Network-Based Isoform Quantification with RNA-Seq Data for Cancer Transcriptome Analysis. - Wei Zhang 076; Jae-Woong Chang; Lilong Lin; Kay Minn; Baolin Wu; Jeremy Chien; Jeongsik Yong; Hui Zheng; Rui Kuang (PLoS Comput. Biol., 2015)

An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types. - Sunho Park; Seung-Jun Kim 002; Donghyeon Yu; Samuel Peña-Llopis; Jianjiong Gao; Jinsuk Park; Beibei Chen; Jessie Norris; Xinlei Wang 001; Min Chen 014; Min-Su Kim; Jeongsik Yong; et al. (Bioinform., 2016)

Platform-integrated mRNA isoform quantification. - Jiao Sun; Jae-Woong Chang; Teng Zhang 002; Jeongsik Yong; Rui Kuang; Wei Zhang 076 (Bioinform., 2020)

In silico model for miRNA-mediated regulatory network in cancer. - Khandakar Tanvir Ahmed; Jiao Sun; William Chen; Irene Martinez; Sze Cheng; Wencai Zhang; Jeongsik Yong; Wei Zhang 076 (Briefings Bioinform., 2021)

Multi-omics data integration by generative adversarial network. - Khandakar Tanvir Ahmed; Jiao Sun; Sze Cheng; Jeongsik Yong; Wei Zhang 076 (Bioinform., 2021)

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion. - Zhuliu Li; Tianci Song; Jeongsik Yong; Rui Kuang (PLoS Comput. Biol., 2021)

APA-Scan: detection and visualization of 3′-UTR alternative polyadenylation with RNA-seq and 3′-end-seq data. - Naima Ahmed Fahmi; Khandakar Tanvir Ahmed; Jae-Woong Chang; Heba Nassereddeen; Deliang Fan; Jeongsik Yong; Wei Zhang 076 (BMC Bioinform., 2022)

Incomplete time-series gene expression in integrative study for islet autoimmunity prediction. - Khandakar Tanvir Ahmed; Sze Cheng; Qian Li 023; Jeongsik Yong; Wei Zhang 076 (Briefings Bioinform., 2023)

Integrating spatial transcriptomics and bulk RNA-seq: predicting gene expression with enhanced resolution through graph attention networks. - Sudipto Baul; Khandakar Tanvir Ahmed; Qibing Jiang; Guangyu Wang; Qian Li 023; Jeongsik Yong; Wei Zhang 076 (Briefings Bioinform., 2024)