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 …

Gastric cancer immunosuppressive microenvironment heterogeneity: implications for therapy development

T Yasuda, YA Wang - Trends in cancer, 2024 - cell.com
Although immunotherapy has revolutionized solid tumor treatment, durable responses in
gastric cancer (GC) remain limited. The heterogeneous tumor microenvironment (TME) …

Open-ST: High-resolution spatial transcriptomics in 3D

M Schott, D León-Periñán, E Splendiani, L Strenger… - Cell, 2024 - cell.com
Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue
development, homeostasis, or disease. However, there is a need for easy-to-use, high …

Starfysh integrates spatial transcriptomic and histologic data to reveal heterogeneous tumor–immune hubs

S He, Y **, A Nazaret, L Shi, X Chen… - Nature …, 2024 - nature.com
Spatially resolved gene expression profiling provides insight into tissue organization and
cell–cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell …

Hest-1k: A dataset for spatial transcriptomics and histology image analysis

G Jaume, P Doucet, A Song, MY Lu… - Advances in …, 2025 - proceedings.neurips.cc
Spatial transcriptomics enables interrogating the molecular composition of tissue with ever-
increasing resolution and sensitivity. However, costs, rapidly evolving technology, and lack …

Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics

Y Ma, X Zhou - Nature Methods, 2024 - nature.com
Spatially resolved transcriptomics (SRT) studies are becoming increasingly common and
large, offering unprecedented opportunities in map** complex tissue structures and …

BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data

X Fu, Y Lin, DM Lin, D Mechtersheimer, C Wang… - Nature …, 2024 - nature.com
Recent advances in subcellular imaging transcriptomics platforms have enabled high-
resolution spatial map** of gene expression, while also introducing significant analytical …

LIANA+ provides an all-in-one framework for cell–cell communication inference

D Dimitrov, PSL Schäfer, E Farr, P Rodriguez-Mier… - Nature Cell …, 2024 - nature.com
The growing availability of single-cell and spatially resolved transcriptomics has led to the
development of many approaches to infer cell–cell communication, each capturing only a …

Multiscale topology classifies cells in subcellular spatial transcriptomics

K Benjamin, A Bhandari, JD Kepple, R Qi, Z Shang… - Nature, 2024 - nature.com
Spatial transcriptomics measures in situ gene expression at millions of locations within a
tissue, hitherto with some trade-off between transcriptome depth, spatial resolution and …

Spatial landscapes of cancers: insights and opportunities

J Chen, L Larsson, A Swarbrick… - Nature Reviews Clinical …, 2024 - nature.com
Solid tumours comprise many different cell types organized in spatially structured
arrangements, with substantial intratumour and intertumour heterogeneity. Advances in …