Genome Evolution


Spring 2009

Amos Tanay, Tuesday, 11am-1pm, Ziskind 261


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.



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



ppt2      ex1



ppt5       ex2



ppt8       ex3



ppt11     ex4








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