Incorporating biological information in sparse principal component analysis with application to genomic data. - Ziyi Li 001; Sandra E. Safo; Qi Long (BMC Bioinform., 2017)

Dissecting differential signals in high-throughput data from complex tissues. - Ziyi Li 001; Zhijin Wu; Peng Jin; Hao Wu 003 (Bioinform., 2019)

Distributed learning from multiple EHR databases: Contextual embedding models for medical events. - Ziyi Li 001; Kirk Roberts; Xiaoqian Jiang; Qi Long (J. Biomed. Informatics, 2019)

Robust partial reference-free cell composition estimation from tissue expression. - Ziyi Li 001; Zhenxing Guo; Ying Cheng; Peng Jin; Hao Wu 003 (Bioinform., 2020)

Detection of differentially methylated CpG sites between tumor samples with uneven tumor purities. - Weiwei Zhang; Ziyi Li 001; Nana Wei; Hua-Jun Wu; Xiaoqi Zheng (Bioinform., 2020)

Complete deconvolution of DNA methylation signals from complex tissues: a geometric approach. - Weiwei Zhang; Hao Wu 003; Ziyi Li 001 (Bioinform., 2021)

A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq. - Xiaobo Sun; Xiaochu Lin; Ziyi Li 001; Hao Wu 003 (Briefings Bioinform., 2022)

NeuCA web server: a neural network-based cell annotation tool with web-app and GUI. - Daoyu Duan; Sijia He; Emina Huang; Ziyi Li 001; Hao Feng 005 (Bioinform., 2022)

CondiS web app: imputation of censored lifetimes for machine learning-based survival analysis. - Yizhuo Wang 002; Christopher R. Flowers; Ziyi Li 001; Xuelin Huang (Bioinform., 2022)

EDClust: an EM-MM hybrid method for cell clustering in multiple-subject single-cell RNA sequencing. - Xin Wei; Ziyi Li 001; Hongkai Ji; Hao Wu 003 (Bioinform., 2022)

CondiS: A conditional survival distribution-based method for censored data imputation overcoming the hurdle in machine learning-based survival analysis. - Yizhuo Wang 002; Christopher R. Flowers; Ziyi Li 001; Xuelin Huang (J. Biomed. Informatics, 2022)

A machine learning-based method for automatically identifying novel cells in annotating single-cell RNA-seq data. - Ziyi Li 001; Yizhuo Wang 002; Irene Ganan-Gomez; Simona Colla; Kim-Anh Do (Bioinform., 2022)

A comprehensive assessment of cell type-specific differential expression methods in bulk data. - Guanqun Meng; Wen Tang 003; Emina Huang; Ziyi Li 001; Hao Feng 005 (Briefings Bioinform., 2023)

A novel statistical method for decontaminating T-cell receptor sequencing data. - Ruoxing Li; Mehmet Altan; Alexandre Reuben; Ruitao Lin; John V. Heymach; Hai Tran; Runzhe Chen; Latasha Little; Shawna Hubert; Jianjun Zhang; Ziyi Li 001 (Briefings Bioinform., 2023)

SCIntRuler: guiding the integration of multiple single-cell RNA-seq datasets with a novel statistical metric. - Yue Lyu; Steven H. Lin; Hao Wu 003; Ziyi Li 001 (Bioinform., 2024)