{"id":"https://openalex.org/W4413969542","doi":"https://doi.org/10.1093/bib/bbaf411","title":"sCIN: a contrastive learning framework for single-cell multi-omics data integration","display_name":"sCIN: a contrastive learning framework for single-cell multi-omics data integration","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4413969542","doi":"https://doi.org/10.1093/bib/bbaf411","pmid":"https://pubmed.ncbi.nlm.nih.gov/40856525"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf411","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf411","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf411/64137607/bbaf411.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/26/4/bbaf411/64137607/bbaf411.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042133577","display_name":"Amir Ebrahimi","orcid":"https://orcid.org/0000-0001-7698-2264"},"institutions":[{"id":"https://openalex.org/I23946033","display_name":"University of Tehran","ror":"https://ror.org/05vf56z40","country_code":"IR","type":"education","lineage":["https://openalex.org/I23946033"]}],"countries":["IR"],"is_corresponding":true,"raw_author_name":"Amir Ebrahimi","raw_affiliation_strings":["Department of Biotechnology, College of Science, University of Tehran , Ghods 37, Tehran , 1417763135,","Department of Biotechnology, College of Science, University of Tehran, Ghods 37, Tehran, 1417763135, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Biotechnology, College of Science, University of Tehran , Ghods 37, Tehran , 1417763135,","institution_ids":["https://openalex.org/I23946033"]},{"raw_affiliation_string":"Department of Biotechnology, College of Science, University of Tehran, Ghods 37, Tehran, 1417763135, Iran","institution_ids":["https://openalex.org/I23946033"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038344150","display_name":"Alireza Fotuhi Siahpirani","orcid":"https://orcid.org/0000-0002-7804-4084"},"institutions":[{"id":"https://openalex.org/I4210103004","display_name":"Institute of Biochemistry","ror":"https://ror.org/022dvs210","country_code":"HU","type":"facility","lineage":["https://openalex.org/I2800351701","https://openalex.org/I4210103004","https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Alireza Fotuhi Siahpirani","raw_affiliation_strings":["Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran , Ghods 37, Tehran , 1417763135,","Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Ghods 37, Tehran, 1417763135, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran , Ghods 37, Tehran , 1417763135,","institution_ids":["https://openalex.org/I4210103004"]},{"raw_affiliation_string":"Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Ghods 37, Tehran, 1417763135, Iran","institution_ids":["https://openalex.org/I4210103004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063294278","display_name":"H. Montazeri","orcid":null},"institutions":[{"id":"https://openalex.org/I4210103004","display_name":"Institute of Biochemistry","ror":"https://ror.org/022dvs210","country_code":"HU","type":"facility","lineage":["https://openalex.org/I2800351701","https://openalex.org/I4210103004","https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Hesam Montazeri","raw_affiliation_strings":["Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran , Ghods 37, Tehran , 1417763135,","Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Ghods 37, Tehran, 1417763135, Iran"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran , Ghods 37, Tehran , 1417763135,","institution_ids":["https://openalex.org/I4210103004"]},{"raw_affiliation_string":"Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Ghods 37, Tehran, 1417763135, Iran","institution_ids":["https://openalex.org/I4210103004"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5042133577"],"corresponding_institution_ids":["https://openalex.org/I23946033"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.685,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.85716604,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"26","issue":"4","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":0.9998999834060669,"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":0.9998999834060669,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9958000183105469,"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":0.994700014591217,"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":0.6489840149879456},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.6459103226661682},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4365561306476593},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.2100110650062561},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1865428388118744}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6489840149879456},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.6459103226661682},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4365561306476593},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2100110650062561},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1865428388118744}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","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/bib/bbaf411","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf411","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf411/64137607/bbaf411.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40856525","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40856525","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:11187554","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12378934","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf411","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf411","pdf_url":"https://academic.oup.com/bib/article-pdf/26/4/bbaf411/64137607/bbaf411.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413969542.pdf","grobid_xml":"https://content.openalex.org/works/W4413969542.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W2025341678","https://openalex.org/W2264481086","https://openalex.org/W2739492614","https://openalex.org/W2744040456","https://openalex.org/W2794083495","https://openalex.org/W2797310920","https://openalex.org/W2800392236","https://openalex.org/W2808845633","https://openalex.org/W2887910040","https://openalex.org/W2917724292","https://openalex.org/W2949177718","https://openalex.org/W2952602120","https://openalex.org/W2979911343","https://openalex.org/W2984472267","https://openalex.org/W3013823153","https://openalex.org/W3027051073","https://openalex.org/W3093858607","https://openalex.org/W3129866267","https://openalex.org/W3155656876","https://openalex.org/W4205421285","https://openalex.org/W4210826564","https://openalex.org/W4225278475","https://openalex.org/W4283689887","https://openalex.org/W4289335819","https://openalex.org/W4295508821","https://openalex.org/W4313424570","https://openalex.org/W4327675690","https://openalex.org/W4361190647","https://openalex.org/W4379521442","https://openalex.org/W4382632237","https://openalex.org/W4387138272","https://openalex.org/W4392251634","https://openalex.org/W4399986066","https://openalex.org/W4402716083","https://openalex.org/W4402716457","https://openalex.org/W4405754608"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052"],"abstract_inverted_index":{"The":[0,92],"rapid":[1],"advancement":[2],"of":[3,26,130,138,154],"single-cell":[4,9,13,54],"omics":[5,62,157,246],"technologies":[6,152],"such":[7],"as":[8],"RNA":[10,119],"sequencing":[11,21],"and":[12,29,43,74,88,103,105,118,127,132,134,141,179,194,211,255],"assay":[14],"for":[15,81,202,214,237],"transposase-accessible":[16],"chromatin":[17,142],"with":[18,121],"high":[19],"throughput":[20],"has":[22],"transformed":[23],"our":[24],"understanding":[25],"cellular":[27,128],"heterogeneity":[28],"regulatory":[30],"mechanisms.":[31],"However,":[32],"integrating":[33],"these":[34],"data":[35,99,149],"types":[36],"remains":[37],"challenging":[38],"due":[39],"to":[40,77,96,147,232],"distributional":[41],"discrepancies":[42],"distinct":[44],"feature":[45],"spaces.":[46],"To":[47],"address":[48],"this,":[49],"we":[50],"present":[51],"a":[52,65,174],"novel":[53],"Contrastive":[55],"INtegration":[56],"framework":[57,93],"(sCIN)":[58],"that":[59,183],"integrates":[60,245],"different":[61,156,170],"modalities":[63,87,247],"into":[64],"shared":[66],"low-dimensional":[67],"latent":[68,79],"space.":[69],"sCIN":[70,184,218,243],"uses":[71],"modality-specific":[72],"encoders":[73],"contrastive":[75],"learning":[76],"generate":[78],"representations":[80],"each":[82],"modality,":[83],"aligning":[84],"cells":[85],"across":[86,196],"removing":[89],"technology-specific":[90],"biases.":[91],"was":[94,106,219],"designed":[95],"rigorously":[97],"prevent":[98],"leakage":[100],"between":[101],"training":[102],"testing,":[104],"extensively":[107],"evaluated":[108,220],"on":[109,177,221],"three":[110],"real-world":[111],"paired":[112,178,227,254],"datasets":[113,145,166,181,224],"namely":[114],"simultaneous":[115],"high-throughput":[116],"ATAC":[117],"expression":[120,140],"sequencing,":[122],"10X":[123],"PBMC":[124],"(10k":[125],"version),":[126],"indexing":[129],"transcriptomes":[131],"epitopes,":[133],"one":[135],"unpaired":[136,165,180,223,256],"dataset":[137],"gene":[139],"accessibility.":[143],"Paired":[144],"refer":[146],"multi-omics":[148],"generated":[150],"using":[151],"capable":[153],"capturing":[155],"features":[158],"from":[159,169,173,226],"the":[160],"same":[161],"cell":[162,171,206,208],"population":[163],"while":[164,248],"are":[167],"measured":[168],"populations":[172],"tissue.":[175],"Results":[176],"show":[182],"outperforms":[185],"state-of-the-art":[186],"models,":[187],"including":[188],"scGLUE,":[189],"scBridge,":[190],"sciCAN,":[191],"Con-AAE,":[192],"Harmony,":[193],"MOFA+,":[195],"multiple":[197],"metrics:":[198],"average":[199],"silhouette":[200],"width":[201],"clustering":[203],"quality,":[204],"Recall@k,":[205],"type@k,":[207],"type":[209],"accuracy,":[210],"median":[212],"rank":[213],"integration":[215],"quality.":[216],"Moreover,":[217],"simulated":[222],"derived":[225],"data,":[228],"demonstrating":[229],"its":[230],"ability":[231],"leverage":[233],"available":[234],"biological":[235,250],"information":[236],"effective":[238],"multimodal":[239],"integration.":[240],"In":[241],"summary,":[242],"reliably":[244],"preserving":[249],"meaning":[251],"in":[252],"both":[253],"settings.":[257]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}