{"id":"https://openalex.org/W4309165889","doi":"https://doi.org/10.1093/bioinformatics/btac739","title":"scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data","display_name":"scAWMV: an adaptively weighted multi-view learning framework for the integrative analysis of parallel scRNA-seq and scATAC-seq data","publication_year":2022,"publication_date":"2022-11-16","ids":{"openalex":"https://openalex.org/W4309165889","doi":"https://doi.org/10.1093/bioinformatics/btac739","pmid":"https://pubmed.ncbi.nlm.nih.gov/36383176"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac739","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac739","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac739/48448772/btac739.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac739/48448772/btac739.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006697904","display_name":"Pengcheng Zeng","orcid":"https://orcid.org/0000-0002-0724-5313"},"institutions":[{"id":"https://openalex.org/I30809798","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786","country_code":"CN","type":"education","lineage":["https://openalex.org/I30809798"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengcheng Zeng","raw_affiliation_strings":["Institute of Mathematical Sciences, ShanghaiTech University , Shanghai 201210, China"],"raw_orcid":"https://orcid.org/0000-0002-0724-5313","affiliations":[{"raw_affiliation_string":"Institute of Mathematical Sciences, ShanghaiTech University , Shanghai 201210, China","institution_ids":["https://openalex.org/I30809798"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061864295","display_name":"Yuanyuan Ma","orcid":"https://orcid.org/0000-0001-9103-5513"},"institutions":[{"id":"https://openalex.org/I4210117382","display_name":"Anyang Normal University","ror":"https://ror.org/02g9nss57","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210117382"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Ma","raw_affiliation_strings":["School of Computer and Information Engineering, Anyang Normal University , Henan 455000, China"],"raw_orcid":"https://orcid.org/0000-0001-9103-5513","affiliations":[{"raw_affiliation_string":"School of Computer and Information Engineering, Anyang Normal University , Henan 455000, China","institution_ids":["https://openalex.org/I4210117382"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5014111636","display_name":"Zhixiang Lin","orcid":"https://orcid.org/0000-0001-9301-947X"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":true,"raw_author_name":"Zhixiang Lin","raw_affiliation_strings":["Department of Statistics, The Chinese University of Hong Kong , Hong Kong SAR, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, The Chinese University of Hong Kong , Hong Kong SAR, China","institution_ids":["https://openalex.org/I177725633"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5014111636"],"corresponding_institution_ids":["https://openalex.org/I177725633"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.4197,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.58185831,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":98},"biblio":{"volume":"39","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9991999864578247,"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":0.9991999864578247,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":9.999999747378752e-05,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5309709310531616},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5140587091445923},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.444742351770401},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40245747566223145},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3300948739051819}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5309709310531616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5140587091445923},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.444742351770401},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40245747566223145},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3300948739051819},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":true},{"descriptor_ui":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","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":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":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":"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},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btac739","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac739","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac739/48448772/btac739.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36383176","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36383176","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:9805575","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9805575","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btac739","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac739","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/1/btac739/48448772/btac739.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.46000000834465027,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[{"id":"https://openalex.org/G768243115","display_name":null,"funder_award_id":"4930181","funder_id":"https://openalex.org/F4320322942","funder_display_name":"Chinese University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320322942","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48"},{"id":"https://openalex.org/F4320327675","display_name":"ShanghaiTech University","ror":"https://ror.org/030bhh786"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4309165889.pdf","grobid_xml":"https://content.openalex.org/works/W4309165889.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W2131681506","https://openalex.org/W2136787567","https://openalex.org/W2144359569","https://openalex.org/W2198371822","https://openalex.org/W2222000795","https://openalex.org/W2296221004","https://openalex.org/W2572375651","https://openalex.org/W2598326928","https://openalex.org/W2766959028","https://openalex.org/W2792598873","https://openalex.org/W2793965282","https://openalex.org/W2794480084","https://openalex.org/W2798368076","https://openalex.org/W2887910040","https://openalex.org/W2889236955","https://openalex.org/W2895456557","https://openalex.org/W2928665623","https://openalex.org/W2934716754","https://openalex.org/W2948469692","https://openalex.org/W2949177718","https://openalex.org/W2949329924","https://openalex.org/W2951343553","https://openalex.org/W2952644935","https://openalex.org/W2953251392","https://openalex.org/W2953322088","https://openalex.org/W2979464975","https://openalex.org/W2979911343","https://openalex.org/W2985765936","https://openalex.org/W3003444384","https://openalex.org/W3010560083","https://openalex.org/W3012788672","https://openalex.org/W3027051073","https://openalex.org/W3042292144","https://openalex.org/W3093858607","https://openalex.org/W3099768174","https://openalex.org/W3112466552","https://openalex.org/W3131450268","https://openalex.org/W3139114765","https://openalex.org/W3164692211","https://openalex.org/W3165062450","https://openalex.org/W3165519561","https://openalex.org/W4213009331","https://openalex.org/W4214854288","https://openalex.org/W6761319427","https://openalex.org/W6774820075"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W1971568933"],"abstract_inverted_index":{"MOTIVATION:":[0],"Technological":[1],"advances":[2],"have":[3,66],"enabled":[4],"us":[5,16],"to":[6,21,28,65,159,172],"profile":[7],"single-cell":[8,39,44,177],"multi-omics":[9,35,80,128,178],"data":[10,48,59,72,81,111,129,194],"from":[11,50,113],"the":[12,23,51,79,85,89,103,114,120,131,135,138,150],"same":[13,52,115],"cells,":[14],"providing":[15],"with":[17],"an":[18,95,169],"unprecedented":[19],"opportunity":[20],"understand":[22],"cellular":[24,90,174],"phenotype":[25],"and":[26,34,43,63,109,130,140,152,185],"links":[27],"its":[29],"genotype.":[30],"The":[31,75,183],"available":[32,188,196],"protocols":[33],"datasets":[36,162,186],"[including":[37],"parallel":[38,107],"RNA":[40],"sequencing":[41,46],"(scRNA-seq)":[42],"ATAC":[45],"(scATAC-seq)":[47],"profiled":[49,112],"cell]":[53],"are":[54,60,187,195],"growing":[55],"increasingly.":[56],"However,":[57],"such":[58],"highly":[61],"sparse":[62],"tend":[64],"high":[67],"level":[68],"of":[69,87,106,134],"noise,":[70],"making":[71],"analysis":[73,105],"challenging.":[74],"methods":[76],"that":[77,164],"integrate":[78],"can":[82],"potentially":[83],"improve":[84],"capacity":[86],"revealing":[88],"heterogeneity.":[91],"RESULTS:":[92],"We":[93],"propose":[94],"adaptively":[96],"weighted":[97],"multi-view":[98],"learning":[99],"(scAWMV)":[100],"method":[101,171],"for":[102,149,176],"integrative":[104],"scRNA-seq":[108,139],"scATAC-seq":[110,141],"cell.":[116],"scAWMV":[117,167],"considers":[118],"both":[119],"difference":[121],"in":[122,127,137],"importance":[123],"across":[124],"different":[125],"modalities":[126],"biological":[132],"connection":[133],"features":[136],"data.":[142,179],"It":[143],"generates":[144],"biologically":[145],"meaningful":[146],"low-dimensional":[147],"representations":[148],"transcriptomic":[151],"epigenomic":[153],"profiles":[154],"via":[155],"unsupervised":[156],"learning.":[157],"Application":[158],"four":[160],"real":[161],"demonstrates":[163],"our":[165],"framework":[166],"is":[168],"efficient":[170],"dissect":[173],"heterogeneity":[175],"AVAILABILITY":[180],"AND":[181],"IMPLEMENTATION:":[182],"software":[184],"at":[189,197],"https://github.com/pengchengzeng/scAWMV.":[190],"SUPPLEMENTARY":[191],"INFORMATION:":[192],"Supplementary":[193],"Bioinformatics":[198],"online.":[199]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2}],"updated_date":"2026-06-18T08:10:14.011955","created_date":"2025-10-10T00:00:00"}
