{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,13]],"date-time":"2025-11-13T01:58:21Z","timestamp":1762999101029},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: Elementary flux modes (EFMs) are important structural tools for the analysis of metabolic networks. It is known that many topologically feasible EFMs are biologically irrelevant. Therefore, tools are needed to find the relevant ones. We present thermodynamic tEFM analysis (tEFMA) which uses the cellular metabolome to avoid the enumeration of thermodynamically infeasible EFMs. Specifically, given a metabolic network and a not necessarily complete metabolome, tEFMA efficiently returns the full set of thermodynamically feasible EFMs consistent with the metabolome. Compared with standard approaches, tEFMA strongly reduces the memory consumption and the overall runtime. Thus tEFMA provides a new way to analyze unbiasedly hitherto inaccessible large-scale metabolic networks.<\/jats:p><jats:p>Availability and implementation: https:\/\/github.com\/mpgerstl\/tEFMA<\/jats:p><jats:p>Contact: christian.jungreuthmayer@boku.ac.at or juergen.zanghellini@boku.ac.at<\/jats:p><jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btv111","type":"journal-article","created":{"date-parts":[[2015,2,21]],"date-time":"2015-02-21T15:10:09Z","timestamp":1424531409000},"page":"2232-2234","source":"Crossref","is-referenced-by-count":35,"title":["tEFMA: computing thermodynamically feasible elementary flux modes in metabolic networks"],"prefix":"10.1093","volume":"31","author":[{"given":"Matthias P.","family":"Gerstl","sequence":"first","affiliation":[{"name":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"},{"name":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christian","family":"Jungreuthmayer","sequence":"additional","affiliation":[{"name":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"},{"name":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"J\u00fcrgen","family":"Zanghellini","sequence":"additional","affiliation":[{"name":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"},{"name":"1 Austrian Centre of Industrial Biotechnology, Vienna, Austria and 2Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Austria"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2015,2,19]]},"reference":[{"key":"2023020202134956100_btv111-B1","doi-asserted-by":"crossref","DOI":"10.1002\/0471332607","volume-title":"Thermodynamics of Biochemical Reactions","author":"Alberty","year":"2003"},{"key":"2023020202134956100_btv111-B2","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1038\/nchembio.186","article-title":"Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli","volume":"5","author":"Bennett","year":"2009","journal-title":"Nat. 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