Mabuchi is an Alfred P. Sloan Research Fellow, an Office of Naval Research (ONR) Young Investigator, and a MacArthur Fellow. His path-breaking research on quantum optics and atomic physics includes fundamental studies in quantum measurement, conditional dynamics of observed quantum systems, real-time quantum feedback, and closed-loop quantum control. He is also known for his work on optical biophysics, which focuses on the use of experimental and mathematical methods from quantum optics to enable biophysical investigations at the few- or single-molecule level.