Metabolic network reconstruction
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Ebook "Systems biology of tuberculosis" starts with a general introduction into the relevance of systems biology for understanding tuberculosis. This will be followed by several chapters which describe the application of systems biology to various aspects of the study of the pathogen, Mycobacterium tuberculosis, and its interaction with the host. The book provides the reader with an account of how the new science of systems biology is providing novel insights into the ancient scourge of tuberculosis.
238p ladongphongthanh1008 22-04-2024 3 2 Download
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Ebook "Systems biology and biotechnology of Escherichia coli" covered include genomics and functional genomics, resources for systems biology, network analysis, genome-scale metabolic reconstruction, modelling and simulation, dynamic modelling and simulation, systems-level analysis of evolution, plasmids and expression systems, protein synthesis, production and export, engineering the central metabolism, synthetic biology, and systems metabolic engineering of E. coli. This book provides readers with guidance on how a complex biological system can be studied using E. coli as a model organism.
470p cotieubac1004 15-03-2024 2 0 Download
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Inference of protein’s membership in metabolic pathways has become an important task in functional annotation of protein. The membership information can provide valuable context to the basic functional annotation and also aid reconstruction of incomplete pathways. Previous works have shown success of inference by using various similarity measures of gene ontology.
10p vitzuyu2711 29-09-2021 19 1 Download
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A central challenge to understanding the ecological and biogeochemical roles of microorganisms in natural and human engineered ecosystems is the reconstruction of metabolic interaction networks from environmental sequence information.
10p viwyoming2711 16-12-2020 13 1 Download
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Despite several recent advances in the automated generation of draft metabolic reconstructions, the manual curation of these networks to produce high quality genome-scale metabolic models remains a labour-intensive and challenging task.
6p vikentucky2711 26-11-2020 16 2 Download
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The explosive growth of microbiome research has yielded great quantities of data. These data provide us with many answers, but raise just as many questions. 16S rDNA—the backbone of microbiome analyses—allows us to assess α-diversity, β-diversity, and microbe-microbe associations, which characterize the overall properties of an ecosystem.
10p vioklahoma2711 19-11-2020 12 0 Download
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Constraint-based analysis has become a widely used method to study metabolic networks. While some of the associated algorithms can be applied to genome-scale network reconstructions with several thousands of reactions, others are limited to small or medium-sized models.
10p vioklahoma2711 19-11-2020 7 0 Download
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Constraint-based modeling is a widely used and powerful methodology to assess the metabolic phenotypes and capabilities of an organism. The starting point and cornerstone of all such modeling is a genome-scale metabolic network reconstruction.
11p vicoachella2711 27-10-2020 12 1 Download
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Genome-scale metabolic network reconstructions are low level chemical representations of biological organisms. These models allow the system-level investigation of metabolic phenotypes using a variety of computational approaches.
8p vicoachella2711 27-10-2020 9 0 Download
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The green microalga Dunaliella salina accumulates a high proportion of β-carotene during abiotic stress conditions. To better understand the intracellular flux distribution leading to carotenoid accumulation, this work aimed at reconstructing a carbon core metabolic network for D. salina CCAP 19/18 based on the recently published nuclear genome and its validation with experimental observations and literature data.
9p vicolorado2711 23-10-2020 15 1 Download
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The reconstruction of metabolic networks and the three-dimensional coverage of protein structures have reached the genome-scale in the widely studied Escherichia coli K-12 MG1655 strain. The combination of the two leads to the formation of a structural systems biology framework, which we have used to analyze differences between the reactive oxygen species (ROS) sensitivity of the proteomes of sequenced strains of E. coli.
23p vicolorado2711 22-10-2020 5 0 Download
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In this paper, we develop a computational method for the metabolic network reconstruction that can uncover not only pairwise interactions but also interactions involving more than two substrates/products such as triple interactions, quartic interactions, etc.
13p nguynthithuylinh 02-06-2017 18 2 Download
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The topology of central carbon metabolism ofAspergillus nigerwas identified and the metabolic network reconstruc-ted, by integrating genomic, biochemical and physiological information available for this microorganism and other related fungi. The reconstructed network may serve as a valuabledatabase for annotationof genes identified in future genome sequencing projects on aspergilli. Based on the metabolic reconstruction, a stoichiometric model was set up that includes 284metabolites and335reactions,...
11p tumor12 20-04-2013 24 2 Download
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The metabolic network is an important biological network which consists of enzymes and chemical compounds. However, a large number of meta-bolic pathways remains unknown, and most organism-specific metabolic pathways contain many missing enzymes. We present a novel method to identify the genes coding for missing enzymes using available genomic and chemical information from bacterial genomes.
12p galaxyss3 19-03-2013 41 2 Download