Models of Cellular Regulation

Models of Cellular Regulation

Volumn , Issue , 2008, Pages 1-194

  Aguda, Baltazar ^a   Friedman, Avner ^a  

^a OHIO STATE UNIVERSITY   (United States)

Author keywords

Biological processes; Biomolecules; Cell cycle; Cell death; Cell senescence; Cells; Differentiation; Dna replication; Gene regulatory networks; Human genome

Indexed keywords

EID: 67349134905     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1093/acprof:oso/9780198570912.001.0001     Document Type: Book

References (72)

1. Aguda, B. D. and Tang, Y. 1999. 'The kinetic origins of the restriction point in the mammalian cell cycle', Cell Proliferation 32, 321-335.
2. Aguda, B. D. )1999a). 'Instabilities in phosphorylation-dephosphorylation cascades and cell cycle checkpoints', Oncogene 18, 2846-2851.
3. Aguda, B. D. )1999b). 'A quantitative analysis of the kinetics of the G2 DNA damage checkpoint system', Proceedings of the National Academy of Sciences of the USA 96, 11352-11357.
4. Bartek, J. and Lukas, J. 2001. 'Mammalian G1- and S-phase checkpoints in response to DNA damage', Current Opinion in Cell Biology 13, 738-747.
5. Doncic, A., Ben-Jacob, E. and Barkai, N. 2006. 'Evaluating putative mechanisms of the mitotic spindle checkpoint', Proceedings of the National Academy of Sciences of the USA 102, 6332-6337.
6. Ekholm, S. V., Zickert, P., Reed, S. I., Zetterberg, A. (2001). 'Accumulation of cyclin E is not a prerequisite for passage through the restriction point,', Molecular Cell Biology 21, 3256-3265.
7. Elledge, S. J. 1996. 'Cell cycle checkpoints: preventing an identity crisis', Science 274, 1664-1672.
8. Pines, J. (1999) 'Four-dimensional control of the cell cycle,' Nature Cell Biology 1, E73-E79.
9. Pardee, A. B. 1974. 'A Restriction Point for Control of Normal Animal Cell Proliferation', Proceedings of the National Academy of Sciences of the USA 71, 1286-1290.
10. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002) Molecular biology of the cell, 4th edn. Garland Science, New York.
11. Roeder, I. (2003) 'Dynamical Modeling of Hematopoietic Stem Cell Organization', PhD Thesis, University of Leipzig, Germany.
12. Op den Buijs, J., Musters, M., Verrips, T., Post, J. A., Braam, B. and van Riel, N. (2004). 'Mathematical modeling of vascular endothelial layer maintenance: the role of endothelial cell division, progenitor cell homing, and telomere shortening', American Journal of Physiology, Heart and Circulatory Physiology 287, H2651-H2658.
13. Roeder, I. and Loeffler, M. (2002). 'A novel dynamic model of hematopoietic stem cell organization based on the concept of within-tissue plasticity,', Experimental Hematology 30, 853-861.
14. Wang, Y., Aguda, B. D. and Friedman, A. (2007) A continuum mathematical model of endothelial layer maintenance and senescence. Theoretical Biology and Medical Modelling 4, 30.
15. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. (2002) Molecular biology of the cell, 4th edn. Garland Publishing, New York.
16. Beere, H. M. (2005). 'Death versus survival: functional interaction between the apoptotic and stress-inducible heat shock protein pathways,', Journal of Clinical Investigation 115, 2633-2639.
17. Eissing, T., Conzelmann, H., Gilles, E. D., Allgower, F., Bullinger, E., Scheurich, P. (2004) 'Bistability analyses of a caspase activation model for receptor-induced apoptosis', Journal of Biological Chemistry. 279, 36892-36897.
18. Fussenegger, M., Bailey, J. E., and Varner, J. (2000). 'A mathematical model of caspase function in apoptosis,', Nature Biotechnology 18, 768-774.
19. Lai, R. and Jackson, T. L. (2004). 'A mathematical model of receptor-mediated apoptosis: dying to know why FASL is a trimer,', Mathematical Biosciences and Engineering 1, 325-338.
20. Legewie, S., Bluthgen, N., and Herzel, H. (2006) 'Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability,' PLoS Computational Biology 2(9), e120.
21. Philchenkov, A. (2004). 'Caspases: potential targets for regulating cell death,', Journal of Cellular and Molecular Medicine 8, 432-444.
22. Ashe, H. L. and Briscoe, J. 2006. 'The interpretation of morphogen gradients', Development 133, 385-394.
23. Cinquin, O. and Demongeot, J. 2005. 'High-dimensional switches and the modeling of cellular differentiation', Journal of Theoretical Biology 233, 391-411.
24. Mariani, L., Lohning, M., Radbruch, A., and Hofer, T. 2004. 'Transcriptional control networks of cell differentiation: insights from helper T lymphocytes', Progress in Biophysics & Molecular Biology 86, 45-76.
25. Yates, A., Callard, R., and Stark J. 2004. 'Combining cytokine signalling with T-bet and GATA-3 regulation in TH1 and Th2 differentiation: a model for cellular decision-making', Journal of Theoretical Biology 231, 181-196.
26. Browning, S. T., Castellanos, M., and Shuler, M. L. (2004). 'Robust control of initiation of prokaryotic chromosome replication: Essential considerations for a minimal cell,', Biotechnology and Bioengineering 88, 575-584.
27. Hansen, F. G., Christensen, B. B., and Atlung, T. (1991). 'The initiator titration model: computer simulation of chromosome and minichromosome control,', Research in Microbiology 142, 161-167.
28. Mahaffy, J. M. and Zyskind, J. W. (1989). 'A model for the initiation of replication in Escherichia coli,', Journal of Theoretical Biology 140, 453-477.
29. Pritchard, R. H., Barth, P. T., and Collins, J. (1969). 'Control of DNA synthesis in bacteria,', Symposium of the Society for General Microbiology 19, 263-297.
30. Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K., and Walter, P. (2002) Molecularbiology of the cell. 4th edn. Garland Science, New York.
31. Cooper, G. M. and Hausman, R. E. (2006) The cell: a molecular approach. 4th edn. Sinauer Associates, Inc., Sunderland, MA, USA.
32. Harold, F. M. (2001) The way of the cell: molecules, organisms and the order of life. Oxford University Press, New York, NY.
33. Judson, H. F. (1996) The eighth day of creation: makers of the revolution in biology. Cold Spring Harbor Laboratory Press.
34. Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. E. (1999) Molecular cell biology W. H. Freeman & Co., New York, NY.
35. Guckenheimer, J. and Holmes, P. (1983) Nonlinear oscillations, dynamical systems, and bifurcation of vector fields. Springer Verlag, New York.
36. Kitano, H. 2004. 'Biological Robustness', Nature Reviews Genetics 5, 826-837.
37. Nicolis, G. and Prigogine, I. (1977) Self-organization in nonequilibrium systems. Wiley, New York.
38. Ross, J., Muller, S. C. and Vidal, C. 1988. 'Chemical Waves', Science 240, 460-465.
39. Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D., and Darnell, J. E. (1999) Molecular cell biology. W. H. Freeman & Co., New York.
40. Ma, H-W., Buer, J., and Zeng, A.-P. (2004) 'Hierarchical structure and modules in the Escherichia coli transcriptional regulatory network revealed by a new top-down approach,' BMC Bioinformatics 5, 199.
41. Martinez-Antonio, A., Janga, S. C., Salgado, H., and Collado-Vides, J. (2006). 'Internalsensing machinery directs the activity of the regulatory network in Escherichia coli,', Trends in Microbiology 14, 22-27.
42. Ozbudak, E. M., Thattai, M., Lim, H. N., Shraiman, B. I., and van Oudenaarden, A. (2004). 'Multistability in the lactose utilization network of Escherichia coli,', Nature 427, 737-740.
43. Santillan, M., Mackey, M. C., and Zeron, E. S. (2007). 'Origin of Bistability in the lac Operon,', Biophysical Journal 92, 3830-3842.
44. Santillan, M. and Zeron, E. S. (2004). 'Dynamic influence of feedback enzyme inhibition and transcription attenuation on the tryptophan operon response to nutritional shifts,', Journal of Theoretical Biology 231, 287-298.
45. Clarke, B. L. 1980. 'Stability of Complex Reaction Networks', Advances in Chemical Physics 43, 1-215.
46. Feinberg, M. (1980) 'Lectures on Chemical Reaction Networks.' Technical Report of the Mathematics Research Center, University of Wisconsin-Madison.
47. Gillespie, D. T. (1976). 'A general method for numerically simulating the stochastic time evolution of coupled chemical reactions,', Journal of Computational Physics 22, 403-434.
48. Gillespie, D. T. 1977. 'Exact stochastic simulation of coupled chemical reactions', Journal of Physics Chemistry 81, 2340-2361.
49. Gillespie, D. T. (2001). 'Approximate accelerated stochastic simulation of chemically reacting systems,', Journal of Chemical Physics 115, 1716-1733.
50. Goldbeter, A. (1996) Biochemical oscillations and cellular rhythms. Cambridge University Press.
51. Guckenheimer, J. and Holmes, P. (1983). Nonlinear oscillations, dynamical systems, and bifurcation of vector fields, Springer Verlag, New York.
52. Kurtz, T. G. (1972)'The relationship between stochastic and deterministic models for chemical reactions,' Chemical Physics 57, 2976-2978.
53. Oppenheim, I., Shuler, K. E., and Weiss, G. H. (1969). 'Stochastic and deterministic formulation of chemical rate equations,', Journal of Chemical Physics 50, 460-466.
54. Bazaliy, B. and Friedman, A. 2003. 'A free boundary problem for an ellipticparabolic system: Application to a model of tumor growth', Communications in Partial Differential Equations 28, 517-560.
55. Chen, X. and Friedman, A. 2003. 'A free boundary problem for an elliptic-hyperbolic system: An application to tumor growth', SIAM Journal of Mathematical Analysis 35, 974-986.
56. Cui, S. and Friedman, A. 2003. 'A hyperbolic free boundary problem modeling of tumor growth', Interfaces and Free Boundaries 5, 159-182.
57. Dorie, M. J., Kallman, R. F., and Coyne, M. A. 1986. 'Effect of cytochalasin b, nocodazole and irradiation on migration and internalization of cells and microspheres in tumor cell spheroids', Experimental Cell Research 166, 370-378.
58. Dorie, M. J., Kallman, R. F., Rapacchietta, D. F., van Antwer, D., and Huang, Y. R. 1982. 'Migration and internalization of cells and polystyrene microspheres in tumor cell spheroids', Experimental Cell Research 141, 201-209.
59. Fontelos, M. A. and Friedman, A. 2003. 'Symmetry-breaking bifurcations of free boundary problems in three dimensions', Asymptotic Analysis 35, 187-206.
60. Friedman, A. (2006) 'Cancer models and their mathematical analysis', in Tutorials in mathematical biosciences III (A. Friedman, ed.). Springer-Verlag, Berlin. 223-246.
61. Friedman, A. and Reitich, F. 1999. 'Analysis of a mathematical model for growth of tumors', Journal of Mathematical Biology 38, 262-284.
62. Hanahan, D. and Weinberg, R. A. 2000. 'The Hallmarks of Cancer', Cell 100, 57-70.
63. Jiang, Y., Pjesivac-Grbovic, J., Cantrell, C., and Freyer, J. P. 2005. 'A Multiscale Model for Avascular Tumor Growth'. Biophysical Journal 89, 3884-3894.
64. Pettet, G., Please, C. P., Tindal, M., and McElwain, D. 2001. 'The migration of cells in multicell tumor spheroids', Bullation of Mathematical Biology 63, 231-257.
65. Ribba, B., Colin, T., and Schnell, S. (2006). 'A multiscale mathematical model of cancer and its use in analyzing irradiation therapies', Theoretical Biology and Medical Modelling 3, 7.
66. Webb, G. F. (1986) 'Logistic models of structured population growth', International Journal of Computational Mathematic and Applications 12A, 527-529.
67. Webb, G. F. 1987. 'An operator-theoretic formulation of asynchronous exponential growth', Transactions of the American Mathematical Society 303, 751-763.
68. Csikasz-Nagy, A., Battogtokh, D., Chen, K. C., Novak, B., and Tyson, J. J., )2006). 'Analysis of a generic model of eukaryotic cell-cycle regulation,', Biophysical Journal 90, 4361-4379.
69. Goldbeter A. (1991). 'A minimal cascade for the mitotic oscillator involving cyclin and cdc2 kinase,', Proceeding of National Academy of Sciences of the USA 88, 9107-9111.
70. Murray, A. W. and Kirschner, M. W. (1989). 'Dominoes and clocks: The union of two views of the cell cycle,', Science 246, 614-621.
71. Novak, B. and Tyson, J. J. (1993). 'Numerical analysis of a comprehensive model of Mphase control in Xenopus oocyte extracts and intact embryos,', Journal of Cell Science 106, 1153-1168.
72. Tyson, J. J. and Novak, B. (2001). 'Regulation of the eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible transitions,', Journal of Theoretical Biology 210, 249-263.