scholarly journals Enzyme allocation problems in kinetic metabolic networks: Optimal solutions are elementary flux modes

2014 ◽  
Vol 347 ◽  
pp. 182-190 ◽  
Author(s):  
Stefan Müller ◽  
Georg Regensburger ◽  
Ralf Steuer
Keyword(s):  
Metabolic Networks ◽  
Optimal Solutions ◽  
Elementary Flux Modes ◽  
Allocation Problems

scholarly journals Hierarchical decomposition of metabolic networks using k-modules

2015 ◽  
Vol 43 (6) ◽  
pp. 1146-1150 ◽  
Author(s):  
Arne C. Reimers
Keyword(s):  
Metabolic Networks ◽  
Null Space ◽  
Tca Cycle ◽  
Primary Objective ◽  
Hierarchical Decomposition ◽  
Matroid Theory ◽  
Optimal Solutions ◽  
Algorithmic Problems ◽  
Branch Decompositions

The optimal solutions obtained by flux balance analysis (FBA) are typically not unique. Flux modules have recently been shown to be a very useful tool to simplify and decompose the space of FBA-optimal solutions. Since yield-maximization is sometimes not the primary objective encountered in vivo, we are also interested in understanding the space of sub-optimal solutions. Unfortunately, the flux modules are too restrictive and not suited for this task. We present a generalization, called k-module, which compensates the limited applicability of flux modules to the space of sub-optimal solutions. Intuitively, a k-module is a sub-network with low connectivity to the rest of the network. Recursive application of k-modules yields a hierarchical decomposition of the metabolic network, which is also known as branch decomposition in matroid theory. In particular, decompositions computed by existing methods, like the null-space-based approach, introduced by Poolman et al. [(2007) J. Theor. Biol. 249, 691–705] can be interpreted as branch decompositions. With k-modules we can now compare alternative decompositions of metabolic networks to the classical sub-systems of glycolysis, tricarboxylic acid (TCA) cycle, etc. They can be used to speed up algorithmic problems [theoretically shown for elementary flux modes (EFM) enumeration] and have the potential to present computational solutions in a more intuitive way independently from the classical sub-systems.

scholarly journals Boosting the extraction of elementary flux modes in genome-scale metabolic networks using the linear programming approach

2020 ◽  
Vol 36 (14) ◽  
pp. 4163-4170
Author(s):  
Francisco Guil ◽  
José F Hidalgo ◽  
José M García
Keyword(s):  
Linear Programming ◽  
Metabolic Networks ◽  
Supplementary Information ◽  
Programming Approach ◽  
Supplementary Data ◽  
Main Interest ◽  
Elementary Flux Modes ◽  
Order Of Magnitude ◽  
Genome Scale ◽  
Efficiency Rate

Abstract Motivation Elementary flux modes (EFMs) are a key tool for analyzing genome-scale metabolic networks, and several methods have been proposed to compute them. Among them, those based on solving linear programming (LP) problems are known to be very efficient if the main interest lies in computing large enough sets of EFMs. Results Here, we propose a new method called EFM-Ta that boosts the efficiency rate by analyzing the information provided by the LP solver. We base our method on a further study of the final tableau of the simplex method. By performing additional elementary steps and avoiding trivial solutions consisting of two cycles, we obtain many more EFMs for each LP problem posed, improving the efficiency rate of previously proposed methods by more than one order of magnitude. Availability and implementation Software is freely available at https://github.com/biogacop/Boost_LP_EFM. Contact [email protected] Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks

2015 ◽  
Vol 31 (13) ◽  
pp. 2232-2234 ◽  
Author(s):  
Matthias P. Gerstl ◽  
Christian Jungreuthmayer ◽  
Jürgen Zanghellini
Keyword(s):  
Metabolic Networks ◽  
Elementary Flux Modes

scholarly journals Computing the shortest elementary flux modes in genome-scale metabolic networks

2009 ◽  
Vol 25 (23) ◽  
pp. 3158-3165 ◽  
Author(s):  
Luis F. de Figueiredo ◽  
Adam Podhorski ◽  
Angel Rubio ◽  
Christoph Kaleta ◽  
John E. Beasley ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Elementary Flux Modes ◽  
Genome Scale

Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks

2007 ◽  
Vol 97 (6) ◽  
pp. 1535-1549 ◽  
Author(s):  
Intawat Nookaew ◽  
Asawin Meechai ◽  
Chinae Thammarongtham ◽  
Kobkul Laoteng ◽  
Vasimon Ruanglek ◽  
...  
Keyword(s):  
Systems Biology ◽  
Metabolic Networks ◽  
Elementary Flux Modes

scholarly journals Metabolic Networks, Elementary Flux Modes, and Polyhedral Cones

2021 ◽  
Author(s):  
Isaac Klapper ◽  
Daniel B. Szyld ◽  
Kai Zhao
Keyword(s):  
Metabolic Networks ◽  
Polyhedral Cones ◽  
Elementary Flux Modes
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