|
Bao, X., Zhang, Y., Li, H., Teng, Y., Ma, L., Chen, Z., Luo, X., Zheng, J., Zhao, A., Ren, J., et al., 2023. RM2Target: a comprehensive database for targets of writers, erasers and readers of RNA modifications. Nucleic Acids Res. 51, D269-D279.
|
|
Deng, S., Zhang, H., Zhu, K., Li, X., Ye, Y., Li, R., Liu, X., Lin, D., Zuo, Z., Zheng J., 2021. M6A2Target: a comprehensive database for targets of m6A writers, erasers and readers. Briefings Bioinf. 22, bbaa055.
|
|
Duan, D., Tang, W., Wang, R., Guo, Z., Feng, H., 2023. Evaluation of epitranscriptome-wide N6-methyladenosine differential analysis methods. Briefings Bioinf. 24, bbad139.
|
|
Flores-Tellez, D., Tankmar, M. D., von Bulow, S., Chen, J., Lindorff-Larsen, K., Brodersen, P., Arribas-Hernandez, L., 2023. Insights into the conservation and diversification of the molecular functions of YTHDF proteins. PLoS Genet. 19, e1010980.
|
|
Huang, W., Hu, X., Ren, Y., Song, M., Ma, C., Miao, Z., 2023. IPOP: an integrative plant multi-omics platform for cross-species comparison and evolutionary study. Mol. Biol. Evol. 40, msad248.
|
|
Kim, D., Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L., 2019. Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat. Biotechnol. 37, 907-915.
|
|
Lang, X., Yu, C., Shen, M., Gu, L., Qian, Q., Zhou, D., Tan, J., Li, Y., Peng, X., Diao, S., et al., 2024. PRMD: an integrated database for plant RNA modifications. Nucleic Acids Res. 52, D1597-D1613.
|
|
Li, Z., Ma, Y., Sun, W., Ding, P., Bu, Y., Qi, Y., Shi, T., Jia, C., Lei, B., et al., 2025. The N6-methyladenosine reader ECT1 regulates seed germination via gibberellic acid- and phytochrome B-mediated signaling. Plant Physiol. 198, kiaf180.
|
|
Song, M., Zhao, J., Zhang, C., Jia, C., Yang, J., Zhao, H., Zhai, J., Lei, B., Tao, S., Chen, S., et al., 2024. PEA-m6A: an ensemble learning framework for accurately predicting N6-methyladenosine modifications in plants. Plant Physiol. 195, 1200-1213.
|
|
Song, P., Wei, L., Chen, Z., Cai, Z., Lu, Q., Wang, C., Tian, E., Jia, G., 2023. m6A readers ECT2/ECT3/ECT4 enhance mRNA stability through direct recruitment of the poly(A) binding proteins in Arabidopsis. Genome Biol. 24, 103.
|
|
Yang, J., Song, M., Bu, Y., Zhao, H., Liu, C., Zhang, T., Zhang, C., Xu, S., Ma, C., 2025. Machine learning-augmented m6A-Seq analysis without a reference genome. Briefings Bioinf. 26, bbaf235.
|
|
Zhai, J., Song, J., Cheng, Q., Tang, Y., Ma, C., 2018. PEA: an integrated R toolkit for plant epitranscriptome analysis. Bioinformatics 34, 3747-3749.
|
|
Zhai, J., Song, J., Zhang, T., Xie, S., Ma, C., 2020. deepEA: a containerized web server for interactive analysis of epitranscriptome sequencing data. Plant Physiol. 185, 29-33.
|