{"id":"https://openalex.org/W7148582914","doi":"https://doi.org/10.1093/bioinformatics/btag162","title":"A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0","display_name":"A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0","publication_year":2026,"publication_date":"2026-03-30","ids":{"openalex":"https://openalex.org/W7148582914","doi":"https://doi.org/10.1093/bioinformatics/btag162","pmid":"https://pubmed.ncbi.nlm.nih.gov/41923359"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag162","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag162","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btag162","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100938915","display_name":"Yiyan Zhou","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yiyan Zhou","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052373853","display_name":"Jiaheng Hou","orcid":"https://orcid.org/0000-0002-1406-991X"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiaheng Hou","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000868597","display_name":"Haoling Xie","orcid":"https://orcid.org/0000-0003-0001-0631"},"institutions":[{"id":"https://openalex.org/I25254941","display_name":"Beijing Normal University","ror":"https://ror.org/022k4wk35","country_code":"CN","type":"education","lineage":["https://openalex.org/I25254941"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haoling Xie","raw_affiliation_strings":["College of Life Sciences, Beijing Normal University , Beijing 100875,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Sciences, Beijing Normal University , Beijing 100875,","institution_ids":["https://openalex.org/I25254941"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132825955","display_name":"Nuoshi Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Nuoshi Lin","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5132825483","display_name":"Cheng Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cheng Yang","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089781130","display_name":"Hengchuang Yin","orcid":"https://orcid.org/0000-0002-9561-7817"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hengchuang Yin","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":"https://orcid.org/0000-0002-9561-7817","affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049503884","display_name":"Wanqiu Ding","orcid":"https://orcid.org/0000-0002-6650-8662"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wanqiu Ding","raw_affiliation_strings":["Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100552197","display_name":"Huaiqiu Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210096250","display_name":"Beijing Institute of Big Data Research","ror":"https://ror.org/00s1sz824","country_code":"CN","type":"facility","lineage":["https://openalex.org/I20231570","https://openalex.org/I37796252","https://openalex.org/I4210096250"]},{"id":"https://openalex.org/I4210160507","display_name":"Center for Life Sciences","ror":"https://ror.org/05kje8j93","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570","https://openalex.org/I4210160507","https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Huaiqiu Zhu","raw_affiliation_strings":["Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,"],"raw_orcid":"https://orcid.org/0000-0002-6376-218X","affiliations":[{"raw_affiliation_string":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210160507"]},{"raw_affiliation_string":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I4210096250","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5100938915"],"corresponding_institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210096250","https://openalex.org/I4210160507"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.67101933,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.890500009059906,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.890500009059906,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.019700000062584877,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.019700000062584877,"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/annotation","display_name":"Annotation","score":0.7656999826431274},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4269999861717224},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.2563999891281128},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.2533000111579895}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7656999826431274},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.746399998664856},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4269999861717224},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4259999990463257},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.41179999709129333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37389999628067017},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.262800008058548},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2563999891281128},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.25369998812675476},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.2533000111579895}],"mesh":[{"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":"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D062085","descriptor_name":"RNA, Long Noncoding","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag162","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag162","pdf_url":null,"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:41923359","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41923359","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:13090826","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13090826/","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"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/btag162","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag162","pdf_url":null,"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":[{"id":"https://openalex.org/G2051170382","display_name":null,"funder_award_id":"32400535","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5615974555","display_name":null,"funder_award_id":"2025ZD01901200","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"},{"id":"https://openalex.org/G8164357140","display_name":null,"funder_award_id":"32570752","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G920515627","display_name":null,"funder_award_id":"2025ZD01901800","funder_id":"https://openalex.org/F4320329860","funder_display_name":"National Science and Technology Major Project"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320324787","display_name":"Peking University","ror":"https://ror.org/02v51f717"},{"id":"https://openalex.org/F4320329860","display_name":"National Science and Technology Major Project","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W1963740134","https://openalex.org/W1996207018","https://openalex.org/W2048194168","https://openalex.org/W2061548680","https://openalex.org/W2111688179","https://openalex.org/W2117977572","https://openalex.org/W2118023394","https://openalex.org/W2132153341","https://openalex.org/W2138370010","https://openalex.org/W2162547088","https://openalex.org/W2170747616","https://openalex.org/W2507804718","https://openalex.org/W2614461365","https://openalex.org/W2615786037","https://openalex.org/W2764054317","https://openalex.org/W2774210326","https://openalex.org/W2777095407","https://openalex.org/W2791507884","https://openalex.org/W2807607992","https://openalex.org/W2886900083","https://openalex.org/W2897570487","https://openalex.org/W2898598946","https://openalex.org/W2901527454","https://openalex.org/W2901697402","https://openalex.org/W2914698725","https://openalex.org/W2949256546","https://openalex.org/W2951579118","https://openalex.org/W3024997712","https://openalex.org/W3036396116","https://openalex.org/W3096514992","https://openalex.org/W3099929518","https://openalex.org/W3155911001","https://openalex.org/W3158452839","https://openalex.org/W3164382315","https://openalex.org/W3165793769","https://openalex.org/W3168297159","https://openalex.org/W3175752499","https://openalex.org/W3177500196","https://openalex.org/W3189383967","https://openalex.org/W3210024567","https://openalex.org/W4225284443","https://openalex.org/W4294558607","https://openalex.org/W4297265642","https://openalex.org/W4307492630","https://openalex.org/W4308735427","https://openalex.org/W4308834893","https://openalex.org/W4313488537","https://openalex.org/W4382047643","https://openalex.org/W4382490702","https://openalex.org/W4388525423","https://openalex.org/W4389265556","https://openalex.org/W4390621251","https://openalex.org/W4401242470","https://openalex.org/W4401265660","https://openalex.org/W4404411340","https://openalex.org/W4406385600"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"Long":[1],"non-coding":[2],"RNAs":[3],"(lncRNAs)":[4],"have":[5],"emerged":[6],"as":[7,164],"crucial":[8],"players":[9],"in":[10],"diverse":[11],"physiological":[12],"and":[13,42,74,84,94,106,146,150,156,167,173,194],"pathological":[14],"processes,":[15],"yet":[16],"the":[17,21,37,62,111,132],"biological":[18,181],"mechanisms":[19],"of":[20,24,39,135,180],"vast":[22],"majority":[23],"lncRNAs":[25,155],"remain":[26],"elusive.":[27],"To":[28],"fill":[29],"this":[30],"gap,":[31],"it":[32],"is":[33,188],"necessary":[34],"to":[35,57,115,125],"improve":[36],"accuracy":[38],"lncRNA":[40,137,171],"identification":[41,63,172],"functional":[43,98,122,174],"annotation.":[44],"RESULTS:":[45],"Here,":[46],"we":[47],"introduce":[48],"LncADeep":[49,65,83,100,127,160,186],"2.0,":[50],"an":[51,165],"integrated":[52],"deep":[53],"learning":[54,113],"framework":[55],"designed":[56],"meet":[58],"these":[59],"needs.":[60],"In":[61],"module,":[64],"2.0":[66,101,128,161,187],"incorporated":[67],"novel":[68],"peptide":[69],"features":[70],"along":[71],"with":[72,120],"sequence":[73],"structural":[75],"information,":[76],"demonstrating":[77],"superior":[78],"performance":[79,119],"over":[80],"our":[81],"previous":[82],"other":[85],"existing":[86],"tools":[87],"on":[88],"both":[89],"annotated":[90],"transcripts":[91],"from":[92,144],"GENCODE":[93],"RNA-seq":[95,148],"data.":[96,123],"For":[97],"annotation,":[99],"leveraged":[102],"lncRNA-centric":[103],"interaction":[104],"networks":[105],"gene":[107],"ontology":[108],"terms":[109],"through":[110],"transfer":[112],"strategy":[114],"achieve":[116],"robust":[117],"annotation":[118,175],"limited":[121],"Compared":[124],"LncADeep,":[126],"could":[129],"accurately":[130],"elucidate":[131],"general":[133],"functions":[134,143],"given":[136],"sequences,":[138],"predict":[139],"tissue-":[140],"or":[141],"cell-type-specific":[142],"bulk":[145],"single-cell":[147],"data,":[149],"establish":[151],"connections":[152],"between":[153],"tumor-associated":[154],"genomic":[157],"markers.":[158],"Overall,":[159],"stands":[162],"out":[163],"efficient":[166],"reliable":[168],"tool":[169],"for":[170,190],"across":[176],"a":[177],"wide":[178],"spectrum":[179],"processes.":[182],"AVAILABILITY":[183],"AND":[184],"IMPLEMENTATION:":[185],"available":[189],"use":[191],"at":[192],"https://github.com/Jefferson-Chou/LncADeep2":[193],"https://doi.org/10.5281/zenodo.17164767.":[195]},"counts_by_year":[],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2026-04-03T00:00:00"}