{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,9]],"date-time":"2025-11-09T03:23:50Z","timestamp":1762658630784,"version":"3.41.2"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T00:00:00Z","timestamp":1693353600000},"content-version":"vor","delay-in-days":0,"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":["61872063"],"award-info":[{"award-number":["61872063"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shenzhen Science and Technology Program","award":["JCYJ20210324140407021"],"award-info":[{"award-number":["JCYJ20210324140407021"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,9,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single-cell DNA methylation sequencing can assay DNA methylation at single-cell resolution. However, incomplete coverage compromises related downstream analyses, outlining the importance of imputation techniques. With a rising number of cell samples in recent large datasets, scalable and efficient imputation models are critical to addressing the sparsity for genome-wide analyses.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We proposed a novel graph-based deep learning approach to impute methylation matrices based on locus-aware neighboring subgraphs with locus-aware encoding orienting on one cell type. Merely using the CpGs methylation matrix, the obtained GraphCpG outperforms previous methods on datasets containing more than hundreds of cells and achieves competitive performance on smaller datasets, with subgraphs of predicted sites visualized by retrievable bipartite graphs. Besides better imputation performance with increasing cell number, it significantly reduces computation time and demonstrates improvement in downstream analysis.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code is freely available at https:\/\/github.com\/yuzhong-deng\/graphcpg.git.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad533","type":"journal-article","created":{"date-parts":[[2023,8,30]],"date-time":"2023-08-30T21:50:25Z","timestamp":1693432225000},"source":"Crossref","is-referenced-by-count":5,"title":["GraphCpG: imputation of single-cell methylomes based on locus-aware neighboring subgraphs"],"prefix":"10.1093","volume":"39","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-2066-5878","authenticated-orcid":false,"given":"Yuzhong","family":"Deng","sequence":"first","affiliation":[{"name":"School of Automation Engineering, University of Electronic Science and Technology of China , Chengdu 611731, Sichuan, China"}]},{"given":"Jianxiong","family":"Tang","sequence":"additional","affiliation":[{"name":"School of Automation Engineering, University of Electronic Science and Technology of China , Chengdu 611731, Sichuan, China"}]},{"given":"Jiyang","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Automation Engineering, University of Electronic Science and Technology of China , Chengdu 611731, Sichuan, China"}]},{"given":"Jianxiao","family":"Zou","sequence":"additional","affiliation":[{"name":"School of Automation Engineering, University of Electronic Science and Technology of China , Chengdu 611731, Sichuan, China"},{"name":"Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China , Shenzhen 518110, Guangdong, China"}]},{"given":"Que","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Out-patient, The Second Affiliated Hospital of Chongqing Medical University , Chongqing 400010, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2548-3689","authenticated-orcid":false,"given":"Shicai","family":"Fan","sequence":"additional","affiliation":[{"name":"School of Automation Engineering, University of Electronic Science and Technology of China , Chengdu 611731, Sichuan, China"},{"name":"Shenzhen Institute for Advanced Study, University of Electronic Science and Technology of China , Shenzhen 518110, Guangdong, China"}]}],"member":"286","published-online":{"date-parts":[[2023,8,30]]},"reference":[{"key":"2023092221483589400_btad533-B1","doi-asserted-by":"crossref","first-page":"1013","DOI":"10.3390\/biom11071013","article-title":"Introduction to single-cell DNA methylation profiling 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