- *Bharatiya Muslim Politics: A Documentary Record, 1989-1990* (1995)
- *Communal Riots in India* (1996)
- *Religious Dimensions of Indian Nationalism: A Study of RSS* (1998)
- *Islam in India: History and Politics* (1999)
- *Politics of Islam and Identity: Comparative Studies of Muslim Communities* (2002)
- *Modern Orientalism and the Construction of India* (2004)
- *The Muslims of India: A Documentary Record, 1980-2006* (2006)
- *The RSS: A History of the Organization 1925-2005* (2006)
- *Islam and Politics in South Asia* (2007)
- *Islam in Southeast Asia: Politics, Radicalization and Violence* (2012)
- *Pakistan: The State of the Nation* (2014)
- *The Islamic Republic of Iran: Political Development, Religious Ideology, and Foreign Policy* (2015)
- *The Muslim Brotherhood in Egypt: History and Politics* (2016)
- *The Rohingya Crisis: A Genocide Unfolding* (2018)
- *Arab World: A History of Power and Politics* (2019)
Edited Books:
- *The Political Role of Islam* (1988)
- *India and the Gulf* (1992)
- *The Middle East: Evolution of Political Systems* (1993)
- *India: Internal and External Issues* (1994)
- *Religion, Identity, and Politics in India: A Reader* (2007)
- *Rethinking Muslim Identity in India: Cultural, Social and Political Perspectives* (2008)
- *Muslim Politics in India: Emerging Trends* (2009)
- *Understanding Religious Fundamentalism in India: Perspectives on South Asian Islam* (2010)
- *The Global Challenge of Muslim Extremism: A Collection of Essays* (2011)
- *Political Islam and the State: Case Studies from the Asia-Pacific Region* (2013)
- *The Changing Arab World: Internal Dynamics and External Challenges* (2014)
- *The Rise and Fall of the Islamic State: A Documentary Record of Atrocities and Persecution* (2017)
- *Shi'i Politics in the Middle East: From Quietism to Confrontation* (2018)
- *Women, Politics and Islam: A Reader* (2019)
Articles:
- "Muslim Communalism in India: A Historical Perspective" (1989)
- "The Role of the Muslim Personal Law Board in Indian Politics" (1990)
- "The Babri Masjid-Ram Janmabhoomi Controversy: A Historical and Political Perspective" (1992)
- "Islamist Movements in India: A Study of the Jamaat-e-Islami and the Students' Islamic Movement of India" (1993)
- "The Gulf Crisis and India: Implications for Muslim Politics" (1994)
- "The Rise of Hindu Nationalism in India: A Challenge to Secularism" (1995)
- "Muslim Politics in India: A Post-Ayodhya Assessment" (1996)
- "The Taliban in Afghanistan: A New Challenge for Regional Security" (1997)
- "The Kashmir Conflict: A Historical and Political Perspective" (1998)
- "The Role of the Ulema in Indian Politics" (1999)
- "The War Against Terrorism: Implications for Muslim Minorities" (2001)
- "The Gujarat Carnage of 2002: A Crime Against Humanity" (2002)
- "The Rise of Islamic Fundamentalism in Southeast Asia" (2003)
- "9/11 and the Future of Islam in the United States" (2004)
- "The Iraq War and the Muslim World: A New Era of Confrontation" (2005)
- "The Continuing Crisis in Darfur: A Case of Genocide" (2006)
- "The Rise of Hamas in Palestine: A Challenge to the Israeli Occupation" (2007)
- "The Arab Spring: A New Beginning for the Middle East?" (2011)
- "The Syrian Civil War: A Regional and International Crisis" (2012)
- "The Rise of ISIS: A Threat to Global Security" (2014)
- "The Rohingya Crisis: A Call for International Action" (2017)
- "The Assassination of Jamal Khashoggi: A Wake-Up Call for the World" (2018)