{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T12:05:48Z","timestamp":1772021148534,"version":"3.50.1"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2020,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.5"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,5,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem.<\/jats:p>\n               <jats:p>Results: We first review the shortcomings of the existing generic sampling scheme\u2014switch randomization\u2014and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties.<\/jats:p>\n               <jats:p>Contact: \u00a0basler@mpimp-golm.mpg.de; nikoloski@mpimp-golm.mpg.de<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr145","type":"journal-article","created":{"date-parts":[[2011,3,25]],"date-time":"2011-03-25T00:25:33Z","timestamp":1301012733000},"page":"1397-1403","source":"Crossref","is-referenced-by-count":23,"title":["Mass-balanced randomization of metabolic networks"],"prefix":"10.1093","volume":"27","author":[{"given":"Georg","family":"Basler","sequence":"first","affiliation":[{"name":"1 University of Potsdam, Institute for Biochemistry and Biology, D-14476 Potsdam, Germany, 2University of Aberdeen, Institute of Medical Sciences, AB25 2ZD Aberdeen, UK and 3Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam, Germany"}]},{"given":"Oliver","family":"Ebenh\u00f6h","sequence":"additional","affiliation":[{"name":"1 University of Potsdam, Institute for Biochemistry and Biology, D-14476 Potsdam, Germany, 2University of Aberdeen, Institute of Medical Sciences, AB25 2ZD Aberdeen, UK and 3Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam, Germany"}]},{"given":"Joachim","family":"Selbig","sequence":"additional","affiliation":[{"name":"1 University of Potsdam, Institute for Biochemistry and Biology, D-14476 Potsdam, Germany, 2University of Aberdeen, Institute of Medical Sciences, AB25 2ZD Aberdeen, UK and 3Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam, Germany"},{"name":"1 University of Potsdam, Institute for Biochemistry and Biology, D-14476 Potsdam, Germany, 2University of Aberdeen, Institute of Medical Sciences, AB25 2ZD Aberdeen, UK and 3Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam, Germany"}]},{"given":"Zoran","family":"Nikoloski","sequence":"additional","affiliation":[{"name":"1 University of Potsdam, Institute for Biochemistry and Biology, D-14476 Potsdam, Germany, 2University of Aberdeen, Institute of Medical Sciences, AB25 2ZD Aberdeen, UK and 3Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam, Germany"},{"name":"1 University of Potsdam, Institute for Biochemistry and Biology, D-14476 Potsdam, Germany, 2University of Aberdeen, Institute of Medical Sciences, AB25 2ZD Aberdeen, UK and 3Max Planck Institute for Molecular Plant Physiology, D-14476 Potsdam, Germany"}]}],"member":"286","published-online":{"date-parts":[[2011,3,23]]},"reference":[{"key":"2023012511040421900_B1","doi-asserted-by":"crossref","first-page":"4947","DOI":"10.1242\/jcs.02714","article-title":"Scale-free networks in cell biology","volume":"118","author":"Albert","year":"2005","journal-title":"J. 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