[1] | Rust MJ, Markson JS, Lane WS, Fisher DS, O'Shea EK (2007) Ordered phosphorylation governs oscillation of a three-protein circadian clock. Science 318: 809–812.
|
[2] | O'Neill JS, Reddy AB (2011) Circadian clocks in human red blood cells. Nature 469: 498–503.
|
[3] | O'Neill JS, van Ooijen G, Dixon LE, Troein C, Corellou F, et al. (2011) Circadian rhythms persist without transcription in a eukaryote. Nature 469: 554–558.
|
[4] | Dunlap JC (1999) Molecular bases for circadian clocks. Cell 96: 271–290.
|
[5] | Young MW, Kay SA (2001) Time zones: a comparative genetics of circadian clocks. Nat Rev Genet 2: 702–715.
|
[6] | Elowitz MB, Leibler S (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403: 335–338.
|
[7] | Atkinson MR, Savageau MA, Myers JT, Ninfa AJ (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia Coli. Cell 113: 597–607.
|
[8] | Fung E, Wong WW, Suen JK, Bulter T, Lee S, et al. (2005) A synthetic gene-metabolic oscillator. Nature 435: 118–122.
|
[9] | Stricker J, Cookson S, Bennett MR, Mather WH, Tsimring LS, et al. (2008) A fast, robust and tunable synthetic gene oscillator. Nature 456: 516–519.
|
[10] | Tigges M, Marquez-Lago TT, Stelling J, Fussenegger M (2009) A tunable synthetic mammalian oscillator. Nature 457: 309–312.
|
[11] | Toettcher JE, Mock C, Batchelor E, Loewer A, Lahav G (2010) A synthetic-natural hybrid oscillator in human cells. Proc Natl Acad Sci USA 107: 17047–17052.
|
[12] | Danino T, Mondragon-Palomino O, Tsimring L, Hasty J (2010) A synchronized quorum of genetic clocks. Nature 463: 326–330.
|
[13] | Goodwin BC (1965) Oscillatory behavior in enzymatic control processes. Adv Enzyme Regul 3: 425–438.
|
[14] | Goldbeter A (1995) A model for circadian oscillations in the Drosophila period protein (PER). Proc R Soc London Ser B 261: 319–324.
|
[15] | Ruoff P, Rensing L (1996) The temperature-compensated Goodwin model simulates many circadian clock properties. J Theor Biol 179: 275–285.
|
[16] | Leloup JC, Gonze D, Goldbeter A (1999) Limit cycle models for circadian rhythms based on transcriptional regulation in Drosophila and Neurospora. J Biol Rhythms 14: 433–448.
|
[17] | Ruoff P, Vinsjevik M, Monnerjahn C, Rensing L (2001) The Goodwin model: simulating the effect of light pulses on the circadian sporulation rhythm of Neurospora crassa. J Biol Rhythms 209: 29–42.
|
[18] | Gonze D, Halloy J, Goldbeter A (2002) Robustness of circadian rhythms with respect to molecular noise. Proc Natl Acad Sci USA 99: 673–678.
|
[19] | Bratsun D, Volfson D, Tsimring LS, Hasty J (2005) Delay-induced stochastic oscillations in gene regulation. Proc Natl Acad Sci USA 102: 14593–14598.
|
[20] | Griffith JS (1968) Mathematics of cellular control processes I. Negative feedback to one gene. J Theor Biol 20: 202–208.
|
[21] | Novák B, Tyson JJ (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9: 981–991.
|
[22] | Widder S, Schicho J, Schuster P (2007) Dynamic patterns of gene regulation I: Simple two-gene systems. J Theor Biol 246: 395–419.
|
[23] | Reppert SM, Weaver DR (2002) Coordination of circadian timing in mammals. Nature 418: 935–941.
|
[24] | Gallego M, Virshup DM (2007) Post-translationalmodifications regulate the ticking of the circadian clock. Nat Rev Mol Cell Biol 8: 139–148.
|
[25] | Purcell O, Savery NJ, Grierson CS, di Bernardo M (2010) A comparative analysis of synthetic genetic oscillators. J R Soc Interface 7: 1503–1524.
|
[26] | Barkai N, Leibler S (2000) Circadian clocks limited by noise. Nature 403: 267–268.
|
[27] | Smolen P, Baxter DA, Byrne JH (2001) Modeling circadian oscillations with interlocking positive and negative feedback loops. J Neurosci 21: 6644–6656.
|
[28] | Hasty J, Isaacs F, Dolnik M, McMillen D, Collins JJ (2001) Designer gene networks: Towards fundamental cellular control. Chaos 11: 207–220.
|
[29] | Leloup JC, Goldbeter A (2003) Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci USA 100: 7051–7056.
|
[30] | Fran?ois P (2005) A model for the Neurospora circadian clock. Biophys J 88: 2369–2383.
|
[31] | Guantes R, Poyatos JF (2006) Dynamical principles of two-component genetic oscillators. PLoS Comput Biol 2: e30.
|
[32] | Hong CI, Jolma IW, Loros JJ, Dunlap JC, Ruoff P (2008) Simulating dark expressions and interactions of frq and wc-1 in the Neurospora circadian clock. Biophys J 94: 1221–1232.
|
[33] | Conrad E, Mayo AE, Ninfa AJ, Forger DB (2008) Rate constants rather than biochemical mechanism determine behaviour of genetic clocks. J R Soc Interface 5: S9–S15.
|
[34] | Munteanu A, Constante M, Isalan M, Sole R (2010) Avoiding transcription factor competition at promoter level increases the chances of obtaining oscillation. BMC Syst Biol 4: 66.
|
[35] | Becskei A, Seraphin B, Serrano L (2001) Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J 20: 2528–2535.
|
[36] | Ferrell JE (2002) Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability. Curr Opin Cell Biol 14: 140–148.
|
[37] | Tsai TY, Choi YS, Ma W, Pomerening JR, Tang C, et al. (2008) Robust, tunable biological oscillations from interlinked positive and negative feedback loops. Science 321: 126–129.
|
[38] | Vilar JMG, Kueh HY, Barkai N, Leibler S (2002) Mechanisms of noise-resistance in genetic oscillators. Proc Natl Acad Sci USA 99: 5988–5992.
|
[39] | Mondragón-Palomino O, Danino T, Selimkhanov J, Tsimring L, Hasty J (2011) Entrainment of a population of synthetic genetic oscillators. Science 333: 1315–1319.
|
[40] | Griffith JS (1968) Mathematics of cellular control processes II. Positive feedback to one gene. J Theor Biol 20: 209–216.
|
[41] | Elowitz MB, Levine AJ, Siggia ED, Swain PS (2002) Stochastic gene expression in a single cell. Science 297: 1183–1186.
|
[42] | Swain PS, Elowitz MB, Siggia ED (2002) Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc Natl Acad Sci USA 99: 12795–12800.
|
[43] | Murray JD (2002) Mathematical biology I: An introduction. New York: Springer. 551:
|
[44] | Strogatz SH (1994) Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering. Addison-Wesley, Reading, MA. 498:
|
[45] | Tyson JJ, Chen KC, Novák B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221–231.
|
[46] | Gillespie DT (1977) Exact stochastic simulation of coupled chemical reactions. J Phys Chem 81: 2340–2361.
|
[47] | Dublanche Y, Michalodimitrakis K, Kümmerer N, Foglierini M, Serrano L (2006) Noise in transcription negative feedback loops: simulation and experimental analysis. Mol Syst Biol 2: 41.
|
[48] | Fall CP, Marland ES, Wagner JM, Tyson JJ (2002) Computational Cell Biology. Springer, Berlin. 468:
|
[49] | Buchler NE, Louis M (2008) Molecular titration and ultrasensitivity in regulatory networks. J Mol Biol 384: 1106–1119.
|
[50] | Buchler NE, Cross FR (2009) Protein sequestration generates a flexible ultrasensitive response in a genetic network. Mol Syst Biol 5: 272.
|