Modeling signal transduction using P systems

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4361 LNCS, Issue , 2006, Pages 100-122

  Pǎun, Andrei ^a   Perez Jimenez, Mario J ^b   Romero Campero, Francisco J ^b  

^a Louisiana Tech University   (United States)

^b UNIVERSITY OF SEVILLE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

CELL BEHAVIORS; CELLULAR MODEL; CELLULAR SIGNALLING; COMPUTATIONAL MODELING; EFFECTIVE THERAPY; EPIDERMAL GROWTH FACTOR RECEPTORS; NETWORK FUNCTIONS; SIGNALLING CASCADES;

DISEASE CONTROL; SIGNAL TRANSDUCTION;

BIOINFORMATICS;

EID: 77953910025     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11963516_7     Document Type: Conference Paper

References (32)

1. Alimonti, J.B., Ball, T.B., Fowke, K.R. Mechanisms of CD4+ T lymphocyte cell death in human immunodeficiency virus infection and AIDS. Journal of General Virology, 84 (2003), 1649-1661. (Pubitemid 36805899)
2. Bhalla, U.S., Iyengar, R., Emergent properties of networks of biological signaling pathways. Science, 283 (1999), 381-387.
3. Blossey, R., Cardelli, L., Phillips, A. A compositional approach to the stochastic dynamics of gene networks. Transactions on Computational Systems Biology, IV, Lecture Notes in Computer Science, 3939 (2006), 99-122. (Pubitemid 350278761)
4. Cheng, E.H., Wei, M.C., Weiler, S., Flavell, R.A., Mak, T.W., Lindsten, T., Korsmeyer, S.J. BCL-2, BCL-XL sequester BH3 domain-only molecules preventing BAX- and BAK-mediated mitochondrial apoptosis. Molecular Cell, 8 (2001), 705-711. (Pubitemid 32946946)
5. Cheruku, S., A. Pǎun, F.J. Romero, M.J. Pérez- Jiménez, O.H. Ibarra. Simulating FAS-induced apoptosis by using P systems. Proceedings of the First International Conference on Bio-Inspired Computing: Theory and Applications, Wuhan, China, September, 18-22, 2006.
6. Hua, F., Cornejo, M., Cardone, M., Stokes, C., Lauffenburger, D. Effects of Bcl-2 levels on FAS signaling-induced caspase-3 activation: Molecular genetic tests of computational model predictions. The Journal of Immunology, 175, 2 (2005), 985-995 and correction 175, 9 (2005), 6235-6237. (Pubitemid 41094983)
7. Ibarra, O.H., Pǎun, A. Counting time in computing with cells. Proceedings of DNA Based Computing, DNA11, London, Ontario, 25-36, 2005.
8. Kerr, J.F., Wyllie, A.H., Currie, A.R. Apoptosis: a basic biological phenomenon with wide-ranging implications in tissue kinetics. British Journal Cancer, 26 (1972), 239.
9. Pogson, M., Smallwood, R., Qwarnstrom, E., Holcombe, Formal agent-based of intracellular chemical interactions. BioSystems, 85, 1 (2006), 37-45. (Pubitemid 43850654)
10. Holcombe, M., Gheorghe, M., Talbot, N. A hybrid machine model of rice blast fungus, Magnaphorte Grisea. BioSystems, 68, 2-3 (2003), 223-228. (Pubitemid 36197709)
11. Jaatela, M. Multiple cell death pathways as regulators of tumour initiation and progression. Oncogene, 23 (2004), 2746-2756.
12. Jackson, D., Holcombe, M., Ratnieks, F. Trail geometry gives polarity to ant foraging networks. Nature 432 (2004), 907-909. (Pubitemid 40037152)
13. Moehren G., Markevich, N., Demin, O., Kiyatkin, A., Goryanin, I., Hoek, J.B., Kholodenko, B.N. Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model, Biochemistry 41 (2002), 306-320. (Pubitemid 34049408)
14. Moghal, N., Sternberg, P.W. Multiple positive and negative regulators of signaling by the EGFR receptor. Curr. Opin. Cell Biology, 11 (1999), 190-196. (Pubitemid 29164033)
15. Nijhawan, D., Honarpour, N., Wang, X. Apotosis in neural development and disease. Annual Reviews Neuroscience, 23 (2000), 73-87.
16. Oltavi, Z.N., Milliman, C.L., Korsmeyer, S.J. Bcl-2 heterodimerizes in vivo with a conserved homolog, Bax, that accelerates programmed cell death. Cell, 74, 4 (1993), 609-619. (Pubitemid 23259742)
17. Gh. Pǎun, Computing with membranes. Journal of Computer and System Sciences, 61, 1 (2000), 108-143, and Turku Center for Computer Science-TUCS Report Nr. 208, 1998.
18. Gh. Pǎun, Membrane Computing. An Introduction. Springer-Verlag, Berlin, 2002.
19. Gh. Pǎun, G. Rozenberg, A guide to membrane computing. Theoretical Computer Science, 287 (2002), 73-100. (Pubitemid 35019161)
20. Perez-Jimenez, M.J., Romero-Campero, F.J. P systems, a new computationl modelling tool for systems biology, Transactions on Computational Systems Biology VI, LNBI 4220, 2006, 176-197. (Pubitemid 351150659)
21. Perez-Jimenez, M.J., Romero-Campero, F.J. A study of the robustness of the EGFR signalling cascade using continuous membrane systems. Lecture Notes in Computer Science, 3561 (2005), 268 - 278. (Pubitemid 41425208)
22. Regev, A., Shapiro, E. (2004) The 7r-calculus as an abstraction for biomolecular systems. In G. Ciobanu and G. Rozenberg, editors, Modelling in Molecular Biology, Springer Berlin.
23. Scaffidi, C., Fulda. S., Srinivasan, A., Friesen, C., Li, F., Tomaselli, K.J., Debatin, K.M., Krammer, P.H., Peter, M.E. Two CD95 (APO-1/Fas) signaling pathways. The Embo Journal, 17 (1998), 1675-1687. (Pubitemid 28119121)
24. Schoeberl, B., Eichler-Jonsson, C., Gilles, E.D., Muller, G. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors, Nature Biotechnology, 20, 4 (2002), 370-375. (Pubitemid 34286330)
25. Van Kampen, N.G. Stochastics Processes in Physics and Chemistry, Elsevier Science B.V., Amsterdam, 1992.
26. Walker, D.C., Southgate, J., Hill, G., Holcombe, M., Hose, D.R., Wood S.M., Mac-Neil, S., Smallwood, R.H. The epitheliome: modelling the social behaviour of cells. BioSystems, 76, 1-3 (2004), 89-100. (Pubitemid 39207439)
27. Wang, K., Yin, X.M., Chao, D.T., Milliman, C.L., Korsmeyer, S.J. BID: a novel BH3 domain-only death agonist. Genes & Development, 10 (1996), 2859-2869. (Pubitemid 26394246)
28. Wells, A. EGFR-receptor. Int. Journal Biochem. Cell Biology, 31 (1999), 637-643.
29. Wiley, H.S., Shvartsman, S.Y., Lauffenburger, D.A. Computational modeling of the EGFR-receptor system: A paradigm for systems biology. Trends in Cell Biology, 13, 1 (2003), 43-50. (Pubitemid 35453894)
30. ISI web page: http://esi-topics.com/erf/october2003.html
31. SciLab Web Site http://scilabsoft.inria.fr/
32. P Systems Modelling Framework Web Site: http://www.dcs.shef.ac.uk/ ~marian/PSimulatorWeb/P-Systems-applications.htm