Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

An introduction to spatial transcriptomics for biomedical research

CG Williams, HJ Lee, T Asatsuma, R Vento-Tormo… - Genome Medicine, 2022 - Springer
Single-cell transcriptomics (scRNA-seq) has become essential for biomedical research over
the past decade, particularly in developmental biology, cancer, immunology, and …

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 …

[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 …

Fast, sensitive and accurate integration of single-cell data with Harmony

I Korsunsky, N Millard, J Fan, K Slowikowski, F Zhang… - Nature …, 2019 - nature.com
The emerging diversity of single-cell RNA-seq datasets allows for the full transcriptional
characterization of cell types across a wide variety of biological and clinical conditions …

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 …

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

M Efremova, M Vento-Tormo, SA Teichmann… - Nature protocols, 2020 - nature.com
Cell–cell communication mediated by ligand–receptor complexes is critical to coordinating
diverse biological processes, such as development, differentiation and inflammation. To …

Dynamics and specificities of T cells in cancer immunotherapy

G Oliveira, CJ Wu - Nature Reviews Cancer, 2023 - nature.com
Recent advances in cancer immunotherapy—ranging from immune-checkpoint blockade
therapy to adoptive cellular therapy and vaccines—have revolutionized cancer treatment …

RNA sequencing: the teenage years

R Stark, M Grzelak, J Hadfield - Nature Reviews Genetics, 2019 - nature.com
Over the past decade, RNA sequencing (RNA-seq) has become an indispensable tool for
transcriptome-wide analysis of differential gene expression and differential splicing of …

Single-cell RNA sequencing technologies and bioinformatics pipelines

B Hwang, JH Lee, D Bang - Experimental & molecular medicine, 2018 - nature.com
Rapid progress in the development of next-generation sequencing (NGS) technologies in
recent years has provided many valuable insights into complex biological systems, ranging …