Mark R. Davies

MxSure estimates within-host substitution rates and transmission SNP thresholds from pairwise SNP distances, addressing challenges in microbial genome evolution analysis.

This study compares S. pyogenes infection responses in airway and alveolar epithelial cells, finding that alveolar cells show higher cell death and a pro-inflammatory response without cytokine secretion, and that IFN-β treatment reduces infection.

This study benchmarks variant callers on bacterial nanopore data, finding deep learning tools outperform traditional methods and Illumina in accuracy and efficiency.

This study examines genetic diversity in the Vi capsule locus of Salmonella Typhi in Fiji, identifying convergent evolution of tviE mutations globally and highlighting the need for further functional analysis.

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

This study reanalyzes transposon sequencing data from 4 S. pyogenes genotypes across 9 phenotypic conditions to identify highly essential genes and operons, revealing differences in essentiality between in vivo and in vitro environments.

The paper shows extensive genomic overlap between Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis, including shared genes and recombination events, with implications for vaccine development.