Daria Frolova

This paper solves the exact Small Parsimony Problem by introducing a cost to indel operations, enabling tractable solutions for small and recently related genomes.

The paper introduces pling, a tool to cluster plasmid genomes using rearrangement distances, and integrates it with SNP and typing data for genomic epidemiology.

This study tracks clonal and plasmid transmission in colistin- and carbapenem-resistant K. pneumoniae using short and long read sequencing, revealing complex plasmid networks and highlighting the need for full-length sequencing to understand resistance spread.

This paper introduces pling, a tool that uses rearrangement distances to cluster plasmids more accurately by accounting for structural changes and avoiding over-clustering caused by transposable elements.