{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,14]],"date-time":"2026-05-14T20:39:18Z","timestamp":1778791158075,"version":"3.51.4"},"reference-count":41,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T00:00:00Z","timestamp":1762732800000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Mapping the query cells onto a well-constructed reference atlas, known as reference mapping, enables robust, reproducible interpretation of new single-cell RNA-seq data in the context of curated and annotated cell subtypes and states. However, existing methods often rely on complex integration frameworks or require re-access to raw data, limiting their applicability and reproducibility. To address this, we introduce ProjectSVR, a machine learning-based framework that formulates reference mapping as a multi-target regression task. By leveraging ensemble support vector regression (SVR) to learn the relationship between gene set activity scores and low-dimensional reference embeddings, ProjectSVR enables platform-agnostic and integration-independent mapping. Benchmarking across diverse biological contexts\u2014including immune responses, developmental trajectories, and disease states\u2014demonstrates that ProjectSVR achieves comparable accuracy and robustness to state-of-the-art methods, with reduced dependence on data-specific preprocessing. Our findings demonstrate that ProjectSVR is a valuable tool for reference mapping, considerably simplifying the analysis of scRNA-seq data when well-constructed reference atlases are available.<\/jats:p>","DOI":"10.1093\/bib\/bbaf586","type":"journal-article","created":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T15:42:20Z","timestamp":1762789340000},"source":"Crossref","is-referenced-by-count":1,"title":["ProjectSVR: mapping single-cell RNA-seq data to reference atlases by supported vector regression"],"prefix":"10.1093","volume":"26","author":[{"given":"Jianing","family":"Gao","sequence":"first","affiliation":[{"name":"Science Island Branch of Graduate School, University of Science and Technology of China , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Westlake Laboratory of Life Sciences and Biomedicine, School of Life Sciences, Westlake University , 18 Shilongshan Road, Xihu District, Hangzhou, Zhejiang 310024 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0556-1324","authenticated-orcid":false,"given":"Jinman","family":"Fang","sequence":"additional","affiliation":[{"name":"Science Island Branch of Graduate School, University of Science and Technology of China , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Qizhi","family":"Zhu","sequence":"additional","affiliation":[{"name":"Science Island Branch of Graduate School, University of Science and Technology of China , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Department of Oncology, The Second Affiliated Hospital of Anhui Medical University , 678 Furong Road, Shushan District, Hefei, Anhui 230032 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoshu","family":"Li","sequence":"additional","affiliation":[{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziran","family":"Bi","sequence":"additional","affiliation":[{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yue","family":"Hu","sequence":"additional","affiliation":[{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8117-5029","authenticated-orcid":false,"given":"Bo","family":"Hong","sequence":"additional","affiliation":[{"name":"Science Island Branch of Graduate School, University of Science and Technology of China , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuanwei","family":"Zhang","sequence":"additional","affiliation":[{"name":"Science Island Branch of Graduate School, University of Science and Technology of China , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9286-7132","authenticated-orcid":false,"given":"Shipeng","family":"Guo","sequence":"additional","affiliation":[{"name":"Department of Breast and Thyroid Surgery, The First Affiliated Hospital of Chongqing Medical University , 1 Youyi Road, Yuzhong District, Chongqing 400016 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hongzhi","family":"Wang","sequence":"additional","affiliation":[{"name":"Science Island Branch of Graduate School, University of Science and Technology of China , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]},{"name":"Anhui Province Key Laboratory of Medical Physics and Technology, Hefei Cancer Hospital of CAS, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences (CAS) , 350 Shushanhu Road, Shushan District, Hefei, Anhui 230031 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,11,10]]},"reference":[{"key":"2025111010421165900_ref1","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1038\/s41592-021-01336-8","article-title":"Benchmarking atlas-level data integration in single-cell genomics","volume":"19","author":"Luecken","year":"2022","journal-title":"Nat Methods"},{"key":"2025111010421165900_ref2","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1038\/s41586-018-0698-6","article-title":"Single-cell reconstruction of the early maternal-fetal interface in humans","volume":"563","author":"Vento-Tormo","year":"2018","journal-title":"Nature"},{"key":"2025111010421165900_ref3","doi-asserted-by":"publisher","first-page":"303","DOI":"10.1038\/s41586-020-2157-4","article-title":"Construction of a human cell landscape at single-cell level","volume":"581","author":"Han","year":"2020","journal-title":"Nature"},{"key":"2025111010421165900_ref4","doi-asserted-by":"publisher","volume-title":"An Integrated Cell Atlas of the Human Lung in Health and Disease","author":"Luecken","DOI":"10.21203\/rs.3.rs-1438584\/v1"},{"key":"2025111010421165900_ref5","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/s13059-020-1926-6","article-title":"Eleven grand challenges in single-cell data science","volume":"21","author":"Lahnemann","year":"2020","journal-title":"Genome Biol"},{"key":"2025111010421165900_ref6","doi-asserted-by":"crossref","first-page":"194","DOI":"10.1186\/s13059-019-1795-z","article-title":"A comparison of automatic cell identification methods for single-cell RNA sequencing data","volume":"20","author":"Abdelaal","year":"2019","journal-title":"Genome Biol"},{"key":"2025111010421165900_ref7","doi-asserted-by":"publisher","first-page":"267","DOI":"10.1016\/j.gpb.2020.07.004","article-title":"Evaluation of cell type annotation R packages on single-cell RNA-seq data","volume":"19","author":"Huang","year":"2021","journal-title":"Genomics Proteomics Bioinformatics"},{"key":"2025111010421165900_ref8","doi-asserted-by":"publisher","first-page":"961","DOI":"10.1016\/j.csbj.2021.01.015","article-title":"Automated methods for cell type annotation on scRNA-seq data","volume":"19","author":"Pasquini","year":"2021","journal-title":"Comput Struct Biotechnol J"},{"key":"2025111010421165900_ref9","doi-asserted-by":"crossref","first-page":"5271","DOI":"10.1038\/s41467-022-33045-x","article-title":"devCellPy is a machine learning-enabled pipeline for automated annotation of complex multilayered single-cell transcriptomic data","volume":"13","author":"Galdos","year":"2022","journal-title":"Nat Commun"},{"key":"2025111010421165900_ref10","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","journal-title":"Nature Biotechnology"},{"key":"2025111010421165900_ref11","doi-asserted-by":"crossref","first-page":"2965","DOI":"10.1038\/s41467-021-23324-4","article-title":"Interpretation of T cell states from single-cell transcriptomics data using reference atlases","volume":"12","author":"Andreatta","year":"2021","journal-title":"Nat Commun"},{"key":"2025111010421165900_ref12","doi-asserted-by":"publisher","first-page":"1000","DOI":"10.1038\/s41587-021-00867-x","article-title":"Iterative single-cell multi-omic integration using online learning","volume":"39","author":"Gao","year":"2021","journal-title":"Nat Biotechnol"},{"key":"2025111010421165900_ref13","doi-asserted-by":"crossref","first-page":"5890","DOI":"10.1038\/s41467-021-25957-x","article-title":"Efficient and precise single-cell reference atlas mapping with symphony","volume":"12","author":"Kang","year":"2021","journal-title":"Nat Commun"},{"key":"2025111010421165900_ref14","doi-asserted-by":"publisher","first-page":"121","DOI":"10.1038\/s41587-021-01001-7","article-title":"Mapping single-cell data to reference atlases by transfer learning","volume":"40","author":"Lotfollahi","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2025111010421165900_ref15","doi-asserted-by":"crossref","first-page":"6118","DOI":"10.1038\/s41467-022-33758-z","article-title":"Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space","volume":"13","author":"Xiong","year":"2022","journal-title":"Nat Commun"},{"key":"2025111010421165900_ref16","doi-asserted-by":"crossref","first-page":"abe6474","DOI":"10.1126\/science.abe6474","article-title":"Pan-cancer single-cell landscape of tumor-infiltrating T cells","volume":"374","author":"Zheng","year":"2021","journal-title":"Science"},{"key":"2025111010421165900_ref17","doi-asserted-by":"publisher","first-page":"D596","DOI":"10.1093\/nar\/gkab1020","article-title":"DISCO: a database of deeply integrated human single-cell omics data","volume":"50","author":"Li","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025111010421165900_ref18","doi-asserted-by":"publisher","first-page":"1053","DOI":"10.1038\/s41592-018-0229-2","article-title":"Deep generative modeling for single-cell transcriptomics","volume":"15","author":"Lopez","year":"2018","journal-title":"Nat Methods"},{"key":"2025111010421165900_ref19","doi-asserted-by":"publisher","first-page":"1289","DOI":"10.1038\/s41592-019-0619-0","article-title":"Fast, sensitive and accurate integration of single-cell data with harmony","volume":"16","author":"Korsunsky","year":"2019","journal-title":"Nat Methods"},{"key":"2025111010421165900_ref20","doi-asserted-by":"crossref","first-page":"e3529","DOI":"10.1016\/j.cell.2021.04.048","article-title":"Integrated analysis of multimodal single-cell data","volume":"184","author":"Hao","year":"2021","journal-title":"Cell"},{"key":"2025111010421165900_ref21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41421-020-00236-z","article-title":"Single-cell profiling of the human decidual immune microenvironment in patients with recurrent pregnancy loss","volume":"7","author":"Guo","year":"2021","journal-title":"Cell Discov"},{"key":"2025111010421165900_ref22","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1186\/s13059-020-02048-6","article-title":"Systematic assessment of tissue dissociation and storage biases in single-cell and single-nucleus RNA-seq workflows","volume":"21","author":"Denisenko","year":"2020","journal-title":"Genome Biol"},{"key":"2025111010421165900_ref23","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1038\/s41591-021-01323-8","article-title":"A single-cell map of intratumoral changes during anti-PD1 treatment of patients with breast cancer","volume":"27","author":"Bassez","year":"2021","journal-title":"Nat Med"},{"key":"2025111010421165900_ref24","doi-asserted-by":"crossref","first-page":"e1020","DOI":"10.1016\/j.cell.2018.10.038","article-title":"Defining T cell states associated with response to checkpoint immunotherapy in melanoma","volume":"175","author":"Sade-Feldman","year":"2018","journal-title":"Cell"},{"key":"2025111010421165900_ref25","doi-asserted-by":"publisher","volume":"29","journal-title":"Nat Med","DOI":"10.1038\/s41591-023-02327-2"},{"key":"2025111010421165900_ref26","doi-asserted-by":"crossref","first-page":"5233","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci Rep"},{"key":"2025111010421165900_ref27","doi-asserted-by":"publisher","first-page":"110540","DOI":"10.1016\/j.celrep.2022.110540","article-title":"ZFP541 maintains the repression of pre-pachytene transcriptional programs and promotes male meiosis progression","volume":"38","author":"Xu","year":"2022","journal-title":"Cell Rep"},{"key":"2025111010421165900_ref28","doi-asserted-by":"crossref","first-page":"e1612","DOI":"10.1016\/j.molcel.2022.02.034","article-title":"The XRN1-regulated RNA helicase activity of YTHDC2 ensures mouse fertility independently of m(6)a recognition","volume":"82","author":"Li","year":"2022","journal-title":"Mol Cell"},{"key":"2025111010421165900_ref29","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.26116","article-title":"The conserved RNA helicase YTHDC2 regulates the transition from proliferation to differentiation in the germline","volume":"6","author":"Bailey","year":"2017","journal-title":"Elife"},{"key":"2025111010421165900_ref30","doi-asserted-by":"publisher","DOI":"10.7554\/eLife.30919","article-title":"ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2","volume":"7","author":"Jain","year":"2018","journal-title":"Elife"},{"key":"2025111010421165900_ref31","doi-asserted-by":"crossref","first-page":"1758","DOI":"10.1038\/s41467-021-22021-6","article-title":"Nutrient restriction synergizes with retinoic acid to induce mammalian meiotic initiation in vitro","volume":"12","author":"Zhang","year":"2021","journal-title":"Nat Commun"},{"key":"2025111010421165900_ref32","doi-asserted-by":"crossref","first-page":"e1017","DOI":"10.1016\/j.cell.2018.02.001","article-title":"Mapping the mouse cell atlas by microwell-Seq","volume":"172","author":"Han","year":"2018","journal-title":"Cell"},{"key":"2025111010421165900_ref33","doi-asserted-by":"publisher","first-page":"323","DOI":"10.1016\/j.neunet.2020.05.029","article-title":"Energy-efficient and damage-recovery slithering gait design for a snake-like robot based on reinforcement learning and inverse reinforcement learning","volume":"129","author":"Bing","year":"2020","journal-title":"Neural Netw"},{"key":"2025111010421165900_ref34","doi-asserted-by":"crossref","first-page":"832","DOI":"10.1109\/TCDS.2022.3189701","article-title":"Multimodal self-paced locality-preserving learning for diagnosis of Alzheimer\u2019s disease","volume":"15","author":"Hao","year":"2022","journal-title":"IEEE Transactions on Cognitive and Developmental Systems"},{"key":"2025111010421165900_ref35","doi-asserted-by":"publisher","first-page":"126742","DOI":"10.1016\/j.neucom.2023.126742","article-title":"Learning to refine object boundaries","volume":"557","author":"Deng","year":"2023","journal-title":"Neurocomputing"},{"key":"2025111010421165900_ref36","doi-asserted-by":"publisher","first-page":"108661","DOI":"10.1016\/j.knosys.2022.108661","article-title":"Subsampling for partial least-squares regression via an influence function","volume":"245","author":"Xie","year":"2022","journal-title":"Knowledge-Based Systems"},{"key":"2025111010421165900_ref37","doi-asserted-by":"publisher","first-page":"117100","DOI":"10.1016\/j.measurement.2025.117100","article-title":"Multi-scale three-path network (MSTP-net): a new architecture for retinal vessel segmentation","volume":"250","author":"Wang","year":"2025","journal-title":"Measurement"},{"key":"2025111010421165900_ref38","doi-asserted-by":"publisher","first-page":"102361","DOI":"10.1016\/j.inffus.2024.102361","article-title":"A review of cancer data fusion methods based on deep learning","volume":"108","author":"Zhao","year":"2024","journal-title":"Information Fusion"},{"key":"2025111010421165900_ref39","doi-asserted-by":"publisher","first-page":"e0307649","DOI":"10.1371\/journal.pone.0307649","article-title":"DeepDRA: drug repurposing using multi-omics data integration with autoencoders","volume":"19","author":"Mohammadzadeh-Vardin","year":"2024","journal-title":"PloS One"},{"key":"2025111010421165900_ref40","doi-asserted-by":"publisher","first-page":"110442","DOI":"10.1016\/j.compbiomed.2025.110442","article-title":"DFT_ANPD: a dual-feature two-sided attention network for anticancer natural products detection","volume":"194","author":"Norouzi","year":"2025","journal-title":"Comput Biol Med"},{"key":"2025111010421165900_ref41","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1038\/s41587-019-0379-5","article-title":"Droplet scRNA-seq is not zero-inflated","volume":"38","author":"Svensson","year":"2020","journal-title":"Nat Biotechnol"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/6\/bbaf586\/65259385\/bbaf586.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/6\/bbaf586\/65259385\/bbaf586.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,10]],"date-time":"2025-11-10T15:42:32Z","timestamp":1762789352000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf586\/8319947"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,1]]},"references-count":41,"journal-issue":{"issue":"6","published-print":{"date-parts":[[2025,11,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf586","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2025,11]]},"published":{"date-parts":[[2025,11,1]]},"article-number":"bbaf586"}}