Genetic network dynamics, information processing and autoimmune disease

Complexus

Volumn 2, Issue 1, 2004, Pages 7-22

  Gilmore, Stephen ^a  

^a ST VINCENT S HOSPITAL   (Australia)

Author keywords

Autoimmunity; Genetic networks; Information theory

Indexed keywords

AUTOANTIGEN;

ARTICLE; AUTOIMMUNE DISEASE; AUTOIMMUNITY; DYNAMICS; ENTROPY; GENE; GENE EXPRESSION; GENETIC REGULATION; GENETIC TRANSCRIPTION; HUMAN; IMMUNE SYSTEM; IMMUNOPATHOLOGY; INFORMATION PROCESSING; INFORMATION SCIENCE; LYMPHOCYTE; MATHEMATICAL MODEL; MOLECULAR MECHANICS; MORBIDITY; NONHUMAN; POPULATION; PRIORITY JOURNAL; PROTEIN EXPRESSION; STATISTICAL MODEL; TISSUE;

EID: 19044376567     PISSN: 14248492     EISSN: None     Source Type: Journal    
DOI: 10.1159/000087850     Document Type: Article

References (42)

1. Jacobson DL, Gange SJ, Rose NR, Graham NM: Epidemiology and estimated population burden of selected autoimmune diseases in the United States. Clin Immunol Immunopathol 1997; 84: 223-243.
2. Rose NR, Mackay IR: The Autoimmune Diseases. San Diego, Academic Press, 1998.
3. Marrak P, Kappler J, Kotzin BL: Autoimmune disease: Why and where it occurs. Nat Med 2001; 8: 899-905.
4. Kaufmann SA: Metabolic stability and epigenesis in randomly connected nets. J Theor Biol 1969; 22: 437.
5. Kauffman SA: The Origins of Order: Self-Organization and Selection in Evolution. Oxford, Oxford University Press,1993.
6. Wuensche A: Genomic regulation modelled as a network with basins of attraction. Proceedings of the 1998 Pacific Symposium on Biocomputing. Singapore, World Scientific, 1998, vol 4, pp 89-102.
7. Smolen P, Baxter DA, Byrne JH: Modeling transcriptional control in gene networks - Methods, recent results, and future directions. Bull Math Biol 2000; 62: 247-292.
8. Szallasi Z: Genetic network analysis in light of massively parallel biological data acquisition. Pacific Symposium on Biocomputing. Singapore, World Scientific, 1999, pp 5-16.
9. Huang S: Gene expression profiling, genetic networks, and cellular states: An integrating concept for tumorigenesis and drug discovery. J Mol Med 1999; 77: 469-480.
10. Stratmann T, Apostolopoulos V, Mallet-Designe V, Corper AL, Scott CA, Wilson IA, Kang AS, Teyton L: The I-Ag7 MHC class II molecule linked to murine diabetes is a promiscuous peptide binder. J Immunol 2000; 165: 3214-3225.
11. Wagner A: How to reconstruct a large genetic network from n gene perturbations in fewer than n squared easy steps. Bioinformatics 2001; 17: 1183-1197.
12. Weigle WO: Autoimmune processes resulting from pertubations of self-nonself recognition. Recomb DNA Tech Bull 1981; 4: 107-115.
13. Jerne NK: Towards a network theory of the immune system. Ann Immunol (Paris) 1974; 125C:373-389.
14. Carneiro J, Stewart J: Self and nonself revisited: Lessons from modelling the immune network; in Lecture Notes in Artificial Intelligence. Berlin, Springer, 1995, pp 406-420.
15. Nakamura MC, Nakamura RM: Contemporary concepts of autoimmunity and autoimmune diseases. J Clin Lab Anal 1992; 6: 275-289.
16. McAdams HH, Arkin A: It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet 1999; 15: 65-69.
17. Bennett DC: Differentiation in mouse melanoma cells: Initial reversibility and an on-off stochastic model. Cell 1983; 34: 445-453.
18. Cook DL, Gerber AN, Tapscott SJ: Modeling stochastic gene expression: Implications for haploinsufficiency. Proc Natl Acad Sci USA 1989; 95: 15641-15546.
19. Ko MS: Induction mechanisms of a single gene molecule: Stochastic or deterministic. Bioessays 1992; 14: 341-346.
20. Elliott JI, Festenstein R, Tolaini M, Kioussis D: Random activation of a transgene under the control of a hybrid hCD2 locus controlling region/Ig enhancer regulatory element. EMBO J 1995; 14: 575-584.
21. Chelly J, Concordet JP, Kaplan JC, Kahn A: Illegitimate transcription: Transcription of any gene in any cell type. Proc Natl Acad Sci USA 1989; 86: 2617-2621.
22. Weaver DC, Workman CT, Stormo GD: Modeling regulatory networks with weight matrices: Pacific Symposium on Biocomputing. Singapore, World Scientific, 1999, pp 112-123.
23. Shannon CE, Weaver W: The Mathematical Theory of Communication. Urbana-Champaign, University of Illinois Press, 1949.
24. Adami C: Introduction to Artificial Life. New York, Springer, 1998.
25. Langton CG: Life at the edge of chaos; in Langton CG, Farmer JD, Rasmussen S (eds): Artificial Life II. Redwood City, Addison-Wesley, 1990, p 41.
26. Williams GP: Chaos Theory Tamed. Washington, Joseph Henry Press, 1997.
27. Watts DJ, Strogatz SH: Collective dynamics of 'small-world' networks. Nature 1998; 393: 440-442.
28. Thieffry D, Huerta AM, Perez-Rueda E, Collado-Vides J: From specific gene regulation to global regulatory networks: A characterisation of Escherichia coli transcriptional network. Bioessays 1998; 20: 433-440.
29. Uetz PL, Giot L, Cagney G, Mansfield TA, Judson RS, Knight JR, Lockson D, Narayan V, Srinivasan M, Pochart P, Qureshi-Emili A, Li Y, Godwin B, Conover D, Kalbfleisch T, Vijayadamodar G, Yang M, Johnston M, Fields S, Rothberg JM: A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 2000; 403: 623.
30. Bornholdt S: Modeling genetic networks and their evolution: A complex dynamical systems perspective. Biol Chem 2001; 382: 1289-1299.
31. Samuelsson B, Troein C: Superpolynomial growth in the number of attractors in Kauffman networks. Phys Rev Lett 2003; 90: 098701.
32. Socolar JES, Kauffman SA: Scaling in ordered and critical random Boolean networks. Phys Rev Lett 2003; 90: 068702.
33. Langton C: Studying artificial life with cellular automata. Physica 1986; 22D:120-149.
34. Moudgil KD, Sercarz EE: Antigenic determinants involved in induction and propagation of autoimmunity; in Rose NR, Mackay IR (eds): The Autoimmune Diseases. San Diego, Academic Press, 1998, pp 45-58.
35. Krakauer D: From physics to phenomenology. Levels of description and levels of selection; in 'In silico' Simulations of Biological Processes. Chichester, Wiley, 2002, pp 42-52.
36. Hasty J, Pradines J, Doinik M, Collins JJ: Noise-based switches and amplifiers for gene expression. Proc Natl Acad Sci USA 2000; 97: 2075-2080.
37. Bowcock AM, Shannon W, Du F, Duncan J, Cao K, Aftergut K, Catier J, Fernandez-Vina MA, Menter A: Insights into psoriasis and other inflammatory diseases from large-scale gene expression studies. Hum Mol Genet 2001; 10: 1793-1805.
38. Gottleib AB: Psoriasis. Immunopathology and Immunomodulation. Dermatol Clin 2001; 19: 649-657.
39. Ortonne JP: Recent developments in the understanding of the pathogenesis of psoriasis. Br J Dermatol 1999; 140(suppl 54):1-7.
40. Bhalerao J, Bowcock AM: The genetics of psoriasis: A complex disorder of the skin and immune system. Hum Mol Genet 1998; 7: 1537-1545.
41. Harrison LC, McColl GJ: Infection and autoimmune disease; in Rose NR, Mackay IR (eds): The Autoimmune Diseases. San Diego, Academic Press, 1998.
42. Barkai N, Leibler S: Circadian clocks limited by noise. Nature 2000; 403: 267-268.