Bayesian-based selection of metabolic objective functions

Abstract

Additional files, code and a program for carrying out model discrimination are available at http://www.engr.uconn.edu/~srivasta/modisc.html.

Balance de Flujos Metabólicos en Saccharomyces cerevisiae basado en Compartimentalización Intracelular

“…Otros objetivos considerados están asociados con la producción de biomasa, debido a la relevancia de este objetivo en el modelado FBA. La mayoría de los objetivos comparados en trabajos como Schuetz et al (2007) y Knorr et al (2007) quedan incluidos entre las combinaciones estudiadas en este trabajo. Su efectividad ha sido estudiada en la literatura de forma individual sin tener en cuenta compartimentos físicos del microorganismo estudiado (Feist y Palsson, 2010).…”

In silico genome‐scale modeling and analysis for identifying anti‐tubercular drug targets

“…Thus, we resort to optimization algorithms to determine a solution that best reflects the true metabolic state [Price et al, 2004]. The implementation of optimization requires the definition of a cellular objective that is typically assumed to be biomass growth or can be systematically selected using several computational methods depending on the cellular environment [Gianchandani et al, 2008;Knorr et al, 2007;Ow et al, 2009;Schuetz et al, 2007]. Hence, after reconstructing the metabolic model of organism of interest, we can simulate its cellular phenotype by solving the following linear programming (LP) problem: A detailed mathematical formulation can be found in Palsson [2006].…”

Optimization of the bioconversion of glycerol to ethanol using <i>Escherichia coli</i> by implementing a bi-level programming framework for proposing gene transcription control strategies based on genetic algorithms

“…Many efforts have been published related to quantifying each flux in the model as it hypothesizes what is the purpose of the cell when growing in a specific environment. In that matter, Knorr et al [5] proposed a bayesian-based selection model to select metabolic objective functions departing from several hypotheses. Finally, their fitness was tested by comparing the flux obtained with previously published microarrays results [6].…”