Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

Schellenberger, Jan, Que, Richard, Fleming, Ronan M T, Thiele, Ines, Orth, Jeffrey D, Feist, Adam M, Zielinski, Daniel C, Bordbar, Aarash +5 more·2011·Nature Protocols

Cited by (1,002)

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  13. Automated generation of genome-scale metabolic draft reconstructions based on KEGG
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