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Zhou, Jingxian, Wang, Xuan, Wei, Zhen, Meng, Jia ORCID: 0000-0003-3455-205X and Huang, Daiyun (2022) 4acCPred: Weakly supervised prediction of Λl4-acetyldeoxycytosine DNA modification from sequences. MOLECULAR THERAPY-NUCLEIC ACIDS, 30. pp. 337-345.

Song, Zitao, Huang, Daiyun, Song, Bowen, Chen, Kunqi, Song, Yiyou, Liu, Gang, Su, Jionglong, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2021) Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. NATURE COMMUNICATIONS, 12 (1). 4011-.

Huang, Daiyun (2022) DEEP LEARNING-BASED RNA MODIFICATION PREDICTION METHOD DEVELOPMENT. PhD thesis, University of Liverpool.

Huang, Daiyun, Chen, Kunqi, Song, Bowen, Wei, Zhen, Su, Jionglong, Coenen, Frans ORCID: 0000-0003-1026-6649, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 and Meng, Jia ORCID: 0000-0003-3455-205X (2022) Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. NUCLEIC ACIDS RESEARCH, 50 (18). pp. 10290-10310.

Coenen, Frans ORCID: 0000-0003-1026-6649, Chen, Kunqi, Song, Bowen, Zhen, Wei, Huang, Daiyun, Su, Jionglong, de Magalhães, João Pedro, Rigden, Daniel and Meng, Jia (2022) Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. Nucleic Acids Research.

Song, Yiyou, Wang, Yue, Wang, Xuan, Huang, Daiyun, Nguyen, Anh ORCID: 0000-0002-1449-211X and Meng, Jia ORCID: 0000-0003-3455-205X (2023) Multi-task adaptive pooling enabled synergetic learning of RNA modification across tissue, type and species from low-resolution epitranscriptomes. BRIEFINGS IN BIOINFORMATICS, 24 (3). bbad105-.

Song, Sifan, Huang, Daiyun, Hu, Yalun, Yang, Chunxiao, Meng, Jia ORCID: 0000-0003-3455-205X, Ma, Fei ORCID: 0000-0001-6099-480X, Coenen, Frans ORCID: 0000-0003-1026-6649, Zhang, Jiaming and Su, Jionglong (2021) A Novel Application of Image-to-Image Translation: Chromosome Straightening Framework by Learning from a Single Image. In: 2021 14th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI), 2021-10-23 - 2021-10-25.

Liu, Hui, Wang, Guangjie, Song, Sifan ORCID: 0000-0002-7940-650X, Huang, Daiyun and Zhang, Lin (2022) RC-Net: Regression Correction for End-To-End Chromosome Instance Segmentation. FRONTIERS IN GENETICS, 13. 895099-.

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Song, Bowen, Wang, Xuan, Liang, Zhanmin, Ma, Jiongming, Huang, Daiyun, Wang, Yue, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X, Liu, Gang et al (show 2 more authors) , Chen, Kunqi and Wei, Zhen (2023) RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. NUCLEIC ACIDS RESEARCH, 51 (D1). D1388-D1396.

Li, Zhirou, Mao, Jinge, Huang, Daiyun, Song, Bowen and Meng, Jia ORCID: 0000-0003-3455-205X (2022) RNADSN: Transfer-Learning 5-Methyluridine (m<SUP>5</SUP>U) Modification on mRNAs from Common Features of tRNA. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 23 (21). 13493-.

Huang, Daiyun, Song, Bowen, Wei, Jingjue, Su, Jionglong, Coenen, Frans ORCID: 0000-0003-1026-6649 and Meng, Jia ORCID: 0000-0003-3455-205X (2021) Weakly supervised learning of RNA modifications from low-resolution epitranscriptome data. In: 29th Intelligent Systems for Molecular Biology and 20th International Society for Computational Biology (ISMB-ISCB) joint conference, England.

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Liang, Zhanmin, Ye, Haokai, Ma, Jiongming, Wei, Zhen, Wang, Yue, Zhang, Yuxin, Huang, Daiyun, Song, Bowen, Meng, Jia ORCID: 0000-0003-3455-205X, Rigden, Daniel J ORCID: 0000-0002-7565-8937 et al (show 1 more authors) and Chen, Kunqi (2023) m(6) A-Atlas v2.0: updated resources for unraveling the N 6-methyladenosine (m(6)A) epitranscriptome among multiple species. NUCLEIC ACIDS RESEARCH, 52 (D1). D194-D202.

Ma, Jiongming, Song, Bowen, Wei, Zhen, Huang, Daiyun, Zhang, Yuxin, Su, Jionglong, de Magalhães, João Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi (2022) m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. Nucleic acids research, 50 (D1). D196-D203.

Song, Bowen ORCID: 0000-0002-8586-0573, Huang, Daiyun ORCID: 0000-0002-3067-7165, Zhang, Yuxin ORCID: 0000-0003-1900-6712, Wei, Zhen, Su, Jionglong ORCID: 0000-0001-5360-6493, Pedro de Magalhães, João, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi ORCID: 0000-0002-6025-8957 (2023) m6A-TSHub: Unveiling the Context-specific m⁶A Methylation and m⁶A-affecting Mutations in 23 Human Tissues. Genomics, proteomics & bioinformatics, 21 (4). pp. 678-694.