Single-cell atlases: shared and tissue-specific cell types across human organs

R Elmentaite, C Domínguez Conde, L Yang… - Nature Reviews …, 2022 - nature.com
The development of single-cell and spatial transcriptomics methods was instrumental in the
conception of the Human Cell Atlas initiative, which aims to generate an integrated map of …

How many cell types are in the kidney and what do they do?

MS Balzer, T Rohacs, K Susztak - Annual review of physiology, 2022 - annualreviews.org
The kidney maintains electrolyte, water, and acid-base balance, eliminates foreign and
waste compounds, regulates blood pressure, and secretes hormones. There are at least 16 …

Epigenomic and transcriptomic analyses define core cell types, genes and targetable mechanisms for kidney disease

H Liu, T Doke, D Guo, X Sheng, Z Ma, J Park, HMT Vy… - Nature …, 2022 - nature.com
More than 800 million people suffer from kidney disease, yet the mechanism of kidney
dysfunction is poorly understood. In the present study, we define the genetic association with …

Single-cell analysis highlights differences in druggable pathways underlying adaptive or fibrotic kidney regeneration

MS Balzer, T Doke, YW Yang, DL Aldridge… - Nature …, 2022 - nature.com
The kidney has tremendous capacity to repair after acute injury, however, pathways guiding
adaptive and fibrotic repair are poorly understood. We developed a model of adaptive and …

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 integration in the age of million single-cell data

Z Miao, BD Humphreys, AP McMahon… - Nature Reviews …, 2021 - nature.com
An explosion in single-cell technologies has revealed a previously underappreciated
heterogeneity of cell types and novel cell-state associations with sex, disease, development …

Spatial charting of single-cell transcriptomes in tissues

R Wei, S He, S Bai, E Sei, M Hu, A Thompson… - Nature …, 2022 - nature.com
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but
cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile …

A guide to systems-level immunomics

L Bonaguro, J Schulte-Schrepping, T Ulas… - Nature …, 2022 - nature.com
The immune system is highly complex and distributed throughout an organism, with
hundreds to thousands of cell states existing in parallel with diverse molecular pathways …

Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments

X Sheng, Y Guan, Z Ma, J Wu, H Liu, C Qiu, S Vitale… - Nature …, 2021 - nature.com
The functional interpretation of genome-wide association studies (GWAS) is challenging due
to the cell-type-dependent influences of genetic variants. Here, we generated …

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 …