Q-SID: Detecting collusion groups from exam question scores with error quantification
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Beyond differential expression: Differential variability as an underappreciated axis in transcriptomics
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Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr
106. Jiang, C.F., Yin, Y., Robson, P., Li, Y.J., Li, J.J., and Song, D. (2026). Flexible and scalable inference of spatially varying correlation in spatial transcriptomics with spCorr. Genome Research 36(7):1440–1454. [ SOFTWARE ]
CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments
105. Hemminger, Z., Ocampo, H.D., Xie, F., Zhai, Z., Li, J.J., and Wollman, R. (2026). CIPHER: An end-to-end framework for designing optimized aggregated spatial transcriptomics experiments. PLOS Computational Biology 22(6):e1014362. [ SOFTWARE ]
Proteogenomic Features Define Novel Subtypes of Mantle Cell Lymphoma
104. Yan, Y., Chen, W., Ge, X., Sun, J., Yu, L., Garcia-Mansfield, K., Zhang, X., Yu, Y., Xiong, W., Zou, D., An, G., Jia, Z., Pirrotte, P., Li, J.J., Yu, Z., Hao, M., Qiu, L., Qi, J., Wang, L., and Yi, S. (2026). Proteogenomic features define subtypes of mantle cell lymphoma. Blood Advances 10 (10):3529-3540.
ClusterDE: A statistical software package for removing double-dipping bias in post-clustering differential expression analysis.
103. Lee, C., Song, D., Chen, S., and Li, J.J. (2026). ClusterDE: A statistical software package for removing double-dipping bias in post-clustering differential expression analysis. Journal of Computational Biology 33(1):36-42. (RECOMB 2025; software article) [ SOFTWARE ]
mcRigor: A statistical software package for evaluating and optimizing metacell partitioning in single-cell data analysis.
102. Liu, P., and Li, J.J. (2026). mcRigor: A statistical software package for evaluating and optimizing metacell partitioning in single-cell data analysis. Journal of Computational Biology 33(1):43-47. (RECOMB 2025; software article; see Publication 98 for the method article) [ SOFTWARE ]
CellScope: high-performance cell atlas workflow with tree-structured representation
101. Li, B., Lin, R., Ni, T., Yan, G., Burns, M., Li, J.J., and Yao, Z. (2026). CellScope: high-performance cell atlas workflow with tree-structured representation. Nature Communications 17:1130. [ SOFTWARE ]
PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime
100. Lai, Y.*, Song, D.*, Xia, L., and Li, J.J. (2025). PseudotimeDE-fast: fast testing of differential gene expression along cell pseudotime. Bioinformatics 41(11):btaf573. [ SOFTWARE ]
Insights, opportunities, and challenges provided by large cell atlases
99. Hemberg, M., Marini, F., Ghazanfar, S., Al Ajami, A., Abassi, N., Anchang, B., Benayoun, B.A., Cao, Y., Chen, K., Cuesta-Astroz, Y., DeBruine, Z., Dendrou, C.A., De Vlaminck, I., Imkeller, K., Korsunsky, I., Lederer, A.R., Li, J.J., Meysman, P., Miller, C.L., Mullan, K.A., Ohler, U., Panwar, P., Patikas, N., Schuck, J., Siu, J.H.Y., Triche, T.J. […]