Description

Short course taught by Erick Matsen and Trevor Bedford for MITII 2017 Summer School on Modeling Immunology.

An introduction to immunity from an evolutionary perspective. We will introduce basic notions of molecular evolution, phylogenetics, and evolutionary models which will set the foundation for modeling pathogens and antibody-making B cells. We will additionally introduce multistrain compartmental models and introduce the diversity generating mechanisms of B and T cells, and survey repertoire analysis.

Outline

Course introduction

Placing pathogen / immune interactions into the larger ecological / evolutionary context
Strain dynamics and population turnover

Multistrain models and serology

Multistrain compartmental models
Exercise: Dynamics of a two-strain SIR system
Serological binding and neutralization data
Antigenic cartography
Exercise: Antigenic map
Original antigenic sin

Selection and evolution in B cells

General outline of adaptive immunity
VDJ recombination
Germinal center formation and cycling
Somatic hypermutation and mismatch repair
A bit of antibody structure

The coalescent and selection

Introduction to Kingman’s coalescent
Effective population size and demographic inference
Exercise: Skyline plots
Effects of selection on tree topology
Introduction to Wright-Fisher model
Tree-based tests of selection: Tajima’s D, etc…
Exercise: measles vs flu, selection and immunity

Introduction to phylogenetics

Sequence alignment
Types of phylogenetic inference methods
Exercise: Parsimony reconstruction
Intro to likelihood
Exercise: Likelihood surface
Likelihood-based phylogenetics
Intro to Bayesian methods
Exercise: Prior and posterior
Markov-chain Monte Carlo

We thank Sarah Cobey for generously allowing use of materials developed for her SISMID module.

All contents including slides, course materials and code are copyright 2015-2017 Sarah Cobey, Erick Matsen and Trevor Bedford. All slides / course materials (files ending in .html and .md) are licensed under Creative Commons Attribution 4.0 and all code (files ending in .py and .ipynb) is licensed under an MIT License.