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PHYS 699:
Introduction to Mathematical Modelling of the Immune System
(Fall 2002)

(Click here for Winter 2003)


Under the supervision of:

Dr. Jack Tuszynski jtus@phys.ualberta.ca 492-3579
Dr. John Samuel jsamuel@pharmacy.ualberta.ca 492-7469



Report:

Final report: immuno.pdf



Schedule:

December 19, 2002 Reading since last course:
  1. M. Bernaschi and F. Castiglione, "Design and implementation of an immune system simulator", Computers in Biology and Medecine, 31(5):303-331 (2001).

  2. F. Celada and P.E. Seiden, "Modelling immune cognition", Proceedings of the 1998 IEEE International Conference on Systems, Man and Cybernetics, San Diego, CA, 3787-3792, 11-14 October (1998). IEEE Catalog Number 98CH36218.

  3. S. Forrest and S. Hofmeyr, "Engineering an immune system", Graft, 4(5):5-9 (2001).

  4. S. Forrest, R.E. Smith, B. Javornik, and A.S. Perelson, "Using genetic algorithms to explore pattern recognition in the immune system", Evolutionary Computation, 1(3):191-211 (1993).

  5. M. Meier-Schellersheim and G. Mack, "SIMMUNE: a tool for simulating and analyzing immune system behavior", arXiv:cs.MA/9903017 (1999).

  6. A.S. Perelson, R. Hightower, and S. Forrest, "Evolution and somatic learning in V-region genes", Res. Immunol. 147:202-208 (1996).

  7. D.J. Smith, S. Forrest and A.S. Perelson, "Immunological memory is associative", In: International Conference on Multiagent Systems, Workshop notes: Workshop 4: Immunity Based Systems, p.62-70, Kyoto, Japan (1996).

November 15, 2002 This was the last official meeting for the reading class. It was decided that the time had come to start writing up the final report. Other meetings can be arranged if needed by Dr. Samuel, Dr. Tuszynski or I. Additional reading may get posted if I see that I require more information about a particular subject.
November 8, 2002 Assigned reading:
  1. M. V. Voitikova, "Cellular automaton model for immunology of tumor growth", arXiv:comp-gas/9811001, (1998).

  2. Steven A. Hofmeyr and Stephanie Forrest, "Immunity by Design: An Artificial Immune System", Proceedings of the Genetic and Evolutionary Computation Conference (1999).

  3. M. Bernaschi and F. Castiglione, "Selection of escape mutants from immune recognition during HIV", Immunology and Cell Biology, vol. 80, p.207 (2002).

October 25, 2002 Assigned reading:
  1. Steven H. Kleinstein and Philip E. Seiden, "Simulating the Immune System", Computing in Science and Engineering, pp 69-77. July/August 2000.

  2. M. Bezzi, F. Celada, S. Ruffo and P. E. Seiden, "The Transition between Immune and Disease States in a Cellular Automaton Model of Clonal Immune Response", Physica A 245, 145-163 (1997). Also in arXiv: chao-dyn/9701004.

  3. Perelson, A. S., "Modelling viral and immune system dynamics", Nature Rev. Immunol. 2, 28-36 (2002).

October 16, 2002 Assigned reading:
  1. F. Celada, and P. E. Seiden, "Affinity Maturation and Hypermutation in a Simulation of the Humoral Response", European J. Immunology 26, 1350-1358 (1996).

  2. J. J. Stewart, H. Agosto, S. Litwin, J. D. Welsh, M. Shlomchik, M. Weigert and P. E. Seiden, "A Solution to the Rheumatoid Factor Paradox", J. Immunology 159, 1728-1738 (1997).

  3. B. Kohler, R. Puzone, P. E. Seiden and F. Celada, "A systematic approach to vaccine complexity using an automaton model of the cellular and humoral immune system", Vaccine 19, 862-876 (2000).

October 10, 2002 Research CA articles of the immune system, particularily by Seiden and Celada. The goal now will be to investigate the IMMSIM (see link below) in order to later be able to elaborate a more specific model based on it.
Assigned reading:
  1. P. E. Seiden and F. Celada, "A Model for Simulating Cognate Recognition and Response in the Immune System", J. Theor. Biology. 158, 329 (1992).

  2. F. Celada and P. E. Seiden, "A Computer Model of Cellular Interactions in the Immune System", Immunol. Today 13, 56 (1992).
Note: the Immunology class starts this Friday and will be on MWF 1pm to 1:50pm, DP 4114 from October 18 to 25.
October 3, 2002 Assigned reading:
September 27, 2002 Assigned reading:



Interesting links:




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