{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,6]],"date-time":"2026-03-06T21:09:40Z","timestamp":1772831380676,"version":"3.50.1"},"reference-count":27,"publisher":"IGI Global","issue":"1","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<p>In this paper, the authors consider the problem of, given a metabolic network, a set of source compounds and a set of target compounds, finding a minimum size reaction cut, where a Boolean model is used as a model of metabolic networks. The problem has potential applications to measurement of structural robustness of metabolic networks and detection of drug targets. They develop an integer programming-based method for this optimization problem. In order to cope with cycles and reversible reactions, they further develop a novel integer programming (IP) formalization method using a feedback vertex set (FVS). When applied to an E. coli metabolic network consisting of Glycolysis\/Glyconeogenesis, Citrate cycle and Pentose phosphate pathway obtained from KEGG database, the FVS-based method can find an optimal set of reactions to be inactivated much faster than a naive IP-based method and several times faster than a flux balance-based method. The authors also confirm that our proposed method works even for large networks and discuss the biological meaning of our results. <\/p>","DOI":"10.4018\/jkdb.2010100202","type":"journal-article","created":{"date-parts":[[2010,4,19]],"date-time":"2010-04-19T12:16:29Z","timestamp":1271679389000},"page":"14-31","source":"Crossref","is-referenced-by-count":15,"title":["Finding Minimum Reaction Cuts of Metabolic Networks Under a Boolean Model Using Integer Programming and Feedback Vertex Sets"],"prefix":"10.4018","volume":"1","author":[{"given":"Takeyuki","family":"Tamura","sequence":"first","affiliation":[{"name":"Kyoto University, Japan"}]},{"given":"Kazuhiro","family":"Takemoto","sequence":"additional","affiliation":[{"name":"Graduate School of Frontier Sciences, Japan"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[{"name":"Kyoto University, Japan"}]}],"member":"2432","reference":[{"key":"jkdb.2010100202-0","doi-asserted-by":"publisher","DOI":"10.1016\/j.biosystems.2008.06.015"},{"key":"jkdb.2010100202-1","doi-asserted-by":"publisher","DOI":"10.1137\/S0097539796305109"},{"key":"jkdb.2010100202-2","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2007.09.043"},{"key":"jkdb.2010100202-3","doi-asserted-by":"publisher","DOI":"10.1002\/bit.10803"},{"key":"jkdb.2010100202-4","doi-asserted-by":"publisher","DOI":"10.1529\/biophysj.105.069724"},{"key":"jkdb.2010100202-5","doi-asserted-by":"publisher","DOI":"10.1007\/PL00009191"},{"key":"jkdb.2010100202-6","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm150"},{"key":"jkdb.2010100202-7","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2007.10.036"},{"key":"jkdb.2010100202-8","doi-asserted-by":"publisher","DOI":"10.1007\/s00239-005-0027-1"},{"key":"jkdb.2010100202-9","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2007.0229"},{"key":"jkdb.2010100202-10","doi-asserted-by":"publisher","DOI":"10.1038\/35036627"},{"key":"jkdb.2010100202-11","doi-asserted-by":"publisher","DOI":"10.1002\/bit.22237"},{"key":"jkdb.2010100202-12","doi-asserted-by":"publisher","DOI":"10.1038\/ng1523"},{"key":"jkdb.2010100202-13","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm882"},{"key":"jkdb.2010100202-14","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm740"},{"key":"jkdb.2010100202-15","doi-asserted-by":"publisher","DOI":"10.1038\/nrc1300"},{"key":"jkdb.2010100202-16","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btg395"},{"key":"jkdb.2010100202-17","doi-asserted-by":"publisher","DOI":"10.1023\/A:1020390132244"},{"key":"jkdb.2010100202-18","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2008.03.003"},{"key":"jkdb.2010100202-19","doi-asserted-by":"publisher","DOI":"10.1126\/science.298.5594.824"},{"key":"jkdb.2010100202-20","doi-asserted-by":"publisher","DOI":"10.1016\/S0968-0004(03)00064-1"},{"key":"jkdb.2010100202-21","doi-asserted-by":"publisher","DOI":"10.1016\/S0167-7799(98)01290-6"},{"key":"jkdb.2010100202-22","doi-asserted-by":"publisher","DOI":"10.1142\/9789812776136_0029"},{"key":"jkdb.2010100202-23","doi-asserted-by":"publisher","DOI":"10.1038\/nature01166"},{"key":"jkdb.2010100202-24","doi-asserted-by":"crossref","unstructured":"Tamura, T., Takemoto, K., & Akutsu, T. 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Measuring structural robustness of metabolic networks under a Boolean model using integer programming and feedback vertex sets. 2nd International Workshop on Intelligent Informatics in Biology and Medicine (IIBM2009), A Part of Proceedings of 3rd International Conference on Complex, Intelligent and Software Intensive Systems (pp. 819\u2013824).","DOI":"10.1109\/CISIS.2009.49"},{"key":"jkdb.2010100202-25","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl267"},{"key":"jkdb.2010100202-26","doi-asserted-by":"publisher","DOI":"10.1098\/rspb.2001.1711"}],"container-title":["International Journal of Knowledge Discovery in Bioinformatics"],"original-title":[],"language":"ng","link":[{"URL":"https:\/\/www.igi-global.com\/viewtitle.aspx?TitleId=40969","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,6,2]],"date-time":"2022-06-02T04:19:52Z","timestamp":1654143592000},"score":1,"resource":{"primary":{"URL":"https:\/\/services.igi-global.com\/resolvedoi\/resolve.aspx?doi=10.4018\/jkdb.2010100202"}},"subtitle":[""],"short-title":[],"issued":{"date-parts":[[2010,1,1]]},"references-count":27,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,1]]}},"URL":"https:\/\/doi.org\/10.4018\/jkdb.2010100202","relation":{},"ISSN":["1947-9115","1947-9123"],"issn-type":[{"value":"1947-9115","type":"print"},{"value":"1947-9123","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,1,1]]}}}