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Modelling gene and protein regulatory networks with answer set pogramming

Timur Fayruzov (UGent) , Jeroen Janssen (UGent) , Dirk Vermeir, Chris Cornelis (UGent) and Martine De Cock (UGent)
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Recently, many approaches to model regulatory networks have been proposed in the systems biology domain. However, the task is far from being solved. In this paper, we propose an Answer Set Programming (ASP)-based approach to model interaction networks. We build a general ASP framework that describes the network semantics and allows modelling specific networks with little effort. ASP provides a rich and flexible toolbox that allows expanding the framework with desired features. In this paper, we tune our framework to mimic Boolean network behaviour and apply it to model the Budding Yeast and Fission Yeast cell cycle networks. The obtained steady states of these networks correspond to those of the Boolean networks.
Keywords
systems biology, ASP, answer set programming, network modelling, budding yeast, fission yeast, cell cycle, steady state, steady cycle

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Citation

Please use this url to cite or link to this publication:

Chicago
Fayruzov, Timur, Jeroen Janssen, Dirk Vermeir, Chris Cornelis, and Martine De Cock. 2011. “Modelling Gene and Protein Regulatory Networks with Answer Set Pogramming.” International Journal of Data Mining and Bioinformatics 5 (2): 209–229.
APA
Fayruzov, T., Janssen, J., Vermeir, D., Cornelis, C., & De Cock, M. (2011). Modelling gene and protein regulatory networks with answer set pogramming. INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS, 5(2), 209–229.
Vancouver
1.
Fayruzov T, Janssen J, Vermeir D, Cornelis C, De Cock M. Modelling gene and protein regulatory networks with answer set pogramming. INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS. 2011;5(2):209–29.
MLA
Fayruzov, Timur, Jeroen Janssen, Dirk Vermeir, et al. “Modelling Gene and Protein Regulatory Networks with Answer Set Pogramming.” INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS 5.2 (2011): 209–229. Print.
@article{1108340,
  abstract     = {Recently, many approaches to model regulatory networks have been proposed in the systems biology domain. However, the task is far from being solved. In this paper, we propose an Answer Set Programming (ASP)-based approach to model interaction networks. We build a general ASP framework that describes the network semantics and allows modelling specific networks with little effort. ASP provides a rich and flexible toolbox that allows expanding the framework with desired features. In this paper, we tune our framework to mimic Boolean network behaviour and apply it to model the Budding Yeast and Fission Yeast cell cycle networks. The obtained steady states of these networks correspond to those of the Boolean networks.},
  author       = {Fayruzov, Timur and Janssen, Jeroen and Vermeir, Dirk and Cornelis, Chris and De Cock, Martine},
  issn         = {1748-5673},
  journal      = {INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS},
  keyword      = {systems biology,ASP,answer set programming,network modelling,budding yeast,fission yeast,cell cycle,steady state,steady cycle},
  language     = {eng},
  number       = {2},
  pages        = {209--229},
  title        = {Modelling gene and protein regulatory networks with answer set pogramming},
  url          = {http://dx.doi.org/10.1504/IJDMB.2011.039178},
  volume       = {5},
  year         = {2011},
}

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