{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:48:42Z","timestamp":1782308922961,"version":"3.54.5"},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,6,4]],"date-time":"2026-06-04T00:00:00Z","timestamp":1780531200000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFE0213800"],"award-info":[{"award-number":["2024YFE0213800"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62225109"],"award-info":[{"award-number":["62225109"]}],"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":["62272094"],"award-info":[{"award-number":["62272094"]}],"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":["62372142"],"award-info":[{"award-number":["62372142"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The advent of single-cell RNA sequencing (scRNA-seq) technology has allowed researchers to measure gene expression profiles at the single-cell level, providing valuable insights into cellular heterogeneity. However, due to the limitations of current sequencing platforms, scRNA-seq data often contain significant noise, particularly severe dropout events, which pose major challenges for subsequent analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this study, we developed a new method called topology-aware contrastive learning (scTACL). This approach uses contrastive learning between a cell similarity graph and a cell embedding similarity graph, employing a zero-inflated negative binomial (ZINB) distribution to model the reconstructed data. This alignment helps the processed data better reflect true biological signals. It delivers superior results in key tasks such as data imputation, clustering, batch effect correction, and cell\u2013cell interaction. Additionally, scTACL successfully identified two distinct subtypes of epithelial cells in lung adenocarcinoma tissues, further demonstrating its effectiveness and usefulness in complex biological settings. Notably, without relying on spatial location information, scTACL still effectively distinguished the epithelial and mesenchymal regions in the spatial transcriptome data of liver cancer and identified the COLLAGEN signaling pathway, which plays a crucial role in the epithelial\u2013mesenchymal transition process through intercellular communication analysis.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag361","type":"journal-article","created":{"date-parts":[[2026,6,3]],"date-time":"2026-06-03T11:47:45Z","timestamp":1780487265000},"source":"Crossref","is-referenced-by-count":0,"title":["scTACL: a multitask topology-aware contrastive learning approach for single-cell transcriptomics analysis"],"prefix":"10.1093","volume":"42","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9634-8164","authenticated-orcid":false,"given":"Murong","family":"Zhou","sequence":"first","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Lu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5905-2820","authenticated-orcid":false,"given":"Yingjian","family":"Liang","sequence":"additional","affiliation":[{"name":"Hepatobiliary and Pancreatic Surgery, Harbin Medical University Cancer Hospital , Harbin 150080,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfred Wei Chieh","family":"Kow","sequence":"additional","affiliation":[{"name":"Division of Hepatobiliary & Pancreatic Surgery, Department of Surgery, National University Hospital , Singapore, 119074,","place":["Singapore"]},{"name":"Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore , Singapore, 119228,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7381-2374","authenticated-orcid":false,"given":"Guohua","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin 150040,","place":["China"]},{"name":"Department of Computer Science and Technology, Faculty of Computing, Harbin Institute of Technology , Harbin 150001,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiaoming","family":"Liu","sequence":"additional","affiliation":[{"name":"School of Artificial Intelligence, Henan University , Zhengzhou 450000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7219-0999","authenticated-orcid":false,"given":"Yuming","family":"Zhao","sequence":"additional","affiliation":[{"name":"School of Computer Science and Artificial Intelligence, Northeast Forestry University , Harbin 150040,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,6,4]]},"reference":[{"key":"2026062409122127700_btag361-B1","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1038\/s41590-018-0276-y","article-title":"Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage","volume":"20","author":"Aran","year":"2019","journal-title":"Nat Immunol"},{"key":"2026062409122127700_btag361-B2","doi-asserted-by":"crossref","first-page":"6748","DOI":"10.1038\/s41388-021-02054-3","article-title":"Single-cell RNA sequencing reveals distinct 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