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 …

Impact of the Human Cell Atlas on medicine

JE Rood, A Maartens, A Hupalowska, SA Teichmann… - Nature medicine, 2022 - nature.com
Single-cell atlases promise to provide a 'missing link'between genes, diseases and
therapies. By identifying the specific cell types, states, programs and contexts where disease …

Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease

A Garrido-Trigo, AM Corraliza, M Veny, I Dotti… - Nature …, 2023 - nature.com
Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with
perplexing heterogeneity in disease manifestation and response to treatment. While the …

Spatial profiling technologies illuminate the tumor microenvironment

O Elhanani, R Ben-Uri, L Keren - Cancer Cell, 2023 - cell.com
The tumor microenvironment (TME) is composed of many different cellular and acellular
components that together drive tumor growth, invasion, metastasis, and response to …

SODB facilitates comprehensive exploration of spatial omics data

Z Yuan, W Pan, X Zhao, F Zhao, Z Xu, X Li, Y Zhao… - Nature …, 2023 - nature.com
Spatial omics technologies generate wealthy but highly complex datasets. Here we present
Spatial Omics DataBase (SODB), a web-based platform providing both rich data resources …

[PDF][PDF] hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data

S Morabito, F Reese, N Rahimzadeh, E Miyoshi… - Cell reports …, 2023 - cell.com
Biological systems are immensely complex, organized into a multi-scale hierarchy of
functional units based on tightly regulated interactions between distinct molecules, cells …

Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development

F Jiang, X Zhou, Y Qian, M Zhu, L Wang, Z Li, Q Shen… - Nature …, 2023 - nature.com
The brain is a complex tissue whose function relies on coordinated anatomical and
molecular features. However, the molecular annotation of the spatial organization of the …

SpatialData: an open and universal data framework for spatial omics

L Marconato, G Palla, KA Yamauchi, I Virshup… - Nature …, 2024 - nature.com
Spatially resolved omics technologies are transforming our understanding of biological
tissues. However, the handling of uni-and multimodal spatial omics datasets remains a …

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 …

Benchmarking spatial clustering methods with spatially resolved transcriptomics data

Z Yuan, F Zhao, S Lin, Y Zhao, J Yao, Y Cui… - Nature …, 2024 - nature.com
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …