{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,9]],"date-time":"2026-04-09T16:33:56Z","timestamp":1775752436639,"version":"3.50.1"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T00:00:00Z","timestamp":1732233600000},"content-version":"vor","delay-in-days":21,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>The ever-growing amount of genome-wide omics data paved the way for solving life science problems in a data-driven manner. Among others, enrichment analysis is part of the standard analysis arsenal to determine systemic signals in any given transcriptomic or proteomic data. Only a part of the members of the fungal kingdom, however, can be analyzed via public web applications, despite the global rise of fungal pathogens and their increasing resistance to antimycotics. We present FungiFun3, a major update of our user-friendly gene set enrichment web application dedicated to fungi. FungiFun3 was rebuilt from scratch to support a modern and easy-to-use web interface and supports &amp;gt;4-fold more fungal strains (n\u2009=\u20091287 in total) than its predecessor. In addition, it also allows ranked gene set enrichment analysis at the genomic scale. FungiFun3 thus serves as a starting hub for identifying molecular signals in omics datasets related to a vast amount of available fungal strains including human fungal pathogens of the WHO\u2019s priority list and far beyond.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>FungiFun3, including sample data and FAQ, is freely available at https:\/\/fungifun3.hki-jena.de\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae620","type":"journal-article","created":{"date-parts":[[2024,11,22]],"date-time":"2024-11-22T16:50:50Z","timestamp":1732294250000},"source":"Crossref","is-referenced-by-count":14,"title":["FungiFun3: systemic gene set enrichment analysis for fungal species"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5455-9227","authenticated-orcid":false,"given":"Albert","family":"Garcia Lopez","sequence":"first","affiliation":[{"name":"Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (Leibniz-HKI) , 07745 Jena,","place":["Germany"]}]},{"given":"Daniela","family":"Albrecht-Eckardt","sequence":"additional","affiliation":[{"name":"Biocontrol Jena GmbH , 07745 Jena,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9393-124X","authenticated-orcid":false,"given":"Gianni","family":"Panagiotou","sequence":"additional","affiliation":[{"name":"Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (Leibniz-HKI) , 07745 Jena,","place":["Germany"]},{"name":"Institute of Microbiology, Faculty of Biological Sciences, Faculty of Medicine, Friedrich Schiller University Jena Jena, 07743,","place":["Germany"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3862-6546","authenticated-orcid":false,"given":"Sascha","family":"Sch\u00e4uble","sequence":"additional","affiliation":[{"name":"Department of Microbiome Dynamics, Leibniz Institute for Natural Product Research and Infection Biology \u2013 Hans-Kn\u00f6ll-Institute (Leibniz-HKI) , 07745 Jena,","place":["Germany"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,22]]},"reference":[{"key":"2024112517553967500_btae620-B1","doi-asserted-by":"crossref","first-page":"39","DOI":"10.3390\/jof4010039","article-title":"FungiDB: an integrated bioinformatic resource for fungi and oomycetes","volume":"4","author":"Basenko","year":"2018","journal-title":"JoF"},{"key":"2024112517553967500_btae620-B2","doi-asserted-by":"crossref","first-page":"D523","DOI":"10.1093\/nar\/gkac1052","article-title":"UniProt: the Universal Protein Knowledgebase in 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