Summing up the noise in gene networks (original) (raw)

References

  1. Schroedinger, E. What is Life? (Cambridge Univ. Press, Cambridge, 1944)
    Google Scholar
  2. Novick, A. & Weiner, M. Enzyme induction as an all-or-none phenomenon. Proc. Natl Acad. Sci. USA 43, 553–566 (1957)
    Article ADS CAS Google Scholar
  3. Maloney, P. C. & Rotman, B. Distribution of suboptimally induced β-d-galactosidase in Escherichia coli. The enzyme content of individual cells. J. Mol. Biol 73, 77–91 (1973)
    Article CAS Google Scholar
  4. Løbner-Olesen, A. Distribution of minichromosomes in individual Escherichia coli cells: implications for replication control. EMBO J. 18, 1712–1721 (1999)
    Article Google Scholar
  5. Becskei, A. & Serrano, L. Engineering stability in gene networks by autoregulation. Nature 405, 590–593 (2000)
    Article ADS CAS Google Scholar
  6. Ozbudak, E. M., Thattai, M., Kurtser, I., Grossman, A. D. & van Oudenaarden, A. Regulation of noise in the expression of a single gene. Nature Genet. 31, 69–73 (2002)
    Article CAS Google Scholar
  7. Elowitz, M. B., Levine, A. J., Siggia, E. D. & Swain, P. S. Stochastic gene expression in a single cell. Science 297, 183–186 (2002)
    Article Google Scholar
  8. Blake, W. J., Kærn, M., Cantor, C. R. & Collins, J. J. Noise in eukaryotic gene expression. Nature 422, 633–637 (2003)
    Article ADS CAS Google Scholar
  9. Xie, X. S. Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics. J. Chem. Phys. 117, 11024–11032 (2002)
    Article ADS Google Scholar
  10. Zwanzig, R. Nonequilibrium Statistical Mechanics (Oxford Univ. Press, New York, 2001)
    MATH Google Scholar
  11. van Kampen, N. G. Stochastic Processes in Physics and Chemistry (North-Holland, Amsterdam, 1992)
    MATH Google Scholar
  12. Elf, J., Paulsson, J., Berg, O. G. & Ehrenberg, M. Near-critical phenomena in intracellular metabolite pools. Biophys. J. 84, 154–170 (2003)
    Article ADS CAS Google Scholar
  13. Keizer, K. Statistical Thermodynamics of Nonequilibrium Processes (Springer, Berlin, 1987)
    Book Google Scholar
  14. Elf, J. & Ehrenberg, M. Fast evaluations of fluctuations in biochemical networks with the linear noise approximation. Genome Res. 13, 2475–2484 (2003)
    Article CAS Google Scholar
  15. Kacser, H. & Burns, J. A. The control of flux. Symp. Soc. Exp. Biol. 27, 65–104 (1973)
    CAS PubMed Google Scholar
  16. Westerhoff, H. V. & Van Dam, K. Thermodynamics and Control of Biological Free Energy Transduction (Elsevier, Amsterdam, 1987)
    Google Scholar
  17. Savageau, M. A. Biochemical Systems Analysis (Addison-Wesley, Reading, 1976)
    MATH Google Scholar
  18. Savageau, M. A. Parameter sensitivity as a criterion for evaluating and comparing the performance of biochemical systems. Nature 229, 542–544 (1971)
    Article ADS CAS Google Scholar
  19. Paulsson, J. & Ehrenberg, M. Noise in a minimal regulatory network: plasmid copy number control. Q. Rev. Biophys. 34, 1–59 (2001)
    Article CAS Google Scholar
  20. Dogterom, M. & Leibler, S. Physical aspects of the growth and regulation of microtubule structures. Phys. Rev. Lett. 70, 1347–1350 (1993)
    Article ADS CAS Google Scholar
  21. Berg, O. G., Paulsson, J. & Ehrenberg, M. Fluctuations and quality of control in biological cells: zero-order ultrasensitivity reinvestigated. Biophys. J. 79, 1228–1236 (2000)
    Article CAS Google Scholar
  22. Rigney, D. R. & Schieve, W. C. Stochastic model of linear, continuous protein-synthesis in bacterial populations. J. Theor. Biol. 69, 761–766 (1977)
    Article CAS Google Scholar
  23. Berg, O. G. A model for statistical fluctuations of protein numbers in a microbial-population. J. Theor. Biol. 173, 307–320 (1978)
    Article Google Scholar
  24. McAdams, H. H. & Arkin, A. Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. USA 94, 814–819 (1997)
    Article ADS CAS Google Scholar
  25. Paulsson, J., Berg, O. G. & Ehrenberg, M. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl Acad. Sci. USA 97, 7148–7153 (2000)
    Article ADS CAS Google Scholar
  26. Thattai, M. & van Oudenaarden, A. Intrinsic noise in gene regulatory networks. Proc. Natl Acad. Sci. USA 98, 8614–8619 (2001)
    Article ADS CAS Google Scholar
  27. Peccoud, J. & Ycart, B. Markovian modelling of gene-product synthesis. Theor. Popul. Biol. 48, 222–234 (1995)
    Article Google Scholar
  28. Kepler, T. B. & Elston, T. C. Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations. Biophys. J. 81, 3116–3136 (2001)
    Article ADS CAS Google Scholar
  29. Sasai, M. & Wolynes, P. G. Stochastic gene expression as a many-body problem. Proc. Natl Acad. Sci. USA 100, 2374–2379 (2003)
    Article ADS CAS Google Scholar
  30. Singh, U. N. Polyribosomes and unstable messenger RNA: a stochastic model of protein synthesis. J. Theor. Biol. 25, 444–460 (1969)
    Article CAS Google Scholar
  31. Swain, P. S., Elowitz, M. B. & Siggia, E. D. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl Acad. Sci. USA 99, 12795–12800 (2002)
    Article ADS CAS Google Scholar
  32. Savageau, M. A. Comparison of classical and autogenous systems of regulation in inducible operons. Nature 252, 546–549 (1974)
    Article ADS CAS Google Scholar
  33. Thieffry, D., Huerta, A. M., Perez-Rueda, E. & Collado-Vides, J. From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. Bioessays 20, 433–440 (1998)
    Article CAS Google Scholar
  34. Shen-Orr, S. S., Milo, R., Mangan, S. & Alon, U. Network motifs in the transcriptional regulation network of Escherichia coli. Nature Genet. 31, 64–68 (2002)
    Article CAS Google Scholar
  35. Paulsson, J. Multileveled selection on plasmid replication. Genetics 161, 1373–1384 (2002)
    PubMed PubMed Central Google Scholar
  36. Chattoraj, D. K. Control of plasmid DNA replication by iterons: no longer paradoxical. Mol. Microbiol. 37, 467–476 (2000)
    Article CAS Google Scholar
  37. Vilar, J. M., Kueh, H. Y., Barkai, N. & Leibler, S. Mechanisms of noise-resistance in genetic oscillators. Proc. Natl Acad. Sci. USA 99, 5988–5992 (2002)
    Article ADS CAS Google Scholar
  38. Howard, M. & Rutenberg, A. D. Pattern formation inside bacteria: fluctuations due to the low copy number of proteins. Phys. Rev. Lett. 90, 128102 (2003)
    Article ADS Google Scholar

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