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.
Results
Showing 1 to 20 of 48 for “"Metabolic Networks"”.
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Unravelling the complexity of metabolic networks
… resulting in various types of biological networks. Metabolic networks, in particular, play a fundamental role, since they provide the building blocks essential for cellular function, and thus, have recently received a lot of attention. In particular, recent studies have revealed a number …
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Towards structure and dynamics of metabolic networks
… approaches to cover various aspects of metabolic network modelling, especially regarding the limited availability of detailed kinetic knowledge on reaction rates. It is shown that precise mathematical formulations of problems are needed i) to find appropriate and, if possible, efficient …
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Mass-balanced randomization : a significance measure for metabolic networks
Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein-protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, including small average path …
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A control-theoretic approach to dynamic optimization of metabolic networks
… of general control principles that underpin metabolic dynamics is an important part of systems analysis in biology. It has been long argued that many biological regulatory mechanisms have evolved so as to optimize cellular adaptation in response to external stimuli. In this thesis we use an …
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In Search of Generic Properties of Evolved Systems: From Elasticity of Proteins to Structure of Metabolic Networks
… employed flux balance analysis to predict the metabolic phenotypes of synthetic genotypes sampled from a genotype space determined by empirical metabolic databases. That work identified intriguing properties of the set of viable genotypes: the viable fraction of genotypes is very small, yet 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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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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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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Evolution of protein structure, function, and dynamics in biological systems
… biological systems to capture interactions of subnetworks and enzymes by analyzing evolving metabolic networks and find that hierarchical modularity is a key evolutionary principle of organization. Small world behavior increases at lower levels and decreases at higher levels of organization in …
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In silico systems analysis of biopathways
… have been produced; a number of specific genetic/metabolic databases and computational systems have been developed, which makes it possible for biologists to perform in silico analysis of metabolism. With experimental data from laboratory, biologists wish to systematically conduct their analysis …
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Quantitative dynamic modeling of transcriptional networks of embryonic stem cells using integrated framework of Pareto optimality and energy balance
… Analysis of transcriptional regulatory networks and metabolic networks in ESCs thus requires both a nonequilibrium thermodynamic and mass balance framework for designing and understanding complex ESC network approach as well as an optimality approach which can take cellular objectives …
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Evaluation of network inference algorithms and their effects on network analysis for the study of small metabolomic data sets
… evi- dence has recently mounted for the role of metabolic dysfunction in AD. Metabolomic data has therefore been increasingly used in AD studies. Metabolomic disease studies often suffer from small sample sizes and inflated false discovery rates. It is therefore of great importance to identify …
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Metabolic network design and engineering in Escherichia coli
This thesis is a study of metabolic engineering to design and engineer novel metabolic networks with improved metabolic processes that can increase product yield and enhance cellular properties. The succinate synthesis pathways in E. coli were chosen as the model system for network design and …
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An updated genome scale metabolic reconstruction of methanosarcina barkeri
… barkeri genome was published in 2006 after the metabolic reconstruction of M. barkeri, iAF692, was published. The iAF692 reconstruction preformed the first large scale simulations of an Archaea. Since the publication of iAF692, a deeper understanding of Archaea biology has shed light on …
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Machine learning methods for detecting structure in metabolic flow networks
Metabolic flow networks are large scale, mechanistic biological models with good predictive power. However, even when they provide good predictions, interpreting the meaning of their structure can be very difficult, especially for large networks which model entire organisms. This is an …
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System analysis and metabolic engineering of biocatalytic reaction networks : application to indene bioconversion
Metabolic engineering is a science concerned with the improvement of cellular properties through the application of recombinant DNA technology. To this point, the field has frequently been limited to methodological issues pertaining to gene introduction, expression and control by way of molecular …
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Towards Deep Learning Models of Metabolism
… catalyzing the chemical reactions that underpin metabolic processes in living organisms. Despite their importance, a vast majority of enzymes remain uncharacterized, limiting our understanding of their potential roles in metabolism and disease. This thesis aims to address this gap by leveraging …
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Simulation, sensitivity analysis, and optimization of bioprocesses using dynamic flux balance analysis
… programs (LPs) that are constructed based on the metabolic networks of the microorganisms. FBA can be combined with the mathematical models of dynamical biosystems, resulting in dynamic FBA (DFBA) models. DFBA models are difficult to simulate, sensitivity information is challenging to obtain, and …
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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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