T-Cell Epitope Prediction: Rescaling Can Mask Biological Variation between MHC Molecules. - Aidan MacNamara; Ulrich D. Kadolsky; Charles R. M. Bangham; Becca Asquith (PLoS Comput. Biol., 2009)

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. - Camille Terfve; Thomas Cokelaer; David Henriques; Aidan MacNamara; Emanuel J. V. Gonçalves; Melody K. Morris; Martijn P. van Iersel; Douglas A. Lauffenburger; Julio Saez-Rodriguez (BMC Syst. Biol., 2012)

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. - Jose A. Egea; David Henriques; Thomas Cokelaer; Alejandro Fernández Villaverde; Aidan MacNamara; Diana-Patricia Danciu; Julio R. Banga; Julio Saez-Rodriguez (BMC Bioinform., 2014)