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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).
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Supplementary information
Supplementary Figures Tables and Texts
Supplementary Figures 1–10, Supplementary Tables 1–4, Supplementary Methods and Supplementary Notes 1–7 (PDF 2544 kb)
Supplementary Data set 1
All models in SBML and JSON format (ZIP 3239 kb)
Supplementary Data set 2
Model statistics (XLSX 1008 kb)
Supplementary Data set 3
ROS generating reactions (XLSX 9302 kb)
Supplementary Data set 4
TF Barcode information (XLSX 1073 kb)
Supplementary Data set 5
ALE data for GAM/NGAM calculations (XLSX 13 kb)
Supplementary Data set 6
iML1515 GEM-PRO (XLSX 487 kb)
Supplementary Data set 7
dGPR network in cytoscape format (ZIP 935 kb)
Supplementary Data set 8
iML1515 dGPR Cytoscape Map (PDF 473 kb)
Supplementary Data set 9
OMICs Data Mapping (XLSX 112 kb)
Supplementary Data set 10
Master phenotype database (XLSX 31077 kb)
Supplementary Data set 11
All essential predictions (XLSX 4690 kb)
Supplementary Data set 12
iML-iso (XLSX 262 kb)
Supplementary Data set 13
Gene conservation (XLSX 37116 kb)
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Monk, J., Lloyd, C., Brunk, E. et al. iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol 35, 904–908 (2017). https://doi.org/10.1038/nbt.3956
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DOI: https://doi.org/10.1038/nbt.3956
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