G-NEST: a gene neighborhood scoring tool to identify co-conserved, co-expressed genes. - Danielle G. Lemay; William F. Martin; Angie S. Hinrichs; Monique Rijnkels; J. Bruce German; Ian Korf; Katherine S. Pollard (BMC Bioinform., 2012)

Automated glycopeptide analysis - review of current state and future directions. - David C. Dallas; William F. Martin; Serenus Hua; J. Bruce German (Briefings Bioinform., 2013)

Endosymbiotic origin and differential loss of eukaryotic genes. - Chuan Ku; Shijulal Nelson-Sathi; Mayo Roettger; Filipa L. Sousa; Peter J. Lockhart; David Bryant; Einat Hazkani-Covo; James O. McInerney; Giddy Landan; William F. Martin (Nat., 2015)

The origin of symbiogenesis: An annotated English translation of Mereschkowsky's 1910 paper on the theory of two plasma lineages. - Klaus V. Kowallik; William F. Martin (Biosyst., 2021)