Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

scGPT: toward building a foundation model for single-cell multi-omics using generative AI

H Cui, C Wang, H Maan, K Pang, F Luo, N Duan… - Nature …, 2024 - nature.com
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

APOE4/4 is linked to damaging lipid droplets in Alzheimer's disease microglia

MS Haney, R Pálovics, CN Munson, C Long… - Nature, 2024 - nature.com
Several genetic risk factors for Alzheimer's disease implicate genes involved in lipid
metabolism and many of these lipid genes are highly expressed in glial cells. However, the …

[HTML][HTML] Microglia states and nomenclature: A field at its crossroads

RC Paolicelli, A Sierra, B Stevens, ME Tremblay… - Neuron, 2022 - cell.com
Microglial research has advanced considerably in recent decades yet has been constrained
by a rolling series of dichotomies such as" resting versus activated" and" M1 versus M2." …

Applications of single-cell RNA sequencing in drug discovery and development

B Van de Sande, JS Lee, E Mutasa-Gottgens… - Nature Reviews Drug …, 2023 - nature.com
Single-cell technologies, particularly single-cell RNA sequencing (scRNA-seq) methods,
together with associated computational tools and the growing availability of public data …

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 …

Single‐cell RNA sequencing technologies and applications: A brief overview

D Jovic, X Liang, H Zeng, L Lin, F Xu… - Clinical and …, 2022 - Wiley Online Library
Single‐cell RNA sequencing (scRNA‐seq) technology has become the state‐of‐the‐art
approach for unravelling the heterogeneity and complexity of RNA transcripts within …

[HTML][HTML] High-content CRISPR screening

C Bock, P Datlinger, F Chardon, MA Coelho… - Nature Reviews …, 2022 - nature.com
CRISPR screens are a powerful source of biological discovery, enabling the unbiased
interrogation of gene function in a wide range of applications and species. In pooled …

Human SARS-CoV-2 challenge uncovers local and systemic response dynamics

RGH Lindeboom, KB Worlock, LM Dratva, M Yoshida… - Nature, 2024 - nature.com
The COVID-19 pandemic is an ongoing global health threat, yet our understanding of the
dynamics of early cellular responses to this disease remains limited. Here in our SARS-CoV …