Epigenetic patient stratification via contrastive machine learning refines hallmark biomarkers in minoritized children with asthma
Identifying and refining clinically significant patient stratification is a critical step toward
realizing the promise of precision medicine in asthma. Several peripheral blood hallmarks …
realizing the promise of precision medicine in asthma. Several peripheral blood hallmarks …
Leveraging epigenetic signatures to determine the cell-type of origin from long read sequencing data
DNA methylation differs across tissue-and cell-types with important implications for the
analysis of disease-associated differences in tissues such as blood. To uncover the …
analysis of disease-associated differences in tissues such as blood. To uncover the …
Identifying systematic variation at the single-cell level by leveraging low-resolution population-level data
A major limitation in single-cell genomics is a lack of ability to conduct cost-effective
population-level studies. As a result, much of the current research in single-cell genomics …
population-level studies. As a result, much of the current research in single-cell genomics …
A unified model for cell-type resolution genomics from heterogeneous omics data
The vast majority of population-scale genomic datasets collected to date consist of “bulk”
samples obtained from heterogeneous tissues, reflecting mixtures of different cell types. In …
samples obtained from heterogeneous tissues, reflecting mixtures of different cell types. In …
Nonlinear ridge regression improves cell-type-specific differential expression analysis
F Takeuchi, N Kato - BMC bioinformatics, 2021 - Springer
Background Epigenome-wide association studies (EWAS) and differential gene expression
analyses are generally performed on tissue samples, which consist of multiple cell types …
analyses are generally performed on tissue samples, which consist of multiple cell types …
A hierarchical Bayesian interaction model to estimate cell-type-specific methylation quantitative trait loci incorporating priors from cell-sorted bisulfite sequencing data
Background: Methylation Quantitative Trait Loci (meQTLs) are chromosomal regions that
harbor genetic variants affecting DNA methylation levels. The identification of meQTLs can …
harbor genetic variants affecting DNA methylation levels. The identification of meQTLs can …
Cell-Type Heterogeneity in DNA Methylation Studies: Statistical Methods and Guidelines
AE Teschendorff - Epigenetic Epidemiology, 2022 - Springer
Studies in epigenetic epidemiology have reported increasing numbers of epigenetic
biomarkers associated with a wide range of exposures and outcomes. Due to cost and …
biomarkers associated with a wide range of exposures and outcomes. Due to cost and …
The Effect of Model Directionality on Cell-Type-Specific Differential DNA Methylation Analysis
Calling differential methylation at a cell-type level from tissue-level bulk data is a
fundamental challenge in genomics that has recently received more attention. These studies …
fundamental challenge in genomics that has recently received more attention. These studies …
Low variability in the underlying cellular landscape adversely affects the performance of interaction-based approaches for conducting cell-specific analyses of DNA …
R Meier, E Nissen, DC Koestler - Statistical applications in genetics …, 2021 - degruyter.com
Statistical methods that allow for cell type specific DNA methylation (DNAm) analyses based
on bulk-tissue methylation data have great potential to improve our understanding of human …
on bulk-tissue methylation data have great potential to improve our understanding of human …
Modeling population size independent tissue epigenomes by ChIL‐seq with single thin sections
Recent advances in genome‐wide technologies have enabled analyses using small cell
numbers of even single cells. However, obtaining tissue epigenomes with cell‐type …
numbers of even single cells. However, obtaining tissue epigenomes with cell‐type …