{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T21:31:53Z","timestamp":1772919113595,"version":"3.50.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T00:00:00Z","timestamp":1759104000000},"content-version":"vor","delay-in-days":29,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007129","name":"Natural Science Foundation of Shandong Province","doi-asserted-by":"publisher","award":["ZR2023QF081"],"award-info":[{"award-number":["ZR2023QF081"]}],"id":[{"id":"10.13039\/501100007129","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62303271"],"award-info":[{"award-number":["62303271"]}],"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":["U1806202"],"award-info":[{"award-number":["U1806202"]}],"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":["82274320"],"award-info":[{"award-number":["82274320"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,8,31]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The rapid advancement of spatial multi-omics technologies has opened new avenues for dissecting tissue architecture with unprecedented resolution. However, inherent disparities across omics modalities, such as differences in biological hierarchy and resolution, pose significant challenges for integrative analysis. To address this, we present soFusion, a method for representation learning on spatial multi-omics data that enables automated identification of tissue compartmentalization. soFusion employs a graph convolutional network (GCN) to extract latent embeddings from spatial omics profiles. To simultaneously capture both cross-modality relationships and modality-specific features, we introduce a novel strategy for intra- and inter-omics feature learning. Moreover, modality-specific decoders are designed to preserve the unique information embedded in each omics type. We evaluated soFusion on multiple datasets including gene expression, protein expression, and epigenetic features. Across all benchmarks, soFusion consistently outperformed existing methods in delineating anatomical structures and identifying spatial domains with improved continuity and reduced noise. Collectively, soFusion offers an effective solution for spatial multi-omics integration, substantially enhancing the robustness of spatial domain identification.<\/jats:p>","DOI":"10.1093\/bib\/bbaf513","type":"journal-article","created":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T10:50:10Z","timestamp":1759143010000},"source":"Crossref","is-referenced-by-count":1,"title":["soFusion: facilitating tissue structure identification via spatial multi-omics data fusion"],"prefix":"10.1093","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1154-3348","authenticated-orcid":false,"given":"Na","family":"Yu","sequence":"first","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 ,","place":["China"]},{"name":"School of Life Sciences, Westlake University , No. 18, Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024 ,","place":["China"]}]},{"given":"Wenrui","family":"Li","sequence":"additional","affiliation":[{"name":"MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST, Department of Automation, Tsinghua University , No 30, Shuangqing road, Haidian district, Beijing 100084 ,","place":["China"]}]},{"given":"Xue","family":"Sun","sequence":"additional","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 ,","place":["China"]}]},{"given":"Jing","family":"Hu","sequence":"additional","affiliation":[{"name":"Department of Pathology, Qilu Hospital, Shandong University , No. 107, Wenhua Xilu, Lixia District, Jinan, ShanDong 250012 ,","place":["China"]},{"name":"Michigan Center for Translational Pathology, University of Michigan , 1500 E. Medical Center Dr., Rogel Cancer Center, Ann Arbor, MI 48109-0940 ,","place":["United States"]}]},{"given":"Qi","family":"Zou","sequence":"additional","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7742-9161","authenticated-orcid":false,"given":"Zhiping","family":"Liu","sequence":"additional","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 ,","place":["China"]}]},{"given":"Daoliang","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 ,","place":["China"]},{"name":"Institute of Science and Technology for Brain-Inspired Intelligence, MOE Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence, MOE Frontiers Center for Brain Science, Fudan University , No. 825, Zhangheng Road, Pudong New Area, Shanghai 200433 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4264-5758","authenticated-orcid":false,"given":"Wei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 ,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3599-7678","authenticated-orcid":false,"given":"Rui","family":"Gao","sequence":"additional","affiliation":[{"name":"Center of Intelligent Medicine, School of Control Science and Engineering, Shandong University , No. 17923, Jingshi Road, Lixia District, Jinan, Shandong 250061 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