He later served as the founding director of the Wyss Center for Bio and Neuroengineering at Campus Biotech in Geneva, Switzerland.

[5] Donoghue is a founder of the discipline of neuroprosthetics and coordinated the team that developed the brain–computer interface 'BrainGate' to restore movement for people with paralysis.

Beginning in 1999, Donoghue served as the inaugural director of Brown's Brain Science Program.

[8] Donoghue has received several honors for the BrainGate neurotechnology: the Zülch Prize [de] in 2007,[6][9] a Roche-Nature Medicine senior award in 2010,[10] and with Arto Nurmikko the inaugural Moshe Mirilashvili Memorial Fund B.R.A.I.N.

[7] In addition in 2012 with Patrick van der Smagt he won the Erwin Schrödinger Prize of the Helmholtz Association of German Research Centres for a thought-controlled robotic arm developed by BrainGate.