title: Probabilistic Boolean Network Modelling and Analysis Framework for mRNA Translation.
abstract: mRNA translation is a complex process involving the progression of ribosomes on the mRNA, resulting in the synthesis of proteins, and is subject to multiple layers of regulation. This process has been modelled using different formalisms, both stochastic and deterministic. Recently, we introduced a Probabilistic Boolean modelling framework for mRNA translation, which possesses the advantage of tools for numerically exact computation of steady state probability distribution, without requiring simulation. Here, we extend this model to incorporate both random sequential and parallel update rules, and demonstrate its effectiveness in various settings, including its flexibility in accommodating additional static and dynamic biological complexities and its role in parameter sensitivity analysis. In these applications, the results from the model analysis match those of TASEP model simulations. Importantly, the proposed modelling framework maintains the stochastic aspects of mRNA translation and provides a way to exactly calculate probability distributions, providing additional tools of analysis in this context. Finally, the proposed modelling methodology provides an alternative approach to the understanding of the mRNA translation process, by bridging the gap between existing approaches, providing new analysis tools, and contributing to a more robust platform for modelling and understanding translation.
authors.forename: Yun-Bo
authors.initials: YB
authors.lastname: Zhao
authors.forename: J
authors.initials: J
authors.lastname: Krishnan
mesh_terms: D003062:Codon / Q000235:genetics; D019295:Computational Biology; D008957:Models, Genetic; D015233:Models, Statistical; D014176:Protein Biosynthesis / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism
chemical_list: D003062:Codon; D012333:RNA, Messenger