{"id":"https://openalex.org/W7128062543","doi":"https://doi.org/10.1093/bib/bbaf664","title":"Deciphering hierarchical regulatory network of cell fate via an epigenetics-informed heterogeneous graph transformer on single-cell multi-omics data","display_name":"Deciphering hierarchical regulatory network of cell fate via an epigenetics-informed heterogeneous graph transformer on single-cell multi-omics data","publication_year":2025,"publication_date":"2025-11-01","ids":{"openalex":"https://openalex.org/W7128062543","doi":"https://doi.org/10.1093/bib/bbaf664","pmid":"https://pubmed.ncbi.nlm.nih.gov/41643202"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf664","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","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://doi.org/10.1093/bib/bbaf664","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yuhong Huang","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuhong Huang","raw_affiliation_strings":["Department of Oral Pathology, School of Stomatology, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oral Pathology, School of Stomatology, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125196248","display_name":"Chao Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Liu","raw_affiliation_strings":["Department of Oral Pathology, School of Stomatology, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oral Pathology, School of Stomatology, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhiling Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiling Yang","raw_affiliation_strings":["Department of Biomedical Engineering, College of Basic Medical Sciences, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, College of Basic Medical Sciences, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031999976","display_name":"B. Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bo Liu","raw_affiliation_strings":["Institute for Genome Engineered Animal Models of Human Diseases, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute for Genome Engineered Animal Models of Human Diseases, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5123517779","display_name":"Xiao Zhai","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Zhai","raw_affiliation_strings":["Department of System Technology, Library, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of System Technology, Library, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084169433","display_name":"Jiajin Zheng","orcid":"https://orcid.org/0000-0002-8530-9810"},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiajin Zheng","raw_affiliation_strings":["Department of Biomedical Engineering, College of Basic Medical Sciences, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, College of Basic Medical Sciences, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5125107395","display_name":"Jing Xiao","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jing Xiao","raw_affiliation_strings":["Department of Oral Pathology, School of Stomatology, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oral Pathology, School of Stomatology, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5125227124","display_name":"Tao Song","orcid":null},"institutions":[{"id":"https://openalex.org/I191996457","display_name":"Dalian Medical University","ror":"https://ror.org/04c8eg608","country_code":"CN","type":"education","lineage":["https://openalex.org/I191996457"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tao Song","raw_affiliation_strings":["Department of Biomedical Engineering, College of Basic Medical Sciences, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,"],"raw_orcid":"https://orcid.org/0009-0006-0019-1291","affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, College of Basic Medical Sciences, Dalian Medical University , No. 9, Western Section of Lushun South Road, Dalian, Liaoning 116044 ,","institution_ids":["https://openalex.org/I191996457"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5125107395","https://openalex.org/A5125227124"],"corresponding_institution_ids":["https://openalex.org/I191996457"],"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":0.52928839,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"26","issue":"6","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.32519999146461487,"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":0.32519999146461487,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.15559999644756317,"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":0.04910000041127205,"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/cell-fate-determination","display_name":"Cell fate determination","score":0.6909999847412109},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6195999979972839},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.5041000247001648},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.4851999878883362},{"id":"https://openalex.org/keywords/subnetwork","display_name":"Subnetwork","score":0.4778999984264374},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.42750000953674316},{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.4185999929904938},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.39800000190734863},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.39070001244544983}],"concepts":[{"id":"https://openalex.org/C163952510","wikidata":"https://www.wikidata.org/wiki/Q5058196","display_name":"Cell fate determination","level":4,"score":0.6909999847412109},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6259999871253967},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6195999979972839},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5273000001907349},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.5041000247001648},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.4851999878883362},{"id":"https://openalex.org/C2780186347","wikidata":"https://www.wikidata.org/wiki/Q11414","display_name":"Subnetwork","level":2,"score":0.4778999984264374},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.42750000953674316},{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.4185999929904938},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.39800000190734863},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.39070001244544983},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.3822000026702881},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3610000014305115},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.352400004863739},{"id":"https://openalex.org/C158207573","wikidata":"https://www.wikidata.org/wiki/Q5747224","display_name":"Heterogeneous network","level":4,"score":0.34299999475479126},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3393999934196472},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.3314000070095062},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.3305000066757202},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.31520000100135803},{"id":"https://openalex.org/C75564084","wikidata":"https://www.wikidata.org/wiki/Q5597085","display_name":"Graph embedding","level":3,"score":0.29829999804496765},{"id":"https://openalex.org/C2778729363","wikidata":"https://www.wikidata.org/wiki/Q11688946","display_name":"Myeloid leukemia","level":2,"score":0.29499998688697815},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.27950000762939453},{"id":"https://openalex.org/C558772884","wikidata":"https://www.wikidata.org/wiki/Q1508564","display_name":"Graph rewriting","level":3,"score":0.2732999920845032},{"id":"https://openalex.org/C146380142","wikidata":"https://www.wikidata.org/wiki/Q1137726","display_name":"Directed graph","level":2,"score":0.2727999985218048},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.2689000070095062},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.26420000195503235},{"id":"https://openalex.org/C124527596","wikidata":"https://www.wikidata.org/wiki/Q17029359","display_name":"Hierarchical control system","level":3,"score":0.2563000023365021},{"id":"https://openalex.org/C2778086970","wikidata":"https://www.wikidata.org/wiki/Q514525","display_name":"Hematopoietic stem cell","level":4,"score":0.2526000142097473},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.2508000135421753},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.25029999017715454}],"mesh":[{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095028","descriptor_name":"Multiomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":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":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":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","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":"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":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D057890","descriptor_name":"Epigenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":4,"locations":[{"id":"doi:10.1093/bib/bbaf664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf664","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","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:41643202","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41643202","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:11682998","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12875533","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:12875533","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12875533/","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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf664","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf664","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","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":[{"display_name":"Partnerships for the goals","score":0.4066241383552551,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G4953645295","display_name":null,"funder_award_id":"82270949","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6549160121","display_name":null,"funder_award_id":"82370916","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":47,"referenced_works":["https://openalex.org/W2140773464","https://openalex.org/W2796366554","https://openalex.org/W2925075625","https://openalex.org/W3013900499","https://openalex.org/W3027051073","https://openalex.org/W3129866267","https://openalex.org/W3178663566","https://openalex.org/W3182973519","https://openalex.org/W4205421285","https://openalex.org/W4280536633","https://openalex.org/W4289835859","https://openalex.org/W4300862723","https://openalex.org/W4308834893","https://openalex.org/W4309247532","https://openalex.org/W4312354047","https://openalex.org/W4319591822","https://openalex.org/W4321452549","https://openalex.org/W4323348775","https://openalex.org/W4360999291","https://openalex.org/W4378212274","https://openalex.org/W4378212544","https://openalex.org/W4378530717","https://openalex.org/W4382022265","https://openalex.org/W4382632237","https://openalex.org/W4384198561","https://openalex.org/W4385237817","https://openalex.org/W4385972047","https://openalex.org/W4386215940","https://openalex.org/W4387774515","https://openalex.org/W4390011121","https://openalex.org/W4392630817","https://openalex.org/W4393004084","https://openalex.org/W4394764901","https://openalex.org/W4399387478","https://openalex.org/W4400140731","https://openalex.org/W4400140744","https://openalex.org/W4401200595","https://openalex.org/W4401556795","https://openalex.org/W4401731539","https://openalex.org/W4401997224","https://openalex.org/W4403405969","https://openalex.org/W4404668596","https://openalex.org/W4406471462","https://openalex.org/W4407103169","https://openalex.org/W4408129839","https://openalex.org/W4408387458","https://openalex.org/W4415101992"],"related_works":[],"abstract_inverted_index":{"The":[0,125,138,150],"precise":[1],"control":[2],"of":[3,25],"cell":[4,136,156,178,235],"fate":[5,157,236],"is":[6],"driven":[7],"by":[8,79,167],"a":[9,62,84,96,200,228],"hierarchical":[10,51,183,224],"regulatory":[11,42,169],"network":[12,101,133],"(HRNet)":[13],"where":[14],"transcription":[15],"factors":[16],"(TFs)":[17],"and":[18,52,94,106,120,147,208,233,241],"cis-regulatory":[19],"elements":[20],"(CREs)":[21],"orchestrate":[22],"the":[23,182,206],"expression":[24,173],"target":[26],"genes":[27],"(TGs)":[28],"through":[29],"complex":[30],"causal":[31,53,184],"actions.":[32],"While":[33],"single-cell":[34],"multi-omics":[35],"technologies":[36],"provide":[37],"multi-dimensional":[38],"data":[39],"to":[40,48,67,99,135,231],"resolve":[41],"networks,":[43],"existing":[44],"methods":[45],"often":[46],"fail":[47],"capture":[49],"their":[50,148],"properties.":[54],"We":[55],"propose":[56],"SMOGT":[57,70,110,180,226],"(Single-cell":[58],"Multi-Omics":[59],"Graph":[60,76],"Transformer),":[61],"graph":[63],"representation":[64],"learning":[65],"method":[66],"decipher":[68],"HRNet.":[69],"embeds":[71],"epigenetic":[72],"mechanism":[73],"into":[74],"Heterogeneous":[75],"Transformer":[77],"(HGT)":[78],"structuring":[80],"information":[81],"flow":[82],"along":[83],"hierarchical-guided":[85],"meta-path":[86],"(TF-TF":[87],"\u2192":[88,90,92],"TF-CRE":[89],"CRE-CRE":[91],"CRE-TG),":[93],"employs":[95],"semi-supervised":[97],"strategy":[98],"ensure":[100],"accuracy.":[102],"Validated":[103],"against":[104],"ChIP-seq":[105],"HiC-seq":[107],"benchmarked":[108],"datasets,":[109],"showed":[111],"significantly":[112],"higher":[113],"accuracy":[114],"in":[115,155,160,209,238],"predicting":[116],"transcriptional":[117],"regulation":[118],"(TF-CRE)":[119],"long-range":[121],"chromatin":[122],"conformation":[123],"(CRE-CRE).":[124],"HRNet":[126,165],"scaffolds":[127],"downstream":[128],"modules":[129],"that":[130,189],"mechanistically":[131],"link":[132],"architecture":[134],"fate.":[137],"multi-layer":[139],"random":[140],"walk":[141],"(MRWR)":[142],"module":[143,152],"identifies":[144],"driver":[145,187],"regulators":[146],"TGs.":[149],"BioStreamNet":[151],"predicts":[153],"shifts":[154],"trajectories":[158],"following":[159],"silico":[161],"perturbations":[162],"within":[163],"gene-specific":[164],"formed":[166],"extracting":[168],"weights":[170],"during":[171],"TG":[172],"prediction.":[174],"In":[175,193],"hematopoietic":[176],"stem":[177],"differentiation,":[179],"elucidated":[181],"cascade":[185],"from":[186],"TFs":[188],"governs":[190],"lineage":[191],"commitment.":[192],"melanoma":[194],"epithelial-to-mesenchymal":[195],"transition":[196],"(EMT),":[197],"it":[198,214],"revealed":[199],"critical":[201],"therapeutic":[202],"window":[203],"for":[204],"reversing":[205],"process,":[207],"Acute":[210],"Myeloid":[211],"Leukemia":[212],"(AML),":[213],"uncovered":[215],"hub-CREs":[216],"with":[217],"significant":[218],"prognostic":[219],"value.":[220],"By":[221],"accurately":[222],"modeling":[223],"causality,":[225],"provides":[227],"robust":[229],"tool":[230],"dissect":[232],"predict":[234],"dynamics":[237],"both":[239],"development":[240],"disease.":[242]},"counts_by_year":[],"updated_date":"2026-07-21T08:15:58.654021","created_date":"2026-02-07T00:00:00"}