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Cottingham's research focuses on understanding biological complexity from the perspectives of both ecology and genomics. As an ecologist, she explores the dynamics of organisms in natural environments to learn what factors control how species change over time. She also wants to learn to what extent the changes are controlled by external factors, such as weather and human activities, as compared to interactions among species. In genomics, she studies the genetic interplay that determines the structure, function, and behavior of an organism. She also examines how gene expression changes in organisms which live in different habitats. Her two main research projects focus on (1) the dynamics of ecological communities and (2) the ecology of Vibrio cholerae, the bacterium that causes cholera.
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