[HTML][HTML] Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

M Piwecka, N Rajewsky, A Rybak-Wolf - Nature Reviews Neurology, 2023 - nature.com
In the past decade, single-cell technologies have proliferated and improved from their
technically challenging beginnings to become common laboratory methods capable of …

[HTML][HTML] 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 …

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

B Li, W Zhang, C Guo, H Xu, L Li, M Fang, Y Hu… - Nature …, 2022 - nature.com
Spatial transcriptomics approaches have substantially advanced our capacity to detect the
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …

[HTML][HTML] Transcriptional programs of neoantigen-specific TIL in anti-PD-1-treated lung cancers

JX Caushi, J Zhang, Z Ji, A Vaghasia, B Zhang… - Nature, 2021 - nature.com
Abstract PD-1 blockade unleashes CD8 T cells, including those specific for mutation-
associated neoantigens (MANA), but factors in the tumour microenvironment can inhibit …

[HTML][HTML] Metabolic modeling of single Th17 cells reveals regulators of autoimmunity

A Wagner, C Wang, J Fessler, D DeTomaso… - Cell, 2021 - cell.com
Metabolism is a major regulator of immune cell function, but it remains difficult to study the
metabolic status of individual cells. Here, we present Compass, an algorithm to characterize …

[HTML][HTML] Zero-preserving imputation of single-cell RNA-seq data

GC Linderman, J Zhao, M Roulis, P Bielecki… - Nature …, 2022 - nature.com
A key challenge in analyzing single cell RNA-sequencing data is the large number of false
zeros, where genes actually expressed in a given cell are incorrectly measured as …

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

TS Andrews, VY Kiselev, D McCarthy, M Hemberg - Nature protocols, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows
you to profile the whole transcriptome of a large number of individual cells. However, the …

[HTML][HTML] Single-cell RNA-seq technologies and related computational data analysis

G Chen, B Ning, T Shi - Frontiers in genetics, 2019 - frontiersin.org
Single-cell RNA sequencing (scRNA-seq) technologies allow the dissection of gene
expression at single-cell resolution, which greatly revolutionizes transcriptomic studies. A …

Current best practices in single‐cell RNA‐seq analysis: a tutorial

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

[HTML][HTML] scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

J Wang, A Ma, Y Chang, J Gong, Y Jiang, R Qi… - Nature …, 2021 - nature.com
Single-cell RNA-sequencing (scRNA-Seq) is widely used to reveal the heterogeneity and
dynamics of tissues, organisms, and complex diseases, but its analyses still suffer from …