Flanagan research focuses on ecclesiology, ecumenism, and Jewish-Christian dialogue, particularly through the Ecclesiological Investigations Network and the Ecclesiological Investigations Group of the American Academy of Religion. He teaches Marymount's foundational Theological Inquiry course and upper-level courses in ecclesiology, Christology, and sacramental theology. He received his B.A. from the Catholic University of America and his M.A. and Ph.D. from Boston College.