Genome Evolution
Spring 2009
Amos Tanay, Tuesday,
The course main rationale is that with the advent of genomic technologies, the focus of computational molecular biology turns from phylogeny and analysis of proteins to complex modeling of evolution in heterogeneous genomic regions and complex fitness functions. Understanding evolution in such conditions mixes some good old population genetics principles with new probabilistic models that are rich in parameters and structure. The course is therefore introducing both basic principles in population genetics and molecular evolution and computational machinery for inference in directed and undirected graphical models. Many examples from contemporary research on genomics and evolution are discussed.
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Schedule: Lecture 1: Modern challenges in evolution Lecture 2: Population Genetics I: drift and mutation Lecture 3: Population Genetics II: selection Lecture 4: Basic molecular evolution: Species and trees Lecture 5: Inference: Sampling. Phylogenetics Lecture 6: More on mutations. Variational inference Lecture 7: Selection: Protein coding genes Lecture 8: Inference: Loopy belief propagation Lecture 9: Quantitative traits Lecture 10: Comparative genomics: non coding sequences Lecture 11: Comparative genomics: TF binding sites Lecture 12: Epistasis and evolution of gene regulation |
ppt11 ex4 |
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Notes:
25/3/09: Welcome. 2008 course is here
29/3/09: Course day change!! Tuesday 11am, Ziskind 261. (If you have a particular problem with this, email me)
11/4 Ex1 is available, due 28/4
27/5 Math handout is available here