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Author: Stephen D. Bentley

Rankings

  • All-time downloads: 32,261 (rank: 6,515 )
  • Categories:
    • bioinformatics: 2,751 (rank: 6,175 (tie) )
    • evolutionary biology: 3,389 (rank: 1,428 (tie) )
    • genetics: 753 (rank: 22,374 (tie) )
    • genomics: 20,214 (rank: 693 )
    • infectious diseases: 429 (rank: 43,888 (tie) )
    • microbiology: 4,725 (rank: 3,782 )

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Preprints

Emergence of a multidrug resistant and virulent Streptococcus pneumoniae lineage mediates serotype replacement after PCV13

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Antimicrobial exposure in sexual networks drives divergent evolution in modern gonococci

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    • In genomics: 152
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Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes

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    • Site-wide: 8,642
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Patterns of within-host genetic diversity in SARS-CoV-2

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Fast and flexible bacterial genomic epidemiology with PopPUNK

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Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

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    • In genomics: 1,536
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Predicting evolution using frequency-dependent selection in bacterial populations

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    • In evolutionary biology: 621
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PANINI: Pangenome Neighbor Identification for Bacterial Populations

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Heterogeneity Among Estimates Of The Core Genome And Pan-Genome In Different Pneumococcal Populations

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Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice

microbiology more details view paper
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Genome-wide epistasis and co-selection study using mutual information

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    • Site-wide: 24,675
    • In genomics: 2,250
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Evolution and global transmission of a multidrug-resistant, community-associated MRSA lineage from the Indian subcontinent

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    • Site-wide: 25,567
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Fast Hierarchical Bayesian Analysis of Population Structure

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Bayesian inference of ancestral dates on bacterial phylogenetic trees

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    • In bioinformatics: 3,288
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pyseer: a comprehensive tool for microbial pangenome-wide association studies

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    • In bioinformatics: 3,310
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SeroBA: rapid high-throughput serotyping of Streptococcus pneumoniae from whole genome sequence data

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    • Site-wide: 39,236
    • In bioinformatics: 4,189
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Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis

genetics more details view paper
  • Downloaded 753 times
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    • Site-wide: 43,149
    • In genetics: 1,870
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    • Site-wide: 159,887
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SuperDCA for genome-wide epistasis analysis

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    • Site-wide: 46,357
    • In genomics: 3,572
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Temporal population structure of invasive Group B Streptococcus during a period of rising disease incidence shows expansion of a CC17 clone

genomics more details view paper
  • Downloaded 618 times
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    • In genomics: 4,150
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Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

evolutionary biology more details view paper
  • Downloaded 607 times
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    • Site-wide: 58,005
    • In evolutionary biology: 2,836
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The role of interspecies recombinations in the evolution of antibiotic resistant pneumococci

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Joint sequencing of human and pathogen genomes reveals the genetics of pneumococcal meningitis

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    • In genomics: 4,705
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Frequent recombination of pneumococcal capsule highlights future risks of emergence of novel serotypes.

evolutionary biology more details view paper
  • Downloaded 526 times
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    • In evolutionary biology: 3,429
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Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

evolutionary biology more details view paper
  • Downloaded 476 times
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    • In evolutionary biology: 3,881
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Large scale genomic analysis shows no evidence for repeated pathogen adaptation during the invasive phase of bacterial meningitis in humans

genomics more details view paper
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    • In genomics: 5,198
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The effect of recombination on the evolution of a population of Neisseria meningitidis

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    • In evolutionary biology: 4,214
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Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae

microbiology more details view paper
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    • Site-wide: 91,557
    • In microbiology: 6,216
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Identification of colonisation and virulence determinants of Streptococcus pneumoniae via experimental evolution in mouse infection models

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    • In microbiology: 6,379
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Pneumococcal genetic variability influences age-dependent bacterial carriage

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    • In microbiology: 8,811
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A novel mosaic tetracycline resistance gene tet(S/M) detected in a multidrug-resistant pneumococcal CC230 lineage that underwent capsular switching in South Africa

microbiology more details view paper
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Early signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data

genomics more details view paper
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Isolate differences in colonization efficiency during experimental human pneumococcal challenge

infectious diseases more details view paper
  • Downloaded 243 times
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    • In infectious diseases: 5,576
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Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx

infectious diseases more details view paper
  • Downloaded 186 times
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