title: Robust design of microbial strains.
abstract: BACKGROUND
  Metabolic engineering algorithms provide means to optimize a biological process leading to the improvement of a biotechnological interesting molecule. Therefore, it is important to understand how to act in a metabolic pathway in order to have the best results in terms of productions. In this work, we present a computational framework that searches for optimal and robust microbial strains that are able to produce target molecules. Our framework performs three tasks: it evaluates the parameter sensitivity of the microbial model, searches for the optimal genetic or fluxes design and finally calculates the robustness of the microbial strains. We are capable to combine the exploration of species, reactions, pathways and knockout parameter spaces with the Pareto-optimality principle.
  
  
  RESULTS
  Our framework provides also theoretical and practical guidelines for design automation. The statistical cross comparison of our new optimization procedures, performed with respect to currently widely used algorithms for bacteria (e.g. Escherichia coli) over different multiple functions, reveals good performances over a variety of biotechnological products.
  
  
  BACKGROUND
  http://www.dmi.unict.it/nicosia/pathDesign.html.
  
  
  BACKGROUND
  nicosia@dmi.unict.it or pl219@cam.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Mathematics and Computer Science, University of Catania, Viale A. Doria 6, 95125 Catania, Italy.
authors.forename: Jole
authors.initials: J
authors.lastname: Costanza
authors.forename: Giovanni
authors.initials: G
authors.lastname: Carapezza
authors.forename: Claudio
authors.initials: C
authors.lastname: Angione
authors.forename: Pietro
authors.initials: P
authors.lastname: Lió
authors.forename: Giuseppe
authors.initials: G
authors.lastname: Nicosia
mesh_terms: D000465:Algorithms; D001709:Biotechnology / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism; D055786:Gene Knockout Techniques; D060847:Metabolic Engineering / Q000379:methods*; D053858:Metabolic Networks and Pathways