Multiple trajectory alignment reconstructs disease dynamics for discovery and clinical benefit

Biological processes are changes occurring concomitantly over time. Therefore, any comparison ignorant of temporal changes is greatly deficient. Even in longitudinal experimental designs, data is usually collected at fixed intervals, whereas process dynamics vary between individuals. We developed TimeAx, which brings time into the equation by building a comparative framework for capturing biological processes dynamics from omic data. We used TimeAx to study influenza infection dynamics and Urothelial bladder cancer tumorigenesis, discovering molecular mechanisms that drive disease progression as well as promoting clinical symptoms, for short and long term biological processes. Specifically, we detected an inflection point, where the tumor progresses into an advanced, pro-metastatic state. Overall, we present a powerful framework for studying high resolution temporal dynamics, providing improved molecular interoperability and clinical benefit. ### Competing Interest Statement SSO holds equity and is a consultant of CytoReason. FJT reports receiving consulting fees from ImmunAI and ownership interest in Dermagnostix.