Applications of genome-scale metabolic reconstructions

Authors

  • Matthew A Oberhardt,

    1. Department of Biomedical Engineering, University of Virginia, Health System, Charlottesville, VA, USA
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  • Bernhard Ø Palsson,

    1. Department of Bioengineering, University of California at San Diego, La Jolla, CA, USA
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  • Jason A Papin

    Corresponding author
    1. Department of Biomedical Engineering, University of Virginia, Health System, Charlottesville, VA, USA
    • Corresponding author. Department of Biomedical Engineering, University of Virginia, Box 800759, Health System, Charlottesville, VA 22908, USA. Tel.: +1 434 924 8195; Fax: +1 434 982 3870; E-mail: papin@virginia.edu

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Abstract

The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. Reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. In this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology.

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