Kerri M. Malone

Rapidly and reproducibly building a comprehensive catalogueof resistance-associated variants for M. tuberculosis

This paper develops an automated method to build a comprehensive catalogue of resistance-associated variants for M. tuberculosis, achieving comparable performance to existing catalogues without expert rules.

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

This study quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes

Minos integrates variant calls from multiple tools to adjudicate discrepancies and jointly genotype bacterial cohorts, improving accuracy in detecting SNPs and indels.

Nucleotide-resolution bacterial pan-genomics with reference graphs

This paper introduces a pan-genome graph structure and software tool, pandora, to analyze bacterial genomic variation across multiple isolates with higher SNP recovery and lower error rates than existing methods.

Comparative omics analyses differentiate Mycobacterium tuberculosis and Mycobacterium bovis and reveal distinct macrophage responses to infection with the human and bovine tubercle bacilli

This study compares the transcriptomic and proteomic profiles of Mycobacterium tuberculosis and Mycobacterium bovis, revealing distinct host responses in bovine macrophages.

Updated reference genome sequence and annotation of Mycobacterium bovis AF2122/97

The paper updates the reference genome of Mycobacterium bovis AF2122/97 with new annotations, corrected SNPs, and confirms the presence of the RD900 locus.