Jonathan's research is focused on the nature of authoritarianism and the role of ideas and legitimacy in authoritarian systems, particularly in African polities. He is also interested in how 'knowledge' on security and conflict is negotiated and constructed in a range of settings. He is the author of East Africa after Liberation: Conflict, Security and the State since the 1980s (Cambridge University Press, 2020) and (with Nic Cheeseman) Authoritarian Africa: Repression, Resistance and the Power of Ideas (Oxford University Press, 2019).