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Boolean Dynamic Modeling Approaches to Study Plant Gene Regulatory Networks: Integration, Validation, and Prediction

  • José Dávila Velderraín
  • Juan Carlos Martínez-García
  • Elena R. Álvarez-Buylla
Part of the Methods in Molecular Biology book series (MIMB, volume 1629)

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.

Key words

Systems biology Gene regulatory networks Cellular differentiation Cell state dynamics Attractor 

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • José Dávila Velderraín
    • 1
  • Juan Carlos Martínez-García
    • 2
  • Elena R. Álvarez-Buylla
    • 1
    • 3
  1. 1.Centro de Ciencias de la Complejidad (C3)Universidad Nacional Autónoma de México (UNAM)MéxicoMexico
  2. 2.Departamento de Control AutomáticoCinvestav-IPNMéxicoMexico
  3. 3.Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de EcologíaUniversidad Nacional Autónoma de México (UNAM)Mexico CityMexico

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