David R. Stanford

A new epigenetic framework for DNA methylation, hydroxymethylation, and gene expression during brain aging.

The paper shows that cell identity and regulatory logic are preserved during brain aging, but cell-type-specific changes occur in DNA modifications and gene expression.

Functional and molecular profiles of the neuroretina and retinal pigmented epithelium-choroid in response to aging and Nrf2 deletion

The paper examines how aging and Nrf2 deletion affect visual function and gene expression in the retina and RPE-choroid, finding exacerbated age-related declines in Nrf2-deficient mice.

Oligodendrocytes show enriched expression of amyloid precursor protein and GABA B receptor isoform 1a

The paper shows GABABR1a is most expressed in oligodendrocytes and APP is most expressed in oligodendrocytes among five brain cell types.

Methylation Array Signals are Predictive of Chronological Age Without Bisulfite Conversion

The paper shows that non-methylation factors cause age-predictive pseudomethylation signals in methylation arrays, affecting epigenetic clocks.

Late-life short-term dietary restriction ameliorates intestinal stem cell function and impacts intestinal stem cell DNA methylation

This study shows that late-life short-term dietary restriction improves intestinal stem cell function and alters DNA methylation in aged mice.

Differential usage of DNA modifications in neurons, astrocytes, and microglia

The paper identifies differential DNA modifications across CNS cell types and their relationship with gene expression using a novel mouse model and epigenomic sequencing.

Differential regulation of mouse hippocampal gene expression sex differences by chromosomal content and gonadal sex

The paper investigates how chromosomal content and gonadal sex influence gene expression and DNA modification patterns in mouse hippocampi, revealing sex chromosome-specific regulatory effects.

Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia

The paper introduces a NuTRAP method to isolate RNA and DNA from specific CNS cell types, revealing cell type-specific epigenetic and transcriptomic differences in microglia and astrocytes.

Early life DNA methylation profiles are indicative of age-related transcriptome changes

The paper shows that early life DNA methylation patterns predict age-related transcriptome changes in mice, supporting the developmental origins of disease hypothesis.

Caloric restriction mitigates age-associated hippocampal differential CG and non-CG methylation.

This study shows that caloric restriction reduces age-related DNA methylation changes in the hippocampus of mice, including both CG and non-CG sites, and introduces CR-specific methylation patterns linked to gene expression changes.

Sexually divergent DNA methylation programs with hippocampal aging

This study identifies sexually divergent DNA methylation changes in mouse and human hippocampus with aging, revealing sex as a key factor in epigenomic aging.