genome-scale metabolic models
More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes
... A conceptually similar framework is BacArena [96]. BacArena also uses a dynamic form of FBA simulations to model microbes over time, but simulates individual microbes across a 2D grid [96] rather than microbial ...
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Current status and applications of genome scale metabolic models
... only representative microbial species. Thus, the use of GEMs will become more powerful when it becomes possible to identify all (or at least most) microbial species in a given community. For example, key microorganisms ...
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Genome-Scale Metabolic Modeling with Protein Expressions of Normal and Cancerous Colorectal Tissues for Oncogene Inference
... a metabolic disease. The first discovery of metabolic alterations in cancer cells refers to Otto Warburg’s ...in metabolic fluxes that are evident in cancer cells compared with most normal tissue ...
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Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model
... Genome-scale metabolic models (GEMs) are currently the only approach that enables the modeling and global analysis of an organism’s metabolic and transport network by a global analysis ...
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Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement
... 50 genome-scale metabolic models have been reconstructed for over 30 species from three main domains of life, ...of genome-scale metabolic models have been reported ...
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Enumeration of minimal stoichiometric precursor sets in metabolic networks
... Our first goal was to validate our method: we compared the results obtained with sasita to the ones in Monk et al. [16]. We enumerated and compared the minimal precursor sets allowing for biomass production of the E. ...
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Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis
... complete genome of ...the genome sequence showed numerous genes for lignocellulose bioconversion and systematic analysis of the genome sequence annota- tion is necessary to obtain useful ...insights. ...
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Developing a Microbial Consortium for Enhanced Metabolite Production from Simulated Food Waste
... exchange metabolic fluxes of monocultures and pairwise co-cultures using genome-scale metabolic models on a food waste ...the scale of the consortium fermentation proved ...
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Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum
... for metabolic engineering purposes ...silico metabolic models, which help predict the cellular behav- ior and production of useful chemicals, are highly ...the genome-scale ...
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Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27
... silico metabolic modeling and analysis can be considered as one of the promising techniques to characterize the physio- logical behaviour and metabolic states of an organism upon various ...
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In silico reconstruction and experimental validation of Saccharopolyspora erythraea genome-scale metabolic model iZZ1342 that accounts for 1685 ORFs
... ematical models improves the ability to analyze and integrate these omics data (Gehlenborg et ...Abstract genome data and intracellular metabolic pathways are trans- formed into mathematical ...
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Reconstruction of a Genome Scale Metabolic Model of the polyhydroxybutyrate producing methanotroph Methylocystis parvus OBBP
... as Genome Scale Meta- bolic Models (GSMMs) allowing to define metabolic engineering ...industrial scale involves an initial production of bio- mass under nutrient sufficient conditions, ...
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Simulating cyanobacterial phenotypes by integrating flux balance analysis, kinetics, and a light distribution function
... Background: Genome-scale models (GSMs) are widely used to predict cyanobacterial phenotypes in photobiore- actors ...a genome-scale metabolic model of Synechocystis 6803 with ...
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Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling
... A genome-scale metabolic model (GSMM) assembles all biochemical reactions possibly occurring in an organism to predict cellular metabolic functions (16), delineate the mechanisms of ...
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Genome-scale metabolic network reconstruction of Saccharopolyspora spinosa for Spinosad Production improvement
... a genome-scale metabolic network reconstruction (GSMR) for ...its genome information, literature data and experimental data was ...silico metabolic network ...
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Elucidating redox balance shift in Scheffersomyces stipitis’ fermentative metabolism using a modified genome-scale metabolic model
... the scale and complexity involved at genome-scale ...a genome-scale understanding of the cellular metabolism of ...both models have certain ...
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Designing Metabolic Division of Labor in Microbial Communities
... of metabolic reactions allowed in an organism is increasingly ...silico genome-scale ...nonintuitive metabolic division of labor, including, for exam- ple, splitting the tricarboxylic acid ...
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Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
... The genome-scale metabolic network for ...published models of related Clostridia species and two draft ...draft metabolic model was generated using the ModelSEED database ...existing ...
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Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen
... a genome-scale metabolic model of the ...mutans models gen- erated from automated reconstruction pipelines and more complete than other manually curated ...
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Genome-scale metabolic reconstructions and theoretical investigation of methane conversion in Methylomicrobium buryatense strain 5G(B1)
... by metabolic mode- ling of methanol utilization ...phy models, the theoretical calculation of methanotrophy has shown very poor correlation with measured param- eters [18, ...core metabolic ...
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