{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:43:40Z","timestamp":1773290620249,"version":"3.50.1"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The reconstruction of metabolic networks at the genome scale has allowed the analysis of metabolic pathways at an unprecedented level of complexity. Elementary flux modes (EFMs) are an appropriate concept for such analysis. However, their number grows in a combinatorial fashion as the size of the metabolic network increases, which renders the application of EFMs approach to large metabolic networks difficult. Novel methods are expected to deal with such complexity.<\/jats:p>\n               <jats:p>Results: In this article, we present a novel optimization-based method for determining a minimal generating set of EFMs, i.e. a convex basis. We show that a subset of elements of this convex basis can be effectively computed even in large metabolic networks. Our method was applied to examine the structure of pathways producing lysine in Escherichia coli. We obtained a more varied and informative set of pathways in comparison with existing methods. In addition, an alternative pathway to produce lysine was identified using a detour via propionyl-CoA, which shows the predictive power of our novel approach.<\/jats:p>\n               <jats:p>Availability: The source code in C++ is available upon request.<\/jats:p>\n               <jats:p>Contact: \u00a0fplanes@tecnun.es<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq681","type":"journal-article","created":{"date-parts":[[2010,12,12]],"date-time":"2010-12-12T01:33:52Z","timestamp":1292117632000},"page":"534-540","source":"Crossref","is-referenced-by-count":45,"title":["Exploring metabolic pathways in genome-scale networks via generating flux modes"],"prefix":"10.1093","volume":"27","author":[{"given":"A.","family":"Rezola","sequence":"first","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"L. F.","family":"de Figueiredo","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"},{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"M.","family":"Brock","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"J.","family":"Pey","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"A.","family":"Podhorski","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"C.","family":"Wittmann","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"S.","family":"Schuster","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"A.","family":"Bockmayr","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]},{"given":"F. J.","family":"Planes","sequence":"additional","affiliation":[{"name":"1 Biomedical Engineering, CEIT and TECNUN, University of Navarra, Manuel de Lardizabal 15, 20018 San Sebastian, Spain, 2Department of Bioinformatics, Friedrich-Schiller-University Jena, 07743 Jena, Germany, 3PhD Program in Computational Biology, Instituto Gulbenkian de Ci\u00eancia, 2780-156 Oeiras, Portugal, 4Junior Research Group of Microbial Biochemistry and Physiology, Leibniz Institute for Natural Product Research and Infection Biology - Hans Kn\u00f6ll Institute (HKI), 07745 Jena, 5Institute of Biochemical Engineering, Technical University Braunschweig, 38106 Braunschweig and 6DFG-Research Center Matheon, FB Mathematik und Informatik, Freie Universit\u00e4t Berlin, Arnimallee 6, D-14195 Berlin, Germany"}]}],"member":"286","published-online":{"date-parts":[[2010,12,10]]},"reference":[{"key":"2023012511573471200_B1","doi-asserted-by":"crossref","first-page":"3848","DOI":"10.1128\/AEM.68.8.3848-3854.2002","article-title":"Metabolic engineering of a novel propionate-independent pathway for the production of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) in recombinant Salmonella enterica serovar Typhimurium","volume":"68","author":"Aldor","year":"2002","journal-title":"Appl. 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