{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T23:28:05Z","timestamp":1792106885688,"version":"4.4.0"},"reference-count":23,"publisher":"Elsevier BV","license":[{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,1,22]],"date-time":"2024-01-22T00:00:00Z","timestamp":1705881600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000780","name":"European Union","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000780","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Journal of Biomedical Informatics"],"published-print":{"date-parts":[[2024,2]]},"DOI":"10.1016\/j.jbi.2024.104597","type":"journal-article","created":{"date-parts":[[2024,1,23]],"date-time":"2024-01-23T18:00:47Z","timestamp":1706032847000},"page":"104597","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":10,"special_numbering":"C","title":["Adjusting for false discoveries in constraint-based differential metabolic flux analysis"],"prefix":"10.1016","volume":"150","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8518-5352","authenticated-orcid":false,"given":"Bruno G.","family":"Galuzzi","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-2248-798X","authenticated-orcid":false,"given":"Luca","family":"Milazzo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chiara","family":"Damiani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.jbi.2024.104597_b1","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.copbio.2020.02.013","article-title":"Systems metabolomics: From metabolomic snapshots to design principles","volume":"63","author":"Damiani","year":"2020","journal-title":"Curr. Opin. Biotechnol."},{"issue":"1","key":"10.1016\/j.jbi.2024.104597_b2","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.cmet.2020.10.012","article-title":"Metabolic-pathway-based subtyping of triple-negative breast cancer reveals potential therapeutic targets","volume":"33","author":"Gong","year":"2021","journal-title":"Cell Metab."},{"issue":"2","key":"10.1016\/j.jbi.2024.104597_b3","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/s41573-021-00339-6","article-title":"Targeting cancer metabolism in the era of precision oncology","volume":"21","author":"Stine","year":"2022","journal-title":"Nat. Rev. Drug Discov."},{"issue":"2","key":"10.1016\/j.jbi.2024.104597_b4","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1009337","article-title":"INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation","volume":"18","author":"Di Filippo","year":"2022","journal-title":"PLoS Comput. Biol."},{"issue":"6","key":"10.1016\/j.jbi.2024.104597_b5","first-page":"1","article-title":"Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells","volume":"23","author":"Galuzzi","year":"2022","journal-title":"BMC Bioinformatics"},{"issue":"3","key":"10.1016\/j.jbi.2024.104597_b6","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1038\/nbt.1614","article-title":"What is flux balance analysis?","volume":"28","author":"Orth","year":"2010","journal-title":"Nature Biotechnol."},{"issue":"4","key":"10.1016\/j.jbi.2024.104597_b7","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":"Mahadevan","year":"2003","journal-title":"Metab. Eng."},{"issue":"6977","key":"10.1016\/j.jbi.2024.104597_b8","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1038\/nature02289","article-title":"Global organization of metabolic fluxes in the bacterium Escherichia coli","volume":"427","author":"Almaas","year":"2004","journal-title":"Nature"},{"issue":"1","key":"10.1016\/j.jbi.2024.104597_b9","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1111\/pce.13896","article-title":"Metabolic flux from the chloroplast provides signals controlling photosynthetic acclimation to cold in Arabidopsis thaliana","volume":"44","author":"Herrmann","year":"2021","journal-title":"Plant Cell Environ."},{"issue":"1","key":"10.1016\/j.jbi.2024.104597_b10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41540-019-0109-0","article-title":"Flux sampling is a powerful tool to study metabolism under changing environmental conditions","volume":"5","author":"Herrmann","year":"2019","journal-title":"NPJ Syst. Biol. Appl."},{"issue":"9","key":"10.1016\/j.jbi.2024.104597_b11","doi-asserted-by":"crossref","first-page":"5457","DOI":"10.1074\/jbc.R800048200","article-title":"Use of randomized sampling for analysis of metabolic networks","volume":"284","author":"Schellenberger","year":"2009","journal-title":"J. Biol. Chem."},{"issue":"1","key":"10.1016\/j.jbi.2024.104597_b12","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12934-021-01694-0","article-title":"Metabolic flux sampling predicts strain-dependent differences related to aroma production among commercial wine yeasts","volume":"20","author":"Scott","year":"2021","journal-title":"Microb. Cell Factories"},{"key":"10.1016\/j.jbi.2024.104597_b13","series-title":"International Conference on Machine Learning, Optimization, and Data Science","first-page":"234","article-title":"Best practices in flux sampling of constrained-based models","author":"Galuzzi","year":"2022"},{"issue":"9","key":"10.1016\/j.jbi.2024.104597_b14","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1005758","article-title":"A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect","volume":"13","author":"Damiani","year":"2017","journal-title":"PLoS Comput. Biol."},{"issue":"11","key":"10.1016\/j.jbi.2024.104597_b15","doi-asserted-by":"crossref","first-page":"1741","DOI":"10.1093\/bioinformatics\/btx052","article-title":"CHRR: coordinate hit-and-run with rounding for uniform sampling of constraint-based models","volume":"33","author":"Haraldsd\u00f3ttir","year":"2017","journal-title":"Bioinformatics"},{"issue":"1","key":"10.1016\/j.jbi.2024.104597_b16","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":"Kaufman","year":"1998","journal-title":"Oper. Res."},{"issue":"2","key":"10.1016\/j.jbi.2024.104597_b17","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0086587","article-title":"optGpSampler: an improved tool for uniformly sampling the solution-space of genome-scale metabolic networks","volume":"9","author":"Megchelenbrink","year":"2014","journal-title":"PLoS One"},{"issue":"7","key":"10.1016\/j.jbi.2024.104597_b18","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pcbi.1000859","article-title":"Sampling the solution space in genome-scale metabolic networks reveals transcriptional regulation in key enzymes","volume":"6","author":"Bordel","year":"2010","journal-title":"PLoS Comput. Biol."},{"issue":"14","key":"10.1016\/j.jbi.2024.104597_b19","doi-asserted-by":"crossref","first-page":"i311","DOI":"10.1093\/bioinformatics\/btx251","article-title":"popFBA: tackling intratumour heterogeneity with Flux Balance Analysis","volume":"33","author":"Damiani","year":"2017","journal-title":"Bioinformatics"},{"issue":"3","key":"10.1016\/j.jbi.2024.104597_b20","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1038\/nbt.4072","article-title":"Recon3D enables a three-dimensional view of gene variation in human metabolism","volume":"36","author":"Brunk","year":"2018","journal-title":"Nature Biotechnol."},{"issue":"9","key":"10.1016\/j.jbi.2024.104597_b21","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":"Schellenberger","year":"2011","journal-title":"Nat. Protoc."},{"issue":"1","key":"10.1016\/j.jbi.2024.104597_b22","first-page":"7","article-title":"CODA: convergence diagnosis and output analysis for MCMC","volume":"6","author":"Plummer","year":"2006","journal-title":"R News"},{"issue":"3","key":"10.1016\/j.jbi.2024.104597_b23","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen","year":"2020","journal-title":"Nature Methods"}],"container-title":["Journal of Biomedical Informatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1532046424000157?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S1532046424000157?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,2,2]],"date-time":"2025-02-02T01:33:48Z","timestamp":1738460028000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S1532046424000157"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2]]},"references-count":23,"alternative-id":["S1532046424000157"],"URL":"https:\/\/doi.org\/10.1016\/j.jbi.2024.104597","relation":{},"ISSN":["1532-0464"],"issn-type":[{"value":"1532-0464","type":"print"}],"subject":[],"published":{"date-parts":[[2024,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Adjusting for false discoveries in constraint-based differential metabolic flux analysis","name":"articletitle","label":"Article Title"},{"value":"Journal of Biomedical Informatics","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.jbi.2024.104597","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"104597"}}