His main research focus is in microelectromechanical systems (MEMS), which uses microfabrication techniques to create mechanical structures in silicon and other materials that can be added to electronic devices. A key participant in the Microelectronics Research Center and the Microsystems Packaging Research Center, Dr. Allen also serves as a co-director for the Center for MEMS and Microsystems Technologies. He leads the Microsensor and Microactuator Group at Georgia Tech, where he has advised 17 postdoctoral fellows and has graduated 27 Ph.D. students. During his career, he has published almost 90 refereed journal papers and 165 refereed conference papers.

To date, Dr. Allen and his research group have been issued 36 patents, two of which have led to the development of two companies—Redeon and CardioMEMS—that are graduates of the Advanced Technology Development Center. In 1999, Dr. Allen and his colleague Mark Prausnitz of the School of Chemical and Biomolecular Engineering co-founded Redeon, a microneedle company that commercialized microfabrication-based approaches to transdermal delivery of drugs such as insulin. The company was sold to Biovalve, Inc., in 2001. Dr. Allen co-founded his second company, CardioMEMS, with Jay Yadav, MD, of the Cleveland Clinic in 2001, to create endovascularly-implantable wireless MEMS sensors for monitoring physiological conditions within the body. The first devices developed were pressure sensors for monitoring the intrasac pressure in abdominal aortic aneurysms that have been repaired using stent-grafts. CardioMEMS' wireless pressure monitor was recently highlighted by the U.S. Food and Drug Administration in its annual report as a medical device likely to have a significant impact on patient care.