Ghent University Academic Bibliography

Advanced

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 (2011) INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS. 5(2). p.209-229
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
systems biology, ASP, answer set programming, network modelling, budding yeast, fission yeast, cell cycle, steady state, steady cycle
journal title
INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS
Int. J. Data Min. Bioinform.
volume
5
issue
2
pages
209 - 229
Web of Science type
Article
Web of Science id
000288797700006
JCR category
MATHEMATICAL & COMPUTATIONAL BIOLOGY
JCR impact factor
0.429 (2011)
JCR rank
44/46 (2011)
JCR quartile
4 (2011)
ISSN
1748-5673
DOI
10.1504/IJDMB.2011.039178
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1108340
handle
http://hdl.handle.net/1854/LU-1108340
date created
2011-01-21 15:30:04
date last changed
2013-02-27 09:11:23
@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},
}

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.