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)

Items 701–800 of 1,002

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  15. In Silico Insights into the Symbiotic Nitrogen Fixation in Sinorhizobium meliloti via Metabolic Reconstruction
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  26. Path to improving the life cycle and quality of genome-scale models of metabolism
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  27. Current state of genome-scale modeling in filamentous fungi
    Julian Brandl, Mikael Rørdam Andersen · 2015 · Biotechnology Letters
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    Paula Jouhten, Tomasz Boruta, Sergej Andrejev, Filipa M. Pereira, Isabel Rocha, Kiran Raosaheb Patil · 2016 · Scientific Reports
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    2022
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  86. ACBM: An Integrated Agent and Constraint Based Modeling Framework for Simulation of Microbial Communities
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  89. Database and tools for metabolic network analysis
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  91. Dispensability of Escherichia coli ’s latent pathways
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