97. 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 ]
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 ]
64. Zhou, H.J., Li, L., Li, Y., Li, W., and Li, J.J. (2022). PCA outperforms popular hidden variable inference methods for QTL mapping. Genome Biology 23:210. [ Highlight talk at RECOMB 2023 ] [ SOFTWARE ] | [ PDF ]
59. Li, Y.*, Ge, X.*, Peng, F., Li, W., and Li, J.J. (2022). Exaggerated false positives by popular differential expression methods when analyzing human population samples. Genome Biology 23:79. [ UCLA NEWS ] [ CODE ] | [ PDF ]
56. Ge, X.*, Chen, Y.E.*, Song, D., McDermott, M., Woyshner, K., Manousopoulou, A., Wang, N., Li, W., Wang, L.D., and Li, J.J. (2021). Clipper: p-value-free FDR control on high-throughput data from two conditions. Genome Biology 22:288. [ UCLA NEWS ] [ SOFTWARE ] [ CODE ] [ VIDEO ] | [ PDF ]
38. Li, J.J. and Tong, X. (2020). Statistical hypothesis testing versus machine-learning binary classification: distinctions and guidelines. Patterns 1(7):110115. [ UCLA NEWS ] [ PODCAST ]