Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

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 …

Doublet identification in single-cell sequencing data using scDblFinder

PL Germain, A Lun, CG Meixide, W Macnair… - …, 2022 - pmc.ncbi.nlm.nih.gov
Doublets are prevalent in single-cell sequencing data and can lead to artifactual findings. A
number of strategies have therefore been proposed to detect them. Building on the strengths …

Multimodal single cell sequencing implicates chromatin accessibility and genetic background in diabetic kidney disease progression

PC Wilson, Y Muto, H Wu, A Karihaloo… - Nature …, 2022 - nature.com
The proximal tubule is a key regulator of kidney function and glucose metabolism. Diabetic
kidney disease leads to proximal tubule injury and changes in chromatin accessibility that …

Single-cell analysis of chromatin accessibility in the adult mouse brain

S Zu, YE Li, K Wang, EJ Armand, S Mamde, ML Amaral… - Nature, 2023 - nature.com
Recent advances in single-cell technologies have led to the discovery of thousands of brain
cell types; however, our understanding of the gene regulatory programs in these cell types is …

Mapping cells through time and space with moscot

D Klein, G Palla, M Lange, M Klein, Z Piran, M Gander… - Nature, 2025 - nature.com
Single-cell genomic technologies enable the multimodal profiling of millions of cells across
temporal and spatial dimensions. However, experimental limitations hinder the …

Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease

AB Meier, D Zawada, MT De Angelis, LD Martens… - Nature …, 2023 - nature.com
The epicardium, the mesothelial envelope of the vertebrate heart, is the source of multiple
cardiac cell lineages during embryonic development and provides signals that are essential …

Genetic risk converges on regulatory networks mediating early type 2 diabetes

JT Walker, DC Saunders, V Rai, HH Chen, P Orchard… - Nature, 2023 - pmc.ncbi.nlm.nih.gov
Type 2 diabetes mellitus (T2D), a major cause of worldwide morbidity and mortality, is
characterized by dysfunction of insulin-producing pancreatic islet β cells1, 2. T2D genome …

Profound phenotypic and epigenetic heterogeneity of the HIV-1-infected CD4+ T cell reservoir

VH Wu, JML Nordin, S Nguyen, J Joy, F Mampe… - Nature …, 2023 - nature.com
Understanding the complexity of the long-lived HIV reservoir during antiretroviral therapy
(ART) remains a considerable impediment in research towards a cure for HIV. To address …

Calorie restriction increases insulin sensitivity to promote beta cell homeostasis and longevity in mice

C Dos Santos, A Cambraia, S Shrestha… - Nature …, 2024 - nature.com
Caloric restriction (CR) can extend the organism life-and health-span by improving glucose
homeostasis. How CR affects the structure-function of pancreatic beta cells remains …