{"id":"https://openalex.org/W4310107759","doi":"https://doi.org/10.1182/blood-2022-162180","title":"Harmonizing the Annotation of Hematopoietic Populations in Single-Cell Atlases with the Cell Marker Accordion","display_name":"Harmonizing the Annotation of Hematopoietic Populations in Single-Cell Atlases with the Cell Marker Accordion","publication_year":2022,"publication_date":"2022-11-15","ids":{"openalex":"https://openalex.org/W4310107759","doi":"https://doi.org/10.1182/blood-2022-162180"},"language":"en","primary_location":{"id":"doi:10.1182/blood-2022-162180","doi":"https://doi.org/10.1182/blood-2022-162180","is_oa":false,"landing_page_url":"https://doi.org/10.1182/blood-2022-162180","pdf_url":null,"source":{"id":"https://openalex.org/S200071133","display_name":"Blood","issn_l":"0006-4971","issn":["0006-4971","1528-0020"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Blood","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref"],"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/A5071823823","display_name":"Emma Busarello","orcid":"https://orcid.org/0009-0009-7731-9777","observed_orcids":["https://orcid.org/0009-0009-7731-9777"]},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Emma Busarello","raw_affiliation_strings":["1University of Trento, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013990285","display_name":"Zuhairia Ibnat","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Zuhairia Ibnat","raw_affiliation_strings":["2University of Trento, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074200166","display_name":"Giulia Biancon","orcid":"https://orcid.org/0000-0003-0182-7766","observed_orcids":["https://orcid.org/0000-0003-0182-7766"]},"institutions":[{"id":"https://openalex.org/I2802730090","display_name":"Yale Cancer Center","ror":"https://ror.org/03j7sze86","country_code":"US","type":"facility","lineage":["https://openalex.org/I2802730090","https://openalex.org/I4210117499","https://openalex.org/I4210165192"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Giulia Biancon","raw_affiliation_strings":["3Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT","4Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]},{"raw_affiliation_string":"4Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058778175","display_name":"Jennifer VanOudenhove","orcid":"https://orcid.org/0000-0001-8206-5542","observed_orcids":["https://orcid.org/0000-0001-8206-5542"]},"institutions":[{"id":"https://openalex.org/I2802730090","display_name":"Yale Cancer Center","ror":"https://ror.org/03j7sze86","country_code":"US","type":"facility","lineage":["https://openalex.org/I2802730090","https://openalex.org/I4210117499","https://openalex.org/I4210165192"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jennifer VanOudenhove","raw_affiliation_strings":["4Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"4Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088387737","display_name":"Fabio Lauria","orcid":"https://orcid.org/0000-0002-1663-1582","observed_orcids":["https://orcid.org/0000-0002-1663-1582"]},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Fabio Lauria","raw_affiliation_strings":["5Institute of Biophysics, CNR, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5Institute of Biophysics, CNR, Trento, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002934973","display_name":"Gabriella Viero","orcid":"https://orcid.org/0000-0002-6755-285X","observed_orcids":["https://orcid.org/0000-0002-6755-285X"]},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Gabriella Viero","raw_affiliation_strings":["5Institute of Biophysics, CNR, Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"5Institute of Biophysics, CNR, Trento, Italy","institution_ids":["https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054557581","display_name":"Stephanie Halene","orcid":"https://orcid.org/0000-0002-2737-9810","observed_orcids":["https://orcid.org/0000-0002-2737-9810"]},"institutions":[{"id":"https://openalex.org/I2802730090","display_name":"Yale Cancer Center","ror":"https://ror.org/03j7sze86","country_code":"US","type":"facility","lineage":["https://openalex.org/I2802730090","https://openalex.org/I4210117499","https://openalex.org/I4210165192"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stephanie Halene","raw_affiliation_strings":["3Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT","4Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT","6Yale Univ. School of Medicine, New Haven, CT","7Department of Internal Medicine, Section of Hematology, Yale University School of Medicine and Yale Cancer Center, New Haven, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"3Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]},{"raw_affiliation_string":"4Section of Hematology, Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]},{"raw_affiliation_string":"6Yale Univ. School of Medicine, New Haven, CT","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"7Department of Internal Medicine, Section of Hematology, Yale University School of Medicine and Yale Cancer Center, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002300255","display_name":"Toma Tebaldi","orcid":"https://orcid.org/0000-0002-0625-1631","observed_orcids":["https://orcid.org/0000-0002-0625-1631"]},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802730090","display_name":"Yale Cancer Center","ror":"https://ror.org/03j7sze86","country_code":"US","type":"facility","lineage":["https://openalex.org/I2802730090","https://openalex.org/I4210117499","https://openalex.org/I4210165192"]},{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Toma Tebaldi","raw_affiliation_strings":["2University of Trento, Trento, Italy","3Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2University of Trento, Trento, Italy","institution_ids":["https://openalex.org/I193223587"]},{"raw_affiliation_string":"3Section of Hematology, Department of Internal Medicine and Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, CT","institution_ids":["https://openalex.org/I2802730090","https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":2500,"currency":"USD","value_usd":2500},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10857678,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"140","issue":"Supplement 1","first_page":"4968","last_page":"4969"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9994999766349792,"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":0.9994999766349792,"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":0.0,"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"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.0,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/cell-type-identification","display_name":"cell type annotation","score":0.8659999966621399},{"id":"https://openalex.org/keywords/marker-genes","display_name":"marker genes","score":0.9380000233650208},{"id":"https://openalex.org/keywords/cell-ontology","display_name":"Cell Ontology","score":0.9700000286102295},{"id":"https://openalex.org/keywords/single-cell-atlas","display_name":"single-cell atlas","score":0.7459999918937683},{"id":"https://openalex.org/keywords/bone-marrow","display_name":"bone marrow","score":0.7170000076293945},{"id":"https://openalex.org/keywords/hematopoiesis","display_name":"hematopoiesis","score":0.8100000023841858},{"id":"https://openalex.org/keywords/cell-type-classification","display_name":"cell type classification","score":0.3700000047683716}],"concepts":[{"id":"https://openalex.org/C87732919","wikidata":"https://www.wikidata.org/wiki/Q3536726","display_name":"Accordion","level":2,"score":0.7575961947441101},{"id":"https://openalex.org/C2993713153","wikidata":"https://www.wikidata.org/wiki/Q211709","display_name":"Hematopoietic cell","level":4,"score":0.6481029987335205},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5405972599983215},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45193302631378174},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3960266709327698},{"id":"https://openalex.org/C109159458","wikidata":"https://www.wikidata.org/wiki/Q919283","display_name":"Haematopoiesis","level":3,"score":0.31490132212638855},{"id":"https://openalex.org/C28328180","wikidata":"https://www.wikidata.org/wiki/Q48196","display_name":"Stem cell","level":2,"score":0.27369722723960876},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2661806344985962},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1485314965248108},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.09930485486984253}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1182/blood-2022-162180","doi":"https://doi.org/10.1182/blood-2022-162180","is_oa":false,"landing_page_url":"https://doi.org/10.1182/blood-2022-162180","pdf_url":null,"source":{"id":"https://openalex.org/S200071133","display_name":"Blood","issn_l":"0006-4971","issn":["0006-4971","1528-0020"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Blood","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4412093926","https://openalex.org/W3108075014","https://openalex.org/W4307432965","https://openalex.org/W4388292371","https://openalex.org/W4386892697","https://openalex.org/W3210631970","https://openalex.org/W4225858647","https://openalex.org/W4360752286","https://openalex.org/W7202357658","https://openalex.org/W7151386268"],"abstract_inverted_index":{"Motivation":[0],"In":[1],"the":[2,39,73,82,99,111,115,127,130,136,146,230,299,313,321,327,358,366,369,385,405,440,461,472,492,506],"past":[3],"few":[4,66],"years,":[5],"single-cell":[6,35,158,426,498],"and":[7,18,22,31,121,150,170,208,242,287,335,350,432,483],"spatial":[8],"technologies":[9],"have":[10],"significantly":[11,452],"improved":[12,453],"our":[13,410],"knowledge":[14],"of":[15,41,75,85,117,123,153,211,256,279,294,304,324,360,368,388,398,463,471,494,508],"cellular":[16],"heterogeneity":[17],"architecture":[19],"in":[20,34,72,157,317,326,454,497],"health":[21],"disease,":[23],"providing":[24],"unprecedented":[25],"insight":[26],"into":[27,87],"hematopoiesis.":[28],"A":[29],"crucial":[30],"challenging":[32],"step":[33],"data":[36,161],"analysis":[37],"is":[38,54,60,234,343,479],"annotation":[40,84,131,362,493],"cell":[42,51,67,101,124,155,176,214,227,240,265,285,301,306,348,381,401,421,435],"types.":[43,68,266,302],"An":[44],"effective":[45],"way":[46],"to":[47,62,106,229,275,297,319,469,490],"achieve":[48],"an":[49,140,395],"accurate":[50],"type":[52,436],"identification":[53,152,397],"employing":[55],"marker":[56,78,96,258,280,330,345,391],"genes,":[57,392],"whose":[58],"expression":[59,386],"specific":[61],"one":[63],"or":[64],"a":[65,118,236,253,292,341,344,413,481],"The":[69,268,475],"recent":[70],"increase":[71],"number":[74,462],"databases":[76,128,167,249],"collecting":[77,168],"genes":[79,259,281,296,331],"potentially":[80],"simplifies":[81],"automatic":[83],"cells":[86,464],"known":[88],"hematopoietic":[89,154,175,264,305,495],"populations.":[90],"Nevertheless,":[91],"each":[92],"database":[93,448],"contains":[94],"dissimilar":[95],"sets":[97],"for":[98,148,174,239,346],"same":[100],"type,":[102],"which":[103,233],"inevitably":[104],"leads":[105],"inconsistent":[107],"annotations":[108,437,445],"depending":[109],"on":[110,439,505],"source":[112],"choice.":[113],"Furthermore,":[114],"lack":[116],"standard":[119,209],"classification":[120],"nomenclature":[122],"types":[125,156,177,228,241,286,307,402],"across":[126],"increases":[129],"discrepancies.":[132],"Methods":[133],"We":[134,407],"developed":[135],"Cell":[137,201,231,269,314,370,441,476],"Marker":[138,270,371,442,477],"Accordion,":[139,372],"R":[141],"Shiny":[142],"web":[143,272],"app":[144],"addressing":[145],"need":[147],"robust":[149],"reproducible":[151],"datasets.":[159,382],"As":[160],"sources,":[162],"we":[163,373,393,433,451],"considered":[164],"multiple":[165],"published":[166,376],"human":[169,377],"mouse":[171],"gene":[172,342],"markers":[173,216],"(Zhang":[178],"et":[179,183,191,195,199,205,245,429],"al.,":[180,184,192,196,200,206,246,430],"2019;":[181,185],"Franz\u00e9n":[182],"Paisley":[186],"&":[187],"Liu,":[188],"2021;":[189,193,202],"B\u00f6rner":[190],"Liberzon":[194],"2015;":[197],"Hao":[198],"Dom\u00ednguez":[203],"Conde":[204],"2022)":[207],"collections":[210],"widely":[212],"used":[213],"sorting":[215],"(Abcam;":[217],"Thermo":[218],"Fisher":[219],"Scientific).":[220],"Annotations":[221],"were":[222,250],"standardized":[223,263],"by":[224,337,352,457],"mapping":[225],"initial":[226],"Ontology,":[232],"becoming":[235],"reference":[237],"ontology":[238],"states":[243],"(Sutherland":[244],"2021).":[247],"Next,":[248],"integrated":[251],"obtaining":[252],"comprehensive":[254],"set":[255],"7514":[257],"associated":[260,282],"with":[261,283,404,412,425,444,467],"126":[262],"Results":[267],"Accordion":[271,443,478],"interface":[273],"permits":[274],"easily":[276,310],"retrieve":[277],"lists":[278],"input":[284],"also":[288,351],"viceversa,":[289],"starting":[290],"from":[291,416,446],"list":[293],"candidate":[295],"obtain":[298,320],"matching":[300],"Hierarchies":[303],"can":[308,332,487],"be":[309,333,488],"browsed":[311],"following":[312],"Ontology":[315],"structure":[316],"order":[318],"desired":[322],"level":[323,387],"resolution":[325],"markers.":[328],"Importantly,":[329],"ranked":[334],"selected":[336],"specificity,":[338],"indicating":[339],"whether":[340],"different":[347,361],"types,":[349],"their":[353],"evidence":[354],"consistency":[355],"scores,":[356],"measuring":[357],"agreement":[359],"sources.":[363,449],"To":[364],"show":[365],"potential":[367],"automatically":[374],"annotated":[375,466],"bone":[378,399],"marrow":[379,400],"single":[380,447,473],"By":[383],"exploring":[384],"well":[389],"established":[390],"confirmed":[394],"appropriate":[396],"obtained":[403,415],"Accordion.":[406],"further":[408],"validated":[409],"approach":[411],"dataset":[414],"flow":[417],"cytometry":[418],"sorted":[419],"blood":[420],"populations,":[422],"separately":[423],"profiled":[424],"RNA-seq":[427],"(Zheng":[428],"2017),":[431],"compared":[434],"based":[438],"Notably,":[450],"accuracy,":[455],"increasing":[456],"more":[458],"than":[459],"30%":[460],"correctly":[465],"respect":[468],"any":[470],"databases.":[474],"indeed":[480],"user-friendly":[482],"flexible":[484],"tool":[485],"that":[486],"exploited":[489],"improve":[491],"populations":[496],"and,":[499],"potentially,":[500],"spatially":[501],"resolved":[502],"datasets":[503],"focused":[504],"study":[507],"hematogical":[509],"pathologies.":[510],"Figure":[511],"1View":[512,515],"largeDownload":[513,516],"PPTFigure":[514],"PPT":[517],"Close":[518],"modal":[519]},"counts_by_year":[],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2022-11-30T00:00:00"}
