Directionality in protein fold prediction. - Jonathan J. Ellis; Fabien P. E. Huard; Charlotte M. Deane; Sheenal Srivastava; Graham R. Wood (BMC Bioinform., 2010)

PREDIVAC: CD4+ T-cell epitope prediction for vaccine design that covers 95% of HLA class II DR protein diversity. - Patricio Oyarzún; Jonathan J. Ellis; Mikael Bodén; Bostjan Kobe (BMC Bioinform., 2013)

Calypso: a user-friendly web-server for mining and visualizing microbiome-environment interactions. - Martha Zakrzewski; Carla Proietti; Jonathan J. Ellis; Shihab Hasan; Marie-Jo Brion; Bernard Berger; Lutz Krause (Bioinform., 2017)