Stubbe received a B.S. degree in Chemistry from the University of Pennsylvania. She received Ph. D. degree in Organic Chemistry from the University of California, Berkeley. After graduation she became a Postdoctoral researcher at the University of California, Los Angeles.
Stubbe moved to Williams College in 1972 as an assistant professor in the Chemistry Department. In 1977 she became an assistant professor in the Pharmacology Department at Yale University. In 1980 she moved to the University of Wisconsin, serving as assistant professor in the Biochemistry Department.
In 1987 Stubbe became a professor in the MIT Chemistry Department.
Achievements and honors 
- Recipient of the 2009 National Medal of Science "for her groundbreaking experiments establishing the mechanisms of ribonucleotide reductases, polyester synthases, and natural product DNA cleavers — compelling demonstrations of the power of chemical investigations to solve problems in biology." 
- Recipient of the 2010 Benjamin Franklin Medal in Chemistry of The Franklin Institute for uncovering the intricate processes by which cells safely use free radicals, for developing new cancer treatments, and for improving the production of environmentally-friendly polymers.
- Member of United States National Academy of Sciences (Biochemistry section) since 1992
- Myron L. Bender and Muriel S. Bender Distinguished Summer Lecturer, Northwestern University (1992)
- F.A. Cotton Medal for Excellence in Chemical Research of the American Chemical Society in 1998
- Recipient of American Chemical Society's Nakanishi Prize (2009) - for identifying the role of radical intermediates in ribonucleotide reductase functions.
- Pioneered the use of spectroscopic investigations of enzyme interactions.
- Her work has led directly to developing drugs against pancreatic cancer
- Recipient of the 2010 Welch Award for "fundamental research in biochemistry and enzymology."
- Franklin Institute Laureate Page for JoAnne Stubbe
- "Nakanishi Prize", Chemical & Engineering News, 9 February 2009: 41–42
- Daniel G. Nocera, quoted in C&EN/9 Feb. 2009, p. 42
- Welch Award Listing of Recipients
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