Rachel M. Chalmers

Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.

The paper develops and validates a set of 100,000 RNA baits (CryptoCap_100k) to enrich Cryptosporidium DNA from clinical and environmental samples, improving read mapping, coverage, and variant analysis while reducing costs.

Parapipe: a Pipeline for Handling Parasite NGS Datasets and its Application to Cryptosporidium

Parapipe is a bioinformatics pipeline for analyzing Cryptosporidium NGS data, enabling variant calling, MOI analysis, and phylogenomic clustering to improve public health surveillance.

Comparative genomics reveals the emergence of an outbreak-associated Cryptosporidium parvum population in Europe and its spread to the USA

The paper uses whole genome sequencing to identify three distinct populations of Cryptosporidium parvum, showing the emergence and spread of a European population to the USA.

Phylogenomic reconstruction of Cryptosporidium spp. captured directly from clinical samples reveals extensive genetic diversity

This study uses CES-Seq to sequence Cryptosporidium genomes directly from clinical samples, revealing genetic diversity and enabling phylogenomic analysis and GWAS.

Global population genomics of two subspecies of Cryptosporidium hominis during 500 years of evolution

The paper analyzes global population genomics of two C. hominis subspecies over 500 years, identifying divergence, transmission patterns, and introgression between them.