Nature Search

Imaging-based multimodal profiling of single cells with STAMP

In this Tools of the Trade article, Kellie Wise and Anna Pascual-Reguant introduce STAMP (single-cell transcriptomics analysis and multimodal profiling), which harnesses imaging to measure RNA and/or protein expression in fixed cells or nuclei.

Kellie Wise
Anna Pascual-Reguant
Research Highlights21 Aug 2025
Nature Reviews Genetics

P: 1
IL-17A-producing NKp44(−) group 3 innate lymphoid cells accumulate in Familial Adenomatous Polyposis duodenal tissue

Familial adenomatous polyposis (FAP) is an inherited gastrointestinal syndrome associated with duodenal adenoma formation. Here the authors show that IL17A-producing NKp44- group 3 innate lymphoid cells accumulate in FAP duodenal tissue and are associated with duodenal adenoma formation in patients with FAP.

Kim M. Kaiser
Jan Raabe
Jacob Nattermann
ResearchOpen Access25 Apr 2025
Nature Communications

Volume: 16, P: 1-19
Modeling intercellular communication in tissues using spatial graphs of cells

How cells in a tissue communicate is modeled with a graph neural network.

David S. Fischer
Anna C. Schaar
Fabian J. Theis
ResearchOpen Access27 Oct 2022
Nature Biotechnology

Volume: 41, P: 332-336
Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19

Infection with SARS-CoV-2 has been linked with substantive inflammation, lung pathology and development of COVID-19. Here the authors spatially associate CCL18 and CCL21 in distinct tissue niches with lung pathology of severe COVID-19.

Ronja Mothes
Anna Pascual-Reguant
Anja E. Hauser
ResearchOpen Access11 Feb 2023
Nature Communications

Volume: 14, P: 1-16
Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells

Innate lymphoid cells (ILCs) are important regulators of biological processes. Here the authors combine multiplexed imaging and computational pipelines to reveal tonsillar IRF4⁺ ILC3s, and to identify conserved stromal landmarks for ILC localization, thereby providing a platform for future ILC studies.

Anna Pascual-Reguant
Ralf Köhler
Anja E. Hauser
ResearchOpen Access19 Mar 2021
Nature Communications

Volume: 12, P: 1-15
SARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself

Our understanding on the humoral immunity induced by SARS-CoV-2 is still lacking. Here the authors analyze B cell responses at the single cell level to find that, in severe COVID-19 patients, plasmablasts shift from IFN to TGFβ instruction to produce IgA antibodies that are not specific to dominant SARS-CoV-2 antigens.

Marta Ferreira-Gomes
Andrey Kruglov
Mir-Farzin Mashreghi
ResearchOpen Access30 Mar 2021
Nature Communications

Volume: 12, P: 1-14

Search

Filter By:

Imaging-based multimodal profiling of single cells with STAMP

IL-17A-producing NKp44(−) group 3 innate lymphoid cells accumulate in Familial Adenomatous Polyposis duodenal tissue

Modeling intercellular communication in tissues using spatial graphs of cells

Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19

Multiplexed histology analyses for the phenotypic and spatial characterization of human innate lymphoid cells

SARS-CoV-2 in severe COVID-19 induces a TGF-β-dominated chronic immune response that does not target itself

Search

Quick links