Description:

Title: Cell reprogramming and bacterial memory predicted by mathematical modeling and transfer learning

Abstract: Determining how molecular changes propagate to affect the whole cell is a fundamental goal in systems biology. The challenge inherent to this pursuit is the number and diversity of molecular entities that give rise to cell behavior. In this talk, I will show how nonlinear dynamics and machine learning uncover unexpected behaviors in recent studies concerning irreversibility in bacterial regulatory networks [1] and cell reprogramming [2]. In the first study, Boolean networks show that the same DNA sequence can counterintuitively encode multiple behaviors through information stored in the state of the gene regulatory network. In the second study, a machine learning model provides an effective representation of the regulatory interactions between genes and cell phenotype. We use this model to identify gene perturbations that can reprogram cells to different phenotypes. Both contributions demonstrate how the abundance of biological data provide opportunities for mathematical modeling to derive unexpected insights.

[1] Zhao, Y., Wytock, T. P., Reynolds, K. A., & Motter, A. E. (2024). Irreversibility in bacterial regulatory networks. Science Advances, 10(35). https://doi.org/10.1126/sciadv.ado3232

[2] Wytock, T. P., & Motter, A. E. (2024). Cell reprogramming design by transfer learning of functional transcriptional networks. Proceedings of the National Academy of Sciences USA, 121(11). https://doi.org/10.1073/pnas.2312942121

Bio: Thomas P Wytock is a postdoctoral researcher in the Motter Group at Northwestern University. In the Motter Group, Wytock is researching Modeling of Genetic Networks.

More information about Wytock's work is available on ResearchGate.

About the NITMB Seminar Series: The NSF-Simons National Institute for Theory and Mathematics in Biology Seminar Series aims to bring together a mix of mathematicians and biologists to foster discussion and collaboration between the two fields. The seminar series will take place on Fridays from 10am - 11am at the NITMB offices in the John Hancock Center in downtown Chicago. There will be both an in-person and virtual component.