He received his Ph.D. in molecular cell biology from the University of California, Berkeley, where he co-discovered the Semaphorin family of genes, whose protein products function in the processes of brain wiring, leukocyte trafficking, and heart and skeleton development. A recent recipient of the College of Biological Science's Most Engaging Professor Award, Matthes teaches courses in genetics, cell biology, and bioinformatics, and is a pioneer in the development of courses in which students have their genome sequenced and conduct hands-on explorations of the data.