Manfred Denker and I will be holding a working seminar on Molecular Evolution in the Spring semester, 2011. We will be working through Durbin's "Biological Sequence Analysis: Probabilistic models of proteins and nucleic acids" with the intent to understand and find improvements upon the current probabilistic models of molecular evolution.

Topics will include: pairwise and multiple sequence alignments, Markov and hidden Markov models, and phylogenetic tree building. We will meet on Wednesday's from 2:30-3:45 in 315 McAllister Building.


The book (while only $37 for a used version on Amazon.com) is also available on Google books here.

Goal

We aim to use recent advances in the theory of Markov chains (namely, random substitutions and other infinite state Markov chain concepts and tools) to develop "better" models of molecular evolution. We aim to incorporate not only substitutions, but also indels and neighboring sequence effects. Throughout, we will look for applications of various symbolic dynamical system tools (like topological entropy, zeta functions, types of mixing, etc.). Alignment-free analysis will be preferred where possible.

Schedule

Note: all meetings are on Wednesday's from 2:30-3:45 in 315 McAllister Building.

January 19: We will discuss chapter 2 of Durbin's book: pairwise alignment. A nice introduction to the background material can be found in Li's Molecular Evolution, chapter 1: Gene Structure, Genetic Codes, and Mutation.

January 26: We will discuss chapter 3 of Durbin's book: Markov chains and hidden Markov models.

February 2: We will discuss the main techniques and issues regarding the building of phylogenetic trees. This corresponds to chapter 7 in Durbin's book.

February 9: Oscar Reina will continue leading the discussion of the uses and implementations of phylogenetic trees, as well as the underlying biological requirements for the construction of such trees.

February 16: We will discuss multiple sequence alignments (MSA) and identify possible mathematical frameworks that can be employed to accurately encompass the biological assumptions of MSA. This corresponds to chapter 6 in Durbin's book.

February 23: We will continue the discussion of multiple sequence alignment.

March 2: There will be no meeting due to a series of talks I will be giving at UCLA and UC Berkeley.

March 9: There will be no meeting due to spring break.

March 16: We will cover chapter 9 from Durbin's book regarding transformational grammars.

March 23: Russell deForest will discuss the graph-theoretic analysis of protein-protein interactions.

March 30: There will be no meeting this day.

April 6: Bob Harris will be presenting this day on a more sensitive generalization of BLAT-like alignments.