Capturing large genomic contexts for accurately predicting enhancer-promoter interactions. - Ken Chen 006; Huiying Zhao; Yuedong Yang (Briefings Bioinform., 2022)

Fast and accurate protein intrinsic disorder prediction by using a pretrained language model. - Yidong Song; Qianmu Yuan; Sheng Chen; Ken Chen 006; Yaoqi Zhou; Yuedong Yang (Briefings Bioinform., 2023)

Self-supervised learning on millions of primary RNA sequences from 72 vertebrates improves sequence-based RNA splicing prediction. - Ken Chen 006; Yue Zhou 014; Maolin Ding; Yu Wang 027; Zhixiang Ren; Yuedong Yang (Briefings Bioinform., 2024)

Deciphering cell types by integrating scATAC-seq data with genome sequences. - Yuansong Zeng; Mai Luo; Ningyuan Shangguan; Peiyu Shi; Junxi Feng; Jin Xu; Ken Chen 006; Yutong Lu; Weijiang Yu; Yuedong Yang (Nat. Comput. Sci., 2024)