Dr Heffernan is a Professor in the Department of Mathematics and Statistics at York University, and York Research Chair (Tier II). She is also the Director of the Centre for Disease Modelling (CDM), and is on the Board of Directors of the Canadian Applied and Industrial Mathematics Society (CAIMS).

Dr Heffernan's research program centres on understanding the spread and persistence of infectious diseases. Her, Modelling Infection and Immunity Lab (MI2), which is affiliated with the Centre for Disease Modelling (CDM) focuses on the development of new biologically motivated models of infectious diseases (deterministic and stochastic) that describe pathogen dynamics in-host (mathematical immunology) and in a population of hosts (mathematical epidemiology). Models in immuno-epidemiology, which integrate the in-host dynamics with population level models, are also developed.

The goals of the MI2 lab are to:
(1) Determine which biological effects have the largest impact on the pathogen dynamics in-host and in a population
(2) Study the effects of immune memory in the individual and the population
(3) Determine how co-infection, when more than one infectious disease is present affects the dynamics of another, in-host and in a population.
(4) Develop new mathematical and computational tools to facilitate goals (1-3).