Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface. - Jacek Sroka; Lukasz Bieniasz-Krzywiec; Szymon Gwozdz; Dariusz Leniowski; Jakub Lacki; Mateusz Markowski; Claudio Avignone-Rossa; Michael E. Bushell; Johnjoe McFadden; Andrzej M. Kierzek (BMC Bioinform., 2011)

Differential Producibility Analysis (DPA) of Transcriptomic Data with Metabolic Networks: Deconstructing the Metabolic Response of M. tuberculosis. - Bhushan K. Bonde; Dany J. V. Beste; Emma Laing; Andrzej M. Kierzek; Johnjoe McFadden (PLoS Comput. Biol., 2011)

Carving Nature at Its Joints: A Comparison of CEMI Field Theory with Integrated Information Theory and Global Workspace Theory. - Johnjoe McFadden (Entropy, 2023)