Abstract
The purpose of this tutorial is to explain and illustrate an approach to the quantitative modelling of molecular interaction networks which departs from the usual notion of (bio-) chemical reaction. This tutorial is self-contained and supposes no familiarity with molecular biology.
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Keywords
- Association Rule
- Continuous Time Markov Chain
- Epigenetic Information
- Molecular Interaction Network
- Recognition Rule
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
References
Feret, J., Danos, V., Harmer, R., Krivine, J., Fontana, W.: Internal coarse-graining of molecular systems. PNAS (April 2009)
Faeder, J.R., Blinov, M.L., Hlavacek, W.S.: Rule-based modeling of biochemical systems with BioNetGen. In: Systems Biology, vol. 500, pp. 113–167. Humana Press (2009)
Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Rule-based modelling, symmetries, refinements. In: Fisher, J. (ed.) FMSB 2008. LNCS (LNBI), vol. 5054, pp. 103–122. Springer, Heidelberg (2008)
Esteller, M.: Cancer epigenomics: Dna methylomes and histone-modification maps. Nat. Rev. Genet. 8(4), 286–298 (2007)
Dinant, C., Luijsterburg, M.S., Höfer, T., von Bornstaedt, G., Vermeulen, W., Houtsmuller, A.B., van Driel, R.: Assembly of multiprotein complexes that control genome function. J. Cell Biol. 185(1), 21–26 (2009)
Kim, P.M., Lu, L.J., Xia, Y., Gerstein, M.B.: Relating three-dimensional structures to protein networks provides evolutionary insights. Science 314(5807), 1938–1941 (2006)
Danos, V., Feret, J., Fontana, W., Krivine, J.: Scalable simulation of cellular signaling networks. In: Shao, Z. (ed.) APLAS 2007. LNCS, vol. 4807, pp. 139–157. Springer, Heidelberg (2007)
Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Investigation of a biological repair scheme. In: Corne, D.W., Frisco, P., Păun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2009. LNCS, vol. 5391, pp. 1–12. Springer, Heidelberg (2009)
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Krivine, J., Danos, V., Benecke, A. (2009). Modelling Epigenetic Information Maintenance: A Kappa Tutorial. In: Bouajjani, A., Maler, O. (eds) Computer Aided Verification. CAV 2009. Lecture Notes in Computer Science, vol 5643. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02658-4_3
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DOI: https://doi.org/10.1007/978-3-642-02658-4_3
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