{"id":"https://openalex.org/W4393066754","doi":"https://doi.org/10.1093/bib/bbae018","title":"scHybridBERT: integrating gene regulation and cell graph for spatiotemporal dynamics in single-cell clustering","display_name":"scHybridBERT: integrating gene regulation and cell graph for spatiotemporal dynamics in single-cell clustering","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4393066754","doi":"https://doi.org/10.1093/bib/bbae018","pmid":"https://pubmed.ncbi.nlm.nih.gov/38517692"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae018","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae018/56659771/bbae018.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/25/2/bbae018/56659771/bbae018.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101899687","display_name":"Wei Zhang","orcid":"https://orcid.org/0000-0002-9719-554X"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhang Wei","raw_affiliation_strings":["Zhejiang Sci-Tech University , 310028, Hangzhou , China"],"raw_orcid":"https://orcid.org/0000-0002-9719-554X","affiliations":[{"raw_affiliation_string":"Zhejiang Sci-Tech University , 310028, Hangzhou , China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094217905","display_name":"Chenjun Wu","orcid":"https://orcid.org/0009-0004-9181-1366"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wu Chenjun","raw_affiliation_strings":["Zhejiang Sci-Tech University , 310028, Hangzhou , China"],"raw_orcid":"https://orcid.org/0009-0004-9181-1366","affiliations":[{"raw_affiliation_string":"Zhejiang Sci-Tech University , 310028, Hangzhou , China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5094217906","display_name":"Xing Feiyang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210087873","display_name":"Institute for Stem Cell Biology and Regenerative Medicine","ror":"https://ror.org/007wpch15","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3141573830","https://openalex.org/I4210087873","https://openalex.org/I4210134808"]},{"id":"https://openalex.org/I4210128175","display_name":"Shanghai East Hospital","ror":"https://ror.org/038xmzj21","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128175"]}],"countries":["CN","IN"],"is_corresponding":false,"raw_author_name":"Xing Feiyang","raw_affiliation_strings":["Tongji University , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tongji University , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","institution_ids":["https://openalex.org/I4210128175"]},{"raw_affiliation_string":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","institution_ids":["https://openalex.org/I4210087873"]},{"raw_affiliation_string":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China","institution_ids":["https://openalex.org/I4210128175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101022189","display_name":"Jiang Mingfeng","orcid":null},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiang Mingfeng","raw_affiliation_strings":["Zhejiang Sci-Tech University , 310028, Hangzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Sci-Tech University , 310028, Hangzhou , China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhang Yixuan","orcid":null},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhang Yixuan","raw_affiliation_strings":["Zhejiang Sci-Tech University , 310028, Hangzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Sci-Tech University , 310028, Hangzhou , China","institution_ids":["https://openalex.org/I1328775524"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100453248","display_name":"Qi Liu","orcid":"https://orcid.org/0000-0003-2578-1221"},"institutions":[{"id":"https://openalex.org/I4210087873","display_name":"Institute for Stem Cell Biology and Regenerative Medicine","ror":"https://ror.org/007wpch15","country_code":"IN","type":"facility","lineage":["https://openalex.org/I2799351866","https://openalex.org/I3141573830","https://openalex.org/I4210087873","https://openalex.org/I4210134808"]},{"id":"https://openalex.org/I4210128175","display_name":"Shanghai East Hospital","ror":"https://ror.org/038xmzj21","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210128175"]}],"countries":["CN","IN"],"is_corresponding":true,"raw_author_name":"Liu Qi","raw_affiliation_strings":["Tongji University , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tongji University , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","institution_ids":["https://openalex.org/I4210128175"]},{"raw_affiliation_string":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine , Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, , 200092, Shanghai , China","institution_ids":["https://openalex.org/I4210087873"]},{"raw_affiliation_string":"Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Frontier Science Center for Stem Cell Research, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China","institution_ids":["https://openalex.org/I4210128175"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089002910","display_name":"Zhuoxing Shi","orcid":"https://orcid.org/0000-0001-7463-4979"},"institutions":[{"id":"https://openalex.org/I157773358","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71","country_code":"CN","type":"education","lineage":["https://openalex.org/I157773358"]},{"id":"https://openalex.org/I4210127074","display_name":"Zhongshan Hospital","ror":"https://ror.org/032x22645","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210127074"]},{"id":"https://openalex.org/I4401726874","display_name":"Zhongshan Ophthalmic Center, Sun Yat-sen University","ror":"https://ror.org/02z2yec16","country_code":null,"type":"healthcare","lineage":["https://openalex.org/I157773358","https://openalex.org/I4401726874"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shi Zhuoxing","raw_affiliation_strings":["State Key Laboratory of Ophthalmology , Zhongshan Ophthalmic Center, , 510060, Guangzhou , China","Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science , Zhongshan Ophthalmic Center, , 510060, Guangzhou , China","State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China"],"raw_orcid":"https://orcid.org/0000-0001-7463-4979","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Ophthalmology , Zhongshan Ophthalmic Center, , 510060, Guangzhou , China","institution_ids":["https://openalex.org/I4210127074"]},{"raw_affiliation_string":"Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science , Zhongshan Ophthalmic Center, , 510060, Guangzhou , China","institution_ids":["https://openalex.org/I157773358","https://openalex.org/I4401726874"]},{"raw_affiliation_string":"State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, 510060, Guangzhou, China","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013729700","display_name":"Qi Dai","orcid":"https://orcid.org/0000-0003-2675-6511"},"institutions":[{"id":"https://openalex.org/I1328775524","display_name":"Zhejiang Sci-Tech University","ror":"https://ror.org/03893we55","country_code":"CN","type":"education","lineage":["https://openalex.org/I1328775524"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dai Qi","raw_affiliation_strings":["Zhejiang Sci-Tech University , 310028, Hangzhou , China"],"raw_orcid":"https://orcid.org/0000-0003-2675-6511","affiliations":[{"raw_affiliation_string":"Zhejiang Sci-Tech University , 310028, Hangzhou , China","institution_ids":["https://openalex.org/I1328775524"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5013729700","https://openalex.org/A5089002910","https://openalex.org/A5100453248"],"corresponding_institution_ids":["https://openalex.org/I1328775524","https://openalex.org/I157773358","https://openalex.org/I4210087873","https://openalex.org/I4210127074","https://openalex.org/I4210128175","https://openalex.org/I4401726874"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.5598,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.63806554,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":96},"biblio":{"volume":"25","issue":"2","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":0.9858999848365784,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9818999767303467,"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":0.712096095085144},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6900120377540588},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.5536497831344604},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.5088622570037842},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.4738212823867798},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4685674011707306},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.46558159589767456},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4140858054161072},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3472977876663208},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.21815934777259827},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.18138426542282104},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.18108606338500977},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10382542014122009}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.712096095085144},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6900120377540588},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5536497831344604},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5088622570037842},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.4738212823867798},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4685674011707306},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.46558159589767456},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4140858054161072},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3472977876663208},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.21815934777259827},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.18138426542282104},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.18108606338500977},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10382542014122009},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","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":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002450","descriptor_name":"Cell Communication","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019985","descriptor_name":"Benchmarking","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbae018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae018","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae018/56659771/bbae018.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:38517692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38517692","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}],"best_oa_location":{"id":"doi:10.1093/bib/bbae018","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae018","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae018/56659771/bbae018.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":[{"id":"https://openalex.org/G4927119344","display_name":null,"funder_award_id":"62302455","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5072212599","display_name":null,"funder_award_id":"2021C02039","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5595964114","display_name":null,"funder_award_id":"62172369","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6145996950","display_name":null,"funder_award_id":"2021C02039","funder_id":"https://openalex.org/F8142712028","funder_display_name":"Key Research and Development Program of Zhejiang Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F8142712028","display_name":"Key Research and Development Program of Zhejiang Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4393066754.pdf"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W2610774430","https://openalex.org/W2794480084","https://openalex.org/W2798338825","https://openalex.org/W2921230232","https://openalex.org/W2937917790","https://openalex.org/W2953251392","https://openalex.org/W2965552103","https://openalex.org/W2998065416","https://openalex.org/W3084086295","https://openalex.org/W3093900604","https://openalex.org/W3109942090","https://openalex.org/W3131383906","https://openalex.org/W3138479716","https://openalex.org/W3176693948","https://openalex.org/W3196939060","https://openalex.org/W3198412468","https://openalex.org/W3198628780","https://openalex.org/W3204708585","https://openalex.org/W3215916291","https://openalex.org/W4200477198","https://openalex.org/W4206445485","https://openalex.org/W4210714205","https://openalex.org/W4210826564","https://openalex.org/W4213136259","https://openalex.org/W4214611015","https://openalex.org/W4225568512","https://openalex.org/W4297243391","https://openalex.org/W4313424570","https://openalex.org/W4315779449","https://openalex.org/W4316096017","https://openalex.org/W4317888741","https://openalex.org/W4362671013","https://openalex.org/W4377139884","https://openalex.org/W4378212544","https://openalex.org/W4379599555","https://openalex.org/W6808530605","https://openalex.org/W6809048309","https://openalex.org/W6852249784"],"related_works":["https://openalex.org/W2378211422","https://openalex.org/W2745001401","https://openalex.org/W4321353415","https://openalex.org/W2130974462","https://openalex.org/W2028665553","https://openalex.org/W2086519370","https://openalex.org/W972276598","https://openalex.org/W2087343574","https://openalex.org/W4246352526","https://openalex.org/W2121910908"],"abstract_inverted_index":{"Graph":[0],"learning":[1,145],"models":[2,28,146],"have":[3,29],"received":[4],"increasing":[5],"attention":[6],"in":[7,71],"the":[8,83,90,110,117,126,155,169,177],"computational":[9],"analysis":[10],"of":[11,85,92,119,133,179],"single-cell":[12,72,180],"RNA":[13],"sequencing":[14],"(scRNA-seq)":[15],"data.":[16,73],"Compared":[17],"with":[18,151],"conventional":[19],"deep":[20,43],"neural":[21,24,44],"networks,":[22],"graph":[23,144],"networks":[25],"and":[26,76,100,154,187],"language":[27],"exhibited":[30],"superior":[31],"performance":[32,84],"by":[33,183],"extracting":[34],"graph-structured":[35],"data":[36,135],"from":[37],"raw":[38],"gene":[39],"count":[40],"matrices.":[41],"Established":[42],"network-based":[45],"clustering":[46,181],"approaches":[47],"generally":[48],"focus":[49],"on":[50],"temporal":[51],"expression":[52],"patterns":[53],"while":[54],"ignoring":[55],"inherent":[56],"interactions":[57,78],"at":[58,109],"gene-level":[59],"as":[60,62,68],"well":[61],"cell-level,":[63],"which":[64],"could":[65],"be":[66],"regarded":[67],"spatial":[69,107],"dynamics":[70,108],"Both":[74],"gene-gene":[75],"cell-cell":[77],"are":[79,103,147],"able":[80,174],"to":[81,105,115,129,149,175],"boost":[82],"cell":[86,101,120,152,188],"type":[87,121],"detection,":[88,122],"under":[89],"framework":[91],"multi-view":[93,131],"modeling.":[94],"In":[95,113,140],"this":[96,123,141],"study,":[97],"spatiotemporal":[98,138,159,185],"embedding":[99],"graphs":[102,153],"extracted":[104,137],"capture":[106],"molecular":[111],"level.":[112],"order":[114],"enhance":[116,176],"accuracy":[118,178],"study":[124],"proposes":[125],"scHybridBERT":[127,142,171],"architecture":[128],"conduct":[130],"modeling":[132],"scRNA-seq":[134,165],"using":[136],"patterns.":[139],"method,":[143],"employed":[148],"deal":[150],"Performer":[156],"model":[157],"employs":[158],"embeddings.":[160],"Experimental":[161],"outcomes":[162],"about":[163],"benchmark":[164],"datasets":[166],"indicate":[167],"that":[168],"proposed":[170],"method":[172],"is":[173],"tasks":[182],"integrating":[184],"embeddings":[186],"graphs.":[189]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}