{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,25]],"date-time":"2026-02-25T03:46:47Z","timestamp":1771991207135,"version":"3.50.1"},"reference-count":52,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T00:00:00Z","timestamp":1684886400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2018YFA0801405"],"award-info":[{"award-number":["2018YFA0801405"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFA0801801"],"award-info":[{"award-number":["2019YFA0801801"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["31871272"],"award-info":[{"award-number":["31871272"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Chinese Institute for Brain Research","award":["2020-NKX-XM-11"],"award-info":[{"award-number":["2020-NKX-XM-11"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression heterogeneities in diverse cell types underlying homeostasis, development and pathological states. However, the loss of spatial information hinders its applications in deciphering spatially related features, such as cell\u2013cell interactions in a spatial context. Here, we present STellaris (https:\/\/spatial.rhesusbase.com), a web server aimed to rapidly assign spatial information to scRNA-seq data based on their transcriptomic similarity with public spatial transcriptomics (ST) data. STellaris is founded on 101 manually curated ST datasets comprising 823 sections across different organs, developmental stages and pathological states from humans and mice. STellaris accepts raw count matrix and cell type annotation of scRNA-seq data as the input, and maps single cells to spatial locations in the tissue architecture of properly matched ST section. Spatially resolved information for intercellular communications, such as spatial distance and ligand-receptor interactions (LRIs), are further characterized between annotated cell types. Moreover, we also expanded the application of STellaris in spatial annotation of multiple regulatory levels with single-cell multiomics data, using the transcriptome as a bridge. STellaris was applied to several case studies to showcase its utility of adding value to the ever-growing scRNA-seq data from a spatial perspective.<\/jats:p>","DOI":"10.1093\/nar\/gkad419","type":"journal-article","created":{"date-parts":[[2023,5,24]],"date-time":"2023-05-24T22:53:00Z","timestamp":1684968780000},"page":"W560-W568","source":"Crossref","is-referenced-by-count":15,"title":["STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data"],"prefix":"10.1093","volume":"51","author":[{"given":"Xiangshang","family":"Li","sequence":"first","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6577-4064","authenticated-orcid":false,"given":"Chunfu","family":"Xiao","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"}]},{"given":"Juntian","family":"Qi","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"}]},{"given":"Weizhen","family":"Xue","sequence":"additional","affiliation":[{"name":"BGI-Beijing , Beijing \u00a0102601, China"}]},{"given":"Xinwei","family":"Xu","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"},{"name":"College of Life Science, Peking University , Beijing \u00a0100871, China"}]},{"given":"Zelin","family":"Mu","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"},{"name":"School of Basic Medical Sciences, Peking University Health Science Center , Beijing \u00a0100191, China"}]},{"given":"Jie","family":"Zhang","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8008-8430","authenticated-orcid":false,"given":"Chuan-Yun","family":"Li","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"},{"name":"Chinese Institute for Brain Research , Beijing \u00a0102206, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6650-8662","authenticated-orcid":false,"given":"Wanqiu","family":"Ding","sequence":"additional","affiliation":[{"name":"Laboratory of Bioinformatics and Genomic Medicine, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"},{"name":"Bioinformatics Core, Institute of Molecular Medicine, College of Future Technology, Peking University , Beijing \u00a0100871, China"}]}],"member":"286","published-online":{"date-parts":[[2023,5,24]]},"reference":[{"key":"2023070505022536800_B1","doi-asserted-by":"crossref","first-page":"e694","DOI":"10.1002\/ctm2.694","article-title":"Single-cell RNA sequencing technologies and applications: a brief overview","volume":"12","author":"Jovic","year":"2022","journal-title":"Clin. Transl. Med."},{"key":"2023070505022536800_B2","doi-asserted-by":"crossref","first-page":"4307","DOI":"10.1038\/s41467-020-18158-5","article-title":"Single cell transcriptomics comes of age","volume":"11","author":"Aldridge","year":"2020","journal-title":"Nat. Commun."},{"key":"2023070505022536800_B3","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1146\/annurev-genet-120417-031247","article-title":"Power in numbers: single-cell RNA-seq strategies to dissect complex tissues","volume":"52","author":"Birnbaum","year":"2018","journal-title":"Annu. Rev. Genet."},{"key":"2023070505022536800_B4","doi-asserted-by":"crossref","first-page":"e27041","DOI":"10.7554\/eLife.27041","article-title":"The Human cell atlas","volume":"6","author":"Regev","year":"2017","journal-title":"Elife"},{"key":"2023070505022536800_B5","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1038\/s41586-021-03775-x","article-title":"Molecular architecture of the developing mouse brain","volume":"596","author":"La\u00a0Manno","year":"2021","journal-title":"Nature"},{"key":"2023070505022536800_B6","doi-asserted-by":"crossref","first-page":"490","DOI":"10.1038\/s41586-019-0933-9","article-title":"A single-cell molecular map of mouse gastrulation and early organogenesis","volume":"566","author":"Pijuan-Sala","year":"2019","journal-title":"Nature"},{"key":"2023070505022536800_B7","doi-asserted-by":"crossref","first-page":"3236","DOI":"10.1158\/0008-5472.CAN-22-0090","article-title":"Single-cell transcriptome profiling reveals intratumoral heterogeneity and molecular features of ductal carcinoma In situ","volume":"82","author":"Tokura","year":"2022","journal-title":"Cancer Res."},{"key":"2023070505022536800_B8","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1126\/science.aan6828","article-title":"Single-cell transcriptomics to explore the immune system in health and disease","volume":"358","author":"Stubbington","year":"2017","journal-title":"Science"},{"key":"2023070505022536800_B9","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1038\/s41569-022-00805-7","article-title":"Single-cell transcriptomics for the assessment of cardiac disease","volume":"20","author":"Miranda","year":"2022","journal-title":"Nat. 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