{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T21:12:32Z","timestamp":1757452352499,"version":"3.41.2"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"2","license":[{"start":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T00:00:00Z","timestamp":1711065600000},"content-version":"vor","delay-in-days":60,"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":["62302455","62172369"],"award-info":[{"award-number":["62302455","62172369"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100022963","name":"Key Research and Development Plan of Zhejiang Province","doi-asserted-by":"publisher","award":["2021C02039"],"award-info":[{"award-number":["2021C02039"]}],"id":[{"id":"10.13039\/100022963","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,1,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Graph learning models have received increasing attention in the computational analysis of single-cell RNA sequencing (scRNA-seq) data. Compared with conventional deep neural networks, graph neural networks and language models have exhibited superior performance by extracting graph-structured data from raw gene count matrices. Established deep neural network-based clustering approaches generally focus on temporal expression patterns while ignoring inherent interactions at gene-level as well as cell-level, which could be regarded as spatial dynamics in single-cell data. Both gene\u2013gene and cell\u2013cell interactions are able to boost the performance of cell type detection, under the framework of multi-view modeling. In this study, spatiotemporal embedding and cell graphs are extracted to capture spatial dynamics at the molecular level. In order to enhance the accuracy of cell type detection, this study proposes the scHybridBERT architecture to conduct multi-view modeling of scRNA-seq data using extracted spatiotemporal patterns. In this scHybridBERT method, graph learning models are employed to deal with cell graphs and the Performer model employs spatiotemporal embeddings. Experimental outcomes about benchmark scRNA-seq datasets indicate that the proposed scHybridBERT method is able to enhance the accuracy of single-cell clustering tasks by integrating spatiotemporal embeddings and cell graphs.<\/jats:p>","DOI":"10.1093\/bib\/bbae018","type":"journal-article","created":{"date-parts":[[2024,3,22]],"date-time":"2024-03-22T16:57:42Z","timestamp":1711126662000},"source":"Crossref","is-referenced-by-count":3,"title":["scHybridBERT: integrating gene regulation and cell graph for spatiotemporal dynamics in single-cell clustering"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9719-554X","authenticated-orcid":false,"given":"Zhang","family":"Wei","sequence":"first","affiliation":[{"name":"Zhejiang Sci-Tech University , 310028, Hangzhou , 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China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiang","family":"Mingfeng","sequence":"additional","affiliation":[{"name":"Zhejiang Sci-Tech University , 310028, Hangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zhang","family":"Yixuan","sequence":"additional","affiliation":[{"name":"Zhejiang Sci-Tech University , 310028, Hangzhou , China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Liu","family":"Qi","sequence":"additional","affiliation":[{"name":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China"},{"name":"Tongji University , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , 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