{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,22]],"date-time":"2026-07-22T05:26:25Z","timestamp":1784697985912,"version":"3.55.0"},"reference-count":157,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,10]],"date-time":"2025-05-10T00:00:00Z","timestamp":1746835200000},"content-version":"vor","delay-in-days":9,"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":["62272067"],"award-info":[{"award-number":["62272067"]}],"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":["62131004"],"award-info":[{"award-number":["62131004"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Sichuan Science and Technology Program","award":["2023NSFSC0499"],"award-info":[{"award-number":["2023NSFSC0499"]}]},{"name":"Scientific Research Foundation of Sichuan Province","award":["MZGC20230078"],"award-info":[{"award-number":["MZGC20230078"]}]},{"name":"Scientific Research Foundation of Chengdu University of Information Technology","award":["KYQN202208"],"award-info":[{"award-number":["KYQN202208"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The rapid accumulation of single-cell RNA sequencing data has provided unprecedented computational resources for cell type annotation, significantly advancing our understanding of cellular heterogeneity. Leveraging gene expression profiles derived from transcriptomic data, researchers can accurately infer cell types, sparking the development of numerous innovative annotation methods. These methods utilize a range of strategies, including marker genes, correlation-based matching, and supervised learning, to classify cell types. In this review, we systematically examine these annotation approaches based on transcriptomics-specific gene expression profiles and provide a comprehensive comparison and categorization of these methods. Furthermore, we focus on the main challenges in the annotation process, especially the long-tail distribution problem arising from data imbalance in rare cell types. We discuss the potential of deep learning techniques to address these issues and enhance model capability in recognizing novel cell types within an open-world framework.<\/jats:p>","DOI":"10.1093\/bib\/bbaf207","type":"journal-article","created":{"date-parts":[[2025,5,10]],"date-time":"2025-05-10T22:26:58Z","timestamp":1746916018000},"source":"Crossref","is-referenced-by-count":24,"title":["An overview of computational methods in single-cell transcriptomic cell type annotation"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-2952-7788","authenticated-orcid":false,"given":"Tianhao","family":"Li","sequence":"first","affiliation":[{"name":"School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8503-6534","authenticated-orcid":false,"given":"Zixuan","family":"Wang","sequence":"additional","affiliation":[{"name":"College of Electronics and Information Engineering , Sichuan University, No. 24 South Section 1, 1st Ring Road, 610065 Chengdu,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5949-344X","authenticated-orcid":false,"given":"Yuhang","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Applied Sciences , Macao Polytechnic University, 999078 Macao,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0004-4946-0478","authenticated-orcid":false,"given":"Sihan","family":"He","sequence":"additional","affiliation":[{"name":"School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6406-1142","authenticated-orcid":false,"given":"Quan","family":"Zou","sequence":"additional","affiliation":[{"name":"Institute of Fundamental and Frontier Sciences , University of Electronic Science and Technology of China, Shahe Campus: No. 4, Section 2, North Jianshe Road, 611731 Chengdu,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3422-8305","authenticated-orcid":false,"given":"Yongqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science , Chengdu University of Information Technology, No. 24 Block 1, Xuefu Road, 610225 Chengdu,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,10]]},"reference":[{"key":"2025052702073618300_ref1","doi-asserted-by":"publisher","first-page":"1430","DOI":"10.1038\/s41592-024-02353-z","article-title":"Transformers in single-cell omics: a review and new perspectives","volume":"21","author":"Sza\u0142ata","year":"2024","journal-title":"Nat Methods"},{"key":"2025052702073618300_ref2","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/s41569-020-0359-y","article-title":"Single-cell RNA sequencing in cardiovascular development, disease and medicine","volume":"17","author":"Paik","year":"2020","journal-title":"Nat Rev Cardiol"},{"key":"2025052702073618300_ref3","doi-asserted-by":"publisher","first-page":"5840","DOI":"10.1158\/1078-0432.CCR-05-0578","article-title":"New monoclonal antibodies to mesothelin useful for immunohistochemistry, fluorescence-activated cell sorting, western blotting, and ELISA","volume":"11","author":"Onda","year":"2005","journal-title":"Clin Cancer Res"},{"key":"2025052702073618300_ref4","doi-asserted-by":"publisher","first-page":"578","DOI":"10.3390\/cells8060578","article-title":"Extracellular localisation of the c-terminus of ddx4 confirmed by immunocytochemistry and fluorescence-activated cell sorting","volume":"8","author":"Clarkson","year":"2019","journal-title":"Cells"},{"key":"2025052702073618300_ref5","doi-asserted-by":"crossref","first-page":"317","DOI":"10.3389\/fgene.2019.00317","article-title":"Single-cell RNA-seq technologies and related computational data analysis","volume":"10","author":"Chen","year":"2019","journal-title":"Front Genet"},{"key":"2025052702073618300_ref6","doi-asserted-by":"publisher","first-page":"1512","DOI":"10.1039\/b908315d","article-title":"Global signatures of protein and mrna expression levels","volume":"5","author":"de Sousa Abreu","year":"2009","journal-title":"Mol Biosyst"},{"key":"2025052702073618300_ref7","doi-asserted-by":"publisher","first-page":"1202","DOI":"10.1016\/j.cell.2015.05.002","article-title":"Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets","volume":"161","author":"Macosko","year":"2015","journal-title":"Cell"},{"key":"2025052702073618300_ref8","first-page":"339","article-title":"Computational methods for single-cell RNA sequencing. 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