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 …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Museum of spatial transcriptomics

L Moses, L Pachter - Nature methods, 2022 - nature.com
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and
tumors, depends on the spatial organization of their cells. In the past decade, high …

Spatial omics and multiplexed imaging to explore cancer biology

SM Lewis, ML Asselin-Labat, Q Nguyen, J Berthelet… - Nature …, 2021 - nature.com
Understanding intratumoral heterogeneity—the molecular variation among cells within a
tumor—promises to address outstanding questions in cancer biology and improve the …

Squidpy: a scalable framework for spatial omics analysis

G Palla, H Spitzer, M Klein, D Fischer, AC Schaar… - Nature …, 2022 - nature.com
Spatial omics data are advancing the study of tissue organization and cellular
communication at an unprecedented scale. Flexible tools are required to store, integrate and …

Advances in spatial transcriptomic data analysis

R Dries, J Chen, N Del Rossi, MM Khan… - Genome …, 2021 - genome.cshlp.org
Spatial transcriptomics is a rapidly growing field that promises to comprehensively
characterize tissue organization and architecture at the single-cell or subcellular resolution …

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 …

An end-to-end workflow for multiplexed image processing and analysis

J Windhager, VRT Zanotelli, D Schulz, L Meyer… - Nature …, 2023 - nature.com
Multiplexed imaging enables the simultaneous spatial profiling of dozens of biological
molecules in tissues at single-cell resolution. Extracting biologically relevant information …

Differentiation of IL-26+ TH17 intermediates into IL-17A producers via epithelial crosstalk in psoriasis

A Fries, F Saidoune, F Kuonen, I Dupanloup… - Nature …, 2023 - nature.com
Abstract Interleukin (IL)-26 is a TH17 cytokine with known antimicrobial and pro-
inflammatory functions. However, the precise role of IL-26 in the context of pathogenic TH17 …

Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments

Y Feng, T Yang, J Zhu, M Li, M Doyle… - Nature …, 2023 - nature.com
Spatial proteomics technologies have revealed an underappreciated link between the
location of cells in tissue microenvironments and the underlying biology and clinical …