His primary research interests include the politics of militancy, the relationship between aid and political violence, and the organizational aspects of terrorism, insurgency, and security policy. His research has been published in International Security, International Studies Quarterly, Security Studies, Foreign Policy, Military Operations Research, and a number of edited volumes. Shapiro co-directs the Empirical Studies of Conflict Project. He is a member of the editorial board of World Politics, a Research Fellow at the Center for Economic Research Pakistan (CERP), a former Harmony Fellow at the Combating Terrorism Center at the United States Military Academy, and served in the U.S. Navy and Naval Reserve.