{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:44:28Z","timestamp":1792784668937,"version":"4.5.0"},"reference-count":39,"publisher":"American Chemical Society (ACS)","issue":"19","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"DOI":"10.13039\/100017380","name":"Science and Technology Foundation of Shenzhen City","doi-asserted-by":"publisher","award":["JCYJ20241202130212016"],"award-info":[{"award-number":["JCYJ20241202130212016"]}],"id":[{"id":"10.13039\/100017380","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["20720250172"],"award-info":[{"award-number":["20720250172"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["CKL075"],"award-info":[{"award-number":["CKL075"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Scientific Research Foundation of State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory","award":["2025XAKJ0102017"],"award-info":[{"award-number":["2025XAKJ0102017"]}]},{"name":"National Natural Science Foundation of China (NSFC)","award":["12426303"],"award-info":[{"award-number":["12426303"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Natural Science Foundation of China (NSFC)","award":["62272449"],"award-info":[{"award-number":["62272449"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]},{"name":"National Natural Science Foundation of China (NSFC)","award":["U24A20257"],"award-info":[{"award-number":["U24A20257"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>RNA subcellular localization determines the regulatory context in which microRNAs (miRNAs), circular RNAs (circRNAs), and long noncoding RNAs (lncRNAs) exert their functions, yet these RNA classes differ greatly in sequence length and circularity, making fixed-length raw-sequence representations inconvenient for cross-RNA comparison. Here, we present SwinTransRNA, a unified framework that encodes each RNA as a length-normalized 64 \u00d7 64 frequency chaos game representation (FCGR) of 6-mer composition, where every cell carries a fixed 6-mer identity and the matrix entries sum to one, enabling direct comparison across sequence lengths. A hierarchical window-attention network captures localized interactions among neighboring composition regions and enlarges the receptive field through shifted windows and patch merging. On audited benchmark data sets for nuclear\/cytoplasmic lncRNA, nuclear\/cytoplasmic circRNA, and intracellular\/extracellular miRNA classification, SwinTransRNA achieves the highest accuracy and F1 among the compared methods on all three tasks (0.748\/0.723, 0.914\/0.908, and 0.819\/0.823 for lncRNA, miRNA, and circRNA, respectively), surpassing RNALight and RNALoc-LM. Ablations show consistent gains over one-hot Transformer baselines and classical FCGR-based classifiers, while feature-space and curve-level analyses characterize the complementary contributions of the FCGR representation and the window-attention backbone. The main novelty lies in combining an order-traceable FCGR with hierarchical window attention under a reproducible protocol: five-seed repeats, confidence intervals, and paired tests quantify comparison uncertainty, and patch-embedding heatmaps with candidate motif screens expose the patterns prioritized by the model. The unified implementation, traceable sequence processing, and compact 4.25-million-parameter model provide a fixed-dimensional, auditable basis for RNA localization prediction and pattern prioritization.<\/jats:p>","DOI":"10.1021\/acs.jcim.6c02004","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T02:02:02Z","timestamp":1790042522000},"page":"13005-13017","source":"Crossref","is-referenced-by-count":0,"title":["SwinTransRNA: A Swin Transformer-Based Framework for\nAccurate Prediction of RNA Subcellular Localization"],"prefix":"10.1021","volume":"66","author":[{"given":"Bowen","family":"Shi","sequence":"first","affiliation":[{"name":"Xiamen University , , , ,","place":["Xiamen, China, 361005"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuxin","family":"He","sequence":"additional","affiliation":[{"name":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","place":["Shenzhen, China, 518172"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yen-Peng","family":"Chiu","sequence":"additional","affiliation":[{"name":"National Yang Ming Chiao Tung University , , ,","place":["Hsinchu, Taiwan, 300093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhihao","family":"Zhao","sequence":"additional","affiliation":[{"name":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","place":["Shenzhen, China, 518172"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peilin","family":"Xie","sequence":"additional","affiliation":[{"name":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","place":["Shenzhen, China, 518172"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yixian","family":"Huang","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , ,","place":["Shenzhen, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xingchen","family":"Liu","sequence":"additional","affiliation":[{"name":"The Chinese University of Hong Kong, Shenzhen , , 2001 Longxiang Road , ,","place":["Shenzhen, China, 518172"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiangrong","family":"Liu","sequence":"additional","affiliation":[{"name":"Xiamen University , , , ,","place":["Xiamen, China, 361005"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tzong-Yi","family":"Lee","sequence":"additional","affiliation":[{"name":"National Yang Ming Chiao Tung University , , ,","place":["Hsinchu, Taiwan, 300093"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1444-190X","authenticated-orcid":true,"given":"Leyi","family":"Wei","sequence":"additional","affiliation":[{"name":"Macao Polytechnic University , , R. de Lui\u0301s Gonzaga Gomes , ,","place":["Macao, China, 999078"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0584-0637","authenticated-orcid":true,"given":"Jiahui","family":"Guan","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , ,","place":["Hong Kong, China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jijun","family":"Tang","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , ,","place":["Shenzhen, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4554-6827","authenticated-orcid":true,"given":"Lantian","family":"Yao","sequence":"additional","affiliation":[{"name":"Shenzhen University of Advanced Technology , , ,","place":["Shenzhen, China, 518107"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"issue":"2","key":"2026101208080264600_cit1","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1038\/nrm3918","article-title":"In the right place at the right time:\nvisualizing and understanding mrna localization","volume":"16","author":"Buxbaum","year":"2015","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"6","key":"2026101208080264600_cit2","doi-asserted-by":"publisher","DOI":"10.3390\/genes12060856","article-title":"Subcellular\nlocalization of mirnas\nand implications in cellular homeostasis","volume":"12","author":"Jie","year":"2021","journal-title":"Genes"},{"issue":"2","key":"2026101208080264600_cit3","doi-asserted-by":"publisher","DOI":"10.1083\/jcb.202009045","article-title":"Lnccation: lncrna localization and\nfunction","volume":"220","author":"Bridges","year":"2021","journal-title":"J. Cell Biol."},{"issue":"5","key":"2026101208080264600_cit4","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1016\/j.molcel.2019.02.008","article-title":"Global positioning system: understanding\nlong noncoding\nrnas through subcellular localization","volume":"73","author":"Carlevaro-Fita","year":"2019","journal-title":"Mol.\nCell"},{"issue":"2","key":"2026101208080264600_cit5","doi-asserted-by":"publisher","first-page":"96","DOI":"10.1038\/s41580-020-00315-9","article-title":"Gene regulation\nby\nlong non-coding rnas and its biological functions","volume":"22","author":"Statello","year":"2021","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"2","key":"2026101208080264600_cit6","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.tig.2017.11.005","article-title":"Nuclear\nlong noncoding rnas: key regulators of gene\nexpression","volume":"34","author":"Sun","year":"2018","journal-title":"Trends Genet."},{"issue":"1","key":"2026101208080264600_cit7","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1016\/j.cell.2018.03.006","article-title":"Metazoan\nmicrornas","volume":"173","author":"Bartel","year":"2018","journal-title":"Cell"},{"issue":"8","key":"2026101208080264600_cit8","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1038\/s41580-020-0243-y","article-title":"The expanding\nregulatory mechanisms and cellular functions of circular rnas","volume":"21","author":"Chen","year":"2020","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"7441","key":"2026101208080264600_cit9","doi-asserted-by":"publisher","first-page":"384","DOI":"10.1038\/nature11993","article-title":"Natural rna circles\nfunction as efficient microrna sponges","volume":"495","author":"Hansen","year":"2013","journal-title":"Nature"},{"issue":"1","key":"2026101208080264600_cit10","doi-asserted-by":"publisher","first-page":"174","DOI":"10.1016\/j.cell.2007.08.003","article-title":"Global\nanalysis of mrna localization reveals a prominent role in organizing\ncellular architecture and function","volume":"131","author":"Le\u0301cuyer","year":"2007","journal-title":"Cell"},{"issue":"5","key":"2026101208080264600_cit11","doi-asserted-by":"publisher","first-page":"594","DOI":"10.1101\/gad.276931.115","article-title":"Diverse and pervasive subcellular\ndistributions for both coding and long noncoding rnas","volume":"30","author":"Wilk","year":"2016","journal-title":"Genes Dev."},{"issue":"6","key":"2026101208080264600_cit12","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1038\/s41580-022-00566-8","article-title":"Long non-coding rnas: definitions, functions, challenges and recommendations","volume":"24","author":"Mattick","year":"2023","journal-title":"Nat. Rev. Mol. Cell Biol."},{"issue":"2","key":"2026101208080264600_cit13","doi-asserted-by":"publisher","first-page":"473","DOI":"10.1016\/j.cell.2019.05.027","article-title":"Atlas of subcellular rna localization\nrevealed by apex-seq","volume":"178","author":"Fazal","year":"2019","journal-title":"Cell"},{"issue":"4","key":"2026101208080264600_cit14","doi-asserted-by":"publisher","first-page":"719","DOI":"10.1016\/j.cell.2009.01.044","article-title":"mrna localization:\ngene expression in the spatial dimension","volume":"136","author":"Martin","year":"2009","journal-title":"Cell"},{"issue":"24","key":"2026101208080264600_cit15","doi-asserted-by":"publisher","first-page":"4196","DOI":"10.1093\/bioinformatics\/bty508","article-title":"iloc-lncrna: predict\nthe subcellular location of lncrnas by incorporating octamer composition\ninto general pseknc","volume":"34","author":"Su","year":"2018","journal-title":"Bioinformatics"},{"issue":"1","key":"2026101208080264600_cit16","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbac509","article-title":"Rnalight: a machine\nlearning model to identify nucleotide features determining rna subcellular\nlocalization","volume":"24","author":"Yuan","year":"2023","journal-title":"Briefings Bioinf."},{"issue":"2","key":"2026101208080264600_cit17","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btae065","article-title":"Deeplocrna:\nan interpretable\ndeep learning model for predicting rna subcellular localization with\ndomain-specific transfer-learning","volume":"40","author":"Wang","year":"2024","journal-title":"Bioinformatics"},{"issue":"4","key":"2026101208080264600_cit18","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaf127","article-title":"Rnaloc-lm: Rna subcellular\nlocalization prediction\nusing pre-trained rna language model","volume":"41","author":"Zeng","year":"2025","journal-title":"Bioinformatics"},{"issue":"14","key":"2026101208080264600_cit19","doi-asserted-by":"publisher","first-page":"i333","DOI":"10.1093\/bioinformatics\/btz337","article-title":"Prediction\nof mrna subcellular localization\nusing deep recurrent neural networks","volume":"35","author":"Yan","year":"2019","journal-title":"Bioinformatics"},{"issue":"7","key":"2026101208080264600_cit20","doi-asserted-by":"publisher","first-page":"851","DOI":"10.1261\/rna.074161.119","article-title":"Rna-gps predicts\nhigh-resolution rna subcellular localization and highlights the role\nof splicing","volume":"26","author":"Wu","year":"2020","journal-title":"RNA"},{"issue":"11","key":"2026101208080264600_cit21","doi-asserted-by":"publisher","DOI":"10.1016\/j.isci.2021.103298","article-title":"Prediction of rna subcellular\nlocalization: Learning from heterogeneous data sources","volume":"24","author":"Savulescu","year":"2021","journal-title":"iScience"},{"issue":"1","key":"2026101208080264600_cit22","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-025-03507-8","article-title":"Decoding subcellular rna localization\none molecule\nat a time","volume":"26","author":"Biayna","year":"2025","journal-title":"Genome Biol."},{"issue":"D1","key":"2026101208080264600_cit23","doi-asserted-by":"publisher","first-page":"D135","DOI":"10.1093\/nar\/gkw728","article-title":"Rnalocate: a resource for rna subcellular\nlocalizations","volume":"45","author":"Zhang","year":"2017","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"2026101208080264600_cit24","doi-asserted-by":"publisher","first-page":"D333","DOI":"10.1093\/nar\/gkab825","article-title":"Rnalocate\nv2. 0: an updated resource for rna subcellular\nlocalization with increased coverage and annotation","volume":"50","author":"Cui","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"D1","key":"2026101208080264600_cit25","doi-asserted-by":"publisher","first-page":"D284","DOI":"10.1093\/nar\/gkae872","article-title":"Rnalocate\nv3. 0: advancing the repository\nof rna subcellular localization with dynamic analysis and prediction","volume":"53","author":"Wu","year":"2025","journal-title":"Nucleic Acids Res."},{"issue":"8","key":"2026101208080264600_cit26","doi-asserted-by":"publisher","first-page":"2163","DOI":"10.1093\/nar\/18.8.2163","article-title":"Chaos game\nrepresentation of gene structure","volume":"18","author":"Jeffrey","year":"1990","journal-title":"Nucleic Acids\nRes."},{"issue":"10","key":"2026101208080264600_cit27","doi-asserted-by":"publisher","first-page":"1391","DOI":"10.1093\/oxfordjournals.molbev.a026048","article-title":"Genomic signature:\ncharacterization and classification of species assessed by chaos game\nrepresentation of sequences","volume":"16","author":"Deschavanne","year":"1999","journal-title":"Mol. Biol. Evol."},{"issue":"5","key":"2026101208080264600_cit28","doi-asserted-by":"publisher","first-page":"429","DOI":"10.1093\/bioinformatics\/17.5.429","article-title":"Analysis of\ngenomic sequences by chaos game representation","volume":"17","author":"Almeida","year":"2001","journal-title":"Bioinformatics"},{"key":"2026101208080264600_cit29","doi-asserted-by":"publisher","first-page":"6263","DOI":"10.1016\/j.csbj.2021.11.008","article-title":"Chaos game representation\nand its applications in bioinformatics","volume":"19","author":"Lo\u0308chel","year":"2021","journal-title":"Comput.\nStruct. Biotechnol. J."},{"key":"2026101208080264600_cit30","doi-asserted-by":"crossref","unstructured":"Liu, Z.; Lin, Y.; Cao, Y.; Hu, H.; Wei, Y.; Zhang, Z.; Lin, S.; Guo, B. In  Swin Transformer:\nHierarchical Vision Transformer Using Shifted Windows, Proceedings\nof the IEEE\/CVF international conference on computer vision; IEEE, 2021; pp 10012\u201310022.","DOI":"10.1109\/ICCV48922.2021.00986"},{"issue":"D1","key":"2026101208080264600_cit31","doi-asserted-by":"publisher","first-page":"D1179","DOI":"10.1093\/nar\/gkab830","article-title":"Cscd2: an\nintegrated interactional database of cancer-specific circular rnas","volume":"50","author":"Feng","year":"2022","journal-title":"Nucleic Acids Res."},{"issue":"10","key":"2026101208080264600_cit32","doi-asserted-by":"publisher","first-page":"2487","DOI":"10.1093\/nar\/21.10.2487","article-title":"Nucleotide,\ndinucleotide and trinucleotide frequencies explain patterns observed\nin chaos game representations of dna sequences","volume":"21","author":"Goldman","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"2026101208080264600_cit33","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giac119","article-title":"Accurate and fast clade assignment\nvia deep learning and frequency chaos game representation","volume":"12","author":"Avila Cartes","year":"2022","journal-title":"GigaScience"},{"key":"2026101208080264600_cit34","unstructured":"Dosovitskiy, A.; Beyer, L.; Kolesnikov, A.; Weissenborn, D.; Zhai, X.; Unterthiner, T.; Dehghani, M.; Minderer, M.; Heigold, G.; Gelly, S.; et al.\n          An Image is Worth 16\n\u00d7 16 Words: Transformers for Image Recognition at Scale. 2020; arXiv:2010.11929. arXiv.org e-Printarchive. https:\/\/arxiv.org\/abs\/2010.11929."},{"key":"2026101208080264600_cit35","unstructured":"Vaswani, A.; Shazeer, N.; Parmar, N.; Uszkoreit, J.; Jones, L.; Gomez, A. N.; Kaiser, \u0141.; Polosukhin, I. In  Attention\nIs All You Need, Advances in Neural Information Processing\nSystems; NIPS, 2017."},{"issue":"12","key":"2026101208080264600_cit36","doi-asserted-by":"publisher","DOI":"10.3390\/genes11121475","article-title":"Mirlocpredictor: A convnet-based\nmulti-label microrna subcellular\nlocalization predictor by incorporating k-mer positional information","volume":"11","author":"Asim","year":"2020","journal-title":"Genes"},{"issue":"15","key":"2026101208080264600_cit37","doi-asserted-by":"publisher","DOI":"10.3390\/ijms23158221","article-title":"Circ-locnet:\nA computational framework for circular rna sub-cellular localization\nprediction","volume":"23","author":"Asim","year":"2022","journal-title":"Int. J. Mol. Sci."},{"issue":"14","key":"2026101208080264600_cit38","doi-asserted-by":"publisher","first-page":"2499","DOI":"10.1093\/bioinformatics\/bty140","article-title":"ifeature: A python\npackage and web\nserver for features extraction and selection from protein and peptide\nsequences","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"issue":"Supplement_1","key":"2026101208080264600_cit39","doi-asserted-by":"publisher","first-page":"i30","DOI":"10.1093\/bioinformatics\/btad229","article-title":"Phavip: Phage virion\nprotein classification based on chaos game representation and vision\ntransformer","volume":"39","author":"Shang","year":"2023","journal-title":"Bioinformatics"}],"container-title":["Journal of Chemical Information and Modeling"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jcim.6c02004","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/19\/13005\/68588903\/acs.jcim.6c02004.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article-pdf\/66\/19\/13005\/68588903\/acs.jcim.6c02004.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T12:29:50Z","timestamp":1791808190000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jcisd8\/article\/66\/19\/13005\/5434788\/SwinTransRNA-A-Swin-Transformer-Based-Framework"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,21]]},"references-count":39,"journal-issue":{"issue":"19","published-online":{"date-parts":[[2026,9,21]]},"published-print":{"date-parts":[[2026,10,12]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jcim.6c02004","relation":{},"ISSN":["1549-9596","1549-960X"],"issn-type":[{"value":"1549-9596","type":"print"},{"value":"1549-960X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,21]]}}}