{"id":"https://openalex.org/W3202393418","doi":"https://doi.org/10.1093/bioinformatics/btab700","title":"scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets","display_name":"scMRA: a robust deep learning method to annotate scRNA-seq data with multiple reference datasets","publication_year":2021,"publication_date":"2021-10-06","ids":{"openalex":"https://openalex.org/W3202393418","doi":"https://doi.org/10.1093/bioinformatics/btab700","mag":"3202393418","pmid":"https://pubmed.ncbi.nlm.nih.gov/34623390"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab700","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab700","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064410034","display_name":"Musu Yuan","orcid":"https://orcid.org/0000-0002-5674-1639"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Musu Yuan","raw_affiliation_strings":["Center for Quantitative Biology, Peking University , Beijing 100871, China","School of Mathematical Sciences, Peking University , Beijing 100871, China"],"raw_orcid":"https://orcid.org/0000-0002-5674-1639","affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Peking University , Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"School of Mathematical Sciences, Peking University , Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334590","display_name":"Liang Chen","orcid":"https://orcid.org/0000-0002-1915-9199"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Chen","raw_affiliation_strings":["School of Mathematical Sciences, Peking University , Beijing 100871, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences, Peking University , Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091013880","display_name":"Minghua Deng","orcid":"https://orcid.org/0000-0002-9143-1898"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minghua Deng","raw_affiliation_strings":["Center for Quantitative Biology, Peking University , Beijing 100871, China","Center for Statistical Science, Peking University , Beijing 100871, China","School of Mathematical Sciences, Peking University , Beijing 100871, China"],"raw_orcid":"https://orcid.org/0000-0002-9143-1898","affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Peking University , Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Center for Statistical Science, Peking University , Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"School of Mathematical Sciences, Peking University , Beijing 100871, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5091013880"],"corresponding_institution_ids":["https://openalex.org/I20231570"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.7024,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.84972155,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"38","issue":"3","first_page":"738","last_page":"745"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9894999861717224,"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":0.9894999861717224,"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":0.00860000029206276,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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/computer-science","display_name":"Computer science","score":0.8256028890609741},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7797553539276123},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5557966828346252},{"id":"https://openalex.org/keywords/closeness","display_name":"Closeness","score":0.5142230987548828},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5071415901184082},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4887361526489258},{"id":"https://openalex.org/keywords/bioconductor","display_name":"Bioconductor","score":0.45875218510627747},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.45554864406585693},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4387335479259491},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3416537344455719}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8256028890609741},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7797553539276123},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5557966828346252},{"id":"https://openalex.org/C2779545769","wikidata":"https://www.wikidata.org/wiki/Q5135364","display_name":"Closeness","level":2,"score":0.5142230987548828},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5071415901184082},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4887361526489258},{"id":"https://openalex.org/C2779694297","wikidata":"https://www.wikidata.org/wiki/Q2888953","display_name":"Bioconductor","level":3,"score":0.45875218510627747},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.45554864406585693},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4387335479259491},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3416537344455719},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":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":"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":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":"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":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab700","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab700","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:34623390","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34623390","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}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.5699999928474426}],"awards":[{"id":"https://openalex.org/G1419623888","display_name":null,"funder_award_id":"2016YFA0502303","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5690750078","display_name":null,"funder_award_id":"31871342","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W2019552331","https://openalex.org/W2069089843","https://openalex.org/W2105523772","https://openalex.org/W2139838862","https://openalex.org/W2579273737","https://openalex.org/W2598326928","https://openalex.org/W2739009776","https://openalex.org/W2796170779","https://openalex.org/W2894687190","https://openalex.org/W2916020270","https://openalex.org/W2946232537","https://openalex.org/W2949067670","https://openalex.org/W2949177718","https://openalex.org/W2971398276","https://openalex.org/W2971653850","https://openalex.org/W3016453687","https://openalex.org/W3029148360","https://openalex.org/W3042462196","https://openalex.org/W3092295864","https://openalex.org/W3092982430","https://openalex.org/W3093900604","https://openalex.org/W6675865240"],"related_works":["https://openalex.org/W2135678793","https://openalex.org/W2109288169","https://openalex.org/W2157684052","https://openalex.org/W4223449272","https://openalex.org/W2978247079","https://openalex.org/W2166887457","https://openalex.org/W2148708580","https://openalex.org/W43224192","https://openalex.org/W90653389","https://openalex.org/W3124814274"],"abstract_inverted_index":{"MOTIVATION:":[0],"Single-cell":[1],"RNA-seq":[2],"(scRNA-seq)":[3],"has":[4],"been":[5],"widely":[6],"used":[7],"to":[8,21,26,128,175,210,216],"resolve":[9],"cellular":[10],"heterogeneity.":[11],"After":[12],"collecting":[13],"scRNA-seq":[14,230],"data,":[15,219],"the":[16,23,97,130,156,176,200,207,224],"natural":[17],"next":[18],"step":[19],"is":[20,44,80,119,126,165,206,239],"integrate":[22],"accumulated":[24],"data":[25,50,61,191,246],"achieve":[27],"a":[28,52,75,110,123,139,145],"common":[29],"ontology":[30],"of":[31,99,132,159,202,237],"cell":[32,133,160],"types":[33,134,161],"and":[34,39,138,155,220],"states.":[35],"Thus,":[36],"an":[37,182],"effective":[38],"efficient":[40],"cell-type":[41],"identification":[42],"method":[43,227],"urgently":[45],"needed.":[46],"Meanwhile,":[47],"high-quality":[48],"reference":[49,60,106,173,214],"remain":[51],"necessity":[53],"for":[54,228],"precise":[55],"annotation.":[56],"However,":[57],"such":[58],"tailored":[59],"are":[62,247],"always":[63],"lacking":[64],"in":[65,102,135,189],"practice.":[66],"To":[67,199],"address":[68],"this,":[69],"we":[70],"aggregated":[71],"multiple":[72,105,172,212,229],"datasets":[73,215],"into":[74],"meta-dataset":[76],"on":[77,148],"which":[78,100],"annotation":[79,86,187,226],"conducted.":[81],"Existing":[82],"supervised":[83],"or":[84],"semi-supervised":[85],"methods":[87,188],"suffer":[88],"from":[89,171,241],"batch":[90,197],"effects":[91],"caused":[92],"by":[93],"different":[94,136],"sequencing":[95],"platforms,":[96],"effect":[98],"increases":[101],"severity":[103],"with":[104],"datasets.":[107,163,231],"RESULTS:":[108],"Herein,":[109],"robust":[111],"deep":[112],"learning-based":[113],"single-cell":[114],"Multiple":[115],"Reference":[116],"Annotator":[117],"(scMRA)":[118],"introduced.":[120],"In":[121],"scMRA,":[122],"knowledge":[124,170],"graph":[125],"constructed":[127],"represent":[129],"characteristics":[131],"datasets,":[137,174],"graphic":[140],"convolutional":[141],"network":[142],"serves":[143],"as":[144],"discriminator":[146],"based":[147],"this":[149,205],"graph.":[150],"scMRA":[151,164,194,238],"keeps":[152],"intra-cell-type":[153],"closeness":[154],"relative":[157],"position":[158],"across":[162],"remarkably":[166],"powerful":[167],"at":[168,249],"transferring":[169],"unlabeled":[177],"target":[178,218],"domain,":[179],"thereby":[180],"gaining":[181],"advantage":[183],"over":[184],"other":[185],"state-of-the-art":[186],"multi-reference":[190],"experiments.":[192],"Furthermore,":[193],"can":[195],"remove":[196],"effects.":[198],"best":[201,225],"our":[203],"knowledge,":[204],"first":[208],"attempt":[209],"use":[211],"insufficient":[213],"annotate":[217],"it":[221],"is,":[222],"comparatively,":[223],"AVAILABILITY":[232],"AND":[233],"IMPLEMENTATION:":[234],"An":[235],"implementation":[236],"available":[240,248],"https://github.com/ddb-qiwang/scMRA-torch.":[242],"SUPPLEMENTARY":[243],"INFORMATION:":[244],"Supplementary":[245],"Bioinformatics":[250],"online.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":12},{"year":2024,"cited_by_count":7},{"year":2023,"cited_by_count":11},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
