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Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox
The manner in which microorganisms utilize their metabolic processes can be predicted using constraint-based analysis of genome-scale metabolic networks. Herein, we present the constraint-basedExpand
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Global reconstruction of the human metabolic network based on genomic and bibliomic data
Metabolism is a vital cellular process, and its malfunction is a major contributor to human disease. Metabolic networks are complex and highly interconnected, and thus systems-level computationalExpand
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Context-Specific Metabolic Networks Are Consistent with Experiments
TLDR
We present a method called Gene Inactivity Moderated by Metabolism and Expression (GIMME) to achieve this goal. Expand
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Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation
BackgroundSeveral strains of bacteria have sequenced and annotated genomes, which have been used in conjunction with biochemical and physiological data to reconstruct genome-scale metabolic networks.Expand
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Pancreatic trypsin increases matrix metalloproteinase-9 accumulation and activation during acute intestinal ischemia-reperfusion in the rat.
Ischemia-reperfusion of the intestine produces a set of inflammatory mediators, the origin of which has recently been shown to involve pancreatic digestive enzymes. Matrix metalloproteinase-9 (MMP-9)Expand
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Three factors underlying incorrect in silico predictions of essential metabolic genes
TLDR
We show that genes that are falsely predicted to be non-essential (for growth) share three characteristics across multiple organisms and growth media, suggesting incomplete knowledge of metabolism surrounding these genes. Expand
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Wolf dispersal in the Rocky Mountains, Western United States: 1993–2008
Gray wolves (Canis lupus) were extirpated from the northern Rocky Mountains (NRM) of the United States by the 1930s. Dispersing wolves from Canada naturally recolonized Montana and first denned thereExpand
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Habitat selection, condition, and survival of Shiras moose in northwest Wyoming
The purpose of this study was to provide the Wyoming Department of Transportation (WYDOT) and the Wyoming Game and Fish Department (WGFD) with information that could be used to assess the importanceExpand
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Deep Semantic Protein Representation for Annotation, Discovery, and Engineering
TLDR
We present a novel, function-based approach to protein annotation and discovery called D-SPACE (Deep Semantic Protein Annotation Classification and Exploration), comprised of a multi-task, multi-label deep neural network trained on over 70 million proteins. Expand
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Metabolite coupling in genome-scale metabolic networks
TLDR
Metabolite coupling is an important topological property of metabolic networks. Expand
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