- Islam Evolving: Radicalism, Reformation, and the Uneasy Relationship with the Secular West
- 1001 Distortions: How (Not) to Narrate History of Science, Medicine, and Technology in Non-Western Cultures Co-edited with Sonja Brentjes and Lutz Richter-Bernburg.
- An Illusion of Harmony: Science and Religion in Islam
- Science and Nonbelief
- Why Intelligent Design Fails: A Scientific Critique of the New Creationism Co-edited with Matt Young.
- The Ghost in The Universe: God in Light of Modern Science