Methods for qualitative analysis of genetic networks

2009 European Control Conference, ECC 2009

Volumn , Issue , 2014, Pages 671-676

  Chaves, Madalena ^a  

^a INRIA   (France)

Author keywords

[No Author keywords available]

Indexed keywords

DEGRADATION;

BIOLOGICAL MODELING; CONTINUOUS DEGRADATIONS; DETAILED KINETICS; GENETIC REGULATORY NETWORKS; MATRIX OF TRANSITION PROBABILITIES; PIECEWISE LINEAR MODELING; QUALITATIVE ANALYSIS; QUALITATIVE DYNAMICS;

PIECEWISE LINEAR TECHNIQUES;

EID: 84955186588     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.23919/ecc.2009.7074480     Document Type: Conference Paper

References (22)

1. S. Kauffman, The origins of order. Oxford University Press (New York), 1993.
2. R. Thomas, "Boolean formalization of genetic control circuits," J. Theor. Biol., vol. 42, pp. 563-585, 1973.
3. R. Thomas and R. D'Ari, Biological feedback. CRC Press, 1990.
4. L. Glass and S. Kauffman, "The logical analysis of continuous, nonlinear biochemical control networks," J. Theor. Biol., vol. 39, pp. 103-129, 1973.
5. L. Sánchez and D. Thieffry, "A logical analysis of the drosophila gapgene system," J. Theor. Biol., vol. 211, pp. 115-141, 2001.
6. H. de Jong, J. Gouzé, C. Hernandez, M. Page, T. Sari, and J. Geiselmann, "Qualitative simulation of genetic regulatory networks using piecewise linear models," Bull. Math. Biol., vol. 66, pp. 301-340, 2004.
7. M. Chaves, R. Albert, and E. Sontag, "Robustness and fragility of boolean models for genetic regulatory networks," J. Theor. Biol., vol. 235, pp. 431-449, 2005.
8. B. Faryabi, J.-F. Chamberland, G. Vahedi, A. Datta, and E. Dougherty, "Optimal intervention in asynchronous genetic regulatory networks," IEEE Journal of Selected Topics in Signal Processing, vol. 2, no. 3, pp. 412-423, 2008.
9. T. Eissing, H. Conzelmann, E. Gilles, F. Allgöwer, E. Bullinger, and P. Scheurich, "Bistability analysis of a caspase activation model for receptor-induced apoptosis," J. Biol. Chem., vol. 279, pp. 36 892-36 897, 2004.
10. T. Eissing, M. Chaves, and F. Allgöwer, "Live and let die-a systems biology view on cell death," Computers & Chemical Engineering, vol. to appear, 2008.
11. N. Danial and S. Korsmeyer, "Cell death: critical control points," Cell, vol. 116, pp. 205-216, 2004.
12. A. Fauré, A. Naldi, C. Chaouiya, and D. Thieffry, "Dynamical analysis of a generic boolean model for the control of the mammalian cell cycle," Bioinformatics, vol. 22, no. 14, pp. e124-e131, 2006.
13. L. Tournier and M. Chaves, "Uncovering operational interactions in genetic networks using asynchronous boolean dynamics," J. Theor. Biol., p. accepted, 2009.
14. W. Feller, An introduction to probability theory and its applications, 3rd ed. New York, Wiley, 1968.
15. H. de Jong, J. Geiselmann, C. Hernandez, and M. Page, "Genetic network analyzer: Qualitative simulation of genetic regulatory networks," Bioinformatics, vol. 19, pp. 336-344, 2003.
16. D. Ropers, H. de Jong, M. Page, D. Schneider, and J. Geiselmann, "Qualitative simulation of the carbon starvation response in Escherichia coli," Biosystems, vol. 84, no. 2, pp. 124-152, 2006.
17. M. Chaves, E. Sontag, and R. Albert, "Methods of robustness analysis for boolean models of gene control networks," IEE Proc. Syst. Biol., vol. 153, pp. 154-167, 2006.
18. M. Chaves, A. Sengupta, and E. Sontag, "Geometry and topology of parameter space: investigating measures of robustness in regulatory networks," J. Math. Biol., vol. 59(3), pp. 315-358, 2009.
19. M. Chaves, T. Eissing, and F. Allgöwer, "Bistable biological systems: a characterization through local compact input-to-state stability," IEEE Trans. Automatic Control, vol. 53, no. 1, pp. 87-100, 2008.
20. E. Sontag and Y. Wang, "On characterizations of the input-to-state stability property with respect to compact sets," in Proc. IFAC Nonlinear Control Symposium (NOLCOS95), Tahoe City, CA, 1995.
21. E. Sontag, "Smooth stabilization implies coprime factorization," IEEE Trans. Automat. Control, vol. 34, pp. 435-443, 1989.
22. E. Sontag and Y. Wang, "On characterizations of the input-to-state stability property," Systems Control Lett., vol. 24, pp. 351-359, 1995.