scholarly journals MetDFBA: incorporating time-resolved metabolomics measurements into dynamic flux balance analysis

2015 ◽  
Vol 11 (1) ◽  
pp. 137-145 ◽  
Author(s):  
A. Marcel Willemsen ◽  
Diana M. Hendrickx ◽  
Huub C. J. Hoefsloot ◽  
Margriet M. W. B. Hendriks ◽  
S. Aljoscha Wahl ◽  
...  
Keyword(s):  
Time Series ◽  
Hypothesis Testing ◽  
Flux Balance Analysis ◽  
Time Resolved ◽  
New Approach ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis ◽  
Constraint Based Modeling

This paper presents MetDFBA, a new approach incorporating experimental metabolomics time-series into constraint-based modeling. The method can be used for hypothesis testing and predicting dynamic flux profiles.

Dynamic flux balance analysis of biomass and lipid production by Antarctic thraustochytrid Oblongichytrium sp. RT2316‐13

2020 ◽  
Vol 117 (10) ◽  
pp. 3006-3017 ◽  
Author(s):  
Carolina Shene ◽  
Paris Paredes ◽  
Liset Flores ◽  
Allison Leyton ◽  
Juan A. Asenjo ◽  
...  
Keyword(s):  
Flux Balance Analysis ◽  
Lipid Production ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis

A reliable simulator for dynamic flux balance analysis

2012 ◽  
Vol 110 (3) ◽  
pp. 792-802 ◽  
Author(s):  
K. Höffner ◽  
S. M. Harwood ◽  
P. I. Barton
Keyword(s):  
Flux Balance Analysis ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis

scholarly journals Multiscale Metabolic Modeling: Dynamic Flux Balance Analysis on a Whole-Plant Scale

2013 ◽  
Vol 163 (2) ◽  
pp. 637-647 ◽  
Author(s):  
E. Grafahrend-Belau ◽  
A. Junker ◽  
A. Eschenroder ◽  
J. Muller ◽  
F. Schreiber ◽  
...  
Keyword(s):  
Flux Balance Analysis ◽  
Metabolic Modeling ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Whole Plant ◽  
Balance Analysis

scholarly journals Regulatory dynamic enzyme-cost flux balance analysis: A unifying framework for constraint-based modeling

2019 ◽  
Author(s):  
Lin Liu ◽  
Alexander Bockmayr
Keyword(s):  
Flux Balance Analysis ◽  
Optimization Problem ◽  
Linear Optimization ◽  
Production Costs ◽  
Mixed Integer ◽  
Time Interval ◽  
Modeling Framework ◽  
Flux Balance ◽  
Balance Analysis ◽  
Constraint Based Modeling

AbstractIntegrated modeling of metabolism and gene regulation continues to be a major challenge in computational biology. While there exist approaches like regulatory flux balance analysis (rFBA), dynamic flux balance analysis (dFBA), resource balance analysis (RBA) or dynamic enzyme-cost flux balance analysis (deFBA) extending classical flux balance analysis (FBA) in various directions, there have been no constraint-based methods so far that allow predicting the dynamics of metabolism taking into account both macromolecule production costs and regulatory events.In this paper, we introduce a new constraint-based modeling framework named regulatory dynamic enzyme-cost flux balance analysis (r-deFBA), which unifies dynamic modeling of metabolism, cellular resource allocation and transcriptional regulation in a hybrid discrete-continuous setting.With r-deFBA, we can predict discrete regulatory states together with the continuous dynamics of reaction fluxes, external substrates, enzymes, and regulatory proteins needed to achieve a cellular objective such as maximizing biomass over a time interval. The dynamic optimization problem underlying r-deFBA can be reformulated as a mixed-integer linear optimization problem, for which there exist efficient solvers.

Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation

2010 ◽  
Vol 12 (2) ◽  
pp. 150-160 ◽  
Author(s):  
Adam L. Meadows ◽  
Rahi Karnik ◽  
Harry Lam ◽  
Sean Forestell ◽  
Brad Snedecor
Keyword(s):  
Escherichia Coli ◽  
Flux Balance Analysis ◽  
Dynamic Flux Balance Analysis ◽  
Flux Balance ◽  
Balance Analysis
Sign in / Sign up

Export Citation Format

Share Document