{"id":"https://openalex.org/W7225256428","doi":"https://doi.org/10.3390/ijms27219888","title":"scLAP: A Liver-Adapted Contrastive Shared-Latent Framework for Pseudo-Pairing Single-Cell Transcriptomes and Chromatin Accessibility Profiles","display_name":"scLAP: A Liver-Adapted Contrastive Shared-Latent Framework for Pseudo-Pairing Single-Cell Transcriptomes and Chromatin Accessibility Profiles","publication_year":2026,"publication_date":"2026-11-04","ids":{"openalex":"https://openalex.org/W7225256428","doi":"https://doi.org/10.3390/ijms27219888"},"language":"en","primary_location":{"id":"doi:10.3390/ijms27219888","doi":"https://doi.org/10.3390/ijms27219888","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms27219888","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Molecular Sciences","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.3390/ijms27219888","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076483517","display_name":"Hongfei Li","orcid":"https://orcid.org/0000-0002-4298-9983","observed_orcids":["https://orcid.org/0000-0002-4298-9983"]},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongfei Li","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","institution_ids":["https://openalex.org/I150229711"]},{"raw_affiliation_string":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5160704123","display_name":"Jiechen Wang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiechen Wang","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","institution_ids":["https://openalex.org/I150229711"]},{"raw_affiliation_string":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5160718427","display_name":"Huan Yang","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Huan Yang","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu 610054, China","institution_ids":["https://openalex.org/I150229711"]},{"raw_affiliation_string":"Yangtze Delta Region Institute (Quzhou), University of Electronic Science and Technology of China, Quzhou 324003, China","institution_ids":["https://openalex.org/I150229711"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5160718427"],"corresponding_institution_ids":["https://openalex.org/I150229711"],"apc_list":{"value":2900,"currency":"CHF","value_usd":3499},"apc_paid":{"value":2900,"currency":"CHF","value_usd":3499},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.73415888,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"21","first_page":"9888","last_page":"9888"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9984999895095825,"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":0.9984999895095825,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.00039999998989515007,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.6679999828338623},{"id":"https://openalex.org/keywords/single-cell-atac-seq","display_name":"single-cell ATAC-seq","score":0.9350000023841858},{"id":"https://openalex.org/keywords/hepatocellular-carcinoma","display_name":"hepatocellular carcinoma","score":0.9129999876022339},{"id":"https://openalex.org/keywords/contrastive-learning","display_name":"contrastive learning","score":0.7620000243186951},{"id":"https://openalex.org/keywords/shared-latent-representation","display_name":"shared latent representation","score":0.8019999861717224},{"id":"https://openalex.org/keywords/multi-omics-integration","display_name":"multi-omics integration","score":0.550000011920929},{"id":"https://openalex.org/keywords/chromatin-accessibility","display_name":"chromatin accessibility","score":0.7570000290870667},{"id":"https://openalex.org/keywords/transcription-factor-binding-motifs","display_name":"transcription factor binding motifs","score":0.5889999866485596},{"id":"https://openalex.org/keywords/nrcam","display_name":"NrCAM","score":0.6679999828338623},{"id":"https://openalex.org/keywords/met","display_name":"MET","score":0.5839999914169312},{"id":"https://openalex.org/keywords/caveolin-1","display_name":"caveolin-1","score":0.9589999914169312},{"id":"https://openalex.org/keywords/ap-1","display_name":"AP-1","score":0.9629999995231628}],"concepts":[{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.6710000038146973},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6459000110626221},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.49160000681877136},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.45680001378059387},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.36399999260902405},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3467000126838684},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.33500000834465027},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.33079999685287476},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.3100000023841858},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.30709999799728394},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.30250000953674316},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.30230000615119934},{"id":"https://openalex.org/C67258246","wikidata":"https://www.wikidata.org/wiki/Q5065897","display_name":"ChIA-PET","level":5,"score":0.29510000348091125},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.29179999232292175},{"id":"https://openalex.org/C64350747","wikidata":"https://www.wikidata.org/wiki/Q15334993","display_name":"RNA polymerase II","level":5,"score":0.2906999886035919},{"id":"https://openalex.org/C2776449523","wikidata":"https://www.wikidata.org/wiki/Q272631","display_name":"RNA polymerase","level":4,"score":0.2849000096321106},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.2838999927043915},{"id":"https://openalex.org/C189430467","wikidata":"https://www.wikidata.org/wiki/Q7293293","display_name":"Ranking (information retrieval)","level":2,"score":0.27709999680519104},{"id":"https://openalex.org/C2777742833","wikidata":"https://www.wikidata.org/wiki/Q1964083","display_name":"Reciprocal","level":2,"score":0.25699999928474426},{"id":"https://openalex.org/C100924687","wikidata":"https://www.wikidata.org/wiki/Q910324","display_name":"Euchromatin","level":5,"score":0.2563000023365021},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.25119999051094055}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.3390/ijms27219888","doi":"https://doi.org/10.3390/ijms27219888","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms27219888","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Molecular Sciences","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.3390/ijms27219888","doi":"https://doi.org/10.3390/ijms27219888","is_oa":true,"landing_page_url":"https://doi.org/10.3390/ijms27219888","pdf_url":null,"source":{"id":"https://openalex.org/S10623703","display_name":"International Journal of Molecular Sciences","issn_l":"1422-0067","issn":["1422-0067","1661-6596"],"is_oa":true,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","medline","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Molecular Sciences","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4000000059604645}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":29,"referenced_works":["https://openalex.org/W1973287023","https://openalex.org/W2050930814","https://openalex.org/W2104271563","https://openalex.org/W2978708928","https://openalex.org/W2982638381","https://openalex.org/W3093858607","https://openalex.org/W3175283754","https://openalex.org/W3215596355","https://openalex.org/W4205514149","https://openalex.org/W4210774372","https://openalex.org/W4225146220","https://openalex.org/W4311579386","https://openalex.org/W4361190647","https://openalex.org/W4387964910","https://openalex.org/W4388784493","https://openalex.org/W4393111577","https://openalex.org/W4394011009","https://openalex.org/W4395069767","https://openalex.org/W4395113839","https://openalex.org/W4404595570","https://openalex.org/W4404979990","https://openalex.org/W4409645306","https://openalex.org/W4410855348","https://openalex.org/W4411099958","https://openalex.org/W4412699288","https://openalex.org/W4413814840","https://openalex.org/W4413860090","https://openalex.org/W4413911379","https://openalex.org/W7131656026"],"related_works":["https://openalex.org/W7213540448","https://openalex.org/W7223811239","https://openalex.org/W4385851326","https://openalex.org/W3119459981","https://openalex.org/W7135426784","https://openalex.org/W7133230180","https://openalex.org/W4404439240","https://openalex.org/W7221121644","https://openalex.org/W4393073814","https://openalex.org/W4407000208"],"abstract_inverted_index":{"Matched":[0],"single-cell":[1,6,40],"RNA":[2,69],"sequencing":[3,11],"(scRNA-seq)":[4],"and":[5,30,43,71,82,108,132,159,173,185,206,211],"assay":[7],"for":[8,51],"transposase-accessible":[9],"chromatin":[10,32],"(scATAC-seq)":[12],"profiles":[13],"from":[14],"the":[15,116,126,166],"same":[16,167],"cells":[17],"remain":[18],"limited":[19,139],"in":[20],"hepatocellular":[21],"carcinoma":[22],"(HCC),":[23],"hindering":[24],"cell-resolved":[25],"integration":[26],"of":[27,106,112,120,163],"transcriptional":[28],"programs":[29],"regulatory":[31],"states.":[33],"To":[34],"address":[35],"this":[36],"challenge,":[37],"we":[38],"developed":[39],"Liver-adapted":[41],"Alignment":[42],"Pseudo-pairing":[44],"(scLAP),":[45],"a":[46,59,89,109,160,181],"liver-adapted":[47],"contrastive":[48],"shared-latent":[49],"framework":[50],"cross-study":[52],"RNA-ATAC":[53,197],"pseudo-pairing.":[54],"scLAP":[55,97],"was":[56],"trained":[57],"on":[58,165],"paired":[60],"liver":[61],"single-nucleus":[62],"multiome":[63],"reference":[64],"using":[65,149],"2000":[66],"highly":[67],"variable":[68],"features":[70],"697":[72],"ATAC":[73,152],"features,":[74],"including":[75],"647":[76],"transcription":[77],"factor":[78],"motif":[79],"activity":[80],"scores":[81],"50":[83],"latent":[84],"semantic":[85],"indexing":[86],"components.":[87],"On":[88],"prespecified":[90],"cell-level":[91],"test":[92,168],"partition":[93],"(n":[94],"=":[95],"3235),":[96],"achieved":[98,154],"an":[99,202],"ATAC-to-RNA":[100],"Top":[101,156],"10":[102,157],"exact-pair":[103,140],"retrieval":[104,158],"rate":[105],"21.48%":[107],"mean":[110,161],"fraction":[111],"samples":[113],"closer":[114],"than":[115],"true":[117],"match":[118],"(FOSCTTM)":[119],"0.0431.":[121],"In":[122],"six":[123],"leave-one-sample-out":[124],"folds,":[125],"corresponding":[127],"macro":[128],"means":[129],"were":[130],"5.23%":[131],"0.2278,":[133],"respectively,":[134],"indicating":[135],"above-random":[136],"ranking":[137],"but":[138],"transfer":[141],"to":[142,189],"unseen":[143],"samples.":[144],"A":[145],"validation-selected":[146],"scButterfly":[147],"configuration":[148],"20,000":[150],"native":[151],"peaks":[153],"8.93%":[155],"FOSCTTM":[162],"0.0811":[164],"cells;":[169],"comparisons":[170],"with":[171],"Con-AAE":[172],"scMODAL":[174],"remained":[175],"study-specific":[176],"adaptations.":[177],"Applying":[178],"reciprocal":[179],"retrieval,":[180],"validation-derived":[182],"cosine-similarity":[183],"threshold,":[184],"greedy":[186],"one-to-one":[187],"assignment":[188],"independent":[190],"HCC":[191],"datasets":[192],"yielded":[193],"4007":[194],"similarity-filtered":[195],"candidate":[196,205],"pseudo-pairs.":[198],"Downstream":[199],"analyses":[200],"identified":[201],"NRCAM-associated":[203],"accessibility":[204],"separate":[207],"exploratory":[208],"MET-,":[209],"CAV1-,":[210],"AP-1-associated":[212],"observations.":[213]},"counts_by_year":[],"updated_date":"2026-11-06T12:05:46.655746","created_date":"2026-11-05T00:00:00"}