Publications

  • Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
  • Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project [version 2; peer review: 2 approved]
  • Genomic diversity of Salmonella enterica -The UoWUCC 10K genomes project
  • Large scale sequencing of SARS-CoV-2 genomes from one region allows detailed epidemiology and enables local outbreak management
  • Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
  • Extensive microbial diversity within the chicken gut microbiome revealed by metagenomics and culture
  • SARS-CoV2 GISAID submission protocol
  • SARS-CoV2 GISAID submission protocol
  • SARS-CoV-2 variants of concern dominate in Lahore, Pakistan in April 2021
  • Replacement of the Alpha variant of SARS-CoV-2 by the Delta variant in Lebanon between April and June 2021
  • Genomic diversity of Escherichia coli isolates from non-human primates in the Gambia
  • Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia
  • Rapid Mycobacterium tuberculosis spoligotyping from uncorrected long reads using Galru
  • Evolution of Salmonella enterica serotype Typhimurium driven by anthropogenic selection and niche adaptation
  • CoronaHiT: High throughput sequencing of SARS-CoV-2 genomes
  • SARS-CoV2 GISAID submission protocol
  • SARS-CoV-2 EBI submission protocol: ENA, BioSample, and BioProject
  • SOP for populating EBI submission templates (ENA)
  • SARS-CoV2 EBI assembly submission protocol
  • Genomic diversity of Escherichia coli isolates from healthy children in rural Gambia
  • GrapeTree: Visualization of core genomic relationships among 100,000 bacterial pathogens
  • A genomic overview of the population structure of Salmonella
  • GrapeTree: visualization of core genomic relationships among 100,000 bacterial pathogens
  • Pan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia
  • Multiple evolutionary trajectories for non-O157 Shiga toxigenic Escherichia coli
  • The user’s guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades of Salmonella, the phylogeny of ancient and modern Yersinia pestis genomes, and the core genomic diversity of all Escherichia
  • Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
  • Principles of Systems Biology, No. 31
  • Comparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak
  • The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
  • BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.
  • Molecular analysis of asymptomatic bacteriuria Escherichia coli strain VR50 reveals adaptation to the urinary tract by gene acquisition.
  • Mechanisms Involved in Acquisition of blaNDM Genes by IncA/C2 and IncFIIY Plasmids.
  • Genome sequence of the emerging pathogen Aeromonas caviae.
  • Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica
  • Comparison Of Multi-locus Sequence Typing software For next generation sequencing data
  • Accurate Reconstruction of Microbial Strains from Metagenomic Sequencing Using Representative Reference Genomes
  • Comparison of classical multi-locus sequence typing software for next-generation sequencing data

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