Journal Papers
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RgnTX: colocalization analysis of transcriptome elements in the presence of isoform heterogeneity and ambiguity (Under Review).
Yue Wang, Zhen Wei, Jionglong Su, Frans Coenen and Jia Meng(*)
The paper is under review. The package has been accepted by Bioconductor.
[10.18129/B9.bioc.RgnTX]
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m6A-Atlas v2.0: updated resources for unravelling the N6-methyladenosine (m6A) epitranscriptome among multiple species (Under Review).
Zhanmin Liang, Haokai Ye, Jiongming Ma, Zhen Wei, Yue Wang, Yuxin Zhang, Daiyun Huang, Bowen Song, Jia Meng, Daniel J Rigden, Kunqi Chen(*)
The paper is under review.
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Multi-task adaptive pooling enabled synergetic learning of RNA modification across tissue, type and species from low-resolution epitranscriptomes.
Yiyou Song, Yue Wang (*), Xuan Wang, Daiyun Huang, Anh Nguyen, Jia Meng
Briefings in Bioinformatics, bbad105, 2023.
[pdf] [10.1093/bib/bbad105]
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Self-attention enabled deep learning of dihydrouridine (D) modification on mRNAs unveiled a distinct sequence signature from tRNAs.
Yue Wang, Xuan Wang, Xiaodong Cui, Jia Meng, Rong Rong(*)
Molecular Therapy - Nucleic Acids, 31:411-420, 2023.
[10.1016/j.omtn.2023.01.014]
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DirectRMDB: a database of post-transcriptional RNA modifications unveiled from direct RNA sequencing technology.
Yuxin Zhang, Jie Jiang, Jiongming Ma, Zhen Wei(*), Yue Wang, Bowen Song, Jia Meng; Guifang Jia, Joao Pedro de Magalhaes, Daniel J Rigden, Daiyun Hang(*), Kunqi Chen(*)
Nucleic Acids Research, 51(D1):D106–D116, 2023.
[10.1093/nar/gkac1061]
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RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication.
Bowen Song, Xuan Wang, Zhanmin Liang, Jiongming Ma, Daiyun Huang, Yue Wang, João Pedro de Magalhães, Daniel J Rigden, Jia Meng, Gang Liu(*), Kunqi Chen(*), Zhen Wei(*)
Nucleic Acids Research, 51(D1):D1388–D1396, 2022.
[10.1093/nar/gkac750]
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MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis.
Yue Wang, Kunqi Chen, Zhen Wei, Frans Coenen, Jionglong Su, Jia Meng(*)
Bioinformatics, 37(9):1285–1291, 2021.
[pdf] [10.1093/bioinformatics/btaa938]
Conference Papers
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An Improved Algorithm for Estimating the Distribution of RNA-related Genomic Features.
Jinge Wu, Lihan Zhang, Yuanzhe Wang, Jia Meng, Jionglong Su, Yue Wang(*)
Proceedings of the Biological Information and Biomedical Engineering, (BIBE), 2020.
10.1145/3403782.3403785