Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Daniel Machado; Markus J. Herrgård; Isabel Rocha

doi:10.1371/journal.pcbi.1005140

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Open Access

Peer-reviewed

Research Article

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Daniel Machado ,

* E-mail: dmachado@deb.uminho.pt

Current address: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

Affiliation Centre of Biological Engineering, University of Minho, Braga, Portugal

http://orcid.org/0000-0002-2063-5383

⨯
Markus J. Herrgård,

Affiliation The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsølm, Denmark

http://orcid.org/0000-0003-2377-9929

⨯
Isabel Rocha

Affiliation Centre of Biological Engineering, University of Minho, Braga, Portugal

http://orcid.org/0000-0001-9494-3410

⨯

Stoichiometric Representation of Gene–Protein–Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction

Daniel Machado,
Markus J. Herrgård,
Isabel Rocha

Published: October 6, 2016
https://doi.org/10.1371/journal.pcbi.1005140

About the Authors

Daniel Machado

* E-mail: dmachado@deb.uminho.pt

Current address: Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany

Affiliation Centre of Biological Engineering, University of Minho, Braga, Portugal

http://orcid.org/0000-0002-2063-5383

Markus J. Herrgård

Affiliation The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Horsølm, Denmark

http://orcid.org/0000-0003-2377-9929

Isabel Rocha

Affiliation Centre of Biological Engineering, University of Minho, Braga, Portugal

http://orcid.org/0000-0001-9494-3410

Competing Interests

The authors have declared that no competing interests exist.

Author Contributions

Conceived and designed the experiments: DM IR. Performed the experiments: DM. Analyzed the data: DM MJH IR. Wrote the paper: DM MJH IR. Implemented the software: DM.

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Enzymes
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Stoichiometry
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Enzyme metabolism
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Isozymes
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Simulation and modeling
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Deletion mutation
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Gene expression
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Genomics
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