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 …

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 …

An integrated cell atlas of the lung in health and disease

L Sikkema, C Ramírez-Suástegui, DC Strobl… - Nature medicine, 2023 - nature.com
Single-cell technologies have transformed our understanding of human tissues. Yet, studies
typically capture only a limited number of donors and disagree on cell type definitions …

[HTML][HTML] Serotonin reduction in post-acute sequelae of viral infection

AC Wong, AS Devason, IC Umana, TO Cox… - Cell, 2023 - cell.com
Post-acute sequelae of COVID-19 (PASC," Long COVID") pose a significant global health
challenge. The pathophysiology is unknown, and no effective treatments have been found to …

Dictionary learning for integrative, multimodal and scalable single-cell analysis

Y Hao, T Stuart, MH Kowalski, S Choudhary… - Nature …, 2024 - nature.com
Mapping single-cell sequencing profiles to comprehensive reference datasets provides a
powerful alternative to unsupervised analysis. However, most reference datasets are …

Cancer cell states recur across tumor types and form specific interactions with the tumor microenvironment

D Barkley, R Moncada, M Pour, DA Liberman, I Dryg… - Nature …, 2022 - nature.com
Transcriptional heterogeneity among malignant cells of a tumor has been studied in
individual cancer types and shown to be organized into cancer cell states; however, it …

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 …

A neutrophil response linked to tumor control in immunotherapy

J Gungabeesoon, NA Gort-Freitas, M Kiss, E Bolli… - Cell, 2023 - cell.com
Neutrophils accumulate in solid tumors, and their abundance correlates with poor prognosis.
Neutrophils are not homogeneous, however, and could play different roles in cancer …

Cell2location maps fine-grained cell types in spatial transcriptomics

V Kleshchevnikov, A Shmatko, E Dann… - Nature …, 2022 - nature.com
Spatial transcriptomic technologies promise to resolve cellular wiring diagrams of tissues in
health and disease, but comprehensive mapping of cell types in situ remains a challenge …

Single-nucleus profiling of human dilated and hypertrophic cardiomyopathy

M Chaffin, I Papangeli, B Simonson, AD Akkad, MC Hill… - Nature, 2022 - nature.com
Heart failure encompasses a heterogeneous set of clinical features that converge on
impaired cardiac contractile function, and presents a growing public health concern …