Qualitative analysis of genetic regulatory networks in bacteria

Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology

Volumn , Issue , 2011, Pages 111-130

  Baldazzi, Valentina ^a   Monteiro, Pedro T ^a   Page, Michel ^a   Ropers, Delphine ^a   Geiselmann, Johannes ^b   De Jong, Hidde ^a  

^a INRIA RHÔNE ALPES   (France)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84871356301     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4419-7964-3_6     Document Type: Chapter

References (79)

1. T. Ali Azam, A. Iwata, A. Nishimura, S. Ueda, and A. Ishihama. Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J. Bacteriol., 181 (20): 6361-6370, 1999.
2. M. Antoniotti, A. Policriti, N. Ugel, and B. Mishra. Model building and model checking for biochemical processes. Cell Biochem. Biophys., 38 (3): 271-286, 2003.
3. C. A. Ball, R. Osuna, K. C. Ferguson, and R. C. Johnson. Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J. Bacteriol., 174 (24): 8043-8056, 1992.
4. G. Batt, D. Ropers, H. de Jong, J. Geiselmann, R. Mateescu, M. Page, and D. Schneider. Validation of qualitative models of genetic regulatory networks by model checking: Analysis of the nutritional stress response in Escherichia coli. Bioinformatics, 21 (Suppl 1): i19-i28, 2005.
5. G. Batt, B. Yordanov, R. Weiss, and C. Belta. Robustness analysis and tuning of synthetic gene networks. Bioinformatics, 23 (18): 2415-2422, 2007.
6. G. Batt, H. de Jong, M. Page, and J. Geiselmann. Symbolic reachability analysis of genetic regulatory networks using discrete abstractions. Automatica, 44 (4): 982-989, 2008.
7. C. Belta and L. C. G. J. M. Habets. Controlling a class of nonlinear systems on rectangles. IEEE Trans. Autom. Control, 51 (11): 1749-1759, 2006.
8. G. Bernot, J.-P. Comet, A. Richard, and J. Guespin. Application of formal methods to biological regulatory networks: Extending Thomas asynchronous logical approach with temporal logic. J. Theor. Biol., 229 (3): 339-348, 2004.
9. K. Bettenbrock, S. Fischer, A. Kremling, K. Jahreis, T. Sauter, and E. D. Gilles. A quantitative approach to catabolite repression in Escherichia coli. J. Biol. Chem., 281 (5): 2578-2584, 2005.
10. K. Bettenbrock, S. Fischer, A. Kremling, K. Jahreis, T. Sauter, and E. D. Gilles. A quantitative approach to catabolite repression in Escherichia coli. J. Biol. Chem., 281 (5): 2578-2584, 2006.
11. M. Calder, V. Vyshemirsky, D. Gilbert, and R. Orton. Analysis of signalling pathways using the PRISM model checker. In G. Plotkin, editor, Proc. of CMSB, pages 179-190, Edinburgh, Scotland, 2005.
12. R. Casey, H. de Jong, and J.-L. Gouze. Piecewise-linear models of genetic regulatory networks: Equilibria and their stability. J. Math. Biol., 52 (1): 27-56, 2006.
13. N. Chabrier-Rivier, M. Chiaverini, V. Danos, F. Fages, and V. Schachter. Modeling and querying biomolecular interaction networks. Theor. Comput. Sci., 325 (1): 25-44, 2004.
14. C. Chassagnole, N. Noisommit-Rizzi, J. W. Schmid, K. Mauch, and M. Reuss. Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol. Bioeng., 79 (1): 53-73, 2002.
15. M. Chaves, E. D. Sontag, and R. Albert. Methods of robustness analysis for Boolean models of gene control networks. IET Syst. Biol., 153 (4): 154-167, 2006.
16. K. C. Chen, L. Calzone, A. Csikasz-Nagy, F. R. Cross, B. Novak, and J. J. Tyson. Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell, 15 (8): 3841-3862, 2004.
17. A. Cimatti, E. Clarke, E. Giunchiglia, F. Giunchiglia, M. Pistore, M. Roveri, R. Sebastiani, and A. Tacchella. NuSMV2: An OpenSource tool for symbolic model checking. In D. Brinksma and K. G. Larsen, editors, 14th International Conference on Computer Aided Verification (CAV 2002), volume 2404 of LNCS, pages 359-364. Springer, Berlin, 2002.
18. E. M. Clarke, O. Grumberg, and D. A. Peled. Model Checking. MIT, Boston, MA, 1999.
19. A. Cornish-Bowden. Fundamentals of Enzyme Kinetics. Portland Press, London, revised edition, 1995.
20. M. Davidich and S. Bornholdt. The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model. J. Theor. Biol., 255: 269-277, 2008.
21. H. de Jong and M. Page. Search for steady states of piecewise-linear differential equation models of genetic regulatory networks. ACM/IEEE Trans. Comput. Biol. Bioinform., 5 (2): 208-222, 2008.
22. H. de Jong and D. Ropers. Strategies for dealing with incomplete information in the modeling of molecular interaction networks. Brief. Bioinform., 7 (4): 354-363, 2006.
23. H. de Jong, J. Geiselmann, C. Hernandez, and M. Page. Genetic Network Analyzer: Qualitative simulation of genetic regulatory networks. Bioinformatics, 19: 336-344, 2003.
24. H. de Jong, J. Geiselmann, G. Batt, C. Hernandez, and M. Page. Qualitative simulation of the initiation of sporulation in B. subtilis. B. Math. Biol., 66 (2): 261-299, 2004a.
25. H. de Jong, J.-L. Gouze, C. Hernandez, M. Page, T. Sari, and J. Geiselmann. Qualitative simulation of genetic regulatory networks using piecewise-linear models. B. Math. Biol., 66 (2): 301-340, 2004b.
26. R. Edwards. Analysis of continuous-time switching networks. Phys. D, 146 (1-4): 165-199, 2000.
27. J. Fisher, N. Piterman, A. Hajnal, and T. A. Henzinger. Predictive modeling of signaling crosstalk during C. elegans vulval development. PLoS Comput. Biol., 3 (5): e92, 2007.
28. T. S. Gardner, C. R. Cantor, and J. J. Collins. Construction of a genetic toggle switch in escherichia coli. Nature, 403 (6767): 339-342, 2000.
29. T. S. Gardner, D. di Bernardo, D. Lorenz, and J. J. Collins. Inferring genetic networks and identifying compound mode of action via expression profiling. Science, 301 (5629): 102-105, 2003.
30. R. Ghosh and C. J. Tomlin. Symbolic reachable set computation of piecewise affine hybrid automata and its application to biological modelling: Delta-Notch protein signalling. IET Syst. Biol., 1 (1): 170-183, 2004.
31. L. Glass and S. A. Kauffman. The logical analysis of continuous non-linear biochemical control networks. J. Theor. Biol., 39 (1): 103-129, 1973.
32. A. Gonzalez Gonzalez, A. Naldi, L. Sanchez, D. Thieffry, and C. Chaouiya. GINsim: a software suit for the qualitative modelling, simulation and analysis of regulatory networks. Biosystems, 84 (2): 91-100, 2006.
33. J.-L. Gouze and T. Sari. A class of piecewise linear differential equations arising in biological models. Dyn. Syst., 17 (4): 299-316, 2002.
34. R. M. Gutierrez-R?os, J. A. Freyre-Gonzalez, O. Resendis, J. Collado-Vides, M. Saier, and G. Gosset. Identification of regulatory network topological units coordinating the genome-wide transcriptional response to glucose in Escherichia coli. BMC Microbiol., 7: 53-53, 2007.
35. A. Halasz, V. Kumar, M. Imielinski, C. Belta, O. Sokolsky, S. Pathak, and H. Rubin. Analysis of lactose metabolism in E. coli using reachability analysis of hybrid systems. IET Syst. Biol., 1 (2): 130-48, 2007.
36. T. Hardiman, K. Lemuth, M. A. Keller, M. Reuss, and M. Siemann-Herzberg. Topology of the global regulatory network of carbon limitation in Escherichia coli. J. Biotechnol., 132: 359-374, 2007.
37. J. J. Heijnen. Approximative kinetic formats used in metabolic network modeling. Biotechnol. Bioeng., 91 (5): 534-545, 2005.
38. R. Heinrich and S. Schuster. The regulation of cellular systems. Chapman & Hall, New York, 1996.
39. G. W. Huisman, M. M. Siegele D. A., Zambrano, and Kolter R. Morphological and physiological changes during stationary phase. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger, editors, Escherichia coli and Salmonella: Cellular and Molecular Biology, pages 1672-1682. ASM, Washington D.C., 1996.
40. H. Ishizuka, A. Hanamura, T. Inada, and H. Aiba. Mechanism of the down-regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene. EMBO J., 13 (13): 3077-3082, 1994.
41. S. A. Kauffman. The origins of order: Self-organization and selection in evolution. Oxford University Press, New York, 1993.
42. S. A. Kauffman. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol., 22 (3): 437-467, 1969.
43. E. Klipp, B. Nordlander, R. Kruger, P. Gennemark, and S. Hohmann. Integrative model of the response of yeast to osmotic shock. Nat. Biotechnol., 23 (8): 975-982, 2005.
44. K. W. Kohn. Molecular interaction maps as information organizers and simulation guides. Chaos, 11 (1): 84-97, 2001.
45. A. Kremling, S. Kremling, and K. Bettenbrock. Catabolite repression in Escherichia coli- A comparison of modelling approaches. FEBS J., 276: 594-602, 2009.
46. L. Kuepfer, M. Peter, U. Sauer, and J. Stelling. Ensemble modeling for analysis of cell signaling dynamics. Nat. Biotechnol., 25 (9): 1001-1006, 2007.
47. J.-C. Leloup and A. Goldbeter. Toward a detailed computational model for the mammalian circadian clock. Proc. Nat. Acad. Sci. USA, 100 (12): 7051-7056, 2003.
48. L. Mendoza, D. Thieffry, and E. R. Alvarez-Buylla. Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis. Bioinformatics, 15 (7-8): 593-606, 1999.
49. T. Mestl, E. Plahte, and S. W. Omholt. A mathematical framework for describing and analysing gene regulatory networks. J. Theor. Biol., 176 (2): 291-300, 1995.
50. T. Millat, E. Bullinger, J. Rohwer, and O. Wolkenhauer. Approximations and their consequences for dynamic modelling of signal transduction pathways. Math. Biosci., 207 (1): 40-57, 2007.
51. C. G. Moles, P. Mendes, and J. R. Banga. Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res., 13 (11): 2467-2474, 2003.
52. P. T. Monteiro, D Ropers, R Mateescu, A. T. Freitas, and H. de Jong. Temporal logic patterns for querying dynamic models of cellular interaction networks. Bioinformatics, 24: i227-i233, 2008.
53. M. S. Okino and M. L. Mavrovouniotis. Simplification of mathematical models of chemical reaction systems. Chem. Rev., 98 (2): 391-408, 1998.
54. J. A. Papin, J. Stelling, N. D. Price, S. Klamt, S. Schuster, and B. O. Palsson. Comparison of network-based pathway analysis methods. Trends Biotechnol., 22 (8): 400-405, 2004.
55. E. Pecou. Splitting the dynamics of large biochemical interaction networks. J. Theor. Biol., 232 (3): 375-384, 2005.
56. E. Plahte and S. Kjoglum. Analysis and generic properties of gene regulatory networks with graded response functions. Phys. D, 201 (1): 150-176, 2005.
57. R. Porreca, S. Drulhe, H. de Jong, and G. Ferrari-Trecate. Structural identification of piecewiselinear models of genetic regulatory networks. J. Comput. Biol., 15 (10): 1365-1380, 2008.
58. T. S. Pratt, T. Steiner, L. S. Feldman, K. A. Walker, and R. Osuna. Deletion analysis of the fis promoter region in Escherichia coli: antagonistic effects of integration host factor and Fis. J. Bacteriol., 179 (20): 6367-6377, 1997.
59. M. Quach, N. Brunel, and F. dAlche Buc. Estimating parameters and hidden variables in nonlinear state-space models based on ODEs for biological networks inference. Bioinformatics, 23 (23): 3209-3216, 2007.
60. Y. Reyes-Dominguez, G. Contreras-Ferrat, J. Ramirez-Santos, J.Membrillo-Hernandez, and M. C. Gomez-Eichelmann. Plasmid DNA supercoiling and gyrase activity in Escherichia coli wildtype and rpoS stationary-phase cells. J. Bacteriol., 185 (3): 1097-1100, 2003.
61. J. M. Rohwer, N. D. Meadow, S. Roseman, H. V. Westerhoff, and P. W. Postma. Understanding glucose transport by the bacterial phosphoenolpyruvate: glycose phosphotransferase system on the basis of kinetic measurements in vitro. J. Biol. Chem., 275 (45): 34909-34921, 2000.
62. M. Ronen, R. Rosenberg, B. I. Shraiman, and U. Alon. Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc. Natl. Acad. Sci. USA, 99 (16): 10555-10560, 2002.
63. D. Ropers, H. de Jong, M. Page, D. Schneider, and J. Geiselmann. Qualitative simulation of the carbon starvation response in Escherichia coli. Biosystems, 84 (2): 124-152, 2006.
64. D. Ropers, V. Baldazzi, and H. de Jong. Model reduction using piecewise-linear approximations preserves dynamic properties of the carbon starvation response in Escherichia coli. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (1): 166-181, 2011.
65. M. R. Roussel and S. J. Fraser. Invariant manifold methods for metabolic model reduction. Chaos, 11 (1): 196-206, 2001.
66. L. Sanchez and D. Thieffry. Segmenting the fly embryo: A logical analysis of the pair-rule crossregulatory module. J. Theor. Biol., 224 (4): 517-537, 2003.
67. M. A. Savageau. Design principles for elementary gene circuits: Elements, methods, and examples. Chaos, 11 (1): 142-159, 2001.
68. B. Schoeberl, C. Eichler-Jonsson, E.-D. Gilles, and G. Mller. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol., 20 (4): 370-375, 2002.
69. J.-A. Sepulchre, S. Reverchon, and W. Nasser. Modeling the onset of virulence in a pectinolytic bacterium. J. Theor. Biol., 44 (2): 239-257, 2007.
70. M. Sugita. Functional analysis of chemical systems in vivo using a logical circuit equivalent: II. The idea of a molecular automaton. J. Theor. Biol., 4: 179-192, 1963.
71. R. Thomas. Boolean formalization of genetic control circuits. J. Theor. Biol., 42 (3): 563-585, 1973.
72. R. Thomas and R. dAri. Biological feedback. CRC, Boca Raton, FL, 1990.
73. R. Thomas and M. Kaufman. Multistationarity, the basis of cell differentiation and memory: II. Logical analysis of regulatory networks in terms of feedback circuits. Chaos, 11 (1): 180-195, 2001.
74. A. Usseglio Viretta and M. Fussenegger. Modeling the quorum sensing regulatory network of human-pathogenic Pseudomonas aeruginosa. Biotechnol. Prog., 20 (3): 670-678, 2004.
75. N. A.W. van Riel and E. D. Sontag. Parameter estimation in models combining signal transduction and metabolic pathways: The dependent input approach. IET Syst. Biol., 153 (4): 263-274, 2006.
76. M. Vilela, I. Chou, S. Vinga, A. Vasconcelos, E. Voit, and J. Almeida. Parameter optimization in S-system models. BMC Syst. Biol., 2: 35, 2008.
77. R. L. Westra, G. Hollanders, G. J. Bex, M. Gyssens, and K. Tuyls. The identification of dynamic gene-protein networks. In K. Tuyls, R. Westra, Y. Saeys, and A. Nowe, editors, Proc. KDECB 2006, volume 4366 of LNCS, pages 157-170. Springer, Berlin, 2007.
78. C.-H. Yuh, H. Bolouri, and E. H. Davidson. Genomic cis-regulatory logic: Experimental and computational analysis of a sea urchin gene. Science, 279: 1896-1902, 1998.
79. J. W. Zwolak, J. J. Tyson, and L. T.Watson. Parameter estimation for a mathematical model of the cell cycle in frog eggs. J. Comput. Biol., 12 (1): 48-63, 2005