Shifley's research interests include mathematical modeling and computer simulation of tree and stand dynamics; structure and composition of old-growth hardwood forests in the Midwest; and modeling impacts of disturbance on forest landscapes. He is currently directing a regional analysis of structural and compositional characteristics of remnant old-growth forests in Missouri, Illinois and Iowa. He is also co-directing development of a landscape model simulating the effects of disturbance (natural and anthropogenic) on ecosystem characteristics. Past research has concentrated on development of individual-tree-based models of tree growth and survival and on stand-level models to forecast forest in-growth.