Eva S. Deutekom

The paper evaluates factors affecting protein interaction prediction using phylogenetic profiles in eukaryotes, finding that orthologous group and interactome selection have greater impact than genome selection.

This paper evaluates orthology methods by comparing their ability to recapitulate patterns of eukaryotic genome evolution, finding similar overall behavior but significant differences in inferred orthologous groups.

PhyRepID quantifies protein repeat evolution across 14 vertebrate species by detecting repeats, optimizing detection, and using phylogenetics to derive a PRD score for large-scale comparison.