PancanQTL: systematic identification of cis-eQTLs and trans-eQTLs in 33 cancer types. - Jing Gong; Shufang Mei; Chun-Jie Liu; Yu Xiang; Youqiong Ye; Zhao Zhang; Jing Feng; Renyan Liu; Lixia Diao; An-Yuan Guo; Xiaoping Miao; Leng Han (Nucleic Acids Res., 2018)

H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development. - Xiaolong Chen; Youqiong Ye; Liang Gu; Jin Sun; Yanhua Du; Wen-Ju Liu; Wei Li; Xiaobai Zhang; Cizhong Jiang (Genom. Proteom. Bioinform., 2019)

APAatlas: decoding alternative polyadenylation across human tissues. - Wei Hong; Hang Ruan; Zhao Zhang; Youqiong Ye; Yaoming Liu; Shengli Li 005; Ying Jing; Huiwen Zhang; Lixia Diao; Han Liang; Leng Han (Nucleic Acids Res., 2020)

DeepAlloDriver: a deep learning-based strategy to predict cancer driver mutations. - Qianqian Song; Mingyu Li; Qian Li; Xun Lu; Kun Song 003; Ziliang Zhang; Jiale Wei; Liang Zhang; Jiacheng Wei; Youqiong Ye; Jinyin Zha; Qiufen Zhang; et al. (Nucleic Acids Res., 2023)

A novel computational model ITHCS for enhanced prognostic risk stratification in ESCC by correcting for intratumor heterogeneity. - Tong Lu; Wei Guo; Wei Guo; Wangyang Meng; Tianyi Han; Zizhen Guo; Chengqiang Li; Shugeng Gao; Youqiong Ye; Hecheng Li (Briefings Bioinform., 2024)

SemanticST: Spatially Informed Semantic Graph Learning for Clustering, Integration, and Scalable Analysis of Spatial Transcriptomics. - Roxana Zahedi; Ahmadreza Argha; Nona Farbehi; Ivan Bakhshayeshi; Youqiong Ye; Nigel H. Lovell; Hamid Alinejad-Rokny (CoRR, 2025)