{"id":"https://openalex.org/W7214027272","doi":"https://doi.org/10.64898/2026.09.18.752607","title":"DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference","display_name":"DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference","publication_year":2026,"publication_date":"2026-09-22","ids":{"openalex":"https://openalex.org/W7214027272","doi":"https://doi.org/10.64898/2026.09.18.752607"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.18.752607","doi":"https://doi.org/10.64898/2026.09.18.752607","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.18.752607","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/22/2026.09.18.752607.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/22/2026.09.18.752607.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087265062","display_name":"Gabriele Partel","orcid":"https://orcid.org/0000-0002-4482-3119","observed_orcids":["https://orcid.org/0000-0002-4482-3119"]},"institutions":[{"id":"https://openalex.org/I4210153928","display_name":"VIB-KU Leuven Center for Brain & Disease Research","ror":"https://ror.org/045c7t348","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4210153928","https://openalex.org/I99464096"]},{"id":"https://openalex.org/I4405260244","display_name":"VIB.AI","ror":"https://ror.org/03fds3g42","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4405260244"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Gabriele Partel","raw_affiliation_strings":["KU Leuven Department of Human Genetics, Leuven, Belgium","VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-4482-3119","affiliations":[{"raw_affiliation_string":"KU Leuven Department of Human Genetics, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","institution_ids":["https://openalex.org/I4405260244"]},{"raw_affiliation_string":"VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium","institution_ids":["https://openalex.org/I4210153928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039340595","display_name":"Seppe De Winter","orcid":"https://orcid.org/0000-0001-7907-1247","observed_orcids":["https://orcid.org/0000-0001-7907-1247"]},"institutions":[{"id":"https://openalex.org/I4210153928","display_name":"VIB-KU Leuven Center for Brain & Disease Research","ror":"https://ror.org/045c7t348","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4210153928","https://openalex.org/I99464096"]},{"id":"https://openalex.org/I4405260244","display_name":"VIB.AI","ror":"https://ror.org/03fds3g42","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4405260244"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Seppe De Winter","raw_affiliation_strings":["KU Leuven Department of Human Genetics, Leuven, Belgium","VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium"],"raw_orcid":"https://orcid.org/0000-0001-7907-1247","affiliations":[{"raw_affiliation_string":"KU Leuven Department of Human Genetics, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","institution_ids":["https://openalex.org/I4405260244"]},{"raw_affiliation_string":"VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium","institution_ids":["https://openalex.org/I4210153928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048605038","display_name":"Vasileios Konstantakos","orcid":"https://orcid.org/0000-0002-0332-7506","observed_orcids":["https://orcid.org/0000-0002-0332-7506"]},"institutions":[{"id":"https://openalex.org/I4210153928","display_name":"VIB-KU Leuven Center for Brain & Disease Research","ror":"https://ror.org/045c7t348","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4210153928","https://openalex.org/I99464096"]},{"id":"https://openalex.org/I4405260244","display_name":"VIB.AI","ror":"https://ror.org/03fds3g42","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4405260244"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Vasileios Konstantakos","raw_affiliation_strings":["KU Leuven Department of Human Genetics, Leuven, Belgium","VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-0332-7506","affiliations":[{"raw_affiliation_string":"KU Leuven Department of Human Genetics, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","institution_ids":["https://openalex.org/I4405260244"]},{"raw_affiliation_string":"VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium","institution_ids":["https://openalex.org/I4210153928"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5116887518","display_name":"Casper H. Blaauw","orcid":"https://orcid.org/0000-0001-8145-9726","observed_orcids":["https://orcid.org/0000-0001-8145-9726"]},"institutions":[{"id":"https://openalex.org/I4210115206","display_name":"Hubrecht Institute for Developmental Biology and Stem Cell Research","ror":"https://ror.org/023qc4a07","country_code":"NL","type":"facility","lineage":["https://openalex.org/I1322597698","https://openalex.org/I4210115206"]},{"id":"https://openalex.org/I4210153928","display_name":"VIB-KU Leuven Center for Brain & Disease Research","ror":"https://ror.org/045c7t348","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4210153928","https://openalex.org/I99464096"]},{"id":"https://openalex.org/I4405260244","display_name":"VIB.AI","ror":"https://ror.org/03fds3g42","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4405260244"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE","NL"],"is_corresponding":false,"raw_author_name":"Casper H. Blaauw","raw_affiliation_strings":["Hubrecht Institute for Developmental Biology and Stem Cell Research,","KU Leuven Department of Human Genetics, Leuven, Belgium","VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium"],"raw_orcid":"https://orcid.org/0000-0001-8145-9726","affiliations":[{"raw_affiliation_string":"Hubrecht Institute for Developmental Biology and Stem Cell Research,","institution_ids":["https://openalex.org/I4210115206"]},{"raw_affiliation_string":"KU Leuven Department of Human Genetics, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","institution_ids":["https://openalex.org/I4405260244"]},{"raw_affiliation_string":"VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium","institution_ids":["https://openalex.org/I4210153928"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002137087","display_name":"Stein Aerts","orcid":"https://orcid.org/0000-0002-8006-0315","observed_orcids":["https://orcid.org/0000-0002-8006-0315"]},"institutions":[{"id":"https://openalex.org/I4210153928","display_name":"VIB-KU Leuven Center for Brain & Disease Research","ror":"https://ror.org/045c7t348","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4210153928","https://openalex.org/I99464096"]},{"id":"https://openalex.org/I4405260244","display_name":"VIB.AI","ror":"https://ror.org/03fds3g42","country_code":"BE","type":"facility","lineage":["https://openalex.org/I2802017950","https://openalex.org/I4405260244"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Stein Aerts","raw_affiliation_strings":["KU Leuven Department of Human Genetics, Leuven, Belgium","VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-8006-0315","affiliations":[{"raw_affiliation_string":"KU Leuven Department of Human Genetics, Leuven, Belgium","institution_ids":["https://openalex.org/I99464096"]},{"raw_affiliation_string":"VIB Center of AI & Computational Biology (VIB.AI), Leuven, Belgium","institution_ids":["https://openalex.org/I4405260244"]},{"raw_affiliation_string":"VIB-KU Leuven Center for Brain and Disease Research, Leuven, Belgium","institution_ids":["https://openalex.org/I4210153928"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5002137087"],"corresponding_institution_ids":["https://openalex.org/I4210153928","https://openalex.org/I4405260244","https://openalex.org/I99464096"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.701200008392334,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.701200008392334,"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":0.2612000107765198,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.023099999874830246,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/gene-regulatory-network-inference","display_name":"gene regulatory network inference","score":0.9210000038146973},{"id":"https://openalex.org/keywords/transfer-learning","display_name":"transfer learning","score":0.800000011920929},{"id":"https://openalex.org/keywords/transcription-factor-binding-motifs","display_name":"transcription factor binding motifs","score":0.7129999995231628},{"id":"https://openalex.org/keywords/chromatin-accessibility","display_name":"chromatin accessibility","score":0.8040000200271606},{"id":"https://openalex.org/keywords/crispri-screen","display_name":"CRISPRi screen","score":0.7570000290870667}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6151999831199646},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.6044999957084656},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.5891000032424927},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5752999782562256},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5252000093460083},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5221999883651733},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.4530999958515167},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45010000467300415},{"id":"https://openalex.org/C158600405","wikidata":"https://www.wikidata.org/wiki/Q5054566","display_name":"Causal inference","level":2,"score":0.4406000077724457},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.40950000286102295},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.3684999942779541},{"id":"https://openalex.org/C150899416","wikidata":"https://www.wikidata.org/wiki/Q1820378","display_name":"Transfer of learning","level":2,"score":0.35409998893737793},{"id":"https://openalex.org/C164614171","wikidata":"https://www.wikidata.org/wiki/Q5204775","display_name":"DECIPHER","level":2,"score":0.34279999136924744},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.3377000093460083},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.3361000120639801},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3230000138282776},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31279999017715454},{"id":"https://openalex.org/C104122410","wikidata":"https://www.wikidata.org/wiki/Q1416406","display_name":"Network model","level":2,"score":0.2953000068664551},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.27559998631477356},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.26989999413490295},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2655999958515167},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.262800008058548},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.25450000166893005},{"id":"https://openalex.org/C11671645","wikidata":"https://www.wikidata.org/wiki/Q5054567","display_name":"Causal model","level":2,"score":0.2535000145435333},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.2517000138759613}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.18.752607","doi":"https://doi.org/10.64898/2026.09.18.752607","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.18.752607","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/22/2026.09.18.752607.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.18.752607","doi":"https://doi.org/10.64898/2026.09.18.752607","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.18.752607","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/22/2026.09.18.752607.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G2895358744","display_name":"Resolving the gene-regulatory dimension of the Fly Cell Atlas using single-cell multi-omics and deep learning","funder_award_id":"G094121N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5513316228","display_name":"SpaceTimeOmics: combining high-throughput spatial omics with AI to model gene regulation in space and time","funder_award_id":"G044124N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"},{"id":"https://openalex.org/G5965395830","display_name":"Cell-cell cOmmuNicaTion As a driver of Cancer cell state identiTy - Decoding the impact of cell-cell communications on the identity of tumor states in skin cancers","funder_award_id":"G0I2722N","funder_id":"https://openalex.org/F4320321730","funder_display_name":"Fonds Wetenschappelijk Onderzoek"}],"funders":[{"id":"https://openalex.org/F4320321730","display_name":"Fonds Wetenschappelijk Onderzoek","ror":"https://ror.org/03qtxy027"},{"id":"https://openalex.org/F4320328144","display_name":"Fondation contre le Cancer","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7214027272.pdf","grobid_xml":"https://content.openalex.org/works/W7214027272.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W2594633041","https://openalex.org/W2605409611","https://openalex.org/W2898981235","https://openalex.org/W4290672942","https://openalex.org/W4382490702","https://openalex.org/W4382603228","https://openalex.org/W4403387533","https://openalex.org/W4403547222","https://openalex.org/W4404666004","https://openalex.org/W4405829527","https://openalex.org/W4410344211","https://openalex.org/W4411701336","https://openalex.org/W7124142393","https://openalex.org/W7133517058","https://openalex.org/W7147749522","https://openalex.org/W7168382988"],"related_works":["https://openalex.org/W4384198561","https://openalex.org/W4392231300","https://openalex.org/W7213760730","https://openalex.org/W4415205355","https://openalex.org/W4414711521","https://openalex.org/W4406878149","https://openalex.org/W4400184583","https://openalex.org/W7140712226","https://openalex.org/W7124443623","https://openalex.org/W4313525378"],"abstract_inverted_index":{"Abstract":[0],"Sequence-to-function":[1],"(S2F)":[2],"deep":[3,66],"learning":[4,67,77],"models":[5,21,80,111],"have":[6],"become":[7],"an":[8],"important":[9],"aid":[10],"to":[11,81,190,209],"decipher":[12],"the":[13,25,55,97,160,181,185],"genomic":[14,59],"cis-":[15,253],"regulatory":[16,39],"code.":[17],"However,":[18],"current":[19],"S2F":[20,79,110,237],"do":[22],"not":[23],"take":[24],"cellular":[26,257],"trans-":[27,256],"environment":[28],"of":[29,58,162],"transcription":[30],"factors":[31],"(TF)":[32],"into":[33],"account.":[34],"Conversely,":[35],"methods":[36],"for":[37,248],"gene":[38,102],"network":[40],"(GRN)":[41],"inference":[42,73],"often":[43],"rely":[44],"on":[45,91],"heuristics":[46],"or":[47],"simple":[48],"position":[49],"weight":[50],"matrices":[51],"(PWMs),":[52],"without":[53,134],"exploiting":[54],"combinatorial":[56],"grammar":[57],"enhancers.":[60],"Here,":[61],"we":[62,206],"present":[63],"DeepSCENIC,":[64],"a":[65,155,172,176,245],"framework":[68,98],"that":[69,96,118],"enables":[70,159],"causal":[71],"GRN":[72],"by":[74,107,169],"performing":[75],"transfer":[76],"from":[78,188],"single-cell":[82,101,241],"multiome":[83],"atlases.":[84],"We":[85,116],"first":[86],"test":[87],"and":[88,104,114,127,193,227,251,255],"validate":[89],"DeepSCENIC":[90,119,156,208,243],"ENCODE":[92],"cell":[93,166,178],"lines,":[94],"demonstrating":[95],"accurately":[99,183],"predicts":[100],"expression":[103],"chromatin":[105],"accessibility":[106],"leveraging":[108],"pretrained":[109],"like":[112],"Enformer":[113],"Borzoi.":[115],"show":[117,197],"recovers":[120],"TF-region":[121],"(TF-RE)":[122],"interactions":[123],"with":[124,200,240],"high":[125,198,216],"fidelity,":[126],"captures":[128],"de":[129],"novo":[130],"TF":[131,220],"binding":[132],"motifs":[133],"prior":[135],"PWM":[136],"knowledge.":[137],"The":[138],"model":[139,182],"improves":[140],"enhancer-gene":[141],"associations":[142],"(RE-TG)":[143],"over":[144],"correlation-based":[145],"baselines":[146],"when":[147],"benchmarked":[148],"against":[149,231],"large-scale":[150],"CRISPRi":[151],"screens.":[152],"After":[153],"training":[154],"model,":[157],"it":[158],"prediction":[161],"perturbation":[163],"effects":[164,196],"during":[165],"state":[167],"changes":[168],"acting":[170],"as":[171],"mechanistic":[173],"simulator.":[174],"In":[175],"melanoma":[177],"line":[179],"atlas,":[180],"recapitulates":[184],"transcriptional":[186],"shift":[187],"melanocytic":[189],"mesenchymal":[191],"states,":[192],"predicted":[194],"knock-down":[195],"concordance":[199,218],"experimental":[201,232],"time":[202],"series":[203],"data.":[204],"Finally,":[205],"use":[207],"identify":[210],"mouse-human":[211],"cortex":[212],"conserved":[213],"GRNs,":[214],"finding":[215],"cross-species":[217],"in":[219],"activity":[221],"programs":[222],"across":[223],"matched":[224],"neuronal":[225],"subclasses":[226],"validating":[228],"top-ranked":[229],"enhancers":[230],"reporter":[233],"assays.":[234],"By":[235],"unifying":[236],"enhancer":[238],"representations":[239],"multiomics,":[242],"provides":[244],"new":[246],"paradigm":[247],"jointly":[249],"modeling":[250],"simulating":[252],"sequence":[254],"perturbations.":[258]},"counts_by_year":[],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2026-09-23T00:00:00"}