Genome-scale microbial in silico models: the constraints-based approach.
@article{Price2003GenomescaleMI, title={Genome-scale microbial in silico models: the constraints-based approach.}, author={Nathan D. Price and Jason A. Papin and Christopher H. Schilling and Bernhard O. Palsson}, journal={Trends in biotechnology}, year={2003}, volume={21 4}, pages={ 162-9 } }
420 Citations
From genomes to in silico cells via metabolic networks.
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This work has shown that a constraint-based reconstruction and analysis approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.
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This chapter introduces the constraint-based modeling approach and focuses on its application to computationally predicting gene essentiality.
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Mixed-integer linear programming was used to calculate and study a subset of the alternate optimal solutions for a genome-scale metabolic model of Escherichia coli (iJR904) under a wide variety of environmental conditions and identified reactions which are used under significantly more environmental conditions suboptimally than optimally.
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Systems biology can be viewed as a genome-scale science that is enabled by the development of highthroughput, or “omics” technologies.
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An integrated genome-scale model for the metabolism and transcriptional regulation in B. subtilis is introduced and a new methodology for the inference of regulatory interactions from gene expression data is proposed, dubbed “atomic regulon inference”.
Use of genome-scale microbial models for metabolic engineering.
- Biology, EngineeringCurrent opinion in biotechnology
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- BiologyMetabolites
- 2014
A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis, and the applicability of the model is demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942.
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- 2014
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Design and application of genome-scale reconstructed metabolic models.
- BiologyMethods in molecular biology
- 2008
In this chapter, the process for the reconstruction of genome-scale metabolic networks is described, and some of the main applications of such models are illustrated. The reconstruction process can…
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