{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T15:10:10Z","timestamp":1759158610830,"version":"3.44.0"},"reference-count":60,"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\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82571316"],"award-info":[{"award-number":["82571316"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007128","name":"Natural Science Foundation of Shaanxi Province","doi-asserted-by":"publisher","award":["2024JC-YBMS-783"],"award-info":[{"award-number":["2024JC-YBMS-783"]}],"id":[{"id":"10.13039\/501100007128","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["xzy012022087"],"award-info":[{"award-number":["xzy012022087"]}],"id":[{"id":"10.13039\/501100012226","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>Single-cell ATAC-seq (scATAC-seq) technology allows the interrogation of chromatin accessibility of individual cells. Dropout events occur while the sequencing data signals at some bona fide chromatin sites of individuals are not captured, and the curse of these dropouts in scATAC-seq data inevitably hinders downstream analysis. It remains a challenge to impute scATAC-seq data due to its high dimensionality, sparsity, and near-binarization properties. Herein, we propose IMATAC, a deep hierarchical network with denoising autoencoder for imputing scATAC-seq data in the form of peak by cell. The network embeds scATAC-seq data into a latent space by a deep hierarchical architecture at two different levels, including bottom level for local details and top level for global information, that helps to characterize the high-dimensional sparse scATAC-seq data. Besides, it is encouraged to learn to reconstruct the original scATAC-seq data from an artificially corrupted version through a denoising autoencoder, so as to acquire an ability to recover the missing values primarily relying on the cells under the same population with the help of a parallel multi-classifier. Using simulated and experimental data, the performance of IMATAC is demonstrated by a comparative analysis with the other competing methods. The results suggest that our method can achieve lower imputation errors, and benefit the downstream analysis, including heterogeneous clustering, differential analysis, and regulatory element discovery. Besides, the contributions of several important network modules in our IMATAC are investigated, and how well it can separate the dropout zeros from biological zeros are discussed.<\/jats:p>","DOI":"10.1093\/bib\/bbaf515","type":"journal-article","created":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T14:37:25Z","timestamp":1759156645000},"source":"Crossref","is-referenced-by-count":0,"title":["IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder"],"prefix":"10.1093","volume":"26","author":[{"given":"Yao","family":"Li","sequence":"first","affiliation":[{"name":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5061-4762","authenticated-orcid":false,"given":"Hongqiang","family":"Lyu","sequence":"additional","affiliation":[{"name":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kexin","family":"Li","sequence":"additional","affiliation":[{"name":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuan","family":"Liu","sequence":"additional","affiliation":[{"name":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xinman","family":"Zhang","sequence":"additional","affiliation":[{"name":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ze","family":"Liu","sequence":"additional","affiliation":[{"name":"College of Water Resources and Architectural Engineering, Northwest A&F University , No. 3 Taicheng Road, Yangling District, Xianyang, Shaanxi 712100 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pengcheng","family":"Jing","sequence":"additional","affiliation":[{"name":"Faculty of Electronic and Information Engineering, School of Automation Science and Engineering, Xi'an Jiaotong University , No. 28 Xianning West Road, Beilin District, Xi'an, Shaanxi 710049 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Peng","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Otorhinolaryngology\u2014Head and Neck Surgery, The First Affiliated Hospital, Xi'an Jiaotong University , No. 277 West Yanta Road, Yanta District, Xi'an, Shaanxi 710061 ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,9,29]]},"reference":[{"key":"2025092910371635000_ref1","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.cell.2007.12.014","article-title":"High-resolution mapping and characterization of open chromatin across the genome","volume":"132","author":"Boyle","year":"2008","journal-title":"Cell"},{"key":"2025092910371635000_ref2","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/s41576-018-0089-8","article-title":"Chromatin accessibility and the regulatory epigenome","volume":"20","author":"Klemm","year":"2019","journal-title":"Nat Rev Genet"},{"key":"2025092910371635000_ref3","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1101\/gr.4074106","article-title":"Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)","volume":"16","author":"Crawford","year":"2006","journal-title":"Genome Res"},{"key":"2025092910371635000_ref4","doi-asserted-by":"publisher","first-page":"823","DOI":"10.1016\/j.cell.2007.05.009","article-title":"High-resolution profiling of histone methylations in the human genome","volume":"129","author":"Barski","year":"2007","journal-title":"Cell"},{"key":"2025092910371635000_ref5","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1016\/j.ymeth.2009.03.003","article-title":"Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (formaldehyde assisted isolation of regulatory elements)","volume":"48","author":"Giresi","year":"2009","journal-title":"Methods"},{"key":"2025092910371635000_ref6","doi-asserted-by":"publisher","first-page":"1213","DOI":"10.1038\/nmeth.2688","article-title":"Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin","volume":"10","author":"Buenrostro","year":"2013","journal-title":"DNA-binding proteins and nucleosome position, Nature Methods"},{"key":"2025092910371635000_ref7","doi-asserted-by":"publisher","first-page":"2497","DOI":"10.1101\/gr.143008.112","article-title":"Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules","volume":"22","author":"Kelly","year":"2012","journal-title":"Genome Res"},{"key":"2025092910371635000_ref8","doi-asserted-by":"publisher","first-page":"E3457","DOI":"10.1073\/pnas.1424804112","article-title":"MPE-seq, a new method for the genome-wide analysis of chromatin structure","volume":"112","author":"Ishii","year":"2015","journal-title":"Proc Natl Acad Sci"},{"key":"2025092910371635000_ref9","doi-asserted-by":"publisher","first-page":"1518","DOI":"10.1038\/s41596-022-00692-9","article-title":"Chromatin accessibility profiling by ATAC-seq","volume":"17","author":"Grandi","year":"2022","journal-title":"Nat Protoc"},{"key":"2025092910371635000_ref10","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1186\/1756-8935-7-33","article-title":"Chromatin accessibility: a window into the genome","volume":"7","author":"Tsompana","year":"2014","journal-title":"Epigenetics Chromatin"},{"key":"2025092910371635000_ref11","doi-asserted-by":"publisher","first-page":"486","DOI":"10.1038\/nature14590","article-title":"Single-cell chromatin accessibility reveals principles of regulatory variation","volume":"523","author":"Buenrostro","year":"2015","journal-title":"Nature"},{"key":"2025092910371635000_ref12","doi-asserted-by":"publisher","first-page":"910","DOI":"10.1126\/science.aab1601","article-title":"Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing","volume":"348","author":"Cusanovich","year":"2015","journal-title":"Science"},{"key":"2025092910371635000_ref13","doi-asserted-by":"publisher","first-page":"4084","DOI":"10.1038\/s41596-021-00583-5","article-title":"A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility","volume":"16","author":"Xu","year":"2021","journal-title":"Nat Protoc"},{"key":"2025092910371635000_ref14","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1186\/s13059-019-1854-5","article-title":"Assessment of computational methods for the analysis of single-cell ATAC-seq data","volume":"20","author":"Chen","year":"2019","journal-title":"Genome Biol"},{"key":"2025092910371635000_ref15","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbab442","article-title":"Are dropout imputation methods for scRNA-seq effective for scATAC-seq data?","volume":"23","author":"Liu","year":"2022","journal-title":"Brief Bioinform"},{"key":"2025092910371635000_ref16","doi-asserted-by":"publisher","first-page":"e2309554","DOI":"10.1002\/advs.202309554","article-title":"Single-cell chromatin accessibility analysis reveals subgroup-specific TF-NTR regulatory circuits in medulloblastoma","volume":"11","author":"Gao","year":"2024","journal-title":"Advanced Science"},{"key":"2025092910371635000_ref17","doi-asserted-by":"publisher","DOI":"10.1093\/bib\/bbae093","article-title":"Incorporating network diffusion and peak location information for better single-cell ATAC-seq data analysis","volume":"25","author":"Yu","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025092910371635000_ref18","doi-asserted-by":"crossref","first-page":"bbad447","DOI":"10.1093\/bib\/bbad447","article-title":"scATAC-seq preprocessing and imputation evaluation system for visualization, clustering and digital footprinting","volume":"25","author":"Akhtyamov","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025092910371635000_ref19","doi-asserted-by":"publisher","first-page":"bbad216","DOI":"10.1093\/bib\/bbad216","article-title":"scDFC: a deep fusion clustering method for single-cell RNA-seq data","volume":"24","author":"Hu","year":"2023","journal-title":"Brief Bioinform"},{"key":"2025092910371635000_ref20","doi-asserted-by":"publisher","first-page":"4576","DOI":"10.1038\/s41467-019-12630-7","article-title":"SCALE method for single-cell ATAC-seq analysis via latent feature extraction","volume":"10","author":"Xiong","year":"2019","journal-title":"Nat Commun"},{"key":"2025092910371635000_ref21","doi-asserted-by":"publisher","first-page":"6386","DOI":"10.1038\/s41467-021-26530-2","article-title":"Chromatin-accessibility estimation from single-cell ATAC-seq data with scOpen","volume":"12","author":"Li","year":"2021","journal-title":"Nat Commun"},{"key":"2025092910371635000_ref22","doi-asserted-by":"publisher","first-page":"i317","DOI":"10.1093\/bioinformatics\/btab303","article-title":"SAILER: scalable and accurate invariant representation learning for single-cell ATAC-seq processing and integration","volume":"37","author":"Cao","year":"2021","journal-title":"Bioinformatics"},{"key":"2025092910371635000_ref23","doi-asserted-by":"publisher","first-page":"100182","DOI":"10.1016\/j.crmeth.2022.100182","article-title":"PeakVI: a deep generative model for single-cell chromatin accessibility analysis","volume":"2","author":"Ashuach","year":"2022","journal-title":"Cell Reports Methods"},{"key":"2025092910371635000_ref24","doi-asserted-by":"publisher","first-page":"1629","DOI":"10.1038\/s41467-024-46045-w","article-title":"scCASE: accurate and interpretable enhancement for single-cell chromatin accessibility sequencing data","volume":"15","author":"Tang","year":"2024","journal-title":"Nat Commun"},{"key":"2025092910371635000_ref25","doi-asserted-by":"publisher","first-page":"716","DOI":"10.1016\/j.cell.2018.05.061","article-title":"Recovering gene interactions from single-cell data using data diffusion","volume":"174","author":"Dijk","year":"2018","journal-title":"Cell"},{"key":"2025092910371635000_ref26","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1038\/s41592-018-0033-z","article-title":"SAVER: gene expression recovery for single-cell RNA sequencing","volume":"15","author":"Huang","year":"2018","journal-title":"Nat Methods"},{"key":"2025092910371635000_ref27","doi-asserted-by":"publisher","first-page":"997","DOI":"10.1038\/s41467-018-03405-7","article-title":"An accurate and robust imputation method scImpute for single-cell RNA-seq data","volume":"9","author":"Li","year":"2018","journal-title":"Nat Commun"},{"key":"2025092910371635000_ref28","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/s13059-019-1837-6","article-title":"DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data","volume":"20","author":"Arisdakessian","year":"2019","journal-title":"Genome Biol"},{"key":"2025092910371635000_ref29","doi-asserted-by":"crossref","first-page":"4021","DOI":"10.1093\/bioinformatics\/btaa278","article-title":"PRIME: a probabilistic imputation method to reduce dropout effects in single-cell RNA sequencing","volume":"36","author":"Jeong","year":"2020","journal-title":"Bioinformatics"},{"key":"2025092910371635000_ref30","doi-asserted-by":"publisher","first-page":"1174","DOI":"10.1093\/bioinformatics\/btz726","article-title":"bayNorm: Bayesian gene expression recovery, imputation and normalization for single-cell RNA-sequencing data","volume":"36","author":"Tang","year":"2020","journal-title":"Bioinformatics"},{"key":"2025092910371635000_ref31","first-page":"217737","volume-title":"K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data","author":"Wagner","year":"2017"},{"volume-title":"2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","author":"Zhong","first-page":"182","key":"2025092910371635000_ref32"},{"key":"2025092910371635000_ref33","doi-asserted-by":"publisher","first-page":"btad453","DOI":"10.1093\/bioinformatics\/btad453","article-title":"simCAS: an embedding-based method for simulating single-cell chromatin accessibility sequencing data","volume":"39","author":"Li","year":"2023","journal-title":"Bioinformatics"},{"key":"2025092910371635000_ref34","doi-asserted-by":"publisher","first-page":"1535","DOI":"10.1016\/j.cell.2018.03.074","article-title":"Integrated single-cell analysis maps the continuous regulatory landscape of human hematopoietic differentiation","volume":"173","author":"Buenrostro","year":"2018","journal-title":"Cell"},{"key":"2025092910371635000_ref35","doi-asserted-by":"crossref","first-page":"5345","DOI":"10.1038\/s41467-018-07771-0","article-title":"A rapid and robust method for single cell chromatin accessibility profiling","volume":"9","author":"Chen","year":"2018","journal-title":"Nat Commun"},{"key":"2025092910371635000_ref36","first-page":"496521","article-title":"Improved peak-calling with MACS2","author":"Gaspar","year":"2018","journal-title":"BioRxiv"},{"key":"2025092910371635000_ref37","doi-asserted-by":"publisher","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"2025092910371635000_ref38a","doi-asserted-by":"publisher","first-page":"264","DOI":"10.1016\/j.compbiomed.2017.08.021","article-title":"A filter feature selection method based on the Maximal Information Coefficient and Gram-Schmidt Orthogonalization for biomedical data mining","volume":"89","author":"Lyu","year":"2017","journal-title":"Computers in Biology and Medicine"},{"key":"2025092910371635000_ref38","doi-asserted-by":"publisher","first-page":"bbae483","DOI":"10.1093\/bib\/bbae483","article-title":"scEGG: an exogenous gene-guided clustering method for single-cell transcriptomic data","volume":"25","author":"Hu","year":"2024","journal-title":"Brief Bioinform"},{"key":"2025092910371635000_ref39","doi-asserted-by":"publisher","first-page":"4448","DOI":"10.1109\/TFUZZ.2024.3399740","article-title":"High-order topology for deep single-cell Multiview fuzzy clustering","volume":"32","author":"Hu","year":"2024","journal-title":"IEEE Trans Fuzzy Syst"},{"author":"Kingma","key":"2025092910371635000_ref40"},{"key":"2025092910371635000_ref41","doi-asserted-by":"publisher","first-page":"94","DOI":"10.1186\/s13059-020-02008-0","article-title":"scATAC-pro: a comprehensive workbench for single-cell chromatin accessibility sequencing data","volume":"21","author":"Yu","year":"2020","journal-title":"Genome Biol"},{"key":"2025092910371635000_ref42","doi-asserted-by":"publisher","first-page":"2382","DOI":"10.1093\/bioinformatics\/btv145","article-title":"ChIPseeker: an R\/Bioconductor package for ChIP peak annotation, comparison and visualization","volume":"31","author":"Yu","year":"2015","journal-title":"Bioinformatics"},{"key":"2025092910371635000_ref43","doi-asserted-by":"publisher","first-page":"W774","DOI":"10.1093\/nar\/gkac238","article-title":"WashU epigenome browser update 2022","volume":"50","author":"Li","year":"2022","journal-title":"Nucleic Acids Res"},{"key":"2025092910371635000_ref44","doi-asserted-by":"publisher","first-page":"978","DOI":"10.1016\/j.bbrc.2006.12.155","article-title":"The suppression of zfpm-1 accelerates the erythropoietic differentiation of human CD34+ cells","volume":"353","author":"Yang","year":"2007","journal-title":"Biochem Biophys Res Commun"},{"key":"2025092910371635000_ref45","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1158\/1541-7786.MCR-07-2115","article-title":"Cell cycle regulator gene CDC5L, a potential target for 6p12-p21 amplicon in osteosarcoma","volume":"6","author":"Lu","year":"2008","journal-title":"Mol Cancer Res"},{"key":"2025092910371635000_ref46","doi-asserted-by":"publisher","first-page":"495","DOI":"10.1038\/nbt.1630","article-title":"GREAT improves functional interpretation of cis-regulatory regions","volume":"28","author":"McLean","year":"2010","journal-title":"Nat Biotechnol"},{"key":"2025092910371635000_ref47","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1038\/s41421-020-00213-6","article-title":"Characterization and generation of human definitive multipotent hematopoietic stem\/progenitor cells","volume":"6","author":"Zhu","year":"2020","journal-title":"Cell Discovery"},{"key":"2025092910371635000_ref48","doi-asserted-by":"publisher","first-page":"477","DOI":"10.1039\/C5MB00663E","article-title":"ReactomePA: an R\/Bioconductor package for reactome pathway analysis and visualization","volume":"12","author":"Yu","year":"2016","journal-title":"Mol Biosyst"},{"key":"2025092910371635000_ref49","first-page":"2:3","article-title":"clusterProfiler 4.0: a universal enrichment tool for interpreting omics data, the","author":"Wu","year":"2021","journal-title":"Innovation"},{"key":"2025092910371635000_ref50","doi-asserted-by":"publisher","first-page":"600","DOI":"10.3109\/10799893.2015.1030412","article-title":"Signaling pathway of MAPK\/ERK in cell proliferation, differentiation, migration, senescence and apoptosis","volume":"35","author":"Sun","year":"2015","journal-title":"Journal of Receptors and Signal Transduction"},{"key":"2025092910371635000_ref51","first-page":"156","article-title":"Signaling pathways implicated in hematopoietic progenitor cell proliferation and differentiation","volume":"232","author":"Bugarski","year":"2007","journal-title":"Exp Biol Med"},{"key":"2025092910371635000_ref52","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.1038\/s41592-021-01282-5","article-title":"Single-cell chromatin state analysis with Signac","volume":"18","author":"Stuart","year":"2021","journal-title":"Nat Methods"},{"key":"2025092910371635000_ref53","doi-asserted-by":"publisher","first-page":"D87","DOI":"10.1093\/nar\/gkz1001","article-title":"JASPAR 2020: update of the open-access database of transcription factor binding profiles","volume":"48","author":"Fornes","year":"2020","journal-title":"Nucleic Acids Res"},{"key":"2025092910371635000_ref54","doi-asserted-by":"publisher","first-page":"E4513","DOI":"10.1073\/pnas.1406985111","article-title":"Mapping of transcription factor motifs in active chromatin identifies IRF5 as key regulator in classical Hodgkin lymphoma","volume":"111","author":"Kreher","year":"2014","journal-title":"Proc Natl Acad Sci"},{"key":"2025092910371635000_ref55","doi-asserted-by":"publisher","first-page":"15","DOI":"10.32607\/20758251-2018-10-1-15-23","article-title":"The role of TAL1 in hematopoiesis and leukemogenesis","volume":"10","author":"Vagapova","year":"2018","journal-title":"Acta Naturae (\u0430\u043d\u0433\u043b\u043e\u044f\u0437\u044b\u0447\u043d\u0430\u044f \u0432\u0435\u0440\u0441\u0438\u044f)"},{"key":"2025092910371635000_ref56","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1189\/jlb.1RU1215-539R","article-title":"Role of the reprogramming factor KLF4 in blood formation","volume":"99","author":"Park","year":"2016","journal-title":"J Leukoc Biol"},{"key":"2025092910371635000_ref57","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/s13287-021-02181-4","article-title":"Melatonin activates ABCA1 via the BiP\/NRF1 pathway to suppress high-cholesterol-induced apoptosis of mesenchymal stem cells","volume":"12","author":"Kim","year":"2021","journal-title":"Stem Cell Research & Therapy"},{"key":"2025092910371635000_ref58","doi-asserted-by":"publisher","first-page":"2206","DOI":"10.1172\/JCI91363","article-title":"The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes","volume":"127","author":"Yip","year":"2017","journal-title":"J Clin Invest"},{"key":"2025092910371635000_ref59","doi-asserted-by":"publisher","first-page":"192","DOI":"10.1038\/s41467-021-27729-z","article-title":"Zero-preserving imputation of single-cell RNA-seq data","volume":"13","author":"Linderman","year":"2022","journal-title":"Nat Commun"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/5\/bbaf515\/64427494\/bbaf515.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/26\/5\/bbaf515\/64427494\/bbaf515.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,9,29]],"date-time":"2025-09-29T14:37:37Z","timestamp":1759156657000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbaf515\/8267888"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,8,31]]},"references-count":60,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2025,8,31]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbaf515","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"type":"print","value":"1467-5463"},{"type":"electronic","value":"1477-4054"}],"subject":[],"published-other":{"date-parts":[[2025,9]]},"published":{"date-parts":[[2025,8,31]]},"article-number":"bbaf515"}}