A yeast cell cycle pulse generator model shows consistency with multiple and mutant datasets

Author(s)

Fox, Julian ; Cummins, Breschine ; Moseley, Robert C. ; Gameiro, Marcio ; Haase, Steven B.

• Document type: Journal article
• Source: MATHEMATICAL BIOSCIENCES; v. 367, p. 19-pg., 2023-12-08.

Abstract

Modeling biological systems holds great promise for speeding up the rate of discovery in systems biology by predicting experimental outcomes and suggesting targeted interventions. However, this process is dogged by an identifiability issue, in which network models and their parameters are not sufficiently constrained by coarse and noisy data to ensure unique solutions. In this work, we evaluated the capability of a simplified yeast cell-cycle network model to reproduce multiple observed transcriptomic behaviors under genomic mutations. We matched time-series data from both cycling and checkpoint arrested cells to model predictions using an asynchronous multi-level Boolean approach. We showed that this single network model, despite its simplicity, is capable of exhibiting dynamical behavior similar to the datasets in most cases, and we demonstrated the drop in severity of the identifiability issue that results from matching multiple datasets. (AU)

• FAPESP's process: 19/06249-7 - Applications of Computational and Topological Methods to Dynamical Systems
• Grantee: Marcio Fuzeto Gameiro
• Support Opportunities: Regular Research Grants