{"id":"https://openalex.org/W7147615056","doi":"https://doi.org/10.1038/s41467-026-70070-6","title":"An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation","display_name":"An end-to-end generalizable deep learning framework to comprehensively analyze transcriptional regulation","publication_year":2026,"publication_date":"2026-04-01","ids":{"openalex":"https://openalex.org/W7147615056","doi":"https://doi.org/10.1038/s41467-026-70070-6","pmid":"https://pubmed.ncbi.nlm.nih.gov/41922356","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/13212934"},"language":"en","primary_location":{"id":"doi:10.1038/s41467-026-70070-6","doi":"https://doi.org/10.1038/s41467-026-70070-6","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41467-026-70070-6","pdf_url":null,"source":{"id":"https://openalex.org/S64187185","display_name":"Nature Communications","issn_l":"2041-1723","issn":["2041-1723"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Communications","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1038/s41467-026-70070-6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101617734","display_name":"Zhaoxi Zhang","orcid":"https://orcid.org/0000-0002-3894-7641","observed_orcids":["https://orcid.org/0000-0002-3894-7641"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhaoxi Zhang","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0002-3894-7641","affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055305202","display_name":"Xiaoya Fan","orcid":"https://orcid.org/0000-0002-5002-6968","observed_orcids":["https://orcid.org/0000-0002-5002-6968"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoya Fan","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0002-5002-6968","affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113976548","display_name":"Jiaxin Zhong","orcid":"https://orcid.org/0009-0000-6474-7582","observed_orcids":["https://orcid.org/0009-0000-6474-7582"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaxin Zhong","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124278122","display_name":"Lijuan Jia","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lijuan Jia","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yuanyuan Han","orcid":"https://orcid.org/0000-0002-3440-0999","observed_orcids":["https://orcid.org/0000-0002-3440-0999"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Han","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0002-3440-0999","affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056390459","display_name":"Chenyi Yang","orcid":"https://orcid.org/0009-0001-0761-7367","observed_orcids":["https://orcid.org/0009-0001-0761-7367"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenyi Yang","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009588567","display_name":"Zengyou He","orcid":"https://orcid.org/0000-0001-9526-8816","observed_orcids":["https://orcid.org/0000-0001-9526-8816"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zengyou He","raw_affiliation_strings":["School of Software Technology, Dalian University of Technology, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China","institution_ids":["https://openalex.org/I27357992"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057749373","display_name":"Xiaodong Li","orcid":"https://orcid.org/0000-0003-2348-926X","observed_orcids":["https://orcid.org/0000-0003-2348-926X","https://orcid.org/0000-0001-7611-845X","https://orcid.org/0009-0003-2088-8799","https://orcid.org/0009-0003-4204-3076"]},"institutions":[{"id":"https://openalex.org/I4210161255","display_name":"Liaoning Cancer Hospital & Institute","ror":"https://ror.org/05d659s21","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210161255"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyan Li","raw_affiliation_strings":["Department of Pathology, Cancer Hospital of Dalian University of Technology, Shenyang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Pathology, Cancer Hospital of Dalian University of Technology, Shenyang, China","institution_ids":["https://openalex.org/I4210161255"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006865040","display_name":"Shing\u2013Tung Yau","orcid":"https://orcid.org/0000-0003-3394-2187","observed_orcids":["https://orcid.org/0000-0003-3394-2187","https://orcid.org/0000-0002-4478-5132"]},"institutions":[{"id":"https://openalex.org/I4403928416","display_name":"Beijing Institute of Mathematical Sciences and Applications","ror":"https://ror.org/05t6hvr95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4403928416","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shing-Tung Yau","raw_affiliation_strings":["Beijing Key Laboratory of Topological Statistics and Applications for Complex Systems, Beijing Institute of Mathematical Sciences and Applications, Beijing, China","Qiuzhen College, Tsinghua University, Beijing, China"],"raw_orcid":"https://orcid.org/0000-0003-3394-2187","affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Topological Statistics and Applications for Complex Systems, Beijing Institute of Mathematical Sciences and Applications, Beijing, China","institution_ids":["https://openalex.org/I4403928416"]},{"raw_affiliation_string":"Qiuzhen College, Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088306828","display_name":"Rongling Wu","orcid":"https://orcid.org/0000-0002-2334-6421","observed_orcids":["https://orcid.org/0000-0002-2334-6421","https://orcid.org/0000-0001-8350-7779","https://orcid.org/0009-0000-0005-1025"]},"institutions":[{"id":"https://openalex.org/I4403928416","display_name":"Beijing Institute of Mathematical Sciences and Applications","ror":"https://ror.org/05t6hvr95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4403928416","https://openalex.org/I99065089"]},{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Rongling Wu","raw_affiliation_strings":["Beijing Key Laboratory of Topological Statistics and Applications for Complex Systems, Beijing Institute of Mathematical Sciences and Applications, Beijing, China. ronglingwu@bimsa.cn","Qiuzhen College, Tsinghua University, Beijing, China. ronglingwu@bimsa.cn"],"raw_orcid":"https://orcid.org/0000-0002-2334-6421","affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Topological Statistics and Applications for Complex Systems, Beijing Institute of Mathematical Sciences and Applications, Beijing, China. ronglingwu@bimsa.cn","institution_ids":["https://openalex.org/I4403928416"]},{"raw_affiliation_string":"Qiuzhen College, Tsinghua University, Beijing, China. ronglingwu@bimsa.cn","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024923108","display_name":"Charles G. Danko","orcid":"https://orcid.org/0000-0002-1999-7125","observed_orcids":["https://orcid.org/0000-0002-1999-7125"]},"institutions":[{"id":"https://openalex.org/I205783295","display_name":"Cornell University","ror":"https://ror.org/05bnh6r87","country_code":"US","type":"education","lineage":["https://openalex.org/I205783295"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Charles G. Danko","raw_affiliation_strings":["Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA. cgd24@cornell.edu","Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA. cgd24@cornell.edu"],"raw_orcid":"https://orcid.org/0000-0002-1999-7125","affiliations":[{"raw_affiliation_string":"Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA. cgd24@cornell.edu","institution_ids":["https://openalex.org/I205783295"]},{"raw_affiliation_string":"Department of Biomedical Sciences, Cornell University, Ithaca, NY, USA. cgd24@cornell.edu","institution_ids":["https://openalex.org/I205783295"]}]},{"author_position":"last","author":{"id":null,"display_name":"Zhong Wang","orcid":"https://orcid.org/0009-0003-5602-1003","observed_orcids":["https://orcid.org/0009-0003-5602-1003"]},"institutions":[{"id":"https://openalex.org/I27357992","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876","country_code":"CN","type":"education","lineage":["https://openalex.org/I27357992"]},{"id":"https://openalex.org/I4403928416","display_name":"Beijing Institute of Mathematical Sciences and Applications","ror":"https://ror.org/05t6hvr95","country_code":"CN","type":"education","lineage":["https://openalex.org/I4403928416","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhong Wang","raw_affiliation_strings":["Beijing Key Laboratory of Topological Statistics and Applications for Complex Systems, Beijing Institute of Mathematical Sciences and Applications, Beijing, China. wangzhong@bimsa.cn","School of Software Technology, Dalian University of Technology, Dalian, China. wangzhong@bimsa.cn"],"raw_orcid":"https://orcid.org/0009-0003-5602-1003","affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory of Topological Statistics and Applications for Complex Systems, Beijing Institute of Mathematical Sciences and Applications, Beijing, China. wangzhong@bimsa.cn","institution_ids":["https://openalex.org/I4403928416"]},{"raw_affiliation_string":"School of Software Technology, Dalian University of Technology, Dalian, China. wangzhong@bimsa.cn","institution_ids":["https://openalex.org/I27357992"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5024923108","https://openalex.org/A5088306828"],"corresponding_institution_ids":["https://openalex.org/I205783295","https://openalex.org/I27357992","https://openalex.org/I4403928416","https://openalex.org/I99065089"],"apc_list":{"value":6990,"currency":"USD","value_usd":6990},"apc_paid":{"value":6990,"currency":"USD","value_usd":6990},"fwci":2.0436,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.83961755,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":96},"biblio":{"volume":"17","issue":"1","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":0.9878000020980835,"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":0.9878000020980835,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0035000001080334187,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.002099999925121665,"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/genome-annotation","display_name":"genome annotation","score":0.8960000276565552},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.8209999799728394},{"id":"https://openalex.org/keywords/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.5619999766349792},{"id":"https://openalex.org/keywords/gene-expression-prediction","display_name":"gene expression prediction","score":0.996999979019165},{"id":"https://openalex.org/keywords/transcription-factor-binding-site-prediction","display_name":"transcription factor binding site prediction","score":0.9750000238418579},{"id":"https://openalex.org/keywords/dna-sequence-features","display_name":"DNA sequence features","score":0.5899999737739563}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7605000138282776},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6003000140190125},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5773000121116638},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5741000175476074},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5414999723434448},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4848000109195709},{"id":"https://openalex.org/C66746571","wikidata":"https://www.wikidata.org/wiki/Q1134833","display_name":"ENCODE","level":3,"score":0.4715000092983246},{"id":"https://openalex.org/C64927066","wikidata":"https://www.wikidata.org/wiki/Q36293","display_name":"Histone","level":3,"score":0.46470001339912415},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.46219998598098755},{"id":"https://openalex.org/C2908923196","wikidata":"https://www.wikidata.org/wiki/Q5205742","display_name":"Gene Annotation","level":4,"score":0.4146000146865845},{"id":"https://openalex.org/C2781162219","wikidata":"https://www.wikidata.org/wiki/Q26250693","display_name":"Replicate","level":2,"score":0.41429999470710754},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.40209999680519104},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.388700008392334},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.3880999982357025},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3840000033378601},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.3824999928474426},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.37709999084472656},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.36959999799728394},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.3538999855518341},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3481000065803528},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3379000127315521},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.33329999446868896},{"id":"https://openalex.org/C27153228","wikidata":"https://www.wikidata.org/wiki/Q3787274","display_name":"Transcriptional regulation","level":4,"score":0.32760000228881836},{"id":"https://openalex.org/C132917006","wikidata":"https://www.wikidata.org/wiki/Q5250436","display_name":"Deep sequencing","level":4,"score":0.31859999895095825},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.3138999938964844},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2955999970436096},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.2939000129699707},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.2858000099658966},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.2727999985218048},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2689000070095062},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.2653000056743622},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.258899986743927}],"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D002460","descriptor_name":"Cell Line","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1038/s41467-026-70070-6","doi":"https://doi.org/10.1038/s41467-026-70070-6","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41467-026-70070-6","pdf_url":null,"source":{"id":"https://openalex.org/S64187185","display_name":"Nature Communications","issn_l":"2041-1723","issn":["2041-1723"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Communications","raw_type":"journal-article"},{"id":"doi:10.21203/rs.3.rs-7242733/v1","doi":"https://doi.org/10.21203/rs.3.rs-7242733/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-7242733/v1","pdf_url":"https://www.researchsquare.com/article/rs-7242733/latest.pdf","source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},{"id":"pmid:41922356","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41922356","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":"Nature communications","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:13212934","doi":null,"is_oa":true,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41922356/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nat Commun","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:c67061fc45d24da78c3eb1de1779ed02","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/c67061fc45d24da78c3eb1de1779ed02","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nature Communications, Vol 17, Iss 1 (2026)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1038/s41467-026-70070-6","doi":"https://doi.org/10.1038/s41467-026-70070-6","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s41467-026-70070-6","pdf_url":null,"source":{"id":"https://openalex.org/S64187185","display_name":"Nature Communications","issn_l":"2041-1723","issn":["2041-1723"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-class-a","anvur-scientific","cwts-core","doaj","dongbi-a","doyens","jufo-3","ki-jl-3","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Communications","raw_type":"journal-article"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G365998636","display_name":null,"funder_award_id":"XLYC2002010","funder_id":"https://openalex.org/F4320329895","funder_display_name":"Liaoning Revitalization Talents Program"},{"id":"https://openalex.org/G8013965529","display_name":null,"funder_award_id":"XLYC2002010","funder_id":"https://openalex.org/F4320321630","funder_display_name":"Dalian University of Technology"}],"funders":[{"id":"https://openalex.org/F4320321630","display_name":"Dalian University of Technology","ror":"https://ror.org/023hj5876"},{"id":"https://openalex.org/F4320329895","display_name":"Liaoning Revitalization Talents Program","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W1567904427","https://openalex.org/W1912127524","https://openalex.org/W1963590871","https://openalex.org/W1964963969","https://openalex.org/W1982881824","https://openalex.org/W1987839415","https://openalex.org/W1997260717","https://openalex.org/W1997590968","https://openalex.org/W2015324225","https://openalex.org/W2015416439","https://openalex.org/W2029903254","https://openalex.org/W2033781392","https://openalex.org/W2044826047","https://openalex.org/W2049266248","https://openalex.org/W2056198580","https://openalex.org/W2060842569","https://openalex.org/W2066777575","https://openalex.org/W2086399711","https://openalex.org/W2090160722","https://openalex.org/W2091533196","https://openalex.org/W2096083625","https://openalex.org/W2096237610","https://openalex.org/W2099035207","https://openalex.org/W2117792884","https://openalex.org/W2124343649","https://openalex.org/W2142184151","https://openalex.org/W2142678031","https://openalex.org/W2158562032","https://openalex.org/W2159164310","https://openalex.org/W2198606573","https://openalex.org/W2211837538","https://openalex.org/W2259938310","https://openalex.org/W2334656801","https://openalex.org/W2336509392","https://openalex.org/W2339142748","https://openalex.org/W2479945688","https://openalex.org/W2556513628","https://openalex.org/W2741124923","https://openalex.org/W2883945062","https://openalex.org/W2896399042","https://openalex.org/W2897250433","https://openalex.org/W2908497471","https://openalex.org/W2911174974","https://openalex.org/W2919115771","https://openalex.org/W2950354537","https://openalex.org/W2951410692","https://openalex.org/W2952239877","https://openalex.org/W3000799818","https://openalex.org/W3014261926","https://openalex.org/W3015468748","https://openalex.org/W3127238141","https://openalex.org/W3137533336","https://openalex.org/W3170841864","https://openalex.org/W3196589510","https://openalex.org/W3203588026","https://openalex.org/W4221036171","https://openalex.org/W4226349074","https://openalex.org/W4239954142","https://openalex.org/W4280512834","https://openalex.org/W4281254649","https://openalex.org/W4283796583","https://openalex.org/W4318669110","https://openalex.org/W4322738638","https://openalex.org/W4361001523","https://openalex.org/W4378071282","https://openalex.org/W4378907379","https://openalex.org/W4412944812","https://openalex.org/W7123865756"],"related_works":["https://openalex.org/W7203571468","https://openalex.org/W4240736919","https://openalex.org/W4311460970","https://openalex.org/W7172433925","https://openalex.org/W4321015480","https://openalex.org/W3096716224","https://openalex.org/W4285891329","https://openalex.org/W4394681169","https://openalex.org/W4283362956","https://openalex.org/W4205751895"],"abstract_inverted_index":{"Abstract":[0],"Genome":[1],"annotation":[2,49,78],"currently":[3],"requires":[4],"performing":[5],"dozens":[6],"of":[7,12,30,83,109,143],"molecular":[8,43],"assays":[9,44],"in":[10,111,116,122],"hundreds":[11],"cell":[13],"and":[14,28,65,86,120,161],"tissue":[15],"samples,":[16],"an":[17,159,171],"expensive":[18],"endeavor":[19],"which":[20],"is":[21,178],"impractical":[22],"to":[23,127,141],"replicate":[24],"across":[25,103,151],"all":[26],"species":[27],"conditions":[29],"interest.":[31],"Here,":[32],"we":[33],"introduce":[34],"BioSeq2Seq,":[35],"a":[36,52,69],"deep":[37],"learning":[38],"model":[39,99],"that":[40,142],"infers":[41],"cell-type-specific":[42,62],"widely":[45],"used":[46],"for":[47,94,164],"genome":[48,77,165],"by":[50,68],"leveraging":[51],"tri-modal":[53],"input:":[54],"evolutionarily":[55],"conserved":[56],"DNA":[57],"sequence":[58],"features,":[59],"together":[60],"with":[61,90,153],"transcriptional":[63],"activity":[64],"directionality":[66],"captured":[67],"single":[70],"run-on":[71],"sequencing":[72],"assay.":[73],"BioSeq2Seq":[74,157,177],"enables":[75],"flexible":[76],"tasks":[79,152],"through":[80],"parameterized":[81],"configurations":[82],"input":[84,155],"features":[85],"output":[87],"targets,":[88],"combined":[89],"gradient-guided":[91],"architectural":[92],"refinement":[93],"specific":[95],"biological":[96],"objectives.":[97],"Our":[98],"demonstrates":[100],"high":[101],"accuracy":[102],"four":[104],"downstream":[105],"tasks,":[106],"showing":[107],"improvements":[108],"10.37%":[110],"histone":[112],"modification":[113],"prediction,":[114,119,136],"2.25%":[115],"functional":[117],"element":[118],"5.02%":[121],"gene":[123],"expression":[124],"prediction":[125,173],"compared":[126],"state-of-the-art":[128],"methods.":[129],"In":[130],"transcription":[131],"factor":[132],"binding":[133],"site":[134],"(TFBS)":[135],"it":[137],"maintains":[138],"performance":[139,150],"comparable":[140],"leading":[144],"existing":[145],"approaches.":[146],"By":[147],"achieving":[148],"competitive":[149],"minimal":[154],"data,":[156],"provides":[158],"efficient":[160],"low-cost":[162],"alternative":[163],"annotation.":[166],"To":[167],"facilitate":[168],"broader":[169],"application,":[170],"online":[172],"service":[174],"based":[175],"on":[176],"publicly":[179],"available":[180],"at":[181],"https://dreg.dnasequence.org.":[182]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2026-04-02T00:00:00"}