The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Open accessAbstract
Motivation: To understand the behaviour of complex biological regulatory networks, a proper integration of molecular data into a full-fledge formal dynamical model is ultimately required. As most available data on regulatory interactions are qualitative, logical modelling offers an interesting framework to delineate the main dynamical properties of the underlying networks. Results: Transposing a generic model of the core network controlling the mammalian cell cycle into the logical framework, we compare different strategies to explore its dynamical properties. In particular, we assess the respective advantages and limits of synchronous versus asynchronous updating assumptions to delineate the asymptotical behaviour of regulatory networks. Furthermore, we propose several intermediate strategies to optimize the computation of asymptotical properties depending on available knowledge. Availability: The mammalian cell cycle model is available in a dedicated XML format (GINML) on our website, along with our logical simulation software GINsim (). Higher resolution state transitions graphs are also found on this web site (Model Repository page). Contact: thieffry@ibdm.univ-mrs.fr
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Cites
The logical analysis of continuous, non-linear biochemical control networks
Glass, L., & Kauffman, S. A. (1973) · Journal of Theoretical Biology · doi:10.1016/0022-5193(73)90208-7 · Cited by 940
The E2F transcriptional network: old acquaintances with new faces
Dimova, D. K., & Dyson, N. J. (2005) · Oncogene · doi:10.1038/sj.onc.1208612 · Cited by 715
Cited by
Boolean network models of cellular regulation: prospects and limitations
Bornholdt, S. (2008) · Journal of The Royal Society Interface · doi:10.1098/rsif.2008.0132.focus · Cited by 394
Logic-Based Models for the Analysis of Cell Signaling Networks
Morris, M. K., Saez-Rodriguez, J., Sorger, P. K., & Lauffenburger, D. A. (2010) · Biochemistry · doi:10.1021/bi902202q · Cited by 332
Synchronous versus asynchronous modeling of gene regulatory networks
Garg, A., Di Cara, A., Xenarios, I., Mendoza, L., & De Micheli, G. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn336 · Cited by 305
Inverse problems in systems biology
Engl, H. W., Flamm, C., Kügler, P., Lu, J., Müller, S., & Schuster, P. (2009) · Inverse Problems · doi:10.1088/0266-5611/25/12/123014 · Cited by 122
BTR: training asynchronous Boolean models using single-cell expression data
Lim, C. Y., Wang, H., Woodhouse, S., Piterman, N., Wernisch, L., Fisher, J., & Göttgens, B. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1235-y · Cited by 81
Metadata
- Authors
- Fauré, A., Naldi, A., Chaouiya, C., & Thieffry, D.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-07-15
- Volume
- 22
- Issue
- 14
- Pages
- e124-e131
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2132935366
- Cited by
- 642
- References
- 2
- FWCI
- 9.70
- Type
- journal article
- Language
- en
- Open access
- bronze
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- Fauré, A., Naldi, A., Chaouiya, C., & Thieffry, D. (2006). Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics. https://doi.org/10.1093/bioinformatics/btl210
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