Krister M. Swenson

The paper introduces two integer linear programming solutions for identifying positional orthologs and evaluates them against existing methods on simulated and real data.

The paper evaluates syntenic block detection methods and their impact on rearrangement phylogeny using Mycobacterium tuberculosis genomes, finding that method choice affects results, especially in low-support branches.

This paper introduces an algorithm to compute the transfer index for all branches in a phylogenetic tree efficiently, improving runtime from O(n²) to O(n log³ n).

RAPPAS provides a fast, alignment-free method for phylogenetic placement of metagenomic sequences, achieving speed improvements over likelihood-based methods while maintaining accuracy.

The paper evaluates a model for inferring ancestral rearrangement scenarios by correlating Hi-C data clustering quality with rearrangement scenario accuracy between Drosophila species.