AUTHOR=Robaina Estévez Semidán , Nikoloski Zoran 

TITLE=Generalized framework for context-specific metabolic model extraction methods

JOURNAL=Frontiers in Plant Science

VOLUME=Volume 5 - 2014

YEAR=2014

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2014.00491

DOI=10.3389/fpls.2014.00491

ISSN=1664-462X

ABSTRACT=Genome-scale metabolic models are increasingly applied to investigate the physiology not only of simple prokaryotes, but also eukaryotes, such as plants, characterized with compartmentalized cells of multiple types. While genome-scale models aim at including the entirety of known metabolic reactions, mounting evidence has indicated that only a subset of these reactions is active in a given context, including: developmental stage, cell type, or environment. As a result, several methods have been proposed to reconstruct context-specific models from existing genome-scale models by integrating various types of high-throughput data. Here we present a mathematical framework that puts all existing methods under one umbrella and provides the means to better understand their functioning, highlight similarities and differences, and to help users in selecting a most suitable method for an application.