Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

By Reuben Moncada, Dalia Barkley, F. Wagner, Marta Chiodin, J. Devlin, Maayan Baron, C. Hajdu, D. Simeone, Itai Yanai. Nature Biotechnology, 2020

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Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution (2022, methodology): “To further quantify the prediction accuracy of each integration method, we adopted three metrics besides PCC: (1) structural similarity index (SSIM), which combines mean value, variance, and covariance to measure the similarity between the predicted result and the ground truth; (2) root mean square ”
Spatial components of molecular tissue biology (2022, positive): “An integrative analysis of scRNA-seq and spatial transcriptomics of the same pancreatic cancer tumors, showed colocalization of stress-response cancer cells and inflammatory fibroblasts 86 forming a cancer-specific cellular neighborhood.”
Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics (2022, neutral): “47).”