{"id":"https://openalex.org/W4402254727","doi":"https://doi.org/10.1093/bib/bbae439","title":"DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs","display_name":"DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs","publication_year":2024,"publication_date":"2024-07-25","ids":{"openalex":"https://openalex.org/W4402254727","doi":"https://doi.org/10.1093/bib/bbae439","pmid":"https://pubmed.ncbi.nlm.nih.gov/39234953"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae439","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae439","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae439/59021567/bbae439.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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/25/5/bbae439/59021567/bbae439.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025609330","display_name":"Jian Zhao","orcid":"https://orcid.org/0000-0001-7857-4766"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jian Zhao","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077171618","display_name":"Zhewei Chen","orcid":"https://orcid.org/0000-0002-7422-095X"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhewei Chen","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100437731","display_name":"Meng Zhang","orcid":"https://orcid.org/0000-0002-2690-5954"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Meng Zhang","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034181138","display_name":"Lingxiao Zou","orcid":"https://orcid.org/0000-0001-7158-4750"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lingxiao Zou","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011186506","display_name":"Shan He","orcid":"https://orcid.org/0000-0003-1694-1465"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shan He","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100442544","display_name":"Jingjing Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jingjing Liu","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100418253","display_name":"Quan Wang","orcid":"https://orcid.org/0000-0002-2821-5017"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Wang","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013359542","display_name":"Xiaofeng Song","orcid":"https://orcid.org/0000-0001-7445-4302"},"institutions":[{"id":"https://openalex.org/I9842412","display_name":"Nanjing University of Aeronautics and Astronautics","ror":"https://ror.org/01scyh794","country_code":"CN","type":"education","lineage":["https://openalex.org/I9842412"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaofeng Song","raw_affiliation_strings":["Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Engineering, Nanjing University of Aeronautics and Astronautics , No. 29 Jiangjun Road, Jiangning District, Nanjing 211106, China","institution_ids":["https://openalex.org/I9842412"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5088850728","display_name":"Jing Wu","orcid":"https://orcid.org/0000-0002-4061-8185"},"institutions":[{"id":"https://openalex.org/I83519826","display_name":"Nanjing Medical University","ror":"https://ror.org/059gcgy73","country_code":"CN","type":"education","lineage":["https://openalex.org/I83519826"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jing Wu","raw_affiliation_strings":["School of Biomedical Engineering and Informatics, Nanjing Medical University , No. 101 Longmian Avenue, Jiangning District, Nanjing 211166, China"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Engineering and Informatics, Nanjing Medical University , No. 101 Longmian Avenue, Jiangning District, Nanjing 211166, China","institution_ids":["https://openalex.org/I83519826"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5025609330"],"corresponding_institution_ids":["https://openalex.org/I9842412"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.7477,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.90871404,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"25","issue":"5","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":0.9983000159263611,"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/T11112","display_name":"Viral Infections and Immunology Research","score":0.9977999925613403,"subfield":{"id":"https://openalex.org/subfields/2705","display_name":"Cardiology and Cardiovascular Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/internal-ribosome-entry-site","display_name":"Internal ribosome entry site","score":0.9638336896896362},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.6746967434883118},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6271815299987793},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5935289859771729},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5591703653335571},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.4998743534088135},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.46907350420951843},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.46477845311164856},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.43153107166290283},{"id":"https://openalex.org/keywords/messenger-rna","display_name":"Messenger RNA","score":0.38398662209510803},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3648851811885834},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.29498690366744995},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.11726579070091248},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10269111394882202},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08027976751327515}],"concepts":[{"id":"https://openalex.org/C77430603","wikidata":"https://www.wikidata.org/wiki/Q166992","display_name":"Internal ribosome entry site","level":5,"score":0.9638336896896362},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.6746967434883118},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6271815299987793},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5935289859771729},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5591703653335571},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.4998743534088135},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.46907350420951843},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.46477845311164856},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.43153107166290283},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.38398662209510803},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3648851811885834},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.29498690366744995},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.11726579070091248},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10269111394882202},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08027976751327515},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000067556","descriptor_name":"Internal Ribosome Entry Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067556","descriptor_name":"Internal Ribosome Entry Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067556","descriptor_name":"Internal Ribosome Entry Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000067556","descriptor_name":"Internal Ribosome Entry Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012367","descriptor_name":"RNA, Viral","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":"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/bib/bbae439","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae439","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae439/59021567/bbae439.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39234953","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39234953","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:11375421","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11375421","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11375421/pdf/bbae439.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae439","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae439","pdf_url":"https://academic.oup.com/bib/article-pdf/25/5/bbae439/59021567/bbae439.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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"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/G2139601656","display_name":null,"funder_award_id":"NS2023017","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G2376276132","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"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/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G59554747","display_name":null,"funder_award_id":"62273175","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"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321605","display_name":"Government of Jiangsu Province","ror":"https://ror.org/004svx814"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402254727.pdf","grobid_xml":"https://content.openalex.org/works/W4402254727.grobid-xml"},"referenced_works_count":71,"referenced_works":["https://openalex.org/W1491993630","https://openalex.org/W1846338561","https://openalex.org/W1964221844","https://openalex.org/W1965594392","https://openalex.org/W1966690209","https://openalex.org/W1969795554","https://openalex.org/W1970949525","https://openalex.org/W1971140237","https://openalex.org/W2006798984","https://openalex.org/W2010755507","https://openalex.org/W2027147867","https://openalex.org/W2043704121","https://openalex.org/W2048731469","https://openalex.org/W2064675550","https://openalex.org/W2066272205","https://openalex.org/W2086561953","https://openalex.org/W2098270395","https://openalex.org/W2101338790","https://openalex.org/W2101975193","https://openalex.org/W2112085782","https://openalex.org/W2120425978","https://openalex.org/W2121359567","https://openalex.org/W2121882364","https://openalex.org/W2122439888","https://openalex.org/W2156125289","https://openalex.org/W2157331557","https://openalex.org/W2158266834","https://openalex.org/W2187089797","https://openalex.org/W2234324103","https://openalex.org/W2325436143","https://openalex.org/W2333784672","https://openalex.org/W2417928515","https://openalex.org/W2464754433","https://openalex.org/W2754335123","https://openalex.org/W2884961061","https://openalex.org/W2911919665","https://openalex.org/W2950219014","https://openalex.org/W2963840672","https://openalex.org/W2966361671","https://openalex.org/W2967169742","https://openalex.org/W2971386099","https://openalex.org/W3005690056","https://openalex.org/W3020147515","https://openalex.org/W3037876193","https://openalex.org/W3047843865","https://openalex.org/W3093048084","https://openalex.org/W3123621644","https://openalex.org/W3130551467","https://openalex.org/W3132383847","https://openalex.org/W3136020393","https://openalex.org/W3136874626","https://openalex.org/W3174855653","https://openalex.org/W3200513961","https://openalex.org/W3201789697","https://openalex.org/W4225012059","https://openalex.org/W4282933430","https://openalex.org/W4285802827","https://openalex.org/W4289521126","https://openalex.org/W4289761856","https://openalex.org/W4293215972","https://openalex.org/W4297786033","https://openalex.org/W4298088395","https://openalex.org/W4307395317","https://openalex.org/W4318977936","https://openalex.org/W4383113554","https://openalex.org/W4384924864","https://openalex.org/W4390621086","https://openalex.org/W6790496477","https://openalex.org/W6811023255","https://openalex.org/W6841546942","https://openalex.org/W6846679498"],"related_works":["https://openalex.org/W1970949525","https://openalex.org/W2865056529","https://openalex.org/W4283746337","https://openalex.org/W2901430522","https://openalex.org/W2999223988","https://openalex.org/W3087325610","https://openalex.org/W1965594392","https://openalex.org/W2119008435","https://openalex.org/W4231970582","https://openalex.org/W2359614599"],"abstract_inverted_index":{"The":[0],"internal":[1],"ribosome":[2],"entry":[3],"site":[4],"(IRES)":[5],"is":[6,19,32,53,99,196],"a":[7,15,82,100,176,197],"cis-regulatory":[8],"element":[9],"that":[10,121,144,166,187],"can":[11,123],"initiate":[12],"translation":[13],"in":[14,93,161,169],"cap-independent":[16],"manner.":[17],"It":[18],"often":[20],"related":[21,189],"to":[22,63,190],"cellular":[23],"processes":[24],"and":[25,38,55,114,130,148,203],"many":[26],"diseases.":[27],"Thus,":[28],"identifying":[29,47,90],"the":[30,173,207],"IRES":[31,48,91,191,201,210],"important":[33],"for":[34,43,88,200],"understanding":[35],"its":[36],"mechanism":[37,208],"finding":[39],"potential":[40,184],"therapeutic":[41],"strategies":[42],"relevant":[44],"diseases":[45],"since":[46],"elements":[49,92],"by":[50],"experimental":[51,163],"method":[52],"time-consuming":[54],"laborious.":[56],"Many":[57],"bioinformatics":[58],"tools":[59,69],"have":[60],"been":[61],"developed":[62],"predict":[64],"IRES,":[65],"but":[66],"all":[67],"these":[68],"are":[70,167,188],"based":[71],"on":[72,139],"structure":[73],"similarity":[74],"or":[75],"machine":[76],"learning":[77,84,178],"algorithms.":[78],"Here,":[79],"we":[80,181],"introduced":[81],"deep":[83,177],"model":[85,102],"named":[86],"DeepIRES":[87,98,122,145,157,195],"precisely":[89],"messenger":[94],"RNA":[95],"(mRNA)":[96],"sequences.":[97],"hybrid":[101],"incorporating":[103],"dilated":[104],"1D":[105],"convolutional":[106],"neural":[107],"network":[108],"blocks,":[109],"bidirectional":[110],"gated":[111],"recurrent":[112],"units,":[113],"self-attention":[115],"module.":[116],"Tenfold":[117],"cross-validation":[118],"results":[119,132],"suggest":[120],"capture":[124],"deeper":[125],"relationships":[126],"between":[127],"sequence":[128],"features":[129],"prediction":[131,150,202],"than":[133,152],"other":[134,153],"baseline":[135],"models.":[136],"Further":[137],"comparison":[138],"independent":[140],"test":[141],"sets":[142],"illustrates":[143],"has":[146],"superior":[147],"robust":[149],"capability":[151],"existing":[154],"methods.":[155],"Moreover,":[156],"achieves":[158],"high":[159],"accuracy":[160],"predicting":[162],"validated":[164],"IRESs":[165],"collected":[168],"recent":[170],"studies.":[171],"With":[172],"application":[174],"of":[175,209],"interpretable":[179],"analysis,":[180],"discover":[182],"some":[183],"consensus":[185],"motifs":[186],"activities.":[192],"In":[193],"summary,":[194],"reliable":[198],"tool":[199],"gives":[204],"insights":[205],"into":[206],"elements.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}