A review of integrative imputation for multi-omics datasets

M Song, J Greenbaum, J Luttrell IV, W Zhou… - Frontiers in …, 2020 - frontiersin.org
Multi-omics studies, which explore the interactions between multiple types of biological
factors, have significant advantages over single-omics analysis for their ability to provide a …

Multi-omics approaches in immunological research

X Chu, B Zhang, VACM Koeken, MK Gupta… - Frontiers in …, 2021 - frontiersin.org
The immune system plays a vital role in health and disease, and is regulated through a
complex interactive network of many different immune cells and mediators. To understand …

Profiling epigenetic age in single cells

A Trapp, C Kerepesi, VN Gladyshev - Nature Aging, 2021 - nature.com
DNA methylation dynamics have emerged as a promising biomarker of mammalian aging,
with multivariate machine learning models ('epigenetic clocks') enabling measurement of …

EpiScanpy: integrated single-cell epigenomic analysis

A Danese, ML Richter, K Chaichoompu… - Nature …, 2021 - nature.com
EpiScanpy is a toolkit for the analysis of single-cell epigenomic data, namely single-cell
DNA methylation and single-cell ATAC-seq data. To address the modality specific …

Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single‐cell analysis

J Castillo‐Fernandez, E Herrera‐Puerta… - Aging …, 2020 - Wiley Online Library
Advancing maternal age causes a progressive reduction in fertility. The decline in
developmental competence of the oocyte with age is likely to be a consequence of multiple …

Deep learning in single-cell analysis

D Molho, J Ding, W Tang, Z Li, H Wen, Y Wang… - ACM Transactions on …, 2024 - dl.acm.org
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of
data generated by single-cell technologies are high dimensional, sparse, and …

Cell types in environmental epigenetic studies: biological and epidemiological frameworks

KA Campbell, JA Colacino, SK Park… - Current environmental …, 2020 - Springer
Abstract Purpose of Review This article introduces the roles of perinatal DNA methylation in
human health and disease, highlights the challenges of tissue and cellular heterogeneity to …

CpG Transformer for imputation of single-cell methylomes

G De Waele, J Clauwaert, G Menschaert… - …, 2022 - academic.oup.com
Motivation The adoption of current single-cell DNA methylation sequencing protocols is
hindered by incomplete coverage, outlining the need for effective imputation techniques …

Experimental and bioinformatic approaches to studying DNA methylation in cancer

A Merkel, M Esteller - Cancers, 2022 - mdpi.com
Simple Summary Aberrations of normal DNA methylation patterns are observed in many
cancers and are associated with chromatin alterations, changes in gene expression and …

Estimating genome-wide DNA methylation heterogeneity with methylation patterns

PY Lin, YT Chang, YC Huang, PY Chen - Epigenetics & Chromatin, 2023 - Springer
Background In a heterogeneous population of cells, individual cells can behave differently
and respond variably to the environment. This cellular diversity can be assessed by …