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M. Marhl, V. Akman

On the correct determination of rotational angles for twisted-profiled sweep objects

Computers & Graphics
18 (1994) 691-694

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Elsevier

M. Marhl, N. Guid, C. Oblonšek, M. Horvat

Extensions of sweep surface constructions

Computers & Graphics
20 (1996) 893-903

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Springer

M. Marhl, M. Brumen, R. Glaser, R. Heinrich

Diffusion layer caused by local ionic transmembrane fluxes

Pflügers Archiv European Journal of Physiology

431 Suppl. 2 (1996) R259-R260

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IoP

T. Schmidt, M. Marhl

A simple mathematical model of a dripping tap

European Journal of Physics

18 (1997) 377-383

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M. Marhl, S. Schuster, M. Brumen, R. Heinrich

Modelling the interrelations between calcium oscillations and ER membrane potential oscillations

Biophysical Chemistry
63 (1997) 221-239

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M. Marhl, S. Schuster, M. Brumen

Mitochondria as an important factor in the maintenance of constant amplitudes of cytosolic calcium oscillations

Biophysical Chemistry
71 (1998) 125-132

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M. Marhl, S. Schuster, M. Brumen, R. Heinrich

Modelling oscillations of calcium and endoplasmic reticulum transmembrane potential - Role of the signalling and buffering proteins and of the size of the Ca2+ sequestering ER subcompartments

Bioelectrochemistry and Bioenergetics
46 (1998) 79-90

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S. Schuster, M. Marhl, M. Brumen, R. Heinrich

Influence of calcium binding to proteins on calcium oscillations and ER membrane potential oscillations. A mathematical model.

In: Holcombe M., Paton R. (Eds.) Information Processing in Cells and Tissues. New York, London, Plenum Press, 1998, 137-150.

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M. Marhl, T. Haberichter, M. Brumen, R. Heinrich

Complex calcium oscillations and the role of mitochondria and cytosolic proteins

Biosystems
57 (2000) 75-86

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T. Haberichter, M. Marhl, R. Heinrich

Birhythmicity, trirhythmicity and chaos in bursting calcium oscillations

Biophysical Chemistry
90 (2001) 17-30

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S. Schuster, M. Marhl

Bifurcation analysis of calcium oscillations. Time-scale separation, canards, and frequency lowering

Journal of Biological Systems
9 (2001) 291-314

Citiran v:

1. Schuster S, Marhl M, Höfer T, Modelling of simple and complex calcium oscillations - From single-cell responses to intercellular signalling, Eur. J. Biochem. 269 (2002) 1333-1355.

2. Chiew SP, Lie ST, Huang ZW, Multi-axes fatigue tests of tubular T-joints under complex loads, Proceedings of the Twelfth (2002) International Offshore and Polar Engineering Conference Vol. 4 (2002) 103-110.

3. Perc M, Marhl M, Sensitivity and flexibility of regular and chaotic calcium oscillations, Biophys. Chem. 104 (2003) 509-522.

4. Volkov EI, Ullner E, Zaikin AA, Kurths J, Oscillatory amplification of stochastic resonance in excitable systems, Phys. Rev. E 68 (2003) art. no. 026214.

5*. Perc M, Marhl M, Noise enhances robustness of intracellular Ca2+ oscillations, Phys. Lett. A 316 (2003) 304-310.

6. Kuhlmann U, Gunther HP, Saul R, Haderle MU, Welded circular hollow section (CHS) joints in bridges, 10th International Symposium on Tubular Structures, Sept. 18-20, 2003 Madrid, Spain, Tubular Structures X (2003) 55-62.

7. Sturm S, Nussbaumer A, Hirt MA, Fatigue behaviour of cast steel nodes in bridge structures, 10th International Symposium on Tubular Structures, Sept. 18-20, 2003 Madrid, Spain, Tubular Structures X (2003) 357-364.

8. Perc M, Marhl M, Frequency dependent stochastic resonance in a model for intracellular Ca2+ oscillations can be explained by local divergence, Physica A - Statistical Mechanics and its Applications 332 (2004) 123-140.

9. Vanag VK, Epstein IR, Stationary and oscillatory localized patterns, and subcritical bifurcations, Phys. Rev. Lett. 92 (2004) art. no. 128301.

10. Chiew SP, Lie ST, Lee CK, Huang ZW, Fatigue performance of cracked tubular T joints under combined loads. I: Experimental, J. Struct. Engineering - ASCE 130 (2004) 562-571.

11. Vanag VK, Waves and patterns in reaction-diffusion systems. Belousov-Zhabotinsky reaction in water-in-oil microemulsions, Phys. Usp. 47 (2004) 923-941.

12*. Ullner E, Noise-induced phenomena of signal transmission in excitable neural models, Dissertation, Institut für Physik, Fakultät Mathematik und Naturwissenschaften, Universität Potsdam, Germany, 2004.

13. Perc M, Marhl M, Amplification of information transfer in excitable systems that reside in a steady state near a bifurcation point to complex oscillatory behavior, Phys. Rev. E 71 (2005) art. no. 026229.

14. Puebla H, Controlling intracellular calcium oscillations and waves, J Biol. Syst. 13 (2005) 173-190.

15. Qian X, Dodds RH, Choo YS, Mode mixity for circular hollow section X joints with weld toe cracks, J. Offshore Mech. Arct. 127 (2005) 269-279.

16. Zhu CL, Jia Y, Liu Q, Yang LJ, Zhan X., A mesoscopic stochastic mechanism of cytosolic calcium oscillations, Biophys. Chem. 125 (2007) 201-212.

17. Knoke B, Marhl M, Perc M, Schuster S, Equality of average and steady-state levels in some nonlinear models of biological oscillations, Theor. Biosci. 127 (2008) 1-14.

18. Durham J, Moehlis J, Feedback control of canards, Chaos 18 (2008) Art. No. 015110.

19. Kapela A, Bezerianos A, Tsoukias NM, A mathematical model of Ca2+ dynamics in rat mesenteric smooth muscle cell: Agonist and NO stimulation, J. theor. Biol. 253 (2008) 238-260.

20. Ma J, Li HY, Hou ZH, Xin HW, System Size Resonance Associated with Canard Phenomenon in a Biological Cell System, Chin. J. Chem. Phys. 21 (2008) 521-525.

21. Surovtsova I, Simus N, Lorenz T, Konig A, Sahle S, Kummer U, Accessible methods for the dynamic time-scale decomposition of biochemical systems, Bioinformatics 25 (2009) 2816-2823.

22. Brons M, Kaasen R, Canards and mixed-mode oscillations in a forest pest model. Theor. Popul. Biol. 77 (2010) 238-242.

23. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

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M. Brumen, A. Fajmut, M. Marhl

Calcium oscillations in the living cell: biological relevance of multi-compartment models

Nonlinear Phenomena in Complex Systems
4 (2001) 280-284

Citiran v:

1*. Fajmut A, Brumen M, Frequency and amplitude analysis of bursting oscillations in the mathematical model of intracellular calcium oscillations, Eur. J. Biochem. 270 Supp. 1 (2003) 228.

 

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V. Grubelnik, A.Z. Larsen, U. Kummer, L.F. Olsen, M. Marhl

Mitochondria regulate the amplitude of simple and complex calcium oscillations

Biophysical Chemistry
94 (2001) 59-74

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T. Haberichter, E. Roux, M. Marhl, J.-P. Mazat

The influence of different InsP3 receptor isoforms on Ca2+ signaling in tracheal smooth muscle cells

Bioelectrochemistry
57 (2002) 129-131

Citiran v:

1*. Dozol H, Etudes inframoléculaires des interactions intramoléculaires de composés polyfonctionnels phosphorylés d'intérêt biologique et thérapeutique, docteur thése de l'Université Louis Pasteur Strasbourg I, Strasbourg, 2003.

2. Koenigsberger M, Sauser R, Meister JJ, Emergent properties of electrically coupled smooth muscle cells, Bull. Math. Biol. 67 (2005) 1253-1272.

3. Brumen M, Fajmut A, Dobovišek A, Roux E, Mathematical modelling of Ca2+ oscillations in airway smooth muscle cells, J. Biol. Phys. 31 (2005) 515-524.

4. Roux E, Noble PJ, Noble D, Marhl M, Modelling of calcium handling in airway myocytes, Prog. Biophys. Mol. Biol. 90 (2006) 64-87.

5. Dupont G, Combettes L, Modelling the effect of specific inositol 1,4,5-trisphosphate receptor isoforms on cellular Ca2+ signals, Biol. Cell 98 (2006) 171-182.

6. Marhl M, Perc M, Schuster S, A minimal model for decoding of time-limited Ca2+ oscillations, Biophys. Chem. 120 (2006) 161-167.

7*. Gharib Naseri MK, Heidari A, Spasmolytic effect of Vitis vinifera leaf extract on rat trachea, J. Medicinal Plants 5 (2006) 39-49.

8. Marhl M, Noble D, Roux E, Modeling of molecular and cellular mechanisms involved in Ca2+ signal encoding in airway myocytes, Cell Biochem. Biophys. 46 (2006) 285-302.

9. Hirota S, Helli P, Janssen LJ, Ionic mechanisms and Ca2+ handling in airway smooth muscle, Eur. Respir. J. 30 (2007) 114-133.

10. Bai Y, Edelmann M, Sanderson MJ, The contribution of inositol 1,4,5-trisphosphate and ryanodine receptors to agonist-induced Ca2+ signaling of airway smooth muscle cells, Am. J. Physiol. - Lung. C. 297 (2009) L347-L361.

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S. Schuster, M. Marhl, T. Höfer

Modelling of simple and complex calcium oscillations. From single-cell responses to intercellular signalling

European Journal of Biochemistry
269 (2002) 1333-1355

Citiran v:

1. Williams CJ, Signalling mechanisms of mammalian oocyte activation, Human Reproduction Update 8 (2002) 313-321.

2. Nash MS, Schell MJ, Atkinson PJ, Johnston NR, Nahorski SR, Challiss RAJ, Determinants of metabotropic glutamate receptor-5-mediated Ca2+ and inositol 1,4,5-trisphosphate oscillation frequency - Receptor density versus agonist concentration, J. Biol. Chem. 277 (2002) 35947-35960.

3. Goldbeter A, Computational approaches to cellular rhythms, Nature 420 (2002): 238-245.

4. Rengifo J, Rosales R, Gonzalez A, Cheng HP, Stern MD, Rios E, Intracellular Ca2+ release as irreversible Markov process, Biophys. J. 83 (2002) 2511-2521.

5. Vetter SW, Leclerc E, Novel aspects of calmodulin target recognition and activation, Eur. J. Biochem. 270 (2003) 404-414.

6. Mooren FC, Exercise-dependent modulation of intracellular calcium signalling pathways, Deutsche Zeitschrift fur Sportmedizin 53 (2002) 368-375.

7. Salazar C, Höfer T, Allosteric regulation of the transcription factor NFAT1 by multiple phosphorylation sites: A mathematical analysis, J. Mol. Biol. 327 (2003) 31-45.

8. Weijer CJ, Visualizing signals moving in cells, Science 300 (2003) 96-100.

9. Falcke M, Buffers and oscillations in intracellular Ca2+ dynamics, Biophys. J. 84 (2003) 28-41.

10. Pribyl M, Muratov CB, Shvartsman SY, Long-range signal transmission in autocrine relays, Biophys. J. 84 (2003) 883-896.

11. McDonald AG, Implications of enzyme kinetics, Biochem. Soc. Trans. 31 (2003) 719-722.

12. Kawano S, Otsu K, Shoji S, Yamagata K, Hiraoka M, Ca2+ oscillations regulated by Na+-Ca2+ exchanger and plasma membrane Ca2+ pump induce fluctuations of membrane currents and potentials in human mesenchymal stem cells, Cell Calcium 34 (2003) 145-156.

13. Perc M, Marhl M, Different types of bursting calcium oscillations in non-excitable cells, Chaos, Solitons & Fractals 18 (2003) 759-773.

14. Perc M, Marhl M, Sensitivity and flexibility of regular and chaotic calcium oscillations, Biophys. Chem. 104 (2003) 509-522.

15. Brostrom MA, Brostrom CO, Calcium dynamics and endoplasmic reticular function in the regulation of protein synthesis: implications for cell growth and adaptability, Cell Calcium 34 (2003) 345-363.

16. Nahorski SR, Young KW, Challiss RAJ, Nash MS, Visualizing phosphoinositide signalling in single neurons gets a green light, Trends in Neurosciences 26 (2003) 444-452.

17. Perc M, Marhl M, Resonance effects determine the frequency of bursting Ca2+ oscillations, Chem. Phys. Lett. 376 (2003) 432-437.

18. Skodt H, Sorensen PG, Antispirals in an artificial tissue of oscillatory cells, Phys. Rev. E 68 (2003) art. no. 020902.

19. Astashkin EI, Belikova NA, Til'kunova NA, Zalepugin DY, Glezer MG, Grachev SV, The effect of allicin on lymphocyte plasma membrane Ca2+-extrusion system, Biologicheskie Membrany 20 (2003) 341-348.

20. Marhl M, Schuster S, Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations, J. theor. Biol. 224 (2003) 491-500.

21. Webb AAR, The physiology of circadian rhythms in plants, New Phytologist 160 (2003) 281-303.

22. Straube R, Muller SC, Hauser MJB, Bursting oscillations in the revised mechanism of the hemin - Hydrogen peroxide - Sulfite oscillator, Zeitschrift fur Physik. Chem. - Int. J. Res. Phys. Chem. & Chem. Phys. 217 (2003) 1427-1442.

23. Dupont G, Houart G, De Koninck P, Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations: a simple model, Cell Calcium 34 (2003) 485-497.

24. Nadkarni S, Jung P, Spontaneous oscillations of dressed neurons: A new mechanism for epilepsy?, Phys. Rev. Lett. 91 (2003) art. no. 268101.

25*. Humetsky R, Mathematical modelling of oscillatory dynamics of embryo cells biolectrical characteristics, Visnik of L'viv Univ. Biology Series. 33 (2003) 12-21.

26. Clark JW, Eggebrecht AT, The small world of the nobel nematode caenorhabditis Elegans, Cond. Mat. Th. 18 (2003) 389-406.

27. Dellen BK, Barber MJ, Ristig M, Calcium oscillations in living cells, Cond. Mat. Th. 18 (2003) 407-416.

28. Vazquez-Coutino GA, Serrano-Luna G, Canedo-Dorantes L, Godina-Nava JJ, Rodriguez-Segura MA, Complex Systems Theory to understand extremely low frequency magnetic fields interaction with immune cells, AIP Conference Proceedings 682 (2003) 251-257.

29. Sinnecker D, Schaefer M, Real-time analysis of phospholipase C activity during different patterns of receptor-induced Ca2+ responses in HEK293 cells, Cell Calcium 35 (2004) 29-38.

30. Larsen AZ, Olsen LF, Kummer U, On the encoding and decoding of calcium signals in hepatocytes, Biophys. Chem. 107 (2004) 83-99.

31. Li Y, Wang GX, Xin M, Yang HM, Wu XJ, Li T, The parameters of guard cell calcium oscillation encodes stomatal oscillation and closure in Vicia faba, Plant Science 166 (2004) 415-421.

32. Wagner J, Fall CP, Hong F, Sims CE, Allbritton NL, Fontanilla RA, Moraru II, Loew LM, Nuccitelli R, A wave Of IP3 production accompanies the fertilization Ca2+ wave in the egg of the frog, Xenopus laevis: theoretical and experimental support, Cell Calcium 35 (2004) 433-447.

33. Spat A, Hunyady L, Control of aldosterone secretion: A model for convergence in cellular signaling pathways, Physiol. Rev. 84 (2004) 489-539.

34. Roux E, Marhl M, Role of sarcoplasmic reticulum and mitochondria in Ca2+ removal in airway myocytes, Biophys. J. 86 (2004) 2583-2595.

35. You LC, Toward computational systems biology, Cell Biochem. Biophys. 40 (2004) 167-184.

36. Love J, Dodd AN, Webb AAR, Circadian and diurnal calcium oscillations encode photoperiodic information in Arabidopsis, Plant Cell 16 (2004) 956-966.

37. Perc M, Marhl M, Local dissipation and coupling properties of cellular oscillators - A case study on calcium oscillations, Bioelectrochemistry 62 (2004) 1-10.

38. Falcke M, Reading the patterns in living cells - the physics of Ca2+ signaling, Adv. Phys. 53 (2004) 255-440.

39. Chernykh AM, Dolgacheva LP, Kaimachnikov NP, Zinchenko VP, Analysis of the kinetics of Ca2+ signals in Ehrlich ascites tumor cells upon the inhibition of the mitochondrial Na+/Ca2+ exchanger, Biofizika 49 (2004) 511-518.

40. Knox CD, Belous AE, Pierce JM, Wakata A, Nicoud IB, Anderson CD, Pinson CW, Chari RS, Novel role of phospholipase C-delta 1: regulation of liver mitochondrial Ca2+ uptake, Am. J. Physiol.-Gastr. L. 287 (2004) G533-G540.

41. Lukas TJ, A signal transduction pathway model prototype I: From agonist to cellular endpoint, Biophys. J. 87 (2004) 1406-1416.

42. Goldstein BN, Ermakov G, Centelles JJ, Westerhoff HV, Cascante M, What makes biochemical networks tick? A graphical tool for the identification of oscillophores, Eur. J. Biochem. 271 (2004) 3877-3887.

43*. Schuster S, A Systems Biology perspective on the modelling of metabolic systems. Book of Abstracts, pp.199, 5th International Conference on Systems Biology, Heidelberg, 2004.

44. Dupont G, Dumollard R, Simulation of calcium waves in ascidian eggs: insights into the origin of the pacemaker sites and the possible nature of the sperm factor
J. Cell Sci. 117 (2004) 4313-4323.

45. Ma CY, Chen CY, Cui ZJ, Selective use of a reserved mechanism for inducing calcium oscillations, Cell. Signal. 16 (2004) 1435-1440.

46. Perc M, Marhl M, Synchronization of regular and chaotic oscillations: The role of local divergence and the slow passage effect - A case study on calcium oscillations, Int. J. Bifurcat. Chaos 14 (2004) 2735-2751.

47*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

48. Fall CP, Wagner JM, Loew LM, Nuccitelli R, Cortically restricted production of IP3 leads to propagation of the fertilization Ca2+ wave along the cell surface in a model of the Xenopus egg, J. theor. Biol. 231 (2004) 487-496.

49. De Blasio BF, Iversen JG, Rottingen JA, Intercellular calcium signalling in cultured renal epithelia: a theoretical study of synchronization mode and pacemaker activity, Eur. Biophys. J. Biophy. 33 (2004) 657-670.

50*. Wang K, Rappel W-J, Levine H, Cooperativity can reduce stochasticity in intracellular calcium dynamics, Phys. Biol. 1 (2004) 27-34.

51. Nadkarni S, Jung P, Dressed neurons: modeling neural-glial interactions, Phys. Biol. 1 (2004) 35-41.

52. Wang K, Rappel WJ, Levine H, Cooperativity can reduce stochasticity in intracellular calcium dynamics, Phys. Biol. 1 (2004) 27-34.

53*. Salazar C, Politi A, Höfer T, Decoding of calcium oscillations by phosphorylation cycles. In: Mamitsuka H, Smith T, Holzhütter HG, Kanehisa M, DeLisi C, Heinrich R, Miyano S (Eds.), Proceedings of Fourth International Workshop on Bioinformatics and Systems Biology, Kyoto, 2004, pp. 50-51.

54. Politi A, Höfer T, Modelling of periodic intercellular Ca2+ waves, Math. Biosci. Interact. pp. 99 (2004).

55. Tien JH, Lyles D, Zeeman ML, A potential role of modulating inositol 1,4,5-trisphosphate receptor desensitization and recovery rates in regulating ovulation, J. theor. Biol. 232 (2005) 105-117.

56. Fioretti B, Franciolini F, Catacuzzeno L, A model of intracellular Ca2+ oscillations based on the activity of the intermediate-conductance Ca2+-activated K+ channels, Biophys. Chem. 113 (2005) 17-23.

57. Op den Buijs J, Miklos Z, van Riel NAW, Prestia CM, Szenczi O, Toth A, Van der Vusse GJ, Szabo C, Ligeti L, Ivanics T, Beta-adrenergic activation reveals impaired cardiac calcium handling at early stage of diabetes, Life Sci. 76 (2005) 1083-1098.

58. Simpson D, Kirk V, Sneyd J, Complex oscillations and waves of calcium in pancreatic acinar cells, Physica D 200 (2005) 303-324.

59. Aalkjaer C, Nilsson H, Vasomotion: cellular background for the oscillator and for the synchronization of smooth muscle cells, Brit. J. Pharmacol. 144 (2005) 605-616.

60. Oxhamre C, Richter-Dahlfors A, Zhdanov VP, Kasemo B, A minimal generic model of bacteria-induced intracellular Ca2+ oscillations in epithelial cells, Biophys. J. 88 (2005) 2976-2981.

61. Tiveci S, Akin A, Cakir T, Saybasili H, Ulgen K, Modelling of calcium dynamics in brain energy metabolism and Alzheimer's disease, Comput. Biol. Chem. 29 (2005) 151-162.

62. Wood AW, Cadusch PJ, Cell calcium oscillations: the origin of their variability, Med. Biol. Eng. Comput. 43 (2005) 200-205.

63. Goldstein BN, Mayevsky AA, Zakrjevskaya DT, Influence of Ca2+ oscillatory influx on membrane Ca2+-ATPase activity: a kinetic model, Biochemistry-Moscow 70 (2005) 445-448.

64. Schuster S, Knoke B, Marhl M, Differential regulation of proteins by bursting calcium oscillations - a theoretical study, BioSystems 81 (2005) 49-63.

65. Puebla H, Controlling intracellular calcium oscillations and waves, J Biol. Syst. 13 (2005) 173-190.

66. De Bono M, Maricq AV, Neuronal substrates of complex behaviors in C-elegans, Annu. Rev. Neurosci. 28 (2005) 451-501.

67. Estevez AY, Strange K, Calcium feedback mechanisms regulate oscillatory activity of a TRP-like Ca2+ conductance in C-elegans intestinal cells, J. Physiol. - London 567 (2005) 239-251.

68. Sneyd J, Falcke M, Models of the inositol trisphosphate receptor, Prog. Biophys. Mol. Bio. 89 (2005) 207-245.

69. Kummer U, Krajnc B, Pahle J, Green AK, Dixon CJ, Marhl M, Transition from stochastic to deterministic behavior in calcium oscillations, Biophys. J. 89 (2005) 1603-1611.

70. Yi YB, Wang H, Sastry AM, Lastoskie CM, Direct stochastic simulation of Ca2+ motion in Xenopus eggs, Phys. Rev. E 72 (2005) art. no. 021913.

71. Marhl M, Perc M, Schuster S, Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations, FEBS Lett. 579 (2005) 5461-5465.

72. Dellen BK, Barber MJ, Ristig ML, Hescheler J, Sauer H, Wartenberg M, [Ca2+] oscillations in a model of energy-dependent Ca2+ uptake by the endoplasmic reticulum, J. theor. Biol. 237 (2005) 279-290.

73*. Book: Mathematics and 21th Century Biology (2005), Chapter 4: Understanding Cells. The National Academies Press, Washington, 2005, pp. 51-79.

74*. Schuster S, Klipp E, Marhl M, The predictive power of molecular network modelling - case studies of predictions with subsequent experimental verification; In Discovering Biomolecular Mechanisms with Computational Biology. F. Eisenhaber (Ed.) Landes Bioscience, Georgetown, 2005 pp. 115-127.

75. Wolf J, Becker-Weimann S, Heinrich R, Analysing the robustness of cellular rhythms, Syst. Biol. 2 (2005) 35-41.

76. Kusters JMAM, Dernison MM, van Meerwijk WPM, Ypey DL, Theuvenet APR, Gielen CCAM, Stabilizing role of calcium store-dependent plasma membrane calcium channels in action-potential firing and intracellular calcium oscillations. Biophys. J. 89 (2005) 3741-3756.

77. Shi XM, Liu ZR, An intracellular calcium oscillations model including mitochondrial calcium cycling. Chin. Phys. Lett. 22 (2005) 3206-3209.

78. Sneyd J, Modeling IP3-dependent calcium dynamics in non-excitable cells, Lect. Notes Math. 1867 (2005) 15-61.

79*. Chae HJ, Kang TH, Park JH, Calcium ion dynamics after dexamethasone treatment in organotypic cultured hippocampal slice, Korean J. Physiol. Pharmacol. 9 (2005) 363-369.

80. Roux E, Noble PJ, Noble D, Marhl M, Modelling of calcium handling in airway myocytes, Prog. Biophys. Mol. Biol. 90 (2006) 64-87.

81. Burdakov D, Verkhratsky A, Biophysical re-equilibration of Ca2+ fluxes as a simple biologically plausible explanation for complex intracellular Ca2+ release patterns, FEBS Lett. 580 (2006) 463-468.

82. Sneyd J, Tsaneva-Atanasova K, Reznikov V, Bai Y, Sanderson MJ, Yule DI, A method for determining the dependence of calcium oscillations on inositol trisphosphate oscillations. Proc. Nat. Acad. Sci. USA, 103 (2006) 1675-1680.

83. Mora R, Maldonado A, Valverde B, Gutierrez JM, Calcium plays a key role in the effects induced by a snake venom Lys49 phospholipase A(2) homologue on a lymphoblastoid cell line. Toxicon 47 (2006) 75-86.

84. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

85. Dupont G, Combettes L, Modelling the effect of specific inositol 1,4,5-trisphosphate receptor isoforms on cellular Ca2+ signals, Biol. Cell 98 (2006) 171-182.

86. Kawano S, Otsu K, Kuruma A, Shoji S, Yanagida E, Muto Y, Yoshikawa F, Hirayama Y, Mikoshiba K, Furuichi T, ATP autocrine/paracrine signaling induces calcium oscillations and NFAT activation in human mesenchymal stem cells, Cell Calcium 39 (2006) 313-324.

87. Marhl M, Perc M, Schuster S, A minimal model for decoding of time-limited Ca2+ oscillations, Biophys. Chem. 120 (2006) 161-167.

88. Politi A, Gaspers LD, Thomas AP, Höfer T, Models of IP3 and Ca2+ oscillations: Frequency encoding and identification of underlying feedbacks, Biophys. J. 90 (2006) 3120-3133.

89. Perc M, Gosak M, Marhl M, From stochasticity to determinism in the collective dynamics of diffusively coupled cells, Chem. Phys. Lett. 421 (2006) 106-110.

90. Higgins ER, Cannell MB, Sneyd J, A buffering SERCA pump in models of calcium dynamics. Biophys. J. 91 (2006) 151-163.

91. Hetherington JPJ, Warner A, Seymour RM, Simplification and its consequences in biological modelling: conclusions from a study of calcium oscillations in hepatocytes, J. R. Soc. Interface 3 (2006) 319-331.

92. Yang HM, Zhang XY, Wang GX, Zhang JH, Water channels are involved in stomatal oscillations encoded by parameter-specific cytosolic calcium oscillations. J. Integ. Plant Biol. 48 (2006) 790-799.

93. Malho R, Kaloriti D, Sousa E, Calcium and rhythms in plant cells, Biol. Rhythm Res. 37 (2006) 297-314.

94. Yong-Chun S, Di L, Xiao-Dan T, Ai-Rong D, Hui-Yong T, Shen-Qiu L, Qin-Kai D, Mathematical model of phosphatidylinositol-4,5-bisphosphate hydrolysis mediated by epidermal growth factor receptor generating diacylglycerol, J. Biotechnol. 124 (2006) 574-591.

95. Yamashita M, 'Quantal' Ca2+ release reassessed - a clue to oscillation and synchronization, FEBS Lett. 580 (2006) 4979-4983.

96. Jung SR, Kim K, Hille B, Nguyen TD, Koh DS, Pattern of Ca2+ increase determines the type of secretory mechanism activated in dog pancreatic duct epithelial cells, J. Physiol.-London 576 (2006) 163-178.

97. Domijan M, Murray R, Sneyd J, Dynamical probing of the mechanisms underlying calcium oscillations, J. Nonlinear Sci. 16 (2006) 483-506.

98. Ventura AC, Sneyd J, Calcium oscillations and waves generated by multiple release mechanisms in pancreatic acinar cells, B. Math. Biol. 68 (2006) 2205-2231.

99. Roose T, Chapman SJ, Maini PK, A mathematical model for simultaneous spatio-temporal dynamics of calcium and inositol 1,4,5-trisphosphate in Madin-Darby canine kidney epithelial cells, B. Math. Biol. 68 (2006) 2027-2051.

100. Kowalewski JM, Uhlen P, Kitano H, Brismar H, Modeling the impact of store-operated Ca2+ entry on intracellular Ca2+ oscillations, Math. Biosci. 204 (2006) 232-249.

101. Marhl M, Noble D, Roux E, Modeling of molecular and cellular mechanisms involved in Ca2+ signal encoding in airway myocytes, Cell Biochem. Biophys. 46 (2006) 285-302.

102. Margoninski O, Saffrey P, Hetherington J, Finkelstein A, Warner A, A specification language and a framework for the execution of composite models in systems biology, Lect. Notes Comput. Sc. 4230 (2006) 163-184.

103*. Valeyev NV, Downing AK, Skorinkin AI, Campbell ID, Kotov NV, A calcium dependent de-adhesion mechanism regulates the direction and rate of cell migration: a mathematical model, In Silico Biology 6 (2006) 0050.

104*. Ali R, Evans ND, Campbell L, Errington RJ, Godfrey KR, Smith PJ, Chappell MJ, Control of cell proliferation by an anti-cancer agent: modelling, validation & sensitivity, IET Seminar Digest 2006 (11576), pp. 247-259.

105. Zhu CL, Jia Y, Liu Q, Yang LJ, Zhan X., A mesoscopic stochastic mechanism of cytosolic calcium oscillations, Biophys. Chem. 125 (2007) 201-212.

106. Marhl M, Grubelnik V, Role of cascades in converting oscillatory signals into stationary step-like responses, Biosystems 87 (2007) 58-67.

107. Perc M, Marhl M, Noise-induced spatial dynamics in the presence of memory loss, Physica A 375 (2007) 72-80.

108. Kusters JMAM, Cortes JM, van Meerwijk WPM, Ypey DL, Theuvenet APR, Gielen CCAM, Hysteresis and bistability in a realistic cell model for calcium oscillations and action potential firing, Phys. Rev. Lett. 98 (2007) Art. No. 098107.

109. Berridge MJ, Inositol trisphosphate and calcium oscillations, Biochem. Soc. Symp. 74 (2007) 1-7.

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111. Peifer M, Timmer J, Parameter estimation in ordinary differential equations for biochemical processes using the method of multiple shooting, IET Syst. Biol. 1 (2007) 78-88.

112. Perc M, Gosak M, Marhl M, Periodic calcium waves in coupled cells induced by internal noise, Chem. Phys. Lett. 437 (2007) 143-147.

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122. Goldstein BN, Aksirov AM, Zaknjevskaya DT, Calmodulin can induce and control damped oscillations in plasma membrane Ca2+-ATPase activity: a kinetic model, Biofizika 52 (2007) 1067-1072.

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124. Walsh F, Balasubramaniam S, Botvich D, Donnelly W, Review of communication mechanisms for biological nano and MEMS devices, Proceedings of the Bio-Inspired Models of Network, Information, and Computing Systems, Bionetics 2007, Art. No. 4610134, pp. 307-312.

125. Kang M, Othmer HG, The variety of cytosolic calcium responses and possible roles of PLC and PKC, Phys. Biol. 4 (2007) 325-343.

126. Lu J, Engl HW, Machne R, Schuster P, Inverse bifurcation analysis of a model for the mammalian G1/S regulatory module, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 4414 LNBI (2007) pp. 168-184.

127*. Minelli TA, Balduzzo M, Milone FF, Nofrate V, Modeling cell dynamics under mobile phone radiation, Nonlinear Dynamics, Psychology, and Life Sciences 11 (2007) 197-218.

128. Goldbeter A, Biological rhythms as temporal dissipative structures, Adv. Chem. Phys. 135 (2007) 253-295.

129. Skupin A, Falcke M, Statistical properties and information content of calcium oscillations, Genome Inform. Ser. 18 (2007) 44-53.

130. Knoke B, Marhl M, Schuster S, Selective regulation of protein activity by complex Ca2+ oscillations: A theoretical study, Conference Information: European Conference on Mathematical and Theoretical Biology (ECMTB 2005), Jul. 2005, Dresden, Germany. Source: Mathematical Modeling of Biological Systems, Vol. I - Cellular Biophysics, Regulatory Networks, Development, Medicine, and Data Analysis. Book Series: Modelling and Simulation in Science, Engineering & Technology. pp.11-22 (2007).

131. Perc M, Green AK, Dixon CJ, Marhl M, Establishing the stochastic nature of intracellular calcium oscillations from experimental data, Biophys. Chem. 132 (2008) 33-38.

132. Salazar C, Politi AZ, Hofer T, Decoding of calcium oscillations by phosphorylation cycles: Analytic results, Biophys. J. 94 (2008) 1203-1215.

133. Knoke B, Marhl M, Perc M, Schuster S, Equality of average and steady-state levels in some nonlinear models of biological oscillations, Theor. Biosci. 127 (2008) 1-14.

134. Shen CS, Chen HS, Zhang JQ, Synchronized anti-phase and in-phase oscillations of intracellular calcium ions in two coupled Hepatocytes system, Chinese Phys. Lett. 25 (2008) 870-873.

135. Corrias A, Buist ML, Quantitative cellular description of gastric slow wave activity, Am. J. Physiol. - Gastr. L. 294 (2008) G989-G995.

136. Gosak M, Marhl M, Perc M, Chaos out of internal noise in the collective dynamics of diffusively coupled cells, Eur. Phys. J. B 62 (2008) 171-177.

137. Harris AL, Connexin specificity of second messenger permeation: Real numbers at last, J. Gen. Physiol. 131 (2008) 287-292 .

138. Pahle J, Green AK, Dixon CJ, Kummer U, Information transfer in signaling pathways: A study using coupled simulated and experimental data, BMC Bioinformatics 9 (2008) Art. No. 139.

139. Lang XF, Li QS, Roles of external noise correlation in optimal intracellular calcium signaling, J. Chem. Phys. 128 (2008) Art. No. 205102.

140. Marhl M, Gosak M, Perc M, Dixon CJ, Green AK, Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes, J. theor. Biol. 252 (2008) 419-426.

141. Wang Y, Li QS, System-size resonance for intracellular and intercellular calcium signaling, Biophys. Chem. 136 (2008) 32-37.

142. Chen XF, Li CX, Wang PY, Li M, Wang WC, Dynamic simulation of the effect of calcium-release activated calcium channel on cytoplasmic Ca2+ oscillation, Biophys. Chem. 136 (2008) 87-95.

143. Mincheva M, Craciun G, Multigraph conditions for multistability, oscillations and pattern formation in biochemical reaction networks, P. IEEE 96 (2008) 1281-1291.

144. Rogers KL, Martin JR, Renaud O, Karplus E, Nicola MA, Nguyen M, Picaud S, Shorte SL, Brulet P, Electron-multiplying charge-coupled detector-based bioluminescence recording of single-cell Ca2+, J. Biomed. Opt. 13 (2008) Art. No. 031211.

145. Dupont G, Abou-Lovergne A, Combettes L, Stochastic aspects of oscillatory Ca2+ dynamics in hepatocytes, Biophys. J. 95 (2008) 2193-2202.

146. Shi XM, Zheng YF, Liu ZR, Yang WZ, A model of calcium signaling and degranulation dynamics induced by laser irradiation in mast cells, Chinese Sci. Bull. 53 (2008) 2315-2325.

147. Harding AS, Hancock JF, Using plasma membrane nanoclusters to build better signaling circuits, Trends Cell Biol. 18 (2008) 364-371.

148. Stiefs D, Gross T, Steuer R, Feudel U, Computation and Visualization of Bifurcation Surfaces, Int. J. Bifurcat. Chaos 18 (2008) 2191-2206.

149. Lu QS, Gu HG, Yang ZQ, Shi X, Duan LX, Zheng YH, Dynamics of firing patterns, synchronization and resonances in neuronal electrical activities: experiments and analysis, Acta Mech. Sinica 24 (2008) 593-628.

150. Santini CC, Tyrrell AM, The manipulation of calcium oscillations by harnessing self-organisation, BioSystems 94 (2008) 153-163.

151. Nittala A, Wang X, The hyperbolic effect of density and strength of inter beta-cell coupling on islet bursting: A theoretical investigation, Theoretical Biology and Medical Modelling 5 (2008) Art. No. 17.

152. Kong H, Fan Y, Xie J, Ding JH, Sha LL, Shi XR, Sun XL, Hu G, AQP4 knockout impairs proliferation, migration and neuronal differentiation of adult neural stem cells, J. Cell Sci. 121(2008) 4029-4036.

153. Ishida S, Yuasa T, Nakata M, Takahashi Y, A Tobacco Calcium-Dependent Protein Kinase, CDPK1, Regulates the Transcription Factor REPRESSION OF SHOOT GROWTH in Response to Gibberellins, Plant Cell 20 (2008) 3273-3288.

154. Linderman JJ, Modeling of G-protein-coupled Receptor Signaling Pathways, J. Biol. Chem. 284 (2009) 5427-5431.

155. McAinsh MR, Pittman JK, Shaping the calcium signature, New Phytol. 181 (2009) 275-294.

156. Gosak M, Marhl M, Perc M, Pacemaker-guided noise-induced spatial periodicity in excitable media, Physica D 238 (2009) 506-515.

157. Mazel T, Raymond R, Raymond-Stintz M, Jett S, Wilson BS, Stochastic Modeling of Calcium in 3D Geometry, Biophys. J. 96 (2009) 1691-1706.

158. Harris LA, Piccirilli AM, Majusiak ER, Clancy P, Quantifying stochastic effects in biochemical reaction networks using partitioned leaping, Phys. Rev. E 79 (2009) Art. No. 051906.

159. Newman SA, EE Just's "Independent Irritability" Revisited: The Activated Egg as Excitable Soft Matter, Mol. Reprod. Dev. 76 (2009) 966-974.

160. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

161. Chen ML, Wang FS, Dynamic sensitivity analysis of oscillating biochemical systems using modified collocation method, J. Taiwan Inst. Chem. E 40 (2009) 371-379.

162. Curis E, Nicolis I, Bensaci J, Deschamps P, Benazeth S, Mathematical modeling in metal metabolism: Overview and perspectives, Biochimie 91 (2009) 1238-1254.

163. Zeng SA, Li B, Zeng SQ, Chen SB, Simulation of Spontaneous Ca2+ Oscillations in Astrocytes Mediated by Voltage-Gated Calcium Channels, Biophys. J. 97 (2009) 2429-2437.

164. Siso-Nadal F, Fox JJ, Laporte SA, Hebert TE, Swain PS, Cross-Talk between Signaling Pathways Can Generate Robust Oscillations in Calcium and cAMP. PloS ONE 4 (2009) Art. No. e7189.

165. Hazledine S, Sun J, Wysham D, Downie JA, Oldroyd GED, Morris RJ, Nonlinear Time Series Analysis of Nodulation Factor Induced Calcium Oscillations: Evidence for Deterministic Chaos? PloS ONE 4 (2009) Art. No. e6637.

166. Bewick S, Yang RT, Zhang MJ, Complex mathematical models of biology at the nanoscale. Wiley Interdisc. Rev. - Nanomed. Nanotech. 1 (2009) 650-659.

167. Aguilar-Lopez R, Martinez-Guerra R, Puebla H, Hernandez-Suarez R, High order sliding-mode dynamic control for chaotic intracellular calcium oscillations, Nonlinear Anal.-Real 11 (2010) 217-231.

168. Yi FX, Boeldt DS, Gifford SM, Sullivan JA, Grummer MA, Magness RR, Bird IM, Pregnancy Enhances Sustained Ca2+ Bursts and Endothelial Nitric Oxide Synthase Activation in Ovine Uterine Artery Endothelial Cells Through Increased Connexin 43 Function. Biol. Reprod. 82 (2010) 66-75.

169. Solovey G, Dawson SP, Intra-Cluster Percolation of Calcium Signals. PloS ONE 5 (2010) Art. No. e8997.

170. Sotero RC, Martinez-Cancino R, Dynamical Mean Field Model of a Neural-Glial Mass. Neural. Comput. 22 (2010) 969-997.

171. Ye WM, Huang XD, Huang XH, Li PF, Xia QZ, Hu G, Self-sustained oscillations of complex genomic regulatory networks. Phys. Lett. A 374 (2010) 2521-2526.

172. Knoke B, Bodenstein C, Marhl M, Perc M, Schuster S, Jensen's inequality as a tool for explaining the effect of oscillations on the average cytosolic calcium concentration, Theor. Biosci. 129 (2010) 25-38.

173. Ito T, Nakata M, Fukazawa J, Ishida S, Takahashi Y, Alteration of Substrate Specificity: The Variable N-Terminal Domain of Tobacco Ca2+-Dependent Protein Kinase Is Important for Substrate Recognition. Plant Cell 22 (2010) 1592-1604.

174. Chignola R, Del Fabbro A, Milotti E, Dynamics of intracellular Ca2+ oscillations in the presence of multisite Ca2+-binding proteins. Physica A 389 (2010) 3172-3178.

175. Ye B, Ca2+ Oscillations and Its Transporters in Mesenchymal Stem Cells. Physiol. Res. 59 (2010) 323-329.

176. Majumder P, Crispino G, Rodriguez L, Ciubotaru CD, Anselmi F, Piazza V, Bortolozzi M, Mammano F, ATP-mediated cell-cell signaling in the organ of Corti: the role of connexin channels. Purinergic Signalling 6 (2010) 167-187.

177. Pandey R, Gupta S, Tandon S, Wolkenhauer O, Vera J, Gupta SK, Baccoside A suppresses epileptic-like seizure/convulsion in Caenorhabditis elegans. Seizure-Eur. J. Epilepsy 19 (2010) 439-442.

178. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

179. Calabrese A, Fraiman D, Zysman D, Dawson SP, Stochastic fire-diffuse-fire model with realistic cluster dynamics. Phys. Rev. E 82 (2010) Art. No. 031910.

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M. Perc, M. Marhl

Sensitivity and flexibility of regular and chaotic calcium oscillations

Biophysical Chemistry
104 (2003) 509-522

 

Citiran v:

1*. Perc M, Marhl M, Different types of bursting calcium oscillations in non-excitable cells, Chaos, Solitons & Fractals 18 (2003) 759-773.

2. Perc M, Marhl M, Noise enhances robustness of intracellular Ca2+ oscillations, Phys. Lett. A 316 (2003) 304-310.

3. Perc M, Marhl M, Frequency dependent stochastic resonance in a model for intracellular Ca2+ oscillations can be explained by local divergence, Physica A - Statistical Mechanics and its Applications 332 (2004) 123-140.

4. Perc M, Marhl M, Local dissipation and coupling properties of cellular oscillators - A case study on calcium oscillations, Bioelectrochemistry 62 (2004) 1-10.

5. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

6. Perc M, Marhl M, Synchronization of regular and chaotic oscillations: The role of local divergence and the slow passage effect - A case study on calcium oscillations, Int. J. Bifurcat. Chaos 14 (2004) 2735-2751.

7*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

8. Kummer U, Krajnc B, Pahle J, Green AK, Dixon CJ, Marhl M, Transition from stochastic to deterministic behavior in calcium oscillations, Biophys. J. 89 (2005) 1603-1611.

9*. Savi MA, Chaos and order in biomedical rhythms, J. of the Braz. Soc. of Mech. Sci. & Eng. 27 (2005) 157-169.

10. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

11. Li HY, Bi JH, Ma J, Constructive Role of Internal Noise for the Detection of Weak Stimulation in a Coupled Biological Cell System, Acta Phys.-Chim. Sin. 25 (2009) 1327-1331.

12. Hazledine S, Sun J, Wysham D, Downie AJ, Oldroyd GED, Morris RJ, Nonlinear time series analysis of nodulation factor induced calcium oscillations: Evidence for deterministic chaos? PLoS ONE 4 (2009) Art. No. e6637.

13*. Li H-Y, Bi J-H, Ma J, Constructive role of internal noise for the detection of weak stimulation in a coupled biological cell system. Wuli Huaxue Xuebao/Acta Physico - Chimica Sinica 25 (2009) 1327-1331.

14. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes. Biophys. Chem. 148 (2010) 42-50.

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M. Perc, M. Marhl

Different types of bursting calcium oscillations in non-excitable cells

Chaos, Solitons & Fractals
18 (2003) 759-773

 

Citiran v:

1. Perc M, Marhl M, Resonance effects determine the frequency of bursting Ca2+ oscillations, Chem. Phys. Lett. 376 (2003) 432-437.

2. Perc M, Marhl M, Frequency dependent stochastic resonance in a model for intracellular Ca2+ oscillations can be explained by local divergence, Physica A - Statistical Mechanics and its Applications 332 (2004) 123-140.

3. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

4. Perc M, Marhl M, Synchronization of regular and chaotic oscillations: The role of local divergence and the slow passage effect - A case study on calcium oscillations, Int. J. Bifurcat. Chaos 14 (2004) 2735-2751.

5*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

6. Wang HX, Lu QS, Wang QY, Generation of firing rhythm, patterns and synchronization in the Morris-Lecar neuron model, Int. J. Nonlinear Sci. 6 (2005) 7-12.

7. Perc M, Marhl M, Amplification of information transfer in excitable systems that reside in a steady state near a bifurcation point to complex oscillatory behavior, Phys. Rev. E 71 (2005) art. no. 026229.

8. Schuster S, Knoke B, Marhl M, Differential regulation of proteins by bursting calcium oscillations - a theoretical study, BioSystems 81 (2005) 49-63.

9. Perc M, Marhl M, Chaos in temporarily destabilized regular systems with the slow passage effect, Chaos Solitons & Fractals 27 (2006) 395-403.

10*. Savi MA, Chaos and order in biomedical rhythms, J. of the Braz. Soc. of Mech. Sci. & Eng. 27 (2005) 157-169.

11. Duan LX, Lu QS, Bursting oscillations near codimension-two bifurcations in the Chay neuron model, Int. J. Nonlin. Sci. Num. Simulat. 7 (2006) 59-63.

12. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

13. Perc M, Effects of small-world connectivity on noise-induced temporal and spatial order in neural media, Chaos Solitons & Fractals 31 (2007) 280-291.

14. Zhang F, Lu QS, Duan LX, Dynamics analysis and transition mechanism of bursting calcium oscillations in non-excitable cells, Chinese Phys. Lett. 24 (2007) 3344-3346.

15*. Wang Y, Li QS, Explicit stochastic resonance of bursting behavior in a calcium system, Beijing Ligong Daxue Xuebao / Transaction of Beijing Institute of Technology 27 (2007), 1039-1041.

16. Knoke B, Marhl M, Schuster S, Selective regulation of protein activity by complex Ca2+ oscillations: A theoretical study, Conference Information: European Conference on Mathematical and Theoretical Biology (ECMTB 2005), Jul. 2005, Dresden, Germany. Source: Mathematical Modeling of Biological Systems, Vol. I - Cellular Biophysics, Regulatory Networks, Development, Medicine, and Data Analysis. Book Series: Modelling and Simulation in Science, Engineering & Technology. pp.11-22 (2007).

17. Wang HX, Lu QS, Wang QY, Bursting and synchronization transition in the coupled modified ML neurons, Communication Nonlin. Sci. Num. Simulat. 13 (2008) 1668-1675.

18. Wang QY, Duan ZS, Feng ZS, Chen GR, Lu QS, Synchronization transition in gap-junction-coupled leech neurons, Physica A 387 (2008) 4404-4410.

19. Ji QB, Lu QS, Yang ZQ, Duan LX, Bursting Ca2+ Oscillations and Synchronization in Coupled Cells, Chinese Phys. Lett. 25 (2008) 3879-3882.

20. Duan L, Lu Q, Wang Q, Two-parameter bifurcation analysis of firing activities in the Chay neuronal model, Neurocomputing 72 (2008) 341-351.

21. Zhou YZ, Zhou J, Liu ZH, Influence of network topology on the abnormal phase order, EPL 84 (2009) Art. No. 60001.

22. Wang Y, Li QS, Luo J, Explicit calcium bursting stochastic resonance, Biophys. Chem. 142 (2009) 40-45.

23. Zhang F, Lu QS, Su JZ, Transition in complex calcium bursting induced by IP3 degradation, Chaos Solitons & Fractals 41 (2009) 2285-2290.

24. Meng P, Lu QS, Dynamical Effect of Calcium Pump on Cytosolic Calcium Bursting Oscillations with IP3 Degradation. Chinese Phys. Lett. 27 (2010) Art. No. 010502.

25. Peng GJ, Jiang YL, Two routes to chaos in the fractional Lorenz system with dimension continuously varying. Physica A 389 (2010) 4140-4148.

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M. Marhl, S. Schuster

Under what conditions signal transduction pathways are highly flexible in response to external forcing? A case study on calcium oscillations

Journal of Theoretical Biology
224 (2003) 491-500

Citiran v:

1. Perc M, Marhl M, Frequency dependent stochastic resonance in a model for intracellular Ca2+ oscillations can be explained by local divergence, Physica A - Statistical Mechanics and its Applications 332 (2004) 123-140.

2. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

3. Perc M, Marhl M, Synchronization of regular and chaotic oscillations: The role of local divergence and the slow passage effect - A case study on calcium oscillations, Int. J. Bifurcat. Chaos 14 (2004) 2735-2751.

4*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

5. Puebla H, Controlling intracellular calcium oscillations and waves, J Biol. Syst. 13 (2005) 173-190.

6. Kummer U, Krajnc B, Pahle J, Green AK, Dixon CJ, Marhl M, Transition from stochastic to deterministic behavior in calcium oscillations, Biophys. J. 89 (2005) 1603-1611.

7. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

8. Klipp E, Liebermeister W, Mathematical modeling of intracellular signaling pathways, BMC Neuroscience 7 (2006) S10, doi:10.1186/1471-2202-7-S1-S10.

9*. Valeyev NV, Downing AK, Skorinkin AI, Campbell ID, Kotov NV, A calcium dependent de-adhesion mechanism regulates the direction and rate of cell migration: a mathematical model, In Silico Biology 6 (2006) 0050.

10*. Battogtokh D, Tyson JJ, Periodic forcing of a mathematical model of the eukaryotic cell cycle, Phys. Rev. E 73 (2006) art. no. 011910.

11. Aguilar-Lopez R, Martinez-Guerra R, Puebla H, Hernandez-Suarez R, High order sliding-mode dynamic control for chaotic intracellular calcium oscillations, Nonlinear Anal.-Real 11 (2010) 217-231.

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------------------------------------------------------------------------

M. Perc, M. Marhl

Resonance effects determine the frequency of bursting Ca2+ oscillations

Chemical Physics Letters
376 (2003) 432-437

Citiran v:

1. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

2. Perc M, Marhl M, Amplification of information transfer in excitable systems that reside in a steady state near a bifurcation point to complex oscillatory behavior, Phys. Rev. E 71 (2005) art. no. 026229.

3. Perc M, Effects of small-world connectivity on noise-induced temporal and spatial order in neural media, Chaos Solitons & Fractals 31 (2007) 280-291.

4. Bi QS, The mechanism of bursting phenomena in Belousov-Zhabotinsky (BZ) chemical reaction with multiple time scales. Sci. China-Technol. Sciences 53 (2010) 748-760.

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M. Perc, M. Marhl

Noise enhances robustness of intracellular Ca2+ oscillations

Physics Letters A
316 (2003) 304-310

Citiran v:

1. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

2*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

3. Goldstein BN, Mayevsky AA, Zakrjevskaya DT, Influence of Ca2+ oscillatory influx on membrane Ca2+-ATPase activity: a kinetic model, Biochemistry-Moscow 70 (2005) 445-448.

4. Li HY, Hou ZH, Xin HW, Internal noise stochastic resonance for intracellular calcium oscillations in a cell system, Phys. Rev. E 71 (2005) art. no. 061916.

5. Zhang JQ, Hou ZH, Xin HW, Stochastic bi-resonance induced by external noise for Ca2+ signaling in hepatocytes, Sci. China Ser. B 48 (2005) 286-291.

6. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

7. Perc M, Marhl M, Pacemaker enhanced noise-induced synchrony in cellular arrays, Phys. Lett. A 353 (2006) 372-377.

8. Chen HS, Zhang JQ, Liu JQ, Selective effects of external noise on Ca2+ signal in mesoscopic scale biochemical cell systems, Biophys. Chem. 125 (2007) 397-402.

9. Chuan-Sheng S, Ji-Qianl Z, Han-Shuang C, System size selected effects induced by clustering in two-dimensional coupled cell systems, Acta. Phys. Sin.-Ch. Ed. 56 (2007) 6315-6320.

10. Lang XF, Li QS, Roles of external noise correlation in optimal intracellular calcium signaling, J. Chem. Phys. 128 (2008) Art. No. 205102.

11. Ma J, Li HY, Hou ZH, Xin HW, System Size Resonance Associated with Canard Phenomenon in a Biological Cell System, Chin. J. Chem. Phys. 21 (2008) 521-525.

12. Pahle J, Biochemical simulations: stochastic, approximate stochastic and hybrid approaches, Brief. Bioinform. 10 (2009) 53-64.

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M. Perc, M. Marhl

Frequency dependent stochastic resonance in a model for intracellular Ca2+ oscillations can be explained by local divergence

Physica A
332 (2004) 123-140

Citiran v:

1. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

2*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

3. Chassin DP, Malard J, Posse C, Managing Complexity, CCCT-04 invited session, Austin Texas, August 2004, 7 pages.

4. Perc M, Marhl M, Amplification of information transfer in excitable systems that reside in a steady state near a bifurcation point to complex oscillatory behavior, Phys. Rev. E 71 (2005) art. no. 026229.

5. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

6. Perc M, Gosak M, Marhl M, From stochasticity to determinism in the collective dynamics of diffusively coupled cells, Chem. Phys. Lett. 421 (2006) 106-110.

7. Perc M, Marhl M, Pacemaker enhanced noise-induced synchrony in cellular arrays, Phys. Lett. A 353 (2006) 372-377.

8. Perc M, Marhl M, Noise-induced spatial dynamics in the presence of memory loss, Physica A 375 (2007) 72-80.

9. Gandhimathi VM, Rajasekar S, Vibrational and stochastic resonances in two coupled overdamped anharmonic oscillators driven by an amplitude modulated force, Phys. Scripta 76 (2007) 693-698.

10*. Minelli TA, Balduzzo M, Milone FF, Nofrate V, Modeling cell dynamics under mobile phone radiation, Nonlinear Dynamics, Psychology, and Life Sciences 11 (2007) 197-218.

11. Lang XF, Li QS, Roles of external noise correlation in optimal intracellular calcium signaling, J. Chem. Phys. 128 (2008) Art. No. 205102.

12. Chignola R, Del Fabbro A, Milotti E, Dynamics of intracellular Ca2+ oscillations in the presence of multisite Ca2+-binding proteins. Physica A 16 (2010) 3172-3178.

13. Lang XF, Lu QS, Kurths J, Phase synchronization in noise-driven bursting neurons. Phys. Rev. E 82 (2010) Art. No. 021909.

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M. Perc, M. Marhl

Local dissipation and coupling properties of cellular oscillators - A case study on calcium oscillations

Bioelectrochemistry
62 (2004) 1-10

Citiran v:

1. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

2*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

3. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

4. Harris AL, Connexin channel permeability to cytoplasmic molecules, Prog. Biophys. Mol. Bio. 94 (2007) 120-143.

5. Harris AL, Connexin specificity of second messenger permeation: Real numbers at last, J. Gen. Physiol. 131 (2008) 287-292.

6. Zhu XL, Sang JP, Wang LL, Huang SY, Zou XW, Structure properties and synchronizability of cobweb-like networks, Physica A 387 (2008) 6646-6656.

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M. Perc, M. Marhl

Synchronisation of regular and chaotic oscillations: The role of local divergence and the slow passage effect. A case study on calcium oscillations

International Journal of Bifurcation and Chaos
14 (2004) 2735-2751

Citiran v:

1*. Perc M, Marhl M, Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor, Phys. Rev. E 70 (2004) art. no. 016204.

2*. Marhl M, Perc M, Determining the robustness of signal transduction systems - A case study on neurons, WSEAS Trans. Biol. Biomed. 1 (2004) 379-383.

3. Perc M, Marhl M, Chaos in temporarily destabilized regular systems with the slow passage effect, Chaos Solitons & Fractals 27 (2006) 395-403.

4. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

5. Zhu XL, Sang JP, Wang LL, Huang SY, Zou XW, Structure properties and synchronizability of cobweb-like networks, Physica A 387 (2008) 6646-6656.

6. Puebla H, Del Muro Cuellar B, Aguilar-Lopez R, Synchronization of coupled calcium oscillators: A robust feedback control approach, Chinese Control and Decision Conference, CCDC 2008 (2008) Art. No. 4598143, pp. 4309-4312.

7. Ma J, Zhang AH, Xia YF, Zhang LP, Optimize design of adaptive synchronization controllers and parameter observers in different hyperchaotic systems. Appl. Math. Comput 215 (2010) 3318-3326.

8. Wang CN, Li SR, Ma J, Jin WY, Synchronization transition in degenerate optical parametric oscillators induced by nonlinear coupling. Appl. Math. Comput 216 (2010) 647-654.

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E. Roux, M. Marhl

Role of sarcoplasmic reticulum and mitochondria in Ca2+ removal in airway myocytes

Biophysical Journal
86 (2004) 2583-2595

Citiran v:

1. Dai JZ, Kuo KH, Leo JM, van Breemen C, Lee CH, Rearrangement of the close contact between the mitochondria and the sarcoplasmic reticulum in airway smooth muscle, Cell Calcium 37 (2005) 333-340.

2. Brumen M, Fajmut A, Dobovisek A, Roux E, Mathematical modelling of Ca2+ oscillations in airway smooth muscle cells, J. Biol. Phys. 31 (2005) 515-524.

3. Roux E, Noble PJ, Noble D, Marhl M, Modelling of calcium handling in airway myocytes, Prog. Biophys. Mol. Biol. 90 (2006) 64-87.

4. Marhl M, Perc M, Schuster S, A minimal model for decoding of time-limited Ca2+ oscillations, Biophys. Chem. 120 (2006) 161-167.

5. McCarron JG, Chalmers S, Bradley KN, MacMillan D, Muir TC, Ca2+ microdomains in smooth muscle, Cell Calcium 40 (2006) 461-493.

6. Marhl M, Noble D, Roux E, Modeling of molecular and cellular mechanisms involved in Ca2+ signal encoding in airway myocytes, Cell Biochem. Biophys. 46 (2006) 285-302.

7. Mbikou P, Fajmut A, Brumen M, Roux E, Theoretical and experimental investigation of calcium-contraction coupling in airway smooth muscle, Cell Biochem. Biophys. 46 (2006) 233-251.

8. Zayas R, Groshong JS, Gomez CM, Inositol-1,4,5-triphosphate receptors mediate activity-induced synaptic Ca2+ signals in muscle fibers and Ca2+ overload in slow-channel syndrome, Cell Calcium 41 (2007) 343-352.

9. Hirota S, Helli P, Janssen LJ, Ionic mechanisms and Ca2+ handling in airway smooth muscle, Eur. Respir. J. 30 (2007) 114-133.

10. Chalmers S, Olson ML, MacMillan D, Rainbow RD, McCarron JG, Ion channels in smooth muscle: Regulation by the sarcoplasmic reticulum and mitochondria, Cell Calcium 42 (2007) 447-466.

11. Marhl M, Gosak M, Perc M, Dixon CJ, Green AK, Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes, J. theor. Biol. 252 (2008) 419-426.

12. Nakamura N, Yamazawa T, Okubo Y, Iino M, Temporal switching and cell-to-cell variability in Ca2+ release activity in mammalian cells, Mol. Syst. Biol. 5 (2009) Art. No. 247.

13. Wray S, Burdyga T, Sarcoplasmic Reticulum Function in Smooth Muscle. Physiol. Rev. 90 (2010) 113-178.

14. Wang IY, Bai Y, Sanderson MJ, Sneyd J, A Mathematical Analysis of Agonist- and KCI-Induced Ca2+ Oscillations in Mouse Airway Smooth Muscle Cells. Biophys. J. 98 (2010) 1170-1181.

15. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes. Biophys. Chem. 148 (2010) 42-50.

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APS

M. Perc, M. Marhl

Detecting and controlling unstable periodic orbits that are not part of a chaotic attractor

Physical Review E
70 (2004) art. no. 016204

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IoP

S. Kodba, M. Perc, M. Marhl

Detecting chaos from a time series

European Journal of Physics
26 (2005) 205-215

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S. Schuster, B. Knoke, M. Marhl

Differential regulation of proteins by bursting calcium oscillations - a theoretical study

Biosystems
81 (2005) 49-63

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APS

M. Perc and M. Marhl

Amplification of information transfer in excitable systems that reside in a steady state near a bifurcation point to complex oscillatory behavior

Physical Review E
71 (2005) art. no. 026229

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U. Kummer, B. Krajnc, J. Pahle. A.K. Green, C.J. Dixon, M. Marhl

Transition from Stochastic to deterministic behavior in calcium oscillations

Biophysical Journal
89 (2005) 1603-1611

Citiran v:

1. Perc M, Gosak M, Marhl M, From stochasticity to determinism in the collective dynamics of diffusively coupled cells, Chem. Phys. Lett. 421 (2006) 106-110.

2. Müller M, Wegner K, Kummer U, Baier G, Quantification of cross correlations in complex spatiotemporal systems, Phys. Rev. E 73 (2006) art. no. 046106.

3. Manninen T, Linne M-L, Ruohonen K, Developing Itô stochastic differential equation models for neuronal signal transduction pathways, Comput. Biol. Chem. 30 (2006) 280-291.

4. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U, COPASI- A COmplex PAthway SImulator, Bioinformatics 22 (2006) 3067-3074.

5. Song H, Smolen P, Av-Ron E, Baxter DA, Byrne JH, Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins, Biophys. J. 92 (2007) 3407-3424.

6. McKane AJ, Nagy JD, Newman TJ, Stefanini MO, Amplified biochemical oscillations in cellular systems, J. Stat. Phys. 128 (2007) 165-191.

7. Hemberg M, Barahona M, Perfect sampling of the master equation for gene regulatory networks, Biophys. J. 93 (2007) 401-410.

8. Dupont G, Combettes L, Leybaert L, Calcium dynamics: Spatio-temporal organization from the subcellular to the organ level, Int. Rev. Cytol. 261 (2007) 193-245.

9. Ullah M, Wolkenhauer O, Family tree of Markov models in systems biology, IET Syst. Biol. 1 (2007) 247-254.

10. Kang M, Othmer HG, The variety of cytosolic calcium responses and possible roles of PLC and PKC, Phys. Biol. 4 (2007) 325-343.

11*. Wang Y, Li QS, Explicit stochastic resonance of bursting behavior in a calcium system, Beijing Ligong Daxue Xuebao / Transaction of Beijing Institute of Technology 27 (2007), 1039-1041.

12. Perc M, Green AK, Dixon CJ, Marhl M, Establishing the stochastic nature of intracellular calcium oscillations from experimental data, Biophys. Chem. 132 (2008) 33-38.

13. Gosak M, Marhl M, Perc M, Chaos out of internal noise in the collective dynamics of diffusively coupled cells, Eur. Phys. J. B 62 (2008) 171-177.

14. Pahle J, Green AK, Dixon CJ, Kummer U, Information transfer in signaling pathways: A study using coupled simulated and experimental data, BMC Bioinformatics 9 (2008) Art. No. 139.

15. Wang Y, Li QS, System-size resonance for intracellular and intercellular calcium signaling, Biophys. Chem. 136 (2008) 32-37.

16. Kosuta S, Hazledine S, Sun J, Miwa H, Morris RJ, Downie JA, Oldroyd GED, Differential and chaotic calcium signatures in the symbiosis signaling pathway of legumes, P. Natl. Acad. Sci. USA 105 (2008) 9823-9828.

17. Dupont G, Abou-Lovergne A, Combettes L, Stochastic aspects of oscillatory Ca2+ dynamics in hepatocytes, Biophys. J. 95 (2008) 2193-2202.

18. Lederhendler A, Biham O, Validity of rate equation results for reaction rates in reaction networks with fluctuations, Phys. Rev. E 78 (2008) Art. No. 041105.

19. Pahle J, Biochemical simulations: stochastic, approximate stochastic and hybrid approaches, Brief. Bioinform. 10 (2009) 53-64.

20. Armbruster D, Nagy JD, van de Rijt EAF, Rooda JE, Dynamic Simulations of Single-Molecule Enzyme Networks, J. Phys. Chem. B 113 (2009) 5537-5544.

21. Wang Y, Li QS, Luo J, Explicit calcium bursting stochastic resonance, Biophys. Chem. 142 (2009) 40-45.

22. Harris LA, Piccirilli AM, Majusiak ER, Clancy P, Quantifying stochastic effects in biochemical reaction networks using partitioned leaping, Phys. Rev. E 79 (2009) Art. No. 051906.

23. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

24. Dupont G, Combettes L, What can we learn from the irregularity of Ca2+ oscillations? Chaos 19 (2009) Art. No.: 037112.

25. Hazledine S, Sun J, Wysham D, Downie JA, Oldroyd GED, Morris RJ, Nonlinear Time Series Analysis of Nodulation Factor Induced Calcium Oscillations: Evidence for Deterministic Chaos? Plos ONE 4 (2009) Art. No. e6637.

26. Aguilar-Lopez R, Martinez-Guerra R, Puebla H, Hernandez-Suarez R, High order sliding-mode dynamic control for chaotic intracellular calcium oscillations. Nonlinear Anal.-Real World Applications 11 (2010) 217-231.

27. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes. Biophys. Chem. 148 (2010) 42-50.

28. Brasen JC, Olsen LF, Hallett MB, Cell surface topology creates high Ca2+ signalling microdomains. Cell Calcium 47 (2010) 339-349.

29. Ouattara DA, Abou-Jaoude W, Kaufman M, From structure to dynamics: Frequency tuning in the p53-Mdm2 network. II Differential and stochastic approaches. J. theor. Biol. 264 (2010) 1177-1189.

30. Elson EC, Complex life forms may arise from electrical processes. Theor. Biol. and Med. Modelling 7 (2010) Art. No. 26.

31. Stratton RC, Squires PE, Green AK, 17 beta-Estradiol Elevates cGMP and, via Plasma Membrane Recruitment of Protein Kinase GI alpha, Stimulates Ca2+ Efflux from Rat Hepatocytes. J. Biol. Chem. 285 (2010) 27201-27212.

32. Skupin A, Kettenmann H, Falcke M, Calcium Signals Driven by Single Channel Noise, PLoS Comput. Biol. 6 (2010) Art. No. e1000870.

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M. Marhl, M. Perc, S. Schuster

Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations

FEBS Letters
579 (2005) 5461-5465

 

Citiran v:

1. Marhl M, Perc M, Schuster S, A minimal model for decoding of time-limited Ca2+ oscillations, Biophys. Chem. 120 (2006) 161-167.

2. Zhao J, Yu H, Luo JH, Cao ZW, Li YX, Hierarchical modularity of nested bow-ties in metabolic networks, BMC Bioinformatics 7 (2006) Art. No. 386.

3. Samoilov MS, Arkin AP, Deviant effects in molecular reaction pathways, Nature Biotechnol. 24 (2006) 1235-1240.

4. Marhl M, Grubelnik V, Role of cascades in converting oscillatory signals into stationary step-like responses, Biosystems 87 (2007) 58-67.

5. Marhl M, Noble D, Roux E, Modeling of molecular and cellular mechanisms involved in Ca2+ signal encoding in airway myocytes, Cell Biochem. Biophys. 46 (2006) 285-302.

6. Zhao J, Tao L, Yu H, Luo JH, Cao ZW, Li YX, Bow-tie topological features of metabolic networks and the functional significance, Chinese Sci. Bull. 52 (2007) 1036-1045.

7. Salazar C, Politi AZ, Hofer T, Decoding of calcium oscillations by phosphorylation cycles: Analytic results, Biophys. J. 94 (2008) 1203-1215.

8. Knoke B, Marhl M, Schuster S, Selective regulation of protein activity by complex Ca2+ oscillations: A theoretical study, Conference Information: European Conference on Mathematical and Theoretical Biology (ECMTB 2005), Jul. 2005, Dresden, Germany. Source: Mathematical Modeling of Biological Systems, Vol. I - Cellular Biophysics, Regulatory Networks, Development, Medicine, and Data Analysis. Book Series: Modelling and Simulation in Science, Engineering & Technology. pp.11-22 (2007).

9. Pahle J, Green AK, Dixon CJ, Kummer U, Information transfer in signaling pathways: A study using coupled simulated and experimental data, BMC Bioinformatics 9 (2008) Art. No. 139.

10. Marhl M, Gosak M, Perc M, Dixon CJ, Green AK, Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes, J. theor. Biol. 252 (2008) 419-426.

11. Grubelnik V, Dugonik B, Osebik D, Marhl M, Signal amplification in biological and electrical engineering systems Universal role of cascades, Biophys. Chem. 143 (2009) 132-138.

12. Yi M, Xia KL, Zhan M, Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling. Biophys. Chem. 147 (2010) 130-139.

13. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion. Physica A 389 (2010) 3791-3803.

14. Ylander PJ, Hanninen P, Modelling of multi-component immunoassay kinetics - A new node-based method for simulation of complex assays. Biophys. Chem. 151 (2010) 105-110.

15. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

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APPT

V. Grubelnik and M. Marhl

Drop formation in a falling stream of liquid

American Journal of Physics
73 (2005) 415-419

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M. Perc, M. Marhl

Chaos in temporarily destabilized regular systems with the slow passage effect


Chaos, Solitons & Fractals
27 (2006) 395-403

 

Citiran v:

1. Marhl M, Perc M, Determining the flexibility of regular and chaotic attractors, Chaos Solitons & Fractals 28 (2006) 822-833.

2. Chen JH, Controlling chaos and chaotification in the Chen-Lee system by multiple time delays, Chaos Solitons & Fractals 36 (2008) 843-852.

3. Tam LM, Tou WMS, Parametric study of the fractional-order Chen-Lee system, Chaos Solitons & Fractals 37 (2008) 817-826.

4. Sheu LJ, Chen HK, Chen JH, Tam LM, Chen WC, Lao SK, Lin KT, Complete synchronization of two Chen-Lee systems, J. Phys.: Conf. Ser. 96 (2008) Art. No. 012138 .

5. Chang SC, Lin HP, Synchronization with particular application to the control of a chaotic electromagnetic system, P. I. Mech. Eng. G - J. Aer. 222 (2008) 1047-1053.

6. Ma J, Zhang AH, Xia YF, Zhang LP, Optimize design of adaptive synchronization controllers and parameter observers in different hyperchaotic systems. Appl. Math. Comput. 215 (2010) 3318-3326.

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M. Marhl, M. Perc, S. Schuster

A minimal model for decoding of time-limited Ca2+ oscillations


Biophysical Chemistry
120 (2006) 161-167

 

Citiran v:

1*. Klipp E, Liebermeister W, Mathematical modeling of intracellular signaling pathways, BMC Neuroscience 7 (2006) S10, doi:10.1186/1471-2202-7-S1-S10.

2. Marhl M, Grubelnik V, Role of cascades in converting oscillatory signals into stationary step-like responses, Biosystems 87 (2007) 58-67.

3. Knoke B, Marhl M, Schuster S, Selective regulation of protein activity by complex Ca2+ oscillations: A theoretical study, Conference Information: European Conference on Mathematical and Theoretical Biology (ECMTB 2005), Jul. 2005, Dresden, Germany. Source: Mathematical Modeling of Biological Systems, Vol. I - Cellular Biophysics, Regulatory Networks, Development, Medicine, and Data Analysis. Book Series: Modelling and Simulation in Science, Engineering & Technology. pp.11-22 (2007).

4. Salazar C, Politi AZ, Hofer T, Decoding of calcium oscillations by phosphorylation cycles: Analytic results, Biophys. J. 94 (2008) 1203-1215.

5. Knoke B, Marhl M, Perc M, Schuster S, Equality of average and steady-state levels in some nonlinear models of biological oscillations, Theor. Biosci. 127 (2008) 1-14.

6. Pahle J, Green AK, Dixon CJ, Kummer U, Information transfer in signaling pathways: A study using coupled simulated and experimental data, BMC Bioinformatics 9 (2008) Art. No. 139.

7. Marhl M, Gosak M, Perc M, Dixon CJ, Green AK, Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes, J. theor. Biol. 252 (2008) 419-426.

8. Yi M, Xia KL, Zhan M, Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling, Biophys. Chem. 147 (2010) 130-139.

9. Knoke B, Bodenstein C, Marhl M, Perc M, Schuster S, Jensen's inequality as a tool for explaining the effect of oscillations on the average cytosolic calcium concentration, Theor. Biosci. 129 (2010) 25-38.

10. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion, Physica A 389 (2010) 3791-3803.

11. Ylander PJ, Hanninen P, Modelling of multi-component immunoassay kinetics - A new node-based method for simulation of complex assays, Biophys. Chem. 151 (2010) 105-110.

12. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

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M. Marhl, M. Perc

Determining the flexibility of regular and chaotic attractors


Chaos, Solitons & Fractals
28 (2006) 822-833

 

Citiran v:

1. Zhang GJ, Xu JX, Yao H, Wei RX, Mechanism of bifurcation-dependent coherence resonance of an excitable neuron model, Int. J. Nonlin. Sc. Num. Sim. 7 (2006) 447-450.

2. Perc M, Marhl M, Noise-induced spatial dynamics in the presence of memory loss, Physica A 375 (2007) 72-80.

3. Zhang J, Limit cycle for the Brusselator by He's variational method, Math. Brobl. Eng. (2007) art. no. 85145.

4. Chen JH, Controlling chaos and chaotification in the Chen-Lee system by multiple time delays, Chaos Solitons & Fractals 36 (2008) 843-852.

5. Tam LM, Tou WMS, Parametric study of the fractional-order Chen-Lee system, Chaos Solitons & Fractals 37 (2008) 817-826.

6. Sheu LJ, Chen HK, Chen JH, Tam LM, Chen WC, Lao SK, Lin KT, Complete synchronization of two Chen-Lee systems, J. Phys.: Conf. Ser. 96 (2008) Art. No. 012138 .

7. Chang SC, Lin HP, Synchronization with particular application to the control of a chaotic electromagnetic system, P. I. Mech. Eng. G - J. Aer. 222 (2008) 1047-1053.

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M. Perc, M. Marhl

Evolutionary and dynamical coherence resonances in the pair approximated prisoner's dilemma game


New Journal of Physics
8 (2006) Art. No. 142

 

Citiran v:

1. Perc M, Double resonance in cooperation induced by noise and network variation for an evolutionary prisoner's dilemma, New J. Phys. 8 (2006) Art. No. 183.

2. Perc M, Premature seizure of traffic flow due to the introduction of evolutionary games, New J. Phys. 9 (2007) Art. No. 3.

3. Perc M, Transition from Gaussian to Levy distributions of stochastic payoff variations in the spatial prisoner's dilemma game, Phys. Rev. E 75 (2007) Art. No. 022101.

4. Wu ZX, Wang YH, Cooperation enhanced by the difference between interaction and learning neighborhoods for evolutionary spatial prisoner's dilemma games, Phys. Rev. E 75 Art. No. 041114.

5. Szabo G, Fath G, Evolutionary games on graphs, Phys. Rep. 446 (2007) 97-216.

6. Perc M, Szolnoki A, Noise-guided evolution within cyclical interactions, New J. Phys. 9 (2007) Art. No. 267.

7. Tanimoto J, Promotion of cooperation by payoff noise in a 2x2 game, Phys. Rev. E 76 (2007) Art. No. 041130.

8. Perc M, Uncertainties facilitate aggressive behavior in a spatial hawk-dove game, Int. J. Bifurcat. Chaos 17 (2007) 4223-4227.

9. Chen XJ, Wang L, Promotion of cooperation induced by appropriate payoff aspirations in a small-world networked game, Phys. Rev. E 77 (2008) Art. No. 017103.

10. Gosak M, Marhl M, Perc M, Chaos between stochasticity and periodicity in the prisoner's dilemma game, Int. J. Bifurcat. Chaos 18 (2008) 869-875.

11. Chen XJ, Fu F, Wang L, Promoting cooperation by local contribution under stochastic win-stay-lose-shift mechanism, Physica A 387 (2008) 5609-5615.

12. Fu F, Hauert C, Nowak MA, Wang L, Reputation-based partner choice promotes cooperation in social networks, Phys. Rev. E 78 (2008) Art. No. 026117.

13. Rohl T, Traulsen A, Claussen JC, Schuster HG, Stochastic gain in finite populations, Phys. Rev. E 78 (2008) Art. No. 026108.

14. Liu FM, Ding YS, Dynamics Analysis of Trust Computing Evolution in P2P Networks, Proceedings of the International Conference on Signal Image Technologies & Internet Based Systems (2008) pp. 200-205.

15. Chen XJ, Fu F, Wang L, Effects of Learning Activity on Cooperation in Evolutionary Prisoner's Dilemma Game, Int. J. Mod. Phys. C 19 (2008) 1377-1387.

16. Chen X, Fu F, Wang L, Interaction stochasticity supports cooperation in spatial Prisoner's dilemma, Phys. Rev. E 78 (2008) Art. No. 051120.

17. Altrock PM, Traulsen A, Fixation times in evolutionary games under weak selection, New J. Phys. 11 (2009) Art. No. 013012.

18. Fu F, Wu T, Wang L, Partner switching stabilizes cooperation in coevolutionary prisoner's dilemma, Phys. Rev. E 79 (2009) Art. No. 036101.

19. Yang DP, Shuai JW, Lin H, Wu CX, Individual's strategy characterized by local topology conditions in prisoner's dilemma on scale-free networks, Physica A 388 (2009) 2750-2756.

20. Yang DP, Lin H, Wu CX, Shuai JW, Effect of mortality selection on the emergence of cooperation with network dynamics, New J. Phys. 11 (2009) Art. No. 073048.

21. Wu ZX, Holme P, Effects of strategy-migration direction and noise in the evolutionary spatial prisoner's dilemma, Phys. Rev. E 80 (2009) Art. No. 026108.

22. Wu ZX, Rong ZH, Holme P, Diversity of reproduction time scale promotes cooperation in spatial prisoner's dilemma games, Phys. Rev. E 80 (2009) Art. No. 036106.

23. Jiang LL, Zhao M, Yang HX, Wakeling J, Wang BH, Zhou T, Reducing the heterogeneity of payoffs: An effective way to promote cooperation in the prisoner's dilemma game, Phys. Rev. E 80 (2009) Art. No. 031144.

24. Du WB, Cao XB, Hu MB, Wang WX, Asymmetric cost in snowdrift game on scale-free networks, EPL 87 (2009) Art. No. 60004.

25. Du WB, Cao XB, Hu MB, The effect of asymmetric payoff mechanism on evolutionary networked prisoner's dilemma game, Physica A 388 (2009) 5005-5012.

26. Perc M, Szolnoki A, Coevolutionary games-A mini review. BioSystems 99 (2010) 109-125.

27. Jia CX, Liu RR, Yang HX, Wang BH, Effects of fluctuations on the evolution of cooperation in the prisoner's dilemma game. EPL 90 (2010) Art. No. 30001.

28. Sun JT, Wang SJ, Huang ZG, Yang L, Do Y, Wang YH, Effect of information transmission on cooperative behavior. New J. Phys. 12 (2010) Art. No. 063034.

29. Rong ZH, Wu ZX, Wang WX, Emergence of cooperation through coevolving time scale in spatial prisoner's dilemma. Phys. Rev. E 82 (2010) Art. No. 026101.

30. Wang Z, Perc M, Aspiring to the fittest and promotion of cooperation in the prisoner's dilemma game. Phys. Rev. E 82 (2010) Art. No. 021115.

31. Camargo-Gamboa G, Huerta-Quintanilla R, Rodriguez-Achach M, Ecological competition and the role of an apex predator. Physica A 389 (2010) 4075-4080.

32. Liu RR, Rong ZH, Jia CX, Wang BH, Effects of diverse inertia on scale-free-networked prisoner's dilemma games. EPL 91 (2010) Art. No. 20002.

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APS

M. Perc and M. Marhl

Minimal model for spatial coherence resonance

Physical Review E
73 (2006) art. no. 066205

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E. Roux, P.J. Noble, D. Noble, M. Marhl

Modelling of calcium handling in airway myocytes


Progress in Biophysics & Molecular Biology
90 (2006) 64-87

 

Citiran v:

1. Marhl M, Noble D, Roux E, Modeling of molecular and cellular mechanisms involved in Ca2+ signal encoding in airway myocytes, Cell Biochem. Biophys. 46 (2006) 285-302.

2. Hirota S, Helli P, Janssen LJ, Ionic mechanisms and Ca2+ handling in airway smooth muscle, Eur. Respir. J. 30 (2007) 114-133.

3. Corrias A, Buist ML, Quantitative cellular description of gastric slow wave activity, Am. J. Physiol. - Gastr. L. 294 (2008) G989-G995.

4. Marhl M, Gosak M, Perc M, Dixon CJ, Green AK, Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes, J. theor. Biol. 252 (2008) 419-426.

5. Burrowes KS, Swan AJ, Warren NJ, Tawhai MH, Towards a virtual lung: multi-scale, multi-physics modelling of the pulmonary system, Philos. T. Roy. Soc. A 366 (2008) 3247-3263.

6. Wang IY, Bai Y, Sanderson MJ, Sneyd J, A Mathematical Analysis of Agonist- and KCI-Induced Ca2+ Oscillations in Mouse Airway Smooth Muscle Cells. Biophys. J. 98 (2010) 1170-1181.

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M. Perc, M. Gosak, M. Marhl

From stochasticity to determinism in the collective dynamics of diffusively coupled cells

Chemical Physics Letters
421 (2006) 106-110

Citiran v:

1. Perc M, Gosak M, Marhl M, Periodic calcium waves in coupled cells induced by internal noise, Chem. Phys. Lett. 437 (2007) 143-147.

2. Gosak M, Marhl M, Perc M, Spatial coherence resonance in excitable biochemical media induced by internal noise, Biophys. Chem. 128 (2007) 210-214.

3. Perc M, Green AK, Dixon CJ, Marhl M, Establishing the stochastic nature of intracellular calcium oscillations from experimental data, Biophys. Chem. 132 (2008) 33-38.

4. Gosak M, Marhl M, Perc M, Chaos out of internal noise in the collective dynamics of diffusively coupled cells, Eur. Phys. J. B 62 (2008) 171-177.

5. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

6. Szekely D, Brennan SC, Mun HC, Conigrave AD, Kuchel PW, Effectors of the frequency of calcium oscillations in HEK-293 cells: wavelet analysis and a computer model, Conference Information: 32nd Annual Meeting of the Australian-Society-for-Biophysics, SEP 28-OCT 01, 2008 Australian Natl Univ, Canberra, Australia. Source: Eur. Biophys. J. Biophys. 39 (2009) Issue: 1 Sp. Iss., pp.: 149-165.

7. Li QS, Li HY, Internal noise-driven circadian oscillator in Drosophila, Biophys. Chem. 145 (2009) 57-63.

8. Solovey G, Dawson SP, Intra-Cluster Percolation of Calcium Signals. PloS ONE 5 (2010) Art. No. e8997.

9. Yi M, Xia KL, Zhan M, Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling. Biophys. Chem. 147 (2010) 130-139.

10. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes. Biophys. Chem. 148 (2010) 42-50.

11. Chignola R, Del Fabbro A, Milotti E, Dynamics of intracellular Ca2+ oscillations in the presence of multisite Ca2+-binding proteins. Physica A 389 (2010) 3172-3178.

12. Shi JC, Signal transduction and amplification in a circadian oscillator: Interaction between two colored noises. J. theor. Biol. 265 (2010) 565-571.

13. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion. Physica A 389 (2010) 3791-3803.

14. Calabrese A, Fraiman D, Zysman D, Dawson SP, Stochastic fire-diffuse-fire model with realistic cluster dynamics. Phys. Rev. E 82 (2010) Art. No. 031910.

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M. Perc, M. Marhl

Pacemaker enhanced noise-induced synchrony in cellular arrays

Physics Letters A
353 (2006) 372-377

Citiran v:

1. Perc M, Stochastic resonance on excitable small-world networks via a pacemaker, Phys. Rev. E 76 (2007) Art. No. 066203.

2. Perc M, Gosak M, Pacemaker-driven stochastic resonance on diffusive and complex networks of bistable oscillators, New J. Phys. 10 (2008) Art. No. 053008.

3. Perc M, Stochastic resonance on weakly paced scale-free networks, Phys. Rev. E 78 (2008) Art. No. 036105.

4. Gosak M, Marhl M, Perc M, Pacemaker-guided noise-induced spatial periodicity in excitable media, Physica D 238 (2009) 506-515.

5. Ozer M, Perc M, Uzuntarla M, Stochastic resonance on Newman-Watts networks of Hodgkin-Huxley neurons with local periodic driving, Phys. Lett A 373 (2009) 964-968.

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M. Marhl, D. Noble, E. Roux

Modeling of molecular and cellular mechanisms involved in Ca2+ signal encoding in airway myocytes

Cell Biochemistry and Biophysics
46 (2006) 285-302

Citiran v:

1. Marhl M, Gosak M, Perc M, Dixon CJ, Green AK, Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes, J. theor. Biol. 252 (2008) 419-426.

2. Burrowes KS, Swan AJ, Warren NJ, Tawhai MH, Towards a virtual lung: multi-scale, multi-physics modelling of the pulmonary system, Philos. T. Roy. Soc. A 366 (2008) 3247-3263.

3. Wang IY, Bai Y, Sanderson MJ, Sneyd J, A Mathematical Analysis of Agonist- and KCI-Induced Ca2+ Oscillations in Mouse Airway Smooth Muscle Cells. Biophys. J. 98 (2010) 1170-1181.

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M. Perc, M. Gosak, M. Marhl

Periodic calcium waves in coupled cells induced by internal noise

Chemical Physics Letters
437 (2007) 143-147

Citiran v:

1. Gosak M, Marhl M, Perc M, Spatial coherence resonance in excitable biochemical media induced by internal noise, Biophys. Chem. 128 (2007) 210-214.

2. Chen HH, Zhang JQ, Liu JQ, Enhancement of neuronal coherence by diversity in coupled Rulkov-map models, Physica A 387 (2008) 1071-1076.

3. Gosak M, Marhl M, Perc M, Chaos out of internal noise in the collective dynamics of diffusively coupled cells, Eur. Phys. J. B 62 (2008) 171-177.

4. Perc M, Gosak M, Pacemaker-driven stochastic resonance on diffusive and complex networks of bistable oscillators, New J. Phys. 10 (2008) Art. No. 053008.

5. Perc M, Gosak M, Kralj S, Stochastic resonance in soft matter systems: combined effects of static and dynamic disorder, Soft Matter 4 (2008) 1861-1870.

6. Lu QS, Gu HG, Yang ZQ, Shi X, Duan LX, Zheng YH, Dynamics of firing patterns, synchronization and resonances in neuronal electrical activities: experiments and analysis, Acta Mech. Sinica 24 (2008) 593-628.

7. Gosak M, Cellular diversity promotes intercellular Ca2+ wave propagation, Biophys. Chem. 139 (2009) 53-56.

8. Wang BH, Lu QS, Lu SJ, Lang XF, Spatiotemporal multiple coherence resonances and calcium waves in a coupled hepatocyte system, Chinese Phys. B 18 (2009) 872-880.

9. Ji L, Lang XF, Li YP, Li QS, Stimulus perturbation induced signal: A case study in mesoscopic intracellular calcium system, Biophys. Chem. 141 (2009) 231-235.

10. Wang Y, Li QS, Luo J, Explicit calcium bursting stochastic resonance, Biophys. Chem. 142 (2009) 40-45.

11. Harris LA, Piccirilli AM, Majusiak ER, Clancy P, Quantifying stochastic effects in biochemical reaction networks using partitioned leaping, Phys. Rev. E 79 (2009) Art. No. 051906.

12. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

13. Li QS, Li HY, Internal noise-driven circadian oscillator in Drosophila, Biophys. Chem. 145 (2009) 57-63.

14. Solovey G, Dawson SP, Intra-Cluster Percolation of Calcium Signals. PloS ONE 5 (2010) Art. No. e8997.

15. Shi JC, The cooperation effect of noise and an external signal on implicit and explicit coherence resonances in the brusselator system. Phys. Scripta 81 (2010) Art. No. 045003.

16. Yi M, Xia KL, Zhan M, Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling. Biophys. Chem. 147 (2010) 130-139.

17. Ma J, Tang J, Zhang AH, Jia Y, Robustness and breakup of the spiral wave in a two-dimensional lattice network of neurons. Science China-Phys. Mech. Astronomy 53 (2010) 672-679.

18. Sun XJ, Lu QS, Spatial coherence resonance induced by coloured noise and parameter diversity in a neuronal network. Chinese Phys. B 19 (2010) Art. No. 040504.

19. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes. Biophys. Chem. 148 (2010) 42-50.

20. Wang CN, Yang LJ, Yuan LH, Ma J, Deformation and death of spiral wave induced by asymmetrical diffusion in elastic media. Communication Nonlin. Sci. Num. Simulation 15 (2010) 3913-3918.

21. Chignola R, Del Fabbro A, Milotti E, Dynamics of intracellular Ca2+ oscillations in the presence of multisite Ca2+-binding proteins. Physica A 389 (2010) 3172-3178.

22. Shi JC, Signal transduction and amplification in a circadian oscillator: Interaction between two colored noises. J. theor. Biol. 265 (2010) 565-571.

23. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion. Physica A 389 (2010) 3791-3803.

24. Ylander PJ, Hanninen P, Modelling of multi-component immunoassay kinetics - A new node-based method for simulation of complex assays. Biophys. Chem. 151 (2010) 105-110.

25. Calabrese A, Fraiman D, Zysman D, Dawson SP, Stochastic fire-diffuse-fire model with realistic cluster dynamics. Phys. Rev. E 82 (2010) Art. No. 031910.

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M. Perc, M. Marhl

Noise-induced spatial dynamics in the presence of memory loss

Physica A
375 (2007) 72-80

Citiran v:

1. Perc M, Gosak M, Marhl M, Periodic calcium waves in coupled cells induced by internal noise, Chem. Phys. Lett. 437 (2007) 143-147.

2. Gosak M, Marhl M, Perc M, Spatial coherence resonance in excitable biochemical media induced by internal noise, Biophys. Chem. 128 (2007) 210-214.

3. Perc M, Green AK, Dixon CJ, Marhl M, Establishing the stochastic nature of intracellular calcium oscillations from experimental data, Biophys. Chem. 132 (2008) 33-38.

4. Gosak M, Marhl M, Perc M, Pacemaker-guided noise-induced spatial periodicity in excitable media, Physica D 238 (2009) 506-515.

5. Ma J, Wang CN, Tang J, Jia Y, Eliminate spiral wave in excitable media by using a new feasible scheme. Communication Nonlin. Sci. Num. Simulation 15 (2010) 1768-1776.

6. Wang CN, Yang LJ, Yuan LH, Ma J, Deformation and death of spiral wave induced by asymmetrical diffusion in elastic media. Communication Nonlin. Sci. Num. Simulation 15 (2010) 3913-3918.

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T. Jagric, M. Marhl, D. Stajer, ST Kocjancic, T. Jagric, M. Podbregar, M. Perc

Irregularity test for very short electrocardiogram (ECG) signals as a method for predicting a successful defibrillation in patients with ventricular fibrillation

Translational Research -
The Journal of Laboratory and Clinical Medicine
149 (2007) 145-151

Citiran v:

1. Perc M, Green AK, Dixon CJ, Marhl M, Establishing the stochastic nature of intracellular calcium oscillations from experimental data, Biophys. Chem. 132 (2008) 33-38.

2. Gosak M, Marhl M, Perc M, Chaos out of internal noise in the collective dynamics of diffusively coupled cells, Eur. Phys. J. B 62 (2008) 171-177.

3. Strohmenger HU, Predicting defibrillation success, Current Opinion in Critical Care 14 (2008) 311-316.

4. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

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D. Devetak, B. Mencinger-Vracko, M, Devetak, M. Marhl, A. Spernjak

Sand as a medium for transmission of vibratory signals of prey in antlions Euroleon nostras (Neuroptera : Myrmeleontidae)

Physiological Entomology
32 (2007) 268-274

Citiran v:

1. Mencinger-Vracko B, Devetak D, Orientation of the pit-building antlion larva Euroleon (Neuroptera, Myrmeleontidae) to the direction of substrate vibrations caused by prey, Zoology 111 (2008) 2-8.

2. Devetak D, Substrate particle size-preference of wormlion Vermileo vermileo (Diptera: Vermileonidae) larvae and their interaction with antlions, Eur. J. Entomol. 105 (2008) 631-635.

3. Scharf I, Golan B, Ovadia O, The effect of sand depth, feeding regime, density, and body mass on the foraging behaviour of a pit-building antlion, Ecol. Entomol. 34 (2009) 26-33.

4. Ruxton GD, Non-visual crypsis: a review of the empirical evidence for camouflage to senses other than vision, Philos. T. R. Soc. B 364 (2009) 549-557.

5. Guillette LM, Hollis KL, Markarian A, Learning in a sedentary insect predator: Antlions (Neuroptera: Myrmeleontidae) anticipate a long wait, Behav. Process. 80 (2009) 224-232.

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M. Gosak, M. Marhl, M. Perc

Spatial coherence resonance in excitable biochemical media induced by internal noise


Biophysical Chemistry
128 (2007) 210-214

Citiran v:

1. Tuckwell HC, Nonlinear effects in white-noise driven spatial diffusion: General analytical results and probabilities of exceeding threshold, Physica A 387 (2008) 1455-1463.

2. Perc M, Gosak M, Pacemaker-driven stochastic resonance on diffusive and complex networks of bistable oscillators, New J. Phys. 10 (2008) Art. No. 053008.

3. Sun XJ, Perc M, Lu QS, Lu QS, Kurths J, Spatial coherence resonance on diffusive and small-world networks of Hodgkin-Huxley neurons, Chaos 18 (2008) Art. No. 023102.

4. Tuckwell HC, Analytical and Simulation Results for the Stochastic Spatial Fitzhugh-Nagumo Model Neuron, Neural Comput. 20 (2008) 3003-3033.

5. Lu QS, Gu HG, Yang ZQ, Shi X, Duan LX, Zheng YH, Dynamics of firing patterns, synchronization and resonances in neuronal electrical activities: experiments and analysis, Acta Mech. Sinica 24 (2008) 593-628.

6. Gosak M, Cellular diversity promotes intercellular Ca2+ wave propagation, Biophys. Chem. 139 (2009) 53-56.

7. Li QS, Li HY, Internal noise-driven circadian oscillator in Drosophila, Biophys. Chem. 145 (2009) 57-63.

8. Xie YH, Gong YB, Hao YH, Ma XG, Synchronization transitions on complex thermo-sensitive neuron networks with time delays, Biophys. Chem. 146 (2010) 126-132.

9. Wang CN, Ma J, Tang J, Li YL, Instability and Death of Spiral Wave in a Two-Dimensional Array of Hindmarsh-Rose Neurons, Commun. Theor. Phys. 53 (2010) 382-388.

10. Yi M, Xia KL, Zhan M, Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling, Biophys. Chem. 147 (2010) 130-139.

11. Sun XJ, Lu QS, Spatial coherence resonance induced by coloured noise and parameter diversity in a neuronal network, Chin. Phys. B, 19 (2010) Art. No.: 040504.

12. Chignola R, Del Fabbro A, Milotti E, Dynamics of intracellular Ca2+ oscillations in the presence of multisite Ca2+-binding proteins, Physica A 389 (2010) 3172-3178.

13. Shi JC, Signal transduction and amplification in a circadian oscillator: Interaction between two colored noises, J. theor. Biol. 265 (2010) 565-571.

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M. Marhl, V. Grubelnik

Role of cascades in converting oscillatory signals into stationary step-like responses

Biosystems
87 (2007) 58-67

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B. Knoke, M. Marhl, M. Perc, S. Schuster

Equality of average and steady-state levels in some nonlinear models of biological oscillations


Theory in Biosciences
127 (2008) 1-14

Citiran v:

1. Zhu XL, Sang JP, Wang LL, Huang SY, Zou XW, Structure properties and synchronizability of cobweb-like networks, Physica A 387 (2008) 6646-6656.

2. Knoke B, Bodenstein C, Marhl M, Perc M, Schuster S, Jensen's inequality as a tool for explaining the effect of oscillations on the average cytosolic calcium concentration, Theor. Biocsi. 129 (2010) 25-38.

3. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

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M. Gosak, M. Marhl, M. Perc

Chaos out of internal noise in the collective dynamics of diffusively coupled cells


European Physical Journal B
62 (2008) 171-177

Citiran v:

1. Wang Y, Li QS, Luo J, Explicit calcium bursting stochastic resonance, Biophys. Chem. 142 (2009) 40-45.

2. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

3. Szekely D, Brennan SC, Mun HC, Conigrave AD, Kuchel PW, Effectors of the frequency of calcium oscillations in HEK-293 cells: wavelet analysis and a computer model, Conference Information: 32nd Annual Meeting of the Australian-Society-for-Biophysics, SEP 28-OCT 01, 2008 Australian Natl Univ, Canberra, Australia. Source: Eur. Biophys. J. Biophys. 39 (2009) Issue: 1 Sp. Iss., pp.: 149-165.

4. Li QS, Li HY, Internal noise-driven circadian oscillator in Drosophila, Biophys. Chem. 145 (2009) 57-63.

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M. Perc, A.K. Green, C.J. Dixon, M. Marhl

Establishing the stochastic nature of intracellular calcium oscillations from experimental data


Biophysical Chemistry
132 (2008) 33-38

Citiran v:

1. Dupont G, Abou-Lovergne A, Combettes L, Stochastic aspects of oscillatory Ca2+ dynamics in hepatocytes, Biophys. J. 95 (2008) 2193-2202 .

2. Chao AC, Li HY, Chuang GS, Ho PY, A Positive Real Eigenvalue Condition for the Determination of Unstable Steady States in Chemical Reaction Networks, Z. Naturforsch. A 63 (2008) 778-790.

3. Liu JL, Brazier-Hicks M, Edwards R, A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana, Biophys. Chem. 143 (2009) 85-94.

4. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

5. Dupont G, Combettes L, What can we learn from the irregularity of Ca2+ oscillations? Chaos 19 (2009) Art. No.: 037112.

6. Skupin A, Falcke M, From puffs to global Ca2+ signals: How molecular properties shape global signals, Chaos 19 (2009) Art. No.: 037111.

7. Falcke M, Introduction to Focus Issue: Intracellular Ca2+ Dynamics- A Change of Modeling Paradigm? Chaos 19 (2009) Art. No.: 037101.

8. Szekely D, Brennan SC, Mun HC, Conigrave AD, Kuchel PW, Effectors of the frequency of calcium oscillations in HEK-293 cells: wavelet analysis and a computer model, Conference Information: 32nd Annual Meeting of the Australian-Society-for-Biophysics, SEP 28-OCT 01, 2008 Australian Natl Univ, Canberra, Australia. Source: Eur. Biophys. J. Biophys. 39 (2009) Issue: 1 Sp. Iss., pp.: 149-165.

9. Hazledine S, Sun J, Wysham D, Downie AJ, Oldroyd GED, Morris RJ, Nonlinear time series analysis of nodulation factor induced calcium oscillations: Evidence for deterministic chaos? PLoS ONE 4 (2009) Art. No. e6637.

10. Xie YH, Gong YB, Hao YH, Ma XG, Synchronization transitions on complex thermo-sensitive neuron networks with time delays, Biophys. Chem. 146 (2010) 126-132.

11. Solovey G, Dawson SP, Intra-Cluster Percolation of Calcium Signals, PLoS ONE 5 (2010) Art. No. e8997.

12. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes, Biophys. Chem. 148 (2010) 42-50.

13. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion, Physica A 389 (2010) 3791-3803.

14. Stratton RC, Squires PE, Green AK, 17 beta-Estradiol Elevates cGMP and, via Plasma Membrane Recruitment of Protein Kinase GI alpha, Stimulates Ca2+ Efflux from Rat Hepatocytes, J. Biol. Chem. 285 (2010) 27201-27212.

15. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

16. Calabrese A, Fraiman D, Zysman D, Dawson SP, Stochastic fire-diffuse-fire model with realistic cluster dynamics. Phys. Rev. E 82 (2010) Art. No. 031910.

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M. Marhl, M. Gosak M, M. Perc, C.J. Dixon, Green AK

Spatio-temporal modelling explains the effect of reduced plasma membrane Ca2+ efflux on intracellular Ca2+ oscillations in hepatocytes


Journal of Theoretical Biology
252 (2008) 419-426

Citiran v:

1. Dupont G, Abou-Lovergne A, Combettes L, Stochastic aspects of oscillatory Ca2+ dynamics in hepatocytes. Biophys. J. 95 (2008) 2193-2202.

2. Dupont G, Combettes L, What can we learn from the irregularity of Ca2+ oscillations? Chaos 19 (2009) Art. No.: 037112.

3. Szekely D, Brennan SC, Mun HC, Conigrave AD, Kuchel PW, Effectors of the frequency of calcium oscillations in HEK-293 cells: wavelet analysis and a computer model, Conference Information: 32nd Annual Meeting of the Australian-Society-for-Biophysics, SEP 28-OCT 01, 2008 Australian Natl Univ, Canberra, Australia. Source: Eur. Biophys. J. Biophys. 39 (2009) Issue: 1 Sp. Iss., pp.: 149-165.

4. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion. Physica A 389 (2010) 3791-3803.

5. Stratton RC, Squires PE, Green AK, 17 beta-Estradiol Elevates cGMP and, via Plasma Membrane Recruitment of Protein Kinase GI alpha, Stimulates Ca2+ Efflux from Rat Hepatocytes. J. Biol. Chem. 285 (2010) 27201-27212.

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M. Perc, M. Rupnik, M. Gosak, M. Marhl

Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine


Chaos
19 (2009) art. no. 037113

Citiran v:

1. Falcke M, Introduction to Focus Issue: Intracellular Ca2+ Dynamics- A Change of Modeling Paradigm? Chaos 19 (2009) Art. No.: 037101.

2. Marhl M, Gosak M, Perc M, Roux E, Importance of cell variability for calcium signaling in rat airway myocytes. Biophys. Chem. 148 (2010) 42-50.

3. Yi M, Liu QA, Michaelis-Menten mechanism for single-enzyme and multi-enzyme system under stochastic noise and spatial diffusion. Physica A 389 (2010) 3791-3803.

4. Wlodkowic D, Cooper JM, Microfabricated analytical systems for integrated cancer cytomics, Analytic. Bioanalytic. Chem. 398 (2010) 193-209.

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M. Gosak, M. Marhl, M. Perc

Pacemaker-guided noise-induced spatial periodicity in excitable media


Physica D
238 (2009) 506-515

Citiran v:

1. Perc M, Rupnik M, Gosak M, Marhl M, Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine, Chaos 19 (2009) Art. No.: 037113.

2. Yi M, Xia KL, Zhan M, Theoretical study for regulatory property of scaffold protein on MAPK cascade: A qualitative modeling. Biophys. Chem. 147 (2010) 130-139.

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V. Grubelnik, B. Dugonik, D. Osebik, M. Marhl

Signal amplification in biological and electrical engineering systems: Universal role of cascades

Biophysical Chemistry
143 (2009) 132-138

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B. Knoke, C. Bodenstein, M. Marhl, M. Perc, S. Schuster

Jensen's inequality as a tool for explaining the effect of oscillations on the average cytosolic calcium concentration


Theory in Biosciences
129 (2010) 25-38

Citiran v:

1. Bodenstein C, Knoke B, Marhl M, Perc M, Schuster S, Using Jensen's inequality to explain the role of regular calcium oscillations in protein activation. Phys. Biol. 7 (2010) Art. No. 036009.

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