{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,30]],"date-time":"2026-06-30T02:37:37Z","timestamp":1782787057695,"version":"3.54.5"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"22","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,11,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: An important tool in Systems Biology is the stoichiometric modeling of metabolic networks, where the stationary states of the network are described by a high-dimensional polyhedral cone, the so-called flux cone. Exhaustive descriptions of the metabolism can be obtained by computing the elementary vectors of this cone but, owing to a combinatorial explosion of the number of elementary vectors, this approach becomes computationally intractable for genome scale networks.<\/jats:p><jats:p>Result: Hence, we propose to instead focus on the conversion cone, a projection of the flux cone, which describes the interaction of the metabolism with its external chemical environment. We present a direct method for calculating the elementary vectors of this cone and, by studying the metabolism of Saccharomyces cerevisiae, we demonstrate that such an analysis is computationally feasible even for genome scale networks.<\/jats:p><jats:p>Contact: \u00a0robert.urbanczik@pki.unibe.ch<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti674","type":"journal-article","created":{"date-parts":[[2005,9,28]],"date-time":"2005-09-28T03:23:31Z","timestamp":1127877811000},"page":"4176-4180","source":"Crossref","is-referenced-by-count":47,"title":["Functional stoichiometric analysis of metabolic networks"],"prefix":"10.1093","volume":"21","author":[{"given":"R.","family":"Urbanczik","sequence":"first","affiliation":[{"name":"Institute of Pharmacology, University of Bern \u00a0 Friedb\u00fchlstrasse 49, CH-3010 Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C.","family":"Wagner","sequence":"additional","affiliation":[{"name":"Institute of Pharmacology, University of Bern \u00a0 Friedb\u00fchlstrasse 49, CH-3010 Bern, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2005,9,27]]},"reference":[{"key":"2023061007210129400_b1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1002\/9780470142622.ch1","article-title":"Stability of complex reaction networks","volume-title":"Advances in Chemical Physics","author":"Clarke","year":"1980"},{"key":"2023061007210129400_b2","doi-asserted-by":"crossref","first-page":"255","DOI":"10.1016\/S0303-2647(03)00067-4","article-title":"A method for classifying metabolites in topological pathway analyses based on minimization of pathway number","volume":"70","author":"Dandekar","year":"2003","journal-title":"Biosystems"},{"key":"2023061007210129400_b3","doi-asserted-by":"crossref","first-page":"1298","DOI":"10.1101\/gr.2250904","article-title":"Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model","volume":"14","author":"Duarte","year":"2004","journal-title":"Genome Res."},{"key":"2023061007210129400_b4","volume-title":"Frequently Asked Questions in Polyhedral Computation","author":"Fukuda","year":"2004"},{"key":"2023061007210129400_b5","first-page":"91","article-title":"Double description method revisited","volume-title":"Combinatorics and Computer Science","author":"Fukuda","year":"1995"},{"key":"2023061007210129400_b6","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1080\/00986448908940663","article-title":"The characterization of complex systems of chemical reactions","volume":"83","author":"Happel","year":"1989","journal-title":"Chem. 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