VAN GOETHEM, Simon, Jean-Marie JACQUET, Luboš BRIM and David ŠAFRÁNEK. Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. Online. In 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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Basic information
Original name Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization
Authors VAN GOETHEM, Simon (56 Belgium), Jean-Marie JACQUET (56 Belgium), Luboš BRIM (203 Czech Republic, belonging to the institution) and David ŠAFRÁNEK (203 Czech Republic, guarantor, belonging to the institution).
Edition Neuveden, Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12), p. 67-81, 15 pp. 2013.
Publisher Elsevier
Other information
Original language English
Type of outcome Proceedings paper
Field of Study 10201 Computer sciences, information science, bioinformatics
Country of publisher Czech Republic
Confidentiality degree is not subject to a state or trade secret
Publication form electronic version available online
WWW URL
RIV identification code RIV/00216224:14330/13:00065956
Organization unit Faculty of Informatics
ISSN 1571-0661
Doi http://dx.doi.org/10.1016/j.entcs.2013.02.019
UT WoS 000216918000006
Keywords in English timed automata; gene regulatory networks; UPPAAL
Tags International impact, Reviewed
Changed by Changed by: RNDr. Pavel Šmerk, Ph.D., učo 3880. Changed: 24/4/2014 17:29.
Abstract
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.
Links
GAP202/11/0312, research and development projectName: Vývoj a verifikace softwarových komponent v zapouzdřených systémech (Acronym: Components in Embedded Systems)
Investor: Czech Science Foundation
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