{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T11:43:11Z","timestamp":1753875791151,"version":"3.41.2"},"reference-count":54,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2025,6,23]],"date-time":"2025-06-23T00:00:00Z","timestamp":1750636800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003453","name":"Natural Science Foundation of Guangdong Province","doi-asserted-by":"publisher","award":["2024A1515012364","2025A1515010926"],"award-info":[{"award-number":["2024A1515012364","2025A1515010926"]}],"id":[{"id":"10.13039\/501100003453","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100016804","name":"Natural Science Foundation of Shenzhen Municipality","doi-asserted-by":"publisher","award":["JCYJ20240813150406009"],"award-info":[{"award-number":["JCYJ20240813150406009"]}],"id":[{"id":"10.13039\/100016804","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32100434","82272534"],"award-info":[{"award-number":["32100434","82272534"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Key Laboratory of Bone Tissue Repair and Translational Research","award":["ZDSYS20230626091402006"],"award-info":[{"award-number":["ZDSYS20230626091402006"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>scATAC-seq enables high-resolution mapping of cis-regulatory elements. It has been widely applied to uncover cell-type-specific regulatory networks and complement scRNA-seq analysis in numerous studies. However, a large number of datasets generated by scATAC-seq remain underutilized due to limited exploration of super-enhancers\/typical enhancers and gene markers. A comprehensive resource enabling cell-type-specific annotation of cis-regulatory elements and their dynamic enhancer\u2013gene linkages remains an urgent unmet need for scATAC-seq.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present dbscATAC, a specialized single-cell database for annotating super-enhancers, gene markers, and enhancer\u2013gene interactions derived from scATAC-seq data. Using improved machine learning algorithms, we identified 213\u00a0835 super-enhancers across 520 tissue\/cell types from three species, as well as 347\u00a0484 gene markers, 13\u00a0470\u00a0526 enhancers, and 10\u00a0402\u00a0346 enhancer\u2013gene interactions derived from 1\u00a0668\u00a0076 single cells spanning 1028 tissue\/cell types in 13 species. An easy-to-use online platform with multiple analytic modules and hierarchical query options was developed for searching, browsing and visualizing single-cell super-enhancers, enhancers, and gene markers. dbscATAC provides a comprehensive resource to facilitate the exploration of enhancer landscapes, gene regulation, and cell-type-specific characteristics in single-cell epigenomics.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The database with all the super-enhancer\/enhancer annotation data is available at http:\/\/singlecelldb.com\/dbscATAC\/index.php. And the source code of dbscATAC for prediction of SEs, enhancers, and gene markers are available at https:\/\/github.com\/EvansGao\/dbscATAC. The source code, tissue\/cell type description, and data summary can be downloaded at DOI: 10.6084\/m9.figshare.28706414.<\/jats:p>\n                  <jats:p>scATAC-seq, Database, Super-enhancers\/enhancers, Gene markers<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf364","type":"journal-article","created":{"date-parts":[[2025,6,28]],"date-time":"2025-06-28T20:09:31Z","timestamp":1751141371000},"source":"Crossref","is-referenced-by-count":0,"title":["dbscATAC: a resource of single-cell super-enhancers\/enhancers and gene markers derived from scATAC-seq data"],"prefix":"10.1093","volume":"41","author":[{"given":"Yingmei","family":"Li","sequence":"first","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]},{"name":"Department of Pharmacy, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6694-5590","authenticated-orcid":false,"given":"Shahid","family":"Ullah","sequence":"additional","affiliation":[{"name":"S-Khan Lab , Mardan, Khyber Pakhtunkhwa, Takhtbhai, KP 23200,","place":["Pakistan"]}]},{"given":"Yumei","family":"Xian","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]},{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Yazhou","family":"Sun","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]},{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Zilong","family":"Zheng","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Xiaoyu","family":"Ma","sequence":"additional","affiliation":[{"name":"Big Data Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]},{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Ming","family":"Shi","sequence":"additional","affiliation":[{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Changlin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Gynecology, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1996-9001","authenticated-orcid":false,"given":"Tian","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Gynecology, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Leli","family":"Zeng","sequence":"additional","affiliation":[{"name":"Scientific Research Center, The Seventh Affiliated Hospital of Sun Yat-sen University , Shenzhen 518107,","place":["China"]},{"name":"Digestive Diseases Center, Scientific Research Center, The Biobank, The Seventh Affiliated Hospital of Sun Yat-Sen University , Shenzhen 518107,","place":["China"]}]},{"given":"Jie","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of General Surgery, Shanghai Children\u2019s Medical Center, Shanghai Jiao Tong School of Medicine , Shanghai 200127,","place":["China"]}]},{"given":"Yubin Y 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