Before joining Imperial in 2010, he was a Ph.D. at Cambridge and postdoc at Boston University, in one of the field’s founding groups with Prof James J. Collins. Ellis's research focuses on developing the foundational tools for accelerating and automating design-led synthetic biology, focusing on research projects in yeast (S. cerevisiae) and E. coli model organisms, as well as industrially relevant interesting microbes such as Acetobacter, Geobacillus and Bacillus. He is leader of the UK-funded project to build a synthetic yeast chromosome for the international synthetic yeast project (Sc2.0) and is involved in the global push to develop genome-writing technologies for human cell lines.