Aspirin Challenge–Induced Genome-Wide DNA Methylation Profile of Peripheral Blood Lymphocytes in Aspirin-Exacerbated Respiratory Disease

JU Lee, HS Chang, JS Shim, MH Kim, YJ Cho… - DNA and Cell …, 2024 - liebertpub.com
Genetic variation and epigenetic factors are thought to contribute to the development of
hypersensitivity to aspirin. DNA methylation fluctuates dynamically throughout the day. To …

DESP demixes cell-state profiles from dynamic bulk molecular measurements

A Youssef, I Paul, M Crovella, A Emili - Cell Reports Methods, 2024 - cell.com
Understanding the dynamic expression of proteins and other key molecules driving
phenotypic remodeling in development and pathobiology has garnered widespread interest …

Chromatin-and nucleosome-associated features in liquid biopsy: implications for cancer biomarker discovery

L Penny, SC Main, SD De Michino… - Biochemistry and Cell …, 2024 - cdnsciencepub.com
Cell-free DNA (cfDNA) from the bloodstream has been studied for cancer biomarker
discovery, and chromatin-derived epigenetic features have come into the spotlight for their …

Epigenome-wide association study using prediagnostic bloods identifies new genomic regions associated with pancreatic cancer risk

DS Michaud, M Ruan, DC Koestler, D Pei… - JNCI Cancer …, 2020 - academic.oup.com
Background Epigenome-wide association studies using peripheral blood have identified
specific sites of DNA methylation associated with risk of various cancers and may hold …

[HTML][HTML] Transcriptomic profiling of whole blood in 22q11. 2 reciprocal copy number variants reveals that cell proportion highly impacts gene expression

A Lin, JK Forsyth, GD Hoftman, L Kushan-Wells… - Brain, behavior, & …, 2021 - Elsevier
Abstract 22q11. 2 reciprocal copy number variants (CNVs) offer a powerful quasi-
experimental “reverse-genetics” paradigm to elucidate how gene dosage (ie, deletions and …

LC-MS/MS profiling of post-transcriptional modifications in ginseng tRNA purified by a polysaccharase-aided extraction method

T Yan, K Hu, F Ren, Z Jiang - Biomolecules, 2020 - mdpi.com
Transfer RNAs (tRNAs) are the most heavily modified RNA species in life entities. Post-
transcriptional modifications severely impact the structure and function of tRNAs. To date …

Testing cell-type-specific mediation effects in genome-wide epigenetic studies

X Luo, J Schwartz, A Baccarelli… - Briefings in …, 2021 - academic.oup.com
Epigenome-wide mediation analysis aims to identify DNA methylation CpG sites that
mediate the causal effects of genetic/environmental exposures on health outcomes …

Role of chromatin modification and remodeling in stem cell regulation and meristem maintenance in Arabidopsis

S Singh, A Singh, A Singh, Mahima… - Journal of …, 2020 - academic.oup.com
In higher plants, pluripotent stem cells reside in the specialized microenvironment called
stem cell niches (SCNs) harbored at the shoot apical meristem (SAM) and root apical …

[HTML][HTML] regionalpcs: improved discovery of DNA methylation associations with complex traits

T Eulalio, MW Sun, O Gevaert, MD Greicius, TJ Montine… - bioRxiv, 2024 - ncbi.nlm.nih.gov
We have developed the regional principal components (rPCs) method, a novel approach for
summarizing gene-level methylation. rPCs address the challenge of deciphering complex …

scDeconv: an R package to deconvolve bulk DNA methylation data with scRNA-seq data and paired bulk RNA–DNA methylation data

Y Liu - Briefings in bioinformatics, 2022 - academic.oup.com
Many DNA methylation (DNAm) data are from tissues composed of various cell types, and
hence cell deconvolution methods are needed to infer their cell compositions accurately …