{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T07:17:30Z","timestamp":1784099850415,"version":"3.55.0"},"reference-count":62,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2023,1,9]],"date-time":"2023-01-09T00:00:00Z","timestamp":1673222400000},"content-version":"vor","delay-in-days":8,"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":["62072374"],"award-info":[{"award-number":["62072374"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61772426"],"award-info":[{"award-number":["61772426"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Single-cell multimodal assays allow us to simultaneously measure two different molecular features of the same cell, enabling new insights into cellular heterogeneity, cell development and diseases. However, most existing methods suffer from inaccurate dimensionality reduction for the joint-modality data, hindering their discovery of novel or rare cell subpopulations.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Here, we present VIMCCA, a computational framework based on variational-assisted multi-view canonical correlation analysis to integrate paired multimodal single-cell data. Our statistical model uses a common latent variable to interpret the common source of variances in two different data modalities. Our approach jointly learns an inference model and two modality-specific non-linear models by leveraging variational inference and deep learning. We perform VIMCCA and compare it with 10 existing state-of-the-art algorithms on four paired multi-modal datasets sequenced by different protocols. Results demonstrate that VIMCCA facilitates integrating various types of joint-modality data, thus leading to more reliable and accurate downstream analysis. VIMCCA improves our ability to identify novel or rare cell subtypes compared to existing widely used methods. Besides, it can also facilitate inferring cell lineage based on joint-modality profiles.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The VIMCCA algorithm has been implemented in our toolkit package scbean (\u22650.5.0), and its code has been archived at https:\/\/github.com\/jhu99\/scbean under MIT license.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad005","type":"journal-article","created":{"date-parts":[[2023,1,6]],"date-time":"2023-01-06T17:30:27Z","timestamp":1673026227000},"source":"Crossref","is-referenced-by-count":22,"title":["A multi-view latent variable model reveals cellular heterogeneity in complex tissues for paired multimodal single-cell data"],"prefix":"10.1093","volume":"39","author":[{"given":"Yuwei","family":"Wang","sequence":"first","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Shaanxi 710129, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bin","family":"Lian","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Shaanxi 710129, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haohui","family":"Zhang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Shaanxi 710129, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuanke","family":"Zhong","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Shaanxi 710129, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jie","family":"He","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, School of Public Health, Peking University Health Science Center , Beijing 100191, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fashuai","family":"Wu","sequence":"additional","affiliation":[{"name":"Department of Orthopaedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology , Wuhan 430022, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Knut","family":"Reinert","sequence":"additional","affiliation":[{"name":"Institut f\u00fcr Informatik, Freie Universit\u00e4t Berlin , 14195 Berlin, Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xuequn","family":"Shang","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Shaanxi 710129, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Life Science, Northwestern Polytechnical University , Shaanxi 710072, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3351-8020","authenticated-orcid":false,"given":"Jialu","family":"Hu","sequence":"additional","affiliation":[{"name":"School of Computer Science, Northwestern Polytechnical University , Shaanxi 710129, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,1,9]]},"reference":[{"key":"2023012019094730100_btad005-B1","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1186\/s13059-020-02015-1","article-title":"MOFA+: a statistical framework for comprehensive integration of multi-modal single-cell data","volume":"21","author":"Argelaguet","year":"2020","journal-title":"Genome Biol"},{"key":"2023012019094730100_btad005-B2","doi-asserted-by":"crossref","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 Rep. 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