{"id":"https://openalex.org/W4403235965","doi":"https://doi.org/10.1093/bib/bbae492","title":"MultiSC: a deep learning pipeline for analyzing multiomics single-cell data","display_name":"MultiSC: a deep learning pipeline for analyzing multiomics single-cell data","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4403235965","doi":"https://doi.org/10.1093/bib/bbae492","pmid":"https://pubmed.ncbi.nlm.nih.gov/39376034"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae492","pdf_url":null,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://doi.org/10.1093/bib/bbae492","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057660606","display_name":"Xiang Lin","orcid":"https://orcid.org/0000-0002-7634-5780"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]},{"id":"https://openalex.org/I4210125099","display_name":"Mayo Clinic in Arizona","ror":"https://ror.org/03jp40720","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210125099"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiang Lin","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,","Department of Quantitative Health Sciences, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ 85259,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Department of Quantitative Health Sciences, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ 85259,","institution_ids":["https://openalex.org/I4210125099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063314027","display_name":"Siqi Jiang","orcid":"https://orcid.org/0009-0003-7675-663X"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Siqi Jiang","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047289560","display_name":"Le Gao","orcid":"https://orcid.org/0000-0003-2625-8774"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]},{"id":"https://openalex.org/I4210125099","display_name":"Mayo Clinic in Arizona","ror":"https://ror.org/03jp40720","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210125099"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Le Gao","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,","Department of Quantitative Health Sciences, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ 85259,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,","institution_ids":["https://openalex.org/I118118575"]},{"raw_affiliation_string":"Department of Quantitative Health Sciences, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ 85259,","institution_ids":["https://openalex.org/I4210125099"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001916237","display_name":"Zhi Wei","orcid":"https://orcid.org/0000-0001-6059-4267"},"institutions":[{"id":"https://openalex.org/I118118575","display_name":"New Jersey Institute of Technology","ror":"https://ror.org/05e74xb87","country_code":"US","type":"education","lineage":["https://openalex.org/I118118575"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zhi Wei","raw_affiliation_strings":["Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,"],"raw_orcid":"https://orcid.org/0000-0001-6059-4267","affiliations":[{"raw_affiliation_string":"Department of Computer Science, New Jersey Institute of Technology , 323 Dr Martin Luther King Jr Blvd, Newark, NJ 07102,","institution_ids":["https://openalex.org/I118118575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100704433","display_name":"Junwen Wang","orcid":"https://orcid.org/0000-0002-4432-4707"},"institutions":[{"id":"https://openalex.org/I4210125099","display_name":"Mayo Clinic in Arizona","ror":"https://ror.org/03jp40720","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1330342723","https://openalex.org/I4210125099"]},{"id":"https://openalex.org/I4390039329","display_name":"UNC Lineberger Comprehensive Cancer Center","ror":"https://ror.org/043ehm030","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I114027177","https://openalex.org/I4390039329"]},{"id":"https://openalex.org/I889458895","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86","country_code":"HK","type":"education","lineage":["https://openalex.org/I889458895"]}],"countries":["HK","US"],"is_corresponding":false,"raw_author_name":"Junwen Wang","raw_affiliation_strings":["Center for Individualized Medicine , and Mayo Clinic Comprehensive Cancer Center, , 13400 E Shea Blvd, Scottsdale, AZ 85259,","Department of Quantitative Health Sciences, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ 85259,","Division of Applied Oral Sciences & Community Dental Care , Faculty of Dentistry, , 34 Hospital Road, Sai Ying Pun, Hong Kong SAR,","Mayo Clinic , and Mayo Clinic Comprehensive Cancer Center, , 13400 E Shea Blvd, Scottsdale, AZ 85259,","The University of Hong Kong , Faculty of Dentistry, , 34 Hospital Road, Sai Ying Pun, Hong Kong SAR,"],"raw_orcid":"https://orcid.org/0000-0002-4432-4707","affiliations":[{"raw_affiliation_string":"Center for Individualized Medicine , and Mayo Clinic Comprehensive Cancer Center, , 13400 E Shea Blvd, Scottsdale, AZ 85259,","institution_ids":["https://openalex.org/I4210125099"]},{"raw_affiliation_string":"Department of Quantitative Health Sciences, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ 85259,","institution_ids":["https://openalex.org/I4210125099"]},{"raw_affiliation_string":"Division of Applied Oral Sciences & Community Dental Care , Faculty of Dentistry, , 34 Hospital Road, Sai Ying Pun, Hong Kong SAR,","institution_ids":[]},{"raw_affiliation_string":"Mayo Clinic , and Mayo Clinic Comprehensive Cancer Center, , 13400 E Shea Blvd, Scottsdale, AZ 85259,","institution_ids":["https://openalex.org/I4210125099","https://openalex.org/I4390039329"]},{"raw_affiliation_string":"The University of Hong Kong , Faculty of Dentistry, , 34 Hospital Road, Sai Ying Pun, Hong Kong SAR,","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.9331,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.74352084,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"25","issue":"6","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":1.0,"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"}},"topics":[{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":1.0,"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"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9969000220298767,"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":0.9948999881744385,"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/pipeline","display_name":"Pipeline (software)","score":0.7324473857879639},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7014459371566772},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5030376315116882},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4518345296382904},{"id":"https://openalex.org/keywords/data-integration","display_name":"Data integration","score":0.4380970001220703},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.4128662645816803},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.41065773367881775},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3864074945449829},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34914690256118774},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.337252140045166},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.22919034957885742},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1657845377922058},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.15119808912277222},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1416759490966797}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7324473857879639},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7014459371566772},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5030376315116882},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4518345296382904},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.4380970001220703},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.4128662645816803},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.41065773367881775},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3864074945449829},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34914690256118774},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.337252140045166},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.22919034957885742},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1657845377922058},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.15119808912277222},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1416759490966797},{"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/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep 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":"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":"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":"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":"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":"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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"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":"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":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae492","pdf_url":null,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39376034","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39376034","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:pubmedcentral.nih.gov:11458747","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11458747","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11458747/pdf/bbae492.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae492","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae492","pdf_url":null,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1063217684","display_name":null,"funder_award_id":"2207101590","funder_id":"https://openalex.org/F4320322170","funder_display_name":"University of Hong Kong"},{"id":"https://openalex.org/G1252428628","display_name":null,"funder_award_id":"R15HG012087","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1742171491","display_name":null,"funder_award_id":"1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2206590661","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2956415725","display_name":null,"funder_award_id":"R01LM013438","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G367708065","display_name":null,"funder_award_id":"ACI-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3709464396","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3730782400","display_name":"XSEDE 2.0:  Integrating, Enabling and Enhancing National Cyberinfrastructure with Expanding Community Involvement","funder_award_id":"1548562","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4923476263","display_name":null,"funder_award_id":"R15HG012087","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5631589122","display_name":null,"funder_award_id":"UM1TR004789","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6306877460","display_name":null,"funder_award_id":"P01CA281867","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7453668593","display_name":null,"funder_award_id":"R15 HG012087","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G8907196067","display_name":null,"funder_award_id":"-1548562","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306143","display_name":"Mayo Clinic","ror":"https://ror.org/02qp3tb03"},{"id":"https://openalex.org/F4320322170","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1492083415","https://openalex.org/W1602702667","https://openalex.org/W1917589835","https://openalex.org/W1980888912","https://openalex.org/W1987971958","https://openalex.org/W1988917769","https://openalex.org/W1996555607","https://openalex.org/W2014384102","https://openalex.org/W2015280752","https://openalex.org/W2015587858","https://openalex.org/W2025768430","https://openalex.org/W2035618305","https://openalex.org/W2054590983","https://openalex.org/W2098023402","https://openalex.org/W2100495367","https://openalex.org/W2104675641","https://openalex.org/W2132066963","https://openalex.org/W2167699956","https://openalex.org/W2346483050","https://openalex.org/W2414895359","https://openalex.org/W2555875659","https://openalex.org/W2739492614","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2889749261","https://openalex.org/W2901677030","https://openalex.org/W2937917790","https://openalex.org/W2951381561","https://openalex.org/W2979911343","https://openalex.org/W3013823153","https://openalex.org/W3021145032","https://openalex.org/W3023456235","https://openalex.org/W3027051073","https://openalex.org/W3051806837","https://openalex.org/W3087284804","https://openalex.org/W3099862724","https://openalex.org/W3129866267","https://openalex.org/W3137285774","https://openalex.org/W3164839005","https://openalex.org/W3178265430","https://openalex.org/W3210860076","https://openalex.org/W4200581587","https://openalex.org/W4210799628","https://openalex.org/W4311232381","https://openalex.org/W4382202790"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2159052453","https://openalex.org/W2566616303","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W4386815338","https://openalex.org/W2145836866","https://openalex.org/W2803255133"],"abstract_inverted_index":{"Single-cell":[0],"technologies":[1],"enable":[2],"researchers":[3,195,220],"to":[4,28,122,137,152,182,196],"investigate":[5],"cell":[6,11,202],"functions":[7],"at":[8],"an":[9,38],"individual":[10],"level":[12],"and":[13,56,131,168,204,224],"study":[14],"cellular":[15,33,71,234],"processes":[16],"with":[17],"higher":[18],"resolution.":[19],"Several":[20],"multi-omics":[21,125,159],"single-cell":[22,215],"sequencing":[23],"techniques":[24],"have":[25],"been":[26],"developed":[27],"explore":[29],"various":[30],"aspects":[31],"of":[32,46,59,70,81,90,107,186,201,213,233],"behavior.":[34],"Using":[35],"NEAT-seq":[36,64],"as":[37],"example,":[39],"this":[40,95],"method":[41],"simultaneously":[42],"obtains":[43],"three":[44,88],"kinds":[45],"omics":[47,91,227],"data":[48,126,228],"for":[49,84,104],"each":[50],"cell:":[51],"gene":[52,154,205],"expression,":[53,165],"chromatin":[54],"accessibility,":[55],"protein":[57],"expression":[58],"transcription":[60],"factors":[61],"(TFs).":[62],"Consequently,":[63],"offers":[65],"a":[66,79,99,114,132,143,198],"more":[67],"comprehensive":[68,199],"understanding":[69,232],"activities":[72,203],"in":[73],"multiple":[74],"modalities.":[75],"However,":[76],"there":[77],"is":[78],"lack":[80],"tools":[82],"available":[83],"effectively":[85,222],"integrating":[86],"the":[87,105,124,128,158,175,184,211],"types":[89],"data.":[92,110,160,216],"To":[93],"address":[94],"gap,":[96],"we":[97,146],"propose":[98],"novel":[100],"pipeline":[101,112,193],"called":[102],"MultiSC":[103,176],"analysis":[106],"MULTIomic":[108],"Single-Cell":[109],"Our":[111],"leverages":[113],"multimodal":[115],"constraint":[116,120],"autoencoder":[117],"(single-cell":[118],"hierarchical":[119],"autoencoder)":[121],"integrate":[123,223],"during":[127],"clustering":[129],"process":[130],"matrix":[133],"factorization-based":[134],"model":[135],"(scMF)":[136],"predict":[138,153],"target":[139],"genes":[140],"regulated":[141],"by":[142,208],"TF.":[144],"Moreover,":[145],"utilize":[147],"multivariate":[148],"linear":[149],"regression":[150],"models":[151],"regulatory":[155,206],"networks":[156,207],"from":[157],"Additional":[161],"functionalities,":[162],"including":[163],"differential":[164],"mediation":[166],"analysis,":[167],"causal":[169],"inference,":[170],"are":[171],"also":[172],"incorporated":[173],"into":[174],"pipeline.":[177],"Extensive":[178],"experiments":[179],"were":[180],"conducted":[181],"evaluate":[183],"performance":[185],"MultiSC.":[187],"The":[188],"results":[189],"demonstrate":[190],"that":[191],"our":[192],"enables":[194],"gain":[197],"view":[200],"fully":[209],"leveraging":[210],"potential":[212],"multiomics":[214],"By":[217],"employing":[218],"MultiSC,":[219],"can":[221],"analyze":[225],"diverse":[226],"types,":[229],"enhancing":[230],"their":[231],"processes.":[235]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
