Network reconstruction using computational algebra and gene knockouts

Mathematical Biology Seminar
Wednesday, November 13, 2019 - 11:00am for 1 hour (actually 50 minutes)
Skiles 006
Matthew Macauley – Clemson University – macaule@clemson.edu
Bo Lin

I will discuss an ongoing project to reconstruct a gene network from time-series data from a mammalian signaling pathway. The data is generated from gene knockouts and the techniques involve computational algebra. Specifically, one creates an pseudomonomial "ideal of non-disposable sets" and applies a analogue of Stanley-Reisner theory and Alexander duality to it. Of course, things never work as well in practice, due to issue such as noise, discretization, and scalability, and so I will discuss some of these challenges and current progress.