Eilis J. Hannon

Best Practices for Pre-Processing Large-Scale ATAC-Seq Data: Why Epidemiological Studies Demand Greater Stringency

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.

Optimised fluorescence-activated nuclei sorting for epigenomic analysis of cortical cell types

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.

Cell-type-resolved DNA methylation profiling in the cortex reveals female-specific X chromosome differences in autism

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

Schizophrenia-associated DNA methylation differences in the cortex are neuron-specific

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

Methylomic signatures of tau and amyloid-beta in transgenic mouse models of Alzheimer's disease neuropathology

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.

Neuron-Specific DNA Methylation Differences in the Prefrontal Cortex in Parkinson's Disease

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.

Identification of SENP7 and UTF1/VENTX as new loci influencing clusteredprotocadherin methylation across blood and brain using a genome-wide associationstudy

The paper identifies SENP7 and UTF1/VENTX as new loci influencing cPCDH methylation in blood and brain through a genome-wide association study.

Re-annotating the EPICv2 manifest with genes, intragenic features, and regulatory elements

The paper re-annotates the EPICv2 methylation array manifest to improve compatibility with previous versions and provide more comprehensive annotations for DNA methylation data.

Guidance for the design and analysis of cell-type specific epigenetic epidemiology studies.

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

Imputed DNA methylation outperforms measured loci associations with smoking and chronological age

The paper shows that imputing DNA methylation loci from epigenome-wide data provides stronger associations with smoking and age than directly measured CpGs.

Blood-based multivariate methylation risk score for cognitive impairment and dementia

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.

Leveraging epigenetic signatures to determine the cell-type of origin from long read sequencing data

The paper develops a computational framework to classify blood cell types from long-read sequencing data using DNA methylation patterns, showing accurate classification for some regions and cell types.

An atlas of expressed transcripts in the prenatal and postnatal human cortex

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

Epigenetic age is accelerated in schizophrenia with age- and sex-specific effects and associated with polygenic disease risk

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

Quantifying the proportion of different cell types in the human cortex using DNA methylation profiles

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.

Developmentally dynamic changes in DNA methylation in the human pancreas

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

Long-read transcript sequencing identifies differential isoform expression in the entorhinal cortex in a transgenic model of tau pathology

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.

Genetic impacts on DNA methylation help elucidate regulatory genomic processes

The paper identifies genetic impacts on DNA methylation across 724,499 CpGs in blood samples, revealing co-localisations with disease traits and regulatory mechanisms.

A comparison of feature selection methodologies and learning algorithms in the development of a DNA methylation-based telomere length estimator

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.

Assessing the burden of rare DNA methylation outliers in schizophrenia

This paper introduces a method to detect rare DNA methylation outliers in schizophrenia and finds an increased burden of these outliers in cases compared to controls.

DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types

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

Uncertainty quantification of reference based cellular deconvolution algorithms

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.

Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays

This study compares Nanopore sequencing with DNA methylation microarrays to evaluate its viability for epigenetic epidemiology, finding high correlation and significant smoking-associated methylation sites.

A comparison of blood and brain-derived ageing and inflammation-related DNA methylation signatures and their association with microglial burdens

This study compares DNA methylation signatures of ageing and inflammation in blood and brain tissues, finding divergent correlations and a link between epigenetic age acceleration and microglial burdens in the hippocampus.

Genomic and phenomic insights from an atlas of genetic effects on DNA methylation

The paper identifies genetic variants influencing DNA methylation in blood and shows their associations with complex traits and diseases, but finds limited direct causality.

Sites of active gene regulation in the prenatal frontal cortex and their role in neuropsychiatric disorders

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

DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy

The paper presents a DNA methylation-based sex classifier that predicts sex and identifies sex chromosome aneuploidy using CpG sites from whole blood samples.

Novel epigenetic clock for fetal brain development predicts prenatal age for cellular stem cell models and derived neurons.

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.

Characterizing the properties of bisulfite sequencing data: maximizing power and sensitivity to identify between-group differences in DNA methylation

The paper develops a simulation framework and tool to assess and optimize power for detecting DNA methylation differences in bisulfite sequencing studies.

A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex

This study performs a meta-analysis of DNA methylation data from Alzheimer's disease patients to identify differentially methylated loci across brain regions and cortex.