Emma Louise Dempster

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

The paper identifies cell-type-specific DNA methylation differences in autism, revealing female-specific X chromosome alterations in microglia.

The paper identifies neuron-specific DNA methylation differences in schizophrenia using cell type-resolved epigenome-wide association study in prefrontal cortex nuclei.

This study identifies DNA methylation differences between microsatellite stable and microsatellite instable colorectal cancers, revealing MLH1-independent markers of mismatch repair deficiency and the impact of anatomical location.

The paper identifies DNA methylation changes in transgenic mouse models of Alzheimer's disease, showing distinct patterns for tau and amyloid-beta pathology and some overlap with human AD data.

This study identifies neuron-specific DNA methylation changes in Parkinson's disease prefrontal cortex, revealing hypermethylation at seven novel loci and highlighting the importance of cell-type-specific analysis.

The paper provides guidance for designing and analyzing cell-type specific epigenetic epidemiology studies using DNA methylation data from purified cell populations.

The paper develops a multivariate methylation risk score using blood DNA methylation data to predict dementia risk and cognitive impairment in Alzheimer's and Parkinson's disease cohorts.

The paper characterizes expressed transcripts in the human cortex across development, identifying novel coding sequences with clinical relevance.

The paper investigates epigenetic age acceleration in schizophrenia, finding age- and sex-specific effects and associations with polygenic risk scores.

The paper develops and validates deconvolution models using DNA methylation data to estimate cell-type proportions in the human cortex, finding glial cells are twice as abundant as neurons and linking cell-type proportions to Alzheimer's disease neuropathology.

The paper quantifies DNA methylation changes in human fetal pancreas development, identifying developmental differentially methylated positions and their genomic distribution.

The paper uses long-read transcript sequencing to identify differential isoform expression in the entorhinal cortex of tau transgenic mice, revealing novel isoforms and transcript associations with tau pathology.

The paper investigates DNA methylation and transcriptomic changes in chronic demyelinated MS lesions, showing hypermethylation of myelination-related genes and demonstrating reversible effects through epigenetic editing.

This study compares feature selection methods and machine learning algorithms to develop a DNA methylation-based telomere length estimator, finding that principal component analysis followed by elastic net regression performs best.

The paper identifies DNA methylation signatures in Alzheimer's disease cortex, showing most changes are driven by non-neuronal cell types.

This paper introduces and validates a metric to assess the accuracy of cellular deconvolution in DNA methylation studies, showing it identifies biases in different demographic groups.

The paper maps open chromatin regions in prenatal human frontal cortex and shows enrichment of SNP heritability for neuropsychiatric disorders within these regions.

The paper develops a novel epigenetic clock for fetal brain development to predict prenatal age in iPSCs and derived neurons, showing they remain epigenetically fetal despite differentiation.

This study uses long-read RNA sequencing to analyze isoform diversity in human and mouse cerebral cortex, revealing widespread alternative splicing and novel transcripts.

This study examines gene expression and DNA methylation changes in human astrocytes exposed to acute and recurrent low glucose, identifying UPR-related gene activation and methylation patterns.

This study identifies DNA methylation changes in blood samples from psychosis patients, including treatment-resistant schizophrenia, and links them to biological age, smoking, and cellular composition.

The paper identifies epigenetic aging abnormalities in growth disorders caused by mutations in epigenetic regulatory molecules.