Author: Liam P. Shaw

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Preprints

No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2

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Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

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  • Site-wide: 1,512
  • In bioinformatics: 75
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  • Site-wide: 50,071
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Genomic diversity affects the accuracy of bacterial SNP calling pipelines

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  • Site-wide: 8,903
  • In bioinformatics: 892
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Modelling microbiome recovery after antibiotics using a stability landscape framework

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  • Site-wide: 16,728
  • In microbiology: 902
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  • Site-wide: 107,998
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  • Site-wide: 116,556

Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study

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  • Site-wide: 17,494
  • In microbiology: 974
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A phylogeny-based metric for estimating changes in transmissibility from recurrent mutations in SARS-CoV-2

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  • Site-wide: 17,611
  • In genomics: 1,670
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The phylogenetic range of bacterial and viral pathogens of vertebrates

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  • Site-wide: 18,737
  • In ecology: 254
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The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples

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  • Site-wide: 21,308
  • In microbiology: 1,149
• Year to date:
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  • Site-wide: 172,895

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae

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  • Site-wide: 41,547
  • In microbiology: 2,410
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Flanker: a tool for comparative genomics of gene flanking regions

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  • In bioinformatics: 4,461
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Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture

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Role of the mobilome in the global dissemination of the carbapenem resistance gene blaNDM

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  • In microbiology: 4,092
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  • Site-wide: 66,355
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Pre-existing chromosomal polymorphisms in pathogenic E. coli potentiate the evolution of antibiotic resistance by MCR-1 plasmid acquisition

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  • Site-wide: 104,526
  • In evolutionary biology: 6,259
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Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

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  • Site-wide: 105,253
  • In evolutionary biology: 4,969
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Genomic network analysis of an environmental and livestock IncF plasmid population

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  • In bioinformatics: 9,018
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  • Site-wide: 92,304

Children with cystic fibrosis are infected with multiple subpopulations of Mycobacterium abscessus with different antimicrobial resistance profiles

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  • Site-wide: 113,875
  • In microbiology: 7,150
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Plasmid overlap and evolution between Enterobacterales isolates from bloodstream infections and non-human compartments

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  • Site-wide: 149,259
  • In genomics: None
• Year to date:
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