{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T00:32:16Z","timestamp":1773966736029,"version":"3.50.1"},"reference-count":131,"publisher":"Public Library of Science (PLoS)","issue":"3","license":[{"start":{"date-parts":[[2016,3,4]],"date-time":"2016-03-04T00:00:00Z","timestamp":1457049600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.ploscompbiol.org"],"crossmark-restriction":false},"short-container-title":["PLoS Comput Biol"],"DOI":"10.1371\/journal.pcbi.1004808","type":"journal-article","created":{"date-parts":[[2016,3,4]],"date-time":"2016-03-04T18:41:35Z","timestamp":1457116895000},"page":"e1004808","update-policy":"https:\/\/doi.org\/10.1371\/journal.pcbi.corrections_policy","source":"Crossref","is-referenced-by-count":142,"title":["Reconstruction of Tissue-Specific Metabolic Networks Using CORDA"],"prefix":"10.1371","volume":"12","author":[{"given":"Andr\u00e9","family":"Schultz","sequence":"first","affiliation":[]},{"given":"Amina A.","family":"Qutub","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2016,3,4]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1038\/msb.2009.77","article-title":"Applications of genome-scale metabolic reconstructions","volume":"5","author":"MA Oberhardt","year":"2009","journal-title":"Mol Syst Biol"},{"issue":"4","key":"ref2","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nrmicro2737","article-title":"Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods","volume":"10","author":"NE Lewis","year":"2012","journal-title":"Nat Rev Microbiol"},{"issue":"2","key":"ref3","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nrg3643","article-title":"Constraint-based models predict metabolic and associated cellular functions","volume":"15","author":"A Bordbar","year":"2014","journal-title":"Nat Rev Genet"},{"issue":"2","key":"ref4","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1039\/C2MB25453K","article-title":"Analysis of omics data with genome-scale models of metabolism","volume":"9","author":"DR Hyduke","year":"2013","journal-title":"Mol Biosyst"},{"issue":"6","key":"ref5","doi-asserted-by":"crossref","first-page":"1777","DOI":"10.1073\/pnas.0610772104","article-title":"Global reconstruction of the human metabolic network based on genomic and bibliomic data","volume":"104","author":"NC Duarte","year":"2007","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"2","key":"ref6","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1111\/j.1365-2796.2011.02494.x","article-title":"Using the reconstructed genome-scale human metabolic network to study physiology and pathology","volume":"271","author":"A Bordbar","year":"2012","journal-title":"J Intern Med"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1752-0509-5-155","article-title":"The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions","volume":"5","author":"O Rolfsson","year":"2011","journal-title":"BMC Syst Biol"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1038\/msb.2009.22","article-title":"Predicting metabolic biomarkers of human inborn errors of metabolism","volume":"5","author":"T Shlomi","year":"2009","journal-title":"Mol Syst Biol"},{"issue":"5","key":"ref9","doi-asserted-by":"crossref","first-page":"419","DOI":"10.1038\/nbt.2488","article-title":"A community-driven global reconstruction of human metabolism","volume":"31","author":"I Thiele","year":"2013","journal-title":"Nat Biotechnol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"299","DOI":"10.3389\/fphys.2012.00299","article-title":"Integration of expression data in genome-scale metabolic network reconstructions","volume":"3","author":"AS Blazier","year":"2012","journal-title":"Front Physiol"},{"issue":"18","key":"ref11","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.csbj.2014.08.009","article-title":"Methods for integration of transcriptomic data in genome-scale metabolic models","volume":"11","author":"MK Kim","year":"2014","journal-title":"Comput Struct Biotechnol J"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"39","DOI":"10.1016\/j.copbio.2014.02.011","article-title":"Recent advances in the reconstruction of metabolic models and integration of omics data","volume":"29","author":"R Saha","year":"2014","journal-title":"Curr Opin Biotechnol"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1186\/1752-0509-3-33","article-title":"Reconstruction of metabolic pathways for the cattle genome","volume":"3","author":"S Seo","year":"2009","journal-title":"BMC Syst Biol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1186\/1752-0509-4-140","article-title":"A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1","volume":"4","author":"MI Sigurdsson","year":"2010","journal-title":"BMC Syst Biol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1002\/msb.145122","article-title":"Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling","volume":"10","author":"R Agren","year":"2014","journal-title":"Mol Syst Biol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"8183","DOI":"10.1038\/srep08183","article-title":"Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling","volume":"5","author":"P Ghaffari","year":"2015","journal-title":"Sci Rep"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"501","DOI":"10.1038\/msb.2011.35","article-title":"Predicting selective drug targets in cancer through metabolic networks","volume":"7","author":"O Folger","year":"2011","journal-title":"Mol Syst Biol"},{"issue":"7363","key":"ref18","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1038\/nature10363","article-title":"Haem oxygenase is synthetically lethal with the tumour suppressor fumarate hydratase","volume":"477","author":"C Frezza","year":"2011","journal-title":"Nature"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"10738","DOI":"10.1038\/srep10738","article-title":"Flux balance analysis predicts essential genes in clear cell renal cell carcinoma metabolism","volume":"5","author":"F Gatto","year":"2015","journal-title":"Sci Rep"},{"key":"ref20","first-page":"491","article-title":"Generalized framework for context-specific metabolic model extraction methods","volume":"5","author":"S Robaina Est\u00e9vez","year":"2014","journal-title":"Front Plant Sci"},{"key":"ref21","article-title":"Reconstruction of genome-scale human metabolic models using omics data","author":"JY Ryu","year":"2015","journal-title":"Integr Biol (Camb)"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1038\/msb.2010.62","article-title":"HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology","volume":"6","author":"C Gille","year":"2010","journal-title":"Mol Syst Biol"},{"issue":"13","key":"ref23","doi-asserted-by":"crossref","first-page":"2705","DOI":"10.1093\/hmg\/ddt119","article-title":"Predicting the impact of diet and enzymopathies on human small intestinal epithelial cells","volume":"22","author":"S Sahoo","year":"2013","journal-title":"Hum Mol Genet"},{"issue":"9","key":"ref24","doi-asserted-by":"crossref","first-page":"e1000938","DOI":"10.1371\/journal.pcbi.1000938","article-title":"Drug off-target effects predicted using structural analysis in the context of a metabolic network model","volume":"6","author":"RL Chang","year":"2010","journal-title":"PLoS Comput Biol"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"422","DOI":"10.1038\/msb.2010.68","article-title":"Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions","volume":"6","author":"A Bordbar","year":"2010","journal-title":"Mol Syst Biol"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"180","DOI":"10.1186\/1752-0509-5-180","article-title":"A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology","volume":"5","author":"A Bordbar","year":"2011","journal-title":"BMC Syst Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"649","DOI":"10.1038\/msb.2013.5","article-title":"Integration of clinical data with a genome-scale metabolic model of the human adipocyte","volume":"9","author":"A Mardinoglu","year":"2013","journal-title":"Mol Syst Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"3083","DOI":"10.1038\/ncomms4083","article-title":"Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease","volume":"5","author":"A Mardinoglu","year":"2014","journal-title":"Nat Commun"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"bav068","DOI":"10.1093\/database\/bav068","article-title":"Human metabolic atlas: an online resource for human metabolism","volume":"2015","author":"N Pornputtapong","year":"2015","journal-title":"Database (Oxford)"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1186\/1752-0509-6-153","article-title":"Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE","volume":"6","author":"Y Wang","year":"2012","journal-title":"BMC Syst Biol"},{"issue":"5","key":"ref31","doi-asserted-by":"crossref","first-page":"e1002518","DOI":"10.1371\/journal.pcbi.1002518","article-title":"Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT","volume":"8","author":"R Agren","year":"2012","journal-title":"PLoS Comput Biol"},{"issue":"9","key":"ref32","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/nbt.1487","article-title":"Network-based prediction of human tissue-specific metabolism","volume":"26","author":"T Shlomi","year":"2008","journal-title":"Nat Biotechnol"},{"issue":"9","key":"ref33","doi-asserted-by":"crossref","first-page":"E866","DOI":"10.1073\/pnas.1319196111","article-title":"Chromosome 3p loss of heterozygosity is associated with a unique metabolic network in clear cell renal carcinoma","volume":"111","author":"F Gatto","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1038\/msb.2010.56","article-title":"Computational reconstruction of tissue-specific metabolic models: application to human liver metabolism","volume":"6","author":"L Jerby","year":"2010","journal-title":"Mol Syst Biol"},{"issue":"7","key":"ref35","doi-asserted-by":"crossref","first-page":"e102319","DOI":"10.1371\/journal.pone.0102319","article-title":"Multi-tissue computational modeling analyzes pathophysiology of type 2 diabetes in MKR mice","volume":"9","author":"A Kumar","year":"2014","journal-title":"PLoS One"},{"issue":"6","key":"ref36","doi-asserted-by":"crossref","first-page":"921","DOI":"10.1016\/j.celrep.2015.04.010","article-title":"Proteome- and transcriptome-driven reconstruction of the human myocyte metabolic network and its use for identification of markers for diabetes","volume":"11","author":"L V\u00e4remo","year":"2015","journal-title":"Cell Rep"},{"issue":"5","key":"ref37","doi-asserted-by":"crossref","first-page":"e1000082","DOI":"10.1371\/journal.pcbi.1000082","article-title":"Context-specific metabolic networks are consistent with experiments","volume":"4","author":"SA Becker","year":"2008","journal-title":"PLoS Comput Biol"},{"issue":"22","key":"ref38","doi-asserted-by":"crossref","first-page":"2900","DOI":"10.1093\/bioinformatics\/btt493","article-title":"GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data","volume":"29","author":"BJ Schmidt","year":"2013","journal-title":"Bioinformatics"},{"issue":"7","key":"ref39","doi-asserted-by":"crossref","first-page":"e0131875","DOI":"10.1371\/journal.pone.0131875","article-title":"Context-Specific Metabolic Model Extraction Based on Regularized Least Squares Optimization","volume":"10","author":"S Robaina Est\u00e9vez","year":"2015","journal-title":"PLoS One"},{"issue":"1","key":"ref40","doi-asserted-by":"crossref","first-page":"e1003424","DOI":"10.1371\/journal.pcbi.1003424","article-title":"Fast reconstruction of compact context-specific metabolic network models","volume":"10","author":"N Vlassis","year":"2014","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"ref41","doi-asserted-by":"crossref","first-page":"264","DOI":"10.1016\/j.ymben.2003.09.002","article-title":"The effects of alternate optimal solutions in constraint-based genome-scale metabolic models","volume":"5","author":"R Mahadevan","year":"2003","journal-title":"Metab Eng"},{"issue":"3","key":"ref42","first-page":"245","article-title":"What is flux balance analysis? Nat Biotechnol","volume":"28","author":"JD Orth","year":"2010","journal-title":"What is flux balance analysis? Nat Biotechnol"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"237","DOI":"10.3389\/fphys.2013.00237","article-title":"The evolution of genome-scale models of cancer metabolism","volume":"4","author":"NE Lewis","year":"2013","journal-title":"Front Physiol"},{"issue":"12","key":"ref44","doi-asserted-by":"crossref","first-page":"1248","DOI":"10.1038\/nbt1210-1248","article-title":"Towards a knowledge-based Human Protein Atlas","volume":"28","author":"M Uhlen","year":"2010","journal-title":"Nat Biotechnol"},{"issue":"6220","key":"ref45","doi-asserted-by":"crossref","first-page":"1260419","DOI":"10.1126\/science.1260419","article-title":"Proteomics. Tissue-based map of the human proteome","volume":"347","author":"M Uhl\u00e9n","year":"2015","journal-title":"Science"},{"issue":"4","key":"ref46","doi-asserted-by":"crossref","first-page":"2172","DOI":"10.1529\/biophysj.104.043000","article-title":"Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies","volume":"87","author":"ND Price","year":"2004","journal-title":"Biophys J"},{"issue":"4","key":"ref47","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/j.jtbi.2004.02.006","article-title":"Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space","volume":"228","author":"SJ Wiback","year":"2004","journal-title":"J Theor Biol"},{"issue":"12","key":"ref48","doi-asserted-by":"crossref","first-page":"11683","DOI":"10.1074\/jbc.M409072200","article-title":"Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet","volume":"280","author":"I Thiele","year":"2005","journal-title":"J Biol Chem"},{"issue":"12","key":"ref49","doi-asserted-by":"crossref","first-page":"1279","DOI":"10.1038\/nbt.1711","article-title":"Large-scale in silico modeling of metabolic interactions between cell types in the human brain","volume":"28","author":"NE Lewis","year":"2010","journal-title":"Nat Biotechnol"},{"issue":"18","key":"ref50","doi-asserted-by":"crossref","first-page":"6539","DOI":"10.1021\/jm901869w","article-title":"Novel approaches for targeting thymidylate synthase to overcome the resistance and toxicity of anticancer drugs","volume":"53","author":"D Garg","year":"2010","journal-title":"J Med Chem"},{"issue":"11","key":"ref51","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1097\/FPC.0b013e32834a48a9","article-title":"Gene set analysis of purine and pyrimidine antimetabolites cancer therapies","volume":"21","author":"BL Fridley","year":"2011","journal-title":"Pharmacogenet Genomics"},{"issue":"3","key":"ref52","article-title":"Antimetabolite Treatment for Pancreatic Cancer","volume":"3","author":"MMA Valenzuela","year":"2014","journal-title":"Chemotherapy (Los Angel)"},{"issue":"Suppl 3","key":"ref53","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/bjc.1998.747","article-title":"New antimetabolites in cancer chemotherapy and their clinical impact","volume":"78","author":"SB Kaye","year":"1998","journal-title":"Br J Cancer"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1038\/msb.2010.115","article-title":"Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery","volume":"7","author":"HU Kim","year":"2011","journal-title":"Mol Syst Biol"},{"issue":"15","key":"ref55","doi-asserted-by":"crossref","first-page":"4177","DOI":"10.1046\/j.1432-1327.2001.02329.x","article-title":"The effect of thiamine supplementation on tumour proliferation. A metabolic control analysis study","volume":"268","author":"B Com\u00edn-Anduix","year":"2001","journal-title":"Eur J Biochem"},{"issue":"5\u20136","key":"ref56","doi-asserted-by":"crossref","first-page":"250","DOI":"10.1159\/000225157","article-title":"The thiamin status of early cancer patients with particular reference to those with breast and bronchial carcinomas","volume":"33","author":"TK Basu","year":"1976","journal-title":"Oncology"},{"issue":"4","key":"ref57","first-page":"169","article-title":"The role of thiamine in cancer: possible genetic and cellular signaling mechanisms","volume":"10","author":"KVQ Lu\u2019o\u2019ng","year":"2013","journal-title":"Cancer Genomics Proteomics"},{"issue":"4345","key":"ref58","doi-asserted-by":"crossref","first-page":"252","DOI":"10.1038\/171252a0","article-title":"Inhibition of tumour growth by D-glucosamine","volume":"171","author":"JH QUASTEL","year":"1953","journal-title":"Nature"},{"issue":"2","key":"ref59","doi-asserted-by":"crossref","first-page":"1172","DOI":"10.1073\/pnas.77.2.1172","article-title":"Membrane-active drugs potentiate the killing of tumor cells by D-glucosamine","volume":"77","author":"SJ Friedman","year":"1980","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"4","key":"ref60","doi-asserted-by":"crossref","first-page":"840","DOI":"10.1016\/j.bbrc.2007.06.137","article-title":"D-glucosamine inhibits proliferation of human cancer cells through inhibition of p70S6K","volume":"360","author":"HJ Oh","year":"2007","journal-title":"Biochem Biophys Res Commun"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/1475-2867-14-45","article-title":"Anti-cancer activity of glucosamine through inhibition of N-linked glycosylation","volume":"14","author":"V Chesnokov","year":"2014","journal-title":"Cancer Cell Int"},{"issue":"2","key":"ref62","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1016\/j.cmet.2013.05.017","article-title":"Cellular fatty acid metabolism and cancer","volume":"18","author":"E Currie","year":"2013","journal-title":"Cell Metab"},{"issue":"4","key":"ref63","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nrc2817","article-title":"Targeting metabolic transformation for cancer therapy","volume":"10","author":"DA Tennant","year":"2010","journal-title":"Nat Rev Cancer"},{"issue":"3","key":"ref64","doi-asserted-by":"crossref","first-page":"400","DOI":"10.1016\/j.molcel.2014.09.026","article-title":"A role for the mitochondrial pyruvate carrier as a repressor of the Warburg effect and colon cancer cell growth","volume":"56","author":"JC Schell","year":"2014","journal-title":"Mol Cell"},{"issue":"2 Pt A","key":"ref65","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.canlet.2014.01.031","article-title":"PKM2 contributes to cancer metabolism","volume":"356","author":"N Wong","year":"2015","journal-title":"Cancer Lett"},{"issue":"7","key":"ref66","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1111\/j.1742-4658.2012.08529.x","article-title":"Glycosaminoglycans: key players in cancer cell biology and treatment","volume":"279","author":"N Afratis","year":"2012","journal-title":"FEBS J"},{"issue":"9","key":"ref67","doi-asserted-by":"crossref","first-page":"2139","DOI":"10.1158\/1535-7163.MCT-06-0082","article-title":"Therapeutic value of glycosaminoglycans in cancer","volume":"5","author":"GW Yip","year":"2006","journal-title":"Mol Cancer Ther"},{"issue":"3","key":"ref68","first-page":"385","article-title":"The biological role of chondroitin sulfate in cancer and chondroitin-based anticancer agents","volume":"22","author":"AP Asimakopoulou","year":"2008","journal-title":"In Vivo"},{"issue":"11","key":"ref69","doi-asserted-by":"crossref","first-page":"1931","DOI":"10.1002\/1097-0142(19870601)59:11<1931::AID-CNCR2820591116>3.0.CO;2-7","article-title":"Keratan sulfate levels in sera of patients bearing cartilage tumors","volume":"59","author":"DJ Kliner","year":"1987","journal-title":"Cancer"},{"issue":"9","key":"ref70","doi-asserted-by":"crossref","first-page":"8685","DOI":"10.1007\/s13277-014-2111-x","article-title":"Increased MTHFD2 expression is associated with poor prognosis in breast cancer","volume":"35","author":"F Liu","year":"2014","journal-title":"Tumour Biol"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"3128","DOI":"10.1038\/ncomms4128","article-title":"Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer","volume":"5","author":"R Nilsson","year":"2014","journal-title":"Nat Commun"},{"issue":"1","key":"ref72","doi-asserted-by":"crossref","first-page":"48","DOI":"10.18632\/oncotarget.756","article-title":"High-throughput RNAi screening for novel modulators of vimentin expression identifies MTHFD2 as a regulator of breast cancer cell migration and invasion","volume":"4","author":"L Lehtinen","year":"2013","journal-title":"Oncotarget"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"e877","DOI":"10.1038\/cddis.2013.393","article-title":"Contribution of serine, folate and glycine metabolism to the ATP, NADPH and purine requirements of cancer cells","volume":"4","author":"PM Tedeschi","year":"2013","journal-title":"Cell Death Dis"},{"issue":"4","key":"ref74","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1016\/j.beha.2009.09.004","article-title":"Cancer research: from folate antagonism to molecular targets","volume":"22","author":"JR Bertino","year":"2009","journal-title":"Best Pract Res Clin Haematol"},{"issue":"26","key":"ref75","doi-asserted-by":"crossref","first-page":"18777","DOI":"10.1074\/jbc.M611763200","article-title":"Squalene synthase, a determinant of Raft-associated cholesterol and modulator of cancer cell proliferation","volume":"282","author":"K Brusselmans","year":"2007","journal-title":"J Biol Chem"},{"issue":"4","key":"ref76","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1038\/pcan.2012.14","article-title":"Role of squalene synthase in prostate cancer risk and the biological aggressiveness of human prostate cancer","volume":"15","author":"Y Fukuma","year":"2012","journal-title":"Prostate Cancer Prostatic Dis"},{"issue":"1\u20132","key":"ref77","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1159\/000178871","article-title":"Genome-wide analysis of pancreatic cancer using microarray-based techniques","volume":"9","author":"T Harada","year":"2009","journal-title":"Pancreatology"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1186\/1745-6150-7-21","article-title":"Pathway-based classification of cancer subtypes","volume":"7","author":"S Kim","year":"2012","journal-title":"Biol Direct"},{"issue":"6","key":"ref79","doi-asserted-by":"crossref","first-page":"1151","DOI":"10.3892\/ol.2012.928","article-title":"Energy metabolism of cancer: Glycolysis versus oxidative phosphorylation (Review)","volume":"4","author":"J Zheng","year":"2012","journal-title":"Oncol Lett"},{"issue":"6","key":"ref80","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1111\/j.1742-4658.2007.05686.x","article-title":"Energy metabolism in tumor cells","volume":"274","author":"R Moreno-S\u00e1nchez","year":"2007","journal-title":"FEBS J"},{"issue":"1","key":"ref81","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1016\/j.mam.2009.12.006","article-title":"Bioenergetic pathways in tumor mitochondria as targets for cancer therapy and the importance of the ROS-induced apoptotic trigger","volume":"31","author":"SJ Ralph","year":"2010","journal-title":"Mol Aspects Med"},{"issue":"3","key":"ref82","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1016\/j.bbrc.2003.11.136","article-title":"Cancer metabolism: facts, fantasy, and fiction","volume":"313","author":"XL Zu","year":"2004","journal-title":"Biochem Biophys Res Commun"},{"issue":"5","key":"ref83","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1593\/neo.13314","article-title":"The role of sarcosine metabolism in prostate cancer progression","volume":"15","author":"AP Khan","year":"2013","journal-title":"Neoplasia"},{"issue":"7231","key":"ref84","doi-asserted-by":"crossref","first-page":"910","DOI":"10.1038\/nature07762","article-title":"Metabolomic profiles delineate potential role for sarcosine in prostate cancer progression","volume":"457","author":"A Sreekumar","year":"2009","journal-title":"Nature"},{"issue":"2","key":"ref85","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1016\/0262-1746(85)90084-8","article-title":"Selective killing of human cancer cells by polyunsaturated fatty acids","volume":"19","author":"ME B\u00e9gin","year":"1985","journal-title":"Prostaglandins Leukot Med"},{"issue":"5","key":"ref86","first-page":"1053","article-title":"Differential killing of human carcinoma cells supplemented with n-3 and n-6 polyunsaturated fatty acids","volume":"77","author":"ME B\u00e9gin","year":"1986","journal-title":"J Natl Cancer Inst"},{"issue":"2","key":"ref87","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1097\/00075197-199903000-00005","article-title":"n-3 polyunsaturated fatty acids and cancer","volume":"2","author":"P Bougnoux","year":"1999","journal-title":"Curr Opin Clin Nutr Metab Care"},{"issue":"9","key":"ref88","doi-asserted-by":"crossref","first-page":"1616","DOI":"10.1016\/j.jnutbio.2013.02.002","article-title":"Up-regulation of vitamin B1 homeostasis genes in breast cancer","volume":"24","author":"JA Zastre","year":"2013","journal-title":"J Nutr Biochem"},{"issue":"12","key":"ref89","first-page":"5175","article-title":"DUOX enzyme activity promotes AKT signalling in prostate cancer cells","volume":"32","author":"CA Pettigrew","year":"2012","journal-title":"Anticancer Res"},{"issue":"8","key":"ref90","doi-asserted-by":"crossref","first-page":"578","DOI":"10.2174\/138920210793360925","article-title":"Dihydrofolate reductase gene variations in susceptibility to disease and treatment outcomes","volume":"11","author":"BS Askari","year":"2010","journal-title":"Curr Genomics"},{"issue":"2\u20133","key":"ref91","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1016\/S0946-672X(01)80066-3","article-title":"Oxidase activity of ceruloplasmin and concentrations of copper and zinc in serum of cancer patients","volume":"15","author":"M Zowczak","year":"2001","journal-title":"J Trace Elem Med Biol"},{"issue":"2","key":"ref92","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/S0304-3835(97)00340-6","article-title":"Serum ceruloplasmin as a diagnostic marker of cancer","volume":"121","author":"A Senra Varela","year":"1997","journal-title":"Cancer Lett"},{"issue":"6","key":"ref93","doi-asserted-by":"crossref","first-page":"2108","DOI":"10.1124\/mol.106.026245","article-title":"The H+-linked monocarboxylate transporter (MCT1\/SLC16A1): a potential therapeutic target for high-risk neuroblastoma","volume":"70","author":"J Fang","year":"2006","journal-title":"Mol Pharmacol"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1186\/1471-2407-14-377","article-title":"Alcohol induces cell proliferation via hypermethylation of ADHFE1 in colorectal cancer cells","volume":"14","author":"JW Moon","year":"2014","journal-title":"BMC Cancer"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1186\/1471-2407-13-142","article-title":"Alcohol dehydrogenase, iron containing, 1 promoter hypermethylation associated with colorectal cancer differentiation","volume":"13","author":"CH Tae","year":"2013","journal-title":"BMC Cancer"},{"issue":"6","key":"ref96","first-page":"2046","article-title":"Decreased lymphocyte adenosine deaminase activity in tumor patients","volume":"36","author":"J Uberti","year":"1976","journal-title":"Cancer Res"},{"issue":"2","key":"ref97","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1002\/1097-0142(197708)40:2<796::AID-CNCR2820400230>3.0.CO;2-O","article-title":"Adenosine deaminase activity in patients with renal adenocarcinoma","volume":"40","author":"G Sufrin","year":"1977","journal-title":"Cancer"},{"issue":"2","key":"ref98","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1007\/BF02469742","article-title":"Alteration of adenosine deaminase levels in peripheral blood lymphocytes of patients with gastric cancer","volume":"15","author":"O Kojima","year":"1985","journal-title":"Jpn J Surg"},{"issue":"11","key":"ref99","doi-asserted-by":"crossref","first-page":"e28186","DOI":"10.1371\/journal.pone.0028186","article-title":"FADS2 function loss at the cancer hotspot 11q13 locus diverts lipid signaling precursor synthesis to unusual eicosanoid fatty acids","volume":"6","author":"WJ Park","year":"2011","journal-title":"PLoS One"},{"issue":"2","key":"ref100","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1016\/j.bbrc.2014.01.051","article-title":"MiR-205 modulates abnormal lipid metabolism of hepatoma cells via targeting acyl-CoA synthetase long-chain family member 1 (ACSL1) mRNA","volume":"444","author":"M Cui","year":"2014","journal-title":"Biochem Biophys Res Commun"},{"issue":"2","key":"ref101","doi-asserted-by":"crossref","first-page":"272","DOI":"10.3760\/cma.j.issn.0366-6999.20121121","article-title":"Validation and target gene screening of hsa-miR-205 in lung squamous cell carcinoma","volume":"127","author":"W Huang","year":"2014","journal-title":"Chin Med J (Engl)"},{"issue":"23","key":"ref102","first-page":"8429","article-title":"Fatty acid CoA ligase 4 is up-regulated in colon adenocarcinoma","volume":"61","author":"Y Cao","year":"2001","journal-title":"Cancer Res"},{"issue":"2","key":"ref103","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1016\/j.jhep.2008.07.037","article-title":"Sustained JNK1 activation is associated with altered histone H3 methylations in human liver cancer","volume":"50","author":"Q Chang","year":"2009","journal-title":"J Hepatol"},{"issue":"6802","key":"ref104","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1038\/35030140","article-title":"Superoxide dismutase as a target for the selective killing of cancer cells","volume":"407","author":"P Huang","year":"2000","journal-title":"Nature"},{"key":"ref105","doi-asserted-by":"crossref","first-page":"87","DOI":"10.1146\/annurev.nutr.22.110801.140547","article-title":"Regulation of enzymes of the urea cycle and arginine metabolism","volume":"22","author":"SM Morris Jr","year":"2002","journal-title":"Annu Rev Nutr"},{"issue":"11","key":"ref106","doi-asserted-by":"crossref","first-page":"1915","DOI":"10.1017\/S0007114512003285","article-title":"Vitamin D signalling in adipose tissue","volume":"108","author":"C Ding","year":"2012","journal-title":"Br J Nutr"},{"key":"ref107","first-page":"228","article-title":"Vitamin D and adipose tissue-more than storage","volume":"5","author":"SJ Mutt","year":"2014","journal-title":"Front Physiol"},{"issue":"6","key":"ref108","first-page":"983","article-title":"Elevated stromal chondroitin sulfate glycosaminoglycan predicts progression in early-stage prostate cancer","volume":"3","author":"C Ricciardelli","year":"1997","journal-title":"Clin Cancer Res"},{"issue":"4","key":"ref109","first-page":"963","article-title":"Elevated levels of versican but not decorin predict disease progression in early-stage prostate cancer","volume":"4","author":"C Ricciardelli","year":"1998","journal-title":"Clin Cancer Res"},{"issue":"10","key":"ref110","first-page":"2324","article-title":"Elevated levels of peritumoral chondroitin sulfate are predictive of poor prognosis in patients treated by radical prostatectomy for early-stage prostate cancer","volume":"59","author":"C Ricciardelli","year":"1999","journal-title":"Cancer Res"},{"issue":"6","key":"ref111","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1016\/j.ejca.2004.12.035","article-title":"Molecular markers of prostate cancer outcome","volume":"41","author":"DI Quinn","year":"2005","journal-title":"Eur J Cancer"},{"issue":"10","key":"ref112","doi-asserted-by":"crossref","first-page":"4070","DOI":"10.1210\/jc.2005-2845","article-title":"An orally administered multitarget tyrosine kinase inhibitor, SU11248, is a novel potent inhibitor of thyroid oncogenic RET\/papillary thyroid cancer kinases","volume":"91","author":"DW Kim","year":"2006","journal-title":"J Clin Endocrinol Metab"},{"issue":"4","key":"ref113","doi-asserted-by":"crossref","first-page":"575","DOI":"10.1530\/EJE-13-0825","article-title":"Tyrosine kinase inhibitor treatments in patients with metastatic thyroid carcinomas: a retrospective study of the TUTHYREF network","volume":"170","author":"MH Massicotte","year":"2014","journal-title":"Eur J Endocrinol"},{"issue":"3","key":"ref114","doi-asserted-by":"crossref","first-page":"179","DOI":"10.1007\/BF00620482","article-title":"Accumulation of radioiodinated tyrosine derivatives in the adrenal medulla and in melanomas","volume":"4","author":"G Kloss","year":"1979","journal-title":"Eur J Nucl Med"},{"issue":"5930","key":"ref115","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1126\/science.1160809","article-title":"Understanding the Warburg effect: the metabolic requirements of cell proliferation","volume":"324","author":"MG Vander Heiden","year":"2009","journal-title":"Science"},{"issue":"2","key":"ref116","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1038\/nrc2981","article-title":"Regulation of cancer cell metabolism","volume":"11","author":"RA Cairns","year":"2011","journal-title":"Nat Rev Cancer"},{"issue":"6235","key":"ref117","doi-asserted-by":"crossref","first-page":"660","DOI":"10.1126\/science.aaa0355","article-title":"Human genomics. The human transcriptome across tissues and individuals","volume":"348","author":"M Mel\u00e9","year":"2015","journal-title":"Science"},{"key":"ref118","article-title":"Are acinic cell carcinomas of the breast and salivary glands distinct diseases?","author":"S Piscuoglio","year":"2015","journal-title":"Histopathology"},{"issue":"12","key":"ref119","doi-asserted-by":"crossref","first-page":"1213","DOI":"10.1001\/jamaoto.2014.1998","article-title":"Salivary gland cancer in BRCA-positive families: a retrospective review","volume":"140","author":"TK Shen","year":"2014","journal-title":"JAMA Otolaryngol Head Neck Surg"},{"issue":"7","key":"ref120","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1136\/jcp.56.7.497","article-title":"Salivary gland-like tumours of the breast: surgical and molecular pathology","volume":"56","author":"M Pia-Foschini","year":"2003","journal-title":"J Clin Pathol"},{"issue":"2","key":"ref121","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1016\/S0959-8049(02)00595-6","article-title":"Skin cancer and non-Hodgkin\u2019s lymphoma as second malignancies. markers of impaired immune function?","volume":"39","author":"K Hemminki","year":"2003","journal-title":"Eur J Cancer"},{"issue":"2","key":"ref122","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1002\/ijc.2910600209","article-title":"Cancer risk after renal transplantation in the Nordic countries, 1964\u20131986","volume":"60","author":"SA Birkeland","year":"1995","journal-title":"Int J Cancer"},{"issue":"6","key":"ref123","doi-asserted-by":"crossref","first-page":"1353","DOI":"10.1242\/dmm.011338","article-title":"Hooked on fat: the role of lipid synthesis in cancer metabolism and tumour development","volume":"6","author":"F Baenke","year":"2013","journal-title":"Dis Model Mech"},{"issue":"9","key":"ref124","doi-asserted-by":"crossref","first-page":"1369","DOI":"10.1038\/sj.bjc.6605007","article-title":"De novo fatty-acid synthesis and related pathways as molecular targets for cancer therapy","volume":"100","author":"T Mashima","year":"2009","journal-title":"Br J Cancer"},{"key":"ref125","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1186\/2049-3002-2-10","article-title":"Defects in mitochondrial metabolism and cancer","volume":"2","author":"E Gaude","year":"2014","journal-title":"Cancer Metab"},{"key":"ref126","article-title":"Tumors and Mitochondrial Respiration: A Neglected Connection","author":"A Viale","year":"2015","journal-title":"Cancer Res"},{"issue":"4","key":"ref127","doi-asserted-by":"crossref","first-page":"191","DOI":"10.1016\/j.tibs.2014.02.004","article-title":"Serine and glycine metabolism in cancer","volume":"39","author":"I Amelio","year":"2014","journal-title":"Trends Biochem Sci"},{"key":"ref128","unstructured":"Gurobi Optimizer Reference Manual [Website]; 2014. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.gurobi.com\/index\" xlink:type=\"simple\">http:\/\/www.gurobi.com\/index<\/ext-link>."},{"issue":"9","key":"ref129","doi-asserted-by":"crossref","first-page":"1290","DOI":"10.1038\/nprot.2011.308","article-title":"Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0","volume":"6","author":"J Schellenberger","year":"2011","journal-title":"Nat Protoc"},{"key":"ref130","unstructured":"Qutub AA. The Qutub Lab [Website]; 2015. Available from: <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/qutublab.org\/apps-code-tools.html#Metabolic\" xlink:type=\"simple\">http:\/\/qutublab.org\/apps-code-tools.html#Metabolic<\/ext-link>."},{"issue":"1","key":"ref131","doi-asserted-by":"crossref","first-page":"84","DOI":"10.1287\/opre.46.1.84","article-title":"Direction choice for accelerated convergence in hit-and-run sampling","volume":"46","author":"DE Kaufman","year":"1998","journal-title":"Operations Research"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004808","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,14]],"date-time":"2024-06-14T19:51:35Z","timestamp":1718394695000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1004808"}},"subtitle":[],"editor":[{"given":"Costas D.","family":"Maranas","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2016,3,4]]},"references-count":131,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2016,3,4]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1004808","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,3,4]]}}}