Characterizing cis-regulatory elements using single-cell epigenomics

S Preissl, KJ Gaulton, B Ren - Nature Reviews Genetics, 2023 - nature.com
Cell type-specific gene expression patterns and dynamics during development or in disease
are controlled by cis-regulatory elements (CREs), such as promoters and enhancers …

[HTML][HTML] Applications of single-cell RNA sequencing in drug discovery and development

B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …

[HTML][HTML] An integrated cell atlas of the lung in health and disease

L Sikkema, C Ramírez-Suástegui, DC Strobl… - Nature Medicine, 2023 - nature.com
Single-cell technologies have transformed our understanding of human tissues. Yet, studies
typically capture only a limited number of donors and disagree on cell type definitions …

[HTML][HTML] Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue …

D Adlam, TE Berrandou, A Georges, CP Nelson… - Nature Genetics, 2023 - nature.com
Spontaneous coronary artery dissection (SCAD) is an understudied cause of myocardial
infarction primarily affecting women. It is not known to what extent SCAD is genetically …

Molecular and cellular evolution of the primate dorsolateral prefrontal cortex

S Ma, M Skarica, Q Li, C Xu, RD Risgaard… - Science, 2022 - science.org
The granular dorsolateral prefrontal cortex (dlPFC) is an evolutionary specialization of
primates that is centrally involved in cognition. We assessed more than 600,000 single …

[HTML][HTML] A fast, scalable and versatile tool for analysis of single-cell omics data

K Zhang, NR Zemke, EJ Armand, B Ren - Nature Methods, 2024 - nature.com
Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …

[HTML][HTML] Chitosan/Gamma-Alumina/Fe3O4@5-FU Nanostructures as Promising Nanocarriers: Physiochemical Characterization and Toxicity Activity

N Ajalli, M Pourmadadi, F Yazdian, H Rashedi… - Molecules, 2022 - mdpi.com
Today, cancer treatment is an important issue in the medical world due to the challenges
and side effects of ongoing treatment procedures. Current methods can be replaced with …

Interpreting non-coding disease-associated human variants using single-cell epigenomics

KJ Gaulton, S Preissl, B Ren - Nature Reviews Genetics, 2023 - nature.com
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence
variants in the human genome to common traits and diseases. However, translating this …

scBasset: sequence-based modeling of single-cell ATAC-seq using convolutional neural networks

H Yuan, DR Kelley - Nature Methods, 2022 - nature.com
Single-cell assay for transposase-accessible chromatin using sequencing (scATAC) shows
great promise for studying cellular heterogeneity in epigenetic landscapes, but there remain …

[HTML][HTML] Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition

JL Zhou, G de Guglielmo, AJ Ho, M Kallupi… - Nature …, 2023 - nature.com
The amygdala processes positive and negative valence and contributes to addiction, but the
cell-type-specific gene regulatory programs involved are unknown. We generated an atlas of …