Thomas M. Stubbs

A novel framework to build saliva-based DNA methylation biomarkers: quantifying systemic chronic inflammation as a case study

This paper introduces a framework to build saliva-based DNA methylation biomarkers, demonstrating a new epigenetic clock (InflammAge) that quantifies systemic chronic inflammation and outperforms CRP in several health outcomes.

Multi-omic rejuvenation of human cells by maturation phase transient reprogramming

This paper introduces a method to rejuvenate human fibroblasts by transient reprogramming to the maturation phase of iPSCs, followed by recovery of fibroblast identity, resulting in significant rejuvenation of transcriptome, epigenome, and functional markers.

Transcriptome and epigenome diversity and plasticity of muscle stem cells following transplantation

This study identifies molecular differences between extraocular and limb muscle stem cells, showing that EOM MuSCs reprogram their transcriptome and epigenome after transplantation, with some genes resisting engraftment.

Ageing affects DNA methylation drift and transcriptional cell-to-cell variability in muscle stem cells

This study shows that ageing increases transcriptional heterogeneity and DNA methylation drift in muscle stem cells, disrupting transcriptional networks and stem cell function.

Screening for genes that accelerate the epigenetic ageing clock in humans reveals a role for the H3K36 methyltransferase NSD1

The paper screens for genes affecting epigenetic age acceleration in humans and identifies NSD1 as a key regulator of the epigenetic ageing clock.

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

This paper introduces scNMT-seq, a method for joint profiling of chromatin accessibility, DNA methylation, and transcription in single cells, and validates it in differentiating mouse embryonic stem cells.

Multi-Tissue DNA Methylation Age Predictor In Mouse

The paper develops a DNA methylation age predictor for mice, showing it accurately measures biological age and responds to interventions like ovariectomy and diet.