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* Believing Women in Islam: Unreading Patriarchal Interpretations of the Qur’an (Austin, TX: University of Texas Press, 2002; revised edition, 2019). Published in Indonesian as Cara Quran Membebaskan Perempuan (Jakarta, Serambi, 2005). Published in the U.K. by Saqi Press (2019).
* Believing Women in Islam: A Brief Introduction, co-authored with David R. Finn (Austin, TX: University of Texas Press, 2019).
* Re-Understanding Islam: A Double Critique, Spinoza Lectures (Amsterdam: Van Gorcum, 2008)
* Islam, Muslims, and the U.S.: Essays on Religion and Politics (New Delhi, India: Global Media Publications, 2004).
* Democracy, Nationalism and Communalism: The Colonial Legacy in South Asia (Bounder, CO.: Westview Press, 1995).