The research group of Dr. Cynthia Gibas uses experimental molecular biology and biophysics methods to inform development of computational models.
(1) To develop quantitative approaches to DNA microarray analysis, we manufacture completely controlled microarrays and target mixtures, which we use to determine the binding behavior of the known mixture. Based on these observations, we develop mathematical models which can be used to predict hybridization behavior and to quantitate target based on observed signal. These modeling approaches extend to any context where a molecular biology experiment or process is based on hybridization; for instance the same approaches can be used to assess the efficacy of quantitative PCR, and potentially to understand biases in next-gen sequencing processes. Both types of experiment incorporate a hybridization step and assume that nucleotides are accessible to the chemistry of the reaction; modeling may help us understand whether these assumptions are reliable.
(2) To develop visual analytic tools for genome comparison and rapid analysis of genomic differences, we also rely on the tools of molecular biology. From genomic sequencing to multiplex PCR, we generate data sets that give us relevant problems to study -- like the molecular determinants of pathogenicity in Vibrio vulnificus, a marine microbe that is a major source of food-borne infection -- and then validate our computational predictions in the lab.