{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T04:22:46Z","timestamp":1773289366794,"version":"3.50.1"},"reference-count":26,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2008,4,16]],"date-time":"2008-04-16T00:00:00Z","timestamp":1208304000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2008,12]]},"DOI":"10.1186\/1471-2105-9-199","type":"journal-article","created":{"date-parts":[[2008,4,16]],"date-time":"2008-04-16T18:13:02Z","timestamp":1208369582000},"source":"Crossref","is-referenced-by-count":64,"title":["anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data"],"prefix":"10.1186","volume":"9","author":[{"given":"Nicola","family":"Zamboni","sequence":"first","affiliation":[]},{"given":"Anne","family":"K\u00fcmmel","sequence":"additional","affiliation":[]},{"given":"Matthias","family":"Heinemann","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2008,4,16]]},"reference":[{"key":"2184_CR1","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/1471-2164-7-142","volume":"7","author":"RA van den Berg","year":"2006","unstructured":"van den Berg RA, Hoefsloot HC, Westerhuis JA, Smilde AK, van der Werf MJ: Centering, scaling, and transformations: improving the biological information content of metabolomics data. BMC Genomics 2006, 7: 142. 10.1186\/1471-2164-7-142","journal-title":"BMC Genomics"},{"issue":"6","key":"2184_CR2","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/nbt823","volume":"21","author":"J Allen","year":"2003","unstructured":"Allen J, Davey HM, Broadhurst D, Heald JK, Rowland JJ, Oliver SG, Kell DB: High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat Biotechnol 2003, 21(6):692\u2013696. 10.1038\/nbt823","journal-title":"Nat Biotechnol"},{"issue":"2","key":"2184_CR3","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/S0958-1669(03)00023-5","volume":"14","author":"M Stitt","year":"2003","unstructured":"Stitt M, Fernie AR: From measurements of metabolites to metabolomics: an 'on the fly' perspective illustrated by recent studies of carbon-nitrogen interactions. Curr Opin Biotechnol 2003, 14(2):136\u2013144. 10.1016\/S0958-1669(03)00023-5","journal-title":"Curr Opin Biotechnol"},{"issue":"11","key":"2184_CR4","doi-asserted-by":"publisher","first-page":"544","DOI":"10.1016\/j.tibtech.2005.08.005","volume":"23","author":"J Nielsen","year":"2005","unstructured":"Nielsen J, Oliver S: The next wave in metabolome analysis. Trends Biotechnol 2005, 23(11):544\u2013546. 10.1016\/j.tibtech.2005.08.005","journal-title":"Trends Biotechnol"},{"key":"2184_CR5","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1186\/1471-2105-7-540","volume":"7","author":"IE Nikerel","year":"2006","unstructured":"Nikerel IE, van Winden WA, van Gulik WM, Heijnen JJ: A method for estimation of elasticities in metabolic networks using steady state and dynamic metabolomics data and linlog kinetics. BMC Bioinformatics 2006, 7: 540. 10.1186\/1471-2105-7-540","journal-title":"BMC Bioinformatics"},{"issue":"2","key":"2184_CR6","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1006\/mben.1998.0110","volume":"1","author":"S Vaseghi","year":"1999","unstructured":"Vaseghi S, Baumeister A, Rizzi M, Reuss M: In vivo dynamics of the pentose phosphate pathway in Saccharomyces cerevisiae. Metab Eng 1999, 1(2):128\u2013140. 10.1006\/mben.1998.0110","journal-title":"Metab Eng"},{"issue":"2","key":"2184_CR7","first-page":"83","volume":"5","author":"EO Voit","year":"2005","unstructured":"Voit EO, Marino S, Lall R: Challenges for the identification of biological systems from in vivo time series data. In Silico Biol 2005, 5(2):83\u201392.","journal-title":"In Silico Biol"},{"issue":"7","key":"2184_CR8","doi-asserted-by":"publisher","first-page":"2026","DOI":"10.1021\/ac048657g","volume":"77","author":"A Lafaye","year":"2005","unstructured":"Lafaye A, Labarre J, Tabet JC, Ezan E, Junot C: Liquid chromatography-mass spectrometry and 15N metabolic labeling for quantitative metabolic profiling. Anal Chem 2005, 77(7):2026\u20132033. 10.1021\/ac048657g","journal-title":"Anal Chem"},{"issue":"4","key":"2184_CR9","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1016\/j.ymben.2005.05.003","volume":"7","author":"L Wu","year":"2005","unstructured":"Wu L, van Winden WA, van Gulik WM, Heijnen JJ: Application of metabolome data in functional genomics: a conceptual strategy. Metab Eng 2005, 7(4):302\u2013310. 10.1016\/j.ymben.2005.05.003","journal-title":"Metab Eng"},{"issue":"5824","key":"2184_CR10","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1126\/science.1142502","volume":"316","author":"U Sauer","year":"2007","unstructured":"Sauer U, Heinemann M, Zamboni N: Getting closer to the whole picture. Science 2007, 316(5824):550\u2013551. 10.1126\/science.1142502","journal-title":"Science"},{"key":"2184_CR11","doi-asserted-by":"publisher","first-page":"2006.0034","DOI":"10.1038\/msb4100074","volume":"2","author":"A K\u00fcmmel","year":"2006","unstructured":"K\u00fcmmel A, Panke S, Heinemann M: Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2006, 2: 2006.0034. 10.1038\/msb4100074","journal-title":"Mol Syst Biol"},{"key":"2184_CR12","doi-asserted-by":"publisher","DOI":"10.1002\/0471332607","volume-title":"Thermodynamics of Biochemical Reactions","author":"RA Alberty","year":"2003","unstructured":"Alberty RA: Thermodynamics of Biochemical Reactions. Hoboken, NJ, USA , John Wiley & Sons Inc; 2003."},{"key":"2184_CR13","doi-asserted-by":"publisher","DOI":"10.1002\/047003646X","volume-title":"Biochemical Thermodynamics: Applications of Mathematica","author":"RA Alberty","year":"2006","unstructured":"Alberty RA: Biochemical Thermodynamics: Applications of Mathematica. In Edited by: John Wiley & Sons I. 2006."},{"issue":"22","key":"2184_CR14","doi-asserted-by":"crossref","first-page":"14440","DOI":"10.1016\/S0021-9258(18)98705-3","volume":"266","author":"ML Mavrovouniotis","year":"1991","unstructured":"Mavrovouniotis ML: Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 1991, 266(22):14440\u201314445.","journal-title":"J Biol Chem"},{"key":"2184_CR15","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1038\/msb4100109","volume":"2","author":"U Sauer","year":"2006","unstructured":"Sauer U: Metabolic networks in motion: 13C-based flux analysis. Mol Syst Biol 2006, 2: 62. 10.1038\/msb4100109","journal-title":"Mol Syst Biol"},{"key":"2184_CR16","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/msb4100155","volume":"3","author":"AM Feist","year":"2007","unstructured":"Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO: A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 2007, 3: 121. 10.1038\/msb4100155","journal-title":"Mol Syst Biol"},{"issue":"7","key":"2184_CR17","doi-asserted-by":"publisher","first-page":"850","DOI":"10.1002\/bit.20663","volume":"92","author":"M Heinemann","year":"2005","unstructured":"Heinemann M, Kummel A, Ruinatscha R, Panke S: In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol Bioeng 2005, 92(7):850\u2013864. 10.1002\/bit.20663","journal-title":"Biotechnol Bioeng"},{"key":"2184_CR18","doi-asserted-by":"publisher","first-page":"994","DOI":"10.1038\/nbt1094-994","volume":"12","author":"A Varma","year":"1994","unstructured":"Varma A, Palsson BO: Metabolic flux balancing: Basic concepts, scientific, and practical use. Bio\/Technol 1994, 12: 994\u2013998. 10.1038\/nbt1094-994","journal-title":"Bio\/Technol"},{"key":"2184_CR19","doi-asserted-by":"publisher","first-page":"512","DOI":"10.1186\/1471-2105-7-512","volume":"7","author":"A Kummel","year":"2006","unstructured":"Kummel A, Panke S, Heinemann M: Systematic assignment of thermodynamic constraints in metabolic network models. BMC Bioinformatics 2006, 7: 512. 10.1186\/1471-2105-7-512","journal-title":"BMC Bioinformatics"},{"issue":"5","key":"2184_CR20","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1021\/bp050381q","volume":"22","author":"J Schaub","year":"2006","unstructured":"Schaub J, Schiesling C, Reuss M, Dauner M: Integrated sampling procedure for metabolome analysis. Biotechnol Prog 2006, 22(5):1434\u20131442. 10.1021\/bp050381q","journal-title":"Biotechnol Prog"},{"issue":"9","key":"2184_CR21","doi-asserted-by":"publisher","first-page":"R54","DOI":"10.1186\/gb-2003-4-9-r54","volume":"4","author":"JL Reed","year":"2003","unstructured":"Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM\/GPR). Genome Biol 2003, 4(9):R54. 10.1186\/gb-2003-4-9-r54","journal-title":"Genome Biol"},{"issue":"8","key":"2184_CR22","doi-asserted-by":"publisher","first-page":"1161","DOI":"10.1007\/s10529-007-9383-9","volume":"29","author":"J Hiller","year":"2007","unstructured":"Hiller J, Franco-Lara E, Papaioannou V, Weuster-Botz D: Fast sampling and quenching procedures for microbial metabolic profiling. Biotechnol Lett 2007, 29(8):1161\u20131167. 10.1007\/s10529-007-9383-9","journal-title":"Biotechnol Lett"},{"issue":"5824","key":"2184_CR23","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1126\/science.1132067","volume":"316","author":"N Ishii","year":"2007","unstructured":"Ishii N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M: Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 2007, 316(5824):593\u2013597. 10.1126\/science.1132067","journal-title":"Science"},{"issue":"1","key":"2184_CR24","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1128\/JB.184.1.152-164.2002","volume":"184","author":"M Emmerling","year":"2002","unstructured":"Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, W\u00fcthrich K, Bailey JE, Sauer U: Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. J Bacteriol 2002, 184(1):152\u2013164. 10.1128\/JB.184.1.152-164.2002","journal-title":"J Bacteriol"},{"issue":"44","key":"2184_CR25","doi-asserted-by":"publisher","first-page":"46446","DOI":"10.1074\/jbc.M307968200","volume":"278","author":"E Fischer","year":"2003","unstructured":"Fischer E, Sauer U: A novel metabolic cycle catalyzes glucose oxidation and anaplerosis in hungry Escherichia coli. J Biol Chem 2003, 278(44):46446\u201346451. 10.1074\/jbc.M307968200","journal-title":"J Biol Chem"},{"issue":"2","key":"2184_CR26","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1016\/j.ab.2004.09.001","volume":"336","author":"L Wu","year":"2005","unstructured":"Wu L, Mashego MR, van Dam JC, Proell AM, Vinke JL, Ras C, van Winden WA, van Gulik WM, Heijnen JJ: Quantitative analysis of the microbial metabolome by isotope dilution mass spectrometry using uniformly 13C-labeled cell extracts as internal standards. Anal Biochem 2005, 336(2):164\u2013171. 10.1016\/j.ab.2004.09.001","journal-title":"Anal Biochem"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-199.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-9-199\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-9-199.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,8]],"date-time":"2021-09-08T08:32:41Z","timestamp":1631089961000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-9-199"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2008,4,16]]},"references-count":26,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2008,12]]}},"alternative-id":["2184"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-9-199","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2008,4,16]]},"article-number":"199"}}