MicrobesOnline: an integrated portal for comparative and functional genomics. - Paramvir S. Dehal; Marcin P. Joachimiak; Morgan N. Price; John T. Bates; Jason K. Baumohl; Dylan Chivian; Greg D. Friedland; Katherine H. Huang; Keith Keller; Pavel S. Novichkov; Inna Dubchak; Eric J. Alm; et al. (Nucleic Acids Res., 2010)

GLAMM: Genome-Linked Application for Metabolic Maps. - John T. Bates; Dylan Chivian; Adam P. Arkin (Nucleic Acids Res., 2011)

Proof of principle for epitope-focused vaccine design. - Bruno E. Correia; John T. Bates; Rebecca J. Loomis; Gretchen Baneyx; Chris Carrico; Joseph G. Jardine; Peter Rupert; Colin E. Correnti; Oleksandr Kalyuzhniy; Vinayak Vittal; Mary J. Connell; Eric Stevens; et al. (Nat., 2014)