Selected publications shown on homepage
98. Liu, P. and Li, J.J. (2025). mcRigor: a statistical method to enhance the rigor of metacell partitioning in single-cell data analysis. Nature Communications 16:1802. (Featured in Nature Communications Editors’ Highlights) [ RECOMB 2025 ] [ SOFTWARE ]
91. Song, D., Chen, S., Lee, C., Li, K., Ge, X., and Li, J.J. (2025). Synthetic control removes spurious discoveries from double dipping in single-cell and spatial transcriptomics data analyses. Lecture Notes in Computer Science 15647:400-404; Sankararaman, S., ed.; Springer, Cham. (RECOMB 2025; proceeding)
85. Yan, G., Hua, S.H., and Li, J.J. (2025). Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data. Nature Communications 16:1141.
77. Li, J.J., Zhou, H.J., Tong, X., and Bickel, P.J. (2024). Dissecting gene expression heterogeneity: generalized Pearson correlation squares and the K-lines clustering algorithm. Journal of American Statistical Association 119(548):2450-2463. [ SOFTWARE ] | [ PDF ]
75. Xia, L.*, Lee, C.*, and Li, J.J. (2024). Statistical method scDEED for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters. Nature Communications 15:1753. (Featured in Nature Communications Editors’ Highlights) [ Nature Methods: Seeing data as t-SNE and UMAP do ] [ SOFTWARE ]
73. Song, D., Wang, Q., Yan, G., Liu, T., and Li, J.J. (2024). scDesign3 generates realistic in silico data for multimodal single-cell and spatial omics. Nature Biotechnology 42:247-252. [ SOFTWARE ] [ PDF ]
71. Yan, G., Song, D., and Li, J.J. (2023). scReadSim: a single-cell RNA-seq and ATAC-seq read simulator. Nature Communications 14:7482. [ SOFTWARE ] [ PDF ]