Complementary approaches to understanding the plant circadian clock

Electronic Proceedings in Theoretical Computer Science, EPTCS

Volumn 19, Issue , 2010, Pages 1-19

  Akman, Ozgur E ^a,b   Guerriero, Maria Luisa ^a   Loewe, Laurence ^a   Troein, Carl ^a  

^a UNIVERSITY OF EDINBURGH   (United Kingdom)

^b UNIVERSITY OF EXETER   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; CLOCKS; DIFFERENTIAL EQUATIONS; ORDINARY DIFFERENTIAL EQUATIONS; PLANTS (BOTANY); PROBABILITY DISTRIBUTIONS; RANDOM PROCESSES; STOCHASTIC MODELS; STOCHASTIC SYSTEMS;

COMPUTATIONAL PREDICTIONS; CONTINUOUS APPROXIMATIONS; DIFFERENT ANALYSIS TECHNIQUES; PLANT CIRCADIAN CLOCK; SELF-SUSTAINED OSCILLATIONS; STOCHASTIC PROCESS ALGEBRAS; STOCHASTIC SIMULATION ALGORITHMS; STOCHASTIC SIMULATIONS;

MODEL CHECKING;

EID: 85020231469     PISSN: 20752180     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.4204/EPTCS.19.1     Document Type: Conference Paper

References (21)

1. O.E. Akman, F. Ciocchetta, A. Degasperi & M.L. Guerriero (2009): Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora Crassa Circadian Network. In: Proc. of CMSB'09, LNCS 5688, Springer, pp. 52-67.
2. O.E. Akman, J.C.W. Locke, S. Tang, I. Carré, A.J. Millar & D.A. Rand (2008): Isoform switching facilitates period control in the Neurospora crassa circadian clock. Mol. Sys. Biol. 4, p. 64.
3. A. Aziz, K. Kanwal, V. Singhal & V. Brayton (1996): Verifying continuous time Markov chains. In: Proc. of CAV'96, LNCS 1102, Springer, pp. 269-276.
4. C. Baier, B. Haverkort, H. Hermann & J.-P. Katoen (2003): Model-Checking Algorithms for Continuous-Time Markov Chains. IEEE Trans. on Software Eng. 29(6), pp. 524-541.
5. Bio-PEPA Home Page. http://www.biopepa.org/.
6. F. Ciocchetta & J. Hillston (2009): Bio-PEPA: a Framework for the Modelling and Analysis of Biological Systems. Theoretical Computer Science 410(33-34), pp. 3065-3084.
7. E.M. Clarke, O. Grumberg & D. Peled (1999): Model Checking. The MIT Press.
8. F. Corellou, C. Schwartz, J.-P. Motta, E.B. Djouani-Tahri, F. Sanchez & F.-Y. Bouget (2009): Clocks in the Green Lineage: Comparative Functional Analysis of the Circadian Architecture in the Picoeukaryote Ostreococcus. Plant Cell 21, pp. 3436-3449.
9. E. Derelle, C. Ferraz, S. Rombauts, P. Rouzé, A.Z. Worden, Robbens S. et al. (2006): Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features. Proc. Natl. Acad. Sci. USA 103(31), p. 11647.
10. A. Duguid, S. Gilmore, M.L. Guerriero, J. Hillston & L. Loewe (2009): Design and development of software tools for Bio-PEPA. In: Proc. of WSC'09, pp. 956-967.
11. J.C. Dunlap, J.J. Loros & P.J. DeCoursey (2004): Chronobiology: Biological Timekeeping. Sinauer.
12. D.T. Gillespie (1977): Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), pp. 2340-2361.
13. D. Gonze, J. Halloy & A. Goldbeter (2002): Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA 99(2), pp. 673-678.
14. J. Heath, M. Kwiatkowska, G. Norman, D. Parker & O. Tymchyshyn (2008): Probabilistic Model Checking of Complex Biological Pathways. Theoretical Computer Science 319, pp. 239-257.
15. A. Hinton, M. Kwiatkowska, G. Norman & D. Parker (2006): PRISM: A tool for automatic verification of probabilistic systems. In: Proc. of TACAS'06, LNCS 3920, pp. 441-444.
16. M.A. Jones (2009): Entrainment of the Arabidopsis Circadian Clock. J. Plant Biology 52(3), pp. 202-209.
17. H. Li, Y. Cao, L.R. Petzold & D.T. Gillespie (2008): Algorithms and Software for Stochastic Simulation of Biochemical Reacting Systems. Biotechnology Progress 24(1), pp. 56-61.
18. L. Loewe (2009): A framework for evolutionary systems biology. BMC Systems Biology 3(27).
19. L. Loewe & J. Hillston (2008): The distribution of mutational effects on fitness in a simple circadian clock. In: Proc. of CMSB'08, LNBI 5307, Springer, pp. 156-175.
20. J.S. O'Neill, G. van Ooijen, C. Troein, L. Dixon, F.-Y. Bouget, F. Corellou & A. Millar (2009): Circadian rhythms persisting in the absence of transcription in a eukaryote. Submitted.
21. H.L.S. Younes & R.G. Simmons (2002): Probabilistic verification of discrete event systems using acceptance sampling. In: Proc. of CAV'02, LNCS 2404, Springer, pp. 223-235.