Statistical evolutionary bioinformatics

"Nothing in Biology Makes Sense Except in the Light of Evolution". Theodosius Dobzhansky thus titled an essay to The American Biology Teacher in 1973. The statement can be taken to mean a number of different things. Dobzhansky meant to say that the biological world around us supports theories of evolution in a myriad of ways. Similarly, we cannot gain a clear understanding of the biological world around us without taking into account evolutionary relationships.In the past two decades an enormous amount of data that pertains to evolutionary questions has been generated by large scale sequencing projects. From a statistical perspective, the setting is complex. Sequence data is high-dimensional, multivariate, discrete data. The parameter space of evolutionary trees is unusual as well. This application will implement increasingly realistic evolutionary models that incorporate things like structural energies of proteins, and the now well-accepted phenomenons of variation of rates of evolution over time and across genes. Statistical methods to assess uncertainty in evolutionary inferences will be developed and models and methods for making sense of data in the presence of lateral genetic transfers, as opposed to hereditary ones, will be pursued.