{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T06:54:52Z","timestamp":1789541692483,"version":"build-2803163510"},"reference-count":33,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,1,31]],"date-time":"2026-01-31T00:00:00Z","timestamp":1769817600000},"content-version":"vor","delay-in-days":30,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Scientific Research Innovation Capability Support Project for Young Faculty","award":["ZYGXQNJSKYCXNLZCXM-H8"],"award-info":[{"award-number":["ZYGXQNJSKYCXNLZCXM-H8"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2024YFE0105400"],"award-info":[{"award-number":["2024YFE0105400"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100021171","name":"GuangDong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2024A1515011437"],"award-info":[{"award-number":["2024A1515011437"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100021171","name":"GuangDong Basic and Applied Basic Research Foundation","doi-asserted-by":"crossref","award":["2025A1515011692"],"award-info":[{"award-number":["2025A1515011692"]}],"id":[{"id":"10.13039\/501100021171","id-type":"DOI","asserted-by":"crossref"}]},{"name":"TCL Science and Technology Innovation Fund","award":["20231752"],"award-info":[{"award-number":["20231752"]}]},{"name":"Major Special Project for Innovation and R&D in Henan Province","award":["241100310200"],"award-info":[{"award-number":["241100310200"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,7]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Spatial transcriptomics (ST) technologies have significantly advanced our ability to discern gene expression patterns within intact tissue structures, enabling unprecedented insights into cellular heterogeneity and tissue architecture. However, accurately determining cell-type proportions within spatially aggregated transcriptomic spots remains challenging due to inherent granularity discrepancies, batch effects, and spatial heterogeneity. To address these challenges, we introduce S$^{2}$potAE, a novel spatial spot autoencoder framework that integrates gene expression data, spatial coordinates, and morphological features from histology images for precise spot-level deconvolution. S$^{2}$potAE employs a multilevel feature aggregation strategy, systematically extracting and fusing spatially-aware features through a graph-based spatial encoder and perceptual image embeddings from histological patches. Furthermore, an auxiliary pathological classification task enhances biological relevance and model interpretability. Comprehensive benchmarking across multiple simulated and real datasets\u2014including human breast cancer, mouse brain anterior, and human dorsolateral prefrontal cortex\u2014demonstrates that S$^{2}$potAE consistently surpasses state-of-the-art methods in accuracy, robustness, and biological interpretability. Our approach effectively resolves complex cellular compositions, accurately identifies tumor boundaries, and captures nuanced cell-type distributions, significantly enhancing the utility of ST in biological research and clinical applications.<\/jats:p>","DOI":"10.1093\/bib\/bbag020","type":"journal-article","created":{"date-parts":[[2026,1,12]],"date-time":"2026-01-12T12:18:42Z","timestamp":1768220322000},"source":"Crossref","is-referenced-by-count":2,"title":["S2potAE: multimodal spatial spot autoencoder integrating image and transcriptomic features for deconvolution"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9708-8939","authenticated-orcid":false,"given":"Tianyi","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Tat Chee Avenue, Kowloon Tong, Kowloon 999077 ,","place":["Hong Kong SAR"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wen","family":"Xue","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, South China University of Technology , 381 Wushan Road, Tianhe District, Guangzhou 510006, Guangdong ,","place":["P.R. 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China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongcan","family":"Luo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Tat Chee Avenue, Kowloon Tong, Kowloon 999077 ,","place":["Hong Kong SAR"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cheng","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Computer Science, Shantou University , 243 Daxue Road, Jinping District, Shantou 515063, Guangdong ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenjun","family":"Shen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, Shantou University Medical College , 22 Xinling Road, Jinping District, Shantou 515041 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4022-0852","authenticated-orcid":false,"given":"Si","family":"Wu","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, South China University of Technology , 381 Wushan Road, Tianhe District, Guangzhou 510006, Guangdong ,","place":["P.R. China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hau-San","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Computer Science, City University of Hong Kong , Tat Chee Avenue, Kowloon Tong, Kowloon 999077 ,","place":["Hong Kong SAR"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,1,31]]},"reference":[{"key":"2026013111380216400_ref1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/bs.mie.2016.03.020","article-title":"RNA imaging with multiplexed error-robust fluorescence in situ hybridization (MERFISH)","volume":"572","author":"Moffitt","year":"2016","journal-title":"Methods Enzymol"},{"key":"2026013111380216400_ref2","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1016\/j.cell.2018.05.035","article-title":"Dynamics and spatial genomics of the nascent transcriptome by intron 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