This EMBO Practical Course offers a comprehensive introduction to the principles, tools, and techniques of infectious disease modelling, with a special focus on integrating genomic data to enhance model development. Infectious disease models play a vital role in understanding pathogen dynamics, predicting epidemic trajectories, and informing public health responses—as demonstrated during the COVID-19 pandemic. Participants will explore compartmental models such as the Susceptible-Infectious-Recovered (SIR) framework, learning how to tailor these models to specific pathogens and distinguish between deterministic and stochastic approaches. They will also apply these models to epidemic scenarios to forecast trends in case numbers and disease severity. The course further delves into genomics-informed modelling, teaching participants how to construct timed phylogenies, infer ancestral states, and model pathogen evolution. By combining transmission dynamics with genomic data, participants will be introduced to phylodynamic approaches—powerful tools that allow earlier and more accurate detection of changes in transmission and pathogenicity than traditional models alone.
