Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses

SJ Sun, R Aguirre-Gamboa, LCJ de Bree, J Sanz… - Immunity, 2024 - cell.com
Summary Although the Bacille-Calmette-Guérin (BCG) vaccine is used to prevent
tuberculosis, it also offers protection against a diverse range of non-mycobacterial infections …

Super‐Enhancer Driven LIF/LIFR‐STAT3‐SOX2 Regulatory Feedback Loop Promotes Cancer Stemness in Head and Neck Squamous Cell Carcinoma

J Li, Y Wang, Z Wang, Y Wei, P Diao, Y Wu… - Advanced …, 2024 - Wiley Online Library
Super‐enhancers (SEs) have been recognized as key epigenetic regulators underlying
cancer stemness and malignant traits by aberrant transcriptional control and promising …

[HTML][HTML] Decreased voluntary alcohol intake and ventral striatal epigenetic and transcriptional remodeling in male Acss2 KO mice

G Egervari, G Donahue, NAQ Cardé, DC Alexander… - …, 2025 - Elsevier
Metabolic-epigenetic interactions are emerging as key pathways in regulating alcohol-
related transcriptional changes in the brain. Recently, we have shown that this is mediated …

Annotation and assessment of functional variants in regulatory regions using epigenomic data in farm animals

R Ma, R Kuang, J Zhang, J Sun, Y Xu, X Zhou, Z Han… - bioRxiv, 2024 - biorxiv.org
Background Understanding the functional impact of genetic variants is essential for
advancing animal genomics and improving livestock breeding. Variants that disrupt …

Arid1a-dependent canonical BAF complex suppresses inflammatory programs to drive efficient Germinal Center B cell responses

A Abraham, D Samaniego-Castruita, I Han… - Nature …, 2024 - nature.com
Abstract The mammalian Brg1/Brm-associated factor (BAF) complexes are major regulators
of nucleosomal remodeling that are commonly mutated in several cancers, including …

Differences in maternal diet fiber content influence patterns of gene expression and chromatin accessibility in fetuses and piglets

S Chalabi, L Loonen, J Boekhorst, H Li, L Fang… - Genomics, 2025 - Elsevier
This study investigates the impact of maternal gestation diets with varying fiber contents on
gene expression and chromatin accessibility in fetuses and piglets fed a low fiber diet post …

Dissecting Regulatory Non-Coding Heart Disease GWAS Loci with High-Resolution 3D Chromatin Interactions Reveals Causal Genes with Pathophysiological …

R Gill, D Lu, I Eres, J Lu, J Cui, ZJ Yu, T Yamawaki… - bioRxiv, 2024 - biorxiv.org
Heart failure is caused in part by cardiac remodeling processes that include the death of
cardiac myocytes and their replacement by cardiac fibroblasts. We hypothesized that these …

IVEA: an integrative variational Bayesian inference method for predicting enhancer–gene regulatory interactions

Y Kimura, Y Ono, K Katayama… - Bioinformatics Advances, 2024 - academic.oup.com
Motivation Enhancers play critical roles in cell-type-specific transcriptional control. Despite
the identification of thousands of candidate enhancers, unravelling their regulatory …