[HTML][HTML] 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 …

The expanding vistas of spatial transcriptomics

L Tian, F Chen, EZ Macosko - Nature Biotechnology, 2023 - nature.com
The formation and maintenance of tissue integrity requires complex, coordinated activities
by thousands of genes and their encoded products. Until recently, transcript levels could …

[HTML][HTML] Comparison of methods and resources for cell-cell communication inference from single-cell RNA-Seq data

D Dimitrov, D Türei, M Garrido-Rodriguez… - Nature …, 2022 - nature.com
The growing availability of single-cell data, especially transcriptomics, has sparked an
increased interest in the inference of cell-cell communication. Many computational tools …

[HTML][HTML] 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 …

[PDF][PDF] Unbiased spatial proteomics with single-cell resolution in tissues

A Mund, AD Brunner, M Mann - Molecular Cell, 2022 - cell.com
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify
the entire complement of proteins in cells or tissues. Here, we review challenges and recent …

Spatial biology of cancer evolution

Z Seferbekova, A Lomakin, LR Yates… - Nature Reviews …, 2023 - nature.com
The natural history of cancers can be understood through the lens of evolution given that the
driving forces of cancer development are mutation and selection of fitter clones. Cancer …

[HTML][HTML] Modeling intercellular communication in tissues using spatial graphs of cells

DS Fischer, AC Schaar, FJ Theis - Nature Biotechnology, 2023 - nature.com
Abstract Models of intercellular communication in tissues are based on molecular profiles of
dissociated cells, are limited to receptor–ligand signaling and ignore spatial proximity in situ …

Single-cell profiling to explore pancreatic cancer heterogeneity, plasticity and response to therapy

S Bärthel, C Falcomatà, R Rad, FJ Theis, D Saur - Nature cancer, 2023 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal cancer entity characterized by a
heterogeneous genetic landscape and an immunosuppressive tumor microenvironment …

[HTML][HTML] 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 …

[HTML][HTML] Spatial omics technologies at multimodal and single cell/subcellular level

J Park, J Kim, T Lewy, CM Rice, O Elemento… - Genome Biology, 2022 - Springer
Spatial omics technologies enable a deeper understanding of cellular organizations and
interactions within a tissue of interest. These assays can identify specific compartments or …