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Relevant bibliographies by topics / Genome-Scale Metabolic Network (GSMN) / Dissertations / Theses

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Dissertations / Theses on the topic 'Genome-Scale Metabolic Network (GSMN)'

Author: Grafiati

Published: 25 January 2025

Last updated: 31 July 2025

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1

Negre, Delphine. "Rationalisation de l’Accès aux Produits Naturels Fongiques par une Approche OSMAC in silico : Cas d’étude avec la modélisation du métabolisme de Penicillium rubens." Electronic Thesis or Diss., Nantes Université, 2024. http://www.theses.fr/2024NANU4038.

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Face à la résistance accrue aux antibiotiques menaçant la santé publique, la prospection de nouvelles molécules biologiquement actives est pressante. Les champignons filamenteux se distinguent par leur capacité à synthétiser une large gamme de produits naturels, sous l’influence de clusters de gènes biosynthétiques (BGC) qui orchestrent la production de métabolites spécialisés. Toutefois, de nombreux produits issus de ces BGCs n’ont pas encore été caractérisés et leur chimiodiversité demeure sous-explorée en raison de l’incapacité à activer l’ensemble de leur potentiel en laboratoire. L’approc

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2

Gautam, Jyotshana. "Genome-Scale Metabolic Network Reconstruction of Thermotoga sp.Strain RQ7." Bowling Green State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1605228158638208.

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3

xinjian, qi. "COMPUTATIONAL ANALYSIS, VISUALIZATION AND TEXT MINING OF METABOLIC NETWORKS." Case Western Reserve University School of Graduate Studies / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=case1378479338.

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4

Loira, Nicolas. "Scaffold-based reconstruction method of genome-scale metabolic models." Thesis, Bordeaux 1, 2012. http://www.theses.fr/2012BOR14484/document.

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La compréhension des organismes vivant a été une quête pendant longtemps. Depuisles premiers progrès des derniers siècles, nous sommes arrivés jusqu’au point où desquantités massives de données et d’information sont constamment générées. Bien que,jusqu’au présent la plupart du travail a été concentré sur la génération d’un catalogued’éléments biologiques, ce n’est pas que récemment qu’un effort coordonné pour découvrirles réseaux de relations entre ces parties a été constaté. Nous nous sommes intéressésà comprendre non pas seulement ces réseaux, mais aussi la façon dont, à partir de sesconnexi

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5

Kalapanulak, Saowalak. "High quality genome-scale metabolic network reconstruction of Mycobacterium tuberculosis and comparison with human metabolic network : application for drug targets identification." Thesis, University of Edinburgh, 2009. http://hdl.handle.net/1842/3925.

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Mycobacterium tuberculosis (Mtb), a pathogenic bacterium, is the causative agent in the vast majority of human tuberculosis (TB) cases. Nearly one-third of the world’s population has been affected by TB and annually two million deaths result from the disease. Because of the high cost of medication for a long term treatment with multiple drugs and the increase of multidrug-resistant Mtb strains, faster-acting drugs and more effective vaccines are urgently demanded. Several metabolic pathways of Mtb are attractive for identifying novel drug targets against TB. Hence, a high quality genome-scale

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6

Vieira, Milreu Paulo. "Enumerating functional substructures of genome-scale metabolic networks : stories, precursors and organisations." Phd thesis, Université Claude Bernard - Lyon I, 2012. http://tel.archives-ouvertes.fr/tel-00850704.

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In this thesis, we presented three different methods for enumerating special subnetworks containedin a metabolic network: metabolic stories, minimal precursor sets and chemical organisations. Foreach of the three methods, we gave theoretical results, and for the two first ones, we further providedan illustration on how to apply them in order to study the metabolic behaviour of living organisms.Metabolic stories are defined as maximal directed acyclic graphs whose sets of sources and targets arerestricted to a subset of the nodes. The initial motivation of this definition was to analyse metabol

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7

Griffin, Daniel C. "Investigating the Clostridium botulinum neurotoxin production process using a genome-scale metabolic network enhanced surrogate system." Thesis, University of Surrey, 2016. http://epubs.surrey.ac.uk/809809/.

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Clostridium botulinum (C. botulinum) produces a neurotoxin which can be used in a clinical environment to treat diseases and disorders characterised by muscle hypertension or spasm. However, previous research has mostly focused on the biochemical mode of action of the toxin and the disease it manifests. In order to increase our understanding of the process further, this study aimed to investigate the metabolism of various biomarkers, thought to be correlated with neurotoxin biosynthesis. The objective was to increase our understanding of the metabolism which drives the production of C. botulin

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8

Triana, Dopico Julián. "Model-based analysis and metabolic design of a cyanobacterium for bio-products synthesis." Doctoral thesis, Universitat Politècnica de València, 2014. http://hdl.handle.net/10251/39351.

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The current investigation is aimed at the reconstruction and analysis of genome-scale metabolic models. Specifically, it is focused on the use of mathematical-computational simulations to predict the cellular metabolism behavior towards bio-products production. The photosynthetic cyanobacterium Synechococcus elongatus PCC7942 was studied as biological system. This prokaryotic has been used in several studies as a biological platform for the synthesis of several substances for industrial interest. These studies are based on the advantage of autotrophic systems, which basically requires light a

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9

TAI, HSIAO-HSIEN, and 戴筱銜. "Metabolic Reprogramming of the Genome-scale Metabolic Network of Liver Deficient." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/73na5f.

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碩士<br>國立中正大學<br>化學工程研究所<br>106<br>This study used the liver as the main axis to exploit the significant flux distribution differences between normal cells and cancer cells to find biomarkers or oncogenes under the case of cancer. Based on the human metabolic network model Recon2.2, and use tissue-specific data from the Human Protein Atlas (HPA), the Virtual Metabolic Human (VMH) to provide the nutrients and Cost Optimization Reaction Dependency Assessment (CORDA) algorithm to generate the model reconstructs of liver health and cancer. Through the use of the Nested Hybrid Differential Evolution

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10

Dias, Oscar. "Reconstruction of the genome-scale metabolic network of Kluyveromyces lactis." Doctoral thesis, 2013. http://hdl.handle.net/1822/24859.

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System Biology proposes to study biological components, as well as the interactions between them, to understand and predict systems’ behaviour through the use of mathematical models. Under this scope, Genome-Scale Metabolic Models (GSMMs) can be regarded as mathematical representations of the intrinsic metabolic capabilities of a given organism, encoded in its genome, and can be used in a variety of applications like predicting the phenotypical behaviour of a given organism in different environmental and genetic perturbations. The reconstruction of these models comprehends four fundament

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11

Cruz, Fernando João Pereira da. "Genome-Scale Metabolic Network Reconstruction of the dairy bacterium Streptococcus thermophilus." Master's thesis, 2017. http://hdl.handle.net/1822/56116.

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Dissertação de mestrado em Bioinformatics<br>The dairy food industry is constantly changing as novel biotechnological techniques improve the manufacturing process of dairy products. Widely used over the years in the yogurt and cheese manufacturing, Streptococcus thermophilus is now considered as an extremely valuable lactic acid bacterium for the annual market of the dairy industry. A specific, but of easy-access knowledge regarding the thermophilic bacteria metabolism would be a plus for the continuous growth of such industry. In this work, we present the Genome-Scale Metabolic (GSM) mo

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12

Dias, José Miguel Gonçalves. "Reconstructing the metabolic network of Lactobacillus helveticus on a genome-wide scale." Master's thesis, 2017. http://hdl.handle.net/1822/56112.

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Dissertação de mestrado em Bioinformatics<br>The constant growth of high-throughput data generation and omics approaches require informatics support and (semi) automated processes to be developed. With increasing number of sequenced genomes available, metabolic engineering processes will allow a rational alteration of the genetic architecture to achieve specific phenotypes. These alterations will allow to generate and optimize features of some organisms with economic and health interest. Lactobacillus helveticus is an important industrial lactic-acid bacterium being used in the productio

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13

Hung-Yi, Lin, and 林泓毅. "Structural Analysis And Flux Variability Analysis Of Genome-Scale Metabolic Network Of Hepatocyte." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/p3sqnn.

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碩士<br>國立中正大學<br>化學工程研究所<br>102<br>Metabolic activities in normal cells rely primarily on mitochondrial oxidative phosphorylation to generate ATP for energy. Unlike in normal cells, glycolysis is enhanced and oxidative phosphorylation capacity is reduced in various cancer cells. This phenomenon is corresponding to the Warburg Effect. Recon2 liver model used in this study include 2168 metabolites, 3041 reaction, eight compartments and 1410 genes. For data comparison against other Recon2 sub-model (liver cells, lung macrophages, epidermal cells), analysis of their common features and differences.

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14

Song, Carl Yulun. "Genome-scale Metabolic Network Reconstruction and Constraint-based Flux Balance Analysis of Toxoplasma gondii." Thesis, 2012. http://hdl.handle.net/1807/33538.

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The increasing prevalence of apicomplexan parasites such as Plasmodium, Toxoplasma, and Cryptosporidium represents a significant global healthcare burden. Treatment options are increasingly limited due to the emergence of new resistant strains. We postulate that parasites have evolved distinct metabolic strategies critical for growth and survival during human infections, and therefore susceptible to drug targeting using a systematic approach. I developed iCS306, a fully characterized metabolic network reconstruction of the model organism Toxoplasma gondii via extensive curation of available ge

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15

Konate, Mariam. "Structure-Based Genome Scale Function Prediction and Reconstruction of the Mycobacterium tuberculosis Metabolic Network." Thesis, 2014. https://doi.org/10.7916/D8GT5KRF.

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Due to vast improvements in sequencing methods over the past few decades, the availability of genomic data is rapidly increasing, thus bringing about the need for functional characterization tools. Considering the breadth of data involved, functional assays would be impractical and only a computational method could afford fast and cost-effective functional annotations. Therefore, homology-based computational methods are routinely used to assign putative molecular functions that can later be confirmed with targeted experiments. These methods are particularly well suited to predict the function

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16

SHIU, WEI-SHIANG, and 徐偉翔. "Reconstruction of Colon Cancer Cell Metabolic Network on Genome Scale and Potential Oncogene Discovery." Thesis, 2019. http://ndltd.ncl.edu.tw/handle/jp33w4.

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碩士<br>國立中正大學<br>化學工程研究所<br>107<br>According to the RNA Seq and protein expression, data of various tissues provided by the Cancer Genome Atlas (TCGA) database and the Human Protein Atlas (HPA) website, and based on the human genome-scale metabolic network model (Recon 2.2 Model). This study used two different algorithms: Cost Optimization Reaction Dependency Assessment (CORDA) and Integrative Metabolic Analysis Tool (iMAT) to reconstruct four different metabolic network models of colon cell. Considering the requirements of the experiment, this study used the components of DMEM and RPMI-1640 as

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17

Guerra, André Catarino. "Genome-scale metabolic network reconstruction of Polaromonas sp. strain JS666: analysis of cDCE degradation rates and design of experiments for bioremediation improvement." Master's thesis, 2015. http://hdl.handle.net/10362/15839.

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Release of chloroethene compounds into the environment often results in groundwater contamination, which puts people at risk of exposure by drinking contaminated water. cDCE (cis-1,2-dichloroethene) accumulation on subsurface environments is a common environmental problem due to stagnation and partial degradation of other precursor chloroethene species. Polaromonas sp. strain JS666 apparently requires no exotic growth factors to be used as a bioaugmentation agent for aerobic cDCE degradation. Although being the only suitable microorganism found capable of such, further studies are needed for i

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