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 12 of 12 for “"genome-scale metabolic models"”.
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Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models
… whose fluxes are “coupled"" or correlated in genome-scale models. By identified sets of coupled reactions, modelers can 1.) reduce the dimensionality of genome-scale models, 2.) identify reactions that must be modulated together during metabolic engineering, and 3.) identify sets of important …
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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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Design and optimization of microbial communities
… Synergies between computational methods and genome-scale metabolic models have been explored in the last years, as a way to unravel community interactions and behavior, as demonstrated by the numerous simulation methods developed for application in the context of microbial communities. The …
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Characterizing the higher order metabolism of oral streptococci
… is often explainable by differences in the metabolic networks that underly microbial metabolism. However, closely related microbial species that have structurally conserved metabolic networks with relatively few differences still display diverse growth profiles under the same growth …
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Integration of metabolic modelling with machine learning to identify mechanisms underlying antibiotic killing
… of antibiotics relies critically on downstream metabolic effects, in addition to inhibition of primary targets. Here we present a novel computational pipeline to expedite investigation of these effects: we combine computational modelling of metabolic networks with data from experimental screens …
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Genome Scale Metabolic Modelling of Arabidopsis thaliana and Chlamydomonas reinhardtii
Recent advances in genome sequencing technology have enabled the elucidation of complete genome sequence for plants and algae. Genome scale metabolic models constructed from genome annotations represent the entire metabolic characteristics of the organism and can be used to integrate other data and …
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Genome scale metabolic modelling of Phaeodactylum tricornutum
… work involves construction and analysis of genome scale metabolic models (GSMs) of Phaeodactylum tricornutum, a model diatom, the characterisation of physiological properties and the identification of the potential strategies to optimise the lipid production. GSMs were constructed based on a …
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Improving predictions in metabolic engineering problems by incorporating enzyme structural information
… focuses in the improvement of predictions in metabolic engineering problems by incorporating enzyme structural information. The uncertainty on the usage of NADP(H) or NAD(H) as co-factors was addressed due to the major impact in metabolic engineering applications these molecules have, severely …
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Computational methods for multi-omic models of cell metabolism and their importance for theoretical computer science
… science provides powerful abstraction tools for metabolic networks. Cell metabolism is the set of chemical reactions taking place in a cell, with the aim of maintaining the living state of the cell. Due to the intrinsic complexity of metabolic networks, predicting the phenotypic traits resulting …
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Omics-driven and constraint-based modelling of microbial community metabolism
… of microbial ecology, metagenomics, and metabolic modelling. More specifically, this thesis outlines the development and applications of omics-driven metabolic modelling approaches to understand microbial community metabolism in diverse ecological contexts. I begin by providing background …
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Model-guided Analysis of Plant Metabolism and Design of Metabolic Engineering Strategies
… This has enabled researchers to use models and data to design experiments and guide new discovery as well as test for consistency. One such computational method is constraint-based metabolic flux modeling. This is performed using genome-scale metabolic models (GEMs) that are a …
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ASSESSMENT OF CELL AND METABOLIC IMPACT OF MICROTUBULE TARGETING AGENTS (MTA) IN NEURODEGENERATION AND NEURON MODELS.
… for therapeutic intervention. Based on the metabolic characterization and transcriptomic data, and applying specific metabolic reconstructions after data integration using Genome-Scale Metabolic Models (GSMM) we report that, in PC12 cell model, neuronal differentiation is accompanied by …