Abstract
We introduce a genetic programming (GP) approach for evolving genetic networks that demonstrate desired dynamics when simulated as a discrete stochastic process. Our representation of genetic networks is based on a biochemical reaction model including key elements such as transcription, translation and post-translational modifications. The stochastic, reaction-based GP system is similar but not identical with algorithmic chemistries. We evolved genetic networks with noisy oscillatory dynamics. The results show the practicality of evolving particular dynamics in gene regulatory networks when modelled with intrinsic noise.
Keywords
- Genetic Network
- Genetic Regulatory Network
- Catalytic Degradation
- Stochastic Simulation Algorithm
- Genetic Circuit
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.
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References
Kobayashi, H., Kaern, M., Chung, K., Gardner, T.S., Cantor, C.R., Collins, J.J.: Programmable cells: Interfacing natural and engineered gene networks. In: Proc. Natl. Acad. Sci., vol. 101(22), pp. 8414–8419 (2004)
Isaacs, F.J., Hasty, J., Cantor, C.R., Collins, J.J.: Prediction and measurement of an autoregulatory genetic module. In: Proc. Natl. Acad. Sci., vol. 100(13), pp. 7714–7719 (2003)
Gardner, T.S., Cantor, C.R., Collins, J.J.: Construction of genetic toggle switch in escherichia coli. Nature 403, 6767, 339–342 (2000)
Guet, C.C., Elowitz, M.B., Hsing, W., Leibler, S.: Combinatorial synthesis of genetic networks. Science 296, 1466–1470 (2002)
Mason, J., Linsay, P.S., Collins, J.J., Glass, L.: Evolving complex dynamics in electronic models of genetic networks. Chaos 14(3), 707–715 (2004)
Elowitz, M.B., Leibler, S.: A synthetic oscillatory network of transcriptional regulators. Nature 403(6767), 335–338 (2000)
Yokobayashi, Y., Weiss, R., Arnold, F.H.: Directed evolution of a genetic circuit. In: Proc. Natl. Acad. Sci., vol. 99(26), pp. 16587–16591 (2002)
François, P., Hakim, V.: Design of genetic networks with specified functions by evolution in silico. In: Proc. Natl. Acad. Sci., vol. 101(2), pp. 580–585 (2004)
Kuo, P.D., Banzhaf, W., Leier, A.: Network topology and the evolution of dynamics in an artificial genetic regulatory network model created by whole genome duplication and divergence. BioSystems (2006) (In press)
McAdams, H.H., Arkin, A.: Stochastic mechanisms in gene expression. In: Proc. Natl. Acad. Sci., vol. 94(3), pp. 814–819 (1997)
Arkin, A., Ross, J., McAdams, H.H.: Stochastic kinetic analysis of developmental pathway bifurcation in phage λ–infected Escherichia coli cells. Genetics 149(4), 1633–1648 (1998)
Elowitz, M.B., Levine, A.J., Siggia, E.D., Swain, P.S.: Stochastic gene expression in a single cell. Science 297(5584), 1183–1186 (2002)
Hasty, J., Collins, J.J.: Translating the noise. Nature Genetics 31(1), 13–14 (2002)
Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340–2361 (1977)
Heuett, W.J., Qian, H.: A stochastic model of oscillatory blood testoterone levels. To appear in Bulletin for Mathematical Biology (2005)
Goutsias, J.: Quasiequilibrium approximation of fast reaction kinetics in stochastic biochemical systems. J. Chem. Phys. 122(184102), 1–15 (2005)
Gillespie, D.T.: Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115(4), 1716–1733 (2001)
Tian, T., Burrage, K.: Binomial leap methods for simulating stochastic chemical kinetics. J. Chem. Phys. 121(21), 10356–10364 (2004)
Koza, J.R.: Genetic Programming. MIT Press, Cambridge (1992)
Banzhaf, W., Francone, F.D., Keller, R.E., Nordin, P.: Genetic programming: an introduction. Morgan Kaufmann, San Francisco (1998)
Lasarczyk, C.W.G., Banzhaf, W.: An algorithmic chemistry for genetic programming. In: Keijzer, M., Tettamanzi, A.G.B., Collet, P., van Hemert, J., Tomassini, M. (eds.) EuroGP 2005. LNCS, vol. 3447, pp. 1–12. Springer, Heidelberg (2005)
Tian, T., Burrage, K.: Stochastic models for regulatory networks of the genetic toggle switch. In: Proc. Natl. Acad. Sci. (2005) (submitted)
Barrio, M., Burrage, K.: Oscillatory regulation of hes1: Discrete stochastic delay modelling and simulation. PLoS Computational Biology (2005) (submitted)
Bratsun, D., Volfson, D., Tsimring, L.S., Hasty, J.: Delay-induced stochastic oscillations in gene regulation. In: Proc. Natl. Acad. Sci., vol. 102(41), pp. 14593–14598 (2005)
Monk, N.A.M.: Oscillatory expression of Hes1, p53, and NF-kappaB driven by transcriptional time delays. Curr. Biol. 13(16), 1409–1413 (2003)
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Leier, A., Kuo, P.D., Banzhaf, W., Burrage, K. (2006). Evolving Noisy Oscillatory Dynamics in Genetic Regulatory Networks. In: Collet, P., Tomassini, M., Ebner, M., Gustafson, S., Ekárt, A. (eds) Genetic Programming. EuroGP 2006. Lecture Notes in Computer Science, vol 3905. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11729976_26
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DOI: https://doi.org/10.1007/11729976_26
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-33143-8
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