Professor Waddington leads a team which is focused upon preclinical models of gene therapy, particularly for perinatal gene delivery for early onset, debilitating and often lethal diseases including neurodegenerative diseases, inherited epilepsy and metabolic diseases. He is funded by the UK Medical Research Council Developmental Pathway Funding Scheme for separate projects on Dravet Syndrome and Dopamine Transporter Deficiency Syndrome. He work with Apollo Therapeutics and Dr Ahad Rahim on clinical translation of gene therapy for Gaucher Disease.

He holds an honorary chair at the University of Witwatersrand, South Africa. His team have published more than one hundred and forty peer reviewed publications in journals including Cell, Nature Medicine, Nature Immunology, Cell Metabolism and Blood.