{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,14]],"date-time":"2026-04-14T03:05:51Z","timestamp":1776135951856,"version":"3.50.1"},"reference-count":33,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,12,1]],"date-time":"2018-12-01T00:00:00Z","timestamp":1543622400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["TEC2014-60337-R"],"award-info":[{"award-number":["TEC2014-60337-R"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["DPI2017-89827-R"],"award-info":[{"award-number":["DPI2017-89827-R"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"Ministerio de Econom\u00eda y Competitividad","doi-asserted-by":"publisher","award":["BFU2014-57466-P"],"award-info":[{"award-number":["BFU2014-57466-P"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12859-018-2487-5","type":"journal-article","created":{"date-parts":[[2018,12,21]],"date-time":"2018-12-21T19:47:31Z","timestamp":1545421651000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":113,"title":["FELLA: an R package to enrich metabolomics data"],"prefix":"10.1186","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6426-8204","authenticated-orcid":false,"given":"Sergio","family":"Picart-Armada","sequence":"first","affiliation":[]},{"given":"Francesc","family":"Fern\u00e1ndez-Albert","sequence":"additional","affiliation":[]},{"given":"Maria","family":"Vinaixa","sequence":"additional","affiliation":[]},{"given":"Oscar","family":"Yanes","sequence":"additional","affiliation":[]},{"given":"Alexandre","family":"Perera-Lluna","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2018,12,22]]},"reference":[{"issue":"1","key":"2487_CR1","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/j.aca.2009.11.042","volume":"659","author":"R Madsen","year":"2010","unstructured":"Madsen R, Lundstedt T, Trygg J. Chemometrics in metabolomics \u2013 a review in human disease diagnosis. Anal Chim Acta. 2010; 659(1):23\u201333.","journal-title":"Anal Chim Acta"},{"issue":"19","key":"2487_CR2","doi-asserted-by":"publisher","first-page":"2452","DOI":"10.1093\/bioinformatics\/btt414","volume":"29","author":"N Kessler","year":"2013","unstructured":"Kessler N, Neuweger H, Bonte A, Langenk\u00e4mper G, Niehaus K, Nattkemper TW, Goesmann A. MeltDB 2.0\u2013advances of the metabolomics software system. Bioinformatics. 2013; 29(19):2452\u20139.","journal-title":"Bioinformatics"},{"issue":"13","key":"2487_CR3","doi-asserted-by":"publisher","first-page":"1937","DOI":"10.1093\/bioinformatics\/btu136","volume":"30","author":"F Fern\u00e1ndez-Albert","year":"2014","unstructured":"Fern\u00e1ndez-Albert F, Llorach R, Andr\u00e9s-Lacueva C, Perera A. An R package to analyse LC\/MS metabolomic data: MAIT (Metabolite Automatic Identification Toolkit). Bioinformatics. 2014; 30(13):1937\u20139.","journal-title":"Bioinformatics"},{"issue":"2","key":"2487_CR4","doi-asserted-by":"publisher","first-page":"e1002375","DOI":"10.1371\/journal.pcbi.1002375","volume":"8","author":"P Khatri","year":"2012","unstructured":"Khatri P, Sirota M, Butte AJ. Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol. 2012; 8(2):e1002375.","journal-title":"PLoS Comput Biol"},{"issue":"D1","key":"2487_CR5","doi-asserted-by":"publisher","first-page":"109","DOI":"10.1093\/nar\/gkr988","volume":"40","author":"M Kanehisa","year":"2011","unstructured":"Kanehisa M, Goto S, Sato Y, Furumichi M, Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2011; 40(D1):109\u201314.","journal-title":"Nucleic Acids Res"},{"issue":"Web Server issu","key":"2487_CR6","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1093\/nar\/gkv380","volume":"43","author":"J Xia","year":"2015","unstructured":"Xia J, Sinelnikov IV, Han B, Wishart DS. MetaboAnalyst 3.0 \u2013 making metabolomics more meaningful. Nucleic Acids Res. 2015; 43(Web Server issue):251\u20137.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"2487_CR7","doi-asserted-by":"publisher","first-page":"284","DOI":"10.1089\/omi.2011.0118","volume":"16","author":"G Yu","year":"2012","unstructured":"Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012; 16(5):284\u20137.","journal-title":"OMICS"},{"issue":"20","key":"2487_CR8","doi-asserted-by":"publisher","first-page":"2917","DOI":"10.1093\/bioinformatics\/btr499","volume":"27","author":"A Kamburov","year":"2011","unstructured":"Kamburov A, Cavill R, Ebbels TM, Herwig R, Keun HC. Integrated pathway-level analysis of transcriptomics and metabolomics data with IMPaLA. Bioinformatics. 2011; 27(20):2917\u20138.","journal-title":"Bioinformatics"},{"issue":"2","key":"2487_CR9","doi-asserted-by":"publisher","first-page":"115","DOI":"10.1038\/nmeth.3252","volume":"12","author":"W Huber","year":"2015","unstructured":"Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Ole\u2019s AK, Pag\u00e8s H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M. Orchestrating high-throughput genomic analysis with Bioconductor. Nat Methods. 2015; 12(2):115\u201321.","journal-title":"Nat Methods"},{"issue":"3","key":"2487_CR10","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1089\/cmb.2010.0265","volume":"18","author":"F Vandin","year":"2011","unstructured":"Vandin F, Upfal E, Raphael BJ. Algorithms for detecting significantly mutated pathways in cancer. J Comput Biol. 2011; 18(3):507\u201322.","journal-title":"J Comput Biol"},{"key":"2487_CR11","unstructured":"Page L, Brin S, Motwani R, Winograd T. The pagerank citation ranking: Bringing order to the web. Technical report, Stanford InfoLab. 1999."},{"issue":"12","key":"2487_CR12","doi-asserted-by":"publisher","first-page":"0189012","DOI":"10.1371\/journal.pone.0189012","volume":"12","author":"S Picart-Armada","year":"2017","unstructured":"Picart-Armada S, Fern\u00e1ndez-Albert F, Vinaixa M, Rodriguez MA, Aivio S, Stracker TH, Yanes O, Perera-Lluna A. Null diffusion-based enrichment for metabolomics data. PloS one. 2017; 12(12):0189012.","journal-title":"PloS one"},{"key":"2487_CR13","first-page":"1695","volume":"Complex Systems","author":"G Csardi","year":"2006","unstructured":"Csardi G, Nepusz T. The igraph software package for complex network research. InterJournal. 2006; Complex Systems:1695.","journal-title":"InterJournal"},{"key":"2487_CR14","unstructured":"Chang W, Cheng J, Allaire J, Xie Y, McPherson J. Shiny: Web Application Framework for R. 2018. R package version 1.1.0. \n                    https:\/\/CRAN.R-project.org\/package=shiny\n                    \n                  . Accessed 20 Sept 2018."},{"issue":"7","key":"2487_CR15","doi-asserted-by":"publisher","first-page":"976","DOI":"10.1093\/bioinformatics\/btq064","volume":"26","author":"G Yu","year":"2010","unstructured":"Yu G, Li F, Qin Y, Bo X, Wu Y, Wang S. Gosemsim: an r package for measuring semantic similarity among go terms and gene products. Bioinformatics. 2010; 26(7):976\u20138.","journal-title":"Bioinformatics"},{"issue":"D1","key":"2487_CR16","doi-asserted-by":"publisher","first-page":"1049","DOI":"10.1093\/nar\/gku1179","volume":"43","author":"GO Consortium","year":"2015","unstructured":"Consortium GO, et al. Gene ontology consortium: going forward. Nucleic Acids Res. 2015; 43(D1):1049\u201356.","journal-title":"Nucleic Acids Res"},{"issue":"9","key":"2487_CR17","doi-asserted-by":"publisher","first-page":"3982","DOI":"10.1021\/acs.jproteome.5b00443","volume":"14","author":"L Chen","year":"2015","unstructured":"Chen L, Li J, Guo T, Ghosh S, Koh SK, Tian D, Zhang L, Jia D, Beuerman RW, Aebersold R, et al. Global metabonomic and proteomic analysis of human conjunctival epithelial cells (IOBA-NHC) in response to hyperosmotic stress. J Proteome Res. 2015; 14(9):3982\u201395.","journal-title":"J Proteome Res"},{"issue":"1","key":"2487_CR18","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/s12918-014-0134-y","volume":"8","author":"G Yu","year":"2014","unstructured":"Yu G, Wang L-G, Han Y, He Q-Y. Distinct metabolic responses of an ovarian cancer stem cell line. BMC Syst Biol. 2014; 8(1):134.","journal-title":"BMC Syst Biol"},{"issue":"3","key":"2487_CR19","doi-asserted-by":"publisher","first-page":"0004480","DOI":"10.1371\/journal.pntd.0004480","volume":"10","author":"S Decuypere","year":"2016","unstructured":"Decuypere S, Maltha J, Deborggraeve S, Rattray NJ, Issa G, B\u00e9renger K, Lompo P, Tahita MC, Ruspasinghe T, McConville M, et al. Towards Improving Point-of-Care Diagnosis of Non-malaria Febrile Illness: A Metabolomics Approach. PLoS Negl Trop Dis. 2016; 10(3):0004480.","journal-title":"PLoS Negl Trop Dis"},{"key":"2487_CR20","doi-asserted-by":"publisher","first-page":"624","DOI":"10.1016\/j.chemosphere.2018.08.013","volume":"211","author":"H Ziarrusta","year":"2018","unstructured":"Ziarrusta H, Mijangos L, Picart-Armada S, Irazola M, Perera-Lluna A, Usobiaga A, Prieto A, Etxebarria N, Olivares M, Zuloaga O. Non-targeted metabolomics reveals alterations in liver and plasma of gilt-head bream exposed to oxybenzone. Chemosphere. 2018; 211:624\u201331.","journal-title":"Chemosphere"},{"issue":"6","key":"2487_CR21","doi-asserted-by":"publisher","first-page":"1591","DOI":"10.1007\/s00216-016-0100-1","volume":"409","author":"M Gogiashvili","year":"2017","unstructured":"Gogiashvili M, Edlund K, Gianmoena K, Marchan R, Brik A, Andersson JT, Lambert J, Madjar K, Hellwig B, Rahnenf\u00fchrer J, et al. Metabolic profiling of ob\/ob mouse fatty liver using HR-MAS 1 H-NMR combined with gene expression analysis reveals alterations in betaine metabolism and the transsulfuration pathway. Anal Bioanal Chem. 2017; 409(6):1591\u2013606.","journal-title":"Anal Bioanal Chem"},{"issue":"8","key":"2487_CR22","doi-asserted-by":"publisher","first-page":"634","DOI":"10.1080\/07853890310018458","volume":"35","author":"P Pollard","year":"2003","unstructured":"Pollard P, Wortham N, Tomlinson I. The TCA cycle and tumorigenesis: the examples of fumarate hydratase and succinate dehydrogenase. Ann Med. 2003; 35(8):634\u20139. \n                    https:\/\/doi.org\/10.1080\/07853890310018458\n                    \n                  .","journal-title":"Ann Med"},{"issue":"9","key":"2487_CR23","doi-asserted-by":"publisher","first-page":"755","DOI":"10.1136\/jmg.2006.041087","volume":"43","author":"M Pithukpakorn","year":"2006","unstructured":"Pithukpakorn M, Wei M-H, Toure O, Steinbach PJ, Glenn GM, Zbar B, Linehan WM, Toro JR. Fumarate hydratase enzyme activity in lymphoblastoid cells and fibroblasts of individuals in families with hereditary leiomyomatosis and renal cell cancer. J Med Genet. 2006; 43(9):755\u201362. \n                    https:\/\/doi.org\/10.1136\/jmg.2006.041087\n                    \n                  .","journal-title":"J Med Genet"},{"issue":"5","key":"2487_CR24","doi-asserted-by":"publisher","first-page":"793","DOI":"10.1016\/j.humpath.2006.10.011","volume":"38","author":"HJ Lehtonen","year":"2007","unstructured":"Lehtonen HJ, Blanco I, Piulats JM, Herva R, Launonen V, Aaltonen LA. Conventional renal cancer in a patient with fumarate hydratase mutation. Hum Pathol. 2007; 38(5):793\u20136. \n                    https:\/\/doi.org\/10.1016\/j.humpath.2006.10.011\n                    \n                  .","journal-title":"Hum Pathol"},{"issue":"2","key":"2487_CR25","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/j.ajhg.2008.07.011","volume":"83","author":"Y Ni","year":"2008","unstructured":"Ni Y, Zbuk KM, Sadler T, Patocs A, Lobo G, Edelman E, Platzer P, Orloff MS, Waite KA, Eng C. Germline Mutations and Variants in the Succinate Dehydrogenase Genes in Cowden and Cowden-like Syndromes. Am J Hum Genet. 2008; 83(2):261\u20138. \n                    https:\/\/doi.org\/10.1016\/j.ajhg.2008.07.011\n                    \n                  .","journal-title":"Am J Hum Genet"},{"key":"2487_CR26","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1186\/1476-4598-5-14","volume":"5","author":"KK Singh","year":"2006","unstructured":"Singh KK, Desouki MM, Franklin RB, Costello LC. Mitochondrial aconitase and citrate metabolism in malignant and nonmalignant human prostate tissues. Mol Cancer. 2006; 5:14. \n                    https:\/\/doi.org\/10.1186\/1476-4598-5-14\n                    \n                  .","journal-title":"Mol Cancer"},{"issue":"4","key":"2487_CR27","doi-asserted-by":"publisher","first-page":"746","DOI":"10.1016\/j.bbamcr.2008.09.008","volume":"1793","author":"T Kirkegaard","year":"2009","unstructured":"Kirkegaard T, J\u00e4\u00e4ttel\u00e4 M. Lysosomal involvement in cell death and cancer. Biochim Biophys Acta-Mol Cell Res. 2009; 1793(4):746\u201354. \n                    https:\/\/doi.org\/10.1016\/j.bbamcr.2008.09.008\n                    \n                  .","journal-title":"Biochim Biophys Acta-Mol Cell Res"},{"issue":"7298","key":"2487_CR28","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1038\/465562a","volume":"465","author":"WG Kaelin","year":"2010","unstructured":"Kaelin WG, Thompson CB. Q&A: Cancer: clues from cell metabolism. Nature. 2010; 465(7298):562\u20134. \n                    https:\/\/doi.org\/10.1038\/465562a\n                    \n                  .","journal-title":"Nature"},{"issue":"1","key":"2487_CR29","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1146\/annurev.me.26.020175.000301","volume":"26","author":"WR Beisel","year":"1975","unstructured":"Beisel WR. Metabolic response to infection. Annu Rev Med. 1975; 26(1):9\u201320.","journal-title":"Annu Rev Med"},{"issue":"1","key":"2487_CR30","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1016\/S0925-4439(00)00081-8","volume":"1535","author":"CD Fitch","year":"2000","unstructured":"Fitch CD, Cai G. -z., Shoemaker JD. A role for linoleic acid in erythrocytes infected with plasmodium berghei. Biochim Biophys Acta-Mol Basis Dis. 2000; 1535(1):45\u201349.","journal-title":"Biochim Biophys Acta-Mol Basis Dis"},{"issue":"7503","key":"2487_CR31","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1038\/nature13475","volume":"510","author":"M Maceyka","year":"2014","unstructured":"Maceyka M, Spiegel S. Sphingolipid metabolites in inflammatory disease. Nature. 2014; 510(7503):58.","journal-title":"Nature"},{"issue":"1","key":"2487_CR32","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.cytogfr.2010.12.001","volume":"22","author":"Y-J Seo","year":"2011","unstructured":"Seo Y-J, Alexander S, Hahm B. Does cytokine signaling link sphingolipid metabolism to host defense and immunity against virus infections?Cytokine Growth Factor Rev. 2011; 22(1):55\u201361.","journal-title":"Cytokine Growth Factor Rev."},{"issue":"10","key":"2487_CR33","doi-asserted-by":"publisher","first-page":"2513","DOI":"10.1007\/s00204-016-1761-4","volume":"90","author":"P Godoy","year":"2016","unstructured":"Godoy P, Widera A, Schmidt-Heck W, Campos G, Meyer C, Cadenas C, Reif R, St\u00f6ber R, Hammad S, P\u00fctter L, et al. Gene network activity in cultivated primary hepatocytes is highly similar to diseased mammalian liver tissue. Arch. Toxicol. 2016; 90(10):2513\u201329.","journal-title":"Arch. Toxicol."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2487-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-018-2487-5\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-018-2487-5.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,12,21]],"date-time":"2019-12-21T19:04:33Z","timestamp":1576955073000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-018-2487-5"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12]]},"references-count":33,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["2487"],"URL":"https:\/\/doi.org\/10.1186\/s12859-018-2487-5","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12]]},"assertion":[{"value":"22 February 2018","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 November 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"22 December 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"Francesc Fern\u00e1ndez-Albert has been employed by Takeda Cambridge Ltd. This does not alter our adherence to BioMed Central policies. There are no patents, products in development or marketed products to declare. The commercial affiliation of Francesc Fern\u00e1ndez-Albert did not play any role in the design, analysis and outcome of this article. The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"538"}}