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 …

Vascular endothelial cell development and diversity

E Trimm, K Red-Horse - Nature Reviews Cardiology, 2023 - nature.com
Vascular endothelial cells form the inner layer of blood vessels where they have a key role
in the development and maintenance of the functional circulatory system and provide …

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …

[HTML][HTML] A single-cell atlas of chromatin accessibility in the human genome

K Zhang, JD Hocker, M Miller, X Hou, J Chiou… - Cell, 2021 - cell.com
Current catalogs of regulatory sequences in the human genome are still incomplete and lack
cell type resolution. To profile the activity of gene regulatory elements in diverse cell types …

A human cell atlas of fetal gene expression

J Cao, DR O'day, HA Pliner, PD Kingsley, M Deng… - Science, 2020 - science.org
INTRODUCTION A reference atlas of human cell types is a major goal for the field. Here, we
set out to generate single-cell atlases of both gene expression (this study) and chromatin …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …

Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus

DJ Downes, AR Cross, P Hua, N Roberts… - Nature …, 2021 - nature.com
The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19)
pandemic has caused millions of deaths worldwide. Genome-wide association studies …

Epigenetic encoding, heritability and plasticity of glioma transcriptional cell states

R Chaligne, F Gaiti, D Silverbush, JS Schiffman… - Nature …, 2021 - nature.com
Single-cell RNA sequencing has revealed extensive transcriptional cell state diversity in
cancer, often observed independently of genetic heterogeneity, raising the central question …

Systematic reconstruction of cellular trajectories across mouse embryogenesis

C Qiu, J Cao, BK Martin, T Li, IC Welsh, S Srivatsan… - Nature …, 2022 - nature.com
Mammalian embryogenesis is characterized by rapid cellular proliferation and
diversification. Within a few weeks, a single-cell zygote gives rise to millions of cells …

Single-cell roadmap of human gonadal development

L Garcia-Alonso, V Lorenzi, CI Mazzeo… - Nature, 2022 - nature.com
Gonadal development is a complex process that involves sex determination followed by
divergent maturation into either testes or ovaries. Historically, limited tissue accessibility, a …