He is the author of A Separate Republic (Jerusalem 1990) and of The Jewish Christian Debate on the Eve of Modernity (Jerusalem 2004). He edited The Lion Shall Roar (Jerusalem 2003), and has recently completed a monograph on Jewish culture in medieval Franco-Germany. He is currently conducting an interdisciplinary study of the tombstones of the Jews of Padua, 1550-1850. This year at Stanford Malkiel will teach a survey of medieval and early modern Jewish history in the fall term and a graduate seminar on the reception of philosophy and kabbalah in the Middle Ages and early modern era in the winter term.