Formal executable models of cell signaling primitives

Proceedings - ISoLA 2006: 2nd International Symposium on Leveraging Applications of Formal Methods, Verification and Validation

Volumn , Issue , 2006, Pages 298-302

  Talcott, Carolyn ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77956432671     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ISoLA.2006.66     Document Type: Conference Paper

References (27)

1. J. M. Kyriakis and J. Avruch, "Mammalian mitogen-activated protein ki-nase signal transduction pathways activated by stress and inflammation," Physiol. Rev., vol. 81, pp. 807-869, 2001.
2. G. P. et al., "Mitogen-activated protein (MAP) kinase pathways: regulation and physiological functions," Endocr. Rev., pp. 153-183, 2001.
3. J. E. D. et al., "Cross signaling, cell specificity, and physiology," Am. J. Physiol. Cell. Physiol., vol. 283, pp. C2-C28, 2002.
4. J. Jordan, E. Landau, and R. Iyengar, "Signaling networks: The origins of cellular multitasking," Cell, vol. 103, pp. 193-200, 2000.
5. K. W. Kohn, "Molecular interaction map of the mammalian cell cycle control and DNA repair systems," Mol Biol Cell, vol. 10, pp. 2703-2734, 1999.
6. D. Fambrough, K. McClure, A. Kazlauskas, and E. S. Lander, "Diverse signaling pathways activated by growth factor receptors induce broadly overlapping, rather than independent, sets of genes," Cell, vol. 97, pp. 727-741, 1999.
7. T. Pawson and T. M. Saxton, "Signaling networks-do all roads lead to the same genes?" Cell, vol. 97, pp. 675-678, 1999.
8. A. Gschwind, E. Zwick, N. Prenzel, M. Leserer, and A. Ullrich, "Cell communication networks: epidermal growth factor receptor transactivation as the paradigm for interreceptor signal transmission," Oncogene, vol. 20, pp. 1594-1600, 2001.
9. Y. Yarden and M. X. Sliwkowski, "Untangling the erbb signalling network," Nature Review Molecular Cell Biology, vol. 2, pp. 127-137, 2001.
10. S. Eker, M. Knapp, K. Laderoute, P. Lincoln, J. Meseguer, and K. Sonmez, "Pathway Logic: Symbolic analysis of biological signaling," in Proceedings of the Pacific Symposium on Biocomputing, January 2002, pp. 400-412. [Online]. Available: http://www.csl.sri.com/papers/lincoln-pathway-logic-psb- 2002/
11. S. Eker, M. Knapp, K. Laderoute, P. Lincoln, and C. Talcott, "Pathway Logic: Executable models of biological networks," in Fourth International Workshop on Rewriting Logic and Its Applications (WRLA'2002), Pisa, Italy, September 19 - 21, 2002, ser. Electronic Notes in Theoretical Computer Science, vol. 71. Elsevier, 2002, http://www.elsevier.nl/locate/entcs/ volume71.html.
12. C. Talcott, S. Eker, M. Knapp, P. Lincoln, and K. Laderoute, "Pathway logic modeling of protein functional domains in signal transduction," in Proceedings of the Pacific Symposium on Biocomputing, January 2004.
13. C. Talcott and D. L. Dill, "The pathway logic assistant," in Third International Workshop on Computational Methods in Systems Biology, G. Plotkin, Ed., 2005, pp. 228-239.
14. J. Meseguer, "Conditional Rewriting Logic as a unified model of concurrency," Theoretical Computer Science, vol. 96, no. 1, pp. 73-155, 1992.
15. R. Hofestädt, "A Petri net application to model metabolic processes," Syst. Anal. Mod. Simul., vol. 16, pp. 113-122, 1994.
16. V. N. Reddy, M. N. Liebmann, and M. L. Mavrovouniotis, "Qualitative analysis of biochemical reaction systems," Comput. Biol. Med., vol. 26, pp. 9-24, 1996.
17. I. Zevedei-Oancea and S. Schuster, "Topological analysis of metabolic networks based on Petri net theory," In Silico Biology, vol. 3, no. 0029, 2003. [Online]. Available: \url{http://www.bioinfo.de/isb/abstracts/ 03/0029.html}
18. A. Regev, W. Silverman, and E. Shapiro, "Representation and simulation of biochemical processes using the pi-calculus process algebra," in Pacific Symposium on Biocomputing, R. B. Altman, A. K. Dunker, L. Hunter, and T. E. Klein, Eds., vol. 6. World Scientific Press, 2001, pp. 459-470.
19. C. Priami, A. Regev, E. Shapiro, and W. Silverman, "Application of a stochastic name-passing calculus to representation and simulation of molecular processes," Information Processing Letters, 2001, in press.
20. M. Calder, V. Vyshemirsky, D. Gilbert, and R. Orton, "Analysis of signalling pathways using the PRISM model checker," in Proceedings of the Third International Conference on Computational Methods in System Biology, G. Plotkin, Ed., 2005.
21. A. Hinton, M. Kwiatkowska, G. Norman, and D. Parker, "PRISM: A tool for automatic verification of probabilistic systems," in 12th International Conference on Tools and Algorithms for the Construction and Analysis of Systems (TACAS'06), ser. Lecture Notes in Computer Science, H. Hermanns and J. Palsberg, Eds., vol. 3920. Springer, 2006, pp. 441-444.
22. A. Regev, E. Panina, W. Silverman, L. Cardelli, and E. Shaprio, "Bioambients: An abstraction for biological compartments," 2003, to appear TCS.
23. F. Nielson, H. R. Nielson, C. Priami, and D. Rosa, "Control flow analysis for bioambients," in BioConcur, 2003.
24. L. Cardelli, "Brane calculi interactions of biological membranes," in Computational Methods in Systems Biology. Springer, 2004.
25. S. Efroni, D. Harel, and I. Cohen, "Towards rigorous comprehension of biological complexity: Modeling, execution and visualization of thymic t-cell maturation," Genome Research, 2003, Special issue on Systems Biology, in press.
26. N. Kam, D. Harel, H. Kugler, R. Marelly, A. Pnueli, J. Hubbard, and M. Stern, "Formal modeling of C.elegans development: A scenario-based approach," in First International Workshop on Computational Methods in Systems Biology, ser. Lecture Notes in Computer Science, vol. 2602. Springer, 2003, pp. 4-20.
27. N. Chabrier-Rivier, M. Chiaverini, V. Danos, F. Fages, and V. Schächter, "Modeling and querying biomolecular interaction networks," 2004, to appear in TCS. [Online]. Available: \url{http://pauillac.inria.fr/%7Efages/Papers/CCDFS04tcs.pdf}