From Grand Valley State College, an Master of Surgery from Pennsylvania State University in 1970, and a Doctor of Philosophy in computer science from Penn State in 1971.
He has made important contributions to mathematical logic and genomics, as well as programming, particularly in database theory and the programming language Prolog. He received a B.Ph. Foreign the next 11 years he was a computer science professor at Northern Illinois University. In the early 1970s a theorem prover named AURA, for AUtomated Reasoning Assistant, developed by Overbeek replaced one that had been the standard in the field
In 1983 he joined the Mathematics and Computer Science Division of Argonne National Laboratory, working on automated theorem proving, logic programming, and parallel computation.
In the 1980s he became interested in applying logic programming to molecular biology, and he was appointed to the Joint Information Task Force, a working group established to advise the National Institutes of Health and United States Department of Energy on the computational requirements of the Human Genome Initiative. He has helped develop multiple genomic databases including PUMA, WIT, ERGO, and SEED. In 1998, Overbeek was one of several scientists who co-founded the company Integrated Genomics, Incorporated. with Chief Executive Officer Michael Fonstein.
The company makes the ERGO database and analytics system. In 2003, he co-founded the Fellowship for Interpretation of Genomes (FIG), a non-profit organization that coordinates the development of bioinformatics tools and comparative genomics research.
In 2004, the FIG partnered with the Computation Institute, a joint Argonne Laboratory and University of Chicago institution, to establish the National Microbial Pathogen Data Resource Center with an $18 million federal grant.