Causality-enriched epigenetic age uncouples damage and adaptation
Abstract Machine learning models based on DNA methylation data can predict biological
age but often lack causal insights. By harnessing large-scale genetic data through …
age but often lack causal insights. By harnessing large-scale genetic data through …
Transcription factor expression repertoire basis for epigenetic and transcriptional subtypes of colorectal cancers
YR Bhandari, V Krishna, R Powers… - Proceedings of the …, 2023 - National Acad Sciences
Colorectal cancers (CRCs) form a heterogenous group classified into epigenetic and
transcriptional subtypes. The basis for the epigenetic subtypes, exemplified by varying …
transcriptional subtypes. The basis for the epigenetic subtypes, exemplified by varying …
Deep neural networks with knockoff features identify nonlinear causal relations and estimate effect sizes in complex biological systems
Background Learning the causal structure helps identify risk factors, disease mechanisms,
and candidate therapeutics for complex diseases. However, although complex biological …
and candidate therapeutics for complex diseases. However, although complex biological …
A role for SETD2 loss in tumorigenesis through DNA methylation dysregulation
Abstract SETD2-dependent H3 Lysine-36 trimethylation (H3K36me3) has been recently
linked to the deposition of de-novo DNA methylation. SETD2 is frequently mutated in cancer …
linked to the deposition of de-novo DNA methylation. SETD2 is frequently mutated in cancer …
[HTML][HTML] Machine and deep learning methods for predicting 3D genome organization
BPG Wall, M Nguyen, JC Harrell, MG Dozmorov - ArXiv, 2024 - ncbi.nlm.nih.gov
Abstract Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter
interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B …
interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B …
Genome‐wide methylomic regulation of multiscale gene networks in Alzheimer's disease
INTRODUCTION Recent studies revealed the association of abnormal methylomic changes
with Alzheimer's disease (AD) but there is a lack of systematic study of the impact of …
with Alzheimer's disease (AD) but there is a lack of systematic study of the impact of …
Expression quantitative trait methylation analysis reveals methylomic associations with gene expression in childhood asthma
Background Nasal (airway) epithelial methylation profiles have been associated with
asthma, but the effects of such profiles on expression of distant cis-genes are largely …
asthma, but the effects of such profiles on expression of distant cis-genes are largely …
Genomic effect of DNA methylation on gene expression in colorectal cancer
J Hong, JK Rhee - Biology, 2022 - mdpi.com
Simple Summary Abnormal DNA methylation is known to regulate gene expression, and its
features have been frequently observed in colorectal cancer (CRC) patients. In addition …
features have been frequently observed in colorectal cancer (CRC) patients. In addition …
[PDF][PDF] Causal epigenetic age uncouples damage and adaptation
Machine learning models based on DNA methylation can be used to predict the age of
biological 17 samples, but their interpretability is limited due to the lack of causal inferences …
biological 17 samples, but their interpretability is limited due to the lack of causal inferences …
Whole genome methylation sequencing in blood identifies extensive differential DNA methylation in late‐onset dementia due to Alzheimer's disease
INTRODUCTION DNA microarray‐based studies report differentially methylated positions
(DMPs) in blood between late‐onset dementia due to Alzheimer's disease (AD) and …
(DMPs) in blood between late‐onset dementia due to Alzheimer's disease (AD) and …