A short course in Evolution and Biophysics of the Genome

École Polytechnique Fédérale de Lausanne                                                                        December 2010

Leonid Mirny (MIT)

Lecture 1A Forces of evolution, genetics drift, bionmial re-sampling, diffusion approximation, Backward Kolmogorov equation.
Lecture 1B Selection, Wright's equation, Halden's equation, probability of fixation for neutral, deleterious and advantageous mutations.

                Lecture notes

                Further reading. Short book on population genetics: J.H.Gillespie Population genetics: a concise guide
                                              On effect of the population size on selection in human and mouse: Eyre-Walker(2002)
                Tests for selection
                                           A classical paper McDonald and Kreitman (1991)
                                           A recent review Sabeti et al review (2006)

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Lecture 2A Protein-DNA interactions: specific and non-specific binding.
Lecture 2B Protein-DNA interactions: sequence dependence.
                    see papers   A classical treatment: Berg and von Hippel (1987)
                                           Using Halden's equation to obtain Boltzman distribution of fitness: Berg, Willmann and Lassig (2004)
                                           Information content of motifs, widespread non-functional binding: Wunderlich and Mirny, (2009)
                                           Widespread non-functional binding: Li et al (2008)
                                           Small overlap between binding and expression targets: Hu et al (2007)

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Lecture 3A Protein-DNA interactions: the search problem.
                        Theory: Slutsky and Mirny (2004), Mirny et al J. of Physics A (2009)
                        Single-molecule experiments: Tafvizi et al (2008), a review Gorman and Greene (2008)

Lecture 3B Cooperativity: hemoglobin and protein-DNA interactions. Bintu et al (2005), Mirny, PNAS in press, preprint

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Lecture 4A
Lecture 4B Physical aspects of chromatin packing. Mirny, Chromosome Research in press, preprint