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Modeling the Epigenetic Landscape in Plant Development

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Computational Cell Biology

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1819))

Abstract

Computational mechanistic models enable a systems-level understanding of plant development by integrating available molecular experimental data and simulating their collective dynamical behavior. Boolean gene regulatory network dynamical models have been extensively used as a qualitative modeling framework for such purpose. More recently, network modeling protocols have been extended to model the epigenetic landscape associated with gene regulatory networks. In addition to understanding the concerted action of interconnected genes, epigenetic landscape models aim to uncover the patterns of cell state transition events that emerge under diverse genetic and environmental background conditions. In this chapter we present simple protocols that naturally extend gene regulatory network modeling and demonstrate their use in modeling plant developmental processes under the epigenetic landscape framework. We focus on conceptual clarity and practical implementation, providing directions to the corresponding technical literature. The protocols presented here can be applied to any well-characterized gene regulatory network in plants, animals, or human disease.

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Author information

Authors and Affiliations

  1. Centro de Ciencias de la Complejidad (C3), Universidad Nacional Autónoma de México, Ciudad Universitaria, México D.F, Mexico

    Jose Davila-Velderrain, Jose Luis Caldu-Primo & Elena R. Alvarez-Buylla

  2. Departamento de Control Automático, Cinvestav-IPN, México D.F, Mexico

    Jose Davila-Velderrain & Juan Carlos Martinez-Garcia

  3. MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA

    Jose Davila-Velderrain

  4. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Jose Davila-Velderrain

  5. Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Instituto de Ecología, México D.F, Mexico

    Elena R. Alvarez-Buylla

  6. University of California, Berkeley, Berkley, CA, USA

    Elena R. Alvarez-Buylla

Authors
  1. Jose Davila-Velderrain
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  2. Jose Luis Caldu-Primo
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  3. Juan Carlos Martinez-Garcia
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  4. Elena R. Alvarez-Buylla
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Editor information

Editors and Affiliations

  1. NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Louise von Stechow

  2. Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen, Denmark

    Alberto Santos Delgado

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Davila-Velderrain, J., Caldu-Primo, J.L., Martinez-Garcia, J.C., Alvarez-Buylla, E.R. (2018). Modeling the Epigenetic Landscape in Plant Development. In: von Stechow, L., Santos Delgado, A. (eds) Computational Cell Biology. Methods in Molecular Biology, vol 1819. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8618-7_17

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  • DOI: https://doi.org/10.1007/978-1-4939-8618-7_17

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-8617-0

  • Online ISBN: 978-1-4939-8618-7

  • eBook Packages: Springer Protocols

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