Colin J. Worby

Circling in on plasmids: benchmarking plasmid detection and reconstruction tools for short-read data from diverse species

This study benchmarks plasmid detection and reconstruction tools on short-read assemblies from diverse bacterial species, finding performance varies with database coverage and assembly quality.

Insights into global antimicrobial resistance dynamics through the sequencing of enteric bacteria from U.S. international travelers

This study sequences AMR bacteria from U.S. travelers to identify regional resistance patterns and detect emerging threats.

Strain Tracking with Uncertainty Quantification

ChronoStrain tracks low-abundance microbial strains over time with uncertainty quantification, outperforming existing methods on real and synthetic data.

Distinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection

This study identifies distinct E. coli transcriptional profiles in the guts of recurrent UTI sufferers using a novel pangenome hybrid selection method.

Inter-species geographic signatures for tracing horizontal gene transfer and long-term persistence of carbapenem resistance

The paper develops a method to trace horizontal gene transfer and persistence of carbapenem resistance genes across bacterial species using genomic data from clinical isolates.

StrainGE: A toolkit to track and characterize low-abundance strains in complex microbial communities

StrainGE identifies low-abundance microbial strains from metagenomic data with higher sensitivity and resolution than existing tools.

Bayesian Reconstruction of Transmission within Outbreaks using Genomic Variants

This paper introduces BadTrIP, a Bayesian method to infer host-to-host transmission using genomic variants and epidemiological data, showing improved accuracy over existing approaches.