[HTML][HTML] What is a cell type and how to define it?

H Zeng - Cell, 2022 - cell.com
Cell types are the basic functional units of an organism. Cell types exhibit diverse
phenotypic properties at multiple levels, making them challenging to define, categorize, and …

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 …

A reference cell tree will serve science better than a reference cell atlas

S Domcke, J Shendure - Cell, 2023 - cell.com
Single-cell biology is facing a crisis of sorts. Vast numbers of single-cell molecular profiles
are being generated, clustered and annotated. However, this is overwhelmingly ad hoc, and …

muscat detects subpopulation-specific state transitions from multi-sample multi-condition single-cell transcriptomics data

HL Crowell, C Soneson, PL Germain, D Calini… - Nature …, 2020 - nature.com
Single-cell RNA sequencing (scRNA-seq) has become an empowering technology to profile
the transcriptomes of individual cells on a large scale. Early analyses of differential …

Rethinking organoid technology through bioengineering

E Garreta, RD Kamm, SM Chuva de Sousa Lopes… - Nature materials, 2021 - nature.com
In recent years considerable progress has been made in the development of faithful
procedures for the differentiation of human pluripotent stem cells (hPSCs). An important step …

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

ZA Clarke, TS Andrews, J Atif, D Pouyabahar… - Nature protocols, 2021 - nature.com
Single-cell transcriptomics can profile thousands of cells in a single experiment and identify
novel cell types, states and dynamics in a wide variety of tissues and organisms. Standard …

The evolving concept of cell identity in the single cell era

SA Morris - Development, 2019 - journals.biologists.com
Fueled by recent advances in single cell biology, we are moving away from qualitative and
undersampled assessments of cell identity, toward building quantitative, high-resolution cell …

Vision, challenges and opportunities for a Plant Cell Atlas

SG Jha, AT Borowsky, BJ Cole, N Fahlgren, A Farmer… - Elife, 2021 - elifesciences.org
With growing populations and pressing environmental problems, future economies will be
increasingly plant-based. Now is the time to reimagine plant science as a critical component …

A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans

Y Li, S Chen, W Liu, D Zhao, Y Gao, S Hu, H Liu… - Nature …, 2024 - nature.com
Invariant cell lineage in C. elegans enables spatiotemporal resolution of transcriptional
regulatory mechanisms controlling the fate of each cell. Here, we develop RAPCAT (Robust …

Defining the variety of cell types in developing and adult human kidneys by single-cell RNA sequencing

A Schumacher, MB Rookmaaker, JA Joles… - NPJ Regenerative …, 2021 - nature.com
The kidney is among the most complex organs in terms of the variety of cell types. The
cellular complexity of human kidneys is not fully unraveled and this challenge is further …