{"id":"https://openalex.org/W3007874153","doi":"https://doi.org/10.1093/bioinformatics/btaa137","title":"Ensemble learning for classifying single-cell data and projection across reference atlases","display_name":"Ensemble learning for classifying single-cell data and projection across reference atlases","publication_year":2020,"publication_date":"2020-02-25","ids":{"openalex":"https://openalex.org/W3007874153","doi":"https://doi.org/10.1093/bioinformatics/btaa137","mag":"3007874153","pmid":"https://pubmed.ncbi.nlm.nih.gov/32105316"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa137","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa137","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3585/33329274/btaa137.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3585/33329274/btaa137.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100403152","display_name":"Lin Wang","orcid":"https://orcid.org/0000-0002-2148-1929"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Wang","raw_affiliation_strings":["Department of Neurosurgery , University of California, San Francisco, CA 94158, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurosurgery , University of California, San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000815659","display_name":"Francisca Catalan","orcid":null},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francisca Catalan","raw_affiliation_strings":["Department of Neurosurgery , University of California, San Francisco, CA 94158, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurosurgery , University of California, San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062585561","display_name":"Karin Shamardani","orcid":"https://orcid.org/0000-0003-3376-5758"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Karin Shamardani","raw_affiliation_strings":["Department of Neurosurgery , University of California, San Francisco, CA 94158, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Neurosurgery , University of California, San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054626781","display_name":"Husam Babikir","orcid":"https://orcid.org/0000-0002-3940-047X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Husam Babikir","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5091597843","display_name":"Aar\u00f3n D\u00edaz","orcid":"https://orcid.org/0000-0001-9059-9501"},"institutions":[{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aaron Diaz","raw_affiliation_strings":["Department of Neurosurgery , University of California, San Francisco, CA 94158, USA"],"raw_orcid":"https://orcid.org/0000-0001-9059-9501","affiliations":[{"raw_affiliation_string":"Department of Neurosurgery , University of California, San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I180670191"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091597843"],"corresponding_institution_ids":["https://openalex.org/I180670191"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.8385,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.91907037,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"36","issue":"11","first_page":"3585","last_page":"3587"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9987000226974487,"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":0.9987000226974487,"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":0.00039999998989515007,"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/T11255","display_name":"Microfluidic and Bio-sensing Technologies","score":9.999999747378752e-05,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7905244827270508},{"id":"https://openalex.org/keywords/projection","display_name":"Projection (relational algebra)","score":0.5394919514656067},{"id":"https://openalex.org/keywords/modalities","display_name":"Modalities","score":0.5381091833114624},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49513331055641174},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.4431268870830536},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4388561248779297}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7905244827270508},{"id":"https://openalex.org/C57493831","wikidata":"https://www.wikidata.org/wiki/Q3134666","display_name":"Projection (relational algebra)","level":2,"score":0.5394919514656067},{"id":"https://openalex.org/C2779903281","wikidata":"https://www.wikidata.org/wiki/Q6888026","display_name":"Modalities","level":2,"score":0.5381091833114624},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49513331055641174},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.4431268870830536},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4388561248779297},{"id":"https://openalex.org/C36289849","wikidata":"https://www.wikidata.org/wiki/Q34749","display_name":"Social science","level":1,"score":0.0},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.0},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"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":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":"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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaa137","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa137","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3585/33329274/btaa137.pdf","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:32105316","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32105316","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},{"id":"pmh:ark:/13030/qt6v05q68k","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt6v05q68k","is_oa":false,"landing_page_url":"https://escholarship.org/uc/item/6v05q68k","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 36, iss 11","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7267838","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7267838","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa137","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa137","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/11/3585/33329274/btaa137.pdf","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1601389486","display_name":null,"funder_award_id":"P30 CA082103","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G1625156198","display_name":"Cancer Center Support Grant","funder_award_id":"2p30ca082103-24","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7571040042","display_name":null,"funder_award_id":"IRG-17-180-19","funder_id":"https://openalex.org/F4320306095","funder_display_name":"American Cancer Society"}],"funders":[{"id":"https://openalex.org/F4320306095","display_name":"American Cancer Society","ror":"https://ror.org/02e463172"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W3007874153.pdf"},"referenced_works_count":6,"referenced_works":["https://openalex.org/W2783644856","https://openalex.org/W2794480084","https://openalex.org/W2796170779","https://openalex.org/W2907783748","https://openalex.org/W2971398276","https://openalex.org/W2975379509"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"SUMMARY:":[0],"Single-cell":[1],"data":[2,14,50,84],"are":[3,85],"being":[4],"generated":[5],"at":[6,87],"an":[7,19],"accelerating":[8],"pace.":[9],"How":[10],"best":[11],"to":[12],"project":[13],"across":[15,72],"single-cell":[16],"atlases":[17],"is":[18],"open":[20],"problem.":[21],"We":[22],"developed":[23],"a":[24],"boosted":[25],"learner":[26],"that":[27,55,64],"overcomes":[28],"the":[29,59],"greatest":[30],"challenge":[31],"with":[32,41],"status":[33],"quo":[34],"classifiers:":[35],"low":[36],"sensitivity,":[37],"especially":[38],"when":[39,70],"dealing":[40],"rare":[42],"cell":[43],"types.":[44],"By":[45],"comparing":[46],"novel":[47],"and":[48],"published":[49],"from":[51,58],"distinct":[52],"scRNA-seq":[53],"modalities":[54],"were":[56],"acquired":[57],"same":[60],"tissues,":[61],"we":[62],"show":[63],"this":[65],"approach":[66],"preserves":[67],"cell-type":[68],"labels":[69],"mapping":[71],"diverse":[73],"platforms.":[74],"AVAILABILITY":[75],"AND":[76],"IMPLEMENTATION:":[77],"https://github.com/diazlab/ELSA.":[78],"CONTACT:":[79],"aaron.diaz@ucsf.edu.":[80],"SUPPLEMENTARY":[81],"INFORMATION:":[82],"Supplementary":[83],"available":[86],"Bioinformatics":[88],"online.":[89]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":8},{"year":2021,"cited_by_count":11}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
