Transcriptional Regulation: Effects of Promoter Proximal Pausing on Speed, Synchrony and Reliability. - Alistair N. Boettiger; Peter L. Ralph; Steven N. Evans (PLoS Comput. Biol., 2011)

Efficient pedigree recording for fast population genetics simulation. - Jerome Kelleher; Kevin R. Thornton; Jaime Ashander; Peter L. Ralph (PLoS Comput. Biol., 2018)

Enabling Inference for Context-Dependent Models of Mutation by Bounding the Propagation of Dependency. - Frederick A. Matsen IV; Peter L. Ralph (J. Comput. Biol., 2022)