Building qualitative models of plant regulatory networks with SQUAD

Frontiers in Plant Science

Volumn 3, Issue APR, 2012, Pages

  Weinstein, Nathan ^a   Mendoza, Luis ^a  

^a UNIVERSIDAD NACIONAL AUTÓNOMA DE MÉXICO   (Mexico)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84879181252     PISSN: None     EISSN: 1664462X     Source Type: Journal    
DOI: 10.3389/fpls.2012.00072     Document Type: Article

References (17)

1. Arellano, G., Argil, J., Azpeitia, E., Benitez, M., Carrillo, M., Gongora, P., Rosenblueth, D. A., and Alvarez-Buylla, E. R. (2011). "Antelope": a hybrid-logic model checker for branching-time Boolean GRN analysis. BMC Bioinformatics12, 490. doi:10.1186/1471-2105-12-490
2. Bornholdt, S. (2008). Boolean network models of cellular regulation: prospects and limitations. J. R. Soc. Interface5, S85-S94.
3. Chaouiya, C., Naldi, A., and Thieffry, D. (2012). Logical modelling of gene regulatory networks with GINsim. Methods Mol. Biol. 804, 463-479.
4. Di Cara, A., Garg, A., De Micheli, G., Xenarios, I., and Mendoza, L. (2007). Dynamic simulation of regulatory networks using SQUAD. BMC Bioinformatics 8, 462. doi: 10.1186/1471-2105-8-462
5. Eldar, A., and Elowitz, M. B. (2010). Functional roles for noise in genetic circuits. Nature 467, 167-173.
6. Garg, A., Xenarios, I., Mendoza, L., and DeMicheli, G. (2007). Efficient methods for dynamic analysis of genetic networks and in silico gene perturbation experiments. Lect. Notes Comput. Sci. 4453, 62-76.
7. Kitano, H. (2004). Biological robustness. Nat. Rev. Genet. 5, 826-837.
8. Machado, D., Costa, R. S., Rocha, M., Ferreira, E. C., Tidor, B., and Rocha, I. (2011). Modeling formalisms in systems biology. AMB Express 1, 45.
9. Mendoza, L. (2006). A network model for the control of the differentiation process in Th cells. Biosystems 84, 101-114.
10. Mendoza, L., and Pardo, F. (2010). A robust model to describe the differentiation of T-helper cells. Theory Biosci.129, 283-293.
11. Mendoza, L., and Xenarios, I. (2006). A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Model. 3, 13.
12. Mugler, A., Ziv, E., Nemenman, I., and Wiggins, C. H. (2009). Quantifying evolvability in small biological networks. IET Syst. Biol. 3, 379-387.
13. Müssel, C., Hopfensitz, M., and Kestler, H. A. (2010). BoolNet-an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26, 1378-1380.
14. Ravasz, E., Somera, A. L., Mongru, D. A., Oltvai, Z. N., and Barabasi, A. L. (2002). Hierarchical organization of modularity in metabolic networks. Science 297, 1551-1555.
15. Sánchez-Corrales, Y. E., Alvarez-Buylla, E. R., and Mendoza, L. (2010). The Arabidopsis thaliana flower organ specification gene regulatory network determines a robust differentiation process. J. Theor. Biol. 264, 971-983.
16. Sankar, M., Osmont, K. S., Rolcik, J., Gujas, B., Tarkowska, D., Strnad, M., Xenarios, I., and Hardtke, C. S. (2011). A qualitative continuous model of cellular auxin and brassinosteroid signaling and their crosstalk. Bioinformatics 27, 1404-1412.
17. Scacchi, E., Salinas, P., Gujas, B., Santuari, L., Krogan, N., Ragni, L., Berleth, T., and Hardtke, C. S. (2010). Spatio-temporal sequence of cross-regulatory events in root meristem growth. Proc. Natl. Acad. Sci. U.S.A. 107, 22734-22739