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Gene knockout simulations are relatively straightforward to implement, simply by constraining the flux values of the target reaction to zero, but the identification of reliable gene amplification targets is rather difficult. Here, we report a new algorithm which incorporates physiological data into a model to improve the model\u2019s prediction capabilities and to capitalize on the relationships between genes and metabolic fluxes.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We developed an algorithm, flux variability scanning based on enforced objective flux (FVSEOF) with grouping reaction (GR) constraints, in an effort to identify gene amplification targets by considering reactions that co-carry flux values based on physiological omics data<jats:italic>via<\/jats:italic>\u201cGR constraints\u201d. This method scans changes in the variabilities of metabolic fluxes in response to an artificially enforced objective flux of product formation. The gene amplification targets predicted using this method were validated by comparing the predicted effects with the previous experimental results obtained for the production of shikimic acid and putrescine in<jats:italic>Escherichia coli<\/jats:italic>. Moreover, new gene amplification targets for further enhancing putrescine production were validated through experiments involving the overexpression of each identified targeted gene under condition-controlled batch cultivation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>FVSEOF with GR constraints allows identification of gene amplification targets for metabolic engineering of microbial strains in order to enhance the production of desired bioproducts. The algorithm was validated through the experiments on the enhanced production of putrescine in<jats:italic>E. coli<\/jats:italic>, in addition to the comparison with the previously reported experimental data. The FVSEOF strategy with GR constraints will be generally useful for developing industrially important microbial strains having enhanced capabilities of producing chemicals of interest.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1752-0509-6-106","type":"journal-article","created":{"date-parts":[[2012,8,21]],"date-time":"2012-08-21T08:15:04Z","timestamp":1345536904000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":64,"title":["Flux variability scanning based on enforced objective flux for identifying gene amplification targets"],"prefix":"10.1186","volume":"6","author":[{"given":"Jong Myoung","family":"Park","sequence":"first","affiliation":[]},{"given":"Hye Min","family":"Park","sequence":"additional","affiliation":[]},{"given":"Won Jun","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Hyun Uk","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Tae Yong","family":"Kim","sequence":"additional","affiliation":[]},{"given":"Sang Yup","family":"Lee","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2012,8,21]]},"reference":[{"key":"927_CR1","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1016\/j.tibtech.2005.05.003","volume":"23","author":"SY Lee","year":"2005","unstructured":"Lee SY, Lee DY, Kim TY: Systems biotechnology for strain improvement. 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