cobra toolbox v3 0 (MathWorks Inc)
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cobra toolbox v3 0
Cobra Toolbox V3 0, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 3218 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cobra+toolbox+v3%2E0/Optimization+Toolbox/pmc12830291-50-7-11
Average 96 stars, based on 3218 article reviews
Cobra Toolbox V3 0, supplied by MathWorks Inc, used in various techniques. Bioz Stars score: 96/100, based on 3218 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/cobra+toolbox+v3%2E0/Optimization+Toolbox/pmc12830291-50-7-11
Average 96 stars, based on 3218 article reviews
cobra toolbox v3 0 - by Bioz Stars,
2026-09
96/100 stars
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Knockdown:Article Title: Reconstruction of a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes. Article Snippet: Green microalgae have emerged as beneficial feedstocks for biofuel production.. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction.. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis. Article Title: Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer Article Snippet: Therefore, this method ensures that the enzyme knockdown simulations are context-specific and considered relative to the metabolic behavior observed in the predicted flux distributions from the baseline model. We consider 70 knockdowns out of 74 possible reactions because we do not perturb the reactions responsible for glucose uptake, lactate secretion, glutamine uptake, and biomass pseudo-reaction, as these are fixed constraints set in the model. All constraint-based modeling was done in Article Title: Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans Article Snippet: Metabolic modeling and flux balance analysis were performed using Cobra Toolbox v3.0 ( ) in Article Title: Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Article Snippet: The COBRA Toolbox v3.0 [32, 39] was used in Article Title: Genome-scale reconstruction of the metabolic network in Streptococcus thermophilus S-3 and assess urea metabolism. Article Snippet: BACKGROUND: Streptococcus thermophilus is an important strain widely used in dairy fermentation, with distinct urea metabolism characteristics compared to other lactic acid bacteria.. The conversion of urea by S. thermophilus has been shown to affect the flavor and acidification characteristics of milk.. Additionally, urea metabolism has been found to significantly increase the number of cells and reduce cell damage under acidic pH conditions, resulting in higher activity. Article Title: Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans. Article Snippet: Metabolic modelling and flux balance analysis were performed using Cobra Toolbox v3.0 (66) in Article Title: Elucidating metabolic mechanisms underlying the influence of specific growth rate on alkaline protease synthesis in Bacillus licheniformis through combined omics and computational modeling analysis. Article Snippet: Specific growth rate is a crucial physiological parameter in fermentation.. This study integrates transcriptomics, metabolomics and genome-scale metabolic modeling to uncover the physiological changes in Bacillus licheniformis induced by specific growth rate during fed-batch fermentation.. The results showed that increasing growth rates significantly enhanced both cell growth and alkaline protease activity. Article Title: A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation. Article Snippet: P. putida models26,51 were analyzed with the COBRA Toolbox v3.0 within the Combined Bisulfite Restriction Analysis Assay:Article Title: Reconstruction of a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes. Article Snippet: Green microalgae have emerged as beneficial feedstocks for biofuel production.. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction.. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis. Article Title: Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer Article Snippet: Therefore, this method ensures that the enzyme knockdown simulations are context-specific and considered relative to the metabolic behavior observed in the predicted flux distributions from the baseline model. We consider 70 knockdowns out of 74 possible reactions because we do not perturb the reactions responsible for glucose uptake, lactate secretion, glutamine uptake, and biomass pseudo-reaction, as these are fixed constraints set in the model. All constraint-based modeling was done in Article Title: Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans Article Snippet: Metabolic modeling and flux balance analysis were performed using Cobra Toolbox v3.0 ( ) in Article Title: Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Article Snippet: The COBRA Toolbox v3.0 [32, 39] was used in Article Title: Genome-scale reconstruction of the metabolic network in Streptococcus thermophilus S-3 and assess urea metabolism. Article Snippet: BACKGROUND: Streptococcus thermophilus is an important strain widely used in dairy fermentation, with distinct urea metabolism characteristics compared to other lactic acid bacteria.. The conversion of urea by S. thermophilus has been shown to affect the flavor and acidification characteristics of milk.. Additionally, urea metabolism has been found to significantly increase the number of cells and reduce cell damage under acidic pH conditions, resulting in higher activity. Article Title: Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans. Article Snippet: Metabolic modelling and flux balance analysis were performed using Cobra Toolbox v3.0 (66) in Article Title: Elucidating metabolic mechanisms underlying the influence of specific growth rate on alkaline protease synthesis in Bacillus licheniformis through combined omics and computational modeling analysis. Article Snippet: Specific growth rate is a crucial physiological parameter in fermentation.. This study integrates transcriptomics, metabolomics and genome-scale metabolic modeling to uncover the physiological changes in Bacillus licheniformis induced by specific growth rate during fed-batch fermentation.. The results showed that increasing growth rates significantly enhanced both cell growth and alkaline protease activity. Article Title: A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation. Article Snippet: P. putida models26,51 were analyzed with the COBRA Toolbox v3.0 within the In Silico:Article Title: Reconstruction of a Genome-Scale Metabolic Model of Scenedesmus obliquus and Its Application for Lipid Production under Three Trophic Modes. Article Snippet: Green microalgae have emerged as beneficial feedstocks for biofuel production.. A systems-level understanding of the biochemical network is needed to harness the microalgal metabolic capacity for bioproduction.. Genome-scale metabolic modeling (GEM) showed immense potential in rational metabolic engineering, utilizing biochemical flux distribution analysis. Article Title: Merging metabolic modeling and imaging for screening therapeutic targets in colorectal cancer Article Snippet: Therefore, this method ensures that the enzyme knockdown simulations are context-specific and considered relative to the metabolic behavior observed in the predicted flux distributions from the baseline model. We consider 70 knockdowns out of 74 possible reactions because we do not perturb the reactions responsible for glucose uptake, lactate secretion, glutamine uptake, and biomass pseudo-reaction, as these are fixed constraints set in the model. All constraint-based modeling was done in Article Title: Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans Article Snippet: Metabolic modeling and flux balance analysis were performed using Cobra Toolbox v3.0 ( ) in Article Title: Improved production of Taxol ® precursors in S. cerevisiae using combinatorial in silico design and metabolic engineering. Article Snippet: The COBRA Toolbox v3.0 [32, 39] was used in Article Title: Genome-scale reconstruction of the metabolic network in Streptococcus thermophilus S-3 and assess urea metabolism. Article Snippet: BACKGROUND: Streptococcus thermophilus is an important strain widely used in dairy fermentation, with distinct urea metabolism characteristics compared to other lactic acid bacteria.. The conversion of urea by S. thermophilus has been shown to affect the flavor and acidification characteristics of milk.. Additionally, urea metabolism has been found to significantly increase the number of cells and reduce cell damage under acidic pH conditions, resulting in higher activity. Article Title: Spatial chromosome organization and adaptation of the radiation-resistant extremophile Deinococcus radiodurans. Article Snippet: Metabolic modelling and flux balance analysis were performed using Cobra Toolbox v3.0 (66) in Article Title: Elucidating metabolic mechanisms underlying the influence of specific growth rate on alkaline protease synthesis in Bacillus licheniformis through combined omics and computational modeling analysis. Article Snippet: Specific growth rate is a crucial physiological parameter in fermentation.. This study integrates transcriptomics, metabolomics and genome-scale metabolic modeling to uncover the physiological changes in Bacillus licheniformis induced by specific growth rate during fed-batch fermentation.. The results showed that increasing growth rates significantly enhanced both cell growth and alkaline protease activity. Article Title: A model-driven approach to upcycling recalcitrant feedstocks in Pseudomonas putida by decoupling PHA production from nutrient limitation. Article Snippet: P. putida models26,51 were analyzed with the COBRA Toolbox v3.0 within the |