Xiaohui Wu

This study identifies the m6A-SIRP axis as a regulator of efferocytosis in atherosclerosis, showing myeloid m6A loss increases plaque instability.

Beta-DIA improves proteome profiling by combining deep learning and function-based scores for diaPASEF data, doubling protein group detection in low datasets.

The paper maps liver chromatin architecture using ATAC-seq and shows sex is the main factor driving diet-induced nucleosome dynamics in mice.

This study benchmarks gene set scoring tools for scATAC-seq, showing their comparable performance to scRNA-seq and highlighting the importance of dropout imputation.

The paper introduces stAPAminer, a toolkit for analyzing spatial patterns of alternative polyadenylation in spatial transcriptomics data, revealing reproducible spatial APA dynamics in mouse olfactory bulb.

This paper surveys computational methods for predicting polyadenylation sites from DNA sequences, bulk RNA-seq, and single-cell RNA-seq data, discussing challenges and future directions.

The paper introduces a network-based method for dropout imputation in scRNA-seq data, showing that different genes benefit from different imputation strategies and introducing the ADImpute R-package.

The paper introduces scLAPA, a toolkit that improves cell-cell association and clustering in scRNA-seq by integrating gene expression and alternative polyadenylation data.