Integration of immune models using petri nets

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

Volumn 3239, Issue , 2004, Pages 205-216

  Na, Dokyun ^a   Park, Inho ^a   Lee, Kwang H ^a   Lee, Dohcon ^a  

^a Department of BioSystems ^*  (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

IMMUNE SYSTEM; PETRI NETS;

ARTIFICIAL IMMUNE SYSTEM; CONTINUOUS PETRI NET; DEFENSE MECHANISM; EMERGENT PROPERTY; IMMUNE MECHANISM; MODEL AND ANALYSIS; NEGATIVE SELECTION; SOMATIC HYPERMUTATION;

MODELING LANGUAGES;

EID: 26944469780     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-30220-9_17     Document Type: Article

References (63)

1. Fearon, D.T., Locksley, R.M.: The instinctive role of innate immunity in the acquired immune response. Science 272 (1996) 50-53
2. Dornand, J., Gross, A., Lafont, V., Liautard. J, Oliaro, J., Liautard, J.P.: The innate immune response against Brucella in humans. Veterinary Microbiology 90 (2002)
3. McHeyzer-Williams, M. G.: B cells as effectors. Gurr. Opin. Immunol. 15 (2003) 354-361
4. Baumgarth, N.: A two-phase model of B-cell activation. Immunological Review 176 (2000) 171-180
5. Dutton, R.W., Bradley, L.M., Swain, S.L.: T cell memory. Annu. Rev. Immunol. 16 (1998) 201-213
6. Lanzavecchia A.: Mechanisms of antigen uptake for presentation. Curr. Opin. Immunol. 8 (1996) 348-354
7. Dennert, G.: Molecular mechanism of target lysis by cytotoxic T cells. Int. Rev. Immunol. 14 (1997) 133-152
8. Rosen, H.R.: Hepatitis C pathogenesis: mechanisms of viral clearance and liver injury. Liver Transplantation 9 (2003) S35-S43
9. Surh, C.D., Sprent, J.: T-cell apoptosis detected in situ during positive and negative selection in the thymus. Nature. 372 (1994) 100-103
10. Cornall, R.J., Goodnow, C.C., Cyster, J.G.: The regulation of self-reactive B cells. Curr. Opin. Immunol. 7 (1995) 804-811
11. Mueller, D.L., Jenkins, M.K., Schwartz, R.H.,: Clonal expansion versus functional clonal inactivation: a costimulatory signaling pathway determines the outcome of T cell antigen receptor occupancy. Annu. Rev. Immunol. 7 (1989) 445-480
12. Wagner, S.D, Neuberger, M.S.: Somatic hypermutation of immunoglobulin genes. Annu. Rev. Immunol. 14 (1996) 441-457
13. Mond, J.J., Lees, A., Snapper, C.C.:T cell-independent antigens type 2. Ann. Rev. Immunol. 13 (1995) 655-692
14. Triantafilou, M., Triantafilou, K.: Lipopolysaccharide recognition : CD14, TLRs and the LPS-activation cluster. Trends in Immunology 23 (2002) 301-304
15. Pleiman, C.M., Dambrosio, D., Cambier, J.C.: The B cell antigen receptor complex-structure and signal-transduction. Immunol. Today 15 (1994) 393-399
16. Kidd, P.: Th1/Th2 balance: The hypothesis, its limitations, and implications for health and disease. Altern. Med. Rev 8 (2003) 223-246
17. DeFranco, A.L.: Molecular aspects of B-lymphocyte activation. Ann. Rev. Cell Biol. 3 (1987) 143-178
18. Robbins, F.C., Robbins, J.B.: Current status and prospects for some improved and new bacterial vaccines. Am. J. Pub. Health 7 (1986) 105-125
19. Rene A.W. van Lier, Ineke J.M. ten Berge, Laila E. Gamadia: Human CD+ T-cell differentiation in response to viruses. Nature Rev. Immunol. 3 (2003) 1-8
20. Trambas, C.M., Griffiths, G.M., Delivering the kiss of death. Nature Immunol. 4 (2003) 399-403
21. Kim, J., Bentley, P.J.: Towards an Artificial Immune System for Network Intrusion Detection: An Investigation of Clonal Selection with a Negative Selection Operator, Proc. of the Congress on Evolutionary Computation, (2001) 1244-1252.
22. Bradley, D.W., Tyrrell, A. M.: The Architecture for a Hardware Immune System. Proc. of 3rd NASA/DoD Workshop on Evolvable Hardware. (2001) 193-200.
23. Knight, T., Timmis, J.: AINE: An Immunological Approach to Data Mining. Proc. of the IEEE International Conference on Data Mining. (2001) 297-304
24. th National Conf. on Artificial Intelligence. (1994) 852-857
25. Castiglione, F.: A network of cellular automata for the simulation of the immune system. Int. J. Morden Physics C10 (1999) 677-686
26. Rundell, A., DeCarlo, R., HogenEsch, H., Doerschuk, P.: The humoral immune response to Haemophilus influenzae type b: a mathematical model based on T-zone and germinal center B-cell dynamics. J. Theor. Biol. 194 (1998) 341-381
27. Perelson, A.S.: Immunology for physicists. Reviews of Modern Physics 69 (1997)
28. Perelson, A.S.: Modelling viral and immune system dynamics Nature Rev. Immunol 2 (2002) 28-36
29. Puzone, R., Kohler, B., Seiden, P., Celada, F.: IMMSIM, a flexible model for in machine experiments on immune system responses. Future Generation Computer Systems 18 (2002) 961-972
30. Kesmir, C., De Boer, R. J.; A mathematical model on germinal center kinetics and termination. J. Immunol. 163 (1999) 2463-2469
31. Agrawal, N.G.B., Linderman, J.J.; Mathematical modeling of helper T lymphocyte/antigen-presenting cell interactions: analysis of methods for modifying antigen processing and presentation. J. Theor. Biol. 182 (1996) 487-504
32. Davenport, M.P., Fazou, C., McMichael, A.J., Callan, M.F.C.; Clonal selection, clonal senescence, and clonal succession: the evolution of the T cell response to infection with a persistent virus. J. Immunol. 168 (2002) 3309-3317
33. DeBoer, R.J., Oprea, M., Antia, R., Murali-Krishna, K., Ahmed, R., Perelson, A.S.; Recruitment times, proliferation, and apoptosis rates during the CD8+ T-cell response to lymphocytic choriomeningitis virus. J. Virol. 75 (2001) 10663-10669
34. Bocharov, G.A.; Modeling the dynamics of LCMV infection in mice: conventional and exhaustive CTL responses. J. Theor. Biol. 192 (1998) 283-308
35. Funk, G.A., Barbour, A.D., Hengartner, H., Kalinke, U.; Mathematical model of a virus-neutralizing immunoglobulin response. J. Theor. Biol. 195 (1998) 41-52.
36. Marino, S., Kirschner, D.E.; The human immune response to Mycobacterium tuberculosis in lung and lymph node. J. Theor. Biol. 227 (2004) 463-486.
37. Koguchi, Y., Kwakami, K.; Cryptococcal infection and Th1-Th2 cytokine balance. Intern. Rev. Immunol. 21 (2002) 423-438
38. Hosken, N.A., Shibuya, K., Heath, A.W., Murphy, K.M., O'Garra, A.; The effect of antigen dose on CD4+ T helper cell phenotype development in a T cell receptorαβ-transgenic model. J. Exp. Med. 182 (1995) 1579-1584
39. Edwards, B.M., Barash, S.C., Main, S.H., Choi, G.H., Minter, R., Ullrich, S., Williams, E., Fou, L.D., Wilton, J., Albert, V.R., Ruben, S.M., Vaughan, T.J.; The remarkable flexibility of the human antibody repertoire; isolation of over one thousand different antibodies to a single protein, BLyS. J. Mol. Biol. 334 (2003) 103-118
40. Mehr, R., Globerson, A., Perelson, A.S.; Modeling positive and negative selection and differentiation in the thymus. J. Theor. Biol. 175 (1995) 103-126
41. Guermonprez, P., Valladeau, J., Zitvolgel, L., Thery, C., Amigorena, S.; Antigen presentation and T cell stimulation by dendritic cells. Annu. Rev. Immunol. 20 (2002) 621-667
42. Rogers, P.R., Croft, M.; Peptide dose, affinity, and time of differentiation can contribute to the Th1/Th2 cytokine balance. J. Immunol. 163 (1999) 1205-121343.
43. Foulds, K.E., Zenewicz, L.A., Shedlock, D.J., Jiang, J., Troy, A.E., Shen, H.; Cutting edge: CD4 and CD8 T cells are intrinsically different in their proliferative responses. J. Immunol. 168 (2002) 1528-1532
44. DeBoer, R.J., Homann, D., Perelson, A.S.; Different dynamics of CD4+ and CD8+ T cell responses during and after acute lymphocytic choriomeningitis virus infection. J. Immunol. 171 (2003) 3928-3935
45. Ridge, J.P., Rose, F.D., Matzinger, P.; A conditioned dendritic cell can be a temporal bridge between a CD4+ T-helper and a T-killer cell. Nature 393 (1998) 474-478
46. Badovinac, V.P., Porter, B.B., Harty, J.T.; Programmed contraction of CD8+ T cells after infection. Nat. Immunol. 3 (2002) 619-626
47. Kaech, S.M., Ahmed, R.; Memory CD8+ T cell differentiation: initial antigen encounter triggers a developmental program in naive cells. Nat. Immunol. 2 (2001) 415-422
48. Chao, D.L., Davenport, M.P., Forrest, S., Perelson, A.S.; A stochastic model of cytotoxic T cell responses. J. Theor. Biol. 228 (2004) 227-240
49. Dmitriev, D.A., Massino, Y.S., Sega, O.L.; Kinetic analysis of interactions between bispecific monoclonal antibodies and immobilized antigens using a resonant mirror biosensor. J. Immunol. Methods 280 (2003) 183-202
50. J. L. Peterson: Petri net theory and the modeling of systems. Prentice-Hall, Englewood Cliff, NJ, (1981)
51. T. Murata, Petri nets: Properties, analysis and applications, Proc. IEEE 77 (1989) 541-580
52. Mor Peleg, Iwei Yeh, and Russ B. Altman.: Modelling biological processes using workflow and Petri Net models. Bioinformatics 18 (2002) 825-837
53. H. Alla, R. David: A modeling and analysis tool for discrete event systems: continuous Petri net, Performance Evaluation 33 (1998) 175-199
54. Ridge J.P., et al. A conditioned dendritic cell can be a temporal bridge between a CD4+ T-helper and a T-killer cell. Nature 393 (1998) 474-478
55. Van Stipdonk, M.K., Lemmens, E.E., Schoenberger, S.P.,: Naive CTLs require a single brief period of antigenic stimulation for clonal expansion and differentiation. Nat. Immunol. 2 (2001) 423-429
56. Veiga-Fernandes, H., Walter, U., Bourgeois, C., McLean, A., Rocha, B.: Response of naive and memory CD8+ T cells to antigen stimulation in vivo. Nat. Immunol. 1 (2000) 47-53
57. Bachman, M.F., Kundig, T.M., Kalberer, C.P., Hengartner, H., Zinkernagel, R.M.: How many specific B-cells are needed to protect against a virus? J.Immunol. 152 (1994) 4235-4241
58. Karlsson, M.C.I., Getahun, A., Heyman, B.: Fc γ RIIB in IgG-mediated suppression of antibody responses: different impact in vivo and in vitro. J. Immunol. 167 (2001) 5558-5564
59. Simeone Marino, Denise E. Kirschner.: The human immune response to Mycobacterium tuberculosis in lung and lymph node. J. Theor. Biol. 227 (2004) 463-486
60. Wilson, M., Seymour, R., Henderson, B., Bacterial perturbation of cytokine networks, Infection and Immunity 6 (1998) 2401-2409
61. Heyman, Birgitta: Feedback regulation by IgG antibodies. Immunology Letters 88 (2003) 157-161
62. Pittner, B. T., Snow, E. C.: Strength of signal through BCR determines the fate of cycling B cells by regulating the expression of the Bcl-2 family of survival proteins. Cell. Immunol. 186 (1998) 55-62
63. Scott, D.W.: Activation-induced cell death in B lymphocytes. Cell Research 10 (2000) 179-192