{"id":"https://openalex.org/W4391788775","doi":"https://doi.org/10.1093/bib/bbae040","title":"ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein\u2013DNA binding site prediction","display_name":"ULDNA: integrating unsupervised multi-source language models with LSTM-attention network for high-accuracy protein\u2013DNA binding site prediction","publication_year":2024,"publication_date":"2024-01-22","ids":{"openalex":"https://openalex.org/W4391788775","doi":"https://doi.org/10.1093/bib/bbae040","pmid":"https://pubmed.ncbi.nlm.nih.gov/38349057"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae040","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae040/56663371/bbae040.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae040/56663371/bbae040.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052610760","display_name":"Yiheng Zhu","orcid":"https://orcid.org/0000-0002-3857-1533"},"institutions":[{"id":"https://openalex.org/I119454577","display_name":"Nanjing Agricultural University","ror":"https://ror.org/05td3s095","country_code":"CN","type":"education","lineage":["https://openalex.org/I119454577"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi-Heng Zhu","raw_affiliation_strings":["College of Artificial Intelligence, Nanjing Agricultural University , Nanjing 210095 , China"],"affiliations":[{"raw_affiliation_string":"College of Artificial Intelligence, Nanjing Agricultural University , Nanjing 210095 , China","institution_ids":["https://openalex.org/I119454577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100451904","display_name":"Zi Liu","orcid":"https://orcid.org/0000-0002-1353-4461"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zi Liu","raw_affiliation_strings":["School of Computer Science and Engineering, Nanjing University of Science and Technology , Nanjing 210094 , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology , Nanjing 210094 , China","institution_ids":["https://openalex.org/I36399199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047530483","display_name":"Yan Liu","orcid":"https://orcid.org/0000-0002-5331-3655"},"institutions":[{"id":"https://openalex.org/I78978612","display_name":"Yangzhou University","ror":"https://ror.org/03tqb8s11","country_code":"CN","type":"education","lineage":["https://openalex.org/I78978612"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Liu","raw_affiliation_strings":["School of Information Engineering, Yangzhou University , Yangzhou 225000 , China"],"affiliations":[{"raw_affiliation_string":"School of Information Engineering, Yangzhou University , Yangzhou 225000 , China","institution_ids":["https://openalex.org/I78978612"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102794567","display_name":"Zhiwei Ji","orcid":"https://orcid.org/0000-0002-0891-7118"},"institutions":[{"id":"https://openalex.org/I119454577","display_name":"Nanjing Agricultural University","ror":"https://ror.org/05td3s095","country_code":"CN","type":"education","lineage":["https://openalex.org/I119454577"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhiwei Ji","raw_affiliation_strings":["College of Artificial Intelligence, Nanjing Agricultural University , Nanjing 210095 , China"],"affiliations":[{"raw_affiliation_string":"College of Artificial Intelligence, Nanjing Agricultural University , Nanjing 210095 , China","institution_ids":["https://openalex.org/I119454577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008960436","display_name":"Dong\u2010Jun Yu","orcid":"https://orcid.org/0000-0002-6786-8053"},"institutions":[{"id":"https://openalex.org/I36399199","display_name":"Nanjing University of Science and Technology","ror":"https://ror.org/00xp9wg62","country_code":"CN","type":"education","lineage":["https://openalex.org/I36399199"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Dong-Jun Yu","raw_affiliation_strings":["School of Computer Science and Engineering, Nanjing University of Science and Technology , Nanjing 210094 , China"],"affiliations":[{"raw_affiliation_string":"School of Computer Science and Engineering, Nanjing University of Science and Technology , Nanjing 210094 , China","institution_ids":["https://openalex.org/I36399199"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5008960436","https://openalex.org/A5102794567"],"corresponding_institution_ids":["https://openalex.org/I119454577","https://openalex.org/I36399199"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":8.4568,"has_fulltext":true,"cited_by_count":36,"citation_normalized_percentile":{"value":0.98470934,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"25","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9994999766349792,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991999864578247,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9991000294685364,"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/computer-science","display_name":"Computer science","score":0.6671271324157715},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5252765417098999},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.49426865577697754},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.47991666197776794},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4605258107185364},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.434159517288208},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.43002021312713623},{"id":"https://openalex.org/keywords/decodes","display_name":"Decodes","score":0.42684391140937805},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.42561712861061096},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40330085158348083},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3714863955974579},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20283150672912598},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18471047282218933},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.15948504209518433},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12504085898399353},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.08400830626487732}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6671271324157715},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5252765417098999},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.49426865577697754},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.47991666197776794},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4605258107185364},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.434159517288208},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.43002021312713623},{"id":"https://openalex.org/C2778858076","wikidata":"https://www.wikidata.org/wiki/Q5249539","display_name":"Decodes","level":3,"score":0.42684391140937805},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.42561712861061096},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40330085158348083},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3714863955974579},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20283150672912598},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18471047282218933},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.15948504209518433},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12504085898399353},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.08400830626487732},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000078332","descriptor_name":"Data Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"D001665","descriptor_name":"Binding Sites","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":"D001665","descriptor_name":"Binding Sites","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":"D001665","descriptor_name":"Binding Sites","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":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae040","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae040/56663371/bbae040.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38349057","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38349057","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10939370","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10939370","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10939370/pdf/bbae040.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae040","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae040","pdf_url":"https://academic.oup.com/bib/article-pdf/25/2/bbae040/56663371/bbae040.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5899999737739563,"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1351919236","display_name":null,"funder_award_id":"62306142","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1702080893","display_name":null,"funder_award_id":"62372234","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2082826544","display_name":null,"funder_award_id":"Postdoctoral","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2651717945","display_name":null,"funder_award_id":"20211210","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3008817052","display_name":null,"funder_award_id":"201304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4021502096","display_name":null,"funder_award_id":"BK20201304","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4181105620","display_name":null,"funder_award_id":"2020130","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5939423041","display_name":null,"funder_award_id":"Technology","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7227913532","display_name":null,"funder_award_id":"2021121","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7608752429","display_name":null,"funder_award_id":"Talent","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7719334545","display_name":null,"funder_award_id":"62072243","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8019139419","display_name":null,"funder_award_id":"BK2021","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8745099089","display_name":null,"funder_award_id":"6177227","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8879126380","display_name":null,"funder_award_id":"61772273","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391788775.pdf"},"referenced_works_count":75,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1964940342","https://openalex.org/W1971894358","https://openalex.org/W1973356821","https://openalex.org/W1980825481","https://openalex.org/W1997401305","https://openalex.org/W2005423065","https://openalex.org/W2038670706","https://openalex.org/W2043638247","https://openalex.org/W2076048958","https://openalex.org/W2089716128","https://openalex.org/W2096986143","https://openalex.org/W2108067237","https://openalex.org/W2115547583","https://openalex.org/W2119948329","https://openalex.org/W2122137509","https://openalex.org/W2128533758","https://openalex.org/W2130479394","https://openalex.org/W2130768139","https://openalex.org/W2138769522","https://openalex.org/W2140538197","https://openalex.org/W2144347309","https://openalex.org/W2149997286","https://openalex.org/W2153153865","https://openalex.org/W2153187042","https://openalex.org/W2156125289","https://openalex.org/W2156136208","https://openalex.org/W2158714788","https://openalex.org/W2160800572","https://openalex.org/W2161652323","https://openalex.org/W2165745599","https://openalex.org/W2166248605","https://openalex.org/W2216946510","https://openalex.org/W2441124914","https://openalex.org/W2531919408","https://openalex.org/W2557595285","https://openalex.org/W2767813457","https://openalex.org/W2799900537","https://openalex.org/W2803187616","https://openalex.org/W2905281057","https://openalex.org/W2933350524","https://openalex.org/W2949342052","https://openalex.org/W2951433247","https://openalex.org/W2971227267","https://openalex.org/W2995514860","https://openalex.org/W2998259324","https://openalex.org/W3121281384","https://openalex.org/W3126876258","https://openalex.org/W3136918052","https://openalex.org/W3146944767","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3208957581","https://openalex.org/W4205989901","https://openalex.org/W4224266664","https://openalex.org/W4225438928","https://openalex.org/W4280609620","https://openalex.org/W4281785626","https://openalex.org/W4282011649","https://openalex.org/W4283011532","https://openalex.org/W4285414302","https://openalex.org/W4288066876","https://openalex.org/W4312097792","https://openalex.org/W4318071656","https://openalex.org/W4318898843","https://openalex.org/W4327550249","https://openalex.org/W4385073318","https://openalex.org/W4386470073","https://openalex.org/W4387583274","https://openalex.org/W6631190155","https://openalex.org/W6682923439","https://openalex.org/W6751420435","https://openalex.org/W6763868836","https://openalex.org/W6791955017","https://openalex.org/W6839782630"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2152664145","https://openalex.org/W2153561273","https://openalex.org/W2079197459","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W2090848290","https://openalex.org/W2146393977","https://openalex.org/W2617836174","https://openalex.org/W2122429294"],"abstract_inverted_index":{"Efficient":[0],"and":[1,18,43],"accurate":[2],"recognition":[3],"of":[4,14,110,124,142],"protein-DNA":[5,35],"interactions":[6],"is":[7,46],"vital":[8],"for":[9,55,194],"understanding":[10],"the":[11,24,29,122,139,164,171,185],"molecular":[12],"mechanisms":[13],"related":[15],"biological":[16],"processes":[17],"further":[19],"guiding":[20],"drug":[21],"discovery.":[22],"Although":[23],"current":[25],"experimental":[26,108],"protocols":[27],"are":[28,87,168],"most":[30],"precise":[31],"way":[32],"to":[33,40,50,67],"determine":[34],"binding":[36],"sites,":[37],"they":[38],"tend":[39],"be":[41],"labor-intensive":[42],"time-consuming.":[44],"There":[45],"an":[47,77],"immediate":[48],"need":[49],"design":[51],"efficient":[52],"computational":[53,115],"approaches":[54],"predicting":[56,195],"DNA-binding":[57,69,111,125,166,182,196],"sites.":[58,112],"Here,":[59],"we":[60],"proposed":[61],"ULDNA,":[62],"a":[63,191,199],"new":[64,192],"deep-learning":[65],"model,":[66],"deduce":[68],"sites":[70,197],"from":[71,92,114,145,205],"protein":[72,105,206],"sequences.":[73],"This":[74],"model":[75],"leverages":[76],"LSTM-attention":[78,174],"architecture,":[79],"embedded":[80],"with":[81,107,130,159,202],"three":[82,147],"unsupervised":[83],"language":[84,149,153],"models":[85,154],"that":[86,118,138],"pre-trained":[88],"on":[89,103,198],"large-scale":[90],"sequences":[91],"multiple":[93],"database":[94],"sources.":[95],"To":[96],"prove":[97],"its":[98],"effectiveness,":[99],"ULDNA":[100,119,143],"was":[101],"tested":[102],"229":[104],"chains":[106],"annotation":[109],"Results":[113],"experiments":[116],"revealed":[117],"significantly":[120],"improves":[121],"accuracy":[123,204],"site":[126],"prediction":[127],"in":[128,162],"comparison":[129],"17":[131],"state-of-the-art":[132],"methods.":[133],"In-depth":[134],"data":[135],"analyses":[136],"showed":[137],"major":[140],"strength":[141],"stems":[144],"employing":[146],"transformer":[148],"models.":[150],"Specifically,":[151],"these":[152],"capture":[155],"complementary":[156],"feature":[157],"embeddings":[158,180],"evolution":[160,178],"diversity,":[161],"which":[163],"complex":[165],"patterns":[167],"buried.":[169],"Meanwhile,":[170],"specially":[172],"crafted":[173],"network":[175],"effectively":[176],"decodes":[177],"diversity-based":[179],"as":[181],"results":[183],"at":[184],"residue":[186],"level.":[187],"Our":[188],"findings":[189],"demonstrated":[190],"pipeline":[193],"large":[200],"scale":[201],"high":[203],"sequence":[207],"alone.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":12}],"updated_date":"2026-03-27T14:29:43.386196","created_date":"2025-10-10T00:00:00"}
