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To fill this gap, it is necessary to improve the accuracy of lncRNA identification and functional annotation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Here, we introduce LncADeep 2.0, an integrated deep learning framework designed to meet these needs. In the identification module, LncADeep 2.0 incorporated novel peptide features along with sequence and structural information, demonstrating superior performance over our previous LncADeep and other existing tools on both annotated transcripts from GENCODE and RNA-seq data. For functional annotation, LncADeep 2.0 leveraged lncRNA-centric interaction networks and gene ontology terms through the transfer learning strategy to achieve robust annotation performance with limited functional data. Compared to LncADeep, LncADeep 2.0 could accurately elucidate the general functions of given lncRNA sequences, predict tissue- or cell-type-specific functions from bulk and single-cell RNA-seq data, and establish connections between tumor-associated lncRNAs and genomic markers. Overall, LncADeep 2.0 stands out as an efficient and reliable tool for lncRNA identification and functional annotation across a wide spectrum of biological processes.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>LncADeep 2.0 is available for use at https:\/\/github.com\/Jefferson-Chou\/LncADeep2 and https:\/\/doi.org\/10.5281\/zenodo.17164767.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag162","type":"journal-article","created":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T11:21:24Z","timestamp":1774869684000},"source":"Crossref","is-referenced-by-count":0,"title":["A novel deep learning-driven framework for improving lncRNA comprehensive annotation with LncADeep 2.0"],"prefix":"10.1093","volume":"42","author":[{"given":"Yiyan","family":"Zhou","sequence":"first","affiliation":[{"name":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","place":["China"]}]},{"given":"Jiaheng","family":"Hou","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","place":["China"]}]},{"given":"Haoling","family":"Xie","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Beijing Normal University , Beijing 100875,","place":["China"]}]},{"given":"Nuoshi","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","place":["China"]}]},{"given":"Cheng","family":"Yang","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9561-7817","authenticated-orcid":false,"given":"Hengchuang","family":"Yin","sequence":"additional","affiliation":[{"name":"Department of Biomedical Engineering, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","place":["China"]},{"name":"Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University , Beijing 100871,","place":["China"]}]},{"given":"Wanqiu","family":"Ding","sequence":"additional","affiliation":[{"name":"Department of Big Data and Biomedical AI, College of Future Technology, Peking University , Beijing 100871,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6376-218X","authenticated-orcid":false,"given":"Huaiqiu","family":"Zhu","sequence":"additional","affiliation":[{"name":"Department of Biomedical 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