This talk focuses on presenting the development of graphical models-based strategies for the study of biological pathways. Biological pathways are structured representations of biological interactions that take place in a cell and can be represented through a graph where genes and their connections are, respectively, nodes and edges of the graph. We can then use graphical models to answer biological questions of great interest, for instance: to refine the structure of the pathway in light of new experimental results, to compare pathways in different experimental conditions and to predict the impact of an external intervention on the system.