This week, Sarah Cobey and I are co-teaching a short course on "Pathogen evolution, selection and immunity" for the 2015 Summer Institute in Statistics and Modeling in Infectious Diseases (SISMID). This course is designed as an introduction to epidemiological modeling and evolutionary analysis for antigenically variable pathogens. Here, on the modeling side, we cover immune-mediated competition, multistrain mechanistic models and state-space reconstruction, while on the evolution side we cover the coalescent, phylogenetics and natural selection. We also discuss the immune response in terms of serology and B cell dynamics. I'm very excited about co-teaching this course.
Sarah and I have worked together to put all the course materials online. The course website is here. We include slide decks using Reveal.js for individual topics like competition and the coalescent. We also include introductory exercises for topics like phylogenetics using BEAST and state-space reconstruction. The goal was to have something students could view alongside lectures, but also have something to refer to after the course was finished and to link out to follow-up material. Overall, I'm really quite pleased with this set up.