Julian Parkhill

The paper uses TraDIS to identify genes involved in twitching motility-mediated biofilm expansion in Pseudomonas aeruginosa, revealing both known and novel components.

The paper uses whole genome sequencing to analyze invasive GBS isolates in the Netherlands and identifies the expansion of a CC17 sub-lineage, CC17-1A, as correlated with increased disease incidence.

The paper compares the genomes of Mycobacterium africanum Lineage 5 and 6 from Ghana, finding genomic diversity and selection pressure differences suggesting distinct ecological niches.

This study traces the origin and global spread of a multidrug-resistant MRSA lineage from the Indian subcontinent, showing its emergence through plasmid acquisition and intercontinental transmission.

The paper investigates an Icelandic equine respiratory disease epidemic, identifying Streptococcus zooepidemicus clone ST209 as the causative agent and tracing its origin and spread.

ARIBA rapidly identifies antimicrobial resistance genes and SNPs from sequencing reads, outperforming existing tools on bacterial datasets.

This paper identifies genomic variation associated with pneumococcal carriage duration using longitudinal data and genome-wide association studies.

This paper introduces genomeDCA, a statistical method to identify epistatic interactions in Streptococcus pneumoniae genomes, revealing networks of resistance, virulence, and core genes.

This study analyzes genomic variation in meningitis pathogens to determine if adaptation occurs during the invasive phase, finding no evidence of such adaptation for four species.

This paper reviews microbial genome-wide association studies, discussing their methodologies, current state, and how lessons from human GWAS can guide future research.

The paper compares bacterial genome assembly software for MinION data, finding Canu provides the most accurate assembly while Miniasm is fastest.

This paper introduces a high-throughput pipeline for bacterial genome assembly and improvement, demonstrating robust performance across diverse datasets and achieving high gene completeness.

This paper introduces SEER, a statistical method to identify sequence elements associated with bacterial phenotypes, demonstrating its application in discovering antibiotic resistance and invasiveness factors in Streptococcus species.

Circlator automates genome circularization using long reads, accurately circularizing 26 of 27 test sequences from bacteria and other organisms.

This study investigates the genome evolution of Streptococcus equi, revealing population replacement and genomic decay linked to its host-restricted lifestyle and persistent carriage in horses.

Roary builds large-scale prokaryote pan genomes efficiently, identifying core and dispensable accessory genes using a single CPU in under 5 hours.

This study shows that reagent contamination affects sequence-based microbiome analyses, especially in low biomass samples, and provides mitigation strategies.