{"id":"https://openalex.org/W4385851326","doi":"https://doi.org/10.1093/bioinformatics/btad505","title":"scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization","display_name":"scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization","publication_year":2023,"publication_date":"2023-08-01","ids":{"openalex":"https://openalex.org/W4385851326","doi":"https://doi.org/10.1093/bioinformatics/btad505","pmid":"https://pubmed.ncbi.nlm.nih.gov/37584660"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad505","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad505","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad505/51117245/btad505.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad505/51117245/btad505.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5011286905","display_name":"Xuhua Yan","orcid":"https://orcid.org/0000-0002-3183-3342"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuhua Yan","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University, Changsha, 410083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044328870","display_name":"Ruiqing Zheng","orcid":"https://orcid.org/0000-0001-6372-6798"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ruiqing Zheng","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University, Changsha, 410083, China"],"raw_orcid":"https://orcid.org/0000-0001-6372-6798","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102766473","display_name":"Jinmiao Chen","orcid":"https://orcid.org/0000-0001-7547-6423"},"institutions":[{"id":"https://openalex.org/I115228651","display_name":"Agency for Science, Technology and Research","ror":"https://ror.org/036wvzt09","country_code":"SG","type":"government","lineage":["https://openalex.org/I115228651"]},{"id":"https://openalex.org/I165932596","display_name":"National University of Singapore","ror":"https://ror.org/01tgyzw49","country_code":"SG","type":"education","lineage":["https://openalex.org/I165932596"]},{"id":"https://openalex.org/I2800824516","display_name":"Singapore Immunology Network","ror":"https://ror.org/03vmmgg57","country_code":"SG","type":"facility","lineage":["https://openalex.org/I115228651","https://openalex.org/I2800824516","https://openalex.org/I2801752549"]}],"countries":["SG"],"is_corresponding":false,"raw_author_name":"Jinmiao Chen","raw_affiliation_strings":["Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS) , Singapore 117545, Singapore","Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR) , Singapore 138648, Singapore","Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore","Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117545, Singapore"],"raw_orcid":"https://orcid.org/0000-0001-7547-6423","affiliations":[{"raw_affiliation_string":"Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS) , Singapore 117545, Singapore","institution_ids":["https://openalex.org/I165932596"]},{"raw_affiliation_string":"Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR) , Singapore 138648, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I2800824516"]},{"raw_affiliation_string":"Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore","institution_ids":["https://openalex.org/I115228651","https://openalex.org/I2800824516"]},{"raw_affiliation_string":"Immunology Translational Research Program, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore, 117545, Singapore","institution_ids":["https://openalex.org/I165932596"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100719013","display_name":"Min Li","orcid":"https://orcid.org/0000-0002-0188-1394"},"institutions":[{"id":"https://openalex.org/I139660479","display_name":"Central South University","ror":"https://ror.org/00f1zfq44","country_code":"CN","type":"education","lineage":["https://openalex.org/I139660479"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Min Li","raw_affiliation_strings":["School of Computer Science and Engineering, Central South University , Changsha 410083, China","School of Computer Science and Engineering, Central South University, Changsha, 410083, China"],"raw_orcid":"https://orcid.org/0000-0002-0188-1394","affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University , Changsha 410083, China","institution_ids":["https://openalex.org/I139660479"]},{"raw_affiliation_string":"School of Computer Science and Engineering, Central South University, Changsha, 410083, China","institution_ids":["https://openalex.org/I139660479"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5044328870","https://openalex.org/A5100719013"],"corresponding_institution_ids":["https://openalex.org/I139660479"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1249,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.76342447,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"39","issue":"8","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":0.8248000144958496,"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":0.8248000144958496,"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":0.1265999972820282,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.009700000286102295,"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/regularization","display_name":"Regularization (linguistics)","score":0.5492954254150391},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5229169130325317},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2814270257949829}],"concepts":[{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.5492954254150391},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5229169130325317},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2814270257949829}],"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":"D000092386","descriptor_name":"Single-Cell Gene Expression Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","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":"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":"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":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":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":3,"locations":[{"id":"doi:10.1093/bioinformatics/btad505","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad505","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad505/51117245/btad505.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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:37584660","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37584660","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:10457667","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10457667","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10457667/pdf/btad505.pdf","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/btad505","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad505","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad505/51117245/btad505.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":[{"id":"https://metadata.un.org/sdg/11","score":0.5400000214576721,"display_name":"Sustainable cities and communities"}],"awards":[{"id":"https://openalex.org/G8663586063","display_name":null,"funder_award_id":"62225209","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":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4385851326.pdf"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W2040810212","https://openalex.org/W2064977507","https://openalex.org/W2068881679","https://openalex.org/W2093458639","https://openalex.org/W2112128403","https://openalex.org/W2133966135","https://openalex.org/W2345356016","https://openalex.org/W2617293585","https://openalex.org/W2747877289","https://openalex.org/W2766959028","https://openalex.org/W2887910040","https://openalex.org/W2894687190","https://openalex.org/W2918882492","https://openalex.org/W2947608130","https://openalex.org/W2978997241","https://openalex.org/W2981916830","https://openalex.org/W2989061519","https://openalex.org/W2990138404","https://openalex.org/W3017348419","https://openalex.org/W3092982430","https://openalex.org/W3096805028","https://openalex.org/W3099179344","https://openalex.org/W3103797259","https://openalex.org/W3113863876","https://openalex.org/W3132715010","https://openalex.org/W3134128419","https://openalex.org/W3145969289","https://openalex.org/W3159800610","https://openalex.org/W3164692211","https://openalex.org/W3164839005","https://openalex.org/W3176693948","https://openalex.org/W3210860076","https://openalex.org/W4205514149","https://openalex.org/W4225278475","https://openalex.org/W4281958589","https://openalex.org/W4283067429","https://openalex.org/W4283689887","https://openalex.org/W4288384188","https://openalex.org/W4293237882","https://openalex.org/W4321611764","https://openalex.org/W6763509818"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"MOTIVATION:":[0],"scATAC-seq":[1,28,53,98,126,201],"has":[2,39],"enabled":[3],"chromatin":[4],"accessibility":[5],"landscape":[6],"profiling":[7],"at":[8],"the":[9,46,90,122],"single-cell":[10],"level,":[11],"providing":[12],"opportunities":[13],"for":[14,68,169],"determining":[15],"cell-type-specific":[16],"regulation":[17],"codes.":[18],"However,":[19,55],"high":[20],"dimension,":[21],"extreme":[22],"sparsity,":[23],"and":[24,85,143,152,165,185,209],"large":[25],"scale":[26],"of":[27,92,125,177],"data":[29,49,210],"have":[30],"posed":[31],"great":[32],"challenges":[33],"to":[34,50,60,65,88,120,147,187],"cell-type":[35,197],"identification.":[36],"Thus,":[37],"there":[38],"been":[40],"a":[41,75,139],"growing":[42],"interest":[43],"in":[44,128,199,212,218],"leveraging":[45],"well-annotated":[47],"scRNA-seq":[48,64,151],"help":[51,195],"annotate":[52],"data.":[54],"substantial":[56],"computational":[57],"obstacles":[58],"remain":[59],"transfer":[61,77,168],"information":[62,113],"from":[63],"scATAC-seq,":[66],"especially":[67],"their":[69],"heterogeneous":[70,93],"features.":[71,94],"RESULTS:":[72],"We":[73],"propose":[74],"new":[76],"learning":[78,87,119],"method,":[79],"scNCL,":[80],"which":[81],"utilizes":[82],"prior":[83,106],"knowledge":[84],"contrastive":[86,118],"tackle":[89],"problem":[91],"Briefly,":[95],"scNCL":[96,115,137,160,180,193],"transforms":[97],"features":[99],"into":[100],"gene":[101],"activity":[102],"matrix":[103],"based":[104],"on":[105,155],"knowledge.":[107],"Since":[108],"feature":[109,130,140],"transformation":[110],"can":[111,194,215],"cause":[112],"loss,":[114],"introduces":[116],"neighborhood":[117,123],"preserve":[121],"structure":[124],"cells":[127],"raw":[129],"space.":[131],"To":[132],"learn":[133],"transferable":[134],"latent":[135],"features,":[136],"uses":[138],"projection":[141],"loss":[142,146],"an":[144],"alignment":[145],"harmonize":[148],"embeddings":[149],"between":[150],"scATAC-seq.":[153],"Experiments":[154],"various":[156],"datasets":[157],"demonstrated":[158],"that":[159],"not":[161],"only":[162],"realizes":[163],"accurate":[164],"robust":[166],"label":[167],"common":[170],"types,":[171],"but":[172],"also":[173,182],"achieves":[174],"reliable":[175],"detection":[176],"novel":[178],"types.":[179],"is":[181],"computationally":[183],"efficient":[184],"scalable":[186],"million-scale":[188],"datasets.":[189],"Moreover,":[190],"we":[191],"prove":[192],"refine":[196],"annotations":[198],"existing":[200],"atlases.":[202],"AVAILABILITY":[203],"AND":[204],"IMPLEMENTATION:":[205],"The":[206],"source":[207],"code":[208],"used":[211],"this":[213],"paper":[214],"be":[216],"found":[217],"https://github.com/CSUBioGroup/scNCL-release.":[219]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}