This manuscript provides a summary of the research I have conducted or supervised between 2010 and 2024, in the field of biostatistics applied to the mathematical modeling of infectious diseases. My presentation is structured into three parts: the methodological development for the use of mechanistic models, their application to the intra-host modeling of viral dynamics and the immune system, and to the population-level evaluation of epidemic control interventions. The primary applications include HIV, Ebola, the Nipah virus, and Sars-CoV-2. I conclude by presenting my future research directions and my vision of the significant advances expected from these models.