On the dynamics of random Boolean networks subject to noise: Attractors, ergodic sets and cell types

Journal of Theoretical Biology

Volumn 265, Issue 2, 2010, Pages 185-193

  Serra, R ^a,b   Villani, M ^a,b   Barbieri, A ^a   Kauffman, S A ^c   Colacci, A ^d  

^a UNIVERSITY OF MODENA AND REGGIO EMILIA   (Italy)

^b EUROPEAN CENTRE FOR LIVING TECHNOLOGY   (Italy)

^c UNIVERSITY OF VERMONT   (United States)

^d Regional Health Agency of Emilia Romagna   (Italy)

Author keywords

Differentiation; Dynamical systems; Noise; Pluripotent cells; Random Boolean networks

Indexed keywords

CELL ORGANELLE; GENE EXPRESSION; MODELING; NOISE;

ARTICLE; BIOLOGICAL ACTIVITY; CELL DIFFERENTIATION; CELL TYPE; COMPUTER MODEL; GENE ACTIVATION; GENE EXPRESSION REGULATION; GENE OVEREXPRESSION; GENETIC MODEL; HUMAN; MATHEMATICAL ANALYSIS; NONHUMAN; PLURIPOTENT STEM CELL; PRIORITY JOURNAL; RANDOM BOOLEAN NETWORK; REGULATOR GENE; SIGNAL NOISE RATIO;

CELL DIFFERENTIATION; CELLS; MODELS, BIOLOGICAL;

EID: 77953671724     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2010.04.012     Document Type: Article

References (26)

1. Aldana, M., Coppersmith, S., Kadanoff, L.P., 2003. Boolean dynamics with random couplings. In: Kaplan, E., Marsden, J.E., Sreenivasan, K.R. (Eds), Perspectives and Problems in Nonlinear Science. A Celebratory Volume in Honor of Lawrence Sirovich. Springer Applied Mathematical Sciences Series.
2. Aldana M., Balleza E., Kauffman S.A., Resendiz O. Robustness and evolvability in genetic regulatory networks. Journal of Theoretical Biology 2007, 245:433-448.
3. Andrecut M., Foster D., Carteret H., Kauffman S.A. Maximal information transfer and behavior diversity in random threshold networks. Journal of Computational Biology 2009, 16(7):909-916. 10.1089/cmb.2009.0007.
4. Barbieri A., Villani M., Serra R., Kauffman S.A., Colacci A. The influence of noise on the dynamic of random Boolean networks. Proceedings of Wirn 2009 2009, IOS Press, Amsterdam, (in press). C. Morabito (Ed.).
5. Chang H.H., Hemberg M., Barahona M., Ingber D.E., Huang S. Transcriptome-wide noise controls lineage choice in mammalian protenitor cells. Nature 2008, 453:544-548.
6. Furusawa C., Kaneko K. Chaotic expression dynamics implies pluripotency: when theory and experiment meet. Biology Direct 2009, 4(1):17. 10.1186/1745-6150-4-17.
7. Glass L., Hill C. Ordered and disordered dynamics in random networks. Europhysics Letters 1998, 41(6):599-604. 10.1209/epl/i1998-00199-0.
8. Hayashi K., de Sousa Lopes S.M.C., Tang F., Surani M.A. Dynamic equilibrium and heterogeneity of mouse pluripotent stem cells with Distinct Functional and Epigenetic States. Cell Stem Cell 2008, 3(4):391-440. 10.1016/j.stem.2008.07.027.
9. Hornstein E., Shomron N. Canalization of development by microRNAs. Nature Genetics 2006, 38(Supplementary):S20-S24. 10.1038/ng1803.
10. Hu M., Krause D., Greaves M., Sharkis S., Dexter M., Heyworth C., Enver T. Multilineage gene expression precedes commitment in the hemopoietic system. Genes & Development 1997, 11(6):774-785.
11. Huang S. Reprogramming cell fates: reconciling rarity with robustness. Bioessays 2009, 31(5):546-560. 10.1002/bies.200800189.
12. Huang S., Ernberg I., Kauffman S.A. Cancer attractors: a systems view of tumors from a gene network dynamics and developmental perspective. Seminars in Cell & Developmental Biology 2009, 20(7):869-876. 10.1016/j.semcdb.2009.07.003.
13. Kaneko K. LIfe: An Introduction to Complex System Biology 2006, Springer-Verlag, Berlin, New York.
14. Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 1969, 22(3):437-467. 10.1016/0022-5193(69)90015-0.
15. Kauffman S.A. The Origins of Order 1993, New York, Oxford University Press.
16. Kauffman S.A. At Home in the Universe 1995, New York, Oxford University Press.
17. Langton C.G. Life at the edge of chaos. Artificial Life II 1992, 41-91. Addison-Wesley, Reading MA. C.G. Langton, C. Taylor, J.D. Farmer, S. Rasmussen (Eds.).
18. Ramo P., Kesseli J., Yli-Harja O. Perturbation avalanches and criticality in gene regulatory networs. Journal of Theoretical Biology 2006, 242(1):160-164.
19. Ribeiro A.S., Kauffman S.A. Noisy attractors and ergodic sets in models of gene regulatory networks. Journal of Theoretical Biology 2007, 247(4):743-755. 10.1016/j.jtbi.2007.04.020.
20. Serra R., Villani M., Semeria A. Genetic network models and statistical properties of gene expression data in knock-out experiments. Journal of Theoretical Biology 2004, 227(1):149-157. 10.1016/j.jtbi.2003.10.018.
21. Serra, R., Villani, M., Graudenzi, A., Kauffman, S.A., 2006. On the distribution of small avalanches in random Boolean networks. In Ruusovori, P. et al. (Eds.), Proceedings of the Fourth TICSP Workshop on Computational Systems Biology, Juvenes print, Tampere, pp. 93-96.
22. 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. Journal of Theoretical Biology 2007, 249(3):449-460. 10.1016/j.jtbi.2007.01.012.
23. Shmulevich I., Kauffman S.A., Aldana M. Eukaryotic cells are dynamically ordered or critical but not chaotic. PNAS 2005, 102(38):13439-13444. 10.1073/pnas.0506771102.
24. Takahashi K., Yamanaka S. Induction of pluripotent stem cells from mouse embryonic and adult fibroblasts cultures by dfined factors. Cell 2006, 126(4):663-676.
25. Takahashi K., Tanabe K., Ohnuki M., Narita M., Ichisaka T., Tomoda K., Yamanaka S. Induction of pluripotent stem cells from adult human fibroblasts by defined factors. Cell 2007, 131(5):861-872.
26. Villani, M., Serra, R., Ingrami, P., Kauffman, S.A., 2006. Coupled random Boolean networks forming an artificial tissue. In: El Yacoubi, S., Chopard, B., Bandini, S. (Eds.), Lecture Notes in Computer Science, vol. 4173. Springer, Berlin, pp. 548-556.