Dr. Thompson has published in a variety of areas. These include multidimensional scaling and unfolding, psychiatric methods, longitudinal data analysis and the analysis of variance. He is currently leading the development of the Web Data Entry System, used for data management and data entry for multicenter clinical trials. His current projects involve evaluations of latent growth curve models for opthamological data analysis, family risk score utility in Alzheimer's disease and the application of multivariate models for steroid data.

Most of his applications have been in the areas of psychiatry, diabetes, and stroke rehabilitation. Dr. Thompson is the PI or Co-PI of several Coordinating Centers or Data Coordinating Centers for a number of NHLBI-sponsored multicenter clinical trials, including the CRISP study (Consortium for Radiologic Imaging Studies of Polycystic Kidney Disease), and the EXCITe study (Extremity Constraint Induced Therapy Evaluation).