Accelerated discovery via a whole-cell model

Nat Methods. 2013 Dec;10(12):1192-5. doi: 10.1038/nmeth.2724. Epub 2013 Nov 3.

Abstract

To test the promise of whole-cell modeling to facilitate scientific inquiry, we compared growth rates simulated in a whole-cell model with experimental measurements for all viable single-gene disruption Mycoplasma genitalium strains. Discrepancies between simulations and experiments led to predictions about kinetic parameters of specific enzymes that we subsequently validated. These findings represent, to our knowledge, the first application of whole-cell modeling to accelerate biological discovery.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Bacterial Proteins / metabolism
  • Catalysis
  • Computational Biology / methods*
  • Computer Simulation
  • Gene Expression Profiling
  • Gene Expression Regulation, Bacterial
  • Gene Regulatory Networks
  • Genes, Bacterial / genetics
  • Models, Biological*
  • Mycoplasma genitalium / genetics*
  • Mycoplasma genitalium / metabolism*
  • Phenotype
  • Regression Analysis
  • Reproducibility of Results
  • Systems Biology*

Substances

  • Bacterial Proteins