{"id":"https://openalex.org/W3164882886","doi":"https://doi.org/10.1093/bioinformatics/btab409","title":"<i>CyAnno</i> : a semi-automated approach for cell type annotation of mass cytometry datasets","display_name":"<i>CyAnno</i> : a semi-automated approach for cell type annotation of mass cytometry datasets","publication_year":2021,"publication_date":"2021-05-24","ids":{"openalex":"https://openalex.org/W3164882886","doi":"https://doi.org/10.1093/bioinformatics/btab409","mag":"3164882886","pmid":"https://pubmed.ncbi.nlm.nih.gov/34037686"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab409","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab409","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9502137","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053474897","display_name":"Abhinav Kaushik","orcid":"https://orcid.org/0000-0001-5682-0209"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Abhinav Kaushik","raw_affiliation_strings":["Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"],"affiliations":[{"raw_affiliation_string":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004532609","display_name":"Diane Dunham","orcid":null},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Diane Dunham","raw_affiliation_strings":["Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"],"affiliations":[{"raw_affiliation_string":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050108806","display_name":"Ziyuan He","orcid":"https://orcid.org/0000-0003-3556-8248"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ziyuan He","raw_affiliation_strings":["Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"],"affiliations":[{"raw_affiliation_string":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066092294","display_name":"Monali Manohar","orcid":"https://orcid.org/0000-0002-1869-2645"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Monali Manohar","raw_affiliation_strings":["Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"],"affiliations":[{"raw_affiliation_string":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032969374","display_name":"Manisha Desai","orcid":"https://orcid.org/0000-0002-6949-2651"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Manisha Desai","raw_affiliation_strings":["Quantitative Sciences Unit, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"],"affiliations":[{"raw_affiliation_string":"Quantitative Sciences Unit, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028760615","display_name":"Kari C. Nadeau","orcid":"https://orcid.org/0000-0002-2146-2955"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kari C Nadeau","raw_affiliation_strings":["Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA"],"affiliations":[{"raw_affiliation_string":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083348332","display_name":"Sandra Andorf","orcid":"https://orcid.org/0000-0002-3093-2568"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]},{"id":"https://openalex.org/I92156820","display_name":"University of Cincinnati Medical Center","ror":"https://ror.org/02p72h367","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I92156820"]},{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Sandra Andorf","raw_affiliation_strings":["Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH 45229, USA","Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children\u2019s Hospital Medical Center , Cincinnati, OH 45229, USA","Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA"],"affiliations":[{"raw_affiliation_string":"Department of Pediatrics, University of Cincinnati College of Medicine , Cincinnati, OH 45229, USA","institution_ids":["https://openalex.org/I92156820"]},{"raw_affiliation_string":"Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children\u2019s Hospital Medical Center , Cincinnati, OH 45229, USA","institution_ids":["https://openalex.org/I1285204247"]},{"raw_affiliation_string":"Sean N Parker Center for Allergy and Asthma Research at Stanford University, Stanford University Department of Medicine, , Stanford, CA 94305\u20135101, USA","institution_ids":["https://openalex.org/I97018004"]},{"raw_affiliation_string":"Divisions of Biomedical Informatics and Allergy & Immunology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5083348332"],"corresponding_institution_ids":["https://openalex.org/I1285204247","https://openalex.org/I92156820","https://openalex.org/I97018004"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3588,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.89652417,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"37","issue":"22","first_page":"4164","last_page":"4171"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9983999729156494,"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":0.994700014591217,"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/annotation","display_name":"Annotation","score":0.8800983428955078},{"id":"https://openalex.org/keywords/mass-cytometry","display_name":"Mass cytometry","score":0.8403091430664062},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6689860820770264},{"id":"https://openalex.org/keywords/flow-cytometry","display_name":"Flow cytometry","score":0.4681701064109802},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4254646599292755},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4081076681613922},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35536691546440125},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3358454704284668},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1866997480392456},{"id":"https://openalex.org/keywords/molecular-biology","display_name":"Molecular biology","score":0.09984156489372253},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.06081533432006836}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8800983428955078},{"id":"https://openalex.org/C2778015335","wikidata":"https://www.wikidata.org/wiki/Q17051163","display_name":"Mass cytometry","level":4,"score":0.8403091430664062},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6689860820770264},{"id":"https://openalex.org/C553184892","wikidata":"https://www.wikidata.org/wiki/Q1141429","display_name":"Flow cytometry","level":2,"score":0.4681701064109802},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4254646599292755},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4081076681613922},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35536691546440125},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3358454704284668},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1866997480392456},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.09984156489372253},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.06081533432006836},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002477","descriptor_name":"Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab409","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab409","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:34037686","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34037686","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:oai:pubmedcentral.nih.gov:9502137","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9502137","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":"pmh:oai:pubmedcentral.nih.gov:9502137","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9502137","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"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G222296539","display_name":null,"funder_award_id":"P30-DK116074","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3583994267","display_name":null,"funder_award_id":"5U19 AI104209-07","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4612420534","display_name":null,"funder_award_id":"P30-CA124435","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5151875122","display_name":null,"funder_award_id":"UL1-TR003142","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6650714014","display_name":null,"funder_award_id":"R01AI140134-01","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W1498436455","https://openalex.org/W1631320694","https://openalex.org/W1924107806","https://openalex.org/W2038254572","https://openalex.org/W2095664313","https://openalex.org/W2119821739","https://openalex.org/W2135861494","https://openalex.org/W2286340588","https://openalex.org/W2295984635","https://openalex.org/W2358421111","https://openalex.org/W2533463831","https://openalex.org/W2585665652","https://openalex.org/W2618433578","https://openalex.org/W2761095749","https://openalex.org/W2797701944","https://openalex.org/W2807534769","https://openalex.org/W2884964182","https://openalex.org/W2886347923","https://openalex.org/W2894143091","https://openalex.org/W2896353945","https://openalex.org/W2900653572","https://openalex.org/W2920999075","https://openalex.org/W2927148996","https://openalex.org/W2945493637","https://openalex.org/W2952923426","https://openalex.org/W2955980564","https://openalex.org/W2959295202","https://openalex.org/W2972623358","https://openalex.org/W2997055652","https://openalex.org/W3044528691","https://openalex.org/W4239510810","https://openalex.org/W4240098044","https://openalex.org/W6679885933","https://openalex.org/W6753772479"],"related_works":["https://openalex.org/W4251194061","https://openalex.org/W2414055539","https://openalex.org/W3000152097","https://openalex.org/W2176701861","https://openalex.org/W2738798767","https://openalex.org/W4200474388","https://openalex.org/W2593722891","https://openalex.org/W2939944564","https://openalex.org/W2911530547","https://openalex.org/W2999230806"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":18},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":4}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2021-06-07T00:00:00"}
