We utilize mathematical and statistical models to infer mechanisms driving the spread of infectious diseases and to predict future outbreaks. In contrast to traditional epidemiology research, which often focuses on the dynamics of a single pathogen, we aim to understand the dynamics of pathogen community as a whole. For example, how do immunological, virological, and environmental factors shape pathogen community dynamics across time and space? How might interventions such as vaccination or broader drivers like climate change affect future pathogen communities? To address these questions, we seek to develop methods for integrating serological and genomic data into inferences of infectious disease dynamics.