Timed Modelling of Gene Networks with Arbitrary Expression
Level Discretization

D 2013

Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization

VAN GOETHEM, Simon, Jean-Marie JACQUET, Luboš BRIM and David ŠAFRÁNEK

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

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

Czech Republic

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

RIV identification code

RIV/00216224:14330/13:00065956

Organization unit

Faculty of Informatics

ISSN

DOI

http://dx.doi.org/10.1016/j.entcs.2013.02.019

UT WoS

000216918000006

Keywords in English

timed automata; gene regulatory networks; UPPAAL

Abstract

V originále

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 project

Name: Vývoj a verifikace softwarových komponent v zapouzdřených systémech (Acronym: Components in Embedded Systems)

Investor: Czech Science Foundation

Citovat

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.

@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.

Detailed Information on Publication Record