Daniel James Whiley

In vitro evolution of uropathogenic Escherichia coli to fosfomycin resistance in a 3D cultured human bladder microtissue model

This study evolves uropathogenic E. coli to fosfomycin resistance in a 3D bladder microtissue model and validates mutations in clinical isolates.

Reference-free clustering as an epidemiological tool for Mycobacterium tuberculosis lineage typing

This study evaluates reference-free methods for Mycobacterium tuberculosis lineage typing using simulated Illumina data, finding SKA2 to be the most accurate tool for strain classification.

Evaluating a SNP calling pipeline for Mycobacterium leprae

The paper evaluates a SNP calling pipeline for Mycobacterium leprae using simulated reads and finds it robust and accurate with low false positives.

The Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference

The paper quantifies the MTBC pangenome, revealing a small, closed genome with lineage-specific regions of difference and implications for virulence and drug resistance.