{"id":"https://openalex.org/W4285090748","doi":"https://doi.org/10.1186/s12859-022-04817-5","title":"Detection of cell markers from single cell RNA-seq with sc2marker","display_name":"Detection of cell markers from single cell RNA-seq with sc2marker","publication_year":2022,"publication_date":"2022-07-12","ids":{"openalex":"https://openalex.org/W4285090748","doi":"https://doi.org/10.1186/s12859-022-04817-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/35831796"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-022-04817-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04817-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04817-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04817-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101419740","display_name":"Ronghui Li","orcid":"https://orcid.org/0000-0001-6329-5895"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Ronghui Li","raw_affiliation_strings":["Joint Research Center for Computational Biomedicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001432177","display_name":"Bella Banjanin","orcid":null},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Bella Banjanin","raw_affiliation_strings":["Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073561254","display_name":"Rebekka K. Schneider","orcid":"https://orcid.org/0000-0002-0749-1565"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Rebekka K. Schneider","raw_affiliation_strings":["Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cell Biology, Institute for Biomedical Engineering, RWTH Aachen University, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5057250270","display_name":"Ivan G. Costa","orcid":"https://orcid.org/0000-0003-2890-8697"},"institutions":[{"id":"https://openalex.org/I887968799","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34","country_code":"DE","type":"education","lineage":["https://openalex.org/I887968799"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ivan G. Costa","raw_affiliation_strings":["Joint Research Center for Computational Biomedicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany. ivan.costa@rwth-aachen.de","Joint Research Center for Computational Biomedicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany. ivan.costa@rwth-aachen.de","institution_ids":["https://openalex.org/I887968799"]},{"raw_affiliation_string":"Joint Research Center for Computational Biomedicine, Institute for Computational Genomics, RWTH Aachen University, Aachen, Germany","institution_ids":["https://openalex.org/I887968799"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5101419740"],"corresponding_institution_ids":["https://openalex.org/I887968799"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.9923,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.86994677,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"23","issue":"1","first_page":"276","last_page":"276"},"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/T10773","display_name":"Extracellular vesicles in disease","score":0.9958000183105469,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9817000031471252,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/flow-cytometry","display_name":"Flow cytometry","score":0.6436445713043213},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.606335461139679},{"id":"https://openalex.org/keywords/mass-cytometry","display_name":"Mass cytometry","score":0.49887585639953613},{"id":"https://openalex.org/keywords/stromal-cell","display_name":"Stromal cell","score":0.4664093255996704},{"id":"https://openalex.org/keywords/cell","display_name":"Cell","score":0.4662550687789917},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.45417520403862},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43079665303230286},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4195306599140167},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.35912948846817017},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2626190781593323},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18156570196151733},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1815236508846283},{"id":"https://openalex.org/keywords/phenotype","display_name":"Phenotype","score":0.10363486409187317}],"concepts":[{"id":"https://openalex.org/C553184892","wikidata":"https://www.wikidata.org/wiki/Q1141429","display_name":"Flow cytometry","level":2,"score":0.6436445713043213},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.606335461139679},{"id":"https://openalex.org/C2778015335","wikidata":"https://www.wikidata.org/wiki/Q17051163","display_name":"Mass cytometry","level":4,"score":0.49887585639953613},{"id":"https://openalex.org/C16930146","wikidata":"https://www.wikidata.org/wiki/Q4381253","display_name":"Stromal cell","level":2,"score":0.4664093255996704},{"id":"https://openalex.org/C1491633281","wikidata":"https://www.wikidata.org/wiki/Q7868","display_name":"Cell","level":2,"score":0.4662550687789917},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.45417520403862},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43079665303230286},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4195306599140167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.35912948846817017},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2626190781593323},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18156570196151733},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1815236508846283},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.10363486409187317},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-022-04817-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04817-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04817-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35831796","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35831796","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:461c0041908e464cb83283eb9d9439aa","is_oa":true,"landing_page_url":"https://doaj.org/article/461c0041908e464cb83283eb9d9439aa","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 23, Iss 1, Pp 1-19 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9281170","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9281170","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"doi:10.18154/rwth-conv-250025","is_oa":true,"landing_page_url":"https://doi.org/10.18154/rwth-conv-250025","pdf_url":null,"source":{"id":"https://openalex.org/S4306401033","display_name":"RWTH Publications (RWTH Aachen)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887968799","host_organization_name":"RWTH Aachen University","host_organization_lineage":["https://openalex.org/I887968799"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/s12859-022-04817-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-022-04817-5","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-022-04817-5","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G5842783010","display_name":null,"funder_award_id":"CRU 344","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"},{"id":"https://openalex.org/F4320324232","display_name":"RWTH Aachen University","ror":"https://ror.org/04xfq0f34"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4285090748.pdf","grobid_xml":"https://content.openalex.org/works/W4285090748.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1985255881","https://openalex.org/W2012034410","https://openalex.org/W2055271333","https://openalex.org/W2063996876","https://openalex.org/W2091765669","https://openalex.org/W2104090034","https://openalex.org/W2173763791","https://openalex.org/W2190545194","https://openalex.org/W2286236870","https://openalex.org/W2461073387","https://openalex.org/W2557833574","https://openalex.org/W2569834758","https://openalex.org/W2602123787","https://openalex.org/W2738487912","https://openalex.org/W2788348358","https://openalex.org/W2805619986","https://openalex.org/W2921294441","https://openalex.org/W2949177718","https://openalex.org/W2952923426","https://openalex.org/W2982231537","https://openalex.org/W2995703197","https://openalex.org/W3015701917","https://openalex.org/W3034168389","https://openalex.org/W3080668573","https://openalex.org/W3094585864","https://openalex.org/W3096568637","https://openalex.org/W3112914139","https://openalex.org/W3132661792","https://openalex.org/W3156558106","https://openalex.org/W3164692211","https://openalex.org/W3215916291"],"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":{"BACKGROUND:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"allows":[5],"the":[6,55,74,95,122],"detection":[7,16],"of":[8,17,45,57,81,97,109],"rare":[9,20],"cell":[10,21],"types":[11,22],"in":[12,102,106,125],"complex":[13],"tissues.":[14],"The":[15,114],"markers":[18,87,105],"for":[19,25,30,38,88],"is":[23,71],"useful":[24],"further":[26],"biological":[27],"analysis":[28],"of,":[29],"example,":[31],"flow":[32,89],"cytometry":[33,90],"and":[34,78,99,111],"imaging":[35],"data":[36,108],"sets":[37],"either":[39],"physical":[40],"isolation":[41],"or":[42,91],"spatial":[43],"characterization":[44],"these":[46],"cells.":[47,113],"However,":[48],"only":[49],"a":[50,79,129],"few":[51],"computational":[52],"approaches":[53],"consider":[54],"problem":[56],"selecting":[58],"specific":[59],"marker":[60],"genes":[61],"from":[62],"scRNA-seq":[63,107],"data.":[64],"RESULTS:":[65],"Here,":[66],"we":[67],"propose":[68],"sc2marker,":[69],"which":[70],"based":[72],"on":[73],"maximum":[75],"margin":[76],"index":[77],"database":[80],"proteins":[82],"with":[83],"antibodies,":[84],"to":[85],"select":[86],"imaging.":[92],"We":[93],"evaluated":[94],"performances":[96],"sc2marker":[98,118],"competing":[100,123],"methods":[101,124],"ranking":[103],"known":[104],"immune":[110],"stromal":[112],"results":[115],"showed":[116],"that":[117],"performed":[119],"better":[120],"than":[121],"accuracy,":[126],"while":[127],"having":[128],"competitive":[130],"running":[131],"time.":[132]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2022-07-14T00:00:00"}
