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Profiling cell identity and tissue architecture with single-cell and spatial transcriptomics
Single-cell transcriptomics has broadened our understanding of cellular diversity and gene
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …
expression dynamics in healthy and diseased tissues. Recently, spatial transcriptomics has …
Gastric cancer immunosuppressive microenvironment heterogeneity: implications for therapy development
Although immunotherapy has revolutionized solid tumor treatment, durable responses in
gastric cancer (GC) remain limited. The heterogeneous tumor microenvironment (TME) …
gastric cancer (GC) remain limited. The heterogeneous tumor microenvironment (TME) …
Open-ST: High-resolution spatial transcriptomics in 3D
Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue
development, homeostasis, or disease. However, there is a need for easy-to-use, high …
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
Spatially resolved gene expression profiling provides insight into tissue organization and
cell–cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell …
cell–cell crosstalk; however, sequencing-based spatial transcriptomics (ST) lacks single-cell …
Hest-1k: A dataset for spatial transcriptomics and histology image analysis
Spatial transcriptomics enables interrogating the molecular composition of tissue with ever-
increasing resolution and sensitivity. However, costs, rapidly evolving technology, and lack …
increasing resolution and sensitivity. However, costs, rapidly evolving technology, and lack …
Accurate and efficient integrative reference-informed spatial domain detection for spatial transcriptomics
Spatially resolved transcriptomics (SRT) studies are becoming increasingly common and
large, offering unprecedented opportunities in map** complex tissue structures and …
large, offering unprecedented opportunities in map** complex tissue structures and …
BIDCell: Biologically-informed self-supervised learning for segmentation of subcellular spatial transcriptomics data
Recent advances in subcellular imaging transcriptomics platforms have enabled high-
resolution spatial map** of gene expression, while also introducing significant analytical …
resolution spatial map** of gene expression, while also introducing significant analytical …
LIANA+ provides an all-in-one framework for cell–cell communication inference
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 …
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 …
tissue, hitherto with some trade-off between transcriptome depth, spatial resolution and …
Spatial landscapes of cancers: insights and opportunities
Solid tumours comprise many different cell types organized in spatially structured
arrangements, with substantial intratumour and intertumour heterogeneity. Advances in …
arrangements, with substantial intratumour and intertumour heterogeneity. Advances in …