title: A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.
abstract: To understand the molecular mechanisms that regulate cell cycle progression in eukaryotes, a variety of mathematical modeling approaches have been employed, ranging from Boolean networks and differential equations to stochastic simulations. Each approach has its own characteristic strengths and weaknesses. In this paper, we propose a "standard component" modeling strategy that combines advantageous features of Boolean networks, differential equations and stochastic simulations in a framework that acknowledges the typical sorts of reactions found in protein regulatory networks. Applying this strategy to a comprehensive mechanism of the budding yeast cell cycle, we illustrate the potential value of standard component modeling. The deterministic version of our model reproduces the phenotypic properties of wild-type cells and of 125 mutant strains. The stochastic version of our model reproduces the cell-to-cell variability of wild-type cells and the partial viability of the CLB2-dbΔ clb5Δ mutant strain. Our simulations show that mathematical modeling with "standard components" can capture in quantitative detail many essential properties of cell cycle control in budding yeast.
authors.affiliation: Genetics, Bioinformatics, and Computational Biology Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Teeraphan
authors.initials: T
authors.lastname: Laomettachit
authors.affiliation: Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: Katherine C
authors.initials: KC
authors.lastname: Chen
authors.affiliation: Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: William T
authors.initials: WT
authors.lastname: Baumann
authors.affiliation: Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, United States of America.
authors.forename: John J
authors.identifier: 0000-0001-7560-6013
authors.initials: JJ
authors.lastname: Tyson
mesh_terms: D000465:Algorithms; D059447:Cell Cycle Checkpoints; D002470:Cell Survival / Q000235:genetics; D003198:Computer Simulation; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D053263:Gene Regulatory Networks; D008954:Models, Biological; D009154:Mutation; D010766:Phosphorylation; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D004718:Saccharomycetales / Q000502:physiology; D015003:Yeasts / Q000502:physiology*
chemical_list: D005656:Fungal Proteins; D012333:RNA, Messenger