A New Approach to Flux Coupling Analysis of Metabolic Networks

2006 ◽  
pp. 205-215 ◽  
Author(s):  
Abdelhalim Larhlimi ◽  
Alexander Bockmayr
Keyword(s):  
Metabolic Networks ◽  
Coupling Analysis ◽  
New Approach ◽  
Flux Coupling ◽  
Flux Coupling Analysis

Flux coupling analysis of metabolic networks is sensitive to missing reactions

Biosystems ◽  
2011 ◽  
Vol 103 (1) ◽  
pp. 57-66 ◽  
Author(s):  
Sayed-Amir Marashi ◽  
Alexander Bockmayr
Keyword(s):  
Metabolic Networks ◽  
Coupling Analysis ◽  
Flux Coupling ◽  
Flux Coupling Analysis

scholarly journals FFCA: a feasibility-based method for flux coupling analysis of metabolic networks

2011 ◽  
Vol 12 (1) ◽  
pp. 236 ◽  
Author(s):  
Laszlo David ◽  
Sayed-Amir Marashi ◽  
Abdelhalim Larhlimi ◽  
Bettina Mieth ◽  
Alexander Bockmayr
Keyword(s):  
Metabolic Networks ◽  
Coupling Analysis ◽  
Flux Coupling ◽  
Flux Coupling Analysis

On flux coupling analysis of metabolic subsystems

2012 ◽  
Vol 302 ◽  
pp. 62-69 ◽  
Author(s):  
Sayed-Amir Marashi ◽  
Laszlo David ◽  
Alexander Bockmayr
Keyword(s):  
Coupling Analysis ◽  
Flux Coupling ◽  
Flux Coupling Analysis

scholarly journals Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models

2019 ◽  
Author(s):  
Dikshant Pradhan ◽  
Jason A. Papin ◽  
Paul A. Jensen
Keyword(s):  
Metabolic Engineering ◽  
Mathematical Framework ◽  
Continuous Variables ◽  
Convex Constraints ◽  
Coupling Analysis ◽  
Flux Coupling ◽  
Scale Models ◽  
Metabolic Models ◽  
Genome Scale ◽  
Flux Coupling Analysis

AbstractFlux coupling identifies sets of reactions whose fluxes are “coupled" or correlated in genome-scale models. By identified sets of coupled reactions, modelers can 1.) reduce the dimensionality of genome-scale models, 2.) identify reactions that must be modulated together during metabolic engineering, and 3.) identify sets of important enzymes using high-throughput data. We present three computational tools to improve the efficiency, applicability, and biological interpretability of flux coupling analysis.The first algorithm (cachedFCF) uses information from intermediate solutions to decrease the runtime of standard flux coupling methods by 10-100 fold. Importantly, cachedFCF makes no assumptions regarding the structure of the underlying model, allowing efficient flux coupling analysis of models with non-convex constraints.We next developed a mathematical framework (FALCON) that incorporates enzyme activity as continuous variables in genome-scale models. Using data from gene expression and fitness assays, we verified that enzyme sets calculated directly from FALCON models are more functionally coherent than sets of enzymes collected from coupled reaction sets.Finally, we present a method (delete-and-couple) for expanding enzyme sets to allow redundancies and branches in the associated metabolic pathways. The expanded enzyme sets align with known biological pathways and retain functional coherence. The expanded enzyme sets allow pathway-level analyses of genome-scale metabolic models.Together, our algorithms extend flux coupling techniques to enzymatic networks and models with transcriptional regulation and other non-convex constraints. By expanding the efficiency and flexibility of flux coupling, we believe this popular technique will find new applications in metabolic engineering, microbial pathogenesis, and other fields that leverage network modeling.

Quantitative flux coupling analysis

2018 ◽  
Vol 78 (5) ◽  
pp. 1459-1484 ◽  
Author(s):  
Mojtaba Tefagh ◽  
Stephen P. Boyd
Keyword(s):  
Coupling Analysis ◽  
Flux Coupling ◽  
Flux Coupling Analysis

scholarly journals Generic flux coupling analysis

2015 ◽  
Vol 262 ◽  
pp. 28-35
Author(s):  
Arne C. Reimers ◽  
Yaron Goldstein ◽  
Alexander Bockmayr
Keyword(s):  
Coupling Analysis ◽  
Flux Coupling ◽  
Flux Coupling Analysis

scholarly journals Flux Coupling Analysis of Genome-Scale Metabolic Network Reconstructions

2004 ◽  
Vol 14 (2) ◽  
pp. 301-312 ◽  
Author(s):  
A. P. Burgard
Keyword(s):  
Metabolic Network ◽  
Coupling Analysis ◽  
Flux Coupling ◽  
Genome Scale ◽  
Flux Coupling Analysis

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
Sign in / Sign up

Export Citation Format

Share Document