Mean-field versus stochastic models for transcriptional regulation

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 78, Issue 3, 2008, Pages

  Blossey, R ^a   Giuraniuc, C V ^a  

^a UNIV LILLE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATION ALGORITHMS; ESCHERICHIA COLI; MATHEMATICAL MODELS; REACTION KINETICS; STOCHASTIC CONTROL SYSTEMS; STOCHASTIC PROGRAMMING;

BI-STABLE; CELLULAR DEVELOPMENT; E. COLI; EXTERNAL DRIVING; GENE NETWORK; GILLESPIE ALGORITHM; LEVEL OF DETAILS; MEAN FIELDS; MEAN-FIELD APPROXIMATION; MINIMAL MODELING; REPRESSILATOR; STOCHASTIC SIMULATIONS; TRANSCRIPTIONAL REGULATIONS; TRANSCRIPTIONAL REGULATORY NETWORKS;

STOCHASTIC MODELS;

EID: 51849141809     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.78.031909     Document Type: Article

References (37)

1. A. Goldbeter, Biochemical Oscillations and Cellular Rhythms (Cambridge University Press, Cambridge, United Kingdom, 1996).
2. Computational Cell Biology, edited by, C. P. Fall, E. S. Marland, J. M. Wagner, and, J. J. Tyson, (Springer, Heidelberg, Germany, 2002).
3. N. van Kampen, Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 2007).
4. D. T. Gillespie, J. Phys. Chem. JPCHAX 0022-3654 10.1021/j100540a008 81, 2340 (1977).
5. J. M. G. Vilar, H. Y. Kueh, N. Baarkai, and S. Leibler, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.092133899 99, 5988 (2002).
6. P. S. Swain, M. B. Elowitz, and E. D. Siggia, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.162041399 99, 12795 (2002).
7. M. B. Elowitz, A. J. Levine, E. D. Siggia, and P. S. Swain, Science SCIEAS 0036-8075 10.1126/science.1070919 297, 1183 (2002).
8. J. Paulsson, Nature (London) NATUAS 0028-0836 10.1038/nature02257 427, 415 (2004).
9. J. Paulsson, Phys. Life. Rev. ZZZZZZ 1571-0645 2, 157 (2005).
10. H. de Jong, J. Geiselmann, C. Hernandez, and M. Page, Bioinformatics BOINFP 1367-4803 10.1093/bioinformatics/btf851 19, 336 (2003).
11. L. Glass and S. A. Kauffman, J. Theor. Biol. JTBIAP 0022-5193 10.1016/0022-5193(73)90208-7 39, 103 (1973).
12. R. Thomas, J. Theor. Biol. JTBIAP 0022-5193 10.1016/0022-5193(73)90247-6 42, 565 (1973).
13. R. Bundschuh, F. Hayot, and C. Jayaprakash, Biophys. J. BIOJAU 0006-3495 84, 1606 (2003).
14. S. Müller, J. Hofbauer, L. Endler, C. Flamm, S. Widder, and P. Schuster, J. Math. Biol. JMBLAJ 0303-6812 10.1007/s00285-006-0035-9 53, 905 (2006).
15. S. Widder, J. Schicho, and P. Schuster, J. Theor. Biol. JTBIAP 0022-5193 10.1016/j.jtbi.2007.01.004 246, 395 (2007).
16. U. Alon, An Introduction to Systems Biology (CRC Chapman and Hall, London, United Kingdom, 2006).
17. M. B. Elowitz and S. Leibler, Nature (London) NATUAS 0028-0836 10.1038/35002125 403, 335 (2000).
18. Y. Saka and J. C. Smith, BMC Evol. Biol. BEBMCG 1471-2148 7, 47 (2007).
19. M. Madan Babu and S. A. Teichmann, Nucleic Acids Res. NARHAD 0305-1048 10.1093/nar/gkg210 31, 1234 (2003).
20. J. N. Weiss, FASEB J. FAJOEC 0892-6638 11, 835 (1997).
21. J. L. Cherry and F. R. Adler, J. Theor. Biol. JTBIAP 0022-5193 10.1006/jtbi.2000.1068 203, 117 (2000).
22. R. Milner, Communicating and Mobile Systems: The π -Calculus (Cambridge University Press, Cambridge, 1999).
23. C. Priami, A. Regev, W. Silverman, and E. Shapiro, Inf. Process. Lett. IFPLAT 0020-0190 10.1016/S0020-0190(01)00214-9 80, 25 (2001).
24. R. Blossey, L. Cardelli, and A. Phillips, T. Comp. Sys. Bio. IV, 99 (2006).
25. R. Blossey, L. Cardelli, and A. Phillips, HFSP J. HJFOA5 1955-2068 10.2976/1.2804749 2, 17 (2008).
26. A. Phillips and L. Cardelli, Computational Methods in Systems Biology, Lect. Notes Comput. Sci. Vol. 4695 (Springer, New York, 2007), p. 184.
27. http://research.microsoft.com/~aphillip/
28. A. Lipshtat, A. Loinger, N. Q. Balaban, and O. Biham, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.96.188101 96, 188101 (2006).
29. A. Loinger and O. Biham, Phys. Rev. E PLEEE8 1063-651X 10.1103/PhysRevE.76.051917 76, 051917 (2007).
30. D. Gonze, J. Halloy, and A. Goldbeter, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.022628299 99, 673 (2002).
31. D. Gonze, J. Halloy, and P. Gaspard, J. Chem. Phys. JCPSA6 0021-9606 10.1063/1.1475765 116, 10997 (2002).
32. J. Paulsson, O. G. Berg, and M. Ehrenberg, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.110057697 97, 7148 (2004).
33. P. B. Warren and P. R. ten Wolde, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.92.128101 92, 128101 (2004).
34. R. J. Allen, P. B. Warren, and P. R. ten Wolde, Phys. Rev. Lett. PRLTAO 0031-9007 10.1103/PhysRevLett.94.018104 94, 018104 (2005).
35. A. M. Walczak, J. Onuchic, and P. G. Wolynes, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0509547102 102, 18926 (2005).
36. M. J. Morelli, S. Tanase-Nicola, R. J. Allen, and P. R. ten Wolde, Biophys. J. BIOJAU 0006-3495 94, 3413 (2008).
37. M. Scott, T. Hwa, and B. Ingalls, Proc. Natl. Acad. Sci. U.S.A. PNASA6 0027-8424 10.1073/pnas.0610468104 104, 7402 (2007).