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Nicholas Eriksson : Combinatorial methods in evolutionary biology



My research focuses in three areas of evolutionary biology: the structure of viral populations, the evolution of drug resistance, and phylogenetics. Knowledge of the diversity of viral populations is important for understanding disease progression, vaccine design, and drug resistance, yet it is poorly understood. New technologies (pyrosequencing) allow us to read short, error-prone DNA sequences from an entire population at once. I will show how to assemble the reads into genomes using graph theory, allowing us to determine the population structure. Next, I will describe a new class of graphical models inspired by poset theory that describe the accumulation of (genetic) events with constraints on the order of occurrence. Applications of these models include calculating the risk of drug resistance in HIV and understanding cancer progression. Finally, I'll describe a polyhedral method for determining the sensitivity of phylogenetic algorithms to changes in the parameters. We will analyze several datasets where small changes in parameters lead to completely different trees and see how discrete geometry can be used to average out the uncertainty in parameter choice.

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