Eleven grand challenges in single-cell data science

D Lähnemann, J Köster, E Szczurek, DJ McCarthy… - Genome biology, 2020 - Springer
The recent boom in microfluidics and combinatorial indexing strategies, combined with low
sequencing costs, has empowered single-cell sequencing technology. Thousands—or even …

Single-cell transcriptome analysis in plants: advances and challenges

R Shaw, X Tian, J Xu - Molecular Plant, 2021 - cell.com
The rapid and enthusiastic adoption of single-cell RNA sequencing (scRNA-seq) has
demonstrated that this technology is far more than just another way to perform transcriptome …

Cellular and transcriptional dynamics of human neutrophils at steady state and upon stress

E Montaldo, E Lusito, V Bianchessi, N Caronni… - Nature …, 2022 - nature.com
Traditionally viewed as poorly plastic, neutrophils are now recognized as functionally
diverse; however, the extent and determinants of neutrophil heterogeneity in humans remain …

[HTML][HTML] DoubletDecon: deconvoluting doublets from single-cell RNA-sequencing data

EAK DePasquale, DJ Schnell, PJ Van Camp… - Cell reports, 2019 - cell.com
Methods for single-cell RNA sequencing (scRNA-seq) have greatly advanced in recent
years. While droplet-and well-based methods have increased the capture frequency of cells …

In situ mapping identifies distinct vascular niches for myelopoiesis

J Zhang, Q Wu, CB Johnson, G Pham, JM Kinder… - Nature, 2021 - nature.com
In contrast to nearly all other tissues, the anatomy of cell differentiation in the bone marrow
remains unknown. This is owing to a lack of strategies for examining myelopoiesis—the …

[HTML][HTML] PKM2-dependent metabolic skewing of hepatic Th17 cells regulates pathogenesis of non-alcoholic fatty liver disease

ME Moreno-Fernandez, DA Giles, JR Oates, CC Chan… - Cell metabolism, 2021 - cell.com
Emerging evidence suggests a key contribution to non-alcoholic fatty liver disease (NAFLD)
pathogenesis by Th17 cells. The pathogenic characteristics and mechanisms of hepatic …

Guided construction of single cell reference for human and mouse lung

M Guo, MP Morley, C Jiang, Y Wu, G Li, Y Du… - Nature …, 2023 - nature.com
Accurate cell type identification is a key and rate-limiting step in single-cell data analysis.
Single-cell references with comprehensive cell types, reproducible and functionally …

Quantifying the effect of experimental perturbations at single-cell resolution

DB Burkhardt, JS Stanley III, A Tong, AL Perdigoto… - Nature …, 2021 - nature.com
Current methods for comparing single-cell RNA sequencing datasets collected in multiple
conditions focus on discrete regions of the transcriptional state space, such as clusters of …

Aging human hematopoietic stem cells manifest profound epigenetic reprogramming of enhancers that may predispose to leukemia

ER Adelman, HT Huang, A Roisman, A Olsson… - Cancer discovery, 2019 - AACR
Aging is associated with functional decline of hematopoietic stem cells (HSC) as well as an
increased risk of myeloid malignancies. We performed an integrative characterization of …

An immunophenotype-coupled transcriptomic atlas of human hematopoietic progenitors

X Zhang, B Song, MJ Carlino, G Li, K Ferchen… - Nature …, 2024 - nature.com
Abstract Analysis of the human hematopoietic progenitor compartment is being transformed
by single-cell multimodal approaches. Cellular indexing of transcriptomes and epitopes by …