Abstract
Mathematical models based on dynamical systems theory are well-suited tools for the integration of available molecular experimental data into coherent frameworks in order to propose hypotheses about the cooperative regulatory mechanisms driving developmental processes. Computational analysis of the proposed models using well-established methods enables testing the hypotheses by contrasting predictions with observations. Within such framework, Boolean gene regulatory network dynamical models have been extensively used in modeling plant development. Boolean models are simple and intuitively appealing, ideal tools for collaborative efforts between theorists and experimentalists. In this chapter we present protocols used in our group for the study of diverse plant developmental processes. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Alvarez-Buylla ER, Benítez M, Davila EB, Chaos A, Espinosa-Soto C, Padilla-Longoria P (2007) Gene regulatory network models for plant development. Curr Opin Plant Biol 10(1):83–91
Huang S, Kauffman S (2009) Complex gene regulatory networks—from structure to biological observables: cell fate determination. In: Meyers RA (ed) Encyclopedia of complexity and systems science. Springer, Heidelberg, pp 1180–1213
Albert I, Thakar J, Li S, Zhang R, Albert R (2008) Boolean network simulations for life scientists. Source Code Biol Med 3:16
Azpeitia E, Davila-Velderrain J, Villarreal C et al (2014) Gene regulatory network models for floral organ determination. In: Riechmann JL, Wellmer F (eds) Flower development. Springer, New York, NY, pp 441–469
Davila-Velderrain J, Martinez-Garcia JC, Alvarez-Buylla ER (2015) Modeling the epigenetic attractors landscape: toward a post-genomic mechanistic understanding of development. Front Genet 6:160
Kauffman S (1969) Homeostasis and differentiation in random genetic control networks. Nature 224:177–178
Mendoza L, Alvarez-Buylla ER (1998) Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis. J Theor Biol 193(2):307–319
Azpeitia E, Benítez M, Vega I, Villarreal C, Alvarez-Buylla ER (2010) Single-cell and coupled GRN models of cell patterning in the Arabidopsis thaliana root stem cell niche. BMC Syst Biol 4:134
Benítez M, Espinosa-Soto C, Padilla-Longoria P, Alvarez-Buylla ER (2008) Interlinked nonlinear subnetworks underlie the formation of robust cellular patterns in Arabidopsis epidermis: a dynamic spatial model. BMC Syst Biol 2(1):98
Pérez-Ruiz RV, García-Ponce B, Marsch-Martínez N et al (2015) XAANTAL2 (AGL14) is an important component of the complex gene regulatory network that underlies arabidopsis shoot apical meristem transitions. Mol Plant 8(5):796–813
Müssel C, Hopfensitz M, Kestler HA (2010) BoolNet—an R package for generation, reconstruction and analysis of Boolean networks. Bioinformatics 26(10):1378–1380
Kaplan D, Glass L (2012) Understanding nonlinear dynamics. Springer, New York, NY
Ellner SP, Guckenheimer J (2011) Dynamic models in biology. Princeton University Press, Princeton, NY
Garg A, Mohanram K, De Micheli G, Xenarios I (2012) Implicit methods for qualitative modeling of gene regulatory networks In Gene Regulatory Networks. Humana, New York, NY, pp 397–443
Espinosa-Soto C, Padilla-Longoria P, Alvarez-Buylla ER (2004) A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles. Plant Cell 16(11):2923–2939
Gershenfeld N (1998) The nature of mathematical modeling. Cambridge University Press, Cambridge
Arellano G, Argil J, Azpeitia E et al (2011) “Antelope”: a hybrid-logic model checker for branching-time Boolean GRN analysis. BMC Bioinformatics 12:490
Naldi A, Berenguier D, Fauré A et al (2009) Logical modeling of regulatory networks with ginsim 2.3. Biosystems 97(2):134–139
Corblin F, Fanchon E, Trilling L (2010) Applications of a formal approach to decipher discrete genetic networks. BMC Bioinformatics 11(1):385
De Jong H, Geiselmann J, Hernandez C et al (2003) Genetic network analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 19(3):336–344
Calzone L, Fages F, Soliman S (2006) Biocham: an environment for modeling biological systems and formalizing experimental knowledge. Bioinformatics 22(14):1805–1807
Yuan R, Zhu X, Radich JP, Ao P (2016) From molecular interaction to acute promyelocytic leukemia: calculating leukemogenesis and remission from endogenous molecular-cellular network. Sci Rep 6:24307
Azpeitia E, Weinstein N, Benítez M, Mendoza L, Alvarez-Buylla ER (2013) Finding missing interactions of the Arabidopsis thaliana root stem cell niche gene regulatory network. Front Plant Sci 4:110
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Velderraín, J.D., Martínez-García, J.C., Álvarez-Buylla, E.R. (2017). Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction. In: Kaufmann, K., Mueller-Roeber, B. (eds) Plant Gene Regulatory Networks. Methods in Molecular Biology, vol 1629. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7125-1_19
Download citation
DOI: https://doi.org/10.1007/978-1-4939-7125-1_19
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-7124-4
Online ISBN: 978-1-4939-7125-1
eBook Packages: Springer Protocols