Department of Computer Science

USM Computer Science Undergraduate Wins National Honor

David J. Gagne, undergraduate USM Computer Science Major from Shapleigh, ME, has been awarded an Honorable Mention from the Computing Research Association (CRA) for the annual Outstanding Undergraduate Researchers Award. According to the CRA web site, "This award program recognizes undergraduate students in North American colleges and universities who show outstanding research potential in an area of computing research."

CRA awarded three winners, four runners up, seven finalists, and 47 honorable mentions in its national competition. Institutions represented among the students honored include Princeton University, Harvard University, UC Berkeley, and many other ivy-league and well-known research universities and elite colleges.

Gagne has been working with Associate Professor of Computer Science Clare Bates Congdon to study elements in noncoding DNA that have been conserved through evolution. While noncoding DNA was once referred to as "junk", it is now known that there are functional elements in the DNA that does not code for genes; these functional elements may cause genes to produce more or less of the proteins that they otherwise would. Since there are approximately 3 billion base pairs in human DNA, and 95% of our DNA is noncoding, the computational identification of candidate functional elements is an important part of the investigation of the human genome.

Gagne has been working on two projects in Dr. Congdon's lab, both addressing facets of the problem of identifying candidate functional elements in noncoding DNA. In the first project, Gagne has extended the existing computational system so that it can find candidate elements of varying length (rather than the user having to chose a length when running the system). In the second project, Gagne has helped design and implement a new system that looks for the candidate elements in modules, since functional elements in DNA are usually part of a set that work together. "Dave is an exceptional undergraduate researcher", says Dr. Congdon, "And both of these projects help significantly improve our ability to identify functional elements in noncoding DNA". Gagne will soon use these new tools as part of a collaboration with Dartmouth Medical School and the University of Maine to study the noncoding elements that may contribute to cystic fibrosis.

Gagne's work on modules began in a summer internship at the Mount Desert Island Biological Lab (MDIBL), where Congdon is an Adjunct Associate Professor and a seasonal researcher. At MDIBL, Congdon and her four USM undergraduate researchers developed bioinformatics tools and conducted computational experiments, attended research talks, and collaborated with biologists from MDIBL. As a result of work at USM and MDIBL, Gagne presented his research at USM's Thinking Matters convocation in the Spring, MDIBL's Student Symposium in the summer, and the IEEE International Conference on Bioinformatics and Biomedicine this Fall.

Gagne is also the recipient of a USM Undergraduate Research Opportunity Program (UROP) grant, which is funding his bioinformatics research this year. The UROP program is headed by Dr. Bruce Thompson of USM's Psychology department. UROP funds student participation in research and creative activities at the undergraduate level. Gagne has also been funded through Dr. Congdon's National Science Foundation CAREER grant and National Institutes of Health COBRE collaboration, and via USM's Maine Economic Incentive Funds.

"Conducting research at USM has been a rewarding experience," says Gagne. "It's been exciting to apply what I've learned here to a real world problem, and it's also been an opportunity to meet and work with some brilliant people, both faculty and students. We've got a great community of researchers here at USM, and I'm glad to be a part of it."