Koonin graduated from Moscow State University, Russia, and received his PhD in molecular biology from the same university in 1983. He has been working in the fields of computational biology and evolutionary genomics since 1984. Koonin moved to the US in 1991, first as a visiting scientist, and then, since 1996, as a senior investigator at the National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD. Koonin's group performs research in many areas of evolutionary genomics.