Descriptive vs. mechanistic network models in plant development in the post-genomic era

Methods in Molecular Biology
J Davila-VelderrainE R Alvarez-Buylla

Abstract

Network modeling is now a widespread practice in systems biology, as well as in integrative genomics, and it constitutes a rich and diverse scientific research field. A conceptually clear understanding of the reasoning behind the main existing modeling approaches, and their associated technical terminologies, is required to avoid confusions and accelerate the transition towards an undeniable necessary more quantitative, multidisciplinary approach to biology. Herein, we focus on two main network-based modeling approaches that are commonly used depending on the information available and the intended goals: inference-based methods and system dynamics approaches. As far as data-based network inference methods are concerned, they enable the discovery of potential functional influences among molecular components. On the other hand, experimentally grounded network dynamical models have been shown to be perfectly suited for the mechanistic study of developmental processes. How do these two perspectives relate to each other? In this chapter, we describe and compare both approaches and then apply them to a given specific developmental module. Along with the step-by-step practical implementation of each approach, we also focus on discussi...Continue Reading

Citations

Feb 18, 2017·BMC Systems Biology·Luis Fernando Méndez-LópezElena R Alvarez-Buylla
Mar 3, 2018·Communicative & Integrative Biology·Wendy Cajero SánchezAdriana Garay-Arroyo
Jun 4, 2015·The New Phytologist·Maria de la Paz SanchezBerenice García-Ponce

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