{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T21:02:56Z","timestamp":1775077376573,"version":"3.50.1"},"reference-count":63,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T00:00:00Z","timestamp":1736208000000},"content-version":"vor","delay-in-days":46,"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":["32470246"],"award-info":[{"award-number":["32470246"]}],"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":["31700199"],"award-info":[{"award-number":["31700199"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003392","name":"Natural Science Foundation of Fujian Province","doi-asserted-by":"publisher","award":["2021J01142"],"award-info":[{"award-number":["2021J01142"]}],"id":[{"id":"10.13039\/501100003392","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008766","name":"Foundation of Fujian Agriculture and Forestry University","doi-asserted-by":"crossref","award":["11899001001"],"award-info":[{"award-number":["11899001001"]}],"id":[{"id":"10.13039\/501100008766","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Spatial transcriptomics (ST) technologies enable dissecting the tissue architecture in spatial context. To perceive the global contextual information of gene expression patterns in tissue, the spatial dependence of cells must be fully considered by integrating both local and non-local features by means of spatial-context-aware. However, the current ST integration algorithm ignores for ST dropouts, which impedes the spatial-aware of ST features, resulting in challenges in the accuracy and robustness of microenvironmental heterogeneity detecting, spatial domain clustering, and batch-effects correction. Here, we developed an STMGraph, a universal dual-view dynamic deep learning framework that combines dual-remask (MASK-REMASK) with dynamic graph attention model (DGAT) to exploit ST data outperforming pre-existing tools. The dual-remask mechanism masks the embeddings before encoding and decoding, establishing dual-decoding-view to share features mutually. DGAT leverages self-supervision to update graph linkage relationships from two distinct perspectives, thereby generating a comprehensive representation for each node. Systematic benchmarking against 10 state-of-the-art tools revealed that the STMGraph has the optimal performance with high accuracy and robustness on spatial domain clustering for the datasets of diverse ST platforms from multi- to sub-cellular resolutions. Furthermore, STMGraph aggregates ST information cross regions by dual-remask to realize the batch-effects correction implicitly, allowing for spatial domain clustering of ST multi-slices. STMGraph is platform independent and superior in spatial-context-aware to achieve microenvironmental heterogeneity detection, spatial domain clustering, batch-effects correction, and new biological discovery, and is therefore a desirable novel tool for diverse ST studies<\/jats:p>","DOI":"10.1093\/bib\/bbae685","type":"journal-article","created":{"date-parts":[[2025,1,7]],"date-time":"2025-01-07T08:18:23Z","timestamp":1736237903000},"source":"Crossref","is-referenced-by-count":3,"title":["STMGraph: spatial-context-aware of transcriptomes via a dual-remasked dynamic graph attention model"],"prefix":"10.1093","volume":"26","author":[{"given":"Lixian","family":"Lin","sequence":"first","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]},{"name":"College of Life Science, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Haoyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Yuxiao","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Yuanyuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Yujie","family":"Xu","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Zhenglin","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Yuemin","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]},{"name":"College of Life Science, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"given":"Kunpeng","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5456-6590","authenticated-orcid":false,"given":"Xiaokai","family":"Ma","sequence":"additional","affiliation":[{"name":"Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]},{"name":"Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration, Fujian Agriculture and Forestry University , No. 15 Shangxiadian Road, Cangshan District, Fuzhou 350002 ,","place":["China"]}]}],"member":"286","published-online":{"date-parts":[[2025,1,6]]},"reference":[{"key":"2025033007272826400_ref1","doi-asserted-by":"crossref","DOI":"10.1002\/bies.201900221","article-title":"Spatially resolved transcriptomes\u2014next generation tools for tissue 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