{"id":"https://openalex.org/W4415819889","doi":"https://doi.org/10.1371/journal.pcbi.1013664","title":"Branch-specific gene discovery in cell differentiation using multi-omics graph attention","display_name":"Branch-specific gene discovery in cell differentiation using multi-omics graph attention","publication_year":2025,"publication_date":"2025-11-03","ids":{"openalex":"https://openalex.org/W4415819889","doi":"https://doi.org/10.1371/journal.pcbi.1013664","pmid":"https://pubmed.ncbi.nlm.nih.gov/41183107"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013664","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013664","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013664","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5111326623","display_name":"Yihao Yin","orcid":"https://orcid.org/0009-0008-3157-0053"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yihao Yin","raw_affiliation_strings":["Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Linzhi Zhuang","orcid":null},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Linzhi Zhuang","raw_affiliation_strings":["Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100374615","display_name":"Yulei Wang","orcid":"https://orcid.org/0000-0002-9057-9786"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yulei Wang","raw_affiliation_strings":["Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054012707","display_name":"Ya-Zhou Shi","orcid":"https://orcid.org/0000-0003-2579-3134"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yazhou Shi","raw_affiliation_strings":["Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5036104736","display_name":"Bengong Zhang","orcid":"https://orcid.org/0000-0002-2766-6502"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bengong Zhang","raw_affiliation_strings":["Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China"],"raw_orcid":"https://orcid.org/0000-0002-2766-6502","affiliations":[{"raw_affiliation_string":"Research Center for Applied Mathematics and Interdisciplinary Studies, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5036104736","https://openalex.org/A5054012707","https://openalex.org/A5100374615","https://openalex.org/A5111326623"],"corresponding_institution_ids":["https://openalex.org/I4210119942"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.25631342,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"11","first_page":"e1013664","last_page":"e1013664"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9139000177383423,"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":0.9139000177383423,"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":0.05290000140666962,"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":0.008100000210106373,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.6761999726295471},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5084999799728394},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4943000078201294},{"id":"https://openalex.org/keywords/cellular-differentiation","display_name":"Cellular differentiation","score":0.4860000014305115},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.39959999918937683},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.3831999897956848},{"id":"https://openalex.org/keywords/cell-fate-determination","display_name":"Cell fate determination","score":0.34860000014305115}],"concepts":[{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.6761999726295471},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5859000086784363},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5084999799728394},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5059999823570251},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4943000078201294},{"id":"https://openalex.org/C148738053","wikidata":"https://www.wikidata.org/wiki/Q210861","display_name":"Cellular differentiation","level":3,"score":0.4860000014305115},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4302000105381012},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.39959999918937683},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.3831999897956848},{"id":"https://openalex.org/C163952510","wikidata":"https://www.wikidata.org/wiki/Q5058196","display_name":"Cell fate determination","level":4,"score":0.34860000014305115},{"id":"https://openalex.org/C33498276","wikidata":"https://www.wikidata.org/wiki/Q2138797","display_name":"Regulator gene","level":4,"score":0.3050999939441681},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.29649999737739563},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.29420000314712524},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.2924000024795532},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2709999978542328},{"id":"https://openalex.org/C189014844","wikidata":"https://www.wikidata.org/wiki/Q189118","display_name":"Cell type","level":3,"score":0.26840001344680786},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.265500009059906},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.2549000084400177},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.25130000710487366}],"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":"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019070","descriptor_name":"Cell Lineage","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059010","descriptor_name":"Single-Cell Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013664","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013664","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41183107","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41183107","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:6f89fea1989b48bfad19baaea8e2a45a","is_oa":true,"landing_page_url":"https://doaj.org/article/6f89fea1989b48bfad19baaea8e2a45a","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 11, p e1013664 (2025)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11403394","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12594343","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"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013664","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013664","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6362099399","display_name":null,"funder_award_id":"32571442","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7104333451","display_name":null,"funder_award_id":"12371500","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":52,"referenced_works":["https://openalex.org/W1963522244","https://openalex.org/W2069089843","https://openalex.org/W2103017472","https://openalex.org/W2157590511","https://openalex.org/W2166643977","https://openalex.org/W2473235403","https://openalex.org/W2515907404","https://openalex.org/W2537679995","https://openalex.org/W2555892463","https://openalex.org/W2616922646","https://openalex.org/W2725171488","https://openalex.org/W2747877289","https://openalex.org/W2794480084","https://openalex.org/W2800392236","https://openalex.org/W2800631768","https://openalex.org/W2802141866","https://openalex.org/W2805650303","https://openalex.org/W2887910040","https://openalex.org/W2916020270","https://openalex.org/W2949177718","https://openalex.org/W2950372712","https://openalex.org/W2950517843","https://openalex.org/W2951506174","https://openalex.org/W2951799803","https://openalex.org/W2989985381","https://openalex.org/W2997280954","https://openalex.org/W3012871709","https://openalex.org/W3021933843","https://openalex.org/W3047725782","https://openalex.org/W3108202858","https://openalex.org/W3138308628","https://openalex.org/W3189065844","https://openalex.org/W3201535265","https://openalex.org/W3210860076","https://openalex.org/W4289979062","https://openalex.org/W4294216483","https://openalex.org/W4295216970","https://openalex.org/W4300672471","https://openalex.org/W4308132330","https://openalex.org/W4321452549","https://openalex.org/W4378212544","https://openalex.org/W4382022265","https://openalex.org/W4385727351","https://openalex.org/W4386602082","https://openalex.org/W4388798453","https://openalex.org/W4389166577","https://openalex.org/W4390636271","https://openalex.org/W4391837732","https://openalex.org/W4392948297","https://openalex.org/W4406860510","https://openalex.org/W4408899008","https://openalex.org/W4414371750"],"related_works":[],"abstract_inverted_index":{"Understanding":[0],"gene":[1,42,64,92,107,135],"regulation":[2,136],"during":[3,138],"cell":[4,30,115],"differentiation":[5,31,46,96,124],"requires":[6],"effective":[7],"integration":[8],"of":[9,73,114,123,131],"multi-omics":[10,147],"single-cell":[11,148],"data.":[12],"In":[13],"this":[14],"study,":[15],"we":[16,44],"propose":[17],"BranchKGN,":[18],"a":[19,40,52,143],"heterogeneous":[20,53],"graph":[21,54,60],"transformer-based":[22],"framework":[23],"for":[24,146],"identifying":[25],"branch-specific":[26],"key":[27,112],"genes":[28,74,86],"along":[29],"trajectories.":[32,97,125],"By":[33],"integrating":[34],"scRNA-seq":[35],"and":[36,50,81,95,141],"scATAC-seq":[37],"data":[38],"into":[39],"unified":[41],"representation,":[43],"infer":[45],"trajectories":[47],"using":[48],"Slingshot":[49],"construct":[51],"capturing":[55],"gene-cell":[56],"relationships.":[57],"Through":[58],"attention-based":[59],"learning,":[61],"BranchKGN":[62,132],"assigns":[63],"importance":[65],"scores":[66],"within":[67],"each":[68],"cell,":[69],"enabling":[70],"the":[71,105,129],"identification":[72],"consistently":[75],"informative":[76],"across":[77],"branch":[78],"point":[79],"cells":[80],"their":[82],"descendant":[83],"lineages.":[84],"These":[85],"are":[87],"then":[88],"used":[89],"to":[90],"reconstruct":[91],"regulatory":[93],"networks":[94],"Validation":[98],"on":[99],"three":[100],"independent":[101],"datasets":[102],"demonstrates":[103],"that":[104],"identified":[106],"sets":[108],"not":[109],"only":[110],"capture":[111],"regulators":[113],"fate":[116],"bifurcation":[117],"but":[118],"also":[119],"support":[120],"accurate":[121],"reconstruction":[122],"Our":[126],"results":[127],"highlight":[128],"effectiveness":[130],"in":[133],"dissecting":[134],"dynamics":[137],"cellular":[139],"transitions":[140],"provide":[142],"valuable":[144],"tool":[145],"analysis.":[149]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-11-03T00:00:00"}
