Donald is the author of over 100 publications. A representative selection includes:
* [http://doi.acm.org/10.1145/174147.174150 Kinodynamic Motion Planning]. Bruce Randall Donald, Patrick G. Xavier, John F. Canny, John H. Reif. J. ACM 40(5): 1048-1066 (1993).
* [http://www.jbc.org/content/278/52/52980.full Phylogenetic classification of protozoa based on the structure of the linker domain in the bifunctional enzyme, dihydrofolate  reductase-thymidylate synthase]. Robert H. O’Neil, Ryan H. Lilien, Bruce R. Donald, Robert M. Stroud and Amy C. Anderson. J Biol Chem 2003. 278(52):52980-7.