Natalie Knox

The paper quantifies bias in proportionality-based association metrics for count data and proposes a logit-normal multinomial model to improve accuracy.

BioHansel rapidly and accurately genotypes bacterial pathogens from WGS data using canonical SNPs, enabling efficient surveillance and outbreak response.

Neptune identifies differentially abundant genomic loci in bacterial populations using k-mer matching and probabilistic models, showing sensitivity and specificity on simulated and real data.

SNVPhyl is a phylogenomics pipeline that identifies SNVs and constructs whole-genome phylogenies from WGS data, showing high sensitivity and specificity in outbreak detection.

Plasmid Profiler is a pipeline for comparative analysis of plasmid content in WGS data without requiring de novo assembly, using read mapping to a plasmid reference database.