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 …
Spatiotemporal omics for biology and medicine
The completion of the Human Genome Project has provided a foundational blueprint for
understanding human life. Nonetheless, understanding the intricate mechanisms through …
understanding human life. Nonetheless, understanding the intricate mechanisms through …
BANKSY unifies cell ty** and tissue domain segmentation for scalable spatial omics data analysis
Spatial omics data are clustered to define both cell types and tissue domains. We present
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …
Building Aggregates with a Neighborhood Kernel and Spatial Yardstick (BANKSY), an …
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 …
The diversification of methods for studying cell–cell interactions and communication
No cell lives in a vacuum, and the molecular interactions between cells define most
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
phenotypes. Transcriptomics provides rich information to infer cell–cell interactions and …
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 …
Benchmarking spatial clustering methods with spatially resolved transcriptomics data
Spatial clustering, which shares an analogy with single-cell clustering, has expanded the
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
scope of tissue physiology studies from cell-centroid to structure-centroid with spatially …
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 …
arrangements, with substantial intratumour and intertumour heterogeneity. Advances in …
Spatial transcriptomic analysis of primary and metastatic pancreatic cancers highlights tumor microenvironmental heterogeneity
Although the spatial, cellular and molecular landscapes of resected pancreatic ductal
adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology …
adenocarcinoma (PDAC) are well documented, the characteristics of its metastatic ecology …
Mitophagy and clear cell renal cell carcinoma: insights from single-cell and spatial transcriptomics analysis
L Jiang, X Ren, J Yang, H Chen, S Zhang… - Frontiers in …, 2024 - frontiersin.org
Background Clear Cell Renal Cell Carcinoma (ccRCC) is the most common type of kidney
cancer, characterized by high heterogeneity and complexity. Recent studies have identified …
cancer, characterized by high heterogeneity and complexity. Recent studies have identified …