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 …

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 …

Cells of the adult human heart

M Litviňuková, C Talavera-López, H Maatz, D Reichart… - Nature, 2020 - nature.com
Cardiovascular disease is the leading cause of death worldwide. Advanced insights into
disease mechanisms and therapeutic strategies require a deeper understanding of the …

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 …

[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 …

Predicting transcriptional outcomes of novel multigene perturbations with GEARS

Y Roohani, K Huang, J Leskovec - Nature Biotechnology, 2024 - nature.com
Understanding cellular responses to genetic perturbation is central to numerous biomedical
applications, from identifying genetic interactions involved in cancer to develo** methods …

Generalizing RNA velocity to transient cell states through dynamical modeling

V Bergen, M Lange, S Peidli, FA Wolf, FJ Theis - Nature biotechnology, 2020 - nature.com
RNA velocity has opened up new ways of studying cellular differentiation in single-cell RNA-
sequencing data. It describes the rate of gene expression change for an individual gene at 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 …

Map** single-cell data to reference atlases by transfer learning

M Lotfollahi, M Naghipourfar, MD Luecken… - Nature …, 2022 - nature.com
Large single-cell atlases are now routinely generated to serve as references for analysis of
smaller-scale studies. Yet learning from reference data is complicated by batch effects …

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 …