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@inproceedings{1076398, author = {Van Goethem, Simon and Jacquet, JeanandMarie and Brim, Luboš and Šafránek, David}, address = {Neuveden}, booktitle = {Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)}, doi = {http://dx.doi.org/10.1016/j.entcs.2013.02.019}, keywords = {timed automata; gene regulatory networks; UPPAAL}, howpublished = {elektronická verze "online"}, language = {eng}, location = {Neuveden}, pages = {67-81}, publisher = {Elsevier}, title = {Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization}, url = {http://www.sciencedirect.com/science/article/pii/S1571066113000212}, year = {2013} }
TY - JOUR ID - 1076398 AU - Van Goethem, Simon - Jacquet, Jean-Marie - Brim, Luboš - Šafránek, David PY - 2013 TI - Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization PB - Elsevier CY - Neuveden KW - timed automata KW - gene regulatory networks KW - UPPAAL UR - http://www.sciencedirect.com/science/article/pii/S1571066113000212 L2 - http://www.sciencedirect.com/science/article/pii/S1571066113000212 N2 - 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. ER -
VAN GOETHEM, Simon, Jean-Marie JACQUET, Luboš BRIM and David ŠAFRÁNEK. Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. Online. In \textit{Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12)}. Neuveden: Elsevier, 2013, p.~67-81. ISSN~1571-0661. Available from: https://dx.doi.org/10.1016/j.entcs.2013.02.019.
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