[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 …

Neuronal cell-type classification: challenges, opportunities and the path forward

H Zeng, JR Sanes - Nature Reviews Neuroscience, 2017 - nature.com
Neurons have diverse molecular, morphological, connectional and functional properties. We
believe that the only realistic way to manage this complexity—and thereby pave the way for …

[HTML][HTML] Comprehensive integration of single-cell data

T Stuart, A Butler, P Hoffman, C Hafemeister… - cell, 2019 - cell.com
Single-cell transcriptomics has transformed our ability to characterize cell states, but deep
biological understanding requires more than a taxonomic listing of clusters. As new methods …

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression

C Hafemeister, R Satija - Genome biology, 2019 - Springer
Single-cell RNA-seq (scRNA-seq) data exhibits significant cell-to-cell variation due to
technical factors, including the number of molecules detected in each cell, which can …

Integrating single-cell transcriptomic data across different conditions, technologies, and species

A Butler, P Hoffman, P Smibert, E Papalexi… - Nature …, 2018 - nature.com
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied
to experiments representing a single condition, technology, or species to discover and …

[HTML][HTML] A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain

Z Yao, CTJ van Velthoven, M Kunst, M Zhang… - Nature, 2023 - nature.com
The mammalian brain consists of millions to billions of cells that are organized into many cell
types with specific spatial distribution patterns and structural and functional properties …

[HTML][HTML] Molecular architecture of the mouse nervous system

A Zeisel, H Hochgerner, P Lönnerberg, A Johnsson… - Cell, 2018 - cell.com
The mammalian nervous system executes complex behaviors controlled by specialized,
precisely positioned, and interacting cell types. Here, we used RNA sequencing of half a …

Non-neuronal expression of SARS-CoV-2 entry genes in the olfactory system suggests mechanisms underlying COVID-19-associated anosmia

DH Brann, T Tsukahara, C Weinreb, M Lipovsek… - Science …, 2020 - science.org
Altered olfactory function is a common symptom of COVID-19, but its etiology is unknown. A
key question is whether SARS-CoV-2 (CoV-2)–the causal agent in COVID-19–affects …

Spatially organized multicellular immune hubs in human colorectal cancer

K Pelka, M Hofree, JH Chen, S Sarkizova, JD Pirl… - Cell, 2021 - cell.com
Immune responses to cancer are highly variable, with mismatch repair-deficient (MMRd)
tumors exhibiting more anti-tumor immunity than mismatch repair-proficient (MMRp) tumors …

Deep generative modeling for single-cell transcriptomics

R Lopez, J Regier, MB Cole, MI Jordan, N Yosef - Nature methods, 2018 - nature.com
Single-cell transcriptome measurements can reveal unexplored biological diversity, but they
suffer from technical noise and bias that must be modeled to account for the resulting …