Translator: A Transfer Learning Approach to Facilitate Single-Cell ATAC-Seq Data Analysis from Reference Dataset. - Siwei Xu; Mario Skarica; Ahyeon Hwang; Yi Dai; Cheyu Lee; Matthew J. Girgenti; Jing Zhang 062 (J. Comput. Biol., 2022)

Venus: An efficient virus infection detection and fusion site discovery method using single-cell and bulk RNA-seq data. - Cheyu Lee; Yuhang Chen; Ziheng Duan; Min Xu 009; Matthew J. Girgenti; Ke Xu 010; Mark Gerstein; Jing Zhang 062 (PLoS Comput. Biol., 2022)

iHerd: an integrative hierarchical graph representation learning framework to quantify network changes and prioritize risk genes in disease. - Ziheng Duan; Yi Dai; Ahyeon Hwang; Cheyu Lee; Kaichi Xie; Chutong Xiao; Min Xu 009; Matthew J. Girgenti; Jing Zhang 062 (PLoS Comput. Biol., 2023)

iMIRACLE: An Iterative Multi-View Graph Neural Network to Model Intercellular Gene Regulation From Spatial Transcriptomic Data. - Ziheng Duan; Siwei Xu; Cheyu Lee; Dylan Riffle; Jing Zhang 062 (CIKM, 2024)

scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. - Ziheng Duan; Siwei Xu; Shushrruth Sai Srinivasan; Ahyeon Hwang; Cheyu Lee; Feng Yue; Mark Gerstein; Yu Luan; Matthew J. Girgenti; Jing Zhang 062 (Briefings Bioinform., 2024)