all-time:
    • Site-wide: 6,875
    • In epidemiology: 565
  • Year to date:
    • Site-wide: 937
  • Since beginning of last month:
    • Site-wide: 164

Early phylodynamics analysis of the COVID-19 epidemics in France

epidemiology more details view paper
  • Downloaded 2,073 times
  • Download rankings, all-time:
    • Site-wide: 8,140
    • In epidemiology: 652
  • Year to date:
    • Site-wide: 3,091
  • Since beginning of last month:
    • Site-wide: 1,723

Rapid SARS-CoV-2 variants spread detected in France using specific RT-PCR testing

epidemiology more details view paper
  • Downloaded 1,651 times
  • Download rankings, all-time:
    • Site-wide: 11,460
    • In epidemiology: 826
  • Year to date:
    • Site-wide: 1,444
  • Since beginning of last month:
    • Site-wide: 14,113

Can Ebola Virus evolve to be less virulent in humans?

evolutionary biology more details view paper
  • Downloaded 1,492 times
  • Download rankings, all-time:
    • Site-wide: 13,233
    • In evolutionary biology: 433
  • Year to date:
    • Site-wide: 64,354
  • Since beginning of last month:
    • Site-wide: 89,956

Epidemiological monitoring and control perspectives: application of a parsimonious modelling framework to the COVID-19 dynamics in France

epidemiology more details view paper
  • Downloaded 1,441 times
  • Download rankings, all-time:
    • Site-wide: 13,977
    • In epidemiology: 960
  • Year to date:
    • Site-wide: 7,072
  • Since beginning of last month:
    • Site-wide: 20,600

Age-structured non-pharmaceutical interventions for optimal control of COVID-19 epidemic

epidemiology more details view paper
  • Downloaded 993 times
  • Download rankings, all-time:
    • Site-wide: 24,306
    • In epidemiology: 1,403
  • Year to date:
    • Site-wide: 23,799
  • Since beginning of last month:
    • Site-wide: 33,867

Modelling the evolution of viral oncogenesis

evolutionary biology more details view paper
  • Downloaded 928 times
  • Download rankings, all-time:
    • Site-wide: 26,783
    • In evolutionary biology: 1,154
  • Year to date:
    • Site-wide: 68,339
  • Since beginning of last month:
    • Site-wide: 78,428

Coevolution of virulence and immunosuppression in multiple infections

evolutionary biology more details view paper
  • Downloaded 918 times
  • Download rankings, all-time:
    • Site-wide: 27,208
    • In evolutionary biology: 1,174
  • Year to date:
    • Site-wide: 100,773
  • Since beginning of last month:
    • Site-wide: 111,171

COUSIN (COdon Usage Similarity INdex): a normalized index of Codon Usage Preferences.

bioinformatics more details view paper
  • Downloaded 913 times
  • Download rankings, all-time:
    • Site-wide: 27,403
    • In bioinformatics: 3,115
  • Year to date:
    • Site-wide: 19,052
  • Since beginning of last month:
    • Site-wide: 14,290

SARS-CoV-2 variants of concern are associated with lower RT-PCR amplification cycles between January and March 2021 in France

epidemiology more details view paper
  • Downloaded 767 times
  • Download rankings, all-time:
    • Site-wide: 34,940
    • In epidemiology: 1,774
  • Year to date:
    • Site-wide: 4,226
  • Since beginning of last month:
    • Site-wide: 8,257

Why human papillomavirus acute infections matter

epidemiology more details view paper
  • Downloaded 650 times
  • Download rankings, all-time:
    • Site-wide: 43,688
    • In epidemiology: 2,118
  • Year to date:
    • Site-wide: 79,735
  • Since beginning of last month:
    • Site-wide: 95,774

Exposing the diversity of multiple infection patterns

epidemiology more details view paper
  • Downloaded 649 times
  • Download rankings, all-time:
    • Site-wide: 43,812
    • In epidemiology: 2,121
  • Year to date:
    • Site-wide: 63,413
  • Since beginning of last month:
    • Site-wide: 37,477

Assessing the accuracy of Approximate Bayesian Computation approaches to infer epidemiological parameters from phylogenies

bioinformatics more details view paper
  • Downloaded 646 times
  • Download rankings, all-time:
    • Site-wide: 44,068
    • In bioinformatics: 4,632
  • Year to date:
    • Site-wide: 122,541
  • Since beginning of last month:
    • Site-wide: 123,378

Detecting within-host interactions from genotype combination prevalence data

epidemiology more details view paper
  • Downloaded 551 times
  • Download rankings, all-time:
    • Site-wide: 53,691
    • In epidemiology: 2,451
  • Year to date:
    • Site-wide: 107,436
  • Since beginning of last month:
    • Site-wide: 92,379

Wearing masks and establishing COVID-19 areas reduces secondary attack risk in nursing homes

geriatric medicine more details view paper
  • Downloaded 518 times
  • Download rankings, all-time:
    • Site-wide: 57,851
    • In geriatric medicine: 27
  • Year to date:
    • Site-wide: 11,823
  • Since beginning of last month:
    • Site-wide: 17,179

Epidemiological and clinical insights from SARS-CoV-2 RT-PCR cycle amplification values

infectious diseases more details view paper
  • Downloaded 509 times
  • Download rankings, all-time:
    • Site-wide: 59,015
    • In infectious diseases: 3,249
  • Year to date:
    • Site-wide: 7,764
  • Since beginning of last month:
    • Site-wide: 38,794

Estimating dates of origin and end of COVID-19 epidemics

epidemiology more details view paper
  • Downloaded 493 times
  • Download rankings, all-time:
    • Site-wide: 61,227
    • In epidemiology: 2,708
  • Year to date:
    • Site-wide: 8,123
  • Since beginning of last month:
    • Site-wide: 21,614

The SARS-CoV-2 B.1.351/V2 variant is outgrowing the B.1.1.7/V1 variant in French regions in April 2021

infectious diseases more details view paper
  • Downloaded 449 times
  • Download rankings, all-time:
    • Site-wide: 67,619
    • In infectious diseases: 3,461
  • Year to date:
    • Site-wide: 9,328
  • Since beginning of last month:
    • Site-wide: 12,738

Inferring SARS-CoV-2 variant within-host kinetics

epidemiology more details view paper
  • Downloaded 441 times
  • Download rankings, all-time:
    • Site-wide: 68,809
    • In epidemiology: 2,992
  • Year to date:
    • Site-wide: 9,555
  • Since beginning of last month:
    • Site-wide: 2,345

Quantifying transmission dynamics of acute hepatitis C virus infections in a heterogeneous population using sequence data

evolutionary biology more details view paper
  • Downloaded 427 times
  • Download rankings, all-time:
    • Site-wide: 71,225
    • In evolutionary biology: 3,752
  • Year to date:
    • Site-wide: 68,267
  • Since beginning of last month:
    • Site-wide: 60,072

Why multiple infections favour virulent parasites

evolutionary biology more details view paper
  • Downloaded 399 times
  • Download rankings, all-time:
    • Site-wide: 76,131
    • In evolutionary biology: 3,996
  • Year to date:
    • Site-wide: 124,493
  • Since beginning of last month:
    • Site-wide: 89,896

Reconstructing contact network structure andcross-immunity patterns from multiple infection histories

ecology more details view paper
  • Downloaded 302 times
  • Download rankings, all-time:
    • Site-wide: 95,787
    • In ecology: 2,885
  • Year to date:
    • Site-wide: 80,921
  • Since beginning of last month:
    • Site-wide: 63,747

Epithelial stratification shapes infection dynamics

systems biology more details view paper
  • Downloaded 273 times
  • Download rankings, all-time:
    • Site-wide: 102,579
    • In systems biology: 2,311
  • Year to date:
    • Site-wide: 140,855
  • Since beginning of last month:
    • Site-wide: 140,698

Rt2: computing and visualising COVID-19 epidemics temporal reproduction number

epidemiology more details view paper
  • Downloaded 269 times
  • Download rankings, all-time:
    • Site-wide: 103,388
    • In epidemiology: 4,315
  • Year to date:
    • Site-wide: 35,363
  • Since beginning of last month:
    • Site-wide: 56,057

Treating symptomatic infections and the co-evolution of virulence and drug resistance

evolutionary biology more details view paper
  • Downloaded 260 times
  • Download rankings, all-time:
    • Site-wide: 105,699
    • In evolutionary biology: 5,414
  • Year to date:
    • Site-wide: 82,875
  • Since beginning of last month:
    • Site-wide: 80,248

HPV cervical infections and serological status in vaccinated and non-vaccinated French women

infectious diseases more details view paper
  • Downloaded 232 times
  • Download rankings, all-time:
    • Site-wide: 112,303
    • In infectious diseases: 4,583
  • Year to date:
    • Site-wide: 71,751
  • Since beginning of last month:
    • Site-wide: 81,523

The source of individual heterogeneity shapes infectious disease outbreaks

epidemiology more details view paper
  • Downloaded 174 times
  • Download rankings, all-time:
    • Site-wide: 126,433
    • In epidemiology: 5,269
  • Year to date:
    • Site-wide: 33,296
  • Since beginning of last month:
    • Site-wide: 37,385

Predicting COVID-19 incidence in French hospitals using human contact network analytics

epidemiology more details view paper
  • Downloaded 112 times
  • Download rankings, all-time:
    • Site-wide: 139,978
    • In epidemiology: 5,743
  • Year to date:
    • Site-wide: 53,142
  • Since beginning of last month:
    • Site-wide: 9,406

Simulating trajectories and phylogenies from population dynamics models with TiPS

bioinformatics more details view paper
  • Downloaded 103 times
  • Download rankings, all-time:
    • Site-wide: 141,465
    • In bioinformatics: 10,906
  • Year to date:
    • Site-wide: 93,837
  • Since beginning of last month:
    • Site-wide: 65,978

Cytokine response following perturbation of the cervicovaginal milieu during HPV genital infection

infectious diseases more details view paper
  • Downloaded 102 times
  • Download rankings, all-time:
    • Site-wide: 141,683
    • In infectious diseases: 5,461
  • Year to date:
    • Site-wide: 58,286
  • Since beginning of last month:
    • Site-wide: 62,728

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