Time series dependent analysis of unparametrized thomas networks

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 9, Issue 5, 2012, Pages 1338-1351

  Klarner, Hannes ^a   Siebert, Heike ^a   Bockmayr, Alexander ^a  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

biology and genetics; constraint satisfaction; model checking; temporal logic; Time series analysis

Indexed keywords

BIOLOGY AND GENETICS; CONSTRAINT SATISFACTION; DATA QUALITY; DISCRETE TIME SERIES; EDGE LABELS; INCOMPLETE MEASUREMENTS; INHIBITORY EFFECT; MONOTONICITY; SAMPLING INTERVAL; SPECIFIC COMPONENT;

GENE EXPRESSION; MODEL CHECKING; TEMPORAL LOGIC;

TIME SERIES ANALYSIS;

ARTICLE; BIOLOGY; GENE REGULATORY NETWORK; GENETICS; METHODOLOGY; SACCHAROMYCES CEREVISIAE; THEORETICAL MODEL;

COMPUTATIONAL BIOLOGY; GENE REGULATORY NETWORKS; MODELS, THEORETICAL; RESEARCH DESIGN; SACCHAROMYCES CEREVISIAE;

EID: 84864949322     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2012.61     Document Type: Article

References (19)

1. J. Barnat, L. Brim, A. Krejci, A. Streck, D. Safranek, M. Vejnar, and T. Vejpustek, "On Parameter Synthesis by Parallel Model Checking," IEEE/ACM Trans. Computational Biology and Bioinfor-matics, vol. 9, no. 3, pp. 693-705, May/June 2012.
2. G. Batt, M. Page, I. Cantone, G. Goessler, P. Monteiro, and H. de Jong, "Efficient Parameter Search for Qualitative Models of Regulatory Networks Using Symbolic Model Checking," Bioinfor-matics, vol. 26, pp. i603-i610, Sept. 2010.
3. G. Bernot, J.-P. Comet, A. Richard, and J. Guespin, "Application of Formal Methods to Biological Regulatory Networks: Extending Thomas' Asynchronous Logical Approach with Temporal Logic," J. Theoretical Biology, vol. 229, no. 3, pp. 339-347, 2004. (Pubitemid 38844938)
4. I. Cantone, L. Marucci, F. Iorio, M.A. Ricci, V. Belcastro, M. Bansal, S. Santini, M. Di Bernardo, D. Di Bernardo, and M.P. Cosma, "A Yeast Synthetic Network for in Vivo Assessment of ReverseEngineering and Modeling Approaches," Cell, vol. 137, no. 1, pp. 172-181, 2009.
5. N. Chabrier-Rivier, M. Chiaverini, V. Danos, F. Fages, and V. Schächter, "Modeling and Querying Biomolecular Interaction Networks," Theoretical Computer Science, vol. 325, no. 1, pp. 25-44, 2004.
6. C. Chaouiya, E. Remy, B. Mossé, and D. Thieffry, "Qualitative Analysis of Regulatory Graphs: A Computational Tool Based on a Discrete Formal Framework," Proc. First Multidisciplinary Int'l Symp. Positive Systemsd Applications, L. Benvenuti, A. De Santis, and L. Farina, eds., pp. 830-832, 2003.
7. A. Cimatti, E.M. Clarke, E. Giunchiglia, F. Giunchiglia, M. Pistore, M. Roveri, R. Sebastiani, and A. Tacchella, "Nusmv 2: An Opensource Tool for Symbolic Model Checking," Proc. 14th Int'l Conf. Computer Aided Verification (CAV '02), pp. 359-364, 2002.
8. F. Corblin, E. Fanchon, and L. Trilling, "Applications of a Formal Approach to Decipher Discrete Genetic Networks," BMC Bioinfor-matics, vol. 11, article 385, July 2010.
9. E.S. Dimitrova, L.D. Garcia-Puente, F. Hinkelmann, A.S. Jarrah, R.C. Laubenbacher, B. Stigler, M. Stillman, and P. Vera-Licona, "Parameter Estimation for Boolean Models of Biological Networks," Theoretical Computer Science, vol. 412, no. 26, pp. 2816-2826, 2011.
10. E.S. Dimitrova, J.J. McGee, and R.C. Laubenbacher, "Discretization of Time Series Data," J. Computational Biology, vol. 17, no. 6, pp. 853-868, 2010.
11. J. Fromentin, J.-P. Comet, P.L. Gall, and O. Roux, "Analysing Gene Regulatory Networks by Both Constraint Programming and Model-Checking." Proc. IEEE 29th Ann. Int'l Conf. Eng. in Medicine and Biology Soc. (EMBC '07), pp. 4595-4598, Aug. 2007.
12. M. Huth and M. Ryan, Logic in Computer Science: Modelling and Reasoning About Systems. Cambridge Univ. Press, 2004.
13. H. Klarner, H. Siebert, and A. Bockmayr, "Parameter Inference for Asynchronous Logical Networks Using Discrete Time Series," Proc. Ninth Int'l Conf. Computational Methods in Systems Biology (CMSB '11), pp. 121-130, 2011.
14. S. Meiers, "Graph Traversal Versus Model Checking in Deciding Compatibility of Time Series with Logical Networks," bachelor's thesis, Freie Universität Berlin, 2011.
15. P.T. Monteiro, D. Ropers, R. Mateescu, A.T. Freitas, and H. de Jong, "Temporal Logic Patterns for Querying Dynamic Models of Cellular Interaction Networks," Bioinformatics, vol. 24, no. 16, pp. i227-i233, 2008.
16. C. Mü ssel, M. Hopfensitz, and H.A. Kestler, "Boolnet-An R Package for Generation, Reconstruction, and Analysis of Boolean Networks," Bioinformatics, vol. 26, no. 10, pp. 1378-1380, 2010.
17. A. Richard, "Negative Circuits and Sustained Oscillations in Asynchronous Automata Networks," Advances in Applied Math., vol. 44, no. 4, pp. 378-392, 2009.
18. I. Shmulevich and W. Zhang, "Binary Analysis and Optimization-Based Normalization of Gene Expression Data," Bioinformatics, vol. 18, no. 4, pp. 555-565, 2002. (Pubitemid 34521045)
19. R. Thomas, "Regulatory Networks Seen as Asynchronous Automata: A Logical Description," J. Theoretical Biology, vol. 153, no. 1, pp. 1-23, 1991.