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2025	DeepMethyGene: a deep-learning model to predict gene expression using DNA methylations BMC Bioinformatics Yuyao Yan, Xinyi Chai, Jiajun Liu, Sijia Wang, Wenran Li, Tao Huang
2025	ETNet: an interpretable transformer framework for enhancer–enhancer interaction prediction with cross-context transferability Briefings in Bioinformatics Shuaibin Wang, Tong Chen, Zhongxin Yang, Zhen Liang, Yin Shen
2022	Machine Learning Methods for Exploring Sequence Determinants of 3D Genome Organization Journal of Molecular Biology Muyu Yang, Jian Ma
2021	DeepYY1: a deep learning approach to identify YY1-mediated chromatin loops Briefings in Bioinformatics Fu-Ying Dao, Hao Lv, Dan Zhang, Zi-Mei Zhang, Li Liu, Hao Lin
2021	Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles Briefings in Bioinformatics Huan Tao, Hao Li, Kang Xu, Hao Hong, Shuai Jiang, Guifang Du, Junting Wang, Yu Sun, Xin Huang, Yang Ding, Fei Li, Xiaofei Zheng, Hebing Chen, Xiaochen Bo
2020	A machine learning framework for the prediction of chromatin folding inDrosophilausing epigenetic features PeerJ Computer Science Michal B. Rozenwald, Aleksandra A. Galitsyna, Grigory V. Sapunov, Ekaterina E. Khrameeva, Mikhail S. Gelfand