{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,26]],"date-time":"2025-09-26T08:30:12Z","timestamp":1758875412152,"version":"3.44.0"},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T00:00:00Z","timestamp":1756684800000},"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":["12301336","72331005"],"award-info":[{"award-number":["12301336","72331005"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Identifying regulatory elements in various chromosomal regions that influence gene expression is a fundamental challenge in epigenomics, with profound implications for understanding gene regulation and disease mechanisms. The advent of paired single-cell RNA sequencing and single-cell ATAC sequencing has created unprecedented opportunities to address this challenge by enabling simultaneous profiling of gene expression and chromatin accessibility at single-cell resolution. However, the inherent signals between them are weak due to the highly sparse and noisy nature of data.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>This article proposes single-cell meta-Path based Omics Embedding (scPOEM), a novel embedding method that jointly projects chromatin accessibility peaks and expressed genes into a shared low-dimensional space. By integrating the relationships among peak\u2013peak, peak\u2013gene, and gene\u2013gene interactions, scPOEM assigns closer representations in the embedding space to related peak\u2013gene pairs. Our experiments demonstrate that scPOEM generates stable representations of peaks and genes, outperforms existing methods in recovering biologically meaningful peak\u2013gene regulatory relationships and enables new insights in subgroup and differential analysis of gene regulation. These results highlight its potential to uncover gene regulatory mechanisms and enhance the understanding of transcriptional regulation at single-cell resolution.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The source code of scPOEM is available at https:\/\/github.com\/Houyt23\/scPOEM. The datasets can be obtained from the 10\u00d7 Genomics (https:\/\/www.10xgenomics.com\/datasets\/pbmc-from-a-healthy-donor-granulocytes-removed-through-cell-sorting-10-k-1-standard-1-0-0) and GEO database under access codes GSE194122 and GSE239916.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaf483","type":"journal-article","created":{"date-parts":[[2025,9,1]],"date-time":"2025-09-01T17:35:23Z","timestamp":1756748123000},"source":"Crossref","is-referenced-by-count":1,"title":["scPOEM: robust co-embedding of peaks and genes revealing peak\u2013gene regulation"],"prefix":"10.1093","volume":"41","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2412-043X","authenticated-orcid":false,"given":"Yan","family":"Zhong","sequence":"first","affiliation":[{"name":"KLATASDS-MOE, School of Statistics, East China Normal University , Shanghai, 200062,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0587-4692","authenticated-orcid":false,"given":"Yuntong","family":"Hou","sequence":"additional","affiliation":[{"name":"KLATASDS-MOE, School of Statistics, East China Normal University , Shanghai, 200062,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4135-5014","authenticated-orcid":false,"given":"Yongjian","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Texas A&M University , College Station, TX 77843,","place":["United States"]}]},{"given":"Xinyue","family":"Zheng","sequence":"additional","affiliation":[{"name":"KLATASDS-MOE, School of Statistics, East China Normal University , Shanghai, 200062,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8081-6725","authenticated-orcid":false,"given":"James J","family":"Cai","sequence":"additional","affiliation":[{"name":"Department of Electrical and Computer Engineering, Texas 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