{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,17]],"date-time":"2026-01-17T10:05:34Z","timestamp":1768644334228,"version":"3.49.0"},"reference-count":75,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,11,27]],"date-time":"2021-11-27T00:00:00Z","timestamp":1637971200000},"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":["61973240"],"award-info":[{"award-number":["61973240"]}],"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":["62072341"],"award-info":[{"award-number":["62072341"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,1,17]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>The rapid development of single-cell RNA-sequencing (scRNA-seq) technology has raised significant computational and analytical challenges. The application of deep learning to scRNA-seq data analysis is rapidly evolving and can overcome the unique challenges in upstream (quality control and normalization) and downstream (cell-, gene- and pathway-level) analysis of scRNA-seq data. In the present study, recent advances and applications of deep learning-based methods, together with specific tools for scRNA-seq data analysis, were summarized. Moreover, the future perspectives and challenges of deep-learning techniques regarding the appropriate analysis and interpretation of scRNA-seq data were investigated. The present study aimed to provide evidence supporting the biomedical application of deep learning-based tools and may aid biologists and bioinformaticians in navigating this exciting and fast-moving area.<\/jats:p>","DOI":"10.1093\/bib\/bbab473","type":"journal-article","created":{"date-parts":[[2021,10,18]],"date-time":"2021-10-18T18:35:29Z","timestamp":1634582129000},"source":"Crossref","is-referenced-by-count":30,"title":["Deep learning-based advances and applications for single-cell RNA-sequencing data analysis"],"prefix":"10.1093","volume":"23","author":[{"given":"Siqi","family":"Bao","sequence":"first","affiliation":[{"name":"School of Information and Communication Engineering, Hainan University, Haikou 570228, P. R. China"},{"name":"School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P. R. China"},{"name":"Hainan Institute of Real World Data, Haikou 570228, P. R. China"}]},{"given":"Ke","family":"Li","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P. R. China"}]},{"given":"Congcong","family":"Yan","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P. R. China"}]},{"given":"Zicheng","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P. R. China"}]},{"given":"Jia","family":"Qu","sequence":"additional","affiliation":[{"name":"School of Information and Communication Engineering, Hainan University, Haikou 570228, P. R. China"},{"name":"School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P. R. China"},{"name":"Hainan Institute of Real World Data, Haikou 570228, P. R. China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9987-9024","authenticated-orcid":false,"given":"Meng","family":"Zhou","sequence":"additional","affiliation":[{"name":"School of Biomedical Engineering, School of Ophthalmology & Optometry and Eye Hospital, Wenzhou Medical University, Wenzhou 325027, P. R. 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