[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 …

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 …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Multi-omics single-cell data integration and regulatory inference with graph-linked embedding

ZJ Cao, G Gao - Nature Biotechnology, 2022 - nature.com
Despite the emergence of experimental methods for simultaneous measurement of multiple
omics modalities in single cells, most single-cell datasets include only one modality. A major …

Comparative cellular analysis of motor cortex in human, marmoset and mouse

TE Bakken, NL Jorstad, Q Hu, BB Lake, W Tian… - Nature, 2021 - nature.com
The primary motor cortex (M1) is essential for voluntary fine-motor control and is functionally
conserved across mammals. Here, using high-throughput transcriptomic and epigenomic …

A multimodal cell census and atlas of the mammalian primary motor cortex

Principal manuscript editors, Analysis coordination… - Nature, 2021 - nature.com
Here we report the generation of a multimodal cell census and atlas of the mammalian
primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network …

Molecularly defined and spatially resolved cell atlas of the whole mouse brain

M Zhang, X Pan, W Jung, AR Halpern, SW Eichhorn… - Nature, 2023 - nature.com
In mammalian brains, millions to billions of cells form complex interaction networks to enable
a wide range of functions. The enormous diversity and intricate organization of cells have …

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

R Fang, C Xia, JL Close, M Zhang, J He, Z Huang… - Science, 2022 - science.org
The human cerebral cortex has tremendous cellular diversity. How different cell types are
organized in the human cortex and how cellular organization varies across species remain …

[HTML][HTML] A single-cell atlas of chromatin accessibility in the human genome

K Zhang, JD Hocker, M Miller, X Hou, J Chiou… - Cell, 2021 - cell.com
Current catalogs of regulatory sequences in the human genome are still incomplete and lack
cell type resolution. To profile the activity of gene regulatory elements in diverse cell types …

Computational principles and challenges in single-cell data integration

R Argelaguet, ASE Cuomo, O Stegle… - Nature biotechnology, 2021 - nature.com
The development of single-cell multimodal assays provides a powerful tool for investigating
multiple dimensions of cellular heterogeneity, enabling new insights into development …