| [1] | Glass L, Kauffman S (1973) The logical analysis of continuous, non-linear biochemical control networks. Journal of Theoretical Biology 39: 103–129.
|
| [2] | Hopfield JJ (1982) Neural networks and physical systems with emergent collective computational abilities. Proc Natl Acad Sci U S A 79: 2554–8.
|
| [3] | Shmulevich I, Dougherty ER, Zhang W (2002) From boolean to probabilistic boolean networks as models of genetic regulatory networks. Proceedings of the IEEE 90: 1778–1792.
|
| [4] | Kuramoto Y (1975) International Symposium on Mathematical Problems in Theoretical Physics, volume 39 of Lecture Notes in Physics. Springer. 420 p.
|
| [5] | Strogatz SH (2003) Sync: the emerging science of spontaneous order. New York: Hyperion, 1st ed edition. 338 p.
|
| [6] | Garcia-Ojalvo J, Elowitz MB, Strogatz SH (2004) Modeling a synthetic multicellular clock: repressilators coupled by quorum sensing. Proc Natl Acad Sci U S A 101: 10955–60.
|
| [7] | Danino T, Mondrag？n-Palomino O, Tsimring L, Hasty J (2010) A synchronized quorum of genetic clocks. Nature 463: 326–30.
|
| [8] | Tu BP, Kudlicki A, Rowicka M, McKnight SL (2005) Logic of the yeast metabolic cycle: temporal compartmentalization of cellular processes. Science 310: 1152–8.
|
| [9] | Klevecz RR, Li CM, Marcus I, Frankel PH (2008) Collective behavior in gene regulation: the cell is an oscillator, the cell cycle a developmental process. FEBS J 275: 2372–84.
|
| [10] | Huang S, Eichler G, Bar-Yam Y, Ingber D (2005) Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys Rev Lett 94: 128701.
|
| [11] | Peskin C (1975) Mathematical Aspects of Heart Physiology. 278 p. Courant Institute Lecture Notes. Courant Institute of Mathematical Sciences.
|
| [12] | Breakspear M, Heitmann S, Daffertshofer A (2010) Generative models of cortical oscillations: neurobiological implications of the kuramoto model. Front Hum Neurosci 4: 190.
|
| [13] | Strogatz SH (1987) Human sleep and circadian rhythms: a simple model based on two coupled oscillators. J Math Biol 25: 327–47.
|
| [14] | Fox JJ, Jayaprakash C, Wang D, Campbell SR (2001) Synchronization in relaxation oscillator networks with conduction delays. Neural Comput 13: 1003–21.
|
| [15] | Cumin D, Unsworth C (2007) Generalizing the Kuramoto model for the study of neuronal synchronization in the brain. Physica D 226: 181–196.
|
| [16] | Wang Q, Duan Z, Perc M, Chen G (2008) Synchronization transitions on small-world neuronal networks: Effects of information transmission delay and rewiring probability. EPL 83: 50008.
|
| [17] | Pérez T, Garcia GC, Eguíluz VM, Vicente R, Pipa G, et al. (2011) Effect of the topology and delayed interactions in neuronal networks synchronization. PLoS One 6: e19900.
|
| [18] | Kunysz A, Shrier A, Glass L (1997) The challenge of complex dynamics for theoretical models of cardiac activity. Journal of Theoretical Medicine 1: 79–90.
|
| [19] | Chang HS, Staras K, Gilbey MP (2000) Multiple oscillators provide metastability in rhythm generation. J Neurosci 20: 5135–43.
|
| [20] | Sato D, Xie LH, Sovari AA, Tran DX, Morita N, et al. (2009) Synchronization of chaotic early afterdepolarizations in the genesis of cardiac arrhythmias. Proc Natl Acad Sci U S A 106: 2983–8.
|
| [21] | Zahanich I, Sirenko SG, Maltseva LA, Tarasova YS, Spurgeon HA, et al. (2011) Rhythmic beating of stem cell-derived cardiac cells requires dynamic coupling of electrophysiology and ca cycling. J Mol Cell Cardiol 50: 66–76.
|
| [22] | Tiana-Alsina J, Garcia-Lopez JH, Torrent M, Garcia-Ojalvo J (2011) Dual-lag synchronization between coupled chaotic lasers due to path-delay interference. Chaos 21: 043102.
|
| [23] | Mondal A, Sinha S, Kurths J (2008) Rapidly switched random links enhance spatiotemporal regularity. Phys Rev E Stat Nonlin Soft Matter Phys 78: 066209.
|
| [24] | Sorrentino F, Ott E (2008) Adaptive synchronization of dynamics on evolving complex networks. Phys Rev Lett 100: 114101.
|
| [25] | Jiang M, Ma P (2009) Coherence resonance induced by rewiring in complex networks. Chaos 19: 013115.
|
| [26] | Volman V, Perc M (2010) Fast random rewiring and strong connectivity impair fast random rewiring and strong connectivity impair subthreshold signal detection in excitable networks. New Journal of Physics 12: 043013.
|
| [27] | Adhikari BM, Prasad A, Dhamala M (2011) Time-delay-induced phase-transition to synchrony in coupled bursting neurons. Chaos 21: 023116.
|
| [28] | G？omez-Gardees J, G？mez S, Arenas A, Moreno Y (2011) Explosive synchronization transitions in scale-free networks. Phys Rev Lett 106: 128701.
|
| [29] | Martens E, Barreto E, Strogatz S, Ott E, So P, et al. (2009) Exact results for the kuramoto model with a bimodal frequency distribution. Phys Rev E 79: 026204.
|
| [30] | Taylor D, Ott E, Restrepo JG (2010) Spontaneous synchronization of coupled oscillator systems with frequency adaptation. Phys Rev E Stat Nonlin Soft Matter Phys 81: 046214.
|
| [31] | Ermentrout B, Ko TW (2009) Delays and weakly coupled neuronal oscillators. Philos Transact A Math Phys Eng Sci 367: 1097–115.
|
| [32] | Wang Q, Perc M, Duan Z, Chen G (2009) Synchronization transitions on scale-free neuronal networks due to finite information transmission delays. Phys Rev E Stat Nonlin Soft Matter Phys 80: 026206.
|
| [33] | Wang Q, Chen G, Perc M (2011) Synchronous bursts on scale-free neuronal networks with attractive and repulsive coupling. PLoS One 6: e15851.
|
| [34] | Alon U (2007) Network motifs: theory and experimental approaches. Nat Rev Genet 8: 450–461.
|
| [35] | Novak B, Tyson JJ (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9: 981–991.
|
| [36] | Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, et al. (2002) Network motifs: simple building blocks of complex networks. Science 298: 824–7.
|
| [37] | Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of escherichia coli. Nat Genet 31: 64–8.
|
| [38] | Rao CV, Arkin AP (2001) Control motifs for intracellular regulatory networks. Annu Rev Biomed Eng 3: 391–419.
|
| [39] | Prill RJ, Iglesias PA, Levchenko A (2005) Dynamic properties of network motifs contribute to biological network organization. PLoS Biol 3: e343.
|
| [40] | Csikász-Nagy A, Novák B, Tyson JJ (2008) Reverse engineering models of cell cycle regulation. Adv Exp Med Biol 641: 88–97.
|
| [41] | Purcell O, Savery NJ, Grierson CS, di Bernardo M (2010) A comparative analysis of synthetic genetic oscillators. J R Soc Interface 7: 1503–24.
|
| [42] | Taylor D, Restrepo JG (2011) Network connectivity during mergers and growth: optimizing the addition of a module. Phys Rev E Stat Nonlin Soft Matter Phys 83: 066112.
|
| [43] | Kim JR, Yoon Y, Cho KH (2008) Coupled feedback loops form dynamic motifs of cellular networks. Biophys J 94: 359–65.
|
| [44] | Tyson JJ, Chen KC, Novak B (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr Opin Cell Biol 15: 221–231.
|
| [45] | Strogatz SH (2000) From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators. Physica D 143: 1–20.
|
| [46] | Edwards R (2000) Analysis of continuous-time switching networks. Physica D 146: 165–199.
|
| [47] | Tyson JJ, Chen K, Novak B (2001) Network dynamics and cell physiology. Nat Rev Mol Cell Biol 2: 908.
|
| [48] | Hanahan D, Weinberg R (2000) The hallmarks of cancer. Cell 100: 57–70.
|
| [49] | Restrepo JG, Ott E, Hunt B (2005) Onset of synchronization in large networks of coupled oscillators. Phys Rev E 71: 036151.
|
| [50] | Restrepo JG, Ott E, Hunt B (2005) Synchronization in large directed networks of coupled phase oscillators. Chaos 16: 015107.
|
| [51] | Restrepo JG, Ott E, Hunt B (2006) Emergence of coherence in complex networks of heterogeneous dynamical systems. Phys Rev Lett 96: 254103.
|
| [52] | Restrepo JG, Ott E, Hunt B (2006) Emergence of synchronization in complex networks of interacting dynamical systems. Physica D 224: 114–122.
|
| [53] | Barabási AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101–13.
|
| [54] | Pikovsky A, Zaikin A, de la Casa MA (2002) System size resonance in coupled noisy systems and in the ising model. Phys Rev Lett 88: 050601.
|
| [55] | Dorogovtsev S (2010) Lectures on Complex Networks. Oxford University Press. 144 p.
|
| [56] | Kaern M, Elston TC, Blake WJ, Collins JJ (2005) Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet 6: 451–464.
|
| [57] | Stein RB, Gossen ER, Jones KE (2005) Neuronal variability: noise or part of the signal? Nat Rev Neurosci 6: 389–97.
|
| [58] | Faisal AA, Selen LPJ, Wolpert DM (2008) Noise in the nervous system. Nat Rev Neurosci 9: 292–303.
|
| [59] | Gillespie DT (2007) Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 58: 35–55.
|
| [60] | Fertig EJ, Danilova LV, Favorov AV, Ochs MF (2011) Hybrid modeling of cell signaling and transcriptional reprogramming and its application in c. elegans development. Frontiers in Bioinformatics and Computational Biology 2: 77.
|
