{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T12:03:13Z","timestamp":1784203393675,"version":"3.55.0"},"reference-count":35,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2026,5,19]],"date-time":"2026-05-19T00:00:00Z","timestamp":1779148800000},"content-version":"vor","delay-in-days":138,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["NRF-2021R1A2C2012002"],"award-info":[{"award-number":["NRF-2021R1A2C2012002"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003725","name":"National Research Foundation of Korea","doi-asserted-by":"publisher","award":["RS-2024-00407104"],"award-info":[{"award-number":["RS-2024-00407104"]}],"id":[{"id":"10.13039\/501100003725","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>The nucleolus is a well-characterized sub-nuclear compartment primarily responsible for ribosomal RNA (rRNA) synthesis and ribosome biogenesis. In addition to these canonical functions, it plays roles in a variety of other cellular processes. Despite its importance, the contributions of the nucleolus to fungal development and pathogenicity remain poorly understood, especially in filamentous fungi. The structure and function of the nucleolus are regulated by numerous proteins that either reside within it or shuttle between the nucleolus and nucleoplasm, often guided by short amino acid motifs known as nucleolar localization signals\u00a0(NoLSs). However, comprehensive resources cataloguing nucleolar proteins and their localization signals in fungi are currently lacking, hindering systematic investigations of nucleolar function across species. To address this gap, we developed FuNGI (Fungal Nucleolar Genomic Inventory), a web-based interactive database for the exploration of fungal proteins containing predicted nucleolar localization signals. The current version of FuNGI includes proteins containing predicted nucleolar localization signals and their associated NoLSs across 769 fungal proteomes spanning eight phyla. The database offers a user-friendly interface that enables browsing, retrieval, and comparison of NoLS-containing proteins across multiple species. Each entry integrates sequence-based predictions and functional annotations to support comparative and functional analyses. To our knowledge, FuNGI is the first comprehensive and interactive database dedicated to fungal proteins containing predicted nucleolar localization signals. By enabling systematic and cross-species analyses, FuNGI provides a valuable resource for advancing our understanding of fungal nucleoli and their roles in fungal biology and pathogenicity.<\/jats:p>","DOI":"10.1093\/database\/baag023","type":"journal-article","created":{"date-parts":[[2026,5,7]],"date-time":"2026-05-07T11:46:30Z","timestamp":1778154390000},"source":"Crossref","is-referenced-by-count":0,"title":["FuNGI: Fungal Nucleolar Genomic Inventory\u2014a comprehensive database of fungal proteins with predicted nucleolar localization signals"],"prefix":"10.1093","volume":"2026","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6617-1804","authenticated-orcid":false,"given":"Gnanendra","family":"Shanmugam","sequence":"first","affiliation":[{"name":"College of Life and Applied Sciences, Yeungnam University Department of Biotechnology, , Gyeongsan, Gyeongbuk 38541 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chaewon","family":"Kim","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Kyung Hee University Department of Convergent Biotechnology and Advanced Materials Science, , Yongin 17104 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Surajit","family":"De\u00a0Mandal","sequence":"additional","affiliation":[{"name":"College of Life and Applied Sciences, Yeungnam University Department of Biotechnology, , Gyeongsan, Gyeongbuk 38541 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Minji","family":"Kim","sequence":"additional","affiliation":[{"name":"College of Life and Applied Sciences, Yeungnam University Department of Biotechnology, , Gyeongsan, Gyeongbuk 38541 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Song Hee","family":"Lee","sequence":"additional","affiliation":[{"name":"College of Life and Applied Sciences, Yeungnam University Department of Biotechnology, , Gyeongsan, Gyeongbuk 38541 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2206-4593","authenticated-orcid":false,"given":"Jaeyoung","family":"Choi","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Kyung Hee University Department of Convergent Biotechnology and Advanced Materials Science, , Yongin 17104 ,","place":["Republic of Korea"]},{"name":"BK21 Interdisciplinary Program in IT-Bio Convergence System, Kyung Hee University , Yongin 17104 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junhyun","family":"Jeon","sequence":"additional","affiliation":[{"name":"College of Life and Applied Sciences, Yeungnam University Department of Biotechnology, , Gyeongsan, Gyeongbuk 38541 ,","place":["Republic of Korea"]},{"name":"Phytobiome Engineering Research Laboratory, Yeungnam University , Gyeongsan, Gyeongbuk 38541 ,","place":["Republic of Korea"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,19]]},"reference":[{"key":"2026071607041629300_bib1","doi-asserted-by":"publisher","first-page":"29","DOI":"10.1007\/978-3-319-38882-3_2","article-title":"The nucleolus: structure and function","volume-title":"The Functional Nucleus","author":"Dubois","year":"2016"},{"key":"2026071607041629300_bib2","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1016\/j.abb.2016.02.018","article-title":"Regulators in the DNA damage response","volume":"594","author":"Liu","year":"2016","journal-title":"Arch Biochem Biophys"},{"key":"2026071607041629300_bib3","doi-asserted-by":"publisher","first-page":"662","DOI":"10.1016\/j.tcb.2018.03.007","article-title":"Nucleolar function in lifespan regulation","volume":"28","author":"Tiku","year":"2018","journal-title":"Trends Cell Biol"},{"key":"2026071607041629300_bib4","doi-asserted-by":"publisher","first-page":"e59065","DOI":"10.1371\/journal.pone.0059065","article-title":"NOA36 protein contains a highly conserved nucleolar localization signal capable of directing functional proteins to the nucleolus in mammalian cells","volume":"8","author":"de\u00a0Melo","year":"2013","journal-title":"PLoS One"},{"key":"2026071607041629300_bib5","doi-asserted-by":"publisher","first-page":"1643","DOI":"10.1080\/15384101.2017.1361568","article-title":"New roles for Dicer in the nucleolus and its relevance to cancer","volume":"16","author":"Roche","year":"2017","journal-title":"Cell Cycle"},{"key":"2026071607041629300_bib6","doi-asserted-by":"publisher","first-page":"2351","DOI":"10.1038\/s41388-017-0121-z","article-title":"Nucleolus as an emerging hub in maintenance of genome stability and cancer pathogenesis","volume":"37","author":"Lindstr\u00f6m","year":"2018","journal-title":"Oncogene"},{"key":"2026071607041629300_bib7","doi-asserted-by":"publisher","first-page":"39","DOI":"10.1615\/CritRevEukaryotGeneExpr.v13.i1.40","article-title":"The dynamics of the nucleolus","volume":"13","author":"Leung","year":"2003","journal-title":"Crit Rev Eukaryot Gene Expr"},{"key":"2026071607041629300_bib8","doi-asserted-by":"publisher","first-page":"984163","DOI":"10.3389\/fpls.2022.984163","article-title":"Nuclear dynamics: formation of bodies and trafficking in plant nuclei","volume":"13","author":"Mu\u00f1oz-D\u00edaz","year":"2022","journal-title":"Front Plant Sci"},{"key":"2026071607041629300_bib9","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1186\/s12964-021-00741-y","article-title":"Types of nuclear localization signals and mechanisms of protein import into the nucleus","volume":"19","author":"Lu","year":"2021","journal-title":"Cell Commun Signal"},{"key":"2026071607041629300_bib10","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1080\/19491034.2015.1079680","article-title":"Principles of protein targeting to the nucleolus","volume":"6","author":"Martin","year":"2015","journal-title":"Nucleus"},{"key":"2026071607041629300_bib11","doi-asserted-by":"publisher","first-page":"E107","DOI":"10.1038\/35014078","article-title":"To be or not to be in the nucleolus","volume":"2","author":"Carmo-Fonseca","year":"2000","journal-title":"Nat Cell Biol"},{"key":"2026071607041629300_bib12","doi-asserted-by":"publisher","first-page":"7388","DOI":"10.1093\/nar\/gkq653","article-title":"Characterization and prediction of protein nucleolar localization sequences","volume":"38","author":"Scott","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib13","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1186\/1471-2105-12-317","article-title":"NoD: a nucleolar localization sequence detector for eukaryotic and viral proteins","volume":"12","author":"Scott","year":"2011","journal-title":"BMC Bioinf"},{"key":"2026071607041629300_bib14","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1111\/tra.12310","article-title":"Mechanisms regulating protein localization","volume":"16","author":"Bauer","year":"2015","journal-title":"Traffic"},{"key":"2026071607041629300_bib15","doi-asserted-by":"publisher","first-page":"e31433","DOI":"10.1002\/jcp.31433","article-title":"Identification and functional characterization of the nuclear and nucleolar localization signals in the intrinsically disordered region of nucleomethylin","volume":"239","author":"Shrikondawar","year":"2024","journal-title":"J Cell Physiol"},{"key":"2026071607041629300_bib16","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/s12929-015-0136-0","article-title":"Identification and characterization of nuclear and nucleolar localization signals in 58-kDa microspherule protein (MSP58)","volume":"22","author":"Yang","year":"2015","journal-title":"J Biomed Sci"},{"key":"2026071607041629300_bib17","doi-asserted-by":"publisher","first-page":"D218","DOI":"10.1093\/nar\/gkj004","article-title":"NOPdb: nucleolar proteome database","volume":"34","author":"Leung","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib18","doi-asserted-by":"publisher","first-page":"214","DOI":"10.1080\/12298093.2024.2379623","article-title":"The unknown within the known: nucleolus, understudied compartment in the filamentous fungi","volume":"52","author":"Lee","year":"2024","journal-title":"Mycobiology"},{"key":"2026071607041629300_bib19","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.fgb.2005.07.005","article-title":"Nucleolar localization of Aspergillus fumigatus CgrA is temperature-dependent","volume":"43","author":"Bhabhra","year":"2006","journal-title":"Fung Genet Biol"},{"key":"2026071607041629300_bib20","doi-asserted-by":"publisher","first-page":"D480","DOI":"10.1093\/nar\/gkaa1100","article-title":"UniProt: the universal protein knowledgebase in 2021","volume":"49","author":"UniProt Consortium","year":"2021","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib21","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1186\/1471-2105-10-202","article-title":"NLStradamus: a simple Hidden Markov Model for nuclear localization signal prediction","volume":"10","author":"Ba","year":"2009","journal-title":"BMC Bioinf"},{"key":"2026071607041629300_bib22","doi-asserted-by":"publisher","first-page":"W585","DOI":"10.1093\/nar\/gkm259","article-title":"WoLF PSORT: protein localization predictor","volume":"35","author":"Horton","year":"2007","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib23","doi-asserted-by":"publisher","first-page":"10171","DOI":"10.1073\/pnas.0900604106","article-title":"Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs","volume":"106","author":"Kosugi","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"2026071607041629300_bib24","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1093\/nar\/gkg001","article-title":"NLSdb: database of nuclear localization signals","volume":"31","author":"Nair","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib25","doi-asserted-by":"publisher","first-page":"e76864","DOI":"10.1371\/journal.pone.0076864","article-title":"SeqNLS: nuclear localization signal prediction based on frequent pattern mining and linear motif scoring","volume":"8","author":"Lin","year":"2013","journal-title":"PLoS One"},{"key":"2026071607041629300_bib26","doi-asserted-by":"publisher","first-page":"R98","DOI":"10.1186\/gb-2006-7-10-r98","article-title":"An inventory of yeast proteins associated with nucleolar and ribosomal components","volume":"7","author":"Staub","year":"2006","journal-title":"Genome Biol"},{"key":"2026071607041629300_bib27","doi-asserted-by":"publisher","first-page":"W576","DOI":"10.1093\/nar\/gkv402","article-title":"NGL Viewer: a web application for molecular visualization","volume":"43","author":"Rose","year":"2015","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib28","doi-asserted-by":"publisher","first-page":"D439","DOI":"10.1093\/nar\/gkab1061","article-title":"AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models","volume":"50","author":"Varadi","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib29","doi-asserted-by":"publisher","first-page":"W402","DOI":"10.1093\/nar\/gkz297","article-title":"The PSIPRED protein analysis workbench: 20 years on","volume":"47","author":"Buchan","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"2026071607041629300_bib30","doi-asserted-by":"publisher","first-page":"e9469","DOI":"10.15252\/msb.20209469","article-title":"Mapping the nucleolar proteome reveals a spatiotemporal organization related to intrinsic protein disorder","volume":"16","author":"Stenstr\u00f6m","year":"2020","journal-title":"Mol Syst Biol"},{"key":"2026071607041629300_bib31","doi-asserted-by":"publisher","first-page":"367","DOI":"10.1083\/jcb.200501141","article-title":"Mammalian WDR12 is a novel member of the Pes1-Bop1 complex and is required for ribosome biogenesis and cell proliferation","volume":"170","author":"H\u00f6lzel","year":"2005","journal-title":"J Cell Biol"},{"key":"2026071607041629300_bib32","doi-asserted-by":"publisher","first-page":"2650","DOI":"10.1128\/MCB.20.8.2650-2659.2000","article-title":"Synthesis and assembly of the box C+D small nucleolar RNPs","volume":"20","author":"Lafontaine","year":"2000","journal-title":"Mol Cell Biol"},{"key":"2026071607041629300_bib33","article-title":"ESM Cambrian: revealing the mysteries of proteins with unsupervised learning","author":"ESM Team","year":"2024","journal-title":"Evolutionary Scale"},{"key":"2026071607041629300_bib34","first-page":"2579","article-title":"Visualizing data using t-SNE","volume":"9","author":"Maaten","year":"2008","journal-title":"J Mach Learn Res"},{"key":"2026071607041629300_bib35","doi-asserted-by":"publisher","first-page":"jcs237156","DOI":"10.1242\/jcs.237156","article-title":"Passive diffusion through nuclear pore complexes regulates levels of the yeast SAGA and SLIK coactivator complexes","volume":"133","author":"Makio","year":"2020","journal-title":"J Cell Sci"}],"container-title":["Database"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baag023\/68333514\/baag023.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/database\/article-pdf\/doi\/10.1093\/database\/baag023\/68333514\/baag023.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,16]],"date-time":"2026-07-16T11:04:25Z","timestamp":1784199865000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/database\/article\/doi\/10.1093\/database\/baag023\/8687223"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026]]},"references-count":35,"URL":"https:\/\/doi.org\/10.1093\/database\/baag023","relation":{},"ISSN":["1758-0463"],"issn-type":[{"value":"1758-0463","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026]]},"published":{"date-parts":[[2026]]},"article-number":"baag023"}}