Clinical and therapeutic relevance of cancer-associated fibroblasts

Y Chen, KM McAndrews, R Kalluri - Nature reviews Clinical oncology, 2021 - nature.com
Cancer-associated fibroblasts (CAFs) found in primary and metastatic tumours are highly
versatile, plastic and resilient cells that are actively involved in cancer progression through …

Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

Dissection of artifactual and confounding glial signatures by single-cell sequencing of mouse and human brain

SE Marsh, AJ Walker, T Kamath, L Dissing-Olesen… - Nature …, 2022 - nature.com
A key aspect of nearly all single-cell sequencing experiments is dissociation of intact tissues
into single-cell suspensions. While many protocols have been optimized for optimal cell …

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

SK Longo, MG Guo, AL Ji, PA Khavari - Nature Reviews Genetics, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) identifies cell subpopulations within tissue but
does not capture their spatial distribution nor reveal local networks of intercellular …

Identifying phenotype-associated subpopulations by integrating bulk and single-cell sequencing data

D Sun, X Guan, AE Moran, LY Wu, DZ Qian… - Nature …, 2022 - nature.com
Single-cell RNA sequencing (scRNA-seq) distinguishes cell types, states and lineages
within the context of heterogeneous tissues. However, current single-cell data cannot …

Differential abundance testing on single-cell data using k-nearest neighbor graphs

E Dann, NC Henderson, SA Teichmann… - Nature …, 2022 - nature.com
Current computational workflows for comparative analyses of single-cell datasets typically
use discrete clusters as input when testing for differential abundance among experimental …

Single-cell multiomics: technologies and data analysis methods

J Lee, DY Hyeon, D Hwang - Experimental & Molecular Medicine, 2020 - nature.com
Advances in single-cell isolation and barcoding technologies offer unprecedented
opportunities to profile DNA, mRNA, and proteins at a single-cell resolution. Recently, bulk …

Direct cell reprogramming: approaches, mechanisms and progress

H Wang, Y Yang, J Liu, L Qian - Nature Reviews Molecular Cell Biology, 2021 - nature.com
The reprogramming of somatic cells with defined factors, which converts cells from one
lineage into cells of another, has greatly reshaped our traditional views on cell identity and …

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 …

The triumphs and limitations of computational methods for scRNA-seq

PV Kharchenko - Nature methods, 2021 - nature.com
The rapid progress of protocols for sequencing single-cell transcriptomes over the past
decade has been accompanied by equally impressive advances in the computational …