{"id":"https://openalex.org/W3035160657","doi":"https://doi.org/10.1186/s12859-020-03547-w","title":"A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data","display_name":"A flexible network-based imputing-and-fusing approach towards the identification of cell types from single-cell RNA-seq data","publication_year":2020,"publication_date":"2020-06-11","ids":{"openalex":"https://openalex.org/W3035160657","doi":"https://doi.org/10.1186/s12859-020-03547-w","mag":"3035160657","pmid":"https://pubmed.ncbi.nlm.nih.gov/32527285"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-020-03547-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03547-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03547-w","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","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03547-w","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5067302327","display_name":"Qi Yang","orcid":"https://orcid.org/0000-0001-8164-2141"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Qi","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067965165","display_name":"Yang Guo","orcid":"https://orcid.org/0000-0003-0821-9755"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]},{"id":"https://openalex.org/I99418890","display_name":"Northwestern Polytechnic University","ror":"https://ror.org/05wn69s11","country_code":"US","type":"education","lineage":["https://openalex.org/I99418890"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Yang Guo","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China. gyang@mail.nwpu.edu.cn","School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China. gyang@mail.nwpu.edu.cn","institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084001232","display_name":"Huixin Jiao","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huixin Jiao","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China. shang@nwpu.edu.cn","School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China. shang@nwpu.edu.cn","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, 710072, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5009944817","https://openalex.org/A5067965165"],"corresponding_institution_ids":["https://openalex.org/I17145004","https://openalex.org/I99418890"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.8201,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.697903,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"21","issue":"1","first_page":"240","last_page":"240"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9995999932289124,"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":0.9995999932289124,"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":9.999999747378752e-05,"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/imputation","display_name":"Imputation (statistics)","score":0.8873852491378784},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6908854246139526},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6186913251876831},{"id":"https://openalex.org/keywords/data-type","display_name":"Data type","score":0.5545199513435364},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5511993765830994},{"id":"https://openalex.org/keywords/missing-data","display_name":"Missing data","score":0.5053308606147766},{"id":"https://openalex.org/keywords/statistic","display_name":"Statistic","score":0.4519035220146179},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3518567681312561},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34389087557792664},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.12573081254959106},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10642841458320618},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.09861770272254944}],"concepts":[{"id":"https://openalex.org/C58041806","wikidata":"https://www.wikidata.org/wiki/Q1660484","display_name":"Imputation (statistics)","level":3,"score":0.8873852491378784},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6908854246139526},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6186913251876831},{"id":"https://openalex.org/C138958017","wikidata":"https://www.wikidata.org/wiki/Q190087","display_name":"Data type","level":2,"score":0.5545199513435364},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5511993765830994},{"id":"https://openalex.org/C9357733","wikidata":"https://www.wikidata.org/wiki/Q6878417","display_name":"Missing data","level":2,"score":0.5053308606147766},{"id":"https://openalex.org/C89128539","wikidata":"https://www.wikidata.org/wiki/Q1949963","display_name":"Statistic","level":2,"score":0.4519035220146179},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3518567681312561},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34389087557792664},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.12573081254959106},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10642841458320618},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.09861770272254944},{"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}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":4,"locations":[{"id":"doi:10.1186/s12859-020-03547-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03547-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03547-w","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:32527285","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32527285","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:3434a7a86bd94763a0deccdb2332ff7d","is_oa":true,"landing_page_url":"https://doaj.org/article/3434a7a86bd94763a0deccdb2332ff7d","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 21, Iss 1, Pp 1-21 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7291547","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7291547","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"}],"best_oa_location":{"id":"doi:10.1186/s12859-020-03547-w","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-020-03547-w","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-020-03547-w","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/G6915057558","display_name":null,"funder_award_id":"No. 61772426","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8881024869","display_name":"\u53ef\u53d8\u526a\u63a5\u7f51\u7edc\u6784\u5efa\u4e0e\u5206\u6790\u7814\u7a76","funder_award_id":"61772426","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3035160657.pdf","grobid_xml":"https://content.openalex.org/works/W3035160657.grobid-xml"},"referenced_works_count":56,"referenced_works":["https://openalex.org/W839653734","https://openalex.org/W1552434751","https://openalex.org/W1570448133","https://openalex.org/W1580018887","https://openalex.org/W1963621662","https://openalex.org/W1967327758","https://openalex.org/W1988391018","https://openalex.org/W1995450389","https://openalex.org/W1998871699","https://openalex.org/W2010457001","https://openalex.org/W2023887100","https://openalex.org/W2024386053","https://openalex.org/W2025828346","https://openalex.org/W2043764521","https://openalex.org/W2051658465","https://openalex.org/W2052301877","https://openalex.org/W2069295116","https://openalex.org/W2076255419","https://openalex.org/W2095445014","https://openalex.org/W2107680358","https://openalex.org/W2122825543","https://openalex.org/W2122863289","https://openalex.org/W2130410032","https://openalex.org/W2134672568","https://openalex.org/W2135519001","https://openalex.org/W2137460766","https://openalex.org/W2154139219","https://openalex.org/W2155320925","https://openalex.org/W2156001353","https://openalex.org/W2163485494","https://openalex.org/W2187089797","https://openalex.org/W2195294260","https://openalex.org/W2295773288","https://openalex.org/W2473258837","https://openalex.org/W2598326928","https://openalex.org/W2600453489","https://openalex.org/W2612502013","https://openalex.org/W2751468300","https://openalex.org/W2761702546","https://openalex.org/W2792693509","https://openalex.org/W2799922543","https://openalex.org/W2805619986","https://openalex.org/W2805831216","https://openalex.org/W2806989085","https://openalex.org/W2886347923","https://openalex.org/W2888562574","https://openalex.org/W2913898479","https://openalex.org/W2915536738","https://openalex.org/W2950129791","https://openalex.org/W2951217100","https://openalex.org/W2952303649","https://openalex.org/W2958564955","https://openalex.org/W3103613649","https://openalex.org/W4233120011","https://openalex.org/W4235169531","https://openalex.org/W4399569422"],"related_works":["https://openalex.org/W2181530120","https://openalex.org/W4211215373","https://openalex.org/W2024529227","https://openalex.org/W2055961818","https://openalex.org/W1574575415","https://openalex.org/W3144172081","https://openalex.org/W3179858851","https://openalex.org/W3028371478","https://openalex.org/W2081476516","https://openalex.org/W2581984549"],"abstract_inverted_index":{"BACKGROUND:":[0],"Single-cell":[1],"RNA":[2],"sequencing":[3],"(scRNA-seq)":[4],"provides":[5,249],"an":[6,160,250],"effective":[7],"tool":[8],"to":[9,19,54,83,115,130,163,223,261],"investigate":[10],"the":[11,15,20,29,34,44,56,69,95,117,132,140,149,174,181,191,203,213,225,241],"transcriptomic":[12],"characteristics":[13],"at":[14],"single-cell":[16],"resolution.":[17],"Due":[18],"low":[21],"amounts":[22],"of":[23,64,80,97,107,135,155,184,198,205,227,235,243,257],"transcripts":[24],"in":[25,32,60,74,121,217],"single":[26],"cells":[27],"and":[28,42,76,124,143,189,231],"technical":[30],"biases":[31],"experiments,":[33],"raw":[35],"scRNA-seq":[36,58,101,122,168,209,229,266],"data":[37,59,82,102,119,123,136,150,186,193,230,238,260],"usually":[38],"includes":[39],"large":[40],"noise":[41,118,137,185],"makes":[43],"downstream":[45],"analyses":[46],"complicated.":[47],"Although":[48],"many":[49],"methods":[50],"have":[51],"been":[52],"proposed":[53,175,247],"impute":[55],"noisy":[57,228],"recent":[61],"years,":[62],"few":[63],"them":[65],"take":[66],"into":[67],"account":[68],"prior":[70,214],"associations":[71,216],"across":[72],"genes":[73],"imputation":[75,81,128,177,192,226,237],"integrate":[77],"multiple":[78,105,153,196,233,255],"types":[79,99,106,154,166,197,207,234,256,264],"identify":[84,164,262],"cell":[85,98,165,206,244,263],"types.":[86,245],"RESULTS:":[87],"We":[88,110],"present":[89],"a":[90,112,126],"new":[91,127],"framework,":[92],"NetImpute,":[93],"towards":[94],"identification":[96,204,242],"from":[100,167,208,265],"by":[103,138,152],"integrating":[104,139,190,232],"biological":[108,156,199,218,258],"networks.":[109],"employ":[111],"statistic":[113],"method":[114],"detect":[116],"items":[120,187],"develop":[125],"model":[129,178],"estimate":[131,180],"real":[133,182],"values":[134,183],"PPI":[141],"network":[142,259],"gene":[144,215],"pathways.":[145],"Meanwhile,":[146],"based":[147,194],"on":[148,195],"imputed":[151],"networks,":[157],"we":[158],"propose":[159],"integrated":[161],"approach":[162],"data.":[169,210,267],"Comprehensive":[170],"experiments":[171],"demonstrate":[172],"that":[173],"network-based":[176,236],"can":[179,201,220,239],"accurately":[188],"networks":[200,219],"improve":[202,224],"CONCLUSIONS:":[211],"Incorporating":[212],"potentially":[221],"help":[222],"enhance":[240],"The":[246],"NetImpute":[248],"open":[251],"framework":[252],"for":[253],"incorporating":[254]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
