{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T12:19:46Z","timestamp":1784290786290,"version":"3.55.0"},"reference-count":34,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2020,4,30]],"date-time":"2020-04-30T00:00:00Z","timestamp":1588204800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000163","name":"ARC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000163","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Discovery Early Career Researcher Award"},{"name":"DECRA","award":["DE170100759"],"award-info":[{"award-number":["DE170100759"]}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"name":"NHMRC)\/Investigator Grant","award":["1173469"],"award-info":[{"award-number":["1173469"]}]},{"name":"NHMRC\/Career Development Fellowship","award":["1111338"],"award-info":[{"award-number":["1111338"]}]},{"name":"ARC\/Discovery Project","award":["DP170100654"],"award-info":[{"award-number":["DP170100654"]}]},{"name":"Research Training Program"},{"name":"RTP"},{"name":"Chen Family Research Scholarship"},{"name":"ARC Postgraduate Research Scholarship and Children\u2019s Medical Research Institute Postgraduate Scholarship"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,30]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Multi-modal profiling of single cells represents one of the latest technological advancements in molecular biology. Among various single-cell multi-modal strategies, cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) allows simultaneous quantification of two distinct species: RNA and cell-surface proteins. Here, we introduce CiteFuse, a streamlined package consisting of a suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand\u2013receptor interaction analysis and interactive web-based visualization of CITE-seq data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We demonstrate the capacity of CiteFuse to integrate the two data modalities and its relative advantage against data generated from single-modality profiling using both simulations and real-world CITE-seq data. Furthermore, we illustrate a novel doublet detection method based on a combined index of cell hashing and transcriptome data. Finally, we demonstrate CiteFuse for predicting ligand\u2013receptor interactions by using multi-modal CITE-seq data. Collectively, we demonstrate the utility and effectiveness of CiteFuse for the integrative analysis of transcriptome and epitope profiles from CITE-seq data.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>CiteFuse is freely available at http:\/\/shiny.maths.usyd.edu.au\/CiteFuse\/ as an online web service and at https:\/\/github.com\/SydneyBioX\/CiteFuse\/ as an R package.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Contact<\/jats:title>\n                    <jats:p>pengyi.yang@sydney.edu.au<\/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\/btaa282","type":"journal-article","created":{"date-parts":[[2020,4,23]],"date-time":"2020-04-23T07:09:37Z","timestamp":1587625777000},"page":"4137-4143","source":"Crossref","is-referenced-by-count":103,"title":["CiteFuse enables multi-modal analysis of CITE-seq data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1844-3275","authenticated-orcid":false,"given":"Hani Jieun","family":"Kim","sequence":"first","affiliation":[{"name":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"},{"name":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia"},{"name":"Computational Systems Biology Group , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yingxin","family":"Lin","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"},{"name":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thomas A","family":"Geddes","sequence":"additional","affiliation":[{"name":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia"},{"name":"School of Life and Environmental Sciences , Faculty of Science, The University of Sydney, Sydney 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jean Yee Hwa","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"},{"name":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1098-3138","authenticated-orcid":false,"given":"Pengyi","family":"Yang","sequence":"additional","affiliation":[{"name":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"},{"name":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia"},{"name":"Computational Systems Biology Group , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,4,30]]},"reference":[{"key":"2023062304264322500_btaa282-B1","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J. R. Stat. Soc. Ser. B"},{"key":"2023062304264322500_btaa282-B2","doi-asserted-by":"crossref","first-page":"P10008","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"Blondel","year":"2008","journal-title":"J. Stat. Mech. Theory Exp"},{"key":"2023062304264322500_btaa282-B3","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/nbt.3102","article-title":"Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells","volume":"33","author":"Buettner","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023062304264322500_btaa282-B4","first-page":"1","article-title":"The igraph software package for complex network research","volume":"1695","author":"Csardi","year":"2006","journal-title":"InterJ. Compl. Syst"},{"key":"2023062304264322500_btaa282-B5","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1038\/nmeth.4177","article-title":"Pooled CRISPR screening with single-cell transcriptome readout","volume":"14","author":"Datlinger","year":"2017","journal-title":"Nat. Methods"},{"key":"2023062304264322500_btaa282-B6","first-page":"1484","author":"Efremova","year":"2020"},{"key":"2023062304264322500_btaa282-B7","doi-asserted-by":"crossref","first-page":"eaaw8330","DOI":"10.1126\/sciadv.aaw8330","article-title":"Aging promotes reorganization of the CD4 T cell landscape toward extreme regulatory and effector phenotypes","volume":"5","author":"Elyahu","year":"2019","journal-title":"Sci. Adv"},{"key":"2023062304264322500_btaa282-B8","doi-asserted-by":"crossref","first-page":"eaaq0305","DOI":"10.1126\/scitranslmed.aaq0305","article-title":"Mixed-effects association of single cells identifies an expanded effector CD4+ T cell subset in rheumatoid arthritis","volume":"10","author":"Fonseka","year":"2018","journal-title":"Sci. Transl. Med"},{"key":"2023062304264322500_btaa282-B9","doi-asserted-by":"crossref","first-page":"2425","DOI":"10.3389\/fimmu.2018.02425","article-title":"A single-cell sequencing guide for immunologists","volume":"9","author":"Ginhoux","year":"2018","journal-title":"Front. Immunol"},{"key":"2023062304264322500_btaa282-B10","doi-asserted-by":"crossref","first-page":"1458","DOI":"10.1038\/s41587-019-0332-7","article-title":"Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia","volume":"37","author":"Granja","year":"2019","journal-title":"Nat. Biotechnol"},{"key":"2023062304264322500_btaa282-B11","doi-asserted-by":"crossref","first-page":"365","DOI":"10.1186\/1471-2164-10-365","article-title":"Correlations between RNA and protein expression profiles in 23 human cell lines","volume":"10","author":"Gry","year":"2009","journal-title":"BMC Genomics"},{"key":"2023062304264322500_btaa282-B12","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1186\/1471-2172-9-44","article-title":"High-throughput gene expression profiling of memory differentiation in primary human T cells","volume":"9","author":"Haining","year":"2008","journal-title":"BMC Immunol"},{"key":"2023062304264322500_btaa282-B13","doi-asserted-by":"crossref","first-page":"2316","DOI":"10.1093\/bib\/bby076","article-title":"Impact of similarity metrics on single-cell RNA-seq data clustering","volume":"20","author":"Kim","year":"2019","journal-title":"Brief. Bioinform"},{"key":"2023062304264322500_btaa282-B14","doi-asserted-by":"crossref","first-page":"618","DOI":"10.1038\/s41591-020-0769-8","article-title":"Broad immune activation underlies shared set point signatures for vaccine responsiveness in healthy individuals and disease activity in patients with lupus","volume":"26","author":"Kotliarov","year":"2020","journal-title":"Nat. Med"},{"key":"2023062304264322500_btaa282-B15","doi-asserted-by":"crossref","first-page":"9775","DOI":"10.1073\/pnas.1820006116","article-title":"scmerge leverages factor analysis, stable expression, and pseudoreplication to merge multiple single-cell RNA-seq datasets","volume":"116","author":"Lin","year":"2019","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023062304264322500_btaa282-B16","first-page":"535","article-title":"On the dependency of cellular protein levels on mRNA abundance","author":"Liu","year":"2016"},{"key":"2023062304264322500_btaa282-B17","first-page":"2122","article-title":"A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor","volume":"5","author":"Lun","year":"2016","journal-title":"F1000Research"},{"key":"2023062304264322500_btaa282-B18","doi-asserted-by":"crossref","first-page":"519","DOI":"10.1038\/nmeth.3370","article-title":"G&t-seq: parallel sequencing of single-cell genomes and transcriptomes","volume":"12","author":"Macaulay","year":"2015","journal-title":"Nat. Methods"},{"key":"2023062304264322500_btaa282-B19","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1016\/j.cels.2019.03.003","article-title":"DoubletFinder: doublet detection in single-cell RNA sequencing data using artificial nearest neighbors","volume":"8","author":"McGinnis","year":"2019","journal-title":"Cell Syst"},{"key":"2023062304264322500_btaa282-B20","doi-asserted-by":"crossref","first-page":"409","DOI":"10.1038\/s41592-019-0392-0","article-title":"Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells","volume":"16","author":"Mimitou","year":"2019","journal-title":"Nat. Methods"},{"key":"2023062304264322500_btaa282-B21","doi-asserted-by":"crossref","first-page":"1215","DOI":"10.1016\/j.celrep.2017.07.009","article-title":"Single-cell landscape of transcriptional heterogeneity and cell fate decisions during mouse early gastrulation","volume":"20","author":"Mohammed","year":"2017","journal-title":"Cell Rep"},{"key":"2023062304264322500_btaa282-B22","first-page":"849","author":"Ng","year":"2002"},{"key":"2023062304264322500_btaa282-B23","doi-asserted-by":"crossref","first-page":"936","DOI":"10.1038\/nbt.3973","article-title":"Multiplexed quantification of proteins and transcripts in single cells","volume":"35","author":"Peterson","year":"2017","journal-title":"Nat. Biotechnol"},{"key":"2023062304264322500_btaa282-B24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-017-16520-0","article-title":"propr: an r-package for identifying proportionally abundant features using compositional data analysis","volume":"7","author":"Quinn","year":"2017","journal-title":"Sci. Rep"},{"key":"2023062304264322500_btaa282-B25","doi-asserted-by":"crossref","first-page":"495","DOI":"10.1038\/nbt.3192","article-title":"Spatial reconstruction of single-cell gene expression data","volume":"33","author":"Satija","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023062304264322500_btaa282-B26","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1038\/nmeth.4380","article-title":"Simultaneous epitope and transcriptome measurement in single cells","volume":"14","author":"Stoeckius","year":"2017","journal-title":"Nat. Methods"},{"key":"2023062304264322500_btaa282-B27","doi-asserted-by":"crossref","first-page":"224","DOI":"10.1186\/s13059-018-1603-1","article-title":"Cell hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics","volume":"19","author":"Stoeckius","year":"2018","journal-title":"Genome Biol"},{"key":"2023062304264322500_btaa282-B28","doi-asserted-by":"crossref","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2023062304264322500_btaa282-B29","doi-asserted-by":"crossref","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":"2023062304264322500_btaa282-B30","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1038\/nmeth.2810","article-title":"Similarity network fusion for aggregating data types on a genomic scale","volume":"11","author":"Wang","year":"2014","journal-title":"Nat. Methods"},{"key":"2023062304264322500_btaa282-B31","doi-asserted-by":"crossref","first-page":"414","DOI":"10.1038\/nmeth.4207","article-title":"Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning","volume":"14","author":"Wang","year":"2017","journal-title":"Nat. Methods"},{"key":"2023062304264322500_btaa282-B32","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1016\/j.cels.2018.11.005","article-title":"Scrublet: computational identification of cell doublets in single-cell transcriptomic data","volume":"8","author":"Wolock","year":"2019","journal-title":"Cell Syst"},{"key":"2023062304264322500_btaa282-B33","doi-asserted-by":"crossref","first-page":"2611","DOI":"10.1038\/s41467-019-10500-w","article-title":"Simulating multiple faceted variability in single cell RNA sequencing","volume":"10","author":"Zhang","year":"2019","journal-title":"Nat. Commun"},{"key":"2023062304264322500_btaa282-B34","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1038\/nprot.2015.020","article-title":"Palladium-based mass tag cell barcoding with a doublet-filtering scheme and single-cell deconvolution algorithm","volume":"10","author":"Zunder","year":"2015","journal-title":"Nat. Protoc"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa282\/33494850\/btaa282.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/14\/4137\/50677425\/btaa282.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/14\/4137\/50677425\/btaa282.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,8,4]],"date-time":"2024-08-04T11:30:12Z","timestamp":1722771012000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/14\/4137\/5827474"}},"subtitle":[],"editor":[{"given":"Anthony","family":"Mathelier","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2020,4,30]]},"references-count":34,"journal-issue":{"issue":"14","published-print":{"date-parts":[[2020,7,30]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa282","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/854299","asserted-by":"object"}]},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,7,15]]},"published":{"date-parts":[[2020,4,30]]}}}