Tissue-specific macrophages: how they develop and choreograph tissue biology

E Mass, F Nimmerjahn, K Kierdorf… - Nature Reviews …, 2023 - nature.com
Macrophages are innate immune cells that form a 3D network in all our tissues, where they
phagocytose dying cells and cell debris, immune complexes, bacteria and other waste …

CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics

S **, MV Plikus, Q Nie - Nature Protocols, 2025 - nature.com
Recent advances in single-cell sequencing technologies offer an opportunity to explore cell–
cell communication in tissues systematically and with reduced bias. A key challenge is …

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 map** of cell types in situ remains a challenge …

[HTML][HTML] Spatial multiomics map of trophoblast development in early pregnancy

A Arutyunyan, K Roberts, K Troulé, FCK Wong… - Nature, 2023 - nature.com
The relationship between the human placenta—the extraembryonic organ made by the
fetus, and the decidua—the mucosal layer of the uterus, is essential to nurture and protect …

Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression

A Sattiraju, S Kang, B Giotti, Z Chen, VJ Marallano… - Immunity, 2023 - cell.com
Glioblastoma (GBM), a highly lethal brain cancer, is notorious for immunosuppression, but
the mechanisms remain unclear. Here, we documented a temporospatial patterning of tumor …

Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics

GS Gulati, JP D'Silva, Y Liu, L Wang… - … Reviews Molecular Cell …, 2024 - nature.com
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …

Systematic comparison of sequencing-based spatial transcriptomic methods

Y You, Y Fu, L Li, Z Zhang, S Jia, S Lu, W Ren, Y Liu… - Nature …, 2024 - nature.com
Recent developments of sequencing-based spatial transcriptomics (sST) have catalyzed
important advancements by facilitating transcriptome-scale spatial gene expression …

Yolk sac cell atlas reveals multiorgan functions during human early development

I Goh, RA Botting, A Rose, S Webb, J Engelbert… - Science, 2023 - science.org
The extraembryonic yolk sac (YS) ensures delivery of nutritional support and oxygen to the
develo** embryo but remains ill-defined in humans. We therefore assembled a …

An integrated single-cell reference atlas of the human endometrium

M Marečková, L Garcia-Alonso, M Moullet, V Lorenzi… - Nature Genetics, 2024 - nature.com
The complex and dynamic cellular composition of the human endometrium remains poorly
understood. Previous endometrial single-cell atlases profiled few donors and lacked …

GeneCompass: deciphering universal gene regulatory mechanisms with a knowledge-informed cross-species foundation model

X Yang, G Liu, G Feng, D Bu, P Wang, J Jiang, S Chen… - Cell Research, 2024 - nature.com
Deciphering universal gene regulatory mechanisms in diverse organisms holds great
potential for advancing our knowledge of fundamental life processes and facilitating clinical …