Conservation Patterns in cis-Elements Reveal Compensatory Mutations. - Perry Evans; Greg Donahue; Sridhar Hannenhalli (Comparative Genomics, 2006)

Protein-Protein Interaction Network Alignment by Quantitative Simulation. - Perry Evans; Ted Sandler; Lyle H. Ungar (BIBM, 2008)

Estimating a gene's mutation burden by the number of observed synonymous base substitutions. - Perry Evans; Michael Krauthammer (BIBM, 2012)