{"id":"https://openalex.org/W7221762087","doi":"https://doi.org/10.1016/j.xgen.2026.101392","title":"Deep learning uncovers hidden power of low-affinity motifs","display_name":"Deep learning uncovers hidden power of low-affinity motifs","publication_year":2026,"publication_date":"2026-10-01","ids":{"openalex":"https://openalex.org/W7221762087","doi":"https://doi.org/10.1016/j.xgen.2026.101392","pmid":"https://pubmed.ncbi.nlm.nih.gov/42874569","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13689512"},"language":"en","primary_location":{"id":"doi:10.1016/j.xgen.2026.101392","doi":"https://doi.org/10.1016/j.xgen.2026.101392","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.xgen.2026.101392","pdf_url":null,"source":{"id":"https://openalex.org/S4210194377","display_name":"Cell Genomics","issn_l":"2666-979X","issn":["2666-979X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Genomics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1016/j.xgen.2026.101392","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5033390855","display_name":"Grace Bower","orcid":"https://orcid.org/0000-0003-1104-604X","observed_orcids":["https://orcid.org/0000-0003-1104-604X"]},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Grace Bower","raw_affiliation_strings":["Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA","institution_ids":["https://openalex.org/I204250578"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017800668","display_name":"Evgeny Z. Kvon","orcid":"https://orcid.org/0000-0002-1562-0945","observed_orcids":["https://orcid.org/0000-0002-1562-0945"]},"institutions":[{"id":"https://openalex.org/I204250578","display_name":"University of California, Irvine","ror":"https://ror.org/04gyf1771","country_code":"US","type":"education","lineage":["https://openalex.org/I204250578"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Evgeny Z. Kvon","raw_affiliation_strings":["Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Department of Systems Biology, University of California, Irvine, Irvine, CA, USA. Electronic address: ekvon@uci.edu"],"raw_orcid":"https://orcid.org/0000-0002-1562-0945","affiliations":[{"raw_affiliation_string":"Department of Developmental and Cell Biology, University of California, Irvine, Irvine, CA, USA; Department of Systems Biology, University of California, Irvine, Irvine, CA, USA. Electronic address: ekvon@uci.edu","institution_ids":["https://openalex.org/I204250578"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5017800668"],"corresponding_institution_ids":["https://openalex.org/I204250578"],"apc_list":{"value":8900,"currency":"USD","value_usd":8900},"apc_paid":{"value":8900,"currency":"USD","value_usd":8900},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.6548606,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"6","issue":"10","first_page":"101392","last_page":"101392"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9970999956130981,"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":0.9970999956130981,"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/T12820","display_name":"Chromatin Remodeling and Cancer","score":0.0010000000474974513,"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/T10269","display_name":"Epigenetics and DNA Methylation","score":0.0003000000142492354,"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/pioneer-transcription-factors","display_name":"pioneer transcription factors","score":0.9350000023841858},{"id":"https://openalex.org/keywords/chromatin-opening","display_name":"chromatin opening","score":0.6759999990463257},{"id":"https://openalex.org/keywords/mouse-embryonic-stem-cells","display_name":"mouse embryonic stem cells","score":0.9399999976158142},{"id":"https://openalex.org/keywords/chromatin-accessibility","display_name":"chromatin accessibility","score":0.6209999918937683},{"id":"https://openalex.org/keywords/deep-learning","display_name":"deep learning","score":0.5540000200271606}],"concepts":[{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7886000275611877},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6208000183105469},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6050000190734863},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.5950999855995178},{"id":"https://openalex.org/C153083717","wikidata":"https://www.wikidata.org/wiki/Q6535263","display_name":"Leverage (statistics)","level":2,"score":0.5839999914169312},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5467000007629395},{"id":"https://openalex.org/C145103041","wikidata":"https://www.wikidata.org/wiki/Q1151519","display_name":"Embryonic stem cell","level":3,"score":0.5424000024795532},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5242999792098999},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.4422000050544739},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4260999858379364},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.40950000286102295},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.33809998631477356},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.3352999985218048},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.3127000033855438},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.29989999532699585},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.28859999775886536},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.274399995803833},{"id":"https://openalex.org/C2781039887","wikidata":"https://www.wikidata.org/wiki/Q1391724","display_name":"Factor (programming language)","level":2,"score":0.2680000066757202},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.260699987411499},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2574000060558319},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2524999976158142}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1016/j.xgen.2026.101392","doi":"https://doi.org/10.1016/j.xgen.2026.101392","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.xgen.2026.101392","pdf_url":null,"source":{"id":"https://openalex.org/S4210194377","display_name":"Cell Genomics","issn_l":"2666-979X","issn":["2666-979X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Genomics","raw_type":"journal-article"},{"id":"pmid:42874569","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42874569","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,"listed_in":[],"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":"Cell genomics","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:9e1b307ddfcc4c428b14b39ec4dc11d5","doi":null,"is_oa":false,"landing_page_url":"https://doaj.org/article/9e1b307ddfcc4c428b14b39ec4dc11d5","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Cell Genomics, Vol 6, Iss 10, Pp 101392- (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1016/j.xgen.2026.101392","doi":"https://doi.org/10.1016/j.xgen.2026.101392","is_oa":true,"landing_page_url":"https://doi.org/10.1016/j.xgen.2026.101392","pdf_url":null,"source":{"id":"https://openalex.org/S4210194377","display_name":"Cell Genomics","issn_l":"2666-979X","issn":["2666-979X"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["cwts-core","doaj","dongbi-c","jufo-1","ki-jl-1","medline","norway-1","oarl","poland-20","vabb-shw"],"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Cell Genomics","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G5564759017","display_name":"Decoding the Mechanism of Pathogenic Enhancer Mutations In Congenital Limb Disorders","funder_award_id":"1r01hd115268-01a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000872201","display_name":"Deciphering the mechanism of long-range gene regulation in vivo","funder_award_id":"DP2GM149555","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G9000908109","display_name":"Center for Modeling Non-Coding Disease Variants","funder_award_id":"1u54od039864-01","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G9000915676","display_name":"Characterizing a mechanism of enhancer-promoter interaction in vivo","funder_award_id":"F31HD112201","funder_id":"https://openalex.org/F4320337611","funder_display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337349","display_name":"NIH Office of the Director","ror":"https://ror.org/00fj8a872"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337611","display_name":"Eunice Kennedy Shriver National Institute of Child Health and Human Development","ror":"https://ror.org/04byxyr05"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":8,"referenced_works":["https://openalex.org/W1986683530","https://openalex.org/W2462656404","https://openalex.org/W2944831967","https://openalex.org/W3083703986","https://openalex.org/W3121486818","https://openalex.org/W4390940878","https://openalex.org/W4409502882","https://openalex.org/W7172393996"],"related_works":["https://openalex.org/W4416385841","https://openalex.org/W7204162191","https://openalex.org/W3035587935","https://openalex.org/W7099774808","https://openalex.org/W3088452016","https://openalex.org/W7133619111","https://openalex.org/W4408022801","https://openalex.org/W4313527127","https://openalex.org/W3130819465","https://openalex.org/W3180669414"],"abstract_inverted_index":{"Low-affinity":[0],"transcription":[1],"factor":[2,35],"binding":[3,36],"sites":[4,37,47],"are":[5],"functionally":[6],"important":[7],"but":[8],"difficult":[9],"to":[10,30,49],"map":[11,32],"and":[12,43],"mechanistically":[13],"poorly":[14],"understood.":[15],"In":[16],"this":[17],"issue":[18],"of":[19],"Cell":[20],"Genomics,":[21],"Weilert":[22],"et":[23],"al.":[24],"leverage":[25],"sequence-to-function":[26],"deep":[27],"learning":[28],"models":[29],"systematically":[31],"low-affinity":[33],"pioneer":[34],"in":[38],"mouse":[39],"embryonic":[40],"stem":[41],"cells":[42],"reveal":[44],"how":[45],"these":[46],"contribute":[48],"chromatin":[50],"opening":[51],"through":[52],"soft-syntax":[53],"nucleosomal":[54],"cooperativity.":[55]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-10-15T00:00:00"}