genome-scale
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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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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X-Chromosome Control of Genome-Scale Recombination Rates in House Mice
... of genome-scale crossover rate, autosomal crossover rate mod- ifiers should have evolved as increases in recombination rate along the PWD lineage and/or decreases in recombina- tion rate along the CAST ...
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Development and experimental verification of a genome-scale metabolic model for Corynebacterium glutamicum
... The genome-scale metabolic network was based on the pathways in the Bio- Cyc database collection ...the genome-scale model constructed using only pub- lic databases contains incorrect and ...
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Revisiting the in vivo GlnR binding sites at the genome scale in Bacillus subtilis
... Despite knowledge of GlnR-regulated genes, a global iden- tification of the TnrA/GlnR motifs directly bound by GlnR was still missing. Here, we used chromatin immunoprecipi- tation of GlnR-DNA complexes coupled with ...
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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
... provide genome-scale models of high qual- ity, in terms of usability and standards, has become a priority during the last ...of genome-scale models to ensure high-qual- ity outputs, not only ...
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Cofactors revisited - Predicting the impact of flavoprotein-related diseases on a genome scale
... Flavin adenine dinucleotide (FAD) and its precursor flavin mononucleotide (FMN) are redox cofactors that are required for the activity of more than hundred human enzymes. Mutations in the genes encoding these proteins ...
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RNA-guided CRISPR-Cas technologies for genome-scale investigation of disease processes
... A similar large-scale study also utilized the CRISPR- Cas9 system to develop a lentiviral library containing 73,000 sgRNAs against 7,114 genes that was used for genetic screens in human cells [41]. The library was ...
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Genome Scale Identification of Resistance Functions in Pseudomonas aeruginosa Using Tn seq
... ABSTRACT We describe a deep-sequencing procedure for tracking large numbers of transposon mutants of Pseudomonas aerugi- nosa. The procedure employs a new Tn-seq methodology based on the generation and amplification of ...
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Genome-scale data resolve ancestral rock-inhabiting lifestyle in Dothideomycetes (Ascomycota)
... of genome-scale data to resolve long-standing evolutionary and taxonomic issues (Chan and Ragan 2013), phylogenomic ap- proaches are rather uncommon for Dothideomycetes, although about 250 sequenced genomes ...
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Genome-Scale Evolution and Phylodynamics of Equine H3N8 Influenza A Virus
... H3N8 genome most likely arose in the 1950s (95% between 1943 and 1962; Table 2), which is consistent with previous hypotheses of H3N8 viruses circulating in South America (59) some years before the 1963 ...
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Genome-Scale Phylogeny of the Alphavirus Genus Suggests a Marine Origin
... overall genome organization and virion morphology (80), the extensive divergence between the genera of the Togaviridae means that there remains no significant sequence homology remaining between the ...
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A genome scale overexpression screen to reveal drug activity in human cells
... To dissect some of these mechanisms by which drugs act within the cell, we postulated that, when overexpressed, genes conferring resistance to a lethal chemical treatment can illuminate the drug mode of action. ...
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A Flexible Genome-Scale SARS-CoV-2 Clone Resource
... Shortly after the outbreak, the complete genome of two SARS-CoV-2 strains were published [7,8]. Using the genome sequence as a reference, Chan et al. identified 12 viral open reading frames (ORFs), ...
12
Genome Scale Patterns of Recombination between Coinfecting Vaccinia Viruses
... One expects that when viruses are passaged five times under these conditions, the passaging should provide an opportunity for repeated rounds of replication and recombination. We also exam- ined what the virus progeny ...
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Genome-scale investigation of phenotypically distinct but nearly clonal Trichoderma strains
... Plant Mini Kit (Qiagen) as per manufacturers’ instructions. DNA samples were sequenced with an Illumina GAII (Solexa) machine by the Massey University Genome Service, New Zealand. The data were analysed to ...
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Genome-scale analysis identifies SERPINE1 and SPARC as diagnostic and prognostic biomarkers in gastric cancer
... Human Genome U133A Array was performed for gene expression profiling ...Human Genome U133 Plus ...Cancer Genome Atlas (TCGA) were downloaded from the Genomic Data Commons Data Portal and were used ...
12
Genome-scale analysis to identify prognostic markers in patients with early-stage pancreatic ductal adenocarcinoma after pancreaticoduodenectomy
... whole genome expression level screening, we identified 1,238 markers that are related to the prognosis of PDAC after pancreaticoduodenectomy and selected 9 genes among these prognosis-related genes by using a ...
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Genome-scale analysis to identify prognostic microRNA biomarkers in patients with early stage pancreatic ductal adenocarcinoma after pancreaticoduodenectomy
... Genome-wide data filtering is one of the most promising tools for the identification of biomarkers and therapeutic targets. The notion that miRNAs are closely related to the prognosis of cancers is increasingly ...
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