Probabilistic Modeling in Computational Biology  

This course reviews the statistical and algorithmic foundations of bioinformatics viewed through the lens of paleogenetics, the science of Jurassic Park, i.e., the reconstruction of ancient genes and genomes by reverse Bayesian inference under various stochastic models of molecular evolution. Such methods, first proposed in the 1960s by Linus Pauling (and others), are now in reach of practical experimentation due to the falling cost of DNA synthesis technology. Applications of these methods are granting insight into the origin of life and of the human species, and may be powerful tools of synthetic biology. Lectures will review the theoretical content; homework and laboratory exercises will involve writing and applying programs for computational reconstruction of ancient protein and DNA sequences and other measurably evolving entities, both biological (e.g., gene families) and otherwise (e.g., natural language).