PhosX: data-driven kinase activity inference from phosphoproteomics experiments. - Alessandro Lussana; Sophia Müller-Dott; Julio Saez-Rodriguez; Evangelia Petsalaki (Bioinform., 2024)

NetworkCommons: bridging data, knowledge, and methods to build and evaluate context-specific biological networks. - Victor Paton; Dénes Türei; Olga Ivanova; Sophia Müller-Dott; Pablo Rodríguez-Mier; Veronica Venafra; Livia Perfetto; Martín Garrido-Rodriguez; Julio Saez-Rodriguez (Bioinform., 2025)