Carlos Reding

OxBreaker: species-agnostic pipeline for the analysis of outbreaks using nanopore sequencing

OxBreaker is a species-agnostic pipeline for analyzing bacterial and plasmid outbreaks using nanopore sequencing, offering high accuracy and accessibility for real-time genomic surveillance.

Plasmid carriage and the unorthodox use of fitness in microbiology

The paper shows that fitness estimates based on growth rate are unreliable, revealing that plasmid carriage can be selectively advantageous even when it reduces growth rate.

Hound: A novel tool for automated mapping of genotype to phenotype in bacterial genomes assembled de novo

Hound maps genotype to phenotype in bacterial genomes by de novo assembly, gene detection, and mutation reporting, demonstrating its utility in predicting antibiotic resistance.