Exploring the gap between dynamic and constraint-based models of metabolism.

scientific article published on 28 January 2012

Exploring the gap between dynamic and constraint-based models of metabolism. is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1016/J.YMBEN.2012.01.003
P932PMC publication ID3465724
P698PubMed publication ID22306209
P5875ResearchGate publication ID221806800

P50authorB TidorQ67689738
Daniel MachadoQ41046566
Isabel RochaQ47449076
Eugénio C. FerreiraQ47449085
P2093author name stringRafael S Costa
P2860cites workDynamic metabolic flux analysis (DMFA): a framework for determining fluxes at metabolic non-steady stateQ51518128
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Metabolic engineeringQ77223941
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Hybrid dynamic/static method for large-scale simulation of metabolismQ24815754
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systemsQ25255639
Evolutionary programming as a platform for in silico metabolic engineeringQ25257616
Analysis of optimality in natural and perturbed metabolic networksQ28213254
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Matrix formalism to describe functional states of transcriptional regulatory systemsQ28469032
Regulatory on/off minimization of metabolic flux changes after genetic perturbationsQ28769658
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growthQ29397612
Systems biology: a brief overviewQ29547514
Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimizationQ29616020
Reconciliation of genome-scale metabolic reconstructions for comparative systems analysisQ30432712
Dynamic analysis of integrated signaling, metabolic, and regulatory networksQ30441717
Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networksQ33286434
Towards a genome-scale kinetic model of cellular metabolismQ33527111
13C metabolic flux analysisQ34084355
Energy balance for analysis of complex metabolic networksQ34178210
Ensemble modeling of metabolic networksQ37008279
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.Q39916365
Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric modelsQ42934732
A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expressionQ43830640
Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux.Q43886395
Constraints-based models: regulation of gene expression reduces the steady-state solution spaceQ45211444
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux spaceQ47417801
Dynamic modeling of the central carbon metabolism of Escherichia coliQ50970929
P433issue2
P304page(s)112-119
P577publication date2012-01-28
P1433published inMetabolic EngineeringQ6822334
P1476titleExploring the gap between dynamic and constraint-based models of metabolism
P478volume14

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cites work (P2860)
Q55402486A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load.
Q38817911Computational Model Predicts the Effects of Targeting Cellular Metabolism in Pancreatic Cancer
Q38579075Constructing kinetic models of metabolism at genome-scales: A review
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Q28083571In Silico Constraint-Based Strain Optimization Methods: the Quest for Optimal Cell Factories
Q57176910In Silico Prediction of Large-Scale Microbial Production Performance: Constraints for Getting Proper Data-Driven Models
Q108126729MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics
Q27144251Metabolomics and systems pharmacology: why and how to model the human metabolic network for drug discovery
Q40393458Modeling the Contribution of Allosteric Regulation for Flux Control in the Central Carbon Metabolism of E. coli
Q45943114Optimization of Multi-Omic Genome-Scale Models: Methodologies, Hands-on Tutorial, and Perspectives.
Q45292349Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks
Q43019726The stimulatory effect of mannitol on levan biosynthesis: Lessons from metabolic systems analysis of Halomonas smyrnensis AAD6(T.).
Q34341551Understanding regulation of metabolism through feasibility analysis.

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