Ellis studied Natural Sciences in Cambridge, focusing on Chemistry, Biochemistry and Plant Sciences. He then went on to the John Innes Centre for his PhD, working in Biological Chemistry on carbohydrate enzymes and algae under the supervision of Rob Field. Ellis then moved to the Scripps Institution of Oceanography at the University of California - San Diego to work on bacterial natural product discovery in the lab of Brad Moore. Ellis joined Oxford, working with Steve Kelly on Eukaryotic synthetic biology, before he was awarded a Glasstone Independent Research Fellowship to work on algal natural products, also holding a Junior Research Fellowship at New College, Oxford. In 2019 Ellis was awarded a Nottingham Research Fellowship to continue his work on algal natural products in the School of Chemistry.