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Fleischer received his PhD from Princeton University in 1982. After leaving Princeton, Fleischer held teaching posts at Washington University in St. Louis and the Ohio State University. In 1988, Fleischer was awarded a genius grant under the prestigious MacArthur Fellows Program. In 1993, Fleischer joined the faculty of the University of Chicago. Fleischer focuses primarily on Ottoman history, specializing in the Age of Suleyman. Currently he is working on a major work on Suleyman the Lawgiver as well as a number of papers dealing with the time period. In addition, he has begun work on Apocalypticism and its relationship to his field of study. Fleischer also sits on the editorial board of a number of publications, including the Cambridge Studies in Early Modern History and the International Journal of Middle Eastern Studies. Fleischer is also a past director of the University Chicago's Center for Middle Eastern Studies and a member of the editorial board of the Historians of the Ottoman Empire.
In September 2011, Fleischer was sentenced in Douglas County, Kansas court to serve two days in jail plus a month on house arrest for drunken driving in April in Lawrence, Kansas with his 3-year-old daughter in the car. Fleischer pleaded guilty in August to a first offense DUI, and as part of a plea agreement prosecutors agreed to drop a child endangerment charge as long as he agreed to serve 30 days on house arrest.
- Bureaucrat and Intellectual in the Ottoman Empire: The Historian Mustafa Âli (1541-1600). Princeton, NJ: Princeton University Press, 1986.