Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization
| Authors | |
|---|---|
| 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 | |
| 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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