Epigenomics and gene regulation in mammalian social systems

TP Guerrero, J Fickel, S Benhaiem, A Weyrich - Current Zoology, 2020 - academic.oup.com
Social epigenomics is a new field of research that studies how the social environment
shapes the epigenome and how in turn the epigenome modulates behavior. We focus on …

Epigenome-augmented eQTL-hotspots reveal genome-wide transcriptional programs in 36 human tissues

H Liu, Q Chen, J Guo, Y Zhou, Z You… - Briefings in …, 2024 - academic.oup.com
Expression quantitative trait loci (eQTLs) are used to inform the mechanisms of
transcriptional regulation in eukaryotic cells. However, the specificity of genome-wide eQTL …

Genome-wide DNA methylation profile of peripheral blood lymphocytes from subjects with nonsteroidal anti-inflammatory drug-induced respiratory diseases

JU Lee, HS Chang, MK Kim, S Park… - Pharmacogenetics …, 2022 - journals.lww.com
Background Significant changes in CpG methylation have been identified in nasal polyps,
which are the main targets of nonsteroidal anti-inflammatory drug-exacerbated respiratory …

[PDF][PDF] Estimating cell type-specific differential expression using deconvolution

MK Jaakkola, LL Elo - Briefings in bioinformatics, 2022 - academic.oup.com
When differentially expressed genes are detected from samples containing different types of
cells, only a very coarse overview without any cell type-specific information is obtained …

swCAM: estimation of subtype-specific expressions in individual samples with unsupervised sample-wise deconvolution

L Chen, CT Wu, CH Lin, R Dai, C Liu, R Clarke… - …, 2022 - academic.oup.com
Motivation Complex biological tissues are often a heterogeneous mixture of several
molecularly distinct cell subtypes. Both subtype compositions and subtype-specific (STS) …

Dynamics and consequences of nutrition-related microbial dysbiosis in early life: study protocol of the VITERBI GUT project

J Tamarelle, MM Creze, V Savathdy, S Phonekeo… - Frontiers in …, 2023 - frontiersin.org
Introduction Early life under-and overnutrition (jointly termed malnutrition) is increasingly
recognized as an important risk factor for adult obesity and metabolic syndrome, a diet …

Multimodal joint deconvolution and integrative signature selection in proteomics

Y Pan, X Wang, J Sun, C Liu, J Peng, Q Li - Communications Biology, 2024 - nature.com
Deconvolution is an efficient approach for detecting cell-type-specific (cs) transcriptomic
signals without cellular segmentation. However, this type of methods may require a …

Identification of cell-specific epigenetic patterns associated with chondroitin sulfate treatment response in an endemic arthritis, Kashin-Beck disease

B Cheng, C Wu, W Wei, H Niu, Y Wen, C Li… - Bone & Joint …, 2024 - boneandjoint.org.uk
Identification of cell-specific epigenetic patterns associated with chondroitin sulfate treatment
response in an endemic arthrit Page 1 Identification of cell-specific epigenetic patterns …

[HTML][HTML] Methods in DNA methylation array dataset analysis: A review

K Sahoo, V Sundararajan - Computational and Structural Biotechnology …, 2024 - Elsevier
Understanding the intricate relationships between gene expression levels and epigenetic
modifications in a genome is crucial to comprehending the pathogenic mechanisms of many …

CAM3. 0: determining cell type composition and expression from bulk tissues with fully unsupervised deconvolution

CT Wu, D Du, L Chen, R Dai, C Liu, G Yu… - …, 2024 - academic.oup.com
Motivation Complex tissues are dynamic ecosystems consisting of molecularly distinct yet
interacting cell types. Computational deconvolution aims to dissect bulk tissue data into cell …