A unified framework for unraveling the functional interaction structure of a biomolecular network based on stimulus‐response experimental data

The approach is based on stationary and/or temporal data obtained from parameter perturbations, and unifies the previous approaches of Kholodenko et al. (PNAS 99 (2002) 12841–12846) and Sontag et al. (Bioinformatics 20 (2004) 1877–1886). By way of demonstration, we apply our unified approach to a network model which cannot be properly identified by existing methods. Finally, we propose an experiment design methodology, which is not limited by the amount of parameter perturbations, and illustrate its use with an in numero example.