Systematic Construction of Kinetic Models from Genome-Scale Metabolic Networks
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November 2013 |
The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization
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November 2016 |
Metabolic states with maximal specific rate carry flux through an elementary flux mode
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February 2014 |
A blueprint for human whole-cell modeling
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February 2018 |
New types of experimental data shape the use of enzyme kinetics for dynamic network modeling
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November 2013 |
The control of flux
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Environments that Induce Synthetic Microbial Ecosystems
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November 2010 |
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
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February 2001 |
Correlation between TCA cycle flux and glucose uptake rate during respiro-fermentative growth of Saccharomyces cerevisiae
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December 2009 |
Incorporating genome-wide DNA sequence information into a dynamic whole-cell model of Escherichia coli: application to DNA replication
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September 2008 |
Gobal optimization of hybrid kinetic/FBA models via outer-approximation
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January 2015 |
Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production
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April 2013 |
Kinetic modeling can describe in vivo glycolysis in Entamoeba histolytica: Modeling Entamoeba glycolysis
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August 2007 |
Large‐scale 13 C‐flux analysis reveals distinct transcriptional control of respiratory and fermentative metabolism in Escherichia coli
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January 2011 |
A diurnal flux balance model of Synechocystis sp. PCC 6803 metabolism
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January 2019 |
Modeling of uncertainties in biochemical reactions
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Rethinking Antibiotic Research and Development: World War II and the Penicillin Collaborative
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March 2013 |
Metabolomics and systems biology: making sense of the soup
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June 2004 |
Approximative kinetic formats used in metabolic network modeling
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January 2005 |
Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.
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January 1994 |
Kinetic models of metabolism that consider alternative steady-state solutions of intracellular fluxes and concentrations
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March 2019 |
Validation and Optimization of a Yeast Dynamic Flux Balance Model using a Parallel Bioreactor System
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January 2013 |
Systematic design and in vitro validation of novel one-carbon assimilation pathways
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December 2019 |
A Whole-Cell Computational Model Predicts Phenotype from Genotype
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July 2012 |
A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains
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December 2016 |
Exploring the gap between dynamic and constraint-based models of metabolism
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March 2012 |
Ensemble Modeling of Metabolic Networks
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December 2008 |
Emergent Biosynthetic Capacity in Simple Microbial Communities
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July 2014 |
Metabolic engineering of Escherichia coli for 1-butanol production
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November 2008 |
Metabolite concentrations, fluxes and free energies imply efficient enzyme usage
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May 2016 |
Transgenic plants in the biopharmaceutical market
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February 2005 |
Design principles and operating principles: the yin and yang of optimal functioning
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March 2003 |
Metabolic flux distributions inCorynebacterium glutamicum during growth and lysine overproduction
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March 2000 |
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry: Do we understand yeast glycolysis?
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September 2000 |
Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis–Menten and approximate kinetic equations
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A probabilistic approach to identify putative drug targets in biochemical networks
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Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.
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January 1993 |
Using Gene Essentiality and Synthetic Lethality Information to Correct Yeast and CHO Cell Genome-Scale Models
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September 2015 |
Reducing the allowable kinetic space by constructing ensemble of dynamic models with the same steady-state flux
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January 2011 |
Kinetic modelling of plant metabolic pathways
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March 2012 |
Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
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May 2011 |
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
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April 2010 |
Structural kinetic modeling of metabolic networks
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July 2006 |
Improving prediction fidelity of cellular metabolism with kinetic descriptions
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December 2015 |
Kinetic modeling of the Calvin cycle identifies flux control and stable metabolomes in Synechocystis carbon fixation
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October 2018 |
Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacterium saccharolyticum
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May 2015 |
Metabolite profiling: from diagnostics to systems biology
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Toward Scalable Whole-Cell Modeling of Human Cells
- Goldberg, Arthur P.; Chew, Yin Hoon; Karr, Jonathan R.
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Proceedings of the 2016 annual ACM Conference on SIGSIM Principles of Advanced Discrete Simulation - SIGSIM-PADS '16
https://doi.org/10.1145/2901378.2901402
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conference
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Expanding a dynamic flux balance model of yeast fermentation to genome-scale
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Models describing the kinetics of ribulose biphosphate carboxylase-oxygenase
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The challenges of in silico biology
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Metabolic Control Analysis under Uncertainty: Framework Development and Case Studies
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Multilevel engineering of the upstream module of aromatic amino acid biosynthesis in Saccharomyces cerevisiae for high production of polymer and drug precursors
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July 2017 |
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism
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February 2014 |
Thermodynamic analysis of the pathway for ethanol production from cellobiose in Clostridium thermocellum
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September 2019 |
Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
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September 2004 |
Something from nothing − bridging the gap between constraint-based and kinetic modelling: Constraint-based meets kinetic modelling
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October 2007 |
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
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December 2006 |
Diurnal Regulation of Cellular Processes in the Cyanobacterium Synechocystis sp. Strain PCC 6803: Insights from Transcriptomic, Fluxomic, and Physiological Analyses
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Simulation of cellular biochemical system kinetics: Simulation of cellular biochemical system kinetics
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Fat synthesis in adipose tissue. An examination of stoichiometric constraints
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Assessing the Metabolic Impact of Nitrogen Availability Using a Compartmentalized Maize Leaf Genome-Scale Model
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Simple constrained-optimization view of acetate overflow inE. coli
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2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis
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Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli
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Control of Bacterial Fermentations
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Metabolic Control Analysis: A Tool for Designing Strategies to Manipulate Metabolic Pathways
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Fed-batch cultivation of animal cells using different medium design concepts and feeding strategies
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January 2006 |
Dynamic Flux Balance Analysis of Diauxic Growth in Escherichia coli
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September 2002 |
Dynamic flux balance modeling to increase the production of high-value compounds in green microalgae
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August 2016 |
Clostridium butyricum population balance model: Predicting dynamic metabolic flux distributions using an objective function related to extracellular glycerol content
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Predictions for oxygen supply control to enhance population stability of engineered production strains
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Multidimensional Optimality of Microbial Metabolism
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Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints
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The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
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January 2007 |
Estimating optimal profiles of genetic alterations using constraint-based models
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January 2004 |
What is flux balance analysis?
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March 2010 |
iML1515, a knowledgebase that computes Escherichia coli traits
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October 2017 |
Glycolysis in Entamoeba histolytica: Biochemical characterization of recombinant glycolytic enzymes and flux control analysis
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March 2005 |
Optimization-driven identification of genetic perturbations accelerates the convergence of model parameters in ensemble modeling of metabolic networks
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June 2013 |