{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T13:48:39Z","timestamp":1782308919526,"version":"3.54.5"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T00:00:00Z","timestamp":1779667200000},"content-version":"vor","delay-in-days":3,"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":["62372209"],"award-info":[{"award-number":["62372209"]}],"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":["62372494"],"award-info":[{"award-number":["62372494"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012245","name":"Science and Technology Planning Project of Guangdong Province","doi-asserted-by":"publisher","award":["20200708112YY"],"award-info":[{"award-number":["20200708112YY"]}],"id":[{"id":"10.13039\/501100012245","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012245","name":"Science and Technology Planning Project of Guangdong Province","doi-asserted-by":"publisher","award":["2020A0505100018"],"award-info":[{"award-number":["2020A0505100018"]}],"id":[{"id":"10.13039\/501100012245","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangdong Universities\u2019 Innovation Team","award":["2021KCXTD015"],"award-info":[{"award-number":["2021KCXTD015"]}]},{"name":"Guangdong Key Disciplines","award":["2021ZDJS138"],"award-info":[{"award-number":["2021ZDJS138"]}]}],"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>Spatial transcriptomics (ST) enables the measurement of gene expression while preserving the spatial context of tissues. However, the sparsity of ST data leads to poor usage of gene expression and spatial information, resulting in the embeddings that are not well represented and challenging for downstream analyses.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we introduced GSG, a generative self-supervised representation learning framework for ST data that leverages a masking mechanism to learn informative representations. For spatial domain identification, GSG consistently outperformed state-of-the-art methods across benchmarking datasets, regardless of sequencing platforms. In addition, we applied GSG to an in-house human fetal heart dataset, revealing anatomically coherent spatial domains and identifying APCDD1 as an endocardial-specific marker potentially involved in congenital heart disease. Our results showcase GSG\u2019s superiority and underscore its valuable contributions to advancing ST analysis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and Implementation<\/jats:title>\n                    <jats:p>Our software package is available at https:\/\/github.com\/keaml-Guan\/GSG.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag333","type":"journal-article","created":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T11:46:12Z","timestamp":1779363972000},"source":"Crossref","is-referenced-by-count":0,"title":["A masked generative graph representation learning framework empowering precise spatial domain identification"],"prefix":"10.1093","volume":"42","author":[{"given":"Chuyao","family":"Wang","sequence":"first","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tongdong","family":"Zhang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hang","family":"Sun","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhipeng","family":"Wu","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuo","family":"Liang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xueting","family":"Wang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meirong","family":"Du","sequence":"additional","affiliation":[{"name":"Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University , Shanghai, 201204,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanchun","family":"Liang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]},{"name":"Zhuhai Sub Laboratory of Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Zhuhai College of Science and Technology , Zhuhai, 519041,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7108-3574","authenticated-orcid":false,"given":"Xin","family":"Gao","sequence":"additional","affiliation":[{"name":"King Abdullah University of Science and Technology, Mathematical and Computer Science and Engineering Division, King Abdullah University of Science and Technology (KAUST) , Thuwal, 23955-6900,","place":["Saudi Arabia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Tang","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4809-0514","authenticated-orcid":false,"given":"Dong","family":"Xu","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Computer Science, Bond Life Sciences Center, University of Missouri , Columbia, MO 65211,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3954-1333","authenticated-orcid":false,"given":"Xiaoyue","family":"Feng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An","family":"Zeng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Cell Biology, Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences , Shanghai, 200031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7162-7826","authenticated-orcid":false,"given":"Renchu","family":"Guan","sequence":"additional","affiliation":[{"name":"Key Laboratory of Symbolic Computation and Knowledge Engineering of the Ministry of Education, College of Computer Science and Technology, Jilin University , Changchun, 130012,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,5,22]]},"reference":[{"key":"2026062409115226700_btag333-B1","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.4463","article-title":"SCENIC: single-cell regulatory network inference and clustering","volume":"14","author":"Aibar","year":"2017","journal-title":"Nat Methods"},{"key":"2026062409115226700_btag333-B2","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1016\/j.cell.2019.11.025","article-title":"A 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