Dynamic Phenotypes and Model Discrimination in Systems Biology

This paper advocates for a shift in focus from steady-state analysis to transient dynamics in understanding biological networks. It emphasizes the importance of dynamic response phenotypes like overshoots and adaptation kinetics, and how these can be used to discriminate between different network architectures. The paper highlights the role of sign structure, interconnection logic, and control-theoretic concepts in analyzing these dynamic behaviors. It suggests that analyzing transient data can falsify entire classes of models and that input-driven dynamics are crucial for understanding, testing, and reverse-engineering biological networks.