{"id":"https://openalex.org/W4405459861","doi":"https://doi.org/10.1093/bib/bbae639","title":"A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks","display_name":"A self-attention-driven deep learning framework for inference of transcriptional gene regulatory networks","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4405459861","doi":"https://doi.org/10.1093/bib/bbae639","pmid":"https://pubmed.ncbi.nlm.nih.gov/39679439"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae639","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae639","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae639/61196044/bbae639.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-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://academic.oup.com/bib/article-pdf/26/1/bbae639/61196044/bbae639.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100724297","display_name":"Yong Liu","orcid":"https://orcid.org/0000-0003-4822-8939"},"institutions":[{"id":"https://openalex.org/I145897649","display_name":"Minzu University of China","ror":"https://ror.org/0044e2g62","country_code":"CN","type":"education","lineage":["https://openalex.org/I145897649"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yong Liu","raw_affiliation_strings":["College of Electronic Information, Guangxi Minzu University , 188 East University Road, Nanning, Guangxi , 530006,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electronic Information, Guangxi Minzu University , 188 East University Road, Nanning, Guangxi , 530006,","institution_ids":["https://openalex.org/I145897649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100316851","display_name":"Le Zhong","orcid":null},"institutions":[{"id":"https://openalex.org/I145897649","display_name":"Minzu University of China","ror":"https://ror.org/0044e2g62","country_code":"CN","type":"education","lineage":["https://openalex.org/I145897649"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Le Zhong","raw_affiliation_strings":["College of Electronic Information, Guangxi Minzu University , 188 East University Road, Nanning, Guangxi , 530006,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electronic Information, Guangxi Minzu University , 188 East University Road, Nanning, Guangxi , 530006,","institution_ids":["https://openalex.org/I145897649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089928380","display_name":"Bin Yan","orcid":"https://orcid.org/0000-0002-5290-4576"},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Bin Yan","raw_affiliation_strings":["Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , 34 Hospital Road, Hong Kong SAR ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , 34 Hospital Road, Hong Kong SAR ,","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhuobin Chen","orcid":null},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuobin Chen","raw_affiliation_strings":["School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University , 66 Gongchang Road, Shenzhen, Guangdong , 518107,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University , 66 Gongchang Road, Shenzhen, Guangdong , 518107,","institution_ids":["https://openalex.org/I157773358"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057132288","display_name":"Yanjia Yu","orcid":"https://orcid.org/0009-0006-2106-1795"},"institutions":[{"id":"https://openalex.org/I145897649","display_name":"Minzu University of China","ror":"https://ror.org/0044e2g62","country_code":"CN","type":"education","lineage":["https://openalex.org/I145897649"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanjia Yu","raw_affiliation_strings":["College of Electronic Information, Guangxi Minzu University , 188 East University Road, Nanning, Guangxi , 530006,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Electronic Information, Guangxi Minzu University , 188 East University Road, Nanning, Guangxi , 530006,","institution_ids":["https://openalex.org/I145897649"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107954022","display_name":"Dan Yu","orcid":null},"institutions":[{"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"],"is_corresponding":false,"raw_author_name":"Dan Yu","raw_affiliation_strings":["Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , 34 Hospital Road, Hong Kong SAR ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , 34 Hospital Road, Hong Kong SAR ,","institution_ids":["https://openalex.org/I889458895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101433660","display_name":"Jing Qin","orcid":"https://orcid.org/0000-0002-8327-8846"},"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"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Qin","raw_affiliation_strings":["School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University , 66 Gongchang Road, Shenzhen, Guangdong , 518107,"],"raw_orcid":"https://orcid.org/0000-0002-8327-8846","affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences (Shenzhen), Shenzhen Campus of Sun Yat-sen University , 66 Gongchang Road, Shenzhen, Guangdong , 518107,","institution_ids":["https://openalex.org/I157773358"]}]},{"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/I2802423016","display_name":"WinnMed","ror":"https://ror.org/02s47w807","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I2802423016"]},{"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/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":["Department of Quantitative Health Sciences, Center for Individualized Medicine, and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ , 85259,","Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , 34 Hospital Road, Hong Kong SAR ,"],"raw_orcid":"https://orcid.org/0000-0002-4432-4707","affiliations":[{"raw_affiliation_string":"Department of Quantitative Health Sciences, Center for Individualized Medicine, and Mayo Clinic Comprehensive Cancer Center, Mayo Clinic , 13400 E Shea Blvd, Scottsdale, AZ , 85259,","institution_ids":["https://openalex.org/I4210125099","https://openalex.org/I2802423016"]},{"raw_affiliation_string":"Division of Applied Oral Sciences & Community Dental Care, Faculty of Dentistry, The University of Hong Kong , 34 Hospital Road, Hong Kong SAR ,","institution_ids":["https://openalex.org/I889458895"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100724297"],"corresponding_institution_ids":["https://openalex.org/I145897649"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.6331,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.69934682,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":97},"biblio":{"volume":"26","issue":"1","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":0.9995999932289124,"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":0.9995999932289124,"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":0.9961000084877014,"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":0.9911999702453613,"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":0.6595754027366638},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6588308811187744},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6442052125930786},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5289775729179382},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5040473341941833},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.501150369644165},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49874138832092285},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.47419577836990356},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41033926606178284},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40203237533569336},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3548632860183716},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2758353352546692},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.15298274159431458}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6595754027366638},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6588308811187744},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6442052125930786},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5289775729179382},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5040473341941833},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.501150369644165},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49874138832092285},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.47419577836990356},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41033926606178284},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40203237533569336},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3548632860183716},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2758353352546692},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.15298274159431458},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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":"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":"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":"D000465","descriptor_name":"Algorithms","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":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"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":"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":"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":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbae639","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae639","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae639/61196044/bbae639.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-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:39679439","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39679439","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:11647272","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11647272","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11647272/pdf/bbae639.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"},{"id":"pmh:oai:hub.hku.hk:10722/355270","is_oa":false,"landing_page_url":"https://hub.hku.hk/handle/10722/355270","pdf_url":null,"source":{"id":"https://openalex.org/S4377196271","display_name":"The HKU Scholars Hub (University of Hong Kong)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I889458895","host_organization_name":"University of Hong Kong","host_organization_lineage":["https://openalex.org/I889458895"],"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":"Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae639","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae639","pdf_url":"https://academic.oup.com/bib/article-pdf/26/1/bbae639/61196044/bbae639.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-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":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G187577613","display_name":null,"funder_award_id":"12071306","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2532324250","display_name":null,"funder_award_id":"6010309","funder_id":"https://openalex.org/F4320322170","funder_display_name":"University of Hong Kong"},{"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/G5603031509","display_name":null,"funder_award_id":"2024A1515011210","funder_id":"https://openalex.org/F4320321921","funder_display_name":"Natural Science Foundation of Guangdong Province"},{"id":"https://openalex.org/G6911122090","display_name":null,"funder_award_id":"207051059","funder_id":"https://openalex.org/F4320322170","funder_display_name":"University of Hong Kong"},{"id":"https://openalex.org/G7073498529","display_name":null,"funder_award_id":"202206193000001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G832256683","display_name":null,"funder_award_id":"32170655","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321160","display_name":"Sun Yat-sen University","ror":"https://ror.org/0064kty71"},{"id":"https://openalex.org/F4320321921","display_name":"Natural Science Foundation of Guangdong Province","ror":null},{"id":"https://openalex.org/F4320322170","display_name":"University of Hong Kong","ror":"https://ror.org/02zhqgq86"},{"id":"https://openalex.org/F4320322816","display_name":"Guangxi University for Nationalities","ror":"https://ror.org/0495efn48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4405459861.pdf","grobid_xml":"https://content.openalex.org/works/W4405459861.grobid-xml"},"referenced_works_count":29,"referenced_works":["https://openalex.org/W1966327575","https://openalex.org/W2076513103","https://openalex.org/W2092194125","https://openalex.org/W2098700236","https://openalex.org/W2103494816","https://openalex.org/W2152575748","https://openalex.org/W2163296115","https://openalex.org/W2332016763","https://openalex.org/W2502949459","https://openalex.org/W2616922646","https://openalex.org/W2757234574","https://openalex.org/W2805198390","https://openalex.org/W2935703330","https://openalex.org/W2951424836","https://openalex.org/W2996140569","https://openalex.org/W2997831639","https://openalex.org/W3005872136","https://openalex.org/W3020930839","https://openalex.org/W3040672684","https://openalex.org/W3099289621","https://openalex.org/W3186348651","https://openalex.org/W4205514149","https://openalex.org/W4206804332","https://openalex.org/W4207068394","https://openalex.org/W4294084745","https://openalex.org/W4295727797","https://openalex.org/W4385245566","https://openalex.org/W4403235965","https://openalex.org/W6682799413"],"related_works":["https://openalex.org/W2950199998","https://openalex.org/W2560421304","https://openalex.org/W2951387065","https://openalex.org/W4385727351","https://openalex.org/W4306798985","https://openalex.org/W2010571965","https://openalex.org/W3151254369","https://openalex.org/W2002709996","https://openalex.org/W2613929436","https://openalex.org/W3128451840"],"abstract_inverted_index":{"The":[0],"interactions":[1,47],"between":[2,69],"transcription":[3],"factors":[4],"(TFs)":[5],"and":[6,71,118,136,139,166,184],"the":[7,72,128,169],"target":[8],"genes":[9],"could":[10,126,140,173],"provide":[11,174],"a":[12,102],"basis":[13],"for":[14,20,177,185],"constructing":[15,90],"gene":[16,29,109,188],"regulatory":[17,67,95,189],"networks":[18,138],"(GRNs)":[19],"mechanistic":[21],"understanding":[22,186],"of":[23,83,179],"various":[24],"biological":[25,181],"complex":[26],"processes.":[27],"From":[28],"expression":[30,110],"data,":[31],"particularly":[32],"single-cell":[33,113],"transcriptomic":[34,116],"data":[35,117],"containing":[36],"rich":[37],"cell-to-cell":[38],"variations,":[39],"it":[40,151],"is":[41],"highly":[42],"desirable":[43],"to":[44,64,86,145,161,167],"infer":[45],"TF-gene":[46],"(TGIs)":[48],"using":[49],"deep":[50,58,103],"learning":[51,104],"technologies.":[52],"Numerous":[53],"models":[54,154],"or":[55,155],"software":[56],"including":[57],"learning-based":[59],"algorithms":[60],"have":[61],"been":[62],"designed":[63],"identify":[65,162],"transcriptional":[66,187],"relationships":[68],"TFs":[70],"downstream":[73],"genes.":[74],"However,":[75],"these":[76],"methods":[77],"do":[78],"not":[79],"significantly":[80],"improve":[81],"predictions":[82],"TGIs":[84,120,165,183],"due":[85],"some":[87],"limitations":[88],"regarding":[89],"underlying":[91],"interactive":[92],"structures":[93],"linking":[94],"components.":[96],"In":[97],"this":[98],"study,":[99],"we":[100],"introduce":[101],"framework,":[105],"DeepTGI,":[106],"that":[107],"encodes":[108],"profiles":[111],"from":[112,131],"and/or":[114],"bulk":[115],"predicts":[119],"with":[121,133,152],"high":[122],"accuracy.":[123],"Our":[124],"approach":[125],"fuse":[127],"features":[129],"extracted":[130],"Auto-encoder":[132],"self-attention":[134],"mechanism":[135],"other":[137,153],"transform":[141],"multihead":[142],"attention":[143],"modules":[144],"define":[146],"representative":[147],"features.":[148],"By":[149],"comparing":[150],"methods,":[156],"DeepTGI":[157],"exhibits":[158],"its":[159],"superiority":[160],"more":[163,180],"potential":[164],"reconstruct":[168],"GRNs":[170],"and,":[171],"therefore,":[172],"broader":[175],"perspectives":[176],"discovery":[178],"meaningful":[182],"mechanisms.":[190]},"counts_by_year":[{"year":2025,"cited_by_count":3}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}