‘Candidatus Phytoplasma solani’ is the agent associated with the most widespread grapevine yellows disease, the “bois noir”, which causes significant economic losses every year. Understanding the interaction between this phytoplasma and the grapevine disease in question remains an intriguing open problem. New approaches developed to improve the understanding of the infection through complex network-based modelling are presented. This computational modelling allows seamless integration of data from multiple sources and provides insights into relationships between genes or other entities of interest. Two approaches and the newly obtained results that further improve the understanding of “bois noir” and other grapevine yellows are reported.