Phone: (510) 642-2028.

Lectures: Tuesdays and Thursdays, 11-12:30pm, 81 Evans.

Office hours: Tuesdays and Thursdays 12:30pm-2pm in 1081 Evans.

Course Control Number: 54949

Algebraic Statistics for Computational Biology by L. Pachter and B. Sturmfels, Cambridge University Press.

Lecture 2: Log linear models

Lecture 3: Markov chains

Lecture 4: Introduction to Gröbner bases

Lecture 5: Hidden Markov models and the EM algorithm

Lecture 6: Tree models I

Lecture 7: Tree models II

Lecture 8: Phylogenetic oranges

Lecture 9: What is an alignment?

Lecture 10: Statistical models for alignment

Lecture 11: The generalized distributive law for alignment

Lecture 12: Inference functions

Lecture 13: The fundamental theorem of phylogenetics I

Lecture 14: The fundamental theorem of phylogenetics II

Lecture 15: Least squares trees

Lecture 16: The neighbor-joining algorithm

Lecture 17: Toric dynamical systems I

Lecture 18: Toric dynamical systems II

Lecture 19: Cyclic split systems

Lecture 20: The neighbor-net algorithm

Lecture 21: Epistasis I

Lecture 22: Epistasis II

Lecture 23: The fundamental theorem of natural selection

Final project presentations April 29: Robert Bradley, Allen Chen, Meromit Schuster

Final project presentations May 1: Maria Cueto, Shaowei Lin, Kevin McLoughlin

Final project presentations May 5: Sudeep Juvekar, Michaeel Kazi, Cynthia Vinzant

Final project presentations May 8: Cordelia Csar, Caroline Uhler, Wenjing Zheng

Statistical models for discrete data, linear and toric models

Week 2 Introduction to computational algebra

Groebner bases and implicitization, maximum likelihood estimation

Week 3 The EM algorithm and biological applications

Week 4 Foundations of graphical models

Hidden Markov models, the Hammersley-Clifford theorem, inference

Week 5 Tropical arithmetic and dynamic programming

Polytopes, linear programming and optimization

Week 6 Sequence analysis

The Needleman-Wunsch algorithm, parametric alignment, the Elizalde-Woods theorem

Week 7 Trees and metrics

The fundamental theorem of phylogenetic combinatorics, the Gromov product, splits

Week 8 The space of trees

Introduction to tropical geometry and the tropical Grassmanian

Week 9 Reconstructing trees

The UPGMA and neighbor-joining algorithms, the robustness theorems, least squares and the minimum evolution polytope

Week 10 Population genetics I

Fisher's fundamental theorem, hapltoypes and genotypes, the coalescent theorem

Week 11 Population genetics II

Reombination, mutation, selection and fitness, the genotope

Week 12 Graphs, networks and dynamical systems

Polynomial dynamical systems, stability, applications to regulatory networks

Week 13 Special topics

Week 14/15 Final project presentations