References

First 15 references in the thesis are listed below:

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Lambert, S.A. et al. The Human Transcription Factors. Cell 172, 650-665 (2018).

Shao, Y. & Zhang, Qiangfeng C. Targeting RNA structures in diseases with small molecules. Essays in Biochemistry 64, 955-966 (2020).

Yu, A.M., Choi, Y.H. & Tu, M.J. RNA Drugs and RNA Targets for Small Molecules: Principles, Progress, and Challenges. Pharmacol Rev 72, 862-898 (2020).

O'Brien, J., Hayder, H., Zayed, Y. & Peng, C. Overview of MicroRNA Biogenesis, Mechanisms of Actions, and Circulation. Front Endocrinol (Lausanne) 9, 402 (2018).

Cannell, I.G., Kong, Y.W. & Bushell, M. How do microRNAs regulate gene expression? Biochem Soc Trans 36, 1224-31 (2008).

Zeng, P., Li, J., Ma, W. & Cui, Q. Rsite: a computational method to identify the functional sites of noncoding RNAs. Sci Rep 5, 9179 (2015).

Zeng, P. & Cui, Q. Rsite2: an efficient computational method to predict the functional sites of noncoding RNAs. Sci Rep 6, 19016 (2016).

Su, M. et al. Comparative Assessment of Scoring Functions: The CASF-2016 Update. J Chem Inf Model 59, 895-913 (2019).

Su, H., Peng, Z. & Yang, J. Recognition of small molecule-RNA binding sites using RNA sequence and structure. Bioinformatics 37, 36-42 (2021).

Wang, K., Zhou, R., Wu, Y. & Li, M. RLBind: a deep learning method to predict RNA-ligand binding sites. Brief Bioinform 24(2023).

Teuwen, J. & Moriakov, N. Chapter 20 - Convolutional neural networks. in Handbook of Medical Image Computing and Computer Assisted Intervention (eds. Zhou, S.K., Rueckert, D. & Fichtinger, G.) 481-501 (Academic Press, 2020).

Liberis, E., Veličković, P., Sormanni, P., Vendruscolo, M. & Liò, P. Parapred: antibody paratope prediction using convolutional and recurrent neural networks. Bioinformatics 34, 2944-2950 (2018).

Jin, W., Wohlwend, J., Barzilay, R. & Jaakkola, T. Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design. arXiv e-prints (2021).

Yuan, Q., Chen, J., Zhao, H., Zhou, Y. & Yang, Y. Structure-aware protein-protein interaction site prediction using deep graph convolutional network. Bioinformatics 38, 125-132 (2021).