Knoepfler received a B.A. in English Literature from Reed College in 1989 and a Ph.D. in Molecular Pathology from the University of California San Diego School of Medicine in 1998 as a Lucille P. Markey Fellow.
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Knoepfler did his postdoctoral studies at the Fred Hutchinson Cancer Research Center in the laboratory of Bob Eisenman, studying Myc regulation of chromatin in stem cells and cancers of the nervous system.
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