Boolean threshold networks: Virtues and limitations for biological modeling

Intelligent Systems Reference Library

Volumn 11, Issue , 2011, Pages 113-151

  Zañudo, Jorge G T ^a   Aldana, Maximino ^a   Martínez Mekler, Gustavo ^a  

^a INSTITUTO DE CIENCIAS FÍSICAS   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84885442446     PISSN: 18684394     EISSN: 18684408     Source Type: Book Series    
DOI: 10.1007/978-3-642-19621-8_6     Document Type: Article

References (43)

1. Glass, L., Kauffman, S.A.: The logical analysis of continous, nonlinear biochemical control networks. J. Theor. Biol. 39, 103-129 (1973)
2. Tyson, J.J., Chen, K.C., Novak, B.: Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Op. Cell Biol. 15, 221-231 (2003)
3. Tyson, J.J., Chen, K.C., Novak, B.: Network dynamics and cell physiology. Nature Rev. Mol. Cell Biol., 908-916 (2001)
4. Bornholdt, S.: Systems biology: Less is more in modeling large genetic networks. Science 310(5747), 449-451 (2005)
5. Albert, R., Othmer, H.G.: But no kinetic details are needed. SIAM News 36(10) (December 2003)
6. Wang, R., Albert, R.: Discrete dynamic modeling of cellular signaling networks. In: Johnson, B.M.L., Brand, L. (eds.) Methods in Enzymology 476: Computer Methods, pp. 281-306. Academic Press, London (2009)
7. Albert, R., Toroczkai, Z., Toroczkai, Z.: Boolean modeling of genetic networks. In: Ben-Naim, E., Frauenfelder, H., Toroczkai, Z. (eds.) Complex Networks. Springer, Heidelberg (2004)
8. Aldana-Gonzalez, M., Coppersmith, S., Kadanoff, L.P.: Boolean Dynamics with Random Couplings. In: Kaplan, E., Marsden, J.E., Sreenivasan, K.R. (eds.) Perspectives and Problems in Nonlinear Science. A celebratory volule in honor of Lawrence Sirovich. Springer Applied Mathematical Sciences Series, pp. 23-89 (2003)
9. Kauffman, S.A.: Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22, 437-467 (1969)
10. Kauffman, S.A.: The Origins of Order: Self-organization and selection in evolution. Oxford University Press, Oxford (1993)
11. Mendoza, L., Thieffry, D., Alvarez-Buylla, E.R.: Genetic control of flower morphogenesis in Arabidopsis Thaliana: a logical analysis. Bioinformatics 15, 593-606 (1999)
12. Espionza-Soto, C., Padilla-Longoria, P., Alvarez-Buylla, E.R.: A gene regulatory network model for cell-fate determination during Arabidopsis Thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell. 16, 2923-2939 (2004)
13. Albert, R., Othmer, H.G.: The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster. J. Theor. Biol. 23, 1-18 (2003)
14. Mendoza, L.: A network model for the control of the differentiation process in Th cells. BioSystems 84, 101-114 (2006)
15. Li, F., Long, T., Lu, Y., Ouyang, Q., Tang, C.: The yeast cell-cycle network is robustly designed. Proc. Natl. Acad. Sci. USA 101, 4781-4786 (2004)
16. Davidich, M.I., Bornholdt, S.: Boolean network model predicts cell cycle sequence of fission yeast. PLoS ONE 3(2), e1672 (2008)
17. Perissi, V., Jepsen, K., Glass, C.K., Rosenfeld, M.G.: Deconstructing repression: evolving models of co-repressor action. Nature Reviews Genetics 11, 109-123 (2010)
18. McCulloch, W., Pitts, W.: A logical calculus of the ideas immanent in nervous activity. Bull. Math. Biophys. 7, 115-133 (1943)
19. Hertz, J., Krogh, A., Palmer, R.G.: Introduction to the Theory of Neural Computation. Santa Fe Institute Studies in the Science of Complexity. Addison-Wesley, Reading (1991)
20. Bornholdt, S.: Boolean network models of cellular regulation: prospects and limitations. J. R. Soc. Interface 5, S85-S94 (2008)
21. Kürten, K.E.: Critical phenomena in model neural networks. Phys. Lett. A 129, 157-160 (1988)
22. Rohlf, T., Bornholdt, S.: Criticality in random threshold networks: annealed approximation and beyond. Physica A 310, 245-259 (2002)
23. Aldana, M., Larralde, H.: Phase transitions in scale-free neural networks: Departure for the standard mean-field universality class. Phys. Rev. E 70, 066130 (2004)
24. Rohlf, T.: Critical line in random threshold networks with inhomogeneous thresholds. Phys. Rev. E 78, 066118 (2008)
25. Kürten, K.E.: Correspondance between neural threshold networks and Kauffman Boolean cellular automata. J. Phys. A 21, L615-L619 (1988)
26. Derrida, B.: Dynamical phase transition in nonsymmetric spin glasses. J. Phys. A: Math. Gen. 20, L721-L725 (1987)
27. Szejka, A., Mihaljev, T., Drossel, B.: The phase diagram of random threshold networks. New Journal of Physics 10, 063009 (2008)
28. Derrida, B., Pomeau, Y.: Random networks of automata: a simple annealed approximation. Europhys. Lett. 1(2), 45-49 (1986)
29. Moreira, A.A., Amaral, L.A.N.: Canalyzing Kauffman networks: Nonergodicity and its effect on their critical behavior. Phys. Rev. Lett. 94, 0218702 (2005)
30. Serra, R., Villani, M., Graudenzi, A., Kauffman, S.A.: Why a simple model of genetic regulatory networks describes the distribution of avalanches in gene expression data. J. Theor. Biol. 246, 449-460 (2007)
31. Serra, R., Villani, M., Semeria, A.: Genetic network models and statistical properties of gene expression data in knock-out experiments. J. Theor. Biol. 227, 149-157 (2004)
32. Shmulevich, I., Kauffman, S., Aldana, M.: Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc. Natl. Acad. Sci. USA 102, 13439-13444 (2005)
33. Nykter, M., Price, N.D., Aldana, M., Ramley, S.A., Kauffman, S.A., Hood, L.E., Yli-Harja, O., Shmulevich, I.: Gene expression dynamics in the macrphage exhibit criticality. Proc. Natl. Acad. Sci. USA 105(6), 1897-1900 (2008)
34. Balleza, E., Alvarez-Buylla, E.R., Chaos, A., Kauffman, S., Shmulevich, I., Aldana, M.: Critical dynamics in genetic regulatory networks: Examples from four kingdoms. PLoS ONE 3(6), e2456 (2008)
35. Derrida, B., Weisbuch, G.: Evolution of overlaps between configurations in random Boolean networks. J. Phys. (Paris) 47, 1297-1303 (1986)
36. Aldana, M.: Boolean dynamics of networks with scale-free topology. Physica D 185, 45-66 (2003)
37. Kesseli, J., Rämö, P., Yli-Harja, O.: Iterated maps for annealed Boolean networks. Phys. Rev. E 74, 046104 (2006)
38. Greil, F., Drossel, B.: Kauffman networks with threshold functions. Eur. Phys. J. B 57, 109-113 (2007)
39. Kauffman, S.A.: Requirements for evolvability in complex systems: orderly dynamics and frozen components. Physica D 42(1-3), 135-152 (1990)
40. Aldana, M., Balleza, E., Kauffman, S.A., Resendiz, O.: Robustness and evolvability in genetic regulatory networks. J. Theor. Biol. 245, 433-448 (2007)
41. Gama-Castrol, S., Jiménez-Jacinto, V., Peralta-Gil, M., Santos-Zavaleta, A., Peñaloza-Spinola, M.I., Contreras-Moreira, B., Segura-Salazar, J., Muñiz-Rascado, L., Martínez-Flores, I., Salgado, H., Bonavides-Martínez, C., Abreu-Goodger, C., Rodríguez-Penagos, C., Miranda-Ríos, J., Morett, E., Merino, E., Huerta, A.M., Treviño-Quintanilla, L., Collado-Vides, J.: RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Research 36, D120-D124 (2008)
42. Braunewell, S., Bornholdt, S.: Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity. J. Theor. Biol. 245, 638-643 (2007)
43. Szejka, A., Drossel, B.: Evolution of Boolean networks under selection for a robust response to external inputs yields an extensive neutral space. Phys. Rev. E 81, 021908 (2010)