An award has been made to the University of Georgia that will provide research training for 10 weeks for 10 student participants, during for the summers of 2011- 2013. This 11-year old program, which began as a partnership between the University of Georgia and Clark Atlanta University, focuses on genomics, computational biology, and epigenetics -- and their integration in the new area of systems biology. There is a wide range of very interesting and exciting projects for the participants. Students are expected to do full-time lab research as well as participate in seminars and workshops, such as the responsible conduct of research, systems biology and molecular genetics research, career opportunities in industry and academia, and the graduate school application process. REU participants have access to a rich array of individual mentor's facilities as well as many interdepartmental laboratories and centers with core facilities for mass spectrometry, microarray analysis, massively parallel sequencing, nuclear magnetic resonance, etc. Visits to the Atlanta University Center of Clark Atlanta University, Morehouse College, and Spellman College as well as Fort Valley State University are made to encourage students from these institutions to apply. Students from other institutions, especially those from underrepresented groups and from institutions with limited opportunities for research, are also encouraged to apply. Participants are selected based on academic record, research interest, and potential for outstanding research in genomics, computational biology, and epigenetics. Student participants are tracked to determine their continued interest in their academic field of study, their career paths, and the lasting influences of the research experience. The program will be assessed by various means, including the REU common assessment tool. More information is available by visiting , or by contacting the PI (Dr. Jonathan Arnold at or the co-PI (Dr. Meagher at

Project Report

The Research Experience for Undergraduates (REU) site is in its 14nth year of operation. The goal of this NSF-funded program is to engage undergraduates, including those from under-represented groups, in research in genomics and computational biology at the University of Georgia for 10 weeks each summer. This REU site is in partnership with Clark Atlanta University. To date, 137 undergraduates have been through the program over 14 years. Over 87% of these undergraduates have gone on in science as a career. Over 66% of these REU participants are from under-represented groups. Over 40% of the REU participants have gone on for higher graduate/professional degrees. At least 20% of them are acknowledged in or coauthors on scientific publications. The program has been in existence long enough that we are now seeing our former REU participants obtaining their PhDs and entering the workforce as postdoctoral fellows. Jereme Doss (2001 REU participant) completed his PhD in Chemistry at Clark Atlanta University in 2013 and has taken a postdoctoral position at NASA. He received an ERN Award for best poster in the Chemical Sciences at the ERN Meeting in Washington, DC in 2012. Part of his dissertation on biofunctional nanofibres appeared in J. Vis. Exp. in 2012. Dr. Cara Altimus completed her PhD in 2010 at Johns Hopkins University and is a postdoctoral fellow at Johns Hopkins University. She published her second paper in Nature on the biological clock on November 22, 2012. She received the national Lindsley Award from the Society of Neuroscience for the best PhD dissertation in 2010. Dr. Eladio Abreu (2004 REU participant) completed his PhD in Biochemistry at the University of Georgia in 2011, and as part of his dissertation work published in Science in 2009. He is now a postdoctoral fellow at Emory University. Dr. BaoHan Vo (2006 REU participant) finished her PhD at Clark Atlanta University in the Department of Biological Sciences in 2013. Her dissertation is on Nodal and TGF-beta signaling in prostate cancer. Her dissertation has led to six publications in Molecular Cancer Research, Carcinogenesis, Prostate, BMC Cell, Endocrinology, and Journal of Natural Medicines. She is now a postdoctoral fellow in the Department of Genetics and Tumor Cell Biology in St. Jude Children's Hospital, Memphis, TN. One of the goals of this REU site is to engage undergraduates in transformative research. Two REU participants, Kimberly Gaines (2012) and Ira Tigner (2010), worked on a project to establish a connection between the process of aging and the biological clock. They helped to establish that two human longevity genes have homologs in the model microbial system, Neurospora crassa, where the homologs also function as longevity genes. Gaines and Tigner also established in N. crassa these two longevity genes affect the biological clock of N. crassa as well. Another process explored by REU participants is how an organism metabolizes a carbon source, like a suger, in this case a carbon compound often found in decaying plant material called quinic acid. How an organism metabolizes a carbon source is one of the oldest problems considered in systems biology. Two REU participants, Allison Mathes (2007) and Kevin Cheng (2009), developed a detailed genetic network (specified by a large systems of ordinary differential equations) describing how the model system, N. crassa, metabolizes quinic acid. The results were published in PLoS ONE in 2011. The genetic network for quinic acid metabolism is one of the largest genetic network characterized in systems biology. Quinic acid metabolism is connected to other interesting processes, such as the biosynthesis of aromatic amino acids and other secondary aromatic metabolites used in plant defense. Another outcome of theis REU site was to support the development of new tools for systems biology, the integration of genomics and computational biology, to understand complex traits, such as aging , the biological clock, development, metabolism, and other processes controlled by many genes. Two new tools from this REU site include one for drawing genetic networks that allows researchers to develop quickly sophisticated models for how complex traits are controlled by underlying biochemical pathways. The graphical specification of these complicated models allows biologists to easily implement the large systems of ordinary differential equations specified by drawing genetic networks. A second tool that was developed on this REU site was a new method to solve large systems of ordinary differential equations arising in systems biology with accuracy comparable to traditional methods. This new method of solving ordinary differential equations will have applications in a number of other areas of science and engineering beyond systems biology.

National Science Foundation (NSF)
Division of Biological Infrastructure (DBI)
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Sally E. O'Connor
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University of Georgia
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