{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T14:14:00Z","timestamp":1742912040757,"version":"3.40.3"},"publisher-location":"Cham","reference-count":29,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319234847"},{"type":"electronic","value":"9783319234854"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2015]]},"DOI":"10.1007\/978-3-319-23485-4_35","type":"book-chapter","created":{"date-parts":[[2015,8,24]],"date-time":"2015-08-24T16:07:15Z","timestamp":1440432435000},"page":"340-352","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["A Critical Evaluation of Methods for the Reconstruction of Tissue-Specific Models"],"prefix":"10.1007","author":[{"given":"Sara","family":"Correia","sequence":"first","affiliation":[]},{"given":"Miguel","family":"Rocha","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,8,25]]},"reference":[{"issue":"5","key":"35_CR1","doi-asserted-by":"publisher","first-page":"e1002518","DOI":"10.1371\/journal.pcbi.1002518","volume":"8","author":"R Agren","year":"2012","unstructured":"Agren, R., Bordel, S., Mardinoglu, A., Pornputtapong, N., Nookaew, I., Nielsen, J.: Reconstruction of Genome-Scale Active Metabolic Networks for 69 Human Cell Types and 16 Cancer Types Using INIT. PLoS Computational Biology 8(5), e1002518 (2012)","journal-title":"PLoS Computational Biology"},{"key":"35_CR2","doi-asserted-by":"publisher","first-page":"721","DOI":"10.1002\/msb.145122","volume":"10","author":"R Agren","year":"2014","unstructured":"Agren, R., Mardinoglu, A., Asplund, A., Kampf, C., Uhlen, M., Nielsen, J.: Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling. Molecular Systems Biology 10, 721 (2014)","journal-title":"Molecular Systems Biology"},{"issue":"suppl 1","key":"35_CR3","doi-asserted-by":"publisher","first-page":"D1005","DOI":"10.1093\/nar\/gkq1184","volume":"39","author":"T Barrett","year":"2011","unstructured":"Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., et al.: NCBI GEO: archive for functional genomics data sets - 10 years on. Nucleic Acids Research 39(suppl 1), D1005\u2013D1010 (2011)","journal-title":"Nucleic Acids Research"},{"key":"35_CR4","unstructured":"Carlson, M.: hgu133plus2.db: Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) (2014). r package version 3.0.0"},{"issue":"6","key":"35_CR5","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1073\/pnas.0610772104","volume":"104","author":"NC Duarte","year":"2007","unstructured":"Duarte, N.C., Becker, S.A., Jamshidi, N., Thiele, I., Mo, M.L., Vo, T.D., Srivas, R., Palsson, B.O.: Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proceedings of the National Academy of Sciences of the United States of America 104(6), 1777\u20131782 (2007)","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"issue":"7","key":"35_CR6","doi-asserted-by":"publisher","first-page":"1298","DOI":"10.1101\/gr.2250904","volume":"14","author":"NC Duarte","year":"2004","unstructured":"Duarte, N.C., Herrg\u00e5rd, M.J., Palsson, B.O.: Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Research 14(7), 1298\u20131309 (2004)","journal-title":"Genome Research"},{"issue":"D1","key":"35_CR7","doi-asserted-by":"publisher","first-page":"D749","DOI":"10.1093\/nar\/gkt1196","volume":"42","author":"P Flicek","year":"2014","unstructured":"Flicek, P., Amode, M.R., Barrell, D., et al.: Ensembl 2014. Nucleic Acids Research 42(D1), D749\u2013D755 (2014)","journal-title":"Nucleic Acids Research"},{"issue":"411","key":"35_CR8","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/msb.2010.62","volume":"6","author":"C Gille","year":"2010","unstructured":"Gille, C., B\u00f6lling, C., Hoppe, A., et al.: HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology. Molecular Systems Biology 6(411), 411 (2010)","journal-title":"Molecular Systems Biology"},{"key":"35_CR9","doi-asserted-by":"publisher","first-page":"393","DOI":"10.1186\/1471-2105-11-393","volume":"11","author":"T Hao","year":"2010","unstructured":"Hao, T., Ma, H.W., Zhao, X.M., Goryanin, I.: Compartmentalization of the Edinburgh Human Metabolic Network. BMC Bioinformatics 11, 393 (2010)","journal-title":"BMC Bioinformatics"},{"key":"35_CR10","doi-asserted-by":"crossref","unstructured":"Ishibashi, H., Nakamura, M., Komori, A., Migita, K., Shimoda, S.: Liver architecture, cell function, and disease. Seminars in Immunopathology 31(3) (2009)","DOI":"10.1007\/s00281-009-0155-6"},{"issue":"20","key":"35_CR11","doi-asserted-by":"publisher","first-page":"5572","DOI":"10.1158\/1078-0432.CCR-12-1856","volume":"18","author":"L Jerby","year":"2012","unstructured":"Jerby, L., Ruppin, E.: Predicting Drug Targets and Biomarkers of Cancer via Genome-Scale Metabolic Modeling. Clinical Cancer Research : An Official Journal of the American Association for Cancer Research 18(20), 5572\u20135584 (2012)","journal-title":"Clinical Cancer Research : An Official Journal of the American Association for Cancer Research"},{"issue":"401","key":"35_CR12","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/msb.2010.56","volume":"6","author":"L Jerby","year":"2010","unstructured":"Jerby, L., Shlomi, T., Ruppin, E.: Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism. Molecular Systems Biology 6(401), 401 (2010)","journal-title":"Molecular Systems Biology"},{"key":"35_CR13","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1146\/annurev.pharmtox.48.113006.094715","volume":"48","author":"R Kaddurah-Daouk","year":"2008","unstructured":"Kaddurah-Daouk, R., Kristal, B., Weinshilboum, R.: Metabolomics: a global biochemical approach to drug response and disease. Annu. Rev. Pharmacol. Toxicol. 48, 653\u2013683 (2008)","journal-title":"Annu. Rev. Pharmacol. Toxicol."},{"issue":"12","key":"35_CR14","doi-asserted-by":"publisher","first-page":"1279","DOI":"10.1038\/nbt.1711","volume":"28","author":"NE Lewis","year":"2010","unstructured":"Lewis, N.E., Schramm, G., Bordbar, A., Schellenberger, J., Andersen, M.P., Cheng, J.K., Patel, N., Yee, A., Lewis, R.A., Eils, R., K\u00f6nig, R., Palsson, B.O.: Large-scale in silico modeling of metabolic interactions between cell types in the human brain. Nature Biotechnology 28(12), 1279\u20131285 (2010)","journal-title":"Nature Biotechnology"},{"key":"35_CR15","doi-asserted-by":"crossref","unstructured":"Mardinoglu, A., Agren, R., Kampf, C., Asplund, A., Uhlen, M., Nielsen, J.: Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nature Communications 5, Jan 2014","DOI":"10.1038\/ncomms4083"},{"issue":"D1","key":"35_CR16","doi-asserted-by":"publisher","first-page":"D938","DOI":"10.1093\/nar\/gkt1204","volume":"42","author":"MN McCall","year":"2014","unstructured":"McCall, M.N., Jaffee, H.A., Zelisko, S.J., Sinha, N., et al.: The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Research 42(D1), D938\u2013D943 (2014)","journal-title":"Nucleic Acids Research"},{"issue":"320","key":"35_CR17","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/msb.2009.77","volume":"5","author":"MA Oberhardt","year":"2009","unstructured":"Oberhardt, M.A., Palsson, B.O., Papin, J.A.: Applications of genome-scale metabolic reconstructions. Molecular Systems Biology 5(320), 320 (2009)","journal-title":"Molecular Systems Biology"},{"issue":"3","key":"35_CR18","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/nbt.1614","volume":"28","author":"JD Orth","year":"2010","unstructured":"Orth, J.D., Thiele, I., Palsson, B.O.: What is flux balance analysis? Nature Biotechnology 28(3), 245\u2013248 (2010)","journal-title":"Nature Biotechnology"},{"key":"35_CR19","doi-asserted-by":"crossref","unstructured":"Parkinson, H., Sarkans, U., Shojatalab, M., Abeygunawardena, N., et al.: ArrayExpress-a public repository for microarray gene expression data at the EBI. Nucleic Acids Research 33(Database issue), Jan 2005","DOI":"10.1093\/nar\/gki056"},{"key":"35_CR20","doi-asserted-by":"crossref","unstructured":"Reed, J.L., Vo, T.D., Schilling, C.H., Palsson, B.O.: An expanded genome-scale model of Escherichia coli K-12 ( i JR904 GSM \/ GPR ) 4(9), 1\u201312 (2003)","DOI":"10.1186\/gb-2003-4-9-r54"},{"issue":"10","key":"35_CR21","doi-asserted-by":"publisher","first-page":"2545","DOI":"10.1039\/c2mb25075f","volume":"8","author":"S Sahoo","year":"2012","unstructured":"Sahoo, S., Franzson, L., Jonsson, J.J., Thiele, I.: A compendium of inborn errors of metabolism mapped onto the human metabolic network. Mol. BioSyst. 8(10), 2545\u20132558 (2012)","journal-title":"Mol. BioSyst."},{"issue":"13","key":"35_CR22","doi-asserted-by":"publisher","first-page":"2705","DOI":"10.1093\/hmg\/ddt119","volume":"22","author":"S Sahoo","year":"2013","unstructured":"Sahoo, S., Thiele, I.: Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells. Human Molecular Genetics 22(13), 2705\u20132722 (2013)","journal-title":"Human Molecular Genetics"},{"issue":"3","key":"35_CR23","doi-asserted-by":"publisher","first-page":"e1002018","DOI":"10.1371\/journal.pcbi.1002018","volume":"7","author":"T Shlomi","year":"2011","unstructured":"Shlomi, T., Benyamini, T., Gottlieb, E., Sharan, R., Ruppin, E.: Genome-scale metabolic modeling elucidates the role of proliferative adaptation in causing the Warburg effect. PLoS Computational Biology 7(3), e1002018 (2011)","journal-title":"PLoS Computational Biology"},{"issue":"263","key":"35_CR24","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/msb.2009.22","volume":"5","author":"T Shlomi","year":"2009","unstructured":"Shlomi, T., Cabili, M.N., Ruppin, E.: Predicting metabolic biomarkers of human inborn errors of metabolism. Molecular Systems Biology 5(263), 263 (2009)","journal-title":"Molecular Systems Biology"},{"key":"35_CR25","unstructured":"Thiele, I., Swainston, N., Fleming, R.M.T., et al.: A community-driven global reconstruction of human metabolism. Nature Biotechnology 31(5), May 2013"},{"issue":"12","key":"35_CR26","doi-asserted-by":"publisher","first-page":"1248","DOI":"10.1038\/nbt1210-1248","volume":"28","author":"M Uhlen","year":"2010","unstructured":"Uhlen, M., Oksvold, P., Fagerberg, L., Lundberg, E., et al.: Towards a knowledge-based Human Protein Atlas. Nat Biotech 28(12), 1248\u20131250 (2010)","journal-title":"Nat Biotech"},{"issue":"1","key":"35_CR27","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1186\/1752-0509-6-153","volume":"6","author":"Y Wang","year":"2012","unstructured":"Wang, Y., Eddy, J.A., Price, N.D.: Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE. BMC Systems Biology 6(1), 153 (2012)","journal-title":"BMC Systems Biology"},{"key":"35_CR28","doi-asserted-by":"crossref","unstructured":"Wishart, D.S., Knox, C., Guo, A.C., Eisner, R., et al.: HMDB: a knowledgebase for the human metabolome. Nucleic Acids Research 37(suppl 1), Jan 2009","DOI":"10.1093\/nar\/gkn810"},{"key":"35_CR29","doi-asserted-by":"crossref","unstructured":"Yizhak, K., Le D\u00e9v\u00e9dec, S.E., Rogkoti, V.M.M., et al.: A computational study of the Warburg effect identifies metabolic targets inhibiting cancer migration. Molecular Systems Biology 10(8) (2014)","DOI":"10.15252\/msb.20134993"}],"container-title":["Lecture Notes in Computer Science","Progress in Artificial Intelligence"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-23485-4_35","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,10]],"date-time":"2023-02-10T11:53:02Z","timestamp":1676029982000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-23485-4_35"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319234847","9783319234854"],"references-count":29,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-23485-4_35","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2015]]},"assertion":[{"value":"25 August 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}