False discovery rate control incorporating phylogenetic tree increases detection power in microbiome-wide multiple testing. - Jian Xiao; Hongyuan Cao; Jun Chen (Bioinform., 2017)

Assessing non-inferiority for incomplete paired-data under non-ignorable missing mechanism. - Hui-Qiong Li; Guo-Liang Tian; Niansheng Tang; Hongyuan Cao (Comput. Stat. Data Anal., 2018)

Asymmetric Tobit Analysis for Correlation Estimation from Censored Data. - Hongyuan Cao; Tsuyoshi Kato (IEICE Trans. Inf. Syst., 2021)

Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. - Frimpong Boadu; Hongyuan Cao; Jianlin Cheng (Bioinform., 2023)