Boolean modeling techniques for protein co-expression networks in systems medicine

ABSTRACTIntroduction: Application of systems biology/systems medicine approaches is promising for proteomics/biomedical research, but requires selection of an adequate modeling type.Areas covered: This article reviews the existing Boolean network modeling approaches, which provide in comparison with alternative modeling techniques several advantages for the processing of proteomics data. Application of methods for inference, reduction and validation of protein co-expression networks that are derived from quantitative high-throughput proteomics measurements is presented. It’s also shown how Boolean models can be used to derive system-theoretic characteristics that describe both the dynamical behavior of such networks as a whole and the properties of different cell states (e.g. healthy or diseased cell states). Furthermore, application of methods derived from control theory is proposed in order to simulate the effects of therapeutic interventions on such networks, which is a promising approach for the compu...