Genome Scale Metabolic Network
Double and multiple knockout simulations for genome-scale metabolic network reconstructions
... double or multiple knockout simulation may significantly reduce the search space, without loosing any information. In this paper, we present an algorithmic framework for double and multiple knockouts in qualitative mod- ...
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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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Genome-scale metabolic network reconstruction and in silico flux analysis of the thermophilic bacterium Thermus thermophilus HB27
... its network connectivity (see Additional file 1 for complete list of reactions ...the network gaps using their amino acid sequences collected from various other organisms against the non-redundant protein ...
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Genomic sequencing, genome-scale metabolic network reconstruction, and in silico flux analysis of the grape endophytic fungus Alternaria sp. MG1
... 50.96%. Genome annotation indicated that MG1 possessed complete biosynthesis pathways for stilbenoids, fla- vonoids, and ...the metabolic diversity of MG1. Furthermore, the first genome-scale ...
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A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress
... The rice protein sequences were downloaded from Gramene’s Rice Ensembl genome. The proteins were submitted to an annotation workflow that included HMM-based annotations from InterPro, SMART, PRINT, Prosite and ...
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Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement
... strain D852. Consequently, it was considered that enhan- cing NADPH availability may improve flux towards the FK506 biosynthesis pathway. However, the recombinant strain HT-PZ expressing both genes showed lower con- ...
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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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Reconstruction of genome-scale metabolic model of Yarrowia lipolytica and its application in overproduction of triacylglycerol
... A genome-scale metabolic model (GSMM) is a power- ful platform for investigation of microorganism’s meta- bolic processes and rational strain design, as a GSMM may represent the metabolic ...
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Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii
... The genome-scale metabolic network for ...draft metabolic model was generated using the ModelSEED database ...existing genome annotations in the SEED ...curated ...
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Integrating kinetic model of E coli with genome scale metabolic fluxes overcomes its open system problem and reveals bistability in central metabolism
... the genome-scale model, initially assuming an uninhibited activity through the two reactions (making up the glyoxylate ...the genome-scale model, we find that of the range of possible flux ...
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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 metabolic ...
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Genome-Scale Metabolic Modeling with Protein Expressions of Normal and Cancerous Colorectal Tissues for Oncogene Inference
... diverse metabolic functions, which are complex and specialized in different tissues and cell ...the metabolic basis of various physiological and pathological ...cell-type-specific metabolic models is ...
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Insights into metabolic osmoadaptation of the ectoines-producer bacterium Chromohalobacter salexigens through a high-quality genome scale metabolic model
... structed metabolic network is its ability to produce flux through the biomass reaction ...automated network that are absent (or, at least, present in a much lower number) in the curated iFP764 ...
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Elucidating redox balance shift in Scheffersomyces stipitis’ fermentative metabolism using a modified genome-scale metabolic model
... With the modified GEM iDH814 being capable of pro- ducing xylitol, we designed and performed additional in silico experiments to gain a more in-depth understand- ing of how S. stipitis adjusts its cellular metabolism in ...
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Comprehensive reconstruction and evaluation of Pichia pastoris genome-scale metabolic model that accounts for 1243 ORFs
... Subsequently, to update the P. pastoris GSMM system- atically, the genome annotation information from mainly three databases (KEGG, UniProtKB, IMG) was gathered and merged (Table 1). To establish the new gene–pro- ...
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In silico identification of metabolic engineering strategies for improved lipid production in Yarrowia lipolytica by genome-scale metabolic modeling
... for metabolic engineering of various industrial hosts, including Escherichia coli and Saccharomyces cerevi- siae ...for metabolic engineering of oleaginous yeasts, several GEMs for ole- aginous yeasts, ...
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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 ...core metabolic arrangements of methane oxidation and/or assimilation could account for this ...whole genome-scale metabolic model ...
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A new genome-scale metabolic model of Corynebacterium glutamicum and its application
... A genome-scale metabolic model (GEM) is con- structed based on experimental data and information on gene annotations and functions, metabolites, reac- tions, enzymes, and their interactions [11, ...
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A systematic assessment of current genome scale metabolic reconstruction tools
... the network comparison for completeness because CarveMe and ModelSEED automatically generate them; as they are non-gene associated reactions, this automatically lowers the scores for the other tools that do not ...
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Capturing the response of Clostridium acetobutylicumto chemical stressors using a regulated genome-scale metabolic model
... different metabolic responses, as also corroborated by the DNA microarray ...regulatory network [3] and the identification of the small RNome [4], the development of an integrated whole cell ...
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