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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.

Wei, Zhen (2020) Applied Data Science Methods in Epitranscriptomic Bioinformatics. PhD thesis, University of Liverpool.

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Liu, Lian, Song, Bowen, Ma, Jiani, Song, Yi, Zhang, Song-Yao, Tang, Yujiao, Wu, Xiangyu, Wei, Zhen, Chen, Kunqi, Su, Jionglong et al (show 10 more authors) , Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Zhang, Lin, Zhang, Shao-Wu, Huang, Yufei, Lei, Xiujuan, Liu, Hui and Meng, Jia ORCID: 0000-0003-3455-205X (2020) Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 18. pp. 1587-1604.

Song, Bowen, Chen, Kunqi, Tang, Yujiao, Wei, Zhen, 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) ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. BRIEFINGS IN BIOINFORMATICS, 22 (6). bbab088-.

Tang, Yujiao, Chen, Kunqi, Wu, Xiangyu, Wei, Zhen, Zhang, Song-Yao, Song, Bowen, Zhang, Shao-Wu, Huang, Yufei and Meng, Jia ORCID: 0000-0003-3455-205X (2019) DRUM: Inference of Disease-Associated m(6)A RNA Methylation Sites From a Multi-Layer Heterogeneous Network. FRONTIERS IN GENETICS, 10 (APR). 266-.

Zhao, Xichen, Zhang, Yuxin, Hang, Daiyun, Meng, Jia ORCID: 0000-0003-3455-205X and Wei, Zhen (2022) Detecting RNA modification using direct RNA sequencing: A systematic review. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 20. pp. 5740-5749.

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Zhang, Yuxin, Jiang, Jie, Ma, Jiongming, Wei, Zhen, Wang, Yue, Song, Bowen, Meng, Jia ORCID: 0000-0003-3455-205X, Jia, Guifang, de Magalhães, João Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937 et al (show 2 more authors) , Hang, Daiyun and Chen, Kunqi (2022) DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology. Nucleic acids research, 51 (D1). gkac1061-gkac1061.

Chen, Kunqi, Wei, Zhen, Liu, Hui, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415 and Meng, Jia ORCID: 0000-0003-3455-205X (2018) Enhancing Epitranscriptome Module Detection from m<SUP>6</SUP>A-Seq Data Using Threshold-Based Measurement Weighting Strategy. BIOMED RESEARCH INTERNATIONAL, 2018. 2075173-.

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.

Cui, Xiaodong, Wei, Zhen, Zhang, Lin, Liu, Hui, Sun, Lei, Zhang, Shao-Wu, Huang, Yufei and Meng, Jia ORCID: 0000-0003-3455-205X (2016) Guitar: An R/Bioconductor Package for Gene Annotation Guided Transcriptomic Analysis of RNA-Related Genomic Features. BIOMED RESEARCH INTERNATIONAL, 2016. 8367534-.

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Liu, Hui, Wang, Huaizhi, Wei, Zhen, Zhang, Songyao, Hua, Gang, Zhang, Shao-Wu, Zhang, Lin, Gao, Shou-Jiang, Meng, Jia ORCID: 0000-0003-3455-205X, Chen, Xing et al (show 1 more authors) and Huang, Yufei (2018) MeT-DB V2.0: elucidating context-specific functions of <i>N</i><SUP>6</SUP>-methyl-adenosine methyltranscriptome. NUCLEIC ACIDS RESEARCH, 46 (D1). D281-D287.

Wang, Yue, Chen, Kunqi, Wei, Zhen, Coenen, Frans ORCID: 0000-0003-1026-6649, Su, Jionglong and Meng, Jia ORCID: 0000-0003-3455-205X (2021) MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. BIOINFORMATICS, 37 (9). pp. 1285-1291.

Song, Bowen, Tang, Yujiao, Wei, Zhen, Liu, Gang, Su, Jionglong, Meng, Jia ORCID: 0000-0003-3455-205X and Chen, Kunqi (2020) PIANO: A Web Server for Pseudouridine-Site (ψ) Identification and Functional Annotation. FRONTIERS IN GENETICS, 11. 88-.

Song, Bowen, Chen, Kunqi, Tang, Yujiao, Ma, Jialin, Meng, Jia ORCID: 0000-0003-3455-205X and Wei, Zhen (2020) PSI-MOUSE: Predicting Mouse Pseudouridine Sites From Sequence and Genome-Derived Features. EVOLUTIONARY BIOINFORMATICS, 16. 1176934320925752-.

Xue, Hao, Wei, Zhen, Chen, Kunqi, Tang, Yujiao, Wu, Xiangyu, Su, Jionglong and Meng, Jia ORCID: 0000-0003-3455-205X (2020) Prediction of RNA Methylation Status From Gene Expression Data Using Classification and Regression Methods. EVOLUTIONARY BIOINFORMATICS, 16. pp. 1-5.

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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.

Chen, Kunqi, Song, Bowen, Tang, Yujiao, Wei, Zhen, Xu, Qingru, 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) RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. NUCLEIC ACIDS RESEARCH, 49 (D1). D1396-D1404.

Coenen, Frans ORCID: 0000-0003-1026-6649, Wang, Yue, Meng, Jia ORCID: 0000-0003-3455-205X, Wei, Zhen and Su, Jionglong (2023) RgnTX: colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity. Computational and Structural Biotechnology Journal, 21. pp. 4110-4117.

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Wei, Zhen, Panneerdoss, Subbarayalu, Timilsina, Santosh, Zhu, Jingting, Mohammad, Tabrez A, Lu, Zhi-Liang ORCID: 0000-0002-3442-1415, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Chen, Yidong, Rong, Rong, Huang, Yufei et al (show 2 more authors) , Rao, Manjeet K and Meng, Jia ORCID: 0000-0003-3455-205X (2018) Topological Characterization of Human and Mouse m<SUP>5</SUP>C Epitranscriptome Revealed by Bisulfite Sequencing. INTERNATIONAL JOURNAL OF GENOMICS, 2018. 1351964-.

Liu, Lian, Song, Bowen, Chen, Kunqi, Zhang, Yuxin, de Magalhaes, Joao Pedro ORCID: 0000-0002-6363-2465, Rigden, Daniel J ORCID: 0000-0002-7565-8937, Lei, Xiujuan and Wei, Zhen (2022) WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction. METHODS, 203. pp. 378-382.

Chen, Kunqi, Wei, Zhen, Zhang, Qing, Wu, Xiangyu, Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415, 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 (2019) WHISTLE: a high-accuracy map of the human N<SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome predicted using a machine learning approach. NUCLEIC ACIDS RESEARCH, 47 (7). e41-.

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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.

Jiang, Jie, Song, Bowen, Tang, Yujiao, Chen, Kunqi, Wei, Zhen and Meng, Jia ORCID: 0000-0003-3455-205X (2020) m5UPred: A Web Server for the Prediction of RNA 5-Methyluridine Sites from Sequences. MOLECULAR THERAPY-NUCLEIC ACIDS, 22. pp. 742-747.

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.

Wu, Xiangyu, Wei, Zhen, Chen, Kunqi, Zhang, Qing, Su, Jionglong, Liu, Hui, Zhang, Lin and Meng, Jia ORCID: 0000-0003-3455-205X (2019) m6Acomet: large-scale functional prediction of individual m<SUP>6</SUP>A RNA methylation sites from an RNA co-methylation network. BMC BIOINFORMATICS, 20 (1). 223-.

Song, Bowen, Tang, Yujiao, Chen, Kunqi, Wei, Zhen, Rong, Rong, Lu, Zhiliang ORCID: 0000-0002-3442-1415, 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 (2020) m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Bioinformatics, 36 (11). pp. 3528-3536.

Zhen, Di, Wu, Yuxuan, Zhang, Yuxin, Chen, Kunqi, Song, Bowen, Xu, Haiqi, Tang, Yujiao, Wei, Zhen and Meng, Jia ORCID: 0000-0003-3455-205X (2020) m<SUP>6</SUP>A Reader: Epitranscriptome Target Prediction and Functional Characterization of <i>N</i><SUP>6</SUP>-Methyladenosine (m<SUP>6</SUP>A) Readers. FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY, 8. 741-.

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Tang, Yujiao, Chen, Kunqi, Song, Bowen, Ma, Jiongming, Wu, Xiangyu, Xu, Qingru, Wei, Zhen, Su, Jionglong, Liu, Gang, Rong, Rong et al (show 4 more authors) , Lu, Zhiliang ORCID: 0000-0002-3442-1415, 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) m<SUP>6</SUP>A-Atlas: a comprehensive knowledgebase for unraveling the <i>N</i><SUP>6</SUP>-methyladenosine (m<SUP>6</SUP>A) epitranscriptome. NUCLEIC ACIDS RESEARCH, 49 (D1). D134-D143.