Ryan C. Fink

ParallelEvolCCM quantifies co-evolutionary patterns among genomic features by integrating phylogenetic signals and offers parallelization and filtering options for improved efficiency.

This study profiles resistance determinants, virulence factors, and mobile genetic elements in 1273 Enterococcus faecium genomes from UK and Canada, showing habitat-associated gene and MGE patterns and a workflow for AMR surveillance.

BugBase assigns pathway coverage and traits (Gram stain, oxygen tolerance, pathogenicity) to individual taxa in 16S or shotgun microbiome data, detecting some functional differences bag-of-genes profiles miss.