On the compromise between retroactivity attenuation and noise amplification in gene regulatory networks

Proceedings of the IEEE Conference on Decision and Control

Volumn , Issue , 2009, Pages 4565-4571

  Jayanthi, Shridhar ^a   Del Vecchio, Domitilla ^a  

^a NONE

Author keywords

[No Author keywords available]

Indexed keywords

DIFFERENTIAL EQUATIONS; FEEDBACK; SIGNAL TO NOISE RATIO; STOCHASTIC SYSTEMS;

AMPLIFICATION GAIN; BIOMOLECULAR SYSTEM; GENE REGULATORY NETWORKS; LANGEVIN EQUATION; LINEARIZED SYSTEMS; NEGATIVE FEEDBACK LOOP; NOISE AMPLIFICATION; STOCHASTIC ANALYSIS;

AMPLIFICATION;

EID: 77950814624     PISSN: 07431546     EISSN: 25762370     Source Type: Conference Proceeding    
DOI: 10.1109/CDC.2009.5400631     Document Type: Conference Paper

References (21)

1. U. Alon. Network motifs: theory and experimental approaches. Nature, 8:450-461, June 2007.
2. D. W. Austin, M. S. Allen, J. M. McCollum, R. D. Dar, J. R. Wilgus, G. S. Sayler, N. F. Samatova, C. D. Cox, and M. L. Simpson. Gene network shaping of inherent noise spectra. Nature, 439(7076):608-611, February 2006.
3. A. Becskei and L. Serrano. Engineering stability in gene networks by autoregulation. Nature, 405:590-593, 2000.
4. D. Del Vecchio and S. Jayanthi. Retroactivity attenuation in transcriptional networks: Design and analysis of an insulation device. Decision and Control, 2008. CDC 2008. 47th IEEE Conference on, pages 774-780, Dec. 2008.
5. D. Del Vecchio, A. J. Ninfa, and E. D. Sontag. Modular cell biology: retroactivity and insulation. Mol Syst Biol, 4, February 2008.
6. J. Elf and M. Ehrenberg. Fast evaluation of fluctuations in biochemical networks with the linear noise approximation. Genome research, 13(11):2475-2484, November 2003.
7. C. W. Gardiner. Handbook of Stochastic Methods: For Physics, Chemistry and the Natural Sciences (Springer Series in Synergetics). Springer, November 1996.
8. W. Gardner and L. Franks. Characterization of cyclostationary random signal processes. Information Theory, IEEE Transactions on, 21(1):4-14, 1975.
9. D. T. Gillespie. Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry, 81:2340-2361, 1977.
10. D. T. Gillespie. The chemical Langevin equation. J. Chem. Physics, 113(1):297-306, 2000.
11. J. Hespanha. Moment closure for biochemical networks. In Communications, Control and Signal Processing, 2008. ISCCSP 2008. 3rd International Symposium on, pages 142-147, 2008.
12. S. Hooshangi and R. Weiss. The effect of negative feedback on noise propagation. Chaos, 16, 2006.
13. I. Lestas, J. Paulsson, N. E. Ross, and G. Vinnicombe. Noise in gene regulatory networks. Automatic Control, IEEE Transactions on, 53(Special Issue):189-200, 2008.
14. J. Paulsson. Summing up the noise in gene networks. Nature, pages 415-418, 2004.
15. K. J. Åström and R. M. Murray. Feedback Systems: An Introduction for Scientists and Engineers. Princeton University Press, illustrated edition edition, April 2008.
16. N. Rosenfeld, J. W. Young, U. Alon, P. S. Swain, and M. B. Elowitz. Gene regulation at the single-cell level. Science, pages 1962-1965, 2005.
17. M. L. Simpson, C. D. Cox, M. S. Allen, J. M. Mccollum, R. D. Dar, D. K. Karig, and J. F. Cooke. Noise in biological circuits. Wiley Interdisciplinary Reviews: Nanomedicine and Nanobiotechnology, 1(2):214-225, 2009.
18. M. L. Simpson, C. D. Cox, and G. S. Sayler. Frequency domain analysis of noise in autoregulated gene circuits. Proc Natl Acad Sci U S A, 100(8):4551-4556, April 2003.
19. Y. Tao, Y. Jia, and G. Dewey. Stochastic fluctuations in gene expression far from equilibrium: Ω expansion and linear noise approximation. Journal of Chemical Physics, 122:124108, 2005.
20. M. Thattai and A. van Oudenaarden. Intrinsic noise in gene regulatory networks. PNAS, pages 8614-8619, 2001.
21. N. G. Van Kampen. Stochastic Processes in Physics and Chemistry, Third Edition (North-Holland Personal Library). North Holland, April 2007.