SSDesign: Computational metabolic pathway design based on flux variability using elementary flux modes

2014 ◽  
Vol 112 (4) ◽  
pp. 759-768 ◽  
Author(s):  
Yoshihiro Toya ◽  
Takanori Shiraki ◽  
Hiroshi Shimizu
Keyword(s):  
Metabolic Pathway ◽  
Elementary Flux Modes ◽  
Flux Variability ◽  
Metabolic Pathway Design

scholarly journals A retrosynthetic biology approach to metabolic pathway design for therapeutic production

2011 ◽  
Vol 5 (1) ◽  
pp. 122 ◽  
Author(s):  
Pablo Carbonell ◽  
Anne-Gaëlle Planson ◽  
Davide Fichera ◽  
Jean-Loup Faulon
Keyword(s):  
Metabolic Pathway ◽  
Metabolic Pathway Design

Thermodynamic constraints for identifying elementary flux modes

2018 ◽  
Vol 46 (3) ◽  
pp. 641-647 ◽  
Author(s):  
Sabine Peres ◽  
Stefan Schuster ◽  
Philippe Dague
Keyword(s):  
Free Energy ◽  
Steady State ◽  
Gibbs Free Energy ◽  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Metabolic Pathway Analysis ◽  
Combinatorial Explosion ◽  
Elementary Flux Modes ◽  
The Real ◽  
Large Systems

Metabolic pathway analysis is a key method to study metabolism and the elementary flux modes (EFMs) is one major concept allowing one to analyze the network in terms of minimal pathways. Their practical use has been hampered by the combinatorial explosion of their number in large systems. The EFMs give the possible pathways at steady state, but the real pathways are limited by biological constraints. In this review, we display three different methods that integrate thermodynamic constraints in terms of Gibbs free energy in the EFMs computation.

Innovative metabolic pathway design for efficient l-glutamate production by suppressing CO2 emission

2007 ◽  
Vol 103 (3) ◽  
pp. 262-269 ◽  
Author(s):  
Akito Chinen ◽  
Yuri I. Kozlov ◽  
Yoshihiko Hara ◽  
Hiroshi Izui ◽  
Hisashi Yasueda
Keyword(s):  
Metabolic Pathway ◽  
Co2 Emission ◽  
Glutamate Production ◽  
Metabolic Pathway Design

scholarly journals From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints

2017 ◽  
Vol 13 (4) ◽  
pp. e1005409 ◽  
Author(s):  
Steffen Klamt ◽  
Georg Regensburger ◽  
Matthias P. Gerstl ◽  
Christian Jungreuthmayer ◽  
Stefan Schuster ◽  
...  
Keyword(s):  
Pathway Analysis ◽  
Metabolic Pathway ◽  
Metabolic Pathway Analysis ◽  
Elementary Flux Modes
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