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2015 | OriginalPaper | Buchkapitel

Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks

verfasst von : Alvis Brazma, Karlis Cerans, Dace Ruklisa, Thomas Schlitt, Juris Viksna

Erschienen in: Hybrid Systems Biology

Verlag: Springer International Publishing

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Abstract

We describe a hybrid system based framework for modeling gene regulation and other biomolecular networks and a method for analysis of the dynamic behavior of such models. A particular feature of the proposed framework is the focus on qualitative experimentally testable properties of the system. With this goal in mind we introduce the notion of the frame of a hybrid system, which allows for the discretisation of the state space of the network. We propose two different methods for the analysis of this state space. The result of the analysis is a set of attractors that characterize the underlying biological system.

Whilst in the general case the problem of finding attractors in the state space is algorithmically undecidable, we demonstrate that our methods work for comparatively complex gene regulatory network model of \(\lambda \)-phage. For this model we are able to identify attractors corresponding to two known biological behaviors of \(\lambda \)-phage: lysis and lysogeny and also to show that there are no other stable behavior regions for this model.

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Vorheriges Kapitel Fluorescent Reporter Genes and the Analysis of Bacterial Regulatory Networks

Nächstes Kapitel Parameter Synthesis Using Parallelotopic Enclosure and Applications to Epidemic Models

For biomolecular networks the value \(''\rightarrow ''\) describing the situation where concentration of some substance does not change is generally reserved for the cases in which concentration is either 0 or the maximal biologically feasible saturation value.

Ahmad, J., Bernot, J., Comet, J., Lime, D., Roux, O.: Hybrid modelling and dynamical analysis of gene regulatory networks with delays. Complexus 3, 231–251 (2007)CrossRef

Alur, R., Belta, C., Ivančić, F., Kumar, V., Mintz, M., Pappas, G.J., Rubin, H., Schug, J.: Hybrid modeling and simulation of biomolecular networks. In: Di Benedetto, M.D., Sangiovanni-Vincentelli, A.L. (eds.) HSCC 2001. LNCS, vol. 2034, pp. 19–32. Springer, Heidelberg (2001) CrossRef

Bartocci, E., Liò, P., Merelli, E., Paoletti, N.: Multiple verification in complex biological systems: the bone remodelling case study. In: Priami, C., Petre, I., de Vink, E. (eds.) Transactions on Computational Systems Biology XIV. LNCS, vol. 7625, pp. 53–76. Springer, Heidelberg (2012) CrossRef

Batt, G., Ben Salah, R., Maler, O.: On timed models of gene networks. In: Raskin, J.-F., Thiagarajan, P.S. (eds.) FORMATS 2007. LNCS, vol. 4763, pp. 38–52. Springer, Heidelberg (2007) CrossRef

Brazma, A., Schlitt, T.: Reverse engineering of gene regulatory networks: a finite state linear model. Genome Biol. 4(P5), 1–31 (2003)

Brazma, R., Cerans, K., Ruklisa, D., Schlitt, T., Viksna, J.: HSM - a hybrid system based approach for modelling intracellular networks. Gene 518, 70–77 (2013)CrossRef

de Jong, H., Gouze, J., Hernandez, C., Page, M., Sari, T., Geiselmann, J.: Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull. Math. Biol. 66, 301–340 (2004)MathSciNetCrossRefMATH

Fromentin, J., Eveillard, D., Roux, O.: Hybrid modeling of biological networks: mixing temporal and qualitative biological properties. BMC Syst. Biol. 4(79), 11 (2010)

Ghosh, R., Tomlin, C.: Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-notch protein signalling. Syst. Biol. 1, 170–183 (2004)CrossRef

10.

Grosu, R., Batt, G., Fenton, F.H., Glimm, J., Le Guernic, C., Smolka, S.A., Bartocci, E.: From cardiac cells to genetic regulatory networks. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 396–411. Springer, Heidelberg (2011) CrossRef

11.

McAdams, H., Shapiro, L.: Circuit simulation of genetic networks. Science 269, 650–656 (1995)CrossRef

12.

Ruklisa, D., Brazma, A., Viksna, J.: Reconstruction of gene regulatory networks under the finite state linear model. Genome Inform. 16, 225–236 (2005)

13.

Schlitt, T., Brazma, A.: Modelling in molecular biology: describing transcription regulatory networks at different scales. Philos. Trans. R. Soc. Lond. B 361, 483–494 (2006)CrossRef

14.

Serra, R., Vilani, M., Barbieri, A., Kaufmfman, S., Colacci, A.: One the dynamics of random boolean networks subject to noise: attractors, ergodic sets and cell types. J. Theor. Biol. 265, 185–193 (2010)CrossRef

15.

Siebert, H., Bockmayr, A.: Temporal constraints in the logical analysis of regulatory networks. Theor. Comput. Sci. 391, 258–275 (2008)MathSciNetCrossRefMATH

16.

Thomas, D., Thieffry, R., Kaufman, M.: Dynamic behaviour of biological regulatory networks. i. biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol. 57, 247–276 (1995)CrossRefMATH

17.

Thomas, D., Thieffry, R., Kaufman, M.: Dynamic behaviour of biological regulatory networks. ii. immunity control in bacteriophage lamda. Bull. Math. Biol. 57, 277–297 (1995)CrossRefMATH

Titel: Modeling and Analysis of Qualitative Behavior of Gene Regulatory Networks
verfasst von: Alvis Brazma
Karlis Cerans
Dace Ruklisa
Thomas Schlitt
Juris Viksna
Verlag: Springer International Publishing
Buch: Hybrid Systems Biology
Print ISBN: 978-3-319-27655-7

Electronic ISBN: 978-3-319-27656-4

Copyright-Jahr: 2015
DOI: https://doi.org/10.1007/978-3-319-27656-4_3

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