Samuel Keir Sheppard

Insertion sequence elements associated with Staphylococcus epidermidis evolution in persistent orthopaedic device-related infections

The paper investigates genetic diversification in Staphylococcus epidermidis during orthopaedic device-related infections, finding that insertion sequence elements drive adaptation without affecting antimicrobial resistance or biofilm formation.

GeneScanner: profiling genetic variation across bacterial populations

GeneScanner links laboratory genetic mutations to natural population variation in bacteria, enabling genotype-phenotype association studies across large genome collections.

Genetic context drives evolution of divergent antibiotic survival phenotypes in Staphylococcus epidermidis

This study shows that antibiotic resistance and tolerance in Staphylococcus epidermidis are genetically linked but phenotypically distinct, shaped by complex epistatic interactions.

Genome co-adaptation and the evolution of methicillin resistant Staphylococcus aureus (MRSA)

The paper introduces a new GWAS method to identify gene-gene associations linked to antimicrobial resistance in Staphylococcus aureus, revealing genetic coalitions beyond known resistance genes.

A stable, hierarchical LIN code system for Campylobacter jejuni and Campylobacter coli: A unified genomic nomenclature for lineage-level typing and global surveillance.

Detecting co-selection through excess linkage disequilibrium in bacterial genomes

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

Urbanization spreads antimicrobial resistant enteric pathogens in wild bird microbiomes

The paper investigates how urbanization affects the spread of antimicrobial resistant Campylobacter jejuni in wild birds, finding a positive correlation between urban proximity and AMR gene prevalence.

Machine learning to predict the source of campylobacteriosis using whole genome data

This paper uses machine learning on whole genome data to improve source attribution of Campylobacter jejuni infections, achieving higher accuracy than traditional methods.

Antimicrobial resistant Salmonella spp. circulating in antibiotic-free organic pig farms of northern-Thailand

The paper investigates Salmonella prevalence in organic pig farms in northern Thailand, finding high antibiotic resistance and linking contamination to conventional farming practices.

Quantifying bacterial evolution in the wild: a birthday problem for Campylobacter lineages

The paper estimates molecular clock rates in Campylobacter using a birthday problem analogy to quantify lineage turnover and diversification in environmental bacteria.

PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria

PIRATE clusters and classifies orthologous gene families in bacterial pangenomes across sequence similarity thresholds and scales efficiently with large datasets.

High-resolution sweep metagenomics using fast probabilistic inference

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.

Hermes: an ensemble machine learning architecture for protein secondary structure prediction

Hermes is an ensemble machine learning model for protein secondary structure prediction that outperforms existing methods with higher accuracy and reduced variability.

Piggy: A Rapid, Large-Scale Pan-Genome Analysis Tool for Intergenic Regions in Bacteria

Piggy analyzes intergenic regions in bacterial pan-genomes, showing divergent IGRs correlate with gene expression differences in Staphylococcus aureus.