{"id":"https://openalex.org/W3023456235","doi":"https://doi.org/10.1093/bioinformatics/btaa282","title":"CiteFuse enables multi-modal analysis of CITE-seq data","display_name":"CiteFuse enables multi-modal analysis of CITE-seq data","publication_year":2020,"publication_date":"2020-04-23","ids":{"openalex":"https://openalex.org/W3023456235","doi":"https://doi.org/10.1093/bioinformatics/btaa282","mag":"3023456235","pmid":"https://pubmed.ncbi.nlm.nih.gov/32353146"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa282","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa282","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5047305525","display_name":"Hani Jieun Kim","orcid":"https://orcid.org/0000-0003-1844-3275"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Hani Jieun Kim","raw_affiliation_strings":["Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","Computational Systems Biology Group , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia","School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"],"raw_orcid":"https://orcid.org/0000-0003-1844-3275","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Computational Systems Biology Group , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia","institution_ids":["https://openalex.org/I129604602","https://openalex.org/I146584863"]},{"raw_affiliation_string":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033771420","display_name":"Yingxin Lin","orcid":"https://orcid.org/0000-0002-4299-7326"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Yingxin Lin","raw_affiliation_strings":["Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027331706","display_name":"Thomas A. Geddes","orcid":null},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas A Geddes","raw_affiliation_strings":["Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","School of Life and Environmental Sciences , Faculty of Science, The University of Sydney, Sydney 2006, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Life and Environmental Sciences , Faculty of Science, The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028524705","display_name":"Jean Yang","orcid":"https://orcid.org/0000-0002-5271-2603"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jean Yee Hwa Yang","raw_affiliation_strings":["Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114375167","display_name":"Pengyi Yang","orcid":"https://orcid.org/0000-0003-1098-3138"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"The University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]},{"id":"https://openalex.org/I146584863","display_name":"Children's Medical Research Institute","ror":"https://ror.org/01bsaey45","country_code":"AU","type":"facility","lineage":["https://openalex.org/I146584863"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Pengyi Yang","raw_affiliation_strings":["Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","Computational Systems Biology Group , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia","School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia"],"raw_orcid":"https://orcid.org/0000-0003-1098-3138","affiliations":[{"raw_affiliation_string":"Charles Perkins Centre , The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"Computational Systems Biology Group , Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Sydney 2145, Australia","institution_ids":["https://openalex.org/I129604602","https://openalex.org/I146584863"]},{"raw_affiliation_string":"School of Mathematics and Statistics , Faculty of Science, The University of Sydney, Sydney 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5114375167"],"corresponding_institution_ids":["https://openalex.org/I129604602","https://openalex.org/I146584863"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":5.2931,"has_fulltext":false,"cited_by_count":116,"citation_normalized_percentile":{"value":0.97001786,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"36","issue":"14","first_page":"4137","last_page":"4143"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9970999956130981,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0006000000284984708,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/modal","display_name":"Modal","score":0.6510838866233826},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6373081207275391},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3220129609107971}],"concepts":[{"id":"https://openalex.org/C71139939","wikidata":"https://www.wikidata.org/wiki/Q910194","display_name":"Modal","level":2,"score":0.6510838866233826},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6373081207275391},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3220129609107971},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C188027245","wikidata":"https://www.wikidata.org/wiki/Q750446","display_name":"Polymer chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000939","descriptor_name":"Epitopes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btaa282","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa282","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32353146","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32353146","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320334705","display_name":"National Health and Medical Research Council","ror":"https://ror.org/011kf5r70"},{"id":"https://openalex.org/F4320338275","display_name":"Division of Arctic Sciences","ror":"https://ror.org/02trddg58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1970170720","https://openalex.org/W1987219048","https://openalex.org/W2010653277","https://openalex.org/W2069089843","https://openalex.org/W2090461073","https://openalex.org/W2100615186","https://openalex.org/W2110065044","https://openalex.org/W2131681506","https://openalex.org/W2161859073","https://openalex.org/W2340761255","https://openalex.org/W2540833380","https://openalex.org/W2577994754","https://openalex.org/W2739492614","https://openalex.org/W2741536364","https://openalex.org/W2752426001","https://openalex.org/W2785085486","https://openalex.org/W2785509713","https://openalex.org/W2817838603","https://openalex.org/W2888562574","https://openalex.org/W2896246287","https://openalex.org/W2897921044","https://openalex.org/W2900144939","https://openalex.org/W2939422961","https://openalex.org/W2942108345","https://openalex.org/W2949177718","https://openalex.org/W2951271761","https://openalex.org/W2953151710","https://openalex.org/W2953251392","https://openalex.org/W2969244270","https://openalex.org/W2991023348","https://openalex.org/W3007282081","https://openalex.org/W3023856724","https://openalex.org/W3099768174","https://openalex.org/W6608852248","https://openalex.org/W6703958248","https://openalex.org/W6728888212"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2051487156","https://openalex.org/W2073681303","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109"],"abstract_inverted_index":{"MOTIVATION:":[0],"Multi-modal":[1],"profiling":[2,101],"of":[3,8,23,33,49,52,76,84,122,148,154],"single":[4],"cells":[5],"represents":[6],"one":[7],"the":[9,82,88,144,151],"latest":[10],"technological":[11],"advancements":[12],"in":[13],"molecular":[14],"biology.":[15],"Among":[16],"various":[17],"single-cell":[18],"multi-modal":[19,138],"strategies,":[20],"cellular":[21],"indexing":[22],"transcriptomes":[24],"and":[25,38,62,72,92,105,125,146,156,176],"epitopes":[26],"by":[27,136],"sequencing":[28],"(CITE-seq)":[29],"allows":[30],"simultaneous":[31],"quantification":[32],"two":[34,89],"distinct":[35],"species:":[36],"RNA":[37,61],"cell-surface":[39],"proteins.":[40],"Here,":[41],"we":[42,110,129,142],"introduce":[43],"CiteFuse,":[44],"a":[45,50,112,119],"streamlined":[46],"package":[47],"consisting":[48],"suite":[51],"tools":[53],"for":[54,132,150],"doublet":[55,114],"detection,":[56],"modality":[57],"integration,":[58],"clustering,":[59],"differential":[60],"protein":[63],"expression":[64],"analysis,":[65],"antibody-derived":[66],"tag":[67],"evaluation,":[68],"ligand-receptor":[69,134],"interaction":[70],"analysis":[71,153],"interactive":[73],"web-based":[74],"visualization":[75],"CITE-seq":[77,107,139,160],"data.":[78,108,127,140,161],"RESULTS:":[79],"We":[80],"demonstrate":[81,130,143],"capacity":[83],"CiteFuse":[85,131,149,165],"to":[86],"integrate":[87],"data":[90,97,188],"modalities":[91],"its":[93],"relative":[94],"advantage":[95],"against":[96],"generated":[98],"from":[99,159],"single-modality":[100],"using":[102,137],"both":[103],"simulations":[104],"real-world":[106],"Furthermore,":[109],"illustrate":[111],"novel":[113],"detection":[115],"method":[116],"based":[117],"on":[118],"combined":[120],"index":[121],"cell":[123],"hashing":[124],"transcriptome":[126,155],"Finally,":[128],"predicting":[133],"interactions":[135],"Collectively,":[141],"utility":[145],"effectiveness":[147],"integrative":[152],"epitope":[157],"profiles":[158],"AVAILABILITY":[162],"AND":[163],"IMPLEMENTATION:":[164],"is":[166],"freely":[167],"available":[168,190],"at":[169,177,191],"http://shiny.maths.usyd.edu.au/CiteFuse/":[170],"as":[171,179],"an":[172,180],"online":[173],"web":[174],"service":[175],"https://github.com/SydneyBioX/CiteFuse/":[178],"R":[181],"package.":[182],"CONTACT:":[183],"pengyi.yang@sydney.edu.au.":[184],"SUPPLEMENTARY":[185],"INFORMATION:":[186],"Supplementary":[187],"are":[189],"Bioinformatics":[192],"online.":[193]},"counts_by_year":[{"year":2026,"cited_by_count":13},{"year":2025,"cited_by_count":17},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":27},{"year":2022,"cited_by_count":20},{"year":2021,"cited_by_count":21},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
