{"id":"https://openalex.org/W4415933716","doi":"https://doi.org/10.1109/jbhi.2025.3628564","title":"TransGRN: A Transfer Learning-Based Framework for Inferring Gene Regulatory Networks Across Cell Lines","display_name":"TransGRN: A Transfer Learning-Based Framework for Inferring Gene Regulatory Networks Across Cell Lines","publication_year":2025,"publication_date":"2025-11-05","ids":{"openalex":"https://openalex.org/W4415933716","doi":"https://doi.org/10.1109/jbhi.2025.3628564","pmid":"https://pubmed.ncbi.nlm.nih.gov/41191474"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2025.3628564","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3628564","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062817621","display_name":"Ge Xu","orcid":"https://orcid.org/0009-0002-5652-7744"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ge Xu","raw_affiliation_strings":["College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Mechatronics and Control Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100389371","display_name":"Ziwei Wang","orcid":"https://orcid.org/0000-0002-1248-7130"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziwei Wang","raw_affiliation_strings":["College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0009-0005-9325-7079","affiliations":[{"raw_affiliation_string":"College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016354648","display_name":"Jiahao Zhou","orcid":"https://orcid.org/0000-0002-4931-9130"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiahao Zhou","raw_affiliation_strings":["College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0000-0002-4931-9130","affiliations":[{"raw_affiliation_string":"College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065833423","display_name":"Weiming Yu","orcid":"https://orcid.org/0000-0002-3024-2938"},"institutions":[{"id":"https://openalex.org/I180726961","display_name":"Shenzhen University","ror":"https://ror.org/01vy4gh70","country_code":"CN","type":"education","lineage":["https://openalex.org/I180726961"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiming Yu","raw_affiliation_strings":["College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China"],"raw_orcid":"https://orcid.org/0009-0007-2682-5288","affiliations":[{"raw_affiliation_string":"College of Electronics and Information Engineering, Shenzhen University, Shenzhen, China","institution_ids":["https://openalex.org/I180726961"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030129372","display_name":"Le Ou-Yang","orcid":"https://orcid.org/0000-0003-4007-4568"},"institutions":[{"id":"https://openalex.org/I4210152380","display_name":"Shenzhen Technology University","ror":"https://ror.org/04qzpec27","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152380"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Ou-Yang","raw_affiliation_strings":["SMBU-MSU-BIT Joint Laboratory on Bioinformatics and Engineering Biology, Shenzhen MSU-BIT University, Shenzhen, China","SMBU-MSU-BIT Joint Laboratory on Bioinformatics and Engineering Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong, China"],"raw_orcid":"https://orcid.org/0000-0003-4007-4568","affiliations":[{"raw_affiliation_string":"SMBU-MSU-BIT Joint Laboratory on Bioinformatics and Engineering Biology, Shenzhen MSU-BIT University, Shenzhen, China","institution_ids":["https://openalex.org/I4210152380"]},{"raw_affiliation_string":"SMBU-MSU-BIT Joint Laboratory on Bioinformatics and Engineering Biology, Shenzhen MSU-BIT University, Shenzhen, Guangdong, China","institution_ids":["https://openalex.org/I4210152380"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.4868,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.68699522,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"30","issue":"5","first_page":"4013","last_page":"4022"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9790999889373779,"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":0.9790999889373779,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.006399999838322401,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.0031999999191612005,"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/gene-regulatory-network","display_name":"Gene regulatory network","score":0.7178000211715698},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6786999702453613},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5609999895095825},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.47029998898506165},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.43140000104904175},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.33180001378059387},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.33160001039505005},{"id":"https://openalex.org/keywords/regulator-gene","display_name":"Regulator gene","score":0.3174000084400177}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7200000286102295},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.7178000211715698},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6786999702453613},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5734999775886536},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5609999895095825},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.47029998898506165},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.43140000104904175},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4032999873161316},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3792000114917755},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3653999865055084},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33180001378059387},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.33160001039505005},{"id":"https://openalex.org/C33498276","wikidata":"https://www.wikidata.org/wiki/Q2138797","display_name":"Regulator gene","level":4,"score":0.3174000084400177},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.3149000108242035},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.3102000057697296},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3095000088214874},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.30059999227523804},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.2928999960422516},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.29249998927116394},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.29190000891685486},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2881999909877777},{"id":"https://openalex.org/C2993684226","wikidata":"https://www.wikidata.org/wiki/Q2662727","display_name":"Human cell","level":3,"score":0.2667999863624573},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.26510000228881836},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.259799987077713}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","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":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","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":2,"locations":[{"id":"doi:10.1109/jbhi.2025.3628564","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2025.3628564","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:41191474","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41191474","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":"IEEE journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1888855023","display_name":null,"funder_award_id":"2022ZDZX1022","funder_id":"https://openalex.org/F4320326279","funder_display_name":"Department of Education of Guangdong Province"},{"id":"https://openalex.org/G1957408769","display_name":null,"funder_award_id":"62173235","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3516314601","display_name":null,"funder_award_id":"62473266","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6698629912","display_name":null,"funder_award_id":"2024B1515020059","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320326279","display_name":"Department of Education of Guangdong Province","ror":null},{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Inferring":[0],"gene":[1,79,120],"regulatory":[2,45,80,114,130],"networks":[3,81],"(GRNs)":[4,82],"is":[5],"critical":[6],"for":[7,57,77],"understanding":[8],"the":[9,30,58],"mechanisms":[10],"that":[11,92,118],"govern":[12],"cellular":[13],"behavior.":[14],"Advances":[15],"in":[16,51,142],"single-cell":[17,26],"RNA":[18],"sequencing":[19],"(scRNA-seq)":[20],"have":[21],"enabled":[22],"GRN":[23,148],"analysis":[24],"at":[25],"resolution":[27],"and":[28,146],"stimulated":[29],"development":[31],"of":[32],"many":[33],"computational":[34],"methods.":[35],"However,":[36],"most":[37],"existing":[38],"approaches":[39],"depend":[40],"heavily":[41],"on":[42],"extensive":[43],"prior":[44],"information,":[46],"which":[47],"limits":[48],"their":[49],"effectiveness":[50],"few-shot":[52,147],"settings":[53],"where":[54],"such":[55],"data":[56,95],"target":[59,135],"cell":[60,84,99,136],"line":[61],"are":[62],"scarce":[63],"or":[64],"unavailable.":[65],"To":[66],"address":[67],"this":[68],"challenge,":[69],"we":[70],"propose":[71],"TransGRN,":[72],"a":[73,88,113],"transfer":[74],"learning-based":[75],"method":[76],"inferring":[78],"across":[83],"lines.":[85],"TransGRN":[86,138],"adopts":[87],"cross-cell-line":[89],"pre-training":[90],"strategy":[91],"combines":[93],"scRNA-seq":[94],"from":[96,105,132],"multiple":[97],"source":[98,133],"lines":[100],"with":[101,123],"biological":[102],"knowledge":[103],"obtained":[104],"large":[106],"language":[107],"models.":[108],"In":[109],"addition,":[110],"it":[111],"includes":[112],"interaction":[115],"extraction":[116],"module":[117],"integrates":[119],"expression":[121],"profiles":[122],"semantic":[124],"information.":[125],"By":[126],"transferring":[127],"generalizable":[128],"gene-gene":[129],"patterns":[131],"to":[134],"lines,":[137],"achieves":[139],"state-of-the-art":[140],"performance":[141],"both":[143],"benchmark":[144],"tests":[145],"inference":[149],"tasks.":[150]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-05-08T13:12:06.581006","created_date":"2025-11-05T00:00:00"}
