This is a preview of subscription content, access via your institution
Relevant articles
Open Access articles citing this article.
-
Accurate prediction of gene deletion phenotypes with Flux Cone Learning
Nature Communications Open Access 26 September 2025
-
Bioenergetic stress potentiates antimicrobial resistance and persistence
Nature Communications Open Access 09 June 2025
-
In silico identification of gene targets to enhance C12 fatty acid production in Escherichia coli
Applied Microbiology and Biotechnology Open Access 08 May 2025
Access options
Access Nature and 54 other Nature Portfolio journals
Get Nature+, our best-value online-access subscription
£17.99 / 30 days
cancel any time
Subscribe to this journal
Receive 12 print issues and online access
£169.00 per year
only £14.08 per issue
Buy this article
- Purchase on SpringerLink
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
References
O'Brien, E.J., Monk, J.M. & Palsson, B.O. Cell 161, 971–987 (2015).
Monk, J., Nogales, J. & Palsson, B.O. Nat. Biotechnol. 32, 447–452 (2014).
Denger, K. et al. Nature 507, 114–117 (2014).
Kamat, S.S., Williams, H.J. & Raushel, F.M. Nature 480, 570–573 (2011).
Hassaninasab, A., Hashimoto, Y., Tomita-Yokotani, K. & Kobayashi, M. Proc. Natl. Acad. Sci. USA 108, 6615–6620 (2011).
Feist, A.M. et al. Mol. Syst. Biol. 3, 121 (2007).
Orth, J.D. et al. Mol. Syst. Biol. 7, 535 (2011).
Reed, J.L., Vo, T.D., Schilling, C.H. & Palsson, B.O. Genome Biol. 4, R54 (2003).
Orth, J.D. & Palsson, B.O. Biotechnol. Bioeng. 107, 403–412 (2010).
Kumar, V.S. & Maranas, C.D. PLOS Comput. Biol. 5, e1000308 (2009).
Brynildsen, M.P., Winkler, J.A., Spina, C.S., MacDonald, I.C. & Collins, J.J. Nat. Biotechnol. 31, 160–165 (2013).
Gama-Castro, S. et al. Nucleic Acids Res. 36, D120–D124 (2008).
Chang, R.L. et al. Science 340, 1220–1223 (2013).
Brunk, E. et al. BMC Syst. Biol. 10, 26 (2016).
Kim, M., Zorraquino, V. & Tagkopoulos, I. PLoS Comput. Biol. 11, e1004127 (2015).
Yamamoto, N. et al. Mol. Syst. Biol. 5, 335 (2009).
Takeuchi, R. et al. BMC Microbiol. 14, 171 (2014).
Schmidt, A. et al. Nat. Biotechnol. 34, 104–110 (2016).
Lukjancenko, O., Wassenaar, T.M. & Ussery, D.W. Microb. Ecol. 60, 708–720 (2010).
Monk, J.M. et al. Proc. Natl. Acad. Sci. USA 110, 20338–20343 (2013).
Scholz, M. et al. Nat. Methods 13, 435–438 (2016).
Karlsson, F.H. et al. Nature 498, 99–103 (2013).
Jensen, K.F. J. Bacteriol. 175, 3401–3407 (1993).
Schellenberger, J. et al. Nat. Protoc. 6, 1290–1307 (2011).
Guzmán, G.I. et al. Proc. Natl. Acad. Sci. USA 112, 929–934 (2015).
Chang, R.L., Xie, L., Bourne, P.E. & Palsson, B.O. BMC Syst. Biol. 7, 102 (2013).
Chung, H. et al. Curr. Opin. Biotechnol. 36, 73–84 (2015).
Notebaart, R.A. et al. Proc. Natl. Acad. Sci. USA 111, 11762–11767 (2014).
Salipante, S.J. et al. Genome Res. 25, 119–128 (2015).
von Mentzer, A. et al. Nat. Genet. 46, 1321–1326 (2014).
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
Authors and Affiliations
Corresponding author
Ethics declarations
Competing interests
The authors declare no competing financial interests.
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)
Rights and permissions
About this article
Cite this article
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
Published:
Issue date:
DOI: https://doi.org/10.1038/nbt.3956
This article is cited by
-
Combining biosensor and metabolic network optimization strategies for enhanced l-threonine production in Escherichia coli
Biotechnology for Biofuels and Bioproducts (2025)
-
MACAW: a method for semi-automatic detection of errors in genome-scale metabolic models
Genome Biology (2025)
-
Design and implementation of aerobic and ambient CO2-reduction as an entry-point for enhanced carbon fixation
Nature Communications (2025)
-
Longitudinal big biological data in the AI era
Molecular Systems Biology (2025)
-
Accurate prediction of gene deletion phenotypes with Flux Cone Learning
Nature Communications (2025)