Efficient Boolean implementation of universal sequence maps (bUSM). - John Schwacke; Jonas S. Almeida (BMC Bioinform., 2002)

iQuantitator: A tool for protein expression inference using iTRAQ. - John Schwacke; Elizabeth G. Hill; Edward L. Krug; Susana Comte-Walters; Kevin L. Schey (BMC Bioinform., 2009)

Revealing functionally coherent subsets using a spectral clustering and an information integration approach. - Adam J. Richards; John Schwacke; Bärbel Rohrer; L. Ashley Cowart; Xinghua Lu (BMC Syst. Biol., 2012)