{"id":"https://openalex.org/W4317702923","doi":"https://doi.org/10.1093/bib/bbad006","title":"Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing","display_name":"Hierarchical cell-type identifier accurately distinguishes immune-cell subtypes enabling precise profiling of tissue microenvironment with single-cell RNA-sequencing","publication_year":2023,"publication_date":"2023-01-02","ids":{"openalex":"https://openalex.org/W4317702923","doi":"https://doi.org/10.1093/bib/bbad006","pmid":"https://pubmed.ncbi.nlm.nih.gov/36681937"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad006","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad006/48810127/bbad006.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad006/48810127/bbad006.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5037005280","display_name":"Joongho Lee","orcid":"https://orcid.org/0000-0003-4729-9938"},"institutions":[{"id":"https://openalex.org/I89015989","display_name":"Dankook University","ror":"https://ror.org/058pdbn81","country_code":"KR","type":"education","lineage":["https://openalex.org/I89015989"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Joongho Lee","raw_affiliation_strings":["Dept. of Computer Science, College of SW Convergence, Dankook University , Yongin-si, Korea, 16890"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, College of SW Convergence, Dankook University , Yongin-si, Korea, 16890","institution_ids":["https://openalex.org/I89015989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100362670","display_name":"Min\u2010Soo Kim","orcid":"https://orcid.org/0000-0002-7184-4396"},"institutions":[{"id":"https://openalex.org/I89015989","display_name":"Dankook University","ror":"https://ror.org/058pdbn81","country_code":"KR","type":"education","lineage":["https://openalex.org/I89015989"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Minsoo Kim","raw_affiliation_strings":["Dept. of Computer Science, College of SW Convergence, Dankook University , Yongin-si, Korea, 16890"],"affiliations":[{"raw_affiliation_string":"Dept. of Computer Science, College of SW Convergence, Dankook University , Yongin-si, Korea, 16890","institution_ids":["https://openalex.org/I89015989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035847757","display_name":"Keunsoo Kang","orcid":"https://orcid.org/0000-0003-0611-9320"},"institutions":[{"id":"https://openalex.org/I89015989","display_name":"Dankook University","ror":"https://ror.org/058pdbn81","country_code":"KR","type":"education","lineage":["https://openalex.org/I89015989"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Keunsoo Kang","raw_affiliation_strings":["Dept. of Microbiology, College of Natural Sciences, Dankook University , Cheonan-si, Korea, 31116"],"affiliations":[{"raw_affiliation_string":"Dept. of Microbiology, College of Natural Sciences, Dankook University , Cheonan-si, Korea, 31116","institution_ids":["https://openalex.org/I89015989"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051050164","display_name":"Chul\u2010Su Yang","orcid":"https://orcid.org/0000-0003-4918-961X"},"institutions":[{"id":"https://openalex.org/I4575257","display_name":"Hanyang University","ror":"https://ror.org/046865y68","country_code":"KR","type":"education","lineage":["https://openalex.org/I4575257"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Chul-Su Yang","raw_affiliation_strings":["Dept. of Molecular and Life Science, Center for Bionano Intelligence Education and Research, Hanyang University , Ansan, Korea, 15588"],"affiliations":[{"raw_affiliation_string":"Dept. of Molecular and Life Science, Center for Bionano Intelligence Education and Research, Hanyang University , Ansan, Korea, 15588","institution_ids":["https://openalex.org/I4575257"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032164323","display_name":"Seokhyun Yoon","orcid":"https://orcid.org/0000-0002-0464-2233"},"institutions":[{"id":"https://openalex.org/I89015989","display_name":"Dankook University","ror":"https://ror.org/058pdbn81","country_code":"KR","type":"education","lineage":["https://openalex.org/I89015989"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Seokhyun Yoon","raw_affiliation_strings":["Dept. of Electronics & Electrical Eng., College of Engineering, Dankook University , Yongin-si Korea, 16890"],"affiliations":[{"raw_affiliation_string":"Dept. of Electronics & Electrical Eng., College of Engineering, Dankook University , Yongin-si Korea, 16890","institution_ids":["https://openalex.org/I89015989"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032164323"],"corresponding_institution_ids":["https://openalex.org/I89015989"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.2638,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.78939693,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"24","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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":1.0,"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/T11313","display_name":"Immune cells in cancer","score":0.9879000186920166,"subfield":{"id":"https://openalex.org/subfields/2403","display_name":"Immunology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10773","display_name":"Extracellular vesicles in disease","score":0.9760000109672546,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cell-type","display_name":"Cell type","score":0.6445157527923584},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6096839308738708},{"id":"https://openalex.org/keywords/immune-system","display_name":"Immune system","score":0.600139856338501},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.5174946784973145},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49982333183288574},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.4558904767036438},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4263593852519989},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.31252777576446533},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.296161413192749},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24736636877059937},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.16535523533821106}],"concepts":[{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.6445157527923584},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6096839308738708},{"id":"https://openalex.org/C8891405","wikidata":"https://www.wikidata.org/wiki/Q1059","display_name":"Immune system","level":2,"score":0.600139856338501},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.5174946784973145},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49982333183288574},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.4558904767036438},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4263593852519989},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.31252777576446533},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.296161413192749},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24736636877059937},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.16535523533821106},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008264","descriptor_name":"Macrophages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D012313","descriptor_name":"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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad006","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad006/48810127/bbad006.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36681937","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36681937","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10025442","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10025442","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10025442/pdf/bbad006.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad006","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad006","pdf_url":"https://academic.oup.com/bib/advance-article-pdf/doi/10.1093/bib/bbad006/48810127/bbad006.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1715513617","display_name":null,"funder_award_id":"NRF-2021R1A4A5032463","funder_id":"https://openalex.org/F4320322349","funder_display_name":"Ministry of Education, Science and Technology"},{"id":"https://openalex.org/G758694678","display_name":null,"funder_award_id":"NRF-2021M3C1C3097212","funder_id":"https://openalex.org/F4320322349","funder_display_name":"Ministry of Education, Science and Technology"},{"id":"https://openalex.org/G8642129062","display_name":null,"funder_award_id":"NRF-2020R1F1A1066320","funder_id":"https://openalex.org/F4320322349","funder_display_name":"Ministry of Education, Science and Technology"}],"funders":[{"id":"https://openalex.org/F4320322349","display_name":"Ministry of Education, Science and Technology","ror":"https://ror.org/01p262204"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4317702923.pdf"},"referenced_works_count":66,"referenced_works":["https://openalex.org/W1580018887","https://openalex.org/W1972825083","https://openalex.org/W2019552331","https://openalex.org/W2069089843","https://openalex.org/W2078621117","https://openalex.org/W2149573463","https://openalex.org/W2332292689","https://openalex.org/W2516455020","https://openalex.org/W2540833380","https://openalex.org/W2598326928","https://openalex.org/W2610509384","https://openalex.org/W2739492614","https://openalex.org/W2796170779","https://openalex.org/W2800392236","https://openalex.org/W2895456557","https://openalex.org/W2897346235","https://openalex.org/W2901677030","https://openalex.org/W2904478560","https://openalex.org/W2905827542","https://openalex.org/W2907514116","https://openalex.org/W2931036699","https://openalex.org/W2942380588","https://openalex.org/W2945777288","https://openalex.org/W2951506174","https://openalex.org/W2951914955","https://openalex.org/W2954871042","https://openalex.org/W2959295202","https://openalex.org/W2963622568","https://openalex.org/W2964643116","https://openalex.org/W2966569571","https://openalex.org/W2971398276","https://openalex.org/W2971653850","https://openalex.org/W2973034691","https://openalex.org/W2980871623","https://openalex.org/W2995410603","https://openalex.org/W3000676906","https://openalex.org/W3004512212","https://openalex.org/W3006566541","https://openalex.org/W3014185549","https://openalex.org/W3016020856","https://openalex.org/W3082125279","https://openalex.org/W3092982430","https://openalex.org/W3095964485","https://openalex.org/W3096486351","https://openalex.org/W3099862724","https://openalex.org/W3107523488","https://openalex.org/W3114373167","https://openalex.org/W3120038393","https://openalex.org/W3126863866","https://openalex.org/W3128961456","https://openalex.org/W3130453114","https://openalex.org/W3134800749","https://openalex.org/W3163661434","https://openalex.org/W3198511950","https://openalex.org/W3208953781","https://openalex.org/W4205288985","https://openalex.org/W4205574430","https://openalex.org/W4206176282","https://openalex.org/W4221065117","https://openalex.org/W4221088064","https://openalex.org/W4226258199","https://openalex.org/W4243363028","https://openalex.org/W4282838697","https://openalex.org/W6728888212","https://openalex.org/W6775999178","https://openalex.org/W6785161123"],"related_works":["https://openalex.org/W4307993920","https://openalex.org/W1898241694","https://openalex.org/W4390695629","https://openalex.org/W2036616013","https://openalex.org/W3157307916","https://openalex.org/W2141091415","https://openalex.org/W2786822253","https://openalex.org/W2895456557","https://openalex.org/W2101753987","https://openalex.org/W4386916799"],"abstract_inverted_index":{"Single-cell":[0],"RNA-seq":[1],"enabled":[2],"in-depth":[3],"study":[4],"on":[5],"tissue":[6],"micro-environment":[7],"and":[8,38,76,91,101,131,140],"immune-profiling,":[9],"where":[10],"a":[11,54,83],"crucial":[12],"step":[13],"is":[14],"to":[15,32,35],"annotate":[16],"cell":[17],"identity.":[18],"Immune":[19],"cells":[20],"play":[21],"key":[22],"roles":[23],"in":[24,82,99,128,138],"many":[25],"diseases,":[26],"whereas":[27],"their":[28,36],"activities":[29],"are":[30],"hard":[31],"track":[33],"due":[34],"diverse":[37],"highly":[39],"variable":[40],"nature.":[41],"Existing":[42],"cell-type":[43,57],"identifiers":[44],"had":[45],"limited":[46],"performance":[47],"for":[48,63,66,125],"this":[49],"purpose.":[50],"We":[51],"present":[52],"HiCAT,":[53],"hierarchical,":[55],"marker-based":[56],"identifier":[58],"utilising":[59,78],"gene":[60],"set":[61],"analysis":[62],"statistical":[64],"scoring":[65],"given":[67],"markers.":[68],"It":[69],"features":[70,134],"successive":[71],"identification":[72],"of":[73,135],"major-type,":[74],"minor-type":[75,102],"subsets":[77,142],"subset":[79],"markers":[80],"structured":[81],"three-level":[84],"taxonomy":[85],"tree.":[86],"Comparison":[87],"with":[88],"manual":[89],"annotation":[90],"pairwise":[92],"match":[93],"test":[94],"showed":[95],"HiCAT":[96,115,121],"outperforms":[97],"others":[98],"major-":[100],"identification.":[103],"For":[104],"subsets,":[105],"we":[106],"qualitatively":[107],"evaluated":[108],"the":[109,117,136],"marker":[110],"expression":[111],"profile":[112],"demonstrating":[113],"that":[114,143],"provide":[116],"clearest":[118],"immune-cell":[119,126],"landscape.":[120],"was":[122],"also":[123],"used":[124],"profiling":[127],"ulcerative":[129],"colitis":[130],"discovered":[132],"distinct":[133],"disease":[137],"macrophage":[139],"T-cell":[141],"could":[144],"not":[145],"be":[146],"identified":[147],"previously.":[148]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":2}],"updated_date":"2026-03-10T16:38:18.471706","created_date":"2025-10-10T00:00:00"}
