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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)
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Organization
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.
Keywords
Boolean functions, biology computing, genetics, physiological models

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MLA
Fayruzov, Timur 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.
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.
Chicago author-date
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.
Chicago author-date (all authors)
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.
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.
IEEE
[1]
T. Fayruzov, J. Janssen, C. Cornelis, D. Vermeir, and M. De Cock, “Extending boolean regulatory network models with answer set programming,” in Proceedings 2010 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW 2010), Hong Kong, PR China, 2010, pp. 207–212.
@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},
  keywords     = {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},
}

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