94. Higgins, C., Li, J.J., Carey, M. (2025). Spatial transcriptomics iterative hierarchical clustering (stIHC): a novel method for identifying spatial gene co-expression modules. Quantitative Biology 13(4):e70011. [ SOFTWARE ]
93. Zhou, H.J., Ge, X., and Li, J.J. (2025). ClipperQTL: ultrafast and powerful eGene identification method. Genome Biology 26:207. [ SOFTWARE ]
92. Zhang, H., Li, X., Song, D., Yukselen, O., Nanda, S., Kucukural, A., Li, J.J., Garber, M., and Walhout, A.J.M. (2025). Worm Perturb-Seq: massively parallel whole-animal RNAi and RNA-seq. Nature Communications 16:4785.
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)
90. Liu, P. and Li, J.J. (2025). mcRigor: A statistical method to enhance the rigor of metacell partitioning in single-cell RNA-seq and ATAC-seq data analysis. Lecture Notes in Computer Science 15647:381-385; Sankararaman, S., ed.; Springer, Cham. (RECOMB 2025; proceeding)
89. Wang, C., Ge, X., Song, D., and Li, J.J. (2025). Comment on Data Fission: Splitting a Single Data Point”-Data Fission for Unsupervised Learning: A Discussion on Post-Clustering Inference and the Challenges of Debiasing. Journal of the American Statistical Association 120(549):174-175.”
88. Fang, L., …, Li, J.J., Palmer, A., Frantz, L., Zhou, H., Zhang, Z., and Liu, G.E. (2025). The farm animal genotype-tissue expression (FarmGTEx) project. Nature Genetics 57:786-796.
87. Song, B., Liu, D., Dai, W., McMyn, N.F., Wang, Q., Yang, D., Krejci, A., Vasilyev, A., Untermoser, N., Loregger, A., Song, D., Williams, B., Rosen, B., Cheng, X., Chao, L., Kale, H.T., Zhang, H., Diao, Y., Bürckstümmer, T., Siliciano, J.D., Li, J.J., Siliciano, R.F., Huangfu, D., & Li, W. (2025). Decoding heterogeneous single-cell perturbation […]
86. Sankaran, K., Kodikara, S., Li, J.J., and Le Cao, K.A. (2025). Semisynthetic simulation for microbiome data analysis. Briefings in Bioinformatics 26(1):bbaf051.