Doherty's research focuses on wartime propaganda[3] and nineteenth-century Irish history, with an emphasis on sectarian grievances and propaganda during the Irish War of Independence. His later work has focused on the Troubles and anti-terrorist policy in Northern Ireland. His published works include:[2]
- Nazi Wireless Propaganda: Lord Haw-Haw and British Public Opinion in the Second World War (Edinburgh: Edinburgh University Press, 2000).
- "Kevin Barry and the Anglo-Irish Propaganda War", Irish Historical Studies, 32:126 (2000), pp. 217–231.
- "The attack on the Altmark: a case study in wartime propaganda", Journal of Contemporary History, 38:2 (2003), pp. 187–200.
- "Religion, community relations and constructive unionism: the Arlow disturbances of 1890-1892", in Murphy, J. H. (ed.), Evangelicals and Catholics in Nineteenth-Century Ireland (Dublin: Four Courts Press, 2005), pp. 223–234.
- "Tackling the terrorists: the experience of internment without trial in Northern Ireland", Journal on European History of Law, 6:1 (2015), pp. 76–83.