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- O’Brien, Edward J, et al. Show all 2 Author
- Current opinion in biotechnology 2015 v.34 pp. 125-134
- models; phenotype; prediction; protein synthesis; proteome; transcriptome
- ... Constraint-based models enable the computation of feasible, optimal, and realized biological phenotypes from reaction network reconstructions and constraints on their operation. To date, stoichiometric reconstructions have largely focused on metabolism, resulting in genome-scale metabolic models (M-Models). Recent expansions in network content to encompass proteome synthesis have resulted in model ...
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- O'Brien, Edward J., et al. Show all 4 Authors
- Metabolic engineering 2017 v.39 pp. 220-227
- Escherichia coli; databases; gene expression; metabolism; models; prediction; secretion
- ... The metabolic byproducts secreted by growing cells can be easily measured and provide a window into the state of a cell; they have been essential to the development of microbiology, cancer biology, and biotechnology. Progress in computational modeling of cells has made it possible to predict metabolic byproduct secretion with bottom-up reconstructions of metabolic networks. However, owing to a lac ...
- O’Brien, Edward J., et al. Show all 3 Authors
- Cell 2015 v.161 pp. 971-987
- antibiotics; evolution; genes; metabolic engineering; models
- ... Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have been under development since the first whole-genome sequences appeared in the mid-1990s. A few years ago, this approach began to demonstrate the ability to predict a range of cellular functions, including cellular growth capabilities on various substrates and the effect of gene knockouts at the genome scale. Thus ...
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