Zoe A. Dyson

AMRgen is an R package that links antimicrobial resistance genotypes to phenotypes through data harmonization, analysis, and visualization, using surveillance data from priority pathogens.

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

The paper introduces TyphiNET, a dashboard for exploring Typhi genomics data to support public health decisions on antimicrobial resistance and vaccine implementation.

EnviroAmpDesigner designs multiplex PCR primer panels for detecting and subtyping specific bacteria in environmental samples, focusing on specificity and minimizing off-target amplification.

AmpliconTyper is a tool for analysing ONT multiplex amplicon sequencing data from environmental samples, using machine learning to classify reads and identify SNPs.

The paper introduces Pathogenwatch, a tool for genomic surveillance of Salmonella Typhi, enabling AMR prediction and population-level risk assessment through global data sharing.

The paper identifies azithromycin-resistant Salmonella Typhi in Northern India, showing independent emergence of resistance and highlighting the need for typhoid conjugate vaccines.

This paper analyzes Salmonella Typhi isolates from Bangladesh 2004-2016 to identify population structure and antimicrobial resistance patterns, finding a decline in H58 genotypes and rise in non-H58 genotypes with fluoroquinolone resistance.

The paper compares fully Bayesian and hybrid methods for inferring demographic parameters in bacterial genomic data, finding hybrid methods are computationally efficient and reliable when data have strong temporal structure.

This study analyzes Salmonella isolates from Nepali children to assess antimicrobial resistance and inform vaccine policy.

This study uses whole genome sequencing to analyze Salmonella Typhi isolates from Thailand before and after a national immunization program, showing that post-vaccine isolates were imported from neighboring countries rather than persisting locally.