Already, we understand that drugs can have multiple effects, including side-effects and repurposing effects, and further that they often act through on- and off- target protein binding. Yet these "secondary effects" are not routinely used for explaining how drugs work. Protein-protein interaction networks are an ideal scaffold for understanding drug secondary effects because these networks can describe downstream and off-target effects. In this talk I will demonstrate how these networks allow us to learn new disease biology - specifically how unintended drug effects on immune system activation are associated with differences in overall survival for patients with amyotrophic lateral sclerosis (ALS), and how drug off-target effects allow us to predict effective drug combinations in oncology.