{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T23:05:52Z","timestamp":1773270352034,"version":"3.50.1"},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Algorithms Mol Biol"],"published-print":{"date-parts":[[2016,12]]},"DOI":"10.1186\/s13015-016-0087-3","type":"journal-article","created":{"date-parts":[[2016,9,19]],"date-time":"2016-09-19T09:59:21Z","timestamp":1474279161000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Enumeration of minimal stoichiometric precursor sets in metabolic networks"],"prefix":"10.1186","volume":"11","author":[{"given":"Ricardo","family":"Andrade","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Wannagat","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia C.","family":"Klein","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vicente","family":"Acu\u00f1a","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alberto","family":"Marchetti-Spaccamela","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paulo V.","family":"Milreu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leen","family":"Stougie","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-France","family":"Sagot","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,9,19]]},"reference":[{"issue":"5","key":"87_CR1","doi-asserted-by":"publisher","first-page":"259","DOI":"10.4103\/2319-4170.138314","volume":"37","author":"C Lin","year":"2014","unstructured":"Lin C, Chang C-J, Lu C-C, Martel J, Ojcius D, Ko Y-F, Young J, Lai H-C. Impact of the gut microbiota, prebiotics, and probiotics on human health and disease. Biomed J. 2014:37(5):259\u2013268. doi: 10.4103\/2319-4170.138314 .","journal-title":"Biomed J"},{"key":"87_CR2","unstructured":"Romero P, Karp P. Nutrition-related analysis of pathway\/genome databases. In: Pacific symposium on biocomputing\u201901. 2001. p. 470\u201382."},{"key":"87_CR3","doi-asserted-by":"publisher","first-page":"530","DOI":"10.1016\/j.jtbi.2007.10.036","volume":"252","author":"T Handorf","year":"2008","unstructured":"Handorf T, Christian N, Ebenh\u00f6h O, Kahn D. An environmental perspective on metabolism. J Theor Biol. 2008;252:530\u20137. doi: 10.1016\/j.jtbi.2007.10.036 .","journal-title":"J Theor Biol"},{"key":"87_CR4","doi-asserted-by":"crossref","unstructured":"Cottret L, Milreu PV, Acuna V, Marchetti-Spaccamela A, Martinez FV, Sagot MF, Stougie L. Enumerating precursor sets of target metabolites in a metabolic network. In: Lecture notes in bioinformatics, vol 5251. 2007. p. 233\u201344.","DOI":"10.1007\/978-3-540-87361-7_20"},{"issue":"19","key":"87_CR5","doi-asserted-by":"crossref","first-page":"2474","DOI":"10.1093\/bioinformatics\/bts423","volume":"28","author":"V Acu\u00f1a","year":"2012","unstructured":"Acu\u00f1a V, Milreu PV, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot M-F. Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Bioinformatics. 2012;28(19):2474\u201383.","journal-title":"Bioinformatics"},{"issue":"7","key":"87_CR6","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1003726","volume":"10","author":"R Zarecki","year":"2014","unstructured":"Zarecki R, Oberhardt MA, Reshef L, Gophna U, Ruppin E. A novel nutritional predictor links microbial fastidiousness with lowered ubiquity, growth rate, and cooperativeness. PLoS Comput Biol. 2014;10(7):1\u201312. doi: 10.1371\/journal.pcbi.1003726 .","journal-title":"PLoS Comput Biol"},{"issue":"8","key":"87_CR7","doi-asserted-by":"publisher","first-page":"2659","DOI":"10.1529\/biophysj.105.069278","volume":"90","author":"M Imieli\u0144ski","year":"2006","unstructured":"Imieli\u0144ski M, Belta C, Rubin H, Hal\u00e1sz \u00c1. Systematic analysis of conservation relations in Escherichia coli genome-scale metabolic network reveals novel growth media. Biophys J. 2006;90(8):2659\u201372. doi: 10.1529\/biophysj.105.069278 .","journal-title":"Biophys J"},{"issue":"1","key":"87_CR8","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/1471-2105-14-114","volume":"14","author":"S Eker","year":"2013","unstructured":"Eker S, Krummenacker M, Shearer A, Tiwari A, Keseler I, Talcott C, Karp P. Computing minimal nutrient sets from metabolic networks via linear constraint solving. BMC Bioinform. 2013;14(1):114. doi: 10.1186\/1471-2105-14-114 .","journal-title":"BMC Bioinform"},{"issue":"6","key":"87_CR9","doi-asserted-by":"publisher","first-page":"1093","DOI":"10.1042\/bst0121093","volume":"12","author":"MR Watson","year":"1984","unstructured":"Watson MR. Metabolic maps for the apple 2. Biochem Soc Trans. 1984;12(6):1093\u20134. doi: 10.1042\/bst0121093 .","journal-title":"Biochem Soc Trans"},{"issue":"2\u20137","key":"87_CR10","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1016\/S0098-1354(00)00323-9","volume":"24","author":"S Lee","year":"2000","unstructured":"Lee S, Phalakornkule C, Domach MM, Grossmann IE. Recursive MILP model for finding all the alternate optima in LP models for metabolic networks. Comput Chem Eng. 2000;24(2\u20137):711\u20136. doi: 10.1016\/S0098-1354(00)00323-9 .","journal-title":"Comput Chem Eng"},{"issue":"23","key":"87_CR11","doi-asserted-by":"publisher","first-page":"3158","DOI":"10.1093\/bioinformatics\/btp564","volume":"25","author":"LF Figueiredo de","year":"2009","unstructured":"de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics. 2009;25(23):3158\u201365. doi: 10.1093\/bioinformatics\/btp564 .","journal-title":"Bioinformatics"},{"issue":"1","key":"87_CR12","doi-asserted-by":"publisher","first-page":"1003378","DOI":"10.1371\/journal.pcbi.1003378","volume":"10","author":"A Kamp von","year":"2014","unstructured":"von Kamp A, Klamt S. Enumeration of smallest intervention strategies in genome-scale metabolic networks. PLoS Comput Biol. 2014;10(1):1003378. doi: 10.1371\/journal.pcbi.1003378 .","journal-title":"PLoS Comput Biol"},{"issue":"2\u20133","key":"87_CR13","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/0166-218X(93)90045-P","volume":"42","author":"G Gallo","year":"1993","unstructured":"Gallo G, Longo G, Nguyen S, Pallottino S. Directed hypergraphs and applications. Discrete Appl Math. 1993;42(2\u20133):177\u2013201.","journal-title":"Discrete Appl Math"},{"key":"87_CR14","doi-asserted-by":"crossref","unstructured":"Ausiello G, Franciosa PG, Frigioni D. Directed hypergraphs: problems, algorithmic results, and a novel decremental approach. In: ICTCS. 2001. p. 312\u201327.","DOI":"10.1007\/3-540-45446-2_20"},{"key":"87_CR15","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1016\/S0166-218X(99)00099-2","volume":"96","author":"V Gurvich","year":"1999","unstructured":"Gurvich V, Khachiyan L. On generating the irredundant conjunctive and disjunctive normal forms of monotone boolean functions. Discrete Appl Math. 1999;96:363\u201373.","journal-title":"Discrete Appl Math"},{"issue":"50","key":"87_CR16","doi-asserted-by":"publisher","first-page":"20338","DOI":"10.1073\/pnas.1307797110","volume":"110","author":"J Monk","year":"2013","unstructured":"Monk J, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson B\u00d8. Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments. Proc Natl Acad Sci. 2013;110(50):20338\u201343. doi: 10.1073\/pnas.1307797110 .","journal-title":"Proc Natl Acad Sci"},{"issue":"5","key":"87_CR17","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1128\/IAI.01435-13","volume":"82","author":"J Meador","year":"2014","unstructured":"Meador J, Caldwell ME, Cohen PS, Conway T. Escherichia coli pathotypes occupy distinct niches in the mouse intestine. Infect Immun. 2014;82(5):1931\u20138.","journal-title":"Infect Immun"},{"key":"87_CR18","doi-asserted-by":"publisher","first-page":"1143","DOI":"10.1128\/iai.01386-07","volume":"76","author":"A Fabich","year":"2008","unstructured":"Fabich A, Jones SA, Chowdhury FZ, Cernosek A, Anderson A, Smalley D, McHargue JW, Hightower GA, Smith JT, Autieri SM, Leatham MP, Lins JJ, Allen RL, Laux DC, Cohen PS, Conway T. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect Immun. 2008;76:1143\u201352. doi: 10.1128\/iai.01386-07 .","journal-title":"Infect Immun"},{"issue":"7","key":"87_CR19","doi-asserted-by":"publisher","first-page":"2876","DOI":"10.1128\/iai.00059-09","volume":"77","author":"M Leatham","year":"2009","unstructured":"Leatham M, Banerjee S, Autieri SM, Mercado-Lubo R, Conway T, Cohen PS. Precolonized human commensal Escherichia coli strains serve as a barrier to E. coli O157:H7 growth in the streptomycin-treated mouse intestine. Infect Immun. 2009;77(7):2876\u201386. doi: 10.1128\/iai.00059-09 .","journal-title":"Infect Immun"},{"issue":"1","key":"87_CR20","doi-asserted-by":"publisher","first-page":"53957","DOI":"10.1371\/journal.pone.0053957","volume":"8","author":"R Maltby","year":"2013","unstructured":"Maltby R, Leatham-Jensen MP, Gibson T, Cohen PS, Conway T. Nutritional basis for colonization resistance by human commensal Escherichia coli strains HS and Nissle 1917 against E. coli O157:H7 in the mouse intestine. PLoS One. 2013;8(1):53957. doi: 10.1371\/journal.pone.0053957 .","journal-title":"PLoS One"}],"container-title":["Algorithms for Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13015-016-0087-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,13]],"date-time":"2019-09-13T15:00:51Z","timestamp":1568386851000},"score":1,"resource":{"primary":{"URL":"http:\/\/almob.biomedcentral.com\/articles\/10.1186\/s13015-016-0087-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,9,19]]},"references-count":20,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2016,12]]}},"alternative-id":["87"],"URL":"https:\/\/doi.org\/10.1186\/s13015-016-0087-3","relation":{},"ISSN":["1748-7188"],"issn-type":[{"value":"1748-7188","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,9,19]]},"article-number":"25"}}