metabolic network
Comparative Analysis of Salmonella Genomes Identifies a Metabolic Network for Escalating Growth in the Inflamed Gut
... large metabolic network that likely epitomizes the “winning strategy” employed by members of the gastrointestinal pathovar to edge out competing microbes in the lumen of the inflamed gut, thereby enhancing ...
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Metabolic network capacity of Escherichia coli for Krebs cycle-dependent proline hydroxylation
... Metabolic modeling and calculation of metabolic fluxes The metabolic network of E. coli was adapted from lit- erature [20, 44] and comprised glycolysis (EMP), pen- tose phosphate pathway ...
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Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for Spinosad Production improvement
... genome-scale metabolic network (GSM) constructed based on genome annotation information provide an integral level to review organism metabol- ...in metabolic engineering as a systems biology tool ...
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Metabolic network as a progression biomarker of premanifest Huntington’s disease
... rate, network activity values were computed on an individual basis in metabolic scans from a separate longitudinal cohort of gene carriers, designated HD3 (Figure 1 and Supplemental Table ...groups, ...
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Double and multiple knockout simulations for genome-scale metabolic network reconstructions
... formulas given as Java strings. As expected we are con- fronted with longer runtimes up to almost 4h for double gene knockouts compared to < 70 min for double reac- tion knockouts. This is due to the fact that we need ...
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The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies
... in metabolic network, utilized to dis- cover potential combinatorial engineering targets, can be revealed by applying grouping reaction constraint to constraints-based flux analysis ...the metabolic ...
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Gene connectivity and enzyme evolution in the human metabolic network
... global metabolic network, we found under positive selec- tion in Europeans (CEU) 13 genes with a complete selective sweep ...of metabolic genes) and 19 genes with an incomplete sweep ...in ...
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A community-driven reconstruction of the Aspergillus niger metabolic network
... its metabolic flexibility with respect to utilizable substrates, there has been sustained research to elucidate the metab- olism of this ...and metabolic network of ...
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Metabolic Network Analysis and Metatranscriptomics Reveal Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI
... In the present report, we present a computational pipeline to predict seed com- pounds using metabolic network reconstructions generated from KBase (8). We apply this pipeline to a collection of 36 ...
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Models of the human metabolic network: aiming to reconcile metabolomics and genomics
... The metabolic syndrome, inborn errors of metabolism, and drug-induced changes to metabolic states all bring about a seemingly bewildering array of alterations in metabolite concentrations; these often occur ...
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Bistability in a Metabolic Network Underpins the De Novo Evolution of Colony Switching in Pseudomonas fluorescens
... central metabolic pathway — the pyrimidine biosynthetic ...these metabolic resources between polymer production (leading to capsulation) and cell division (leading to noncapsulation); this bifurcation marks ...
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Synthesis and Enzymatic Studies of Selenium Derivatized Nucleosides, Nucleotides and Nucleic Acids
... the metabolic pathway data and modeled them as directed ...the metabolic networks, which take into account the similarity of network topology and the enzymes’ ...for metabolic network ...
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In silico model-guided identification of transcriptional regulator targets for efficient strain design
... As mentioned earlier, h-BeReTa utilizes an uninte- grated approach which treats the cellular metabolism and regulation as two modules in the framework and then combines them systematically as previously pro- posed in ...
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Metabolic Pathway Analysis for Nutrient Removal of the Consortium between C. vulgaris and P. aeruginosa
... genome-scale metabolic network for the consortium, the biochemical reactions were ordered in a matrix S with dimension m × n, whose rows (m) represent the mass balance for each metabolite (X), and n is the ...
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In silico characterization of microbial electrosynthesis for metabolic engineering of biochemicals
... Characterizing changes to ATP yield and biomass growth rate are fundamental to understanding how elec- trical enhancement impacts cellular metabolism. To determine the extent to which electrical enhancement can influence ...
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Proteomic analysis of chicken embryonic trachea and kidney tissues after infection in ovo by avian infectious bronchitis coronavirus
... Viral replication requires energy and macromolecular precursors derived from the metabolic network of the host. In the present results obtained using 2-DE, the abundance of some proteins which are ...
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Scalable Graph-Mining Techniques with Applications to Systems Biology.
... organism-wide metabolic net- work that model phenotype-related metabolic ...the metabolic networks of phenotype-expressing organisms and not present in phenotype-non-expressing ...the ...
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TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
... Many additional databases provide information that can complement metabolic network databases. Linking to these other data sources enhances our ability to learn about an organism’s metabolism. TrypanoCyc, ...
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TrypanoCyc : a community led biochemical pathways database for Trypanosoma brucei
... lenge. Metabolic network-based methods offer a means to contextualise and integrate data to help inference of biolog- ical function ...on metabolic networks and pathways are therefore crucial to ...
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Short term metabolic adjustments in Plasmodium falciparum counter hypoxanthine deprivation at the expense of long term viability
... the metabolic network ...given metabolic reaction. c A metabolic network model showing integration of metabolic and transcriptomic ...
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