Dynamical roles of biological regulatory circuits

Briefings in Bioinformatics

Volumn 8, Issue 4, 2007, Pages 220-225

  Thieffry, Denis ^a  

^a Aix Marseille university   (France)

Author keywords

Dynamics; Homeostasis; Multistability; Oscillations; Regulatory circuits; Synthetic biology; Systems biology

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; CELL CYCLE; CELL NUCLEUS; ENZYME MECHANISM; GENETIC ENGINEERING; HOMEOSTASIS; MATHEMATICAL MODEL; MOLECULAR BIOLOGY; MOLECULAR DYNAMICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MOLECULAR INTERACTION; NONHUMAN; POSITIVE FEEDBACK;

ALGORITHMS; BACTERIA; FEEDBACK, BIOCHEMICAL; HOMEOSTASIS; MODELS, GENETIC; SYSTEMS BIOLOGY;

EID: 34548327206     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbm028     Document Type: Article

References (30)

1. Umbarger HE. Evidence for a negative-feedback mechanism in the biosynthesis of isoleucine. Science 1956;123:848.
2. Novick A, Weiner M. Enzyme induction as an all or none phenomenon. Proc Natl Acad Sci USA 1957;43:553-66.
3. Monod J, Jacob F. Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb Symp Quant Biol 1961;26 389-401.
4. Goldberger RF. Autogenous regulation of gene expression. Science 1974;183:810-6.
5. Meinhardt H, Gierer A. Applications of a theory of biological pattern formation based on lateral inhibition. J Cell Sci 1974;15 321-46.
6. Savageau MA. Design of molecular control mechanisms and the demand for gene expression. Proc Natl Acad Sci USA 1977;74:5647-51.
7. Thomas R. On the relation between the logical structure of systems and their ability to generate multiple steady states of sustained oscillations. Springer Series Synergetics 1981; 9:180-93.
8. Thomas R, D'Ari R. Biological Feedback. Boca Raton, Forida: CRC Press 1990.
9. Remy R, Ruet, Thieffry D. Positive or negative regulatory circuit inference from multilevel dynamics. Lect Notes Control Inf Sci 2006;341:263-70.
10. de Jong H, Ropers D. Strategies for dealing with incomplete information in the modeling of molecular interaction networks. Brief Bioinform 2006;7:354-63.
11. Tyson J. Classification of instabilities in chemical reactions systems. Chem Phys 1975;62:1010-15.
12. Thomas R, Kaufman M. Frontier diagrams: Partition of the phase space according to the signs of the eigenvalues or to the sign patterns of the circuits. Int J Bifurcation Chaos 2005; 15:1-24.
13. Thomas R. Positive feedback circuits are a necessary conditions for positive eigenvalues of the Jacobian matrix. Ber Bungenses Phys Chem 1994;98:1148-51.
14. Plahte E, Mestl T, Omholt SW. Feedback loops, stability and multistationarity in dynamical systems. J Biol Syst 1995; 3 409-13.
15. Snoussi EH. Necessary conditions for multistationarity and stable periodicity. J Biol Syst 1998;6:3-9.
16. Gouzé J-L. Positive and negative circuits in dynamical systems. J Biol Syst 1998;6:11-15.
17. Soulé C. Graphic requirements for multistationarity. ComPlex Us 2003;1:123-33.
18. Richard A. Modèle formel pour les réseaux de régulation génétique et influence des circuits de rétroaction. Thesis, University of Evry: France, 2006.
19. Goldbeter A. Computational approaches to cellular rhythms. Nature 2002;420:238-45.
20. Tyson JJ, Chen K, Novak B. Network dynamics and cel physiology. Nat Rev Mol Cell Biol 2001;2:908-16.
21. Remy R, Mossé B, Chaouiya C, Thieffry D. Discrete dynamics of regulatory feedback circuits. Bioinformatics 2003;10:iI172-8.
22. Gardner TS, Cantor CR, Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000;403: 339-42.
23. Elowitz MB, Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000;403:335-8.
24. Becskei A, Serrano L. Engineering stability in gene networks by autoregulation. Nature 2000;405:590-3.
25. Becskei A, Seraphin B, Serrano L. Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion. EMBO J 2001;20:2528-35.
26. Wall ME, Hlavacek WS, Savageau MA. Design of gene circuits: Lessons from bacteria. Nat Rev Genet 2004;5: 34-42.
27. Cinquin O, Demongeot J. High-dimensional switches and the modelling of cellular differentiation. J Theor Biol 2005; 233:391-411.
28. Sánchez L, Thieffry D. Segmenting the fly embryo: A logical analysis of the pair-rule cross-regulatory module. J theor Biol 2003;224 517-37.
29. Eisenfeld J, DeLisi C. On conditions for qualitative instability of regulatory circuits with application to immunological loops. In: Eisenfeld J, DeLisi C, (eds). Mathematics and Computers in Medical Applications. Elsevier Science Publishers, 1985;39-53.
30. Csikasz-Nagy A, Battogtokh D, Chen KC, et al. Analysis of a generic model of eukaryotic cell-cycle regulation. Biophys J 2006;90:4361-79.