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Optimizing genome-scale network reconstructions

Nature Biotechnology volume 32, pages 447–452 (2014)Cite this article

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Metabolic reconstructions remain limited in their scope and content, and improvements in biochemical knowledge and collaborative research are required.

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Figure 1: Expansion of metabolic networks and global reactome coverage over time.
Figure 2: Similarity analysis of GENREs.
Figure 3: Phylogenetic coverage of GENREs.
Figure 4: Factors limiting GENRE completeness and strategies for improvement.

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Acknowledgements

We would like to thank B. Heavner, A. Bordbar, A. Feist and J. Lerman for helpful discussions and critical review of the manuscript. J.M. is funded by US National Institutes of Health grant R01 GM057089. J.N. was funded by the Spanish Ministry of Education through the National Plan for Scientific Research, Development and Technological Innovation (2008–2011).

Author information

Author notes

  1. Juan Nogales

    Present address: Present address: Department of Environmental Biology, Centro de Investigaciones Biológicas, CSIC, Madrid, Spain.,

  2. Jonathan Monk and Juan Nogales: These authors contributed equally to this work.

Authors and Affiliations

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

    Jonathan Monk, Juan Nogales & Bernhard O Palsson

Authors
  1. Jonathan Monk
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  2. Juan Nogales
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  3. Bernhard O Palsson
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Corresponding author

Correspondence to Bernhard O Palsson.

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Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Table 1 (download XLSX )

Names and properties of the 117 metabolic reconstructions published as of February 2013. We are maintaining an up-to-date list on the SBRG website (sbrg.ucsd.edu/optimizing-genres). (XLSX 25 kb)

Supplementary Table 2 (download XLSX )

List of the 53 curated reconstructions analyzed in this study (XLSX 14 kb)

Supplementary Table 3 (download DOCX )

List of quality metrics and their values for selected reconstructions (DOCX 26 kb)

Supplementary Data (download ZIP )

All curated and reconciled metabolic reconstruction content in.xlsx format. (ZIP 7500 kb)

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Monk, J., Nogales, J. & Palsson, B. Optimizing genome-scale network reconstructions. Nat Biotechnol 32, 447–452 (2014). https://doi.org/10.1038/nbt.2870

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