{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,24]],"date-time":"2026-04-24T10:27:42Z","timestamp":1777026462216,"version":"3.51.4"},"reference-count":32,"publisher":"Springer Science and Business Media LLC","issue":"8","license":[{"start":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T00:00:00Z","timestamp":1629417600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T00:00:00Z","timestamp":1629417600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["853995 to SV"],"award-info":[{"award-number":["853995 to SV"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100010767","name":"Innovative Medicines Initiative","doi-asserted-by":"publisher","award":["853995 to SD"],"award-info":[{"award-number":["853995 to SD"]}],"id":[{"id":"10.13039\/501100010767","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002803","name":"Fondazione Cariplo","doi-asserted-by":"publisher","award":["2018-0112 to FU"],"award-info":[{"award-number":["2018-0112 to FU"]}],"id":[{"id":"10.13039\/501100002803","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Fondazione Amici ONLUS ITALIA, research prize to FU"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Comput Sci"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Inflammatory bowel disease (IBD) is a class of chronic disorders whose etiogenesis is still unknown. Despite the high number of IBD-related omics studies, the RNA-sequencing data produced results that are hard to compare because of the experimental variability and different data analysis approaches. We here introduce the IBD Transcriptome and Metatranscriptome Meta-Analysis (TaMMA) framework, a comprehensive survey of publicly available IBD RNA-sequencing datasets. IBD TaMMA is an open-source platform where scientists can explore simultaneously the freely available IBD-associated transcriptomics and microbial profiles thanks to its interactive interface, resulting in a useful tool to the IBD community.<\/jats:p>","DOI":"10.1038\/s43588-021-00114-y","type":"journal-article","created":{"date-parts":[[2021,8,20]],"date-time":"2021-08-20T11:11:53Z","timestamp":1629457913000},"page":"511-515","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":97,"title":["The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) framework"],"prefix":"10.1038","volume":"1","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3975-9148","authenticated-orcid":false,"given":"Luca","family":"Massimino","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9571-2582","authenticated-orcid":false,"given":"Luigi Antonio","family":"Lamparelli","sequence":"additional","affiliation":[]},{"given":"Yashar","family":"Houshyar","sequence":"additional","affiliation":[]},{"given":"Silvia","family":"D\u2019Alessio","sequence":"additional","affiliation":[]},{"given":"Laurent","family":"Peyrin-Biroulet","sequence":"additional","affiliation":[]},{"given":"Stefania","family":"Vetrano","sequence":"additional","affiliation":[]},{"given":"Silvio","family":"Danese","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5395-7795","authenticated-orcid":false,"given":"Federica","family":"Ungaro","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,8,20]]},"reference":[{"key":"114_CR1","doi-asserted-by":"publisher","first-page":"3076","DOI":"10.3390\/ijms22063076","volume":"22","author":"L Aldars-Garc\u00eda","year":"2021","unstructured":"Aldars-Garc\u00eda, L., Marin, A. C., Chaparro, M. & Gisbert, J. P. The interplay between immune system and microbiota in inflammatory bowel disease: a narrative review. Int. J. Mol. Sci. 22, 3076 (2021).","journal-title":"Int. J. Mol. Sci."},{"key":"114_CR2","doi-asserted-by":"publisher","first-page":"1520","DOI":"10.1136\/gutjnl-2019-320065","volume":"69","author":"NS Seyed Tabib","year":"2020","unstructured":"Seyed Tabib, N. S. et al. Big data in IBD: big progress for clinical practice. Gut 69, 1520\u20131532 (2020).","journal-title":"Gut"},{"key":"114_CR3","first-page":"8279619","volume":"2020","author":"X Li","year":"2020","unstructured":"Li, X. et al. Meta-analysis of expression profiling data indicates need for combinatorial biomarkers in pediatric ulcerative colitis. J. Immunol. Res. 2020, 8279619 (2020).","journal-title":"J. Immunol. Res."},{"key":"114_CR4","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1016\/j.cellimm.2018.09.003","volume":"334","author":"S Naz","year":"2018","unstructured":"Naz, S. et al. Transcriptome meta-analysis identifies immune signature comprising of RNA binding proteins in ulcerative colitis patients. Cell. Immunol. 334, 42\u201348 (2018).","journal-title":"Cell. Immunol."},{"key":"114_CR5","doi-asserted-by":"publisher","first-page":"1761","DOI":"10.1016\/j.ygeno.2019.09.019","volume":"112","author":"KE Vennou","year":"2020","unstructured":"Vennou, K. E., Piovani, D., Kontou, P. I., Bonovas, S. & Bagos, P. G. Multiple outcome meta-analysis of gene-expression data in inflammatory bowel disease. Genomics 112, 1761\u20131767 (2020).","journal-title":"Genomics"},{"key":"114_CR6","doi-asserted-by":"publisher","first-page":"999","DOI":"10.1177\/2050640619876787","volume":"7","author":"F Ungaro","year":"2019","unstructured":"Ungaro, F., Massimino, L., D\u2019Alessio, S. & Danese, S. The gut virome in inflammatory bowel disease pathogenesis: from metagenomics to novel therapeutic approaches. United Eur. Gastroenterol. J. 7, 999\u20131007 (2019).","journal-title":"United Eur. Gastroenterol. J."},{"key":"114_CR7","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1186\/s12859-015-0478-3","volume":"16","author":"CK Stein","year":"2015","unstructured":"Stein, C. K. et al. Removing batch effects from purified plasma cell gene expression microarrays with modified ComBat. BMC Bioinformatics 16, 63 (2015).","journal-title":"BMC Bioinformatics"},{"key":"114_CR8","doi-asserted-by":"publisher","first-page":"882","DOI":"10.1093\/bioinformatics\/bts034","volume":"28","author":"JT Leek","year":"2012","unstructured":"Leek, J. T., Johnson, W. E., Parker, H. S., Jaffe, A. E. & Storey, J. D. The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics 28, 882\u2013883 (2012).","journal-title":"Bioinformatics"},{"key":"114_CR9","doi-asserted-by":"publisher","first-page":"702","DOI":"10.1038\/s41575-020-0352-2","volume":"17","author":"M Argollo","year":"2020","unstructured":"Argollo, M., Kotze, P. G., Kakkadasam, P. & D\u2019Haens, G. Optimizing biologic therapy in IBD: how essential is therapeutic drug monitoring? Nat. Rev. Gastroenterol. Hepatol. 17, 702\u2013710 (2020).","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"114_CR10","doi-asserted-by":"publisher","first-page":"580803","DOI":"10.3389\/fmed.2020.580803","volume":"7","author":"F Liu","year":"2020","unstructured":"Liu, F., Lee, S. A., Riordan, S. M., Zhang, L. & Zhu, L. Global studies of using fecal biomarkers in predicting relapse in inflammatory bowel disease. Front. Med. (Lausanne) 7, 580803 (2020).","journal-title":"Front. Med. (Lausanne)"},{"key":"114_CR11","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/j.jcmgh.2017.03.007","volume":"4","author":"E Martini","year":"2017","unstructured":"Martini, E., Krug, S. M., Siegmund, B., Neurath, M. F. & Becker, C. Mend your fences: the epithelial barrier and its relationship with mucosal immunity in inflammatory bowel disease. Cell. Mol. Gastroenterol. Hepatol. 4, 33\u201346 (2017).","journal-title":"Cell. Mol. Gastroenterol. Hepatol."},{"key":"114_CR12","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1136\/gut.2010.207480","volume":"60","author":"S Danese","year":"2011","unstructured":"Danese, S. Role of the vascular and lymphatic endothelium in the pathogenesis of inflammatory bowel disease: \u2018brothers in arms\u2019. Gut 60, 998\u20131008 (2011).","journal-title":"Gut"},{"key":"114_CR13","doi-asserted-by":"publisher","first-page":"656745","DOI":"10.3389\/fmed.2021.656745","volume":"8","author":"A Schulz-Kuhnt","year":"2021","unstructured":"Schulz-Kuhnt, A., Neurath, M. F., Wirtz, S. & Atreya, I. Innate lymphoid cells as regulators of epithelial integrity: therapeutic implications for inflammatory bowel diseases. Front. Med. (Lausanne) 8, 656745 (2021).","journal-title":"Front. Med. (Lausanne)"},{"key":"114_CR14","first-page":"970890","volume":"2015","author":"C Alkim","year":"2015","unstructured":"Alkim, C., Alkim, H., Koksal, A. R., Boga, S. & Sen, I. Angiogenesis in inflammatory bowel disease. Int. J. Inflam. 2015, 970890 (2015).","journal-title":"Int. J. Inflam."},{"key":"114_CR15","doi-asserted-by":"publisher","first-page":"655","DOI":"10.1038\/s41586-019-1237-9","volume":"569","author":"J Lloyd-Price","year":"2019","unstructured":"Lloyd-Price, J. et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature 569, 655\u2013662 (2019).","journal-title":"Nature"},{"key":"114_CR16","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/nature11550","volume":"489","author":"CA Lozupone","year":"2012","unstructured":"Lozupone, C. A., Stombaugh, J. I., Gordon, J. I., Jansson, J. K. & Knight, R. Diversity, stability and resilience of the human gut microbiota. Nature 489, 220\u2013230 (2012).","journal-title":"Nature"},{"key":"114_CR17","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1097\/MPG.0000000000002140","volume":"68","author":"MA Fernandes","year":"2019","unstructured":"Fernandes, M. A. et al. Enteric virome and bacterial microbiota in children with ulcerative colitis and Crohn disease. J. Pediatr. Gastroenterol. Nutr. 68, 30\u201336 (2019).","journal-title":"J. Pediatr. Gastroenterol. Nutr."},{"key":"114_CR18","doi-asserted-by":"publisher","first-page":"1169","DOI":"10.1136\/gutjnl-2018-318131","volume":"68","author":"T Zuo","year":"2019","unstructured":"Zuo, T. et al. Gut mucosal virome alterations in ulcerative colitis. Gut 68, 1169\u20131179 (2019).","journal-title":"Gut"},{"key":"114_CR19","first-page":"1419","volume":"21","author":"W Wang","year":"2015","unstructured":"Wang, W. et al. Metagenomic analysis of microbiome in colon tissue from subjects with inflammatory bowel diseases reveals interplay of viruses and bacteria. Inflamm. Bowel Dis. 21, 1419\u20131427 (2015).","journal-title":"Inflamm. Bowel Dis."},{"key":"114_CR20","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1080\/19490976.2018.1511664","volume":"10","author":"F Ungaro","year":"2019","unstructured":"Ungaro, F. et al. Metagenomic analysis of intestinal mucosa revealed a specific eukaryotic gut virome signature in early-diagnosed inflammatory bowel disease. Gut Microbes 10, 149\u2013158 (2019).","journal-title":"Gut Microbes"},{"key":"114_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1155\/2011\/282507","volume":"2011","author":"M Nguyen","year":"2011","unstructured":"Nguyen, M., Bradford, K., Zhang, X. & Shih, D. Q. Cytomegalovirus reactivation in ulcerative colitis patients. Ulcers 2011, 1\u20137 (2011).","journal-title":"Ulcers"},{"key":"114_CR22","doi-asserted-by":"publisher","first-page":"e8124","DOI":"10.15252\/msb.20178124","volume":"14","author":"R Argelaguet","year":"2018","unstructured":"Argelaguet, R. et al. Multi-omics factor analysis\u2014a framework for unsupervised integration of multi-omics data sets. Mol. Syst. Biol. 14, e8124 (2018).","journal-title":"Mol. Syst. Biol."},{"key":"114_CR23","doi-asserted-by":"publisher","first-page":"2520","DOI":"10.1093\/bioinformatics\/bts480","volume":"28","author":"J K\u00f6ster","year":"2012","unstructured":"K\u00f6ster, J. & Rahmann, S. Snakemake\u2014a scalable bioinformatics workflow engine. Bioinformatics 28, 2520\u20132522 (2012).","journal-title":"Bioinformatics"},{"key":"114_CR24","doi-asserted-by":"publisher","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","volume":"30","author":"AM Bolger","year":"2014","unstructured":"Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114\u20132120 (2014).","journal-title":"Bioinformatics"},{"key":"114_CR25","doi-asserted-by":"publisher","first-page":"D766","DOI":"10.1093\/nar\/gky955","volume":"47","author":"A Frankish","year":"2019","unstructured":"Frankish, A. et al. GENCODE reference annotation for the human and mouse genomes. Nucleic Acids Res. 47, D766\u2013D773 (2019).","journal-title":"Nucleic Acids Res."},{"key":"114_CR26","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","volume":"29","author":"A Dobin","year":"2013","unstructured":"Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15\u201321 (2013).","journal-title":"Bioinformatics"},{"key":"114_CR27","doi-asserted-by":"publisher","first-page":"2184","DOI":"10.1093\/bioinformatics\/bts356","volume":"28","author":"L Wang","year":"2012","unstructured":"Wang, L., Wang, S. & Li, W. RSeQC: quality control of RNA-seq experiments. Bioinformatics 28, 2184\u20132185 (2012).","journal-title":"Bioinformatics"},{"key":"114_CR28","doi-asserted-by":"publisher","first-page":"3047","DOI":"10.1093\/bioinformatics\/btw354","volume":"32","author":"P Ewels","year":"2016","unstructured":"Ewels, P., Magnusson, M., Lundin, S. & K\u00e4ller, M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32, 3047\u20133048 (2016).","journal-title":"Bioinformatics"},{"key":"114_CR29","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0550-8","volume":"15","author":"MI Love","year":"2014","unstructured":"Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).","journal-title":"Genome Biol."},{"key":"114_CR30","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1186\/s12859-016-1250-z","volume":"17","author":"S Subhash","year":"2016","unstructured":"Subhash, S. & Kanduri, C. GeneSCF: a real-time based functional enrichment tool with support for multiple organisms. BMC Bioinformatics 17, 365 (2016).","journal-title":"BMC Bioinformatics"},{"key":"114_CR31","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1891-0","volume":"20","author":"DE Wood","year":"2019","unstructured":"Wood, D. E., Lu, J. & Langmead, B. Improved metagenomic analysis with Kraken 2. Genome Biol. 20, 257 (2019).","journal-title":"Genome Biol."},{"key":"114_CR32","doi-asserted-by":"publisher","unstructured":"Massimino, L., Ungaro, F. & Lamparelli, L. A. IBD TaMMA data (Open Science Framework, 2021); https:\/\/doi.org\/10.17605\/osf.io\/yrxa7","DOI":"10.17605\/osf.io\/yrxa7"}],"updated-by":[{"DOI":"10.1038\/s43588-021-00146-4","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T00:00:00Z","timestamp":1632873600000}}],"container-title":["Nature Computational Science"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00114-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00114-y","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00114-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,12,3]],"date-time":"2022-12-03T16:29:52Z","timestamp":1670084992000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s43588-021-00114-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,8,20]]},"references-count":32,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2021,8]]}},"alternative-id":["114"],"URL":"https:\/\/doi.org\/10.1038\/s43588-021-00114-y","relation":{"has-preprint":[{"id-type":"doi","id":"10.21203\/rs.3.rs-478844\/v1","asserted-by":"object"}]},"ISSN":["2662-8457"],"issn-type":[{"value":"2662-8457","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,8,20]]},"assertion":[{"value":"30 April 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 July 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"20 August 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 September 2021","order":4,"name":"change_date","label":"Change Date","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Correction","order":5,"name":"change_type","label":"Change Type","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"A Correction to this paper has been published:","order":6,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"https:\/\/doi.org\/10.1038\/s43588-021-00146-4","URL":"https:\/\/doi.org\/10.1038\/s43588-021-00146-4","order":7,"name":"change_details","label":"Change Details","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"S.D. has served as a speaker, consultant and advisory board member for Schering-Plough, Abbott (AbbVie) Laboratories, Merck and Co, UCB Pharma, Ferring, Cellerix, Millenium Takeda, Nycomed, Pharmacosmos, Actelion, Alfa Wasserman, Genentech, Grunenthal, Pfizer, AstraZeneca, Novo Nordisk, Vifor and Johnson & Johnson. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}]}}