Mathematical Systems Biology of Infection Dynamics

: Established in June 2024, the MSBID research group studies the microbial world of the human respiratory tract, from the nose to the mouth and throat, and its potential impact on health. We focus on how bacteria and phages interact with one another and with us to help maintain system balance. Changes in the respiratory microbiome may influence susceptibility to viral and bacterial infections. To understand this ecosystem, we build computational models of microbial, viral, and host systems, reconstructing metabolism and simulating how they interact, compete, and adapt. This aligns with our interest in questions that are hard to answer at the bench alone: how a respiratory virus may reshape its host's metabolism, how bacteriophages could be explored as precision antimicrobials against drug-resistant bacteria, or how a microbial community may shift from a healthy to a disease-prone state. We increasingly pair these mechanistic models with machine learning and AI, using data-driven methods to surface patterns and generate hypotheses while keeping the resulting predictions grounded in real biology. Together, these approaches reflect our core fit: a predictive, mechanistic, and AI-informed view of the respiratory ecosystem that may help identify new ways to prevent and treat infection.

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