Jeffrey M. Granja

The paper investigates how Polycomb-mediated genome architecture facilitates long-range H3K27 methylation spreading in ESCs and iPSCs, revealing RNA-dependent DNA looping and developmental gene roles in chromatin organization.

The paper examines dynamic chromatin changes in human CAR T cells during exhaustion, identifying regulatory networks and enhancer roles in exhaustion-associated genes.

The paper introduces Spear-ATAC, a high-throughput scATAC-seq protocol that identifies regulatory networks in cancer by analyzing chromatin accessibility and sgRNA spacer sequences from thousands of cells.

ArchR, an HDF5-backed R suite for end-to-end scATAC-seq analysis, outpaces SnapATAC and Signac and processes over 1.2 million simulated cells within 8 h on a laptop.

The paper uses single-cell epigenomic data to identify functional SNPs associated with Alzheimer's and Parkinson's disease, revealing novel gene-disease associations and regulatory mechanisms.

The paper uses scATAC-seq to analyze chromatin accessibility in immune cell development and tumor microenvironments, identifying regulatory elements and trajectories associated with cell differentiation and therapy response.

This paper develops a single-cell multi-omic framework to identify malignant regulatory signatures in mixed phenotype acute leukemia by analyzing transcriptomic and epigenetic data.

This paper uses HiChIP to map enhancer-promoter interactions in primary human cells, linking disease-associated DNA variants to their target genes.