Stephen Johnston's work centers on developing diagnostic systems for preventative medicine. By testing for inflammation of antibodies in blood, he hopes to be able to detect illness before symptoms appear. Johnston's works in translational sciences and technological development as well as cancer eradication. His team hopes to develop neo-antigens to prevent cancer-causing mutations to occur.

Johnston is the director for the Center for Innovations in Medicine and for the Biological Design Graduate Program. He was a founding member of the Advisory Committee for the Defense Intelligence Agency. He is a member of the Institute of Medicine Forum on Microbial Threats, and is affiliated with the Western Regional Center of Excellence for Biodefense and Emerging Infectious Diseases.