Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization

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Authors

VAN GOETHEM Simon JACQUET Jean-Marie BRIM Luboš ŠAFRÁNEK David

Year of publication 2013
Type Article in Proceedings
Conference Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)
MU Faculty or unit

Faculty of Informatics

Citation
Web http://www.sciencedirect.com/science/article/pii/S1571066113000212
Doi http://dx.doi.org/10.1016/j.entcs.2013.02.019
Field Informatics
Keywords timed automata; gene regulatory networks; UPPAAL
Description In this paper, a novel approach to discrete modeling of gene regulatory networks is presented. The approach is based on timed automata and is new in: (i) reflecting discrete abstraction of gene expression with arbitrary granularity, (ii) combining boolean logic with approximation of Hill kinetics. This is achieved by introducing delays that change dynamically with respect to current activity levels of regulating genes. The approach is implemented in UPPAAL and evaluated on benchmark models and on a biological case study.
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