A modeling framework for immune-related diseases

Mathematical Modelling of Natural Phenomena

Volumn 7, Issue 3, 2012, Pages 40-48

  Castiglione, F ^a   Motta, S ^b   Pappalardo, F ^b   Pennisi, M ^b  

^a CNR   (Italy)

^b UNIVERSITY OF CATANIA   (Italy)

Author keywords

Agent based modeling; Computational biology; CS model; Immunology

Indexed keywords

AGENT-BASED MODELING; CLINICAL RESEARCH; COMPUTATIONAL BIOLOGY; COMPUTATIONAL FRAMEWORK; COMPUTATIONAL MODEL; CS-MODEL; DISCRETE MATHEMATICAL MODELS; IMMUNE SYSTEMS; MODELING FRAMEWORKS;

BIOINFORMATICS; COMPUTATIONAL METHODS; DISEASES; MATHEMATICAL MODELS;

IMMUNOLOGY;

EID: 84863738908     PISSN: 09735348     EISSN: 17606101     Source Type: Journal    
DOI: 10.1051/mmnp/20127304     Document Type: Article

References (38)

1. A.S. Perelson, G. Weisbuch (Eds.). Theoretical Immunology, Part One. Springer, Berlin, 1988.
2. A.S. Perelson (Ed.). Theoretical Immunology, Part Two. Addison Wesley, Redwood City, CA, 1988.
3. A.S. Perelson, G. Weisbuch. Immunology for physicists. Rev. Mod. Phys., 69 (1997), 1219-1267.
4. R. Puzone, B. Kohler, P.E. Seiden, F. Celada. IMMSIM, a flexible model for in machina experiments on immune system responses. Future Gener. Comput. Syst., 18 (2002), No. 7, 961-972.
5. M. Meier-Schellersheim, G. Mack. Simmune: A tool for simulating and analyzing immune system behavior. Das Deutsche Elektronen-Synchrotron Technical Report, 1999.
6. F. Castiglione Agent based modeling. Scholarpedia, 1 (2006), No. 10, 1562.
7. M. Kaufman, J. Urbain, R. Thomas. Towards a logical analysis of the immune response. J. Th. Biol., 114 (1985), 527-561.
8. F. Celada, P.E. Seiden. Affinity maturation and hypermutation in a simulation of the humoral immune response. Eur. J. Immunol., 26 (1996), No. 6, 1350-1358.
9. F. Celada, P.E. Seiden. A computer model of cellular interactions in the immune system. Immunol. Today, 13 (1992), No. 2, 56-62.
10. P.E. Seiden, F. Celada. A model for simulating cognate recognition and response in the immune system. J. Th. Biol., 158 (1992), No. 3, 329-357.
11. D. Morpurgo, R. Serenthà, P.E. Seiden, F. Celada. Modelling thymic functions in a cellular automaton. Int. Immunol., 7 (1995), No. 4, 505-516.
12. F. Castiglione, F. Poccia, G. D'Offizi, M. Bernaschi. Mutation, fitness, viral diversity and predictive markers of disease p rogression in a computational model of HIV-1 infection. AIDS Res. Human Retrovirus, 20 (2004), No. 12, 1316-1325.
13. F. Castiglione, K.A. Duca, A.S. Jarrah, R. Laubenbacher, K. Luzuriaga, D. Hochberg, D.A. Thorley-Lawson. Simulating Epstein-Barr virus infection with C-ImmSim. Bioinformatics, 23 (2007), 1371-1377.
14. F. Castiglione, V. Sleitser, Z. Agur. Analyzing hypersensitivity to chemotherapy in a Cellular Automata model of the immune system, in Cancer Modeling and Simulation, L. Preziosi (Ed.), pages 333-365. Chapman & Hall/CRC Press, London, UK, 2003.
15. F. Pappalardo, P-L. Lollini, F. Castiglione, S. Motta. Modelling and simulation of cancer immunoprevention vaccine. Bioinformatics, 21 (2005), No. 12, 2891-2897.
16. P. Paci, R. Carello, M. Bernaschi, G. D'Offizi, F. Castiglione. Immune control of HIV-1 infection after therapy interruption: immediate versus deferred antiretroviral therapy. BMC Infect. Dis., 9 (2009), 172.
17. J.D. Farmer, N.H. Packard, and A.S. Perelson. The immune system, adaptation and machine learning. Physica D, 22 (1986), 187-204.
18. P. Paci, F. Castiglione, M. Bernaschi, V. Baldazzi. A discrete/continuous model of anti-HIV response and therapy. IEEE Computer Society, Digital library Proceedins UKSIM, pages 481-486, 2008.
19. V. Baldazzi, P. Paci, M. Bernaschi, F. Castiglione. Modeling lymphocytes homing and encounters in lymph nodes. BMC Bioinformatics, 10 (2009), 387.
20. P. Paci, F. Martini, M. Bernaschi, F. D'Offizi, F. Castiglione. Earlier is better: a timely HAART initiation may pave the way for best controllers. BMC Infectious Diseases, 11 (2011), 56.
21. F. Castiglione, P. Paci. Criticality of timing for anti-HIV therapy initiation. PLoS ONE, 5 (2010), No. 12, e15294.
22. L.L. Laichalk, D.A. Thorley-Lawson. Terminal differentiation into plasma cells initiates the replicative cycle of Epstein-Barr virus in vivo. J. Virol., 79 (2005), 1296-1307.
23. A.B. Kay AB. Allergy and allergic diseases. First Part. N. Engl. J. Med., 344 (2001), 30-37.
24. R.A. Goldsby, T.J. Kindt, B.A. Osborne. Kuby Immunology, IV ed.. W.H. Freeman & Co., NY, 2000.
25. A.B. Kay. Allergy and allergic diseases. Second Part. N. Engl. J. Med., 344 (2001), 109-113.
26. S.T. Holgate. Allergic disorders. British Med. J., 320 (2000), 231-234.
27. D. Santoni, M. Pedicini, F. Castiglione. Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hyper-sensitivity reactions. Bioinformatics, 24 (2008), 1374-1380.
28. G.K. Hansson. Inflammation, atherosclerosis, and coronary artery disease. N. Engl. J. Med., 352 (2002), No. 16, 1685-1695.
29. A. Romero-Corral, V.K. Somers, J. Korinek, J. Sierra-Johnson, R.J. Thomas, T.G. Allison, F. Lopez-Jimenez. Update in prevention of atherosclerotic heart disease: management of major cardiovascular risk factors. Rev. Invest. Clin., 58 (2006), No. 3, 237-244.
30. C. Weber, A. Zernecke, P. Libby. The multifaceted contributions of leukocyte subsets to atherosclerosis: lessons from mouse models. Nat. Rev. Immunol., 8 (2008), No. 10, 802-815.
31. F. Pappalardo, S. Musumeci, S. Motta. Modeling immune system control of atherogenesis. Bioinformatics, 24 (2008), No. 15, 1715-1721.
32. M. Meier-Schellersheim. The immune system as a complex system: Description and simulation of the interactions of its constituents. Ph.D. thesis, University of Hamburg, Germany, 2001.
33. S. Efroni, D. Harel, I.R. Cohen. Toward rigorous comprehension of biological complexity: modeling, execution, and visualization of thymic T-cell maturation. Genome Res., 13 (2003), No. 11, 2485-2497.
34. J.K. Kalita, K. Chandrashekar, R. Hans, R. Selvam. Computational modelling and simulation of the immune system. Int. J. Bioinf. Res. Appl., 2 (2006), No. 1, 63-88.
35. V.A. Folcik, G.C. An, C.G. Orosz. The basic immune simulator: an agent-based model to study the interactions between innate and adaptive immunity. Theor. Biol. Med. Model., 4 (2007), 39.
36. R.C. Laubenbacher, A.S. Jarrah, H.S. Mortveit, S.S. Ravi. A mathematical formalism for agent-based modeling. CoRR., (2008), abs/0801.0249.
37. S.Y. Del Valle, P.D. Stroud, J.P. Smith, S.M. Mniszewski, J.M. Riese, S.J. Sydoriak, D.A. Kubicek. Episims: Epidemic simulation system. Los Alamos Unlimited Release (LAUR), (2006), 06-06714.
38. S. Mniszewski, S.Y. Del Valle, P. Stroud, J. Riese, S. Sydoriak. Episims simulation of a multi-component strategy for pandemic influenza. Proceedings of the 2008 Spring Simulation Multiconference, 2008.