2022 publications
• Huang D*, Chen K*, Song B*, Wei Z, Su J, Coenen F, de Magalhães JP, Rigden DJ, Meng J#. Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation. Nucleic Acids Research. 2022 Oct 14;50(18):10290-10310.
[Abstract] [Full Text]
• Song B, Huang D#, Zhang Y, Wei Z, Su J, Pedro de Magalhães J, Rigden DJ, Meng J, Chen K#. m6A-TSHub: Unveiling the Context-specific m(6)A Methylation and m6A-affecting Mutations in 23 Human Tissues. Genomics Proteomics Bioinformatics. 2022 Sep 9:S1672-0229(22)00114-0.
[Abstract] [Full Text]
• Yuan Y*, Wang C*, Zhuang X*, Lin S*, Luo M*, Deng W, Zhou J, Liu L, Mao L, Peng W, Chen J, Wang Q, Shu Y#, Xue Y#, Huang P#. PIM1 promotes hepatic conversion by suppressing reprogramming-induced ferroptosis and cell cycle arrest. Nature Communications. 2022 Sep 6;13(1):5237.
[CKI GitHub] [Abstract] [Full Text]
• Song B*, Wang X*, Liang Z*, Ma J*, Huang D, Wang Y, de Magalhães JP, Rigden DJ, Meng J, Liu G#, Chen K#, Wei Z#. RMDisease V2.0: an updated database of genetic variants that affect RNA modifications with disease and trait implication. Nucleic Acids Research. 2022 Sep 5:gkac750.
[Abstract] [Full Text]
• Tang D*, Han C*, Lin S, Tan X, Zhang W, Peng D, Wang C#, Xue Y#. iPCD: A Comprehensive Data Resource of Regulatory Proteins in Programmed Cell Death. Cells. 2022 Jun 24;11(13):2018.
[Abstract] [Full Text]
• Zhang Y, Huang D, Wei Z, Chen K. Primary sequence-assisted prediction of m(6)A RNA methylation sites from Oxford nanopore direct RNA sequencing data. Methods. 2022 Jul;203:62-69.
[Abstract] [Full Text]
• Wang C*, Tan X*, Tang D, Gou Y, Han C, Ning W, Lin S, Zhang W, Chen M, Peng D, Xue Y#. GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites. Briefings in Bioinformatics. 2022 Mar 10;23(2):bbab574.
[Abstract] [Full Text]
• Ma J*, Song B*, Wei Z#, Huang D, Zhang Y, Su J, de Magalhães JP, Rigden DJ, Meng J, Chen K#. m5C-Atlas: a comprehensive database for decoding and annotating the 5-methylcytosine (m5C) epitranscriptome. Nucleic Acids Research. 2022 Jan 7;50(D1):D196-D203.
[Abstract] [Full Text]
• CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Research. 2022 Jan 7;50(D1):D27-D38.
[Abstract] [Full Text]
• Zhang W*, Tan X*, Lin S, Gou Y, Han C, Zhang C, Ning W, Wang C, Xue Y#. CPLM 4.0: an updated database with rich annotations for protein lysine modifications. Nucleic Acids Research. 2022 Jan 7;50(D1):D451-D459.
[Abstract] [Full Text]
• Liu L*, Song B*, Chen K, Zhang Y, de Magalhães JP, Rigden DJ, Lei X#, Wei Z#. WHISTLE server: A high-accuracy genomic coordinate-based machine learning platform for RNA modification prediction. Methods. 2022 Jul;203:378-382.
[Abstract] [Full Text]
• Jiang J, Song B#, Chen K, Lu Z, Rong R, Zhong Y, Meng J. m6AmPred: Identifying RNA N6, 2'-O-dimethyladenosine (m(6)A(m)) sites based on sequence-derived information. Methods. 2022 Jul;203:328-334.
[Abstract] [Full Text]
2021 publications
• Song Z*, Huang D*, Song B*, Chen K*, Song Y, Liu G, Su J, Magalhães JP, Rigden DJ, Meng J#. Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications. Nature Communications. 2021 Jun 29;12(1):4011.
[Abstract] [Full Text]
• Song B*, Chen K*, Tang Y*, Wei Z, Su J, de Magalhães JP, Rigden DJ, Meng J#. ConsRM: collection and large-scale prediction of the evolutionarily conserved RNA methylation sites, with implications for the functional epitranscriptome. Briefings in Bioinformatics. 2021 Nov 5;22(6):bbab088.
[Abstract] [Full Text]
• Xu Q, Chen K, Meng J. WHISTLE: A Functionally Annotated High-Accuracy Map of Human m(6)A Epitranscriptome. Methods in Molecular Biology. 2021;2284:519-529.
[Abstract] [Full Text]
• Peng D*, Ruan C, Fu S, He C, Song J, Li H, Tu Y, Tang D, Yao L, Lin S, Shi Y, Zhang W, Zhou H, Zhu L, Ma C, Chang C, Ma J, Xie Z, Wang C#, Xue Y#. Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae. Autophagy. 2021 Dec;17(12):4453-4476.
[Abstract] [Full Text]
• Tan W*, Jiang P*, Zhang W*, Hu Z, Lin S, Chen L, Li Y, Peng C, Li Z, Sun A, Chen Y, Zhu W, Xue Y, Yao Y, Li X, Song Q, He F#, Qin W#, Pei H#. Posttranscriptional regulation of de novo lipogenesis by glucose-induced O-GlcNAcylation. Molecular Cell. 2021 May 6;81(9):1890-1904.e7.
[Abstract] [Full Text]
• Klionsky DJ, …, Lin S, …, Tong CK. Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy (4th edition). Autophagy. 2021 Jan;17(1):1-382.
[Abstract] [Full Text]
• CNCB-NGDC Members and Partners. Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2021. Nucleic Acids Research. 2021 Jan 8;49(D1):D18-D28.
[Abstract] [Full Text]
• Chen K*, Song B*, Tang Y*, Wei Z#, Xu Q, Su J, de Magalhães JP, Rigden DJ, Meng J#. RMDisease: a database of genetic variants that affect RNA modifications, with implications for epitranscriptome pathogenesis. Nucleic Acids Research. 2021;49(D1):D1396-D1404.
[Abstract] [Full Text]
• Tang Y*, Chen K*, Song B*, Ma J*, Wu X*, Xu Q, Wei Z, Su J, Liu G, Rong R, Lu Z, de Magalhães JP, Rigden DJ, Meng J#. m6A-Atlas: a comprehensive knowledgebase for unraveling the N6-methyladenosine (m6A) epitranscriptome. Nucleic Acids Research. 2021 Jan 8;49(D1):D134-D143.
[Abstract] [Full Text]
• Lin S*, Wang C*, Zhou J, Shi Y, Ruan C, Tu Y, Yao L, Peng D, Xue Y#. EPSD: a well-annotated data resource of protein phosphorylation sites in eukaryotes. Briefings in Bioinformatics. 2021 Jan 18;22(1):298-307.
[EPSD Website] [Abstract] [Full Text]
2020 publications
• Peng D*, Li H*, Hu B*, Zhang H, Chen L, Lin S, Zuo Z, Xue Y, Ren J#, Xie Y#. PTMsnp: a web server for the identification of driver mutations that affect protein post-translational modification. Frontiers in Cell and Developmental Biology. 2020 Nov 10;8:593661.
[Abstract] [Full Text]
• Jiang J, Song B#, Tang Y, Chen K, Wei Z, Meng J. m5UPred: A Web Server for the Prediction of RNA 5-Methyluridine Sites from Sequences. Molecular Therapy. Nucleic Acids. 2020 Sep 30;22:742-747.
[Abstract] [Full Text]
• Wang Y, Chen K, Wei Z, Coenen F, Su J, Meng J#. MetaTX: deciphering the distribution of mRNA-related features in the presence of isoform ambiguity, with applications in epitranscriptome analysis. Bioinformatics. 2021 Jun 9;37(9):1285-1291.
[Abstract] [Full Text]
• Zhen D*, Wu Y*, Zhang Y*, Chen K#, Song B, Xu H, Tang Y, Wei Z, Meng J. m(6)A Reader: Epitranscriptome Target Prediction and Functional Characterization of N (6)-Methyladenosine (m(6)A) Readers. Frontiers in Cell and Developmental Biology. 2020;8:741. Published 2020 Aug 11.
[Abstract] [Full Text]
• Xue H, Wei Z#, Chen K, Tang Y, Wu X, Su J, Meng J. Prediction of RNA Methylation Status From Gene Expression Data Using Classification and Regression Methods. Evolutionary Bioinformatics. 2020 Jul 20;16:1176934320915707.
[Abstract] [Full Text]
• Liu L*, Song B*, Ma J*, Song Y, Zhang SY, Tang Y, Wu X, Wei Z, Chen K, Su J, Rong R, Lu Z, de Magalhães JP, Rigden DJ, Zhang L, Zhang SW, Huang Y, Lei X#, Liu H#, Meng J#. Bioinformatics approaches for deciphering the epitranscriptome: Recent progress and emerging topics. Computational and Structural Biotechnology Journal. 2020 Jun 13;18:1587-1604.
[Abstract] [Full Text]
• Song B, Chen K, Tang Y, Ma J, Meng J, Wei Z#. PSI-MOUSE: Predicting Mouse Pseudouridine Sites From Sequence and Genome-Derived Features. Evolutionary Bioinformatics. 2020 Jun 9;16:1176934320925752.
[Abstract] [Full Text]
• Wang C*, Shui K*, Ma S, Lin S, Zhang Y, Wen B, Deng W, Xu H, Hu H, Guo A, Xue Y#, Zhang L#. Integrated omics in Drosophila uncover a circadian kinome. Nature Communications. 2020 Jun 1;11(1):2710.
[Abstract] [Full Text]
• Shi Y*, Zhang Y*, Lin S, Wang C, Zhou J, Peng D#, Xue Y#. dbPSP 2.0, an Updated Database of Protein Phosphorylation Sites in Prokaryotes. Scientific Data. 2020 May 29;7(1):164.
[Abstract] [Full Text]
• Guo Y*, Ning W*, Jiang P, Lin S, Wang C, Tan X, Yao L, Peng D, Xue Y#. GPS-PBS: A deep learning framework to predict phosphorylation sites that specifically interact with phosphoprotein-binding domains. Cells. 2020 May 20;9(5):1266.
[Abstract] [Full Text]
• Song B*, Tang Y*, Wei Z, Liu G, Su J, Meng J, Chen K#. PIANO: A Web Server for Pseudouridine-Site (Ψ) Identification and Functional Annotation. Frontiers in Genetics. 2020 Mar 12;11:88.
[Abstract] [Full Text]
• Wang C*, Xu H*, Lin S, Deng W, Zhou J, Zhang Y, Shi Y, Peng D, Xue Y#. GPS 5.0: An Update on the Prediction of Kinase-specific Phosphorylation Sites in Proteins. Genomics Proteomics & Bioinformatics. 2020 Feb;18(1):72-80. doi: 10.1016/j.gpb.2020.01.001.
[Abstract] [Full Text]
• Song B*, Tang Y*, Chen K#, Wei Z, Rong R, Lu Z, Su J, de Magalhães JP, Rigden DJ, Meng J. m7GHub: deciphering the location, regulation and pathogenesis of internal mRNA N7-methylguanosine (m7G) sites in human. Bioinformatics. 2020 Jun 1;36(11):3528-3536.
[Abstract] [Full Text]
• National Genomics Data Center Members and Partners. Database Resources of the National Genomics Data Center in 2020. Nucleic Acids Research. 2020 Jan 8;48(D1):D24-D33.
[Abstract] [Full Text]
• Ning W*, Guo Y*, Lin S*, Mei B, Wu Y, Jiang P, Tan X, Zhang W, Chen G, Peng D, Chu L#, Xue Y#. DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes. Nucleic Acids Research. 2020 Jan 8;48(D1):D288-D295.
[DrLLPS Website] [Abstract] [Full Text]
2019 publications
• Song Y*, Xu Q*, Wei Z, Zhen D, Su J, Chen K#, Meng J#. Predict Epitranscriptome Targets and Regulatory Functions of N (6)-Methyladenosine (m(6)A) Writers and Erasers. Evolutionary Bioinformatics. 2019 Sep 5;15:1176934319871290.
[Abstract] [Full Text]
• Wu X, Wei Z, Chen K, Zhang Q, Su J, Liu H, Zhang L#, Meng J#. m6Acomet: large-scale functional prediction of individual m(6)A RNA methylation sites from an RNA co-methylation network. BMC Bioinformatics. 2019 May 2;20(1):223.
[Abstract] [Full Text]
• Tang Y, Chen K, Wu X, Wei Z, Zhang SY, Song B, Zhang SW, Huang Y, Meng J#. DRUM: Inference of Disease-Associated m(6)A RNA Methylation Sites From a Multi-Layer Heterogeneous Network. Frontiers in Genetics. 2019 Apr 3;10:266.
[Abstract] [Full Text]
• Chen K*, Wei Z*, Zhang Q*, Wu X*, Rong R, Lu Z, Su J, de Magalhães JP, Rigden DJ, Meng J#. WHISTLE: a high-accuracy map of the human N6-methyladenosine (m6A) epitranscriptome predicted using a machine learning approach. Nucleic Acids Research. 2019 Apr 23;47(7):e41.
[Abstract] [Full Text]
• Guo Y*, Peng D*, Zhou J, Lin S, Wang C, Ning W, Xu H, Deng W#, Xue Y#. iEKPD 2.0: an update with rich annotations for eukaryotic protein kinases, protein phosphatases and proteins containing phosphoprotein-binding domains. Nucleic Acids Research. 2019 Jan 8;47(D1):D344-D350.
[Abstract] [Full Text]
• BIG Data Center Members. Database Resources of the BIG Data Center in 2019. Nucleic Acids Research. 2019 Jan 8;47(D1):D8-D14.
[Abstract] [Full Text]
2018 publications
• Xu H*, Wang Y, Lin S, Deng W, Peng D, Cui Q#, Xue Y#. PTMD: A Database of Human Disease-associated Post-translational Modifications. Genomics Proteomics & Bioinformatics. 2018 Aug;16(4):244-251.
[Abstract] [Full Text]
• Chen K, Wei Z, Liu H, de Magalhães JP, Rong R, Lu Z, Meng J#. Enhancing Epitranscriptome Module Detection from m(6)A-Seq Data Using Threshold-Based Measurement Weighting Strategy. BioMed Research International. 2018 Jun 14;2018:2075173.
[Abstract] [Full Text]
• Ning W*, Lin S, Zhou J, Guo Y, Zhang Y, Peng D, Deng W#, Xue Y#. WocEA: The visualization of functional enrichment results in word clouds. Journal of Genetics and Genomics. 2018 Jul 20;45(7):415-417.
[Abstract] [Full Text]
• Zhou J*, Xu Y*, Lin S*, Guo Y, Deng W, Zhang Y, Guo A, Xue Y#. iUUCD 2.0: an update with rich annotations for ubiquitin and ubiquitin-like conjugations. Nucleic Acids Research. 2018 Jan 4;46(D1):D447-D453.
[iUUCD Website] [Abstract] [Full Text]
• BIG Data Center Members. Database Resources of the BIG Data Center in 2018. Nucleic Acids Research. 2018 Jan 4;46(D1):D14-D20.
[Abstract] [Full Text]
Before 2018 publications
• Xu H*, Zhou J, Lin S, Deng W, Zhang Y, Xue Y#. PLMD: An updated data resource of protein lysine modifications. Journal of Genetics and Genomics. 2017 May 20;44(5):243-250.
[Abstract] [Full Text]
• Xu Y*, Zhang S*, Lin S, Guo Y, Deng W, Zhang Y, Xue Y#. WERAM: a database of writers, erasers and readers of histone acetylation and methylation in eukaryotes. Nucleic Acids Research. 2017 Jan 4;45(D1):D264-D270.
[Abstract] [Full Text]
• Ullah S*, Lin S*, Xu Y, Deng W, Ma L, Zhang Y, Liu Z#, Xue Y#. dbPAF: an integrative database of protein phosphorylation in animals and fungi. Scientific Reports. 2016 Mar 24;6:23534.
[Abstract] [Full Text]