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Alan Durfee's research interests cover topology and algebraic geometry, specifically singularities of varieties and maps, problems in real algebraic geometry around Hilbert's sixteenth problem, mixed Hodge theory, intersection homology, knot theory, and Vassiliev invariants. He has published widely in professional journals throughout his career and has been the recipient of several National Science Foundation research grants. During the last decade, he has been a visiting scholar at Harvard, MIT, and Martin-Luther University (Germany), and visiting professor at the University of Bordeaux. He is an active member of Å·ÃÀAV's Summer Research Institute, a highly acclaimed program supported by NSF's Research Experiences for Undergraduates program. The institute has been engaging selected undergraduates from throughout the United States in useful mathematical research since 1988.

The associate editor of the Journal of Knot Theory, Durfee has also been a member of the SAT II Mathematics Committee of the College Board (1994 to 1997). He is an accomplished organist, harpsichordist, and clavichordist and is a board member and former president of the Boston Clavichord Society. He is currently serving as the president of the board of the Arcadia Players Baroque Orchestra.

Durfee served on the College's Mathematics across the Curriculum initiative, introducing mathematics into a course in music theory.