Simon Charles Heath

EpiATLAS - a reference for human epigenomic research

EpiATLAS provides a comprehensive collection of human reference epigenomes to advance epigenomic research and understanding of cellular function and disease.

Mitochondrial leakage and mtDNA damage trigger early immune response in Inclusion Body Myositis.

This study identifies mitochondrial dysfunction and mtDNA damage as early triggers of immune response in PM-Mito and IBM, linking mitochondrial abnormalities to inflammation and disease progression.

cvlr: Finding heterogeneously methylated genomicregions using ONT reads

The paper introduces a method to identify heterogeneously methylated genomic regions using Nanopore reads by analyzing methylation patterns across multiple loci.

Novel method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome

This paper introduces a method to sequence full-length human mitochondrial genomes using Cas9 and long-read sequencing, enabling accurate detection of heteroplasmy and deletion patterns.

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data

DeepMP detects DNA methylation from Nanopore sequencing data using a CNN that combines signals and basecalling errors, outperforming existing methods across multiple datasets.

Selective single molecule sequencing and assembly of a human Y chromosome of African origin

The paper develops a method to sequence and assemble a human Y chromosome of African origin using native DNA and nanopore sequencing, achieving high continuity and enabling epigenetic modification detection.

DNA methylation oscillation defines classes of enhancers

The paper identifies DNA methylation oscillations as a marker for enhancer classification, showing high predictive power compared to other methods.

GEMBS -- high through-put processing for DNA methylation data from Whole Genome Bisulfite Sequencing (WGBS)

The paper introduces GEMBS, a high-throughput processing tool for DNA methylation data from WGBS, aiming to improve efficiency for large datasets.

Inference of genomic spatial organization from a whole genome bisulfite sequencing sample.

The paper predicts the first eigenvector of the Hi-C matrix from whole genome bisulfite sequencing data, showing that methylation variability better predicts chromatin compartments than methylation levels.

Comparative analysis of neutrophil and monocyte epigenomes

This study compares the epigenomes of neutrophils and monocytes to identify regulatory elements and chromatin states, revealing differences in enhancer activity and DNA methylation.