Reconstruction of transcription-translation dynamics with a model of gene networks

Journal of Theoretical Biology

Volumn 255, Issue 4, 2008, Pages 378-386

  Ichinose, N ^a   Yada, T ^a   Gotoh, O ^a   Aihara, K ^b,c  

^a KYOTO UNIVERSITY   (Japan)

^b INSTITUTE OF INDUSTRIAL SCIENCE   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

Gene expression; Hybrid system; Inverse problem

Indexed keywords

MESSENGER RNA; PROTEIN;

GENE EXPRESSION; HYBRID; MODELING; RECONSTRUCTION;

ACCURACY; ARTICLE; CIRCADIAN RHYTHM; GENE EXPRESSION; GENETIC MODEL; GENETIC TRANSCRIPTION; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; RNA TRANSLATION; TRANSCRIPTION REGULATION;

ALGORITHMS; ANIMALS; CIRCADIAN RHYTHM; GENE REGULATORY NETWORKS; MICE; MODELS, GENETIC; PINEAL GLAND; PROTEIN BIOSYNTHESIS; TRANSCRIPTION, GENETIC;

EID: 55949093452     PISSN: 00225193     EISSN: 10958541     Source Type: Journal    
DOI: 10.1016/j.jtbi.2008.09.006     Document Type: Article

References (21)

1. Akutsu T., Miyano S., and Kuhara S. Inferring qualitative relations in genetic networks and metabolic pathways. Bioinformatics 16 (2000) 727-734
2. Bower, J.M., Bolouri, H. (Eds.), 2001. Computational Modeling of Genetic and Biochemical Networks. MIT Press, Cambridge.
3. Chen, T., He, H.L., Church, G.M. 1999. Modeling gene expression with differential equations. In: Proceedings of Pacific Symposium of Biocomputing, vol. 4, pp. 29-40.
4. de Jong H. Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. 9 1 (2002) 67-103
5. Demiriz A., Bennett K.P., and Shawe-Taylor J. Linear programming boosting via column generation. Mach. Learn. 46 1-3 (2002) 225-254
6. Edwards R. Analysis of continuous-time switching networks. Physica D 146 (2000) 167-199
7. Edwards R., and Glass L. Combinatorial explosion in model gene networks. Chaos 10 3 (2000) 691-704
8. Elowitz M.B., and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 403 (2000) 335-338
9. Gardner T.S., Cantor C.R., and Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403 (2000) 339-342
10. Glass L. Classification of biological networks by their qualitative dynamics. J. Theor. Biol. 54 (1975) 85-107
11. Hasty J., Isaacs F., Dolnik M., McMillen D., and Collins J.J. Designer gene networks: towards fundamental cellular control. Chaos 11 1 (2001) 207-220
12. Karolczak M., Burbach G.J., Sties G., Korf H.-W., and Stehle J.H. Clock gene mRNA and protein rhythms in the pineal gland of mice. Eur. J. Neurosci. 19 (2004) 3382-3388
13. Kauffman S.A. Origins of Order: Self-organization and Selection in Evolution (1993), Oxford University Press, Oxford
14. Maki Y., Takahashi Y., Arikawa Y., Watanabe S., Aoshima K., Eguchi Y., Ueda T., Aburatani S., Kuhara S., and Okamoto M. Integrated comprehensive workbench for inferring genetic networks: VOYAGENE. J. Bioinformatics Comput. Biol. 2 (2004) 533-550
15. Mestl T., Plahte E., and Omholt S.W. A mathematical framework for describing and analysing gene regulatory networks. J. Theor. Biol. 176 (1995) 291-300
16. Mestl T., Lemay C., and Glass L. Chaos in high-dimensional neural and gene networks. Physica D 98 (1996) 33-52
17. Mochizuki A. An analytical study of the number of steady states in gene regulatory networks. J. Theor. Biol. 236 (2005) 291-310
18. Rätsch G., Schölkopf B., Smola A.J., Mika S., Onoda T., and Müller K.-R. Robust ensemble learning. In: Smola A.J., Bartlett P.L., Schölkopf B., and Schuurmans D. (Eds). Advances in Large Margin Classifiers (1999), MIT Press, Cambridge, MA pp. 208-222
19. Reppert S.M., and Weaver D.R. Coordination of circadian timing in mammals. Nature 418 (2002) 935-941
20. Snoussi E.H., and Thomas R. Logical identification of all steady states: the concept of feedback loop characteristic states. Bull. Math. Biol. 55 5 (1993) 973-991
21. Thomas R., Thieffry D., and Kaufman M. Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol. 57 2 (1995) 247-276