Leonard Bohnenkämper

This paper introduces a formal framework for deriving synteny blocks directly from sequence data to better capture genomic rearrangements without obscuring structural variation.

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

This paper introduces the CARP problem to address limitations in rearrangement analysis of pangenomic data by unifying concepts from comparative genomics and graphical pangenomics.

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.