Genome-scale models of microbial cells: evaluating the consequences of constraints

Nat Rev Microbiol. 2004 Nov;2(11):886-97. doi: 10.1038/nrmicro1023.


Microbial cells operate under governing constraints that limit their range of possible functions. With the availability of annotated genome sequences, it has become possible to reconstruct genome-scale biochemical reaction networks for microorganisms. The imposition of governing constraints on a reconstructed biochemical network leads to the definition of achievable cellular functions. In recent years, a substantial and growing toolbox of computational analysis methods has been developed to study the characteristics and capabilities of microorganisms using a constraint-based reconstruction and analysis (COBRA) approach. This approach provides a biochemically and genetically consistent framework for the generation of hypotheses and the testing of functions of microbial cells.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Bacterial Physiological Phenomena*
  • Computational Biology
  • Genome, Bacterial*
  • Mathematics
  • Models, Biological*
  • Phenotype
  • Software
  • Systems Theory