Adam D. Ewing

Linking somatic variants to altered methylation profiles in nanopore-derived breast and pancreatic cancer genomes using unduliner

This paper introduces unduliner, a framework that links somatic variants to methylation changes in cancer genomes using nanopore sequencing data.

Substantial genomic and methylation variability between MCF-7 sublines

The paper uses nanopore sequencing to analyze genomic and methylation differences between two MCF-7 sublines, finding substantial methylation divergence and associations with cancer-related genes.

An allele-resolved nanopore-guided tour of the human placental methylome

The paper uses nanopore sequencing to analyze the methylome and transcriptome of human placental trios, identifying new differentially methylated regions and imprinted genes.

Wild type bone marrow-derived microglia-like cells mitigate strain-dependent neuropathology in Csf1r mutant mice.

The paper shows that wild-type bone marrow-derived microglia-like cells reduce strain-dependent neuropathology in Csf1r mutant mice by preventing thalamic calcification.

ProA and ProB repeat sequences shape genome organization in eukaryotes

The paper identifies ProA and ProB repeat sequences as sequence determinants of chromatin compartments, showing their role in genome organization and cancer progression.

Vitamin C activates young LINE-1 elements in mouse embryonic stem cells via H3K9me3 demethylation

This study shows that vitamin C increases young LINE-1 element expression in mouse ESCs through H3K9me3 demethylation by KDM4A/C, without increasing somatic insertion rates.

Mouse L1s fade with age: a methylation-enforced mechanism for attenuation of L1 retrotransposition potential

The paper investigates how L1 retrotransposition potential declines with age through methylation changes and promoter shortening in mice.

Retrotransposon instability dominates the acquired mutation landscape of mouse induced pluripotent stem cells

The paper identifies retrotransposon insertions as the main source of mutations in mouse induced pluripotent stem cells, showing hypomethylation of LINE-1 elements and their impact on gene regulation.

LINE-1 retrotransposon activation intrinsic to interneuron development

The paper shows that SOX6 activates LINE-1 retrotransposons in PV+ interneurons, leading to increased morphological complexity through a novel CAPS2 isoform.

Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID

This study introduces Nanopore-DamID, a method to detect DNA methylation and DNA-protein interactions, revealing methylation's role in transcription factor activity.

No evidence of human genome integration of SARS-CoV-2 found by long-read DNA sequencing

The paper uses long-read sequencing to investigate SARS-CoV-2 integration into the human genome and finds no evidence of such integration in infected cells.

Methylartist: Tools for Visualising Modified Bases from Nanopore Sequence Data

Methylartist provides tools for processing, visualizing, and analyzing nanopore methylation data, supporting multiple methylation types and enabling integrated study of modified bases.

Long-read cDNA sequencing identifies functional pseudogenes in the human transcriptome

This study identifies hundreds of novel transcribed pseudogenes using long-read sequencing and shows their functional relevance through translation and perturbation experiments.

Nanopore sequencing enables comprehensive transposable element epigenomic profiling

This study uses nanopore sequencing and the TLDR tool to profile CpG methylation of transposable elements in human tissues and tumors.

Creating Standards for Evaluating Tumour Subclonal Reconstruction

This study develops quantitative metrics and simulated datasets to evaluate subclonal reconstruction methods in tumours.

Arginine to glutamine mutation in olfactomedin-like 3 (OLFML3) is a candidate for severe goniodysgenesis and glaucoma in the Border Collie dog breed.

The paper identifies a missense variant in OLFML3 as a candidate for severe goniodysgenesis and glaucoma in Border Collies.

LINE-1 retrotransposition impacts the genome of human pre implantation embryos and extraembryonic tissues

This study shows LINE-1 retrotransposition occurs in human pre-implantation embryos and extraembryonic tissues, impacting gene expression and potentially contributing to genomic variation.

Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection

The paper benchmarks somatic structural variant detection methods using synthetic tumors and crowd-sourced submissions, finding that ensembles do not always outperform individual methods.

Human-specific NOTCH-like genes in a region linked to neurodevelopmental disorders affect cortical neurogenesis

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.

Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection

The paper quantifies germline leakage in somatic SNV detection across 259 datasets and introduces a tool to correct it, finding low leakage rates that can be further reduced with pre-filtering.