Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 17 of 17 for “"Metabolic modeling"”.
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Computational strategies for metabolic modeling of yeast
Submission original under an indefinite embargo labeled 'Open Access'. The submission was exported from vireo on 2023-09-01 without embargo terms
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Computational Tools for Metabolic Modeling and Gene Duplication Analysis
… in this area. Next, we delve deeper into the metabolic response of the organism to changing temperatures, and develop methods to model and simulate the fluxes of metabolites occurring through a metabolic network. In particular, we construct a simplified model of aerobic respiration for an …
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Multiscale, multiparadigm metabolic modeling of the keystone diazotrophic cyanobacterium, Trichodesmium erythraeum
… require organisms to interact. Current modeling techniques neglect many of these phenomena, considering cells as separate entities, homogeneous populations, or static members of a population. Biological data conflict with these models: organisms are highly dynamic even in the most ideal …
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Characterization and genome-scale metabolic modeling of catechol-degrading Pseudomonas fluorescens isolated from a petroleum hydrocarbon-impacted site
… performance, catechol, an important metabolic intermediate during monoaromatic hydrocarbon biodegradation, was chosen as the sole carbon source. A set of experiments based on a 23 factorial design was undertaken to investigate how nitrate, sulfate, and phosphate ions affect catechol …
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Is metabolism goal-directed? Investigating the validity of modeling biological systems with cybernetic control via omic data
… models are uniquely juxtaposed to other metabolic modeling frameworks in that they describe the time-dependent regulation of cellular reactions in terms of dynamic "metabolic goals." This approach contrasts starkly with purely mechanistic descriptions of metabolic regulation which seek to …
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Bridging molecular and systems scales in membrane biology
… which integrates molecular simulation and metabolic modeling in the development of a whole-cell model for the photosynthetic bacteria \textit{Procholorococcus marinus} MED4.
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Development of universal stoichiometric coefficients for modeling microalgal cultivation systems
… however, is the lack of robust algae modeling platforms for wastewater treatment that can predict process performance under fluctuating reactor conditions and despite the inevitable biodiversity of influent wastewater. One necessary step towards improved modeling capabilities for algae …
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Constraint-based modeling of host-microbe and microbe-microbe metabolic interactions in the human gut
… computational models. Constraint-based metabolic modeling uses manually curated and validated metabolic reconstructions that constitute a genomically, genetically and biochemically structured knowledge base of a target organism. These reconstructions can be converted into mathematical …
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Strategies for engineering microbial communities
… human health, environmental sustainability, and metabolic engineering. Although it is known that the competition and exchange of nutrients (i.e., metabolic interactions) shape microbial community structure and dynamics, the ability to reliably predict the metabolic interactions and their effect …
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Improving constraint-based metabolic models with deep learning
Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2025-05-01
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Computer-assisted generation and curation of genome-scale metabolic models with case studies in the methanogen genus Methanosarcina
… to other methanogens): the diversity in metabolic capabilities for these organisms enables manipulations of methanogenesis pathways that would be lethal in other methanogens. Genetic manipulation tools have been valuable for identifying functions of individual enzymes and pathways in …
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Dynamic regulation of bacterial metabolic pathways using autonomous, pathway-independent control strategies
Metabolic engineering efforts have so far focused on strain optimization through careful metabolic modeling and tinkering with host genomes, through gene knockouts or knockins, to direct flux in desired channels. These efforts have borne fruit with the development of large manufacturing processes …
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Systems approaches to infer microbial community interactions and their impacts on ecosystem function
… I also highlight how microbial community-scale metabolic models (MCMMs) can be leveraged to predict Clostridioides difficile (C. difficile) colonization in the human gut microbiome, provide mechanistic insights into the niche of C. difficile across different community contexts, and assess …
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A tale of two microbes: Computational investigations of biological processes in escherichia and methanosarcina at multiple scales
… response to stimuli are examined. A variety of modeling approaches are employed to capture phenomena at different scales. Using as model systems Methanosarcina acetivorans, an anaerobic methane producing archaeum adapted to niche environments, and Escherichia coli, a faculative anaerobic …
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Computational methods for integrating metabolomics data with metabolic engineering strain design
… provides data ideal for applications in metabolic engineering. However, many of the computational tools for strain design are built around Flux Balance Analysis (FBA) and were developed using assumptions that preclude direct integration of metabolomics data into the underlying models. To …
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Integrating manual and automated metabolic engineering methods
Made available in DSpace on 2016-07-07T20:27:15Z (GMT). No. of bitstreams: 4 RICHARDS-DISSERTATION-2016.pdf: 3860821 bytes, checksum: cbaf30718ce7594d7f76859b49a220de (MD5) Richards_Matthew.docx: 2576729 bytes, checksum: e2a1076a288d7d31c646df244282d03a (MD5) LICENSE.txt: 4213 bytes, checksum: …