Shengen Shawn Hu

PATTY corrects open chromatin bias in CUT&Tag data using ATAC-seq and machine learning, improving detection of histone modifications and cell clustering in single-cell analyses.

This study identifies age-associated delays in immune resolution to respiratory viral infection by analyzing single-cell RNA sequencing and flow cytometry data from young and aged mice.

HILAMA is a method for high-dimensional mediation analysis with latent confounding, showing improved FDR control and power in simulations and applied to ADNI proteomics-radiomics data.

The paper uses super-resolution microscopy to show that estrogen receptor activity regulates distinct chromatin structures marked by H3K27ac, revealing dynamic epigenetic states and their implications for transcriptional activity and cancer resistance.

This study identifies dysregulated immune-epithelial progenitor interactions in post-viral lung sequelae and shows that targeting IFN-γ, TNF, or IL-1β improves alveolar regeneration and pulmonary function.

The paper uses single-cell ATAC-seq to analyze coronary artery cells from CAD patients, identifying regulatory mechanisms and risk variants associated with disease.

SELMA estimates intrinsic cleavage biases in bulk and single-cell chromatin accessibility data, improving analysis accuracy and cell clustering in single-cell ATAC-seq.

CAM provides a comprehensive quality control pipeline for MNase-seq data, including QC measurements and a reference atlas of 268 datasets from human and mouse.

Dr.seq2 is a QC and analysis pipeline for single cell transcriptome and epigenome data, providing reliable results on published datasets.