{"id":"https://openalex.org/W4398763706","doi":"https://doi.org/10.1093/bioinformatics/btae330","title":"CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism","display_name":"CodonBERT: a BERT-based architecture tailored for codon optimization using the cross-attention mechanism","publication_year":2024,"publication_date":"2024-05-24","ids":{"openalex":"https://openalex.org/W4398763706","doi":"https://doi.org/10.1093/bioinformatics/btae330","pmid":"https://pubmed.ncbi.nlm.nih.gov/38788220"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae330","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae330","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae330/57890129/btae330.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae330/57890129/btae330.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068356154","display_name":"Zilin Ren","orcid":"https://orcid.org/0000-0002-3621-1024"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]},{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zilin Ren","raw_affiliation_strings":["Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","School of Information Science and Technology, Northeast Normal University , Changchun 130117, China"],"affiliations":[{"raw_affiliation_string":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","institution_ids":["https://openalex.org/I4210138501"]},{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , Changchun 130117, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090872577","display_name":"Lili Jiang","orcid":"https://orcid.org/0009-0001-3297-4892"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]},{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lili Jiang","raw_affiliation_strings":["Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","School of Information Science and Technology, Northeast Normal University , Changchun 130117, China"],"affiliations":[{"raw_affiliation_string":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","institution_ids":["https://openalex.org/I4210138501"]},{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , Changchun 130117, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104312514","display_name":"Yaxin Di","orcid":null},"institutions":[{"id":"https://openalex.org/I169572211","display_name":"Northeast Agricultural University","ror":"https://ror.org/0515nd386","country_code":"CN","type":"education","lineage":["https://openalex.org/I169572211"]},{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yaxin Di","raw_affiliation_strings":["Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","College of Veterinary Medicine, Northeast Agricultural University , Harbin 150038, China"],"affiliations":[{"raw_affiliation_string":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","institution_ids":["https://openalex.org/I4210138501"]},{"raw_affiliation_string":"College of Veterinary Medicine, Northeast Agricultural University , Harbin 150038, China","institution_ids":["https://openalex.org/I169572211"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113227127","display_name":"Dufei Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]},{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dufei Zhang","raw_affiliation_strings":["Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","School of Information Science and Technology, Northeast Normal University , Changchun 130117, China"],"affiliations":[{"raw_affiliation_string":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","institution_ids":["https://openalex.org/I4210138501"]},{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , Changchun 130117, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100856677","display_name":"Jianli Gong","orcid":null},"institutions":[{"id":"https://openalex.org/I4210123088","display_name":"Wuhan Technology and Business University","ror":"https://ror.org/0348f9w08","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123088"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianli Gong","raw_affiliation_strings":["Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine , Beijing 100850, China","School of Artificial Intelligence, Wuhan Technology and Business University , Wuhan 340000, China"],"affiliations":[{"raw_affiliation_string":"Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine , Beijing 100850, China","institution_ids":[]},{"raw_affiliation_string":"School of Artificial Intelligence, Wuhan Technology and Business University , Wuhan 340000, China","institution_ids":["https://openalex.org/I4210123088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067176216","display_name":"Jianting Gong","orcid":"https://orcid.org/0000-0002-6072-3150"},"institutions":[{"id":"https://openalex.org/I4210123088","display_name":"Wuhan Technology and Business University","ror":"https://ror.org/0348f9w08","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210123088"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianting Gong","raw_affiliation_strings":["Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine , Beijing 100850, China","School of Artificial Intelligence, Wuhan Technology and Business University , Wuhan 340000, China"],"affiliations":[{"raw_affiliation_string":"Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine , Beijing 100850, China","institution_ids":[]},{"raw_affiliation_string":"School of Artificial Intelligence, Wuhan Technology and Business University , Wuhan 340000, China","institution_ids":["https://openalex.org/I4210123088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078531561","display_name":"Qiwei Jiang","orcid":"https://orcid.org/0000-0002-6048-0582"},"institutions":[{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qiwei Jiang","raw_affiliation_strings":["Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China"],"affiliations":[{"raw_affiliation_string":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","institution_ids":["https://openalex.org/I4210138501"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045149952","display_name":"Zhiguo Fu","orcid":"https://orcid.org/0000-0002-9808-4008"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiguo Fu","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , Changchun 130117, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , Changchun 130117, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5120839754","display_name":"Pingping Sun","orcid":"https://orcid.org/0000-0002-9193-4321"},"institutions":[{"id":"https://openalex.org/I184983240","display_name":"Northeast Normal University","ror":"https://ror.org/02rkvz144","country_code":"CN","type":"education","lineage":["https://openalex.org/I184983240"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Pingping Sun","raw_affiliation_strings":["School of Information Science and Technology, Northeast Normal University , Changchun 130117, China"],"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, Northeast Normal University , Changchun 130117, China","institution_ids":["https://openalex.org/I184983240"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113258459","display_name":"Bo Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I4210138501","display_name":"Chinese Academy of Agricultural Sciences","ror":"https://ror.org/0313jb750","country_code":"CN","type":"government","lineage":["https://openalex.org/I4210127390","https://openalex.org/I4210138501","https://openalex.org/I4210151987"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Bo Zhou","raw_affiliation_strings":["Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China"],"affiliations":[{"raw_affiliation_string":"Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, State Key Laboratory of Pathogen and Biosecurity, Key Laboratory of Jilin Province for Zoonosis Prevention and Control , Changchun 130122, China","institution_ids":["https://openalex.org/I4210138501"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073443345","display_name":"Ming Ni","orcid":"https://orcid.org/0000-0003-0225-4816"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ming Ni","raw_affiliation_strings":["Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine , Beijing 100850, China"],"affiliations":[{"raw_affiliation_string":"Deartment of Regenerative Medicine, Institute of Health Service and Transfusion Medicine , Beijing 100850, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":11,"corresponding_author_ids":["https://openalex.org/A5073443345","https://openalex.org/A5113258459","https://openalex.org/A5120839754"],"corresponding_institution_ids":["https://openalex.org/I184983240","https://openalex.org/I4210138501"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":5.7363,"has_fulltext":true,"cited_by_count":25,"citation_normalized_percentile":{"value":0.96942842,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"40","issue":"7","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":1.0,"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/T11482","display_name":"RNA modifications and cancer","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"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9940000176429749,"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/codon-usage-bias","display_name":"Codon usage bias","score":0.6729316711425781},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5999528169631958},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.5550557971000671},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5355256795883179},{"id":"https://openalex.org/keywords/start-codon","display_name":"Start codon","score":0.4736524820327759},{"id":"https://openalex.org/keywords/translational-efficiency","display_name":"Translational efficiency","score":0.4713076055049896},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.4627549350261688},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4588821828365326},{"id":"https://openalex.org/keywords/amino-acid","display_name":"Amino acid","score":0.44997698068618774},{"id":"https://openalex.org/keywords/machine-translation","display_name":"Machine translation","score":0.4119799733161926},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37260353565216064},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3679828643798828},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32301026582717896},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.3121121823787689},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2152557075023651}],"concepts":[{"id":"https://openalex.org/C87253356","wikidata":"https://www.wikidata.org/wiki/Q1106472","display_name":"Codon usage bias","level":4,"score":0.6729316711425781},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5999528169631958},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.5550557971000671},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5355256795883179},{"id":"https://openalex.org/C176990463","wikidata":"https://www.wikidata.org/wiki/Q1854186","display_name":"Start codon","level":4,"score":0.4736524820327759},{"id":"https://openalex.org/C2775992057","wikidata":"https://www.wikidata.org/wiki/Q16956568","display_name":"Translational efficiency","level":5,"score":0.4713076055049896},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.4627549350261688},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4588821828365326},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.44997698068618774},{"id":"https://openalex.org/C203005215","wikidata":"https://www.wikidata.org/wiki/Q79798","display_name":"Machine translation","level":2,"score":0.4119799733161926},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37260353565216064},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3679828643798828},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32301026582717896},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3121121823787689},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2152557075023651}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003062","descriptor_name":"Codon","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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae330","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae330","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae330/57890129/btae330.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38788220","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38788220","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11226863","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11226863","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11226863/pdf/btae330.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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae330","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae330","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae330/57890129/btae330.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320327282","display_name":"Department of Science and Technology of Jilin Province","ror":null}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4398763706.pdf"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1995661119","https://openalex.org/W2006607348","https://openalex.org/W2086561953","https://openalex.org/W2164618276","https://openalex.org/W2168036974","https://openalex.org/W2259283565","https://openalex.org/W2762868004","https://openalex.org/W3009746164","https://openalex.org/W3093282046","https://openalex.org/W3111061871","https://openalex.org/W3177545102","https://openalex.org/W3214182269","https://openalex.org/W4205773061","https://openalex.org/W4321787045","https://openalex.org/W4362601885","https://openalex.org/W4367681391","https://openalex.org/W6684041852","https://openalex.org/W6797827587"],"related_works":["https://openalex.org/W2151102421","https://openalex.org/W2028165934","https://openalex.org/W2165439827","https://openalex.org/W2887582884","https://openalex.org/W1793475955","https://openalex.org/W2123637623","https://openalex.org/W2752267826","https://openalex.org/W3207681509","https://openalex.org/W2132060660","https://openalex.org/W2399739163"],"abstract_inverted_index":{"CodonBERT":[0],"is":[1],"freely":[2],"available":[3],"on":[4],"https://github.com/FPPGroup/CodonBERT.":[5]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":14},{"year":2024,"cited_by_count":4}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}