All Published – Page 3 – The Junction of Statistics and Biology

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 ]

A genome-wide spectrum of tandem repeat expansions in 338,963 humans

76. Cui, Y., Ye, W., Li, J.S., Li, J.J., Vilain, E., Sallam, T., and Li, W. (2024). A genome-wide spectrum of tandem repeat expansions in 338,963 humans. Cell 187(9):2336-2341. | [ PDF ]

scDEED: a statistical method for detecting dubious 2D single-cell embeddings

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 ]