Transformers in single-cell omics: a review and new perspectives

A Szałata, K Hrovatin, S Becker, A Tejada-Lapuerta… - Nature …, 2024 - nature.com
Recent efforts to construct reference maps of cellular phenotypes have expanded the
volume and diversity of single-cell omics data, providing an unprecedented resource for …

Fibroblast and myofibroblast activation in normal tissue repair and fibrosis

FS Younesi, AE Miller, TH Barker, FMV Rossi… - … Reviews Molecular Cell …, 2024 - nature.com
The term 'fibroblast'often serves as a catch-all for a diverse array of mesenchymal cells,
including perivascular cells, stromal progenitor cells and bona fide fibroblasts. Although …

CZ CELLxGENE Discover: a single-cell data platform for scalable exploration, analysis and modeling of aggregated data

CZI Cell Science Program, S Abdulla… - Nucleic Acids …, 2025 - academic.oup.com
Hundreds of millions of single cells have been analyzed using high-throughput
transcriptomic methods. The cumulative knowledge within these datasets provides an …

Map** spatially resolved transcriptomes in human and mouse pulmonary fibrosis

L Franzén, M Olsson Lindvall, M Hühn, V Ptasinski… - Nature Genetics, 2024 - nature.com
Idiopathic pulmonary fibrosis (IPF) is a progressive lung disease with poor prognosis and
limited treatment options. Efforts to identify effective treatments are thwarted by limited …

Hematopoietic aging promotes cancer by fueling IL-1⍺–driven emergency myelopoiesis

MD Park, J Le Berichel, P Hamon, CM Wilk, M Belabed… - Science, 2024 - science.org
Age is a major risk factor for cancer, but how aging impacts tumor control remains unclear. In
this study, we establish that aging of the immune system, regardless of the age of the stroma …

Precise identification of cell states altered in disease using healthy single-cell references

E Dann, AM Cujba, AJ Oliver, KB Meyer… - Nature Genetics, 2023 - nature.com
Joint analysis of single-cell genomics data from diseased tissues and a healthy reference
can reveal altered cell states. We investigate whether integrated collections of data from …

scTab: scaling cross-tissue single-cell annotation models

F Fischer, DS Fischer, R Mukhin, A Isaev… - Nature …, 2024 - nature.com
Identifying cellular identities is a key use case in single-cell transcriptomics. While machine
learning has been leveraged to automate cell annotation predictions for some time, there …

Diversity of group 1 innate lymphoid cells in human tissues

N Jaeger, AU Antonova, D Kreisel, F Roan… - Nature …, 2024 - nature.com
Group 1 innate lymphoid cells (ILC1s) are cytotoxic and interferon gamma-producing
lymphocytes lacking antigen-specific receptors, which include ILC1s and natural killer (NK) …

[HTML][HTML] Transgenic ferret models define pulmonary ionocyte diversity and function

F Yuan, GN Gasser, E Lemire, DT Montoro… - Nature, 2023 - nature.com
Speciation leads to adaptive changes in organ cellular physiology and creates challenges
for studying rare cell-type functions that diverge between humans and mice. Rare cystic …

Pathology and pathobiology of pulmonary hypertension: current insights and future directions

C Guignabert, J Aman, S Bonnet… - European …, 2024 - publications.ersnet.org
In recent years, major advances have been made in the understanding of the cellular and
molecular mechanisms driving pulmonary vascular remodelling in various forms of …