{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T19:25:34Z","timestamp":1782156334897,"version":"3.54.5"},"reference-count":42,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T00:00:00Z","timestamp":1702857600000},"content-version":"vor","delay-in-days":17,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFC3400300"],"award-info":[{"award-number":["2022YFC3400300"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62102457"],"award-info":[{"award-number":["62102457"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004735","name":"Hunan Provincial Natural Science Foundation of China","doi-asserted-by":"crossref","award":["2023JJ40763"],"award-info":[{"award-number":["2023JJ40763"]}],"id":[{"id":"10.13039\/501100004735","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>There is mounting evidence that the subcellular localization of lncRNAs can provide valuable insights into their biological functions. In the real world of transcriptomes, lncRNAs are usually localized in multiple subcellular localizations. Furthermore, lncRNAs have specific localization patterns for different subcellular localizations. Although several computational methods have been developed to predict the subcellular localization of lncRNAs, few of them are designed for lncRNAs that have multiple subcellular localizations, and none of them take motif specificity into consideration.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we proposed a novel deep learning model, called LncLocFormer, which uses only lncRNA sequences to predict multi-label lncRNA subcellular localization. LncLocFormer utilizes eight Transformer blocks to model long-range dependencies within the lncRNA sequence and shares information across the lncRNA sequence. To exploit the relationship between different subcellular localizations and find distinct localization patterns for different subcellular localizations, LncLocFormer employs a localization-specific attention mechanism. The results demonstrate that LncLocFormer outperforms existing state-of-the-art predictors on the hold-out test set. Furthermore, we conducted a motif analysis and found LncLocFormer can capture known motifs. Ablation studies confirmed the contribution of the localization-specific attention mechanism in improving the prediction performance.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The LncLocFormer web server is available at http:\/\/csuligroup.com:9000\/LncLocFormer. The source code can be obtained from https:\/\/github.com\/CSUBioGroup\/LncLocFormer.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad752","type":"journal-article","created":{"date-parts":[[2023,12,18]],"date-time":"2023-12-18T20:46:16Z","timestamp":1702932376000},"source":"Crossref","is-referenced-by-count":37,"title":["LncLocFormer: a Transformer-based deep learning model for multi-label lncRNA subcellular localization prediction by using localization-specific attention mechanism"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1726-0955","authenticated-orcid":false,"given":"Min","family":"Zeng","sequence":"first","affiliation":[{"name":"School of Computer Science and Engineering, Central South University , Changsha, Hunan 410083, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yifan","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, Central 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