{"id":"https://openalex.org/W4417117319","doi":"https://doi.org/10.1093/bib/bbag330","title":"GatorSC: Multi-Scale Cell and Gene Graphs with Mixture-of-Experts Fusion for Single-Cell Transcriptomics","display_name":"GatorSC: Multi-Scale Cell and Gene Graphs with Mixture-of-Experts Fusion for Single-Cell Transcriptomics","publication_year":2025,"publication_date":"2025-12-07","ids":{"openalex":"https://openalex.org/W4417117319","doi":"https://doi.org/10.1093/bib/bbag330","pmid":"https://pubmed.ncbi.nlm.nih.gov/41409156"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbag330","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag330","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"preprint","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbag330","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100602640","display_name":"Yuxi Liu","orcid":"https://orcid.org/0000-0003-1265-7926"},"institutions":[{"id":"https://openalex.org/I1283055418","display_name":"Indiana University Health","ror":"https://ror.org/01aaptx40","country_code":"US","type":"funder","lineage":["https://openalex.org/I1283055418","https://openalex.org/I4388446366","https://openalex.org/I592451"]},{"id":"https://openalex.org/I4210153792","display_name":"University School","ror":"https://ror.org/05ap66461","country_code":"US","type":"education","lineage":["https://openalex.org/I4210153792"]},{"id":"https://openalex.org/I4394709130","display_name":"Indiana University School of Medicine","ror":"https://ror.org/02ets8c94","country_code":null,"type":"education","lineage":["https://openalex.org/I4394709130","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuxi Liu","raw_affiliation_strings":["Department of Biostatistics and Health Data Science, Indiana University School of Medicine , Indianapolis, 410 W 10th St, IN 46202 ,","Indiana University School of Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine , Indianapolis, 410 W 10th St, IN 46202 ,","institution_ids":[]},{"raw_affiliation_string":"Indiana University School of Medicine","institution_ids":["https://openalex.org/I592451","https://openalex.org/I4210153792","https://openalex.org/I4394709130"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101859518","display_name":"Zhenhao Zhang","orcid":"https://orcid.org/0000-0001-6992-3047"},"institutions":[{"id":"https://openalex.org/I2801534221","display_name":"Agriculture and Forestry University","ror":"https://ror.org/01f60xs15","country_code":"NP","type":"education","lineage":["https://openalex.org/I2801534221"]},{"id":"https://openalex.org/I37802460","display_name":"Northwest University","ror":"https://ror.org/00z3td547","country_code":"CN","type":"education","lineage":["https://openalex.org/I37802460"]}],"countries":["CN","NP"],"is_corresponding":false,"raw_author_name":"Zhenhao Zhang","raw_affiliation_strings":["College of Life Sciences, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100 ,","Northwest Agriculture and Forestry University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences, Northwest A&F University , No. 3 Taicheng Road, Yangling, Shaanxi 712100 ,","institution_ids":[]},{"raw_affiliation_string":"Northwest Agriculture and Forestry University","institution_ids":["https://openalex.org/I2801534221"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Mufan Qiu","orcid":null},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mufan Qiu","raw_affiliation_strings":["Department of Computer Science, The University of North Carolina at Chapel Hill , 232 S Columbia St, NC 27599 ,","The University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Chapel Hill , 232 S Columbia St, NC 27599 ,","institution_ids":[]},{"raw_affiliation_string":"The University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100326208","display_name":"Song Wang","orcid":"https://orcid.org/0000-0002-6462-9866"},"institutions":[{"id":"https://openalex.org/I106165777","display_name":"University of Central Florida","ror":"https://ror.org/036nfer12","country_code":"US","type":"education","lineage":["https://openalex.org/I106165777"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Song Wang","raw_affiliation_strings":["Department of Computer Science, University of Central Florida , 4000 Central Florida Blvd., FL 32816 ,","University of Central Florida"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of Central Florida , 4000 Central Florida Blvd., FL 32816 ,","institution_ids":[]},{"raw_affiliation_string":"University of Central Florida","institution_ids":["https://openalex.org/I106165777"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090893421","display_name":"Flora D. Salim","orcid":"https://orcid.org/0000-0002-1237-1664"},"institutions":[{"id":"https://openalex.org/I31746571","display_name":"UNSW Sydney","ror":"https://ror.org/03r8z3t63","country_code":"AU","type":"education","lineage":["https://openalex.org/I31746571"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Flora D Salim","raw_affiliation_strings":["School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales , High St, Kensington, NSW 2052 ,","University of New South Wales"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Faculty of Engineering, University of New South Wales , High St, Kensington, NSW 2052 ,","institution_ids":[]},{"raw_affiliation_string":"University of New South Wales","institution_ids":["https://openalex.org/I31746571"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018392902","display_name":"Jun Shen","orcid":"https://orcid.org/0000-0001-5171-0035"},"institutions":[{"id":"https://openalex.org/I204824540","display_name":"University of Wollongong","ror":"https://ror.org/00jtmb277","country_code":"AU","type":"education","lineage":["https://openalex.org/I204824540"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jun Shen","raw_affiliation_strings":["School of Computing and Information Technology, Faculty of Engineering and Information Sciences, University of Wollongong , Wollongong, NSW 2522 ,","University of Wollongong"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing and Information Technology, Faculty of Engineering and Information Sciences, University of Wollongong , Wollongong, NSW 2522 ,","institution_ids":[]},{"raw_affiliation_string":"University of Wollongong","institution_ids":["https://openalex.org/I204824540"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103073431","display_name":"Tianlong Chen","orcid":"https://orcid.org/0000-0001-7774-8197"},"institutions":[{"id":"https://openalex.org/I114027177","display_name":"University of North Carolina at Chapel Hill","ror":"https://ror.org/0130frc33","country_code":"US","type":"education","lineage":["https://openalex.org/I114027177"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tianlong Chen","raw_affiliation_strings":["Department of Computer Science, The University of North Carolina at Chapel Hill , 232 S Columbia St, NC 27599 ,","The University of North Carolina at Chapel Hill"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of North Carolina at Chapel Hill , 232 S Columbia St, NC 27599 ,","institution_ids":[]},{"raw_affiliation_string":"The University of North Carolina at Chapel Hill","institution_ids":["https://openalex.org/I114027177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033585021","display_name":"Imran Razzak","orcid":"https://orcid.org/0000-0002-3930-6600"},"institutions":[{"id":"https://openalex.org/I4210113480","display_name":"Mohamed bin Zayed University of Artificial Intelligence","ror":"https://ror.org/0258gkt32","country_code":"AE","type":"education","lineage":["https://openalex.org/I4210113480"]}],"countries":["AE"],"is_corresponding":false,"raw_author_name":"Imran Razzak","raw_affiliation_strings":["Division of Biology and Life Science, Muhammad bin Zayed University of Artificial Intelligence , Building 1B, Masdar City 20302, Abu Dhabi ,","Mohamed bin Zayed University of Artificial Intelligence"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Biology and Life Science, Muhammad bin Zayed University of Artificial Intelligence , Building 1B, Masdar City 20302, Abu Dhabi ,","institution_ids":[]},{"raw_affiliation_string":"Mohamed bin Zayed University of Artificial Intelligence","institution_ids":["https://openalex.org/I4210113480"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Fuyi Li","orcid":null},"institutions":[{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852","https://openalex.org/I4405259444"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["AU","US"],"is_corresponding":true,"raw_author_name":"Fuyi Li","raw_affiliation_strings":["College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100 ,","South Australian immunoGENomics Cancer Institute (SAiGENCI) , The University of Adelaide, AHMS Building, North Terrace, SA 5005 ,","Indiana University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University , Yangling, Shaanxi 712100 ,","institution_ids":[]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI) , The University of Adelaide, AHMS Building, North Terrace, SA 5005 ,","institution_ids":[]},{"raw_affiliation_string":"Indiana University","institution_ids":["https://openalex.org/I592451"]}]},{"author_position":"last","author":{"id":null,"display_name":"Jiang Bian","orcid":null},"institutions":[{"id":"https://openalex.org/I1283055418","display_name":"Indiana University Health","ror":"https://ror.org/01aaptx40","country_code":"US","type":"funder","lineage":["https://openalex.org/I1283055418","https://openalex.org/I4388446366","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jiang Bian","raw_affiliation_strings":["Department of Biostatistics and Health Data Science, Indiana University School of Medicine , Indianapolis, 410 W 10th St, IN 46202 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Health Data Science, Indiana University School of Medicine , Indianapolis, 410 W 10th St, IN 46202 ,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":5,"institutions_distinct_count":12,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210140852","https://openalex.org/I592451"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.29774329,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"27","issue":"3","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":0.9983000159263611,"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":0.9983000159263611,"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/T11307","display_name":"Domain Adaptation and Few-Shot Learning","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.00019999999494757503,"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/graph","display_name":"Graph","score":0.4941999912261963},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4625000059604645},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.39899998903274536},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.3977000117301941},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.39089998602867126},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3695000112056732},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.35030001401901245}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6115999817848206},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5318999886512756},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4941999912261963},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4733999967575073},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4625000059604645},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.39899998903274536},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.3977000117301941},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.39089998602867126},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3695000112056732},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.35580000281333923},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.35030001401901245},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.3449000120162964},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3172000050544739},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.3012000024318695},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.28690001368522644},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.27959999442100525},{"id":"https://openalex.org/C2781170535","wikidata":"https://www.wikidata.org/wiki/Q30587856","display_name":"Noisy data","level":2,"score":0.2741999924182892},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.27320000529289246},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.26489999890327454},{"id":"https://openalex.org/C99498987","wikidata":"https://www.wikidata.org/wiki/Q2210247","display_name":"Noise (video)","level":3,"score":0.2639999985694885},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.2547000050544739}],"mesh":[],"locations_count":8,"locations":[{"id":"doi:10.1093/bib/bbag330","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag330","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.64898/2025.12.03.691688","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2025.12.03.691688","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:41409156","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41409156","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":"bioRxiv : the preprint server for biology","raw_type":null},{"id":"pmid:42308421","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42308421","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:11516109","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12707292","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12707292","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12707292/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:13275018","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13275018/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-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"},{"id":"pmh:oai:scholarworks.indianapolis.iu.edu:1805/52937","is_oa":false,"landing_page_url":"https://hdl.handle.net/1805/52937","pdf_url":null,"source":{"id":"https://openalex.org/S4306400987","display_name":"IUScholarWorks (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PMC","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbag330","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbag330","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":null,"license_id":null,"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/G199177249","display_name":null,"funder_award_id":"R01AG080624","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4027523644","display_name":null,"funder_award_id":"R01AG080991","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4476558940","display_name":null,"funder_award_id":"R01AG076234","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6037199653","display_name":null,"funder_award_id":"RF1AG077820","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7818219098","display_name":null,"funder_award_id":"R01AG083039","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8894638175","display_name":null,"funder_award_id":"RF1AG084178","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":44,"referenced_works":["https://openalex.org/W1631320694","https://openalex.org/W1979283544","https://openalex.org/W2135937351","https://openalex.org/W2150884987","https://openalex.org/W2610509384","https://openalex.org/W2610550445","https://openalex.org/W2794478094","https://openalex.org/W2800392236","https://openalex.org/W2805619986","https://openalex.org/W2894687190","https://openalex.org/W2901677030","https://openalex.org/W2927507212","https://openalex.org/W2937917790","https://openalex.org/W2950976066","https://openalex.org/W2951381561","https://openalex.org/W2951506174","https://openalex.org/W2964643116","https://openalex.org/W2991414673","https://openalex.org/W3021272327","https://openalex.org/W3121168830","https://openalex.org/W3138479716","https://openalex.org/W3159101980","https://openalex.org/W3198628780","https://openalex.org/W3216323060","https://openalex.org/W4205281625","https://openalex.org/W4221010612","https://openalex.org/W4225579877","https://openalex.org/W4225598893","https://openalex.org/W4280596398","https://openalex.org/W4288384137","https://openalex.org/W4290876361","https://openalex.org/W4378348563","https://openalex.org/W4385567478","https://openalex.org/W4393853792","https://openalex.org/W4394881579","https://openalex.org/W4396663708","https://openalex.org/W4398253916","https://openalex.org/W4402100533","https://openalex.org/W4403922429","https://openalex.org/W4403972624","https://openalex.org/W4404783367","https://openalex.org/W4408245847","https://openalex.org/W4408858386","https://openalex.org/W4412053846"],"related_works":[],"abstract_inverted_index":{"Single-cell":[0],"RNA":[1],"sequencing":[2,158],"(scRNA-seq)":[3],"enables":[4],"high-resolution":[5],"characterization":[6],"of":[7,25,47,192],"cellular":[8],"heterogeneity,":[9],"but":[10],"its":[11],"rich,":[12],"complementary":[13],"structure":[14,34],"across":[15],"cells":[16,48],"and":[17,28,49,73,76,93,102,119,128,141,157,170,179,197,217,224],"genes":[18,50],"remains":[19],"underexploited,":[20],"especially":[21],"in":[22,132,201],"the":[23],"presence":[24],"technical":[26],"noise":[27],"sparsity.":[29],"Effectively":[30],"leveraging":[31],"this":[32,56],"multi-scale":[33,71],"is":[35],"essentially":[36],"an":[37,202],"information":[38],"fusion":[39],"problem":[40],"that":[41,66,108,162],"requires":[42],"integrating":[43],"heterogeneous":[44],"graph-based":[45],"views":[46],"into":[51],"robust":[52],"low-dimensional":[53],"representations.":[54],"In":[55],"paper,":[57],"we":[58,124],"introduce":[59],"GatorSC,":[60],"a":[61,80,85,89,94,113,133,209],"unified":[62,134],"representation":[63],"learning":[64,131],"framework":[65],"models":[67],"scRNA-seq":[68,151],"data":[69],"through":[70],"cell":[72,174],"gene":[74,176,195],"graphs":[75],"fuses":[77],"them":[78],"with":[79],"mixture-of-experts":[81],"architecture.":[82],"GatorSC":[83,146,163,207],"constructs":[84],"global":[86,90],"cell-cell":[87],"graph,":[88,92],"gene-gene":[91,96],"local":[95],"graph":[97,104,126,129],"derived":[98],"from":[99],"neighborhood-specific":[100],"subgraphs,":[101],"learns":[103],"neural":[105],"network":[106],"embeddings":[107,121,184],"are":[109,185],"adaptively":[110],"fused":[111],"by":[112],"gating":[114],"network.":[115],"To":[116],"learn":[117],"noise-robust":[118],"structure-preserving":[120],"without":[122],"labels,":[123],"couple":[125],"reconstruction":[127],"contrastive":[130,171],"self-supervised":[135],"objective":[136],"applied":[137],"to":[138,222],"both":[139],"cell-":[140],"gene-level":[142],"graphs.":[143],"We":[144],"evaluate":[145],"on":[147],"19":[148],"publicly":[149],"available":[150],"datasets":[152],"covering":[153],"diverse":[154],"tissues,":[155],"species,":[156],"platforms.":[159],"Experiments":[160],"showed":[161],"consistently":[164],"outperforms":[165],"state-of-the-art":[166],"deep":[167],"generative,":[168],"graph-based,":[169],"methods":[172],"for":[173,187,212],"clustering,":[175],"expression":[177],"imputation,":[178],"cell-type":[180],"annotation.":[181],"The":[182],"learned":[183],"used":[186],"accurate":[188],"trajectory":[189],"inference,":[190],"recovery":[191],"canonical":[193],"marker":[194],"programs,":[196],"cell-type-specific":[198],"pathway":[199],"signatures":[200],"Alzheimer's":[203],"disease":[204],"single-nucleus":[205],"dataset.":[206],"provides":[208],"flexible":[210],"foundation":[211],"comprehensive":[213],"single-cell":[214],"transcriptomic":[215],"analysis":[216],"can":[218],"be":[219],"readily":[220],"extended":[221],"multi-omic":[223],"spatial":[225],"modalities.":[226]},"counts_by_year":[],"updated_date":"2026-07-02T09:51:11.867554","created_date":"2025-12-08T00:00:00"}
