Essential Background Theory for Genomic Epidemiology
These short videos introduce the core concepts of genomic epidemiology, oriented towards genomic epidemiological analysis of viral diseases (although some concepts will hold true for analysis of bacterial evolution). They are designed to get you started with the basics of genomic epidemiology, and avoid mistakes in interpretation when you first start looking at genomic data and phylogenetic analyses. The six are meant to be done sequentially, and we recommend working through the practice questions after each video to check your comprehension of the introduced principles. There are video recordings to answer each of the quiz questions.
- Module 1: The overlapping timescales of pathogen evolution and transmission
- Module 2: From sequences to trees.
- Module 3: Shared terminology for describing phylogenetic trees.
- Module 4: Estimating evolutionary rates (molecular clocks) from sequence data.
- Module 5: Interpreting and working with evolutionary rates.
- Module 6: Using evolutionary rates to infer time trees.