Integration of millions of transcriptomes using batch-aware triplet neural networks. - Lukas M. Simon; Yin-Ying Wang; Zhongming Zhao (Nat. Mach. Intell., 2021)

EmptyNN: A neural network based on positive and unlabeled learning to remove cell-free droplets and recover lost cells in scRNA-seq data. - Fangfang Yan; Zhongming Zhao; Lukas M. Simon (Patterns, 2021)

deCS: A Tool for Systematic Cell Type Annotations of Single-cell RNA Sequencing Data among Human Tissues. - Guangsheng Pei; Fangfang Yan; Lukas M. Simon; Yulin Dai; Peilin Jia; Zhongming Zhao (Genom. Proteom. Bioinform., 2023)