{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T06:15:08Z","timestamp":1784614508994,"version":"3.55.0"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"16","license":[{"start":{"date-parts":[[2021,2,25]],"date-time":"2021-02-25T00:00:00Z","timestamp":1614211200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62073219"],"award-info":[{"award-number":["62073219"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61903248"],"award-info":[{"award-number":["61903248"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61725302"],"award-info":[{"award-number":["61725302"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003399","name":"Science and Technology Commission of Shanghai Municipality","doi-asserted-by":"publisher","award":["20S11902100"],"award-info":[{"award-number":["20S11902100"]}],"id":[{"id":"10.13039\/501100003399","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,8,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Long non-coding RNAs (lncRNAs) are generally expressed in a tissue-specific way, and subcellular localizations of lncRNAs depend on the tissues or cell lines that they are expressed. Previous computational methods for predicting subcellular localizations of lncRNAs do not take this characteristic into account, they train a unified machine learning model for pooled lncRNAs from all available cell lines. It is of importance to develop a cell-line-specific computational method to predict lncRNA locations in different cell lines.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>In this study, we present an updated cell-line-specific predictor lncLocator 2.0, which trains an end-to-end deep model per cell line, for predicting lncRNA subcellular localization from sequences. We first construct benchmark datasets of lncRNA subcellular localizations for 15 cell lines. Then we learn word embeddings using natural language models, and these learned embeddings are fed into convolutional neural network, long short-term memory and multilayer perceptron to classify subcellular localizations. lncLocator 2.0 achieves varying effectiveness for different cell lines and demonstrates the necessity of training cell-line-specific models. Furthermore, we adopt Integrated Gradients to explain the proposed model in lncLocator 2.0, and find some potential patterns that determine the subcellular localizations of lncRNAs, suggesting that the subcellular localization of lncRNAs is linked to some specific nucleotides.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availabilityand implementation<\/jats:title>\n                  <jats:p>The lncLocator 2.0 is available at www.csbio.sjtu.edu.cn\/bioinf\/lncLocator2 and the source code can be found at https:\/\/github.com\/Yang-J-LIN\/lncLocator2.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab127","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T12:32:16Z","timestamp":1614083536000},"page":"2308-2316","source":"Crossref","is-referenced-by-count":101,"title":["lncLocator 2.0: a cell-line-specific subcellular localization predictor for long non-coding RNAs with interpretable deep learning"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8963-5384","authenticated-orcid":false,"given":"Yang","family":"Lin","sequence":"first","affiliation":[{"name":"Department of Automation, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University , Shanghai 200240, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5010-464X","authenticated-orcid":false,"given":"Xiaoyong","family":"Pan","sequence":"additional","affiliation":[{"name":"Department of Automation, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University , Shanghai 200240, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4029-3325","authenticated-orcid":false,"given":"Hong-Bin","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Automation, Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University , Shanghai 200240, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2021,2,25]]},"reference":[{"key":"2023051609131854800_btab127-B1","doi-asserted-by":"crossref","first-page":"2583","DOI":"10.1016\/j.ygeno.2020.02.011","article-title":"Locate-r: subcellular localization of long non-coding RNAs using nucleotide compositions","volume":"112","author":"Ahmad","year":"2020","journal-title":"Genomics"},{"key":"2023051609131854800_btab127-B2","doi-asserted-by":"crossref","first-page":"3387","DOI":"10.1093\/bioinformatics\/btx431","article-title":"Deeploc: prediction of protein subcellular localization using deep learning","volume":"33","author":"Almagro Armenteros","year":"2017","journal-title":"Bioinformatics"},{"key":"2023051609131854800_btab127-B3","first-page":"28","article-title":"The product of the h19 gene may function as an RNA","volume":"10","author":"Brannan","year":"1990","journal-title":"Mol. 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