10th Annual Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID)

Module 12: Evolutionary Dynamics and Molecular Epidemiology of Viruses

Session 4: Wed Jul 18 to Fri Jul 20
Instructor(s):

Module dates/times: Wednesday, July 18, 1:30-5 p.m.; Thursday, July 19, 8:30 a.m.-5 p.m., and Friday, July 20, 8:30 a.m.-5 p.m.

Prerequisites: This module assumes knowledge of the material in Module 1: Probability and Statistical Inference, though not necessarily from taking that module.

This module covers the use of phylogenetic and bioinformatic tools to analyze pathogen genetic variation and to gain insight in the processes that shape their diversity. The module focuses on phylogenies and how these relate to population genetic processes in infectious diseases.

In particular, the module will cover Bayesian Evolutionary Analysis by Sampling Trees (BEAST). This software will be used in class exercises that are mainly focused on estimating epidemic time scales, reconstruction changes in viral population sizes through time and inference of spatial diffusion of viruses. Evolutionary processes including recombination and selection will also be considered.

Access 2017 Course Materials (2018 materials will be uploaded to this page prior to the start of the module)