scPNMF: sparse gene encoding of single cells to facilitate gene selection for targeted gene profiling. - Dongyuan Song; Kexin Li; Zachary Hemminger; Roy Wollman; Jingyi Jessica Li (Bioinform., 2021)

Particle swarm optimization in constrained maximum likelihood estimation a case study. - Elvis Han Cui; Dongyuan Song; Weng Kee Wong (CoRR, 2021)

Single-cell generalized trend model (scGTM): a flexible and interpretable model of gene expression trend along cell pseudotime. - Elvis Han Cui; Dongyuan Song; Weng Kee Wong; Jingyi Jessica Li (Bioinform., 2022)

scSampler: fast diversity-preserving subsampling of large-scale single-cell transcriptomic data. - Dongyuan Song; Nan Miles Xi; Jingyi Jessica Li; Lin Wang 044 (Bioinform., 2022)

Simulating Single-Cell Gene Expression Count Data with Preserved Gene Correlations by scDesign2. - Tianyi Sun; Dongyuan Song; Wei Vivian Li; Jingyi Jessica Li (J. Comput. Biol., 2022)

Synthetic Control Removes Spurious Discoveries from Double Dipping in Single-Cell and Spatial Transcriptomics Data Analyses. - Dongyuan Song; Siqi Chen; Christy Lee; Kexin Li; Xinzhou Ge; Jingyi Jessica Li (RECOMB, 2025)