{"id":"https://openalex.org/W7223347208","doi":"https://doi.org/10.64898/2026.10.22.760916","title":"Reconstructing human gene regulatory evolution using deep learning","display_name":"Reconstructing human gene regulatory evolution using deep learning","publication_year":2026,"publication_date":"2026-10-23","ids":{"openalex":"https://openalex.org/W7223347208","doi":"https://doi.org/10.64898/2026.10.22.760916"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.22.760916","doi":"https://doi.org/10.64898/2026.10.22.760916","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.22.760916","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/23/2026.10.22.760916.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/2026/10/23/2026.10.22.760916.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033683943","display_name":"Tetsuya Yamada","orcid":"https://orcid.org/0000-0001-8601-737X","observed_orcids":["https://orcid.org/0000-0001-8601-737X"]},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tetsuya Yamada","raw_affiliation_strings":["Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-8601-737X","affiliations":[{"raw_affiliation_string":"Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I4210151100"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5059916508","display_name":"Xuefei Yuan","orcid":"https://orcid.org/0000-0001-5193-9964","observed_orcids":["https://orcid.org/0000-0001-5193-9964"]},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Xuefei Yuan","raw_affiliation_strings":["Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-5193-9964","affiliations":[{"raw_affiliation_string":"Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I4210151100"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038144368","display_name":"Hugo Zeberg","orcid":"https://orcid.org/0000-0001-7118-1249","observed_orcids":["https://orcid.org/0000-0001-7118-1249"]},"institutions":[{"id":"https://openalex.org/I28166907","display_name":"Karolinska Institutet","ror":"https://ror.org/056d84691","country_code":"SE","type":"education","lineage":["https://openalex.org/I28166907"]},{"id":"https://openalex.org/I4210118560","display_name":"Max Planck Institute for Evolutionary Anthropology","ror":"https://ror.org/02a33b393","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210118560"]}],"countries":["DE","SE"],"is_corresponding":false,"raw_author_name":"Hugo Zeberg","raw_affiliation_strings":["Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden","Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7118-1249","affiliations":[{"raw_affiliation_string":"Department of Physiology and Pharmacology, Karolinska Institutet, Stockholm, Sweden","institution_ids":["https://openalex.org/I28166907"]},{"raw_affiliation_string":"Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","institution_ids":["https://openalex.org/I4210118560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012130760","display_name":"Volker Soltys","orcid":"https://orcid.org/0009-0008-4568-3040","observed_orcids":["https://orcid.org/0009-0008-4568-3040"]},"institutions":[{"id":"https://openalex.org/I4210118560","display_name":"Max Planck Institute for Evolutionary Anthropology","ror":"https://ror.org/02a33b393","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210118560"]},{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Volker Soltys","raw_affiliation_strings":["Leipzig University, LeiCeM \u2014 Leipzig Center of Metabolism, Leipzig, Germany","Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0009-0008-4568-3040","affiliations":[{"raw_affiliation_string":"Leipzig University, LeiCeM \u2014 Leipzig Center of Metabolism, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]},{"raw_affiliation_string":"Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","institution_ids":["https://openalex.org/I4210118560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100036337","display_name":"Mikel Lana Alberro","orcid":"https://orcid.org/0009-0008-3065-3375","observed_orcids":["https://orcid.org/0009-0008-3065-3375"]},"institutions":[{"id":"https://openalex.org/I4210118560","display_name":"Max Planck Institute for Evolutionary Anthropology","ror":"https://ror.org/02a33b393","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210118560"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mikel Lana Alberro","raw_affiliation_strings":["Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0009-0008-3065-3375","affiliations":[{"raw_affiliation_string":"Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","institution_ids":["https://openalex.org/I4210118560"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007618638","display_name":"Ioannis Sarropoulos","orcid":"https://orcid.org/0000-0002-2242-0562","observed_orcids":["https://orcid.org/0000-0002-2242-0562"]},"institutions":[{"id":"https://openalex.org/I21196054","display_name":"Wellcome/MRC Cambridge Stem Cell Institute","ror":"https://ror.org/05nz0zp31","country_code":"GB","type":"facility","lineage":["https://openalex.org/I21196054","https://openalex.org/I241749","https://openalex.org/I4210087105","https://openalex.org/I87048295","https://openalex.org/I90344618"]},{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Ioannis Sarropoulos","raw_affiliation_strings":["Cambridge Stem Cell Institute and Department of Medicine, University of Cambridge, Cambridge, UK"],"raw_orcid":"https://orcid.org/0000-0002-2242-0562","affiliations":[{"raw_affiliation_string":"Cambridge Stem Cell Institute and Department of Medicine, University of Cambridge, Cambridge, UK","institution_ids":["https://openalex.org/I21196054","https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012216367","display_name":"Svante P\u00e4\u00e4bo","orcid":"https://orcid.org/0000-0002-4670-6311","observed_orcids":["https://orcid.org/0000-0002-4670-6311"]},"institutions":[{"id":"https://openalex.org/I142637625","display_name":"Okinawa Institute of Science and Technology Graduate University","ror":"https://ror.org/02qg15b79","country_code":"JP","type":"education","lineage":["https://openalex.org/I142637625"]},{"id":"https://openalex.org/I4210118560","display_name":"Max Planck Institute for Evolutionary Anthropology","ror":"https://ror.org/02a33b393","country_code":"DE","type":"facility","lineage":["https://openalex.org/I149899117","https://openalex.org/I4210118560"]}],"countries":["DE","JP"],"is_corresponding":false,"raw_author_name":"Svante P\u00e4\u00e4bo","raw_affiliation_strings":["Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan","Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"],"raw_orcid":"https://orcid.org/0000-0002-4670-6311","affiliations":[{"raw_affiliation_string":"Human Evolutionary Genomics Unit, Okinawa Institute of Science and Technology (OIST), Okinawa, Japan","institution_ids":["https://openalex.org/I142637625"]},{"raw_affiliation_string":"Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","institution_ids":["https://openalex.org/I4210118560"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085413454","display_name":"Henrik Kaessmann","orcid":"https://orcid.org/0000-0001-7563-839X","observed_orcids":["https://orcid.org/0000-0001-7563-839X"]},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I4210151100","display_name":"DKFZ-ZMBH Alliance","ror":"https://ror.org/05x8b4491","country_code":"DE","type":"facility","lineage":["https://openalex.org/I1305996414","https://openalex.org/I17937529","https://openalex.org/I223822909","https://openalex.org/I4210151100"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Henrik Kaessmann","raw_affiliation_strings":["Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany"],"raw_orcid":"https://orcid.org/0000-0001-7563-839X","affiliations":[{"raw_affiliation_string":"Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I4210151100"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5085413454"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I4210151100"],"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.798799991607666,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.798799991607666,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.0471000000834465,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.03060000017285347,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/evolution-of-gene-regulation","display_name":"gene regulatory evolution","score":0.7940000295639038},{"id":"https://openalex.org/keywords/cis-regulatory-elements","display_name":"cis-regulatory elements","score":0.9760000109672546},{"id":"https://openalex.org/keywords/human-lineage","display_name":"human lineage","score":0.6150000095367432},{"id":"https://openalex.org/keywords/single-nucleotide-substitution","display_name":"single nucleotide substitution","score":0.8289999961853027},{"id":"https://openalex.org/keywords/alphagenome","display_name":"AlphaGenome","score":0.8270000219345093},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.5329999923706055},{"id":"https://openalex.org/keywords/gene-expression-evolution","display_name":"gene expression evolution","score":0.7020000219345093},{"id":"https://openalex.org/keywords/human-accelerated-regions","display_name":"human accelerated regions","score":0.890999972820282},{"id":"https://openalex.org/keywords/distal-enhancers","display_name":"distal enhancers","score":0.9430000185966492},{"id":"https://openalex.org/keywords/tissue-specific-expression","display_name":"tissue-specific gene expression","score":0.6970000267028809},{"id":"https://openalex.org/keywords/transcription-factor-binding-motifs","display_name":"transcription factor binding motifs","score":0.875},{"id":"https://openalex.org/keywords/neanderthals","display_name":"Neanderthals","score":0.6909999847412109},{"id":"https://openalex.org/keywords/denisovans","display_name":"Denisovans","score":0.9670000076293945},{"id":"https://openalex.org/keywords/phenotypic-innovation","display_name":"phenotypic innovation","score":0.75}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7598000168800354},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.6561999917030334},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6559000015258789},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.6191999912261963},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.588699996471405},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5351999998092651},{"id":"https://openalex.org/C185554395","wikidata":"https://www.wikidata.org/wiki/Q83944","display_name":"Human evolution","level":2,"score":0.5059000253677368},{"id":"https://openalex.org/C167683757","wikidata":"https://www.wikidata.org/wiki/Q5937774","display_name":"Human evolutionary genetics","level":4,"score":0.49390000104904175},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.48980000615119934},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4805999994277954},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.47839999198913574},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.47380000352859497},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4528000056743622},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.44850000739097595},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.41339999437332153},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.40130001306533813},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.3792000114917755},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3725999891757965},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3677999973297119},{"id":"https://openalex.org/C174600577","wikidata":"https://www.wikidata.org/wiki/Q5533491","display_name":"Genome evolution","level":4,"score":0.35530000925064087},{"id":"https://openalex.org/C168601633","wikidata":"https://www.wikidata.org/wiki/Q1044484","display_name":"Evolutionary developmental biology","level":2,"score":0.34940001368522644},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3490000069141388},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.3483000099658966},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.3456999957561493},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.33070001006126404},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.2903999984264374},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.28139999508857727},{"id":"https://openalex.org/C168393362","wikidata":"https://www.wikidata.org/wiki/Q5421706","display_name":"Expression quantitative trait loci","level":5,"score":0.2793000042438507},{"id":"https://openalex.org/C179463898","wikidata":"https://www.wikidata.org/wiki/Q10273301","display_name":"Epigenesis","level":5,"score":0.27720001339912415},{"id":"https://openalex.org/C61727976","wikidata":"https://www.wikidata.org/wiki/Q751748","display_name":"Epistasis","level":3,"score":0.27000001072883606},{"id":"https://openalex.org/C2779987252","wikidata":"https://www.wikidata.org/wiki/Q635162","display_name":"Hominidae","level":3,"score":0.266400009393692},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.26429998874664307},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.262800008058548},{"id":"https://openalex.org/C2988562018","wikidata":"https://www.wikidata.org/wiki/Q1063","display_name":"Biological evolution","level":2,"score":0.2624000012874603}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.10.22.760916","doi":"https://doi.org/10.64898/2026.10.22.760916","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.22.760916","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/23/2026.10.22.760916.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:10.64898/2026.10.22.760916","doi":"https://doi.org/10.64898/2026.10.22.760916","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.22.760916","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/10/23/2026.10.22.760916.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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4000000059604645}],"study_designs":[],"awards":[{"id":"https://openalex.org/G1087913658","display_name":null,"funder_award_id":"INST 35/1804\u20101 LAGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G1244305882","display_name":null,"funder_award_id":"INST 35/1597-1","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G2628649996","display_name":null,"funder_award_id":"INST35/1597\u20101FUGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3336866309","display_name":null,"funder_award_id":"INST 35/1803\u20101 FUGG","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G5284521312","display_name":null,"funder_award_id":"INST 35","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320325162","display_name":"NOMIS Stiftung","ror":"https://ror.org/01zkd3118"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7223347208.pdf","grobid_xml":"https://content.openalex.org/works/W7223347208.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W2101234009","https://openalex.org/W2618851150","https://openalex.org/W4405829527","https://openalex.org/W4415164095","https://openalex.org/W4415354282","https://openalex.org/W7151234819","https://openalex.org/W7161551590","https://openalex.org/W7172393996","https://openalex.org/W7203966855","https://openalex.org/W7212434028","https://openalex.org/W7213745552"],"related_works":["https://openalex.org/W7203966855","https://openalex.org/W2951780082","https://openalex.org/W6886015853","https://openalex.org/W1986588305","https://openalex.org/W3194401437","https://openalex.org/W7099644353","https://openalex.org/W4417482564","https://openalex.org/W7212434028","https://openalex.org/W1991036278","https://openalex.org/W6977028649"],"abstract_inverted_index":{"Understanding":[0],"the":[1,6,35,43,84,94,157,165,219,252],"genetic":[2],"changes":[3,37,243],"that":[4,161,210],"drove":[5],"evolution":[7,104,166,250],"of":[8,28,87,128,136,156,167,241],"human-specific":[9],"traits":[10],"is":[11],"a":[12,25,78,225,237],"central":[13],"goal":[14],"in":[15,18,38,140,170,183,186,216],"biology.":[16],"Changes":[17],"gene":[19,102,153,232,248],"expression":[20,103,249],"are":[21,54,144],"thought":[22],"to":[23,82,93,164,174,180,189,195,231,247],"be":[24,181],"major":[26],"source":[27],"phenotypic":[29],"innovations":[30],"1,2":[31],",":[32,77],"but":[33],"identifying":[34],"underlying":[36],"cis-regulatory":[39,85,114,242],"elements":[40],"(CREs)":[41],"along":[42,251],"human":[44,95,119,253],"lineage":[45,96],"has":[46],"been":[47],"difficult:":[48],"functional":[49],"data":[50],"from":[51,221],"great":[52],"apes":[53],"scarce":[55],"and":[56,61,97,108,123,150,185,206,244],"unobtainable":[57],"for":[58,101,147,151],"extinct":[59],"hominins,":[60,223],"pinpointing":[62],"causal":[63],"substitutions":[64,91,197],"requires":[65],"knowing":[66],"which":[67],"sequences":[68],"determine":[69],"CRE":[70],"activity.":[71],"Here,":[72],"we":[73],"used":[74],"AlphaGenome":[75],"3":[76],"sequence-to-function":[79],"deep-learning":[80],"model,":[81],"predict":[83],"effects":[86],"\u223c17":[88],"million":[89],"single-nucleotide":[90],"specific":[92],"traced":[98,192],"their":[99,245],"consequences":[100],"across":[105],"305":[106],"tissues":[107],"cell":[109],"types.":[110],"The":[111],"71,345":[112],"predicted":[113],"gains":[115,176,213,228],"lie":[116],"mostly":[117],"outside":[118],"accelerated":[120],"regions":[121],"4,5":[122],"arose":[124],"either":[125],"through":[126,134],"creation":[127],"new":[129],"CREs":[130,137],"or,":[131],"more":[132,175,178],"often,":[133],"co-option":[135],"ancestrally":[138],"accessible":[139],"other":[141],"tissues.":[142],"They":[143],"also":[145],"enriched":[146],"distal":[148],"enhancers":[149],"target":[152],"functions":[154],"characteristic":[155],"corresponding":[158],"tissues,":[159],"suggesting":[160],"they":[162],"contributed":[163],"tissue-specific":[168],"biology":[169],"humans.":[171],"Genes":[172],"linked":[173],"were":[177],"likely":[179],"upregulated":[182],"humans,":[184],"silico":[187],"reversion":[188],"ancestral":[190],"alleles":[191],"such":[193],"upregulations":[194],"individual":[196],"creating":[198],"transcription":[199],"factor":[200],"binding":[201],"motifs.":[202],"Comparison":[203],"with":[204],"Neandertal":[205],"Denisovan":[207],"genomes":[208],"revealed":[209],"nearly":[211],"all":[212],"now":[214],"fixed":[215],"humans":[217],"predate":[218],"split":[220],"archaic":[222],"yet":[224],"few":[226],"modern-human-specific":[227],"contribute":[229],"substantially":[230],"upregulation.":[233],"Our":[234],"study":[235],"provides":[236],"genome-wide,":[238],"tissue-resolved":[239],"map":[240],"contribution":[246],"lineage.":[254]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-10-24T00:00:00"}
