Semisynthetic simulation for microbiome data analysis.
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.
Categorization of 34 computational methods to detect spatially variable genes from spatially resolved transcriptomics data
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.
Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA
84. Sun, T., Yuan, J., Zhu, Y., Li, J., Yang, S., Zhou, J., Ge, X., Qu, S., Li, W., Li, J.J., and Li, Y. (2024). Systematic evaluation of methylation-based cell type deconvolution methods for plasma cell-free DNA. Genome Biology 25:318. | [ PDF ]
Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic vulnerabilities in malignant glioma
83. Fernandez, E.G., Mai, W.X., Song, K., Bayley, N.A., Kim, J., Zhu, H., Pioso, M., Young, P., Andrasz, C., Cadet, D., Liau, L.M., Li, G., Yong, W.H., Rodriguez, F., Dixon, S.J., Souers, A.J., Li, J.J., Graeber, T.G., Cloughesy, T.F. & Nathanson, D.A. (2024). Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic […]
Response to “Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives” and “Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samp
82. Ge, X.*, Li, Y.*, Li, W., and Li, J.J. (2024). Response to “Neglecting normalization impact in semi-synthetic RNA-seq data simulation generates artificial false positives” and “Winsorization greatly reduces false positives by popular differential expression methods when analyzing human population samples”. Genome Biology 25:283.
Leadership at the Intersection of Statistics & Genomics: A COPSS-NISS Leadership Webinar with Drs. Rafael Irizarry and Mingyao Li
81. Li, J.J. (2024). Leadership at the Intersection of Statistics & Genomics: A COPSS-NISS Leadership Webinar with Drs. Rafael Irizarry and Mingyao Li. Statistics in Biosciences 16:547-555.
Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms
80. Patowary, A., Zhang, P., Jops, C., Vuong, C.K., Ge, X., Hou, K., Kim, M., Gong, N., Margolis, M., Vo, D., Wang, X., Liu, C., Pasaniuc, B., Li, J.J., Gandal, M.J., and De La Torre-Ubieta, L. (2024). Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms. Science 384(6698):eadh7688.
scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data
79. Wang, W.*, Cen, Y.*, Lu, Z.*, Xu, Y., Sun, T., Xiao, Y., Liu, W., Li, J.J., and Wang, C. (2024). scCDC: a computational method for gene-specific contamination detection and correction in single-cell and single-nucleus RNA-seq data. Genome Biology 25:136. [ SOFTWARE ]
APIR: a universal FDR-control framework for boosting peptide identification power by aggregating multiple proteomics database search algorithms
78. Chen, Y.E.*, Ge, X.*, Woyshner, K.*, McDermott, M.*, Manousopoulou, A., Ficarro, S., Marto, J., Kexin Li, Wang, L.D., and Li, J.J. (2024). APIR: a universal FDR-control framework for boosting peptide identification power by aggregating multiple proteomics database search algorithms. Genomics, Proteomics & Bioinformatics 22(2):qzae042. [ SOFTWARE ] [ CODE ]
Dissecting gene expression heterogeneity: generalized Pearson correlation squares and the K-lines clustering algorithm
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 ]