GeneMerge - Post-genomic Analysis, Data Mining, and Hypothesis Testing. - Cristian I. Castillo-Davis; Daniel L. Hartl (Bioinform., 2003)

A New Take on John Maynard Smith's Concept of Protein Space for Understanding Molecular Evolution. - C. Brandon Ogbunugafor; Daniel L. Hartl (PLoS Comput. Biol., 2016)

Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance. - C. Brandon Ogbunugafor; C. Scott Wylie; Ibrahim Diakite; Daniel M. Weinreich; Daniel L. Hartl (PLoS Comput. Biol., 2016)

Modeling the genetic relatedness of Plasmodium falciparum parasites following meiotic recombination and cotransmission. - Wesley Wong; Edward A. Wenger; Daniel L. Hartl; Dyann Wirth (PLoS Comput. Biol., 2018)