Sarah J. Marzi

The paper introduces PIPPA, a pipeline for processing large-scale ATAC-seq data, showing that peak calling performance varies by dataset and recommending parameters for high-confidence chromatin accessibility profiles.

The paper identifies seven sex-dependent differentially methylated positions in ALS blood samples, suggesting sex-specific biological mechanisms in the disease.

The paper introduces optimized fluorescence-activated nuclei sorting (FANS) protocols to isolate cell-type-specific nuclei from human and mouse brain tissue for multi-omic analysis.

This study identifies cell-type-specific histone acetylation changes in Alzheimer's disease, highlighting MITF's potential role in microglial dysfunction.

CHAS deconvolves bulk H3K27ac profiles to infer cell type-specific signatures in neurological and psychiatric disorders, revealing distinct genetic and epigenetic contributions across cell types.

The paper links genetic risk for neurodegenerative diseases to microglial pathways using genomic and computational methods.

This study benchmarks CUT&Tag against ENCODE ChIP-seq for histone modifications, finding 54% average recall of known peaks and comparable peak caller performance.

The paper investigates how the 17q21.31 locus influences Parkinson's disease through KANSL1 activity, showing haplotype-specific effects on key biological processes.

This study identifies region-specific epigenomic and transcriptomic changes in a rotenone rat model of Parkinson's disease, highlighting immune and synaptic dysregulation in the substantia nigra and cortex.

This study shows that histone mark function, genomic distance, and cellular states collectively influence gene expression predictions using deep learning models, with no single mark consistently predicting expression across contexts.

The paper generates morphologically distinct astrocyte subtypes from human iPSCs and links their shape, function, and reactivity.

This study examines how APOE isoforms affect the transcriptomic and epigenomic features of human microglia in an Alzheimer's disease xenotransplantation model, identifying genotype-dependent differences.

This study investigates whether donor DNA methylation can predict acute graft-versus-host disease (aGVHD) in HCT, finding that a classifier developed from methylation data failed to validate in an independent cohort.

This study shows that genetic variation in rDNA affects epigenetic states and rRNA expression in mice and humans, with species-specific patterns observed.

The paper examines DNA methylation differences between human blood and sperm, finding limited correlation and no significant obesity-related changes in sperm methylation.

This study identifies widespread H3K27ac acetylomic variation in AD cases compared to controls, linking it to disease-related pathways and AD-associated genetic variants.