Critical self-organized self-sustained oscillations in large regulatory networks: Towards understanding the gene expression initiation

Gene Regulation and Systems Biology

Volumn 2011, Issue 5, 2011, Pages 27-40

  Rosenfeld, Simon ^a  

^a NATIONAL CANCER INSTITUTE   (United States)

Author keywords

Genetic regulatory systems; Self organized criticality; Stochastic oscillations; Transcription initiation

Indexed keywords

TRANSCRIPTION FACTOR;

ARTICLE; CELL STRUCTURE; EXCITATION; GENE EXPRESSION REGULATION; GENE FUNCTION; GENE NUMBER; GENE REGULATORY NETWORK; GENETIC CORRELATION; GENETIC ORGANIZATION; GENETIC SELECTION; MITOSIS; OSCILLATION; SIGNAL TRANSDUCTION; STATISTICS; STOCHASTIC MODEL; TRANSLATION INITIATION;

EID: 79958796352     PISSN: 11776250     EISSN: None     Source Type: Journal    
DOI: 10.4137/GRSB.S6804     Document Type: Article

References (23)

1. Rosenfeld S. Stochastic cooperativity in non-linear dynamics of genetic regulatory networks. Math Biosci. 2007;210:121.
2. McAdams HH, Arkin A. Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A. 1997;94:814.
3. McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trends Genet. 1999;15:65.
4. Turcotte DL. Self-organized criticality. Rep Prog Phys. 1999;62:1377.
5. Bak P. How Nature Works. The Science of Self-Organized Criticaliy. Springer Verlag, 1996.
6. Scott A. Encyclopedia of Nonlinear Science, Taylor & Francis Books, Abington, UK, 2005.
7. Turcotte DL, Rundle JB. Self-organized complexity in the physical, biological, and social sciences. Proc Natl Acad Sci U S A. 2002;99 Suppl 1:2463.
8. Johnson NL, Kotz S, Balakrishnan N. Continuous Univariate Distributions, Wiley-Interscience, 1994.
9. Jenkins GM, Watts DG. Spectral Analysis and Its Applications, Holden Day, 1968.
10. Rosenfeld S. A nonlinear continuous stochastic model for genetic regulatory networks. Caveats for microarray data analysis. ALIFE-X, 2006:28-34.
11. Rosenfeld S. Stochastic Oscillations in Genetic Regulatory Networks. Applications to Microarray Experiment, in: A. Rizzi, M. Vichi, editors. COMPSTAT-2006. Physica-Verlag. 2006:1609-1618.
12. Rosenfeld S. Stochastic Oscillations in Genetic Regulatory Networks, EURASIP. Journal of Bioinformatics and Systems Biology. 2006:1.
13. Rosenfeld S. Why do high-dimensional networks seem to be stable?-A reflection on stochasticity of dynamically unstable nonlinear systems, In: Gauges R, Kummer U, Pahle J, Willy P, editors. Fifth Workshop on Computation of Biochemical Pathways and Genetic Networks, University of Heidelberg, Heidelberg, 2008:101-112.
14. Rosenfeld S. Origins of Stochasticity and Burstiness in High-Dimensional Biochemical Networks, EURASIP Journal of Bioinformatics and Systems Biology, 2009.
15. Rosenfeld S. Characteristics of transcriptional activity in nonlinear dynamics of genetic regulatory networks. Gene Regul Syst Bio. 2009;3:159.
16. Rosenfeld S. Patterns of stochastic behavior in dynamically unstable highdimensional biochemical networks. Gene Regul Syst Bio. 2009;3:1.
17. Wolfram S. A New Kind of Science, Wolfram Media, 2002
18. Rapp PE. An Atlas of Cellular Oscillations. Jounal of Experimental Biology. 1979;81:281.
19. Nitabach MN, Blau J. Cellular Clockwork. Nature Genetics. 2002;32:559.
20. Schriber U, Naef F. Cellular oscillations: rhytmic gene expression and metabolism. Current Opinion in Cell Biology. 2005;17:223.
21. Goldbeter A. Complex oscillatory phenomena, including multiple oscillations, in regulated biochemical systems. Biomed Biochim Acta. 1985;44: 881.
22. Goldbeter A. Computational approaches to cellular rhythms. Nature. 2002; 420:238.
23. Reil T. Dynamics of Gene Expression in an Artificial Genome-Implications for Biological and Artificial Ontogeny, Advances in Artificial Life, 5th European Conference, ECAL'99, 1999:457-66.