Population Balances in Biomedical Engineering: Segregation Through the Distribution of Cell States

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Dynamic Flux Balance Analysis of diauxic growth in Escherichia coli. Biophysical Journal. Genome-scale analysis of Saccharomyces cerevisiae metabolism and ethanol production in fed-batch culture. Biotechnology and Bioengineering. Dynamic analysis of integrated signaling, metabolic, and regulatory networks.


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PLoS Computational Biology. Dynamic flux balance analysis of the metabolism of Saccharomyces cerevisiae during the shift from fully respirative or respirofermentative metabolic states to anaerobiosis. FEBS Journal. The application of flux balance analysis in systems biology.


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Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing. Biotechnology Journal. Characterization of Clostridium ljungdahlii OTA1: a non-autotrophic hyper ethanol-producing strain. Exploring complex cellular phenotypes and model-guided strain design with a novel genome-scale metabolic model of Clostridium thermocellum DSM implementing an adjustable cellulosome.

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Long term impact of stressing agents on fermentative hydrogen production: Effect on the hydrogenase flux and population diversity. Renewable Energy. View Article Google Scholar High production of butyric acid by Clostridium tyrobutyricum mutant. Frontiers of Chemical Science and Engineering. In silico analysis of Clostridium acetobutylicum ATCC metabolic response to an external electron supply. Bioprocess and Biosystems Engineering.

Chen J, Henson MA. In silico metabolic engineering of Clostridium ljungdahlii for synthesis gas fermentation.

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Metabolic modeling of clostridia: Current developments and applications. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii. Microbial Cell Factories. Genome-scale metabolic analysis of Clostridium thermocellum for bioethanol production. A review of genome-scale metabolic flux modeling of anaerobiosis in biotechnology.

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Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Molecular Systems Biology. Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: A systems biological analysis. Dynamic flux balance analysis of a genetic engineered cyanobacterium for ethanol production.

Parameter estimation. Chemical Engineering Transactions. Kleessen S, Nikoloski Z. Quantitative modeling of triacylglycerol homeostasis in yeast—Metabolic requirement for lipolysis to promote membrane lipid synthesis and cellular growth. Systematic development of hybrid cybernetic models: Application to recombinant yeast co-consuming glucose and xylose. Eslamloueyan R, Setoodeh P. Optimization of fed-batch recombinant yeast fermentation for ethanol production using a reduced dynamic flux balance model based on artificial neural networks. Chemical Engineering Communications.

Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae. Modeling of yeast metabolism and process dynamics in batch fermentation. Optimization of fed-batch Saccharomyces cerevisiae fermentation using dynamic flux balance models. Biotechnology Progress.

Coupling kinetic expressions and metabolic networks for predicting wine fermentations. Expanding a dynamic flux balance model of yeast fermentation to genome-scale.

Population Balances in Biomedical Engineering: Segregation Through the Distribution of Cell States

Steady-state and dynamic flux balance analysis of ethanol production by Saccharomyces cerevisiae. IET Systems Biology. Construction of robust dynamic genome-scale metabolic model structures of Saccharomyces cerevisiae through iterative re-parameterization. Dynamic behavior of regulatory elements in the hierarchical regulatory network of various carbon sources-grown Escherichia coli. Journal of Microbiology and Biotechnology.

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A fuzzy logic approach for regulation in flux balance analysis. Biochemical Engineering Journal. Dynamic strain scanning optimization: An efficient strain design strategy for balanced yield, titer, and productivity. DySScO strategy for strain design. BMC Biotechnology. Dynamic metabolic engineering for increasing bioprocess productivity. Varma A, Palsson BO. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W Hybrid neural modeling framework for simulation and optimization of diauxie-involved fed-batch fermentative succinate production.

Chemical Engineering Science. Application of dynamic flux balance analysis to an industrial Escherichia coli fermentation. Dynamic metabolic flux analysis demonstrated on cultures where the limiting substrate is changed from carbon to nitrogen and vice versa. Journal of Biomedicine and Biotechnology. Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures. Dynamic flux balance modeling of S. Lisha KP, Sarkar D. Dynamic flux balance analysis of batch fermentation: Effect of genetic manipulations on ethanol production.

A dynamic, genome-scale flux model of Lactococcus lactis to increase specific recombinant protein expression. Nolan RP, Lee K. Dynamic model of CHO cell metabolism. Dynamic modeling of aerobic growth of Shewanella oneidensis. Predicting triauxic growth, flux distributions, and energy requirement for growth. Development of a Chlamydomonas reinhardtii metabolic network dynamic model to describe distinct phenotypes occurring at different CO2 levels. Influence of agricultural activities in the structure and metabolic functionality of paramo soil samples in Colombia studied using a metagenomics analysis in dynamic state.

Ecological Modelling. A reliable simulator for dynamic flux balance analysis. Sensitivity analysis approaches applied to systems biology models. Sensitivity analysis for the reduction of complex metabolism models. Journal of Process Control. Sumner T.

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Sensitivity analysis in systems biology modelling and its application to a multi-scale model of blood glucose homeostasis: University College London; Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nature Reviews Microbiology. A methodology for performing global uncertainty and sensitivity analysis in systems biology.

Journal of Theoretical Biology.