Compositionality, stochasticity, and cooperativity in dynamic models of gene regulation

HFSP Journal

Volumn 2, Issue 1, 2008, Pages 17-28

  Blossey, Ralf ^a   Cardelli, Luca ^b   Phillips, Andrew ^b  

^a CNRS   (France)

^b MICROSOFT RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 51849166317     PISSN: 19552068     EISSN: 1955205X     Source Type: Journal    
DOI: 10.2976/1.2804749     Document Type: Article

References (26)

1. Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K, and Water, P (2002). Molecular Biology of the Cell, 4th ed., Garland Science, London, UK
2. Blossey, R, Cardelli, L, and Phillips, A (2006). "A compositional approach to the stochastic dynamics of gene networks." T. Comp. Sys. Biology, IV, 99-122.
3. Bundschuh, R, Hayot, F, and Jayaprakash, C (2003). "Fluctuations and slow variables in genetic networks." Blood 84, 1606-1615.
4. Cardelli, L (2007). "On process rate semantics," Theoretical Computer Science, Elsevier, NewYork.
5. Cherry, JL, and Adler, FR (2000). "How to make a biological switch." J. Theor. Biol. 203, 117-133.
6. De Jong, H (2002). "Modeling and simulation of genetic regulatory systems: a literature review." J. Comput. Biol. 9, 69-105.
7. Elowitz, MB, and Leibler, S (2000). "A synthetic oscillatory network of transcriptional regulators." Nature (London) 403, 335-338.
8. EPAPS Document No. E-HJFOA5-2-001801 for supplemental material. This document can be reached through a direct link in the online article's HTML reference section or via the EPAPS homepage (http://www.aip.org/pubservs/epaps.html).
9. Fall, CP, Marland, ES, Wagner, JM, and Tyson, JJ (eds.) (2002). Computational Cell Biology, Springer, Heidelberg, Germany.
10. Freidlin, MI (2001). "On stable oscillations and equilibriums induced by small noise." J. Stat. Phys. 103, 283-300.
11. Gillespie, D (1977). "Exact stochastic simulation of coupled chemical reactions." J. Phys. Chem. 81, 2340-2361.
12. Goldbeter, A (1996). Biochemical Oscillations and Cellular Rhythms, Cambridge University Press, Cambridge, UK
13. Kauffman, SA (1969). "Metabolic stability and epigenesis in randomly constructed genetic nets." J. Theor. Biol. 22, 437-467.
14. Kim, J, White, KS, and Winfree, E (2006). "In vitro bistable circuit from synthetic transcriptional activation." Mol. Syst. Biol.
15. Lee Deville, RE, Muratov, CB, and Vanden-Eijnden, E (2006). "Nonmeanfield deterministic limits in chemical reaction kinetics far from equilibrium." J. Chem. Phys. 124, 231102.
16. Milner, R (1999). Communicating and Mobile Systems: the π-calculus, Cambridge University Press, Cambridge, UK.
17. Müller, S, Hofbauer, J, Endler, L, Flamm, C, Widder, S, and Schuster, P (2006). "A generalized model of the repressilator." J. Math. Biol. 53, 905-937.
18. Phillips, A, and Cardelli, L (2007). "Efficient, correct simulation of biological processes in the stochastic Pi-calculus." Comp. Methods. Syst. Biol. 4695, 184-199.
19. Priami, C, Regev, A, Silverman, W, and Shapiro, E (2001). "Application of stochastic process algebras to bioinformatics of molecular processes." Inf. Process. Lett. 80, 25-31.
20. Regev, A (2003). "Computational systems biology: a calculus for biomolecular knowledge." Ph.D. dissertation, Tel Aviv University, Tel Aviv, Israel.
21. Regev, A, and Shapiro, E (2002). "Cellular abstractions: cells as computation." Nature (London) 419, 343.
22. Smolen, P, Baxter, DA, and Byrne, JH (2002). "Modeling transcriptional control in gene networks-methods, recent results, and future directions." Bull. Math. Biol. 62 247-292.
23. Thomas, R (1973). "Boolean formalism of genetic control circuits." J. Theor. Biol. 42, 565-583.
24. Thomas, R (1991). "Regulatory networks seen as asynchronous automata: a logical description." J. Theor. Biol. 153, 1-23.
25. Van Kampen, NG (1992). Stochastic Processes in Physics and Chemistry, Elsevier, Amsterdam, The Netherlands.
26. Widder, S, Schicho, J, and Schuster, P (2007). "Dynamic patterns of gene regulation I: simple two-gene systems." J. Theor. Biol. 246, 395-419.