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

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 Decomposing flux distributions into elementary flux modes in genome-scale metabolic networks

2011 ◽  
Vol 27 (16) ◽  
pp. 2256-2262 ◽  
Author(s):  
Siu Hung Joshua Chan ◽  
Ping Ji
Keyword(s):  
Metabolic Networks ◽  
Elementary Flux Modes ◽  
Genome Scale

scholarly journals Optimization of a modeling platform to predict oncogenes from genome‐scale metabolic networks of non‐small‐cell lung cancers

FEBS Open Bio ◽  
2021 ◽  
Author(s):  
You‐Tyun Wang ◽  
Min‐Ru Lin ◽  
Wei‐Chen Chen ◽  
Wu‐Hsiung Wu ◽  
Feng‐Sheng Wang
Keyword(s):  
Metabolic Networks ◽  
Small Cell ◽  
Small Cell Lung ◽  
Lung Cancers ◽  
Genome Scale

Systematic Investigation of Mouse Models of Parkinson’s Disease by Transcriptome Mapping on a Brain-Specific Genome-Scale Metabolic Network

2021 ◽  
Author(s):  
Ecehan Abdik ◽  
Tunahan Cakir
Keyword(s):  
Parkinson’S Disease ◽  
Parkinson's Disease ◽  
Metabolic Network ◽  
Mouse Models ◽  
Mus Musculus ◽  
Metabolic Networks ◽  
Systematic Investigation ◽  
Omics Data ◽  
Metabolic Alterations ◽  
Genome Scale

Genome-scale metabolic networks enable systemic investigation of metabolic alterations caused by diseases by providing interpretation of omics data. Although Mus musculus (mouse) is one of the most commonly used model...

scholarly journals F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks

2012 ◽  
Vol 13 (1) ◽  
Author(s):  
Abdelhalim Larhlimi ◽  
Laszlo David ◽  
Joachim Selbig ◽  
Alexander Bockmayr
Keyword(s):  
Metabolic Networks ◽  
Flux Coupling ◽  
Genome Scale

scholarly journals Integration of metabolic databases for the reconstruction of genome-scale metabolic networks

2010 ◽  
Vol 4 (1) ◽  
pp. 114 ◽  
Author(s):  
Karin Radrich ◽  
Yoshimasa Tsuruoka ◽  
Paul Dobson ◽  
Albert Gevorgyan ◽  
Neil Swainston ◽  
...  
Keyword(s):  
Metabolic Networks ◽  
Genome Scale

Model-guided identification of novel gene amplification targets for improving succinate production in Escherichia coli NZN111

2017 ◽  
Vol 9 (10) ◽  
pp. 830-835 ◽  
Author(s):  
Xingxing Jian ◽  
Ningchuan Li ◽  
Qian Chen ◽  
Qiang Hua
Keyword(s):  
Escherichia Coli ◽  
Metabolic Engineering ◽  
Gene Amplification ◽  
Metabolic Networks ◽  
Computational Analysis ◽  
Succinate Production ◽  
Novel Gene ◽  
Metabolic Models ◽  
Genome Scale

Reconstruction and application of genome-scale metabolic models (GEMs) have facilitated metabolic engineering by providing a platform on which systematic computational analysis of metabolic networks can be performed.

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