{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T15:03:21Z","timestamp":1764083001071,"version":"3.45.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2025,11,25]],"date-time":"2025-11-25T00:00:00Z","timestamp":1764028800000},"content-version":"vor","delay-in-days":24,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62136004","62276130"],"award-info":[{"award-number":["62136004","62276130"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2023YFF1204803"],"award-info":[{"award-number":["2023YFF1204803"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key Research and Development Plan of Jiangsu Province","award":["BE2022842"],"award-info":[{"award-number":["BE2022842"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Oxford Nanopore Technologies (ONT) direct RNA sequencing (dRNA-seq) offers high-resolution, single-molecule analysis but is hindered by the lack of robust multiplex barcoding methods. Existing approaches struggle to accurately demultiplex raw nanopore signals, failing to capture both local patterns and long-range dependencies. This limitation underscores the requirement for advanced solutions to improve accuracy, efficiency, and adaptability in sequencing workflows. We present DemuxTrans, a hybrid deep learning framework that integrates Multi-Layer Feature Fusion, Transformers, and Temporal Convolutional Networks (TCN) for precise barcode demultiplexing.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>DemuxTrans achieves state-of-the-art performance across multiple datasets by effectively balancing local feature extraction, global context modeling, and long-term dependency capture, excelling in metrics such as accuracy, recall and F1-score. These results demonstrate DemuxTrans as a scalable, efficient solution for barcode demultiplexing in nanopore sequencing, enabling precise identification of multiplexed RNA samples and improving throughput in transcriptomic and epigenomic analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The code and datasets are publicly available on https:\/\/github.com\/LiyuanShu116\/Demuxtrans<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf612","type":"journal-article","created":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T12:57:34Z","timestamp":1762865854000},"source":"Crossref","is-referenced-by-count":0,"title":["DemuxTrans: Transformer and temporal convolution network for accurate barcode demultiplexing in nanopore sequencing"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-6119-4368","authenticated-orcid":false,"given":"Liyuan","family":"Shu","sequence":"first","affiliation":[{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","place":["China"]}]},{"given":"Deyu","family":"Zhuang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","place":["China"]}]},{"given":"Jiao","family":"Tang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","place":["China"]}]},{"given":"Junyong","family":"Zhao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","place":["China"]}]},{"given":"Wei","family":"Shao","sequence":"additional","affiliation":[{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 211106,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3985-3900","authenticated-orcid":false,"given":"Xiaoyu","family":"Guan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics , Nanjing, 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