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Acknowledgements

We would like to thank D. Zielinski, J. Lerman, J. Orth, S. Bowen, and J. Reed for helpful discussions. We'd like to thank M. Abrams for copyediting help. The work was funded by the Novo Nordisk Foundation (Grant NNF10CC1016517) and by grant 1R01GM057089 from the NIH/NIGMS and 1-U01-AI124316-01 from NIH/NIAID. B.O.P., C.J.L., and A.M.F. received support from the Novo Nordisk Foundation Center for Biosustainability (NNF10CC1016517).

Author information

Author notes

    • Jonathan M Monk
    • , Colton J Lloyd
    •  & Elizabeth Brunk

    These authors contributed equally to this work.

Affiliations

  1. Department of Bioengineering, University of California, San Diego, La Jolla, California, USA.

    • Jonathan M Monk
    • , Colton J Lloyd
    • , Elizabeth Brunk
    • , Nathan Mih
    • , Anand Sastry
    • , Zachary King
    • , Zhen Zhang
    • , Adam M Feist
    •  & Bernhard O Palsson
  2. Graduate School of Biological Sciences Nara Institute of Science and Technology Ikoma, Nara, Japan.

    • Rikiya Takeuchi
    • , Wataru Nomura
    •  & Hirotada Mori
  3. The NNF Center for Biosustainability, The Technical University of Denmark, Lyngby, Denmark.

    • Adam M Feist
    •  & Bernhard O Palsson

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Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Bernhard O Palsson.

Supplementary information

PDF files

  1. 1.

    Supplementary Figures Tables and Texts

    Supplementary Figures 1–10, Supplementary Tables 1–4, Supplementary Methods and Supplementary Notes 1–7

  2. 2.

    Supplementary Data set 8

    iML1515 dGPR Cytoscape Map

Zip files

  1. 1.

    Supplementary Data set 1

    All models in SBML and JSON format

  2. 2.

    Supplementary Data set 7

    dGPR network in cytoscape format

Excel files

  1. 1.

    Supplementary Data set 2

    Model statistics

  2. 2.

    Supplementary Data set 3

    ROS generating reactions

  3. 3.

    Supplementary Data set 4

    TF Barcode information

  4. 4.

    Supplementary Data set 5

    ALE data for GAM/NGAM calculations

  5. 5.

    Supplementary Data set 6

    iML1515 GEM-PRO

  6. 6.

    Supplementary Data set 9

    OMICs Data Mapping

  7. 7.

    Supplementary Data set 10

    Master phenotype database

  8. 8.

    Supplementary Data set 11

    All essential predictions

  9. 9.

    Supplementary Data set 12

    iML-iso

  10. 10.

    Supplementary Data set 13

    Gene conservation

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DOI

https://doi.org/10.1038/nbt.3956