Jonathan's research on Islam in Europe has been published in German Politics and Society (2001), French Politics, Culture and Society (2005), International Crisis Group (2007) and Foreign Affairs (2007) and several edited volumes. His first book, Integrating Islam: political and religious challenges in contemporary France (co-authored with Justin Vaisse, Brookings Press 2006 and Odile Jacob 2007) examined Muslims and Islam in French politics and institutions. Jonathan's Ph.D. thesis (Harvard 2006) received the APSA's Laswell prize for best dissertation in public policy.