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 …

Beyond assembly: the increasing flexibility of single-molecule sequencing technology

PW Hook, W Timp - Nature Reviews Genetics, 2023 - nature.com
The maturation of high-throughput short-read sequencing technology over the past two
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …

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 …

Droplet-based single-cell joint profiling of histone modifications and transcriptomes

Y Xie, C Zhu, Z Wang, M Tastemel, L Chang… - Nature Structural & …, 2023 - nature.com
Abstract We previously reported Paired-Tag, a combinatorial indexing-based method that
can simultaneously map histone modifications and gene expression at single-cell resolution …

Advancing CAR T cell therapy through the use of multidimensional omics data

J Yang, Y Chen, Y Jing, MR Green, L Han - Nature Reviews Clinical …, 2023 - nature.com
Despite the notable success of chimeric antigen receptor (CAR) T cell therapies in the
treatment of certain haematological malignancies, challenges remain in optimizing CAR …

A fast, scalable and versatile tool for analysis of single-cell omics data

K Zhang, NR Zemke, EJ Armand, B Ren - Nature Methods, 2024 - nature.com
Single-cell omics technologies have revolutionized the study of gene regulation in complex
tissues. A major computational challenge in analyzing these datasets is to project the large …

Interpreting non-coding disease-associated human variants using single-cell epigenomics

KJ Gaulton, S Preissl, B Ren - Nature Reviews Genetics, 2023 - nature.com
Genome-wide association studies (GWAS) have linked hundreds of thousands of sequence
variants in the human genome to common traits and diseases. However, translating this …

Integration of spatial and single-cell data across modalities with weakly linked features

S Chen, B Zhu, S Huang, JW Hickey, KZ Lin… - Nature …, 2023 - nature.com
Although single-cell and spatial sequencing methods enable simultaneous measurement of
more than one biological modality, no technology can capture all modalities within the same …

New genetic and epigenetic insights into the chemokine system: The latest discoveries aiding progression toward precision medicine

H Xu, S Lin, Z Zhou, D Li, X Zhang, M Yu… - Cellular & Molecular …, 2023 - nature.com
Over the past thirty years, the importance of chemokines and their seven-transmembrane G
protein-coupled receptors (GPCRs) has been increasingly recognized. Chemokine …

The heterocellular heart: identities, interactions, and implications for cardiology

A Lother, P Kohl - Basic Research in Cardiology, 2023 - Springer
The heterocellular nature of the heart has been receiving increasing attention in recent
years. In addition to cardiomyocytes as the prototypical cell type of the heart, non-myocytes …