{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T12:52:45Z","timestamp":1779886365517,"version":"3.53.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2025,5,23]],"date-time":"2025-05-23T00:00:00Z","timestamp":1747958400000},"content-version":"vor","delay-in-days":22,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"name":"Science and Technology Innovation Key R&D Program of Chongqing","award":["CSTB2023TIAD-STX0002"],"award-info":[{"award-number":["CSTB2023TIAD-STX0002"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Spatial omics technologies, generating high-throughput and multimodal data, have necessitated the development of advanced data integration methods to facilitate comprehensive biological and clinical treatment discoveries. Based on the cross-attention concept, we developed an AI learning based toolchain called StereoMM, a graph based fusion model that can incorporate omics data such as gene expression, histological images, and spatial location. StereoMM uses an attention module for omics data interaction and a graph autoencoder to integrate spatial positions and omics data in a self-supervised manner. Applying StereoMM across various cancer types and platforms has demonstrated its robust capability. StereoMM outperforms competitors in identifying spatial regions reflecting tumour progression and shows promise in classifying colorectal cancer patients into deficient mismatch repair and proficient mismatch repair groups. The comprehensive inter-modal integration and efficiency of StereoMM enable researchers to construct spatial views of integrated multimodal features efficiently, advancing thorough tissue and patient characterization.<\/jats:p>","DOI":"10.1093\/bib\/bbaf210","type":"journal-article","created":{"date-parts":[[2025,4,23]],"date-time":"2025-04-23T07:46:45Z","timestamp":1745394405000},"source":"Crossref","is-referenced-by-count":6,"title":["StereoMM: a graph fusion model for integrating spatial transcriptomic data and pathological images"],"prefix":"10.1093","volume":"26","author":[{"given":"Bingying","family":"Luo","sequence":"first","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fei","family":"Teng","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guo","family":"Tang","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weixuan","family":"Cen","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xing","family":"Liu","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinmiao","family":"Chen","sequence":"additional","affiliation":[{"name":"Center for Computational Biology and Program in Cancer and Stem Cell Biology, Duke-NUS Medical School , 8 College Road, Singapore 169857 ,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chi","family":"Qu","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuanzhu","family":"Liu","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xin","family":"Liu","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenyan","family":"Jiang","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Huaqiang","family":"Huang","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Feng","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Genome and Multi-omics Technologies , , Shenzhen 518083 ,","place":["China"]},{"name":"BGI Research, No. 9, Yunhua Road, Yantian District , , Shenzhen 518083 ,","place":["China"]},{"name":"BGI Collaborative Center for Future Medicine, Shanxi Medical University , No. 1258, Xinjiannan Road, Yingze District, Taiyuan 030001 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xue","family":"Zhang","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Min","family":"Jian","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mei","family":"Li","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Xi","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guibo","family":"Li","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sha","family":"Liao","sequence":"additional","affiliation":[{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ao","family":"Chen","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weimiao","family":"Yu","sequence":"additional","affiliation":[{"name":"School of Biological Science, Nanyang Technological University , 60 Nanyang Drive, Singapore 637551 ,","place":["Singapore"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xun","family":"Xu","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]},{"name":"BGI Research , Hangzhou, No. 203, Zhenzhong Road, Xihu District, Hangzhou 310030 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiajun","family":"Zhang","sequence":"additional","affiliation":[{"name":"BGI Research , Chongqing, No. 313, Jinyue road, Jiulongpo District, Chongqing 401329 ,","place":["China"]},{"name":"BGI Research , Shenzhen, No. 9, Yunhua Road, Yantian District, Shenzhen 518083 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,5,23]]},"reference":[{"key":"2025052702074863700_ref1","doi-asserted-by":"publisher","first-page":"5250","DOI":"10.1158\/1078-0432.Ccr-18-0309","article-title":"Quantitative spatial profiling of PD-1\/PD-L1 interaction and HLA-DR\/IDO-1 predicts improved outcomes of anti-PD-1 therapies in metastatic melanoma","volume":"24","author":"Johnson","year":"2018","journal-title":"Clin Cancer Res"},{"key":"2025052702074863700_ref2","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1038\/s41592-022-01560-w","article-title":"Sprod for de-noising spatially resolved transcriptomics data based on position and image information","volume":"19","author":"Wang","year":"2022","journal-title":"Nat Methods"},{"key":"2025052702074863700_ref3","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1186\/s13073-022-01075-1","article-title":"An introduction to spatial transcriptomics for biomedical research","volume":"14","author":"Williams","year":"2022","journal-title":"Genome Med"},{"key":"2025052702074863700_ref4","doi-asserted-by":"publisher","first-page":"3541","DOI":"10.1038\/s41467-021-23913-3","article-title":"Hybrid AI-assistive diagnostic model permits rapid TBS classification of cervical liquid-based thin-layer cell smears","volume":"12","author":"Zhu","year":"2021","journal-title":"Nat Commun"},{"key":"2025052702074863700_ref5","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1038\/s41586-023-06555-x","article-title":"A foundation model for generalizable disease detection from retinal images","volume":"622","author":"Zhou","year":"2023","journal-title":"Nature"},{"key":"2025052702074863700_ref6","doi-asserted-by":"publisher","first-page":"154","DOI":"10.1038\/s41591-021-01620-2","article-title":"Artificial intelligence for diagnosis and Gleason grading of prostate cancer: the PANDA challenge","volume":"28","author":"Bulten","year":"2022","journal-title":"Nat Med"},{"key":"2025052702074863700_ref7","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1038\/s43856-024-00502-1","article-title":"A comprehensive AI model development framework for consistent Gleason grading","volume":"4","author":"Huo","year":"2024","journal-title":"Commun Med"},{"key":"2025052702074863700_ref8","doi-asserted-by":"publisher","first-page":"7739","DOI":"10.1038\/s41467-023-43120-6","article-title":"Robust mapping of spatiotemporal trajectories and cell\u2013cell interactions in healthy and diseased tissues","volume":"14","author":"Pham","year":"2023","journal-title":"Nat Commun"},{"key":"2025052702074863700_ref9","doi-asserted-by":"publisher","first-page":"1342","DOI":"10.1038\/s41592-021-01255-8","article-title":"SpaGCN: integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network, (in eng)","volume":"18","author":"Hu","year":"2021","journal-title":"Nat Methods"},{"key":"2025052702074863700_ref10","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1038\/s41467-022-29439-6","article-title":"deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder, (in eng)","volume":"13","author":"Dong","year":"2022","journal-title":"Nat Commun"},{"key":"2025052702074863700_ref11","doi-asserted-by":"publisher","first-page":"1200","DOI":"10.1038\/s41587-022-01251-z","article-title":"Integrative spatial analysis of cell morphologies and transcriptional states with MUSE","volume":"40","author":"Bao","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2025052702074863700_ref12","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/s13073-024-01283-x","article-title":"Unsupervised spatially embedded deep representation of spatial transcriptomics","volume":"16","author":"Xu","year":"2024","journal-title":"Genome Med"},{"key":"2025052702074863700_ref13","doi-asserted-by":"publisher","first-page":"bbae257","DOI":"10.1093\/bib\/bbae257","article-title":"Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics","volume":"25","author":"Wang","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025052702074863700_ref14","doi-asserted-by":"publisher","first-page":"1777","DOI":"10.1016\/j.cell.2022.04.003","article-title":"spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays, (in eng)","volume":"185","author":"Chen","year":"2022","journal-title":"Cell"},{"key":"2025052702074863700_ref15","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1038\/nature05453","article-title":"genome-wide atlas of gene expression in the adult mouse brain, (in eng)","volume":"445","author":"Lein","year":"2007","journal-title":"Nature"},{"key":"2025052702074863700_ref16","doi-asserted-by":"publisher","first-page":"80","DOI":"10.1038\/s41698-023-00430-8","article-title":"clonal dynamics and stereo-seq resolve origin and phenotypic plasticity of adenosquamous carcinoma, (in eng)","volume":"7","author":"Zhao","year":"2023","journal-title":"NPJ Precis Oncol"},{"key":"2025052702074863700_ref17","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1186\/s13073-022-01089-9","article-title":"Molecular profiling of human non-small cell lung cancer by single-cell RNA-seq","volume":"14","author":"Li","year":"2022","journal-title":"Genome Med"},{"key":"2025052702074863700_ref18","doi-asserted-by":"publisher","first-page":"238","DOI":"10.2741\/4893","article-title":"EMT imparts cancer stemness and plasticity: new perspectives and therapeutic potential, (in eng)","volume":"26","author":"Roy","year":"2021","journal-title":"Front Biosci (Landmark Ed)"},{"key":"2025052702074863700_ref19","doi-asserted-by":"publisher","first-page":"eabn7571","DOI":"10.1126\/scitranslmed.abn7571","article-title":"Triple-negative breast cancer metastasis involves complex epithelial-mesenchymal transition dynamics and requires vimentin","volume":"14","author":"Grasset","year":"2022","journal-title":"(in eng), Sci Transl Med"},{"key":"2025052702074863700_ref20","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1038\/s41556-022-01045-0","article-title":"MLL3 loss drives metastasis by promoting a hybrid epithelial-mesenchymal transition state, (in eng)","volume":"25","author":"Cui","year":"2023","journal-title":"Nat Cell Biol"},{"key":"2025052702074863700_ref21","doi-asserted-by":"publisher","DOI":"10.3390\/cells9071643","article-title":"The E2F pathway score as a predictive biomarker of response to Neoadjuvant therapy in ER+\/HER2- breast cancer","volume":"9","author":"Oshi","year":"2020","journal-title":"Cells"},{"key":"2025052702074863700_ref22","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.semcancer.2023.11.009","article-title":"mutual regulation of TGF\u03b2-induced oncogenic EMT, cell cycle progression and the DDR, (in eng)","volume":"97","author":"Schuhwerk","year":"2023","journal-title":"Semin Cancer Biol"},{"key":"2025052702074863700_ref23","doi-asserted-by":"publisher","first-page":"11432","DOI":"10.1073\/pnas.0403969101","article-title":"Semaphorin 3B (SEMA3B) induces apoptosis in lung and breast cancer, whereas VEGF165 antagonizes this effect, (in eng)","volume":"101","author":"Castro-Rivera","year":"2004","journal-title":"Proc Natl Acad Sci U S A"},{"key":"2025052702074863700_ref24","doi-asserted-by":"publisher","first-page":"109827","DOI":"10.1016\/j.biopha.2020.109827","article-title":"Trefoil factor 1 (TFF1) is a potential prognostic biomarker with functional significance in breast cancers","volume":"124","author":"Yi","year":"2020","journal-title":"(in eng), Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie"},{"key":"2025052702074863700_ref25","doi-asserted-by":"publisher","first-page":"6012","DOI":"10.1038\/s41467-021-26271-2","article-title":"Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions","volume":"12","author":"Andersson","year":"2021","journal-title":"Nat Commun"},{"key":"2025052702074863700_ref26","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1016\/j.fmre.2022.01.036","article-title":"Spatial transcriptome unveils a discontinuous inflammatory pattern in proficient mismatch repair colorectal adenocarcinoma","volume":"3","author":"Zhang","year":"2023","journal-title":"Fundamental Research"},{"key":"2025052702074863700_ref27","doi-asserted-by":"publisher","DOI":"10.3390\/ijms20194915","article-title":"insulin-like growth factor 2 (IGF2) Signaling in colorectal cancer-from basic research to potential clinical applications, (in eng)","volume":"20","author":"Kasprzak","year":"2019","journal-title":"Int J Mol Sci"},{"key":"2025052702074863700_ref28","doi-asserted-by":"publisher","first-page":"5037","DOI":"10.3892\/mmr.2018.8533","article-title":"COL1A1 promotes metastasis in colorectal cancer by regulating the WNT\/PCP pathway, (in eng)","volume":"17","author":"Zhang","year":"2018","journal-title":"Mol Med Rep"},{"key":"2025052702074863700_ref29","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1038\/s41586-021-03634-9","article-title":"exploring tissue architecture using spatial transcriptomics, (in eng)","volume":"596","author":"Rao","year":"2021","journal-title":"Nature"},{"key":"2025052702074863700_ref30","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1038\/s41576-023-00580-2","article-title":"methods and applications for single-cell and spatial multi-omics, (in eng)","volume":"24","author":"Vandereyken","year":"2023","journal-title":"Nat Rev Genet"},{"key":"2025052702074863700_ref31","doi-asserted-by":"publisher","first-page":"e696","DOI":"10.1002\/ctm2.696","article-title":"spatial omics: navigating to the golden era of cancer research, (in eng)","volume":"12","author":"Wu","year":"2022","journal-title":"Clin Transl Med"},{"key":"2025052702074863700_ref32","doi-asserted-by":"publisher","first-page":"152","DOI":"10.1186\/s13073-021-00968-x","article-title":"deep learning in cancer diagnosis, prognosis and treatment selection, (in eng)","volume":"13","author":"Tran","year":"2021","journal-title":"Genome Med"},{"key":"2025052702074863700_ref33","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1038\/s41568-021-00408-3","article-title":"Harnessing multimodal data integration to advance precision oncology","volume":"22","author":"Boehm","year":"2022","journal-title":"Nat Rev Cancer"},{"key":"2025052702074863700_ref34","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1038\/nmeth.4182","article-title":"Prospective identification of hematopoietic lineage choice by deep learning","volume":"14","author":"Buggenthin","year":"2017","journal-title":"Nat Methods"},{"key":"2025052702074863700_ref35","doi-asserted-by":"publisher","first-page":"4870","DOI":"10.1016\/j.csbj.2022.08.043","article-title":"Computational solutions for spatial transcriptomics","volume":"20","author":"Kleino","year":"2022","journal-title":"Comput Struct Biotechnol J"},{"key":"2025052702074863700_ref36","doi-asserted-by":"publisher","first-page":"eabq4964","DOI":"10.1126\/science.abq4964","article-title":"the dawn of spatial omics, (in eng)","volume":"381","author":"Bressan","year":"2023","journal-title":"Science"},{"key":"2025052702074863700_ref37","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: Large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2025052702074863700_ref38","doi-asserted-by":"publisher","first-page":"970","DOI":"10.1038\/s41586-024-07894-z","article-title":"A pathology foundation model for cancer diagnosis and prognosis prediction","volume":"634","author":"Wang","year":"2024","journal-title":"Nature"},{"key":"2025052702074863700_ref39","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1038\/s41593-020-00787-0","article-title":"Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex","volume":"24","author":"Maynard","year":"2021","journal-title":"Nat Neurosci"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/3\/bbaf210\/63308337\/bbaf210.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/3\/bbaf210\/63308337\/bbaf210.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,5,27]],"date-time":"2025-05-27T02:07:56Z","timestamp":1748311676000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf210\/8142327"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,5,1]]},"references-count":39,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2025,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf210","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2024.05.04.592486","asserted-by":"object"}]},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,5]]},"published":{"date-parts":[[2025,5,1]]},"article-number":"bbaf210"}}