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Author: Xavier Didelot

Rankings

  • All-time downloads: 28,329 (rank: 10,088 (tie) )
  • Categories:
    • bioinformatics: 3,239 (rank: 6,092 (tie) )
    • epidemiology: 1,596 (rank: 10,857 (tie) )
    • evolutionary biology: 6,069 (rank: 882 )
    • genetics: 987 (rank: 20,355 (tie) )
    • genomics: 3,188 (rank: 10,057 (tie) )
    • infectious diseases: 679 (rank: 44,940 (tie) )
    • microbiology: 11,243 (rank: 2,029 )

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Preprints

A Phylogenetic Method To Perform Genome-Wide Association Studies In Microbes That Accounts For Population Structure And Recombination

microbiology more details view paper
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Vaccination against antibiotic resistant gonorrhoea for men who have sex with men in England: a modelling study

microbiology more details view paper
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    • Site-wide: 18,860
    • In microbiology: 1,045
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Bayesian inference of infectious disease transmission from whole genome sequence data

genomics more details view paper
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    • In genomics: 1,680
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Why panmictic bacteria are rare

microbiology more details view paper
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    • Site-wide: 22,221
    • In microbiology: 1,315
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The global distribution and spread of the mobilized colistin resistance gene mcr-1

microbiology more details view paper
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    • Site-wide: 22,951
    • In microbiology: 1,281
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Identification of hidden population structure in time-scaled phylogenies

evolutionary biology more details view paper
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    • Site-wide: 23,481
    • In evolutionary biology: 748
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Automated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel

bioinformatics more details view paper
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Genomic infectious disease epidemiology in partially sampled and ongoing outbreaks

epidemiology more details view paper
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Bayesian inference of ancestral dates on bacterial phylogenetic trees

bioinformatics more details view paper
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    • In bioinformatics: 3,788
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Emerging phylogenetic structure of the SARS-CoV-2 pandemic

genetics more details view paper
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    • In genetics: 1,480
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The Clostridioides difficile species problem: global phylogenomic analysis uncovers three ancient, toxigenic, genomospecies

microbiology more details view paper
  • Downloaded 866 times
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    • Site-wide: 47,810
    • In microbiology: 2,908
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Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

evolutionary biology more details view paper
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    • Site-wide: 58,555
    • In evolutionary biology: 2,418
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A two-hit epistasis model prevents core genome disharmony in recombining bacteria

microbiology more details view paper
  • Downloaded 729 times
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    • Site-wide: 61,648
    • In microbiology: 3,754
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Model design for non-parametric phylodynamic inference and applications to pathogen surveillance

bioinformatics more details view paper
  • Downloaded 709 times
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    • Site-wide: 64,110
    • In bioinformatics: 6,217
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Phylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments

microbiology more details view paper
  • Downloaded 708 times
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    • Site-wide: 64,209
    • In microbiology: 3,655
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Modeling the growth and decline of pathogen effective population size provides insight into epidemic dynamics and drivers of antimicrobial resistance

evolutionary biology more details view paper
  • Downloaded 703 times
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    • Site-wide: 64,983
    • In evolutionary biology: 2,841
  • Year to date:
    • Site-wide: 162,972
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    • Site-wide: 117,017

Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree

evolutionary biology more details view paper
  • Downloaded 680 times
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    • Site-wide: 68,040
    • In evolutionary biology: 2,928
  • Year to date:
    • Site-wide: 200,000
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Detection of a bedaquiline / clofazimine resistance reservoir in Mycobacterium tuberculosis predating the antibiotic era

genomics more details view paper
  • Downloaded 677 times
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    • Site-wide: 68,521
    • In genomics: 4,612
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    • Site-wide: 74,845
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Bayesian inference of clonal expansions in a dated phylogeny

evolutionary biology more details view paper
  • Downloaded 640 times
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    • Site-wide: 73,901
    • In evolutionary biology: 3,350
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Declaring a tuberculosis outbreak over with genomic epidemiology

genomics more details view paper
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    • Site-wide: 77,269
    • In genomics: 4,939
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Quantifying The Fitness Benefit And Cost Of Cefixime Resistance In Neisseria gonorrhoeae To Inform Prescription Policy

microbiology more details view paper
  • Downloaded 614 times
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    • Site-wide: 77,980
    • In microbiology: 4,720
  • Year to date:
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    • Site-wide: 205,550

Frequent recombination of pneumococcal capsule highlights future risks of emergence of novel serotypes.

evolutionary biology more details view paper
  • Downloaded 585 times
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    • Site-wide: 82,782
    • In evolutionary biology: 3,787
  • Year to date:
    • Site-wide: 148,305
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The speciation and hybridization history of the genus Salmonella

microbiology more details view paper
  • Downloaded 563 times
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    • Site-wide: 86,862
    • In microbiology: 5,347
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Population genomics and antimicrobial resistance in Corynebacterium diphtheriae

microbiology more details view paper
  • Downloaded 530 times
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    • Site-wide: 93,568
    • In microbiology: 5,852
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Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks

evolutionary biology more details view paper
  • Downloaded 524 times
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    • Site-wide: 94,656
    • In evolutionary biology: 4,918
  • Year to date:
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A scalable analytical approach from bacterial genomes to epidemiology

microbiology more details view paper
  • Downloaded 510 times
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    • Site-wide: 97,756
    • In microbiology: 6,545
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A role for tetracycline selection in the evolution of Clostridium difficile PCR-ribotype 078

microbiology more details view paper
  • Downloaded 487 times
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    • Site-wide: 103,117
    • In microbiology: 6,512
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KPop: An assembly-free and scalable method for the comparative analysis of microbial genomes

bioinformatics more details view paper
  • Downloaded 458 times
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    • Site-wide: 109,729
    • In bioinformatics: 10,447
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Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

evolutionary biology more details view paper
  • Downloaded 456 times
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    • Site-wide: 110,364
    • In evolutionary biology: 5,115
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A dynamic power-law sexual network model of gonorrhoea outbreaks

epidemiology more details view paper
  • Downloaded 446 times
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    • Site-wide: 112,746
    • In epidemiology: 4,736
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The sudden emergence of a Neisseria gonorrhoeae strain with reduced susceptibility to extended-spectrum cephalosporins, Norway

genomics more details view paper
  • Downloaded 422 times
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    • Site-wide: 118,918
    • In genomics: 6,597
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Integrated patient network and genomic plasmid analysis reveal a regional, multi-species outbreak of carbapenemase-producing Enterobacterales carrying both blaIMP and mcr-9 genes

infectious diseases more details view paper
  • Downloaded 377 times
  • Download rankings, all-time:
    • Site-wide: 131,364
    • In infectious diseases: 6,382
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Comparative evaluation of the transmissibility of SARS-CoV-2 variants of concern

infectious diseases more details view paper
  • Downloaded 369 times
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    • Site-wide: 133,777
    • In infectious diseases: 6,354
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Speeding up Inference of Homologous Recombination in Bacteria

evolutionary biology more details view paper
  • Downloaded 309 times
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    • Site-wide: 151,637
    • In evolutionary biology: 6,941
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The bounded coalescent model: conditioning a genealogy on a minimum root date

evolutionary biology more details view paper
  • Downloaded 216 times
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    • Site-wide: 177,875
    • In evolutionary biology: 7,845
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Phylogenetic analysis of the origin and spread of plague in Madagascar

microbiology more details view paper
  • Downloaded 205 times
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    • Site-wide: 180,650
    • In microbiology: 13,835
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    • Site-wide: 43,273
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Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease

evolutionary biology more details view paper
  • Downloaded 173 times
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    • Site-wide: 187,782
    • In evolutionary biology: 8,520
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KmerAperture: Retaining k-mer synteny for alignment-free estimation of within-lineage core and accessory differences

bioinformatics more details view paper
  • Downloaded 166 times
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    • Site-wide: 189,129
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Penicillin Binding Protein Substitutions Co-occur with Fluoroquinolone Resistance in 'Epidemic Lineages of Multi Drug-Resistant Clostridioides difficile

microbiology more details view paper
  • Downloaded 99 times
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