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Extending boolean regulatory network models with answer set programming

Timur Fayruzov UGent, Jeroen Janssen UGent, Chris Cornelis UGent, Dirk Vermeir and Martine De Cock UGent (2010) Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010). p.207-212
abstract
Because of their simplicity, boolean networks are a popular formalism to model gene regulatory networks. However, they have their limitations, including their inability to formally and unambiguously define network behaviour, and their lack of the possibility to model meta interactions, i.e., interactions that target other interactions. In this paper we develop an answer set programming (ASP) framework that supports threshold boolean network semantics and extends it with the capability to model meta interactions. The framework is easy to use but sufficiently flexible to express intricate interactions that go beyond threshold network semantics as we illustrate with an example of a Mammalian cell cycle network. Moreover, readily available answer set solvers can be used to find the steady states of the network.
Please use this url to cite or link to this publication:
author
organization
year
type
conference
publication status
published
subject
keyword
Boolean functions, biology computing, genetics, physiological models
in
Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010)
pages
207 - 212
publisher
IEEE
place of publication
Piscataway, NJ, USA
conference name
2010 IEEE International conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010) : Integrative Data Analysis in Systems Biology (IDASB '10)
conference location
Hong Kong, PR China
conference start
2010-12-18
conference end
2010-12-21
Web of Science type
Conference Paper
Web of Science id
11777683
ISBN
9781424483037
9781424483020
DOI
10.1109/BIBMW.2010.5703800
language
English
UGent publication?
yes
classification
C1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1108292
handle
http://hdl.handle.net/1854/LU-1108292
date created
2011-01-21 15:25:43
date last changed
2011-05-18 16:28:58
@inproceedings{1108292,
  abstract     = {Because of their simplicity, boolean networks are a popular formalism to model gene regulatory networks. However, they have their limitations, including their inability to formally and unambiguously define network behaviour, and their lack of the possibility to model meta interactions, i.e., interactions that target other interactions. In this paper we develop an answer set programming (ASP) framework that supports threshold boolean network semantics and extends it with the capability to model meta interactions. The framework is easy to use but sufficiently flexible to express intricate interactions that go beyond threshold network semantics as we illustrate with an example of a Mammalian cell cycle network. Moreover, readily available answer set solvers can be used to find the steady states of the network.},
  author       = {Fayruzov, Timur and Janssen, Jeroen and Cornelis, Chris and Vermeir, Dirk and De Cock, Martine},
  booktitle    = {Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010)},
  isbn         = {9781424483037},
  keyword      = {Boolean functions,biology computing,genetics,physiological models},
  language     = {eng},
  location     = {Hong Kong, PR China},
  pages        = {207--212},
  publisher    = {IEEE},
  title        = {Extending boolean regulatory network models with answer set programming},
  url          = {http://dx.doi.org/10.1109/BIBMW.2010.5703800},
  year         = {2010},
}

Chicago
Fayruzov, Timur, Jeroen Janssen, Chris Cornelis, Dirk Vermeir, and Martine De Cock. 2010. “Extending Boolean Regulatory Network Models with Answer Set Programming.” In Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010), 207–212. Piscataway, NJ, USA: IEEE.
APA
Fayruzov, T., Janssen, J., Cornelis, C., Vermeir, D., & De Cock, M. (2010). Extending boolean regulatory network models with answer set programming. Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010) (pp. 207–212). Presented at the 2010 IEEE International conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010) : Integrative Data Analysis in Systems Biology (IDASB  ’10), Piscataway, NJ, USA: IEEE.
Vancouver
1.
Fayruzov T, Janssen J, Cornelis C, Vermeir D, De Cock M. Extending boolean regulatory network models with answer set programming. Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010). Piscataway, NJ, USA: IEEE; 2010. p. 207–12.
MLA
Fayruzov, Timur, Jeroen Janssen, Chris Cornelis, et al. “Extending Boolean Regulatory Network Models with Answer Set Programming.” Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010). Piscataway, NJ, USA: IEEE, 2010. 207–212. Print.