Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface
Sign Up to like & getrecommendations! Published in 2021 at "Nature Communications"
DOI: 10.1038/s41467-021-26614-z
Abstract: During tumor progression, cancer cells come into contact with various non-tumor cell types, but it is unclear how tumors adapt to these new environments. Here, we integrate spatially resolved transcriptomics, single-cell RNA-seq, and single-nucleus RNA-seq… read more here.
Keywords: resolved transcriptomics; interface; tumor microenvironment; spatially resolved ... See more keywords
Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder.
Sign Up to like & getrecommendations! Published in 2022 at "Nature communications"
DOI: 10.1038/s41467-022-29439-6
Abstract: Recent advances in spatially resolved transcriptomics have enabled comprehensive measurements of gene expression patterns while retaining the spatial context of the tissue microenvironment. Deciphering the spatial context of spots in a tissue needs to use… read more here.
Keywords: spatially resolved; resolved transcriptomics; spatial domains; attention ... See more keywords
Multi-modal domain adaptation for revealing spatial functional landscape from spatially resolved transcriptomics
Sign Up to like & getrecommendations! Published in 2024 at "Briefings in Bioinformatics"
DOI: 10.1093/bib/bbae257
Abstract: Abstract Spatially resolved transcriptomics (SRT) has emerged as a powerful tool for investigating gene expression in spatial contexts, providing insights into the molecular mechanisms underlying organ development and disease pathology. However, the expression sparsity poses… read more here.
Keywords: spatially resolved; modal domain; resolved transcriptomics; multi modal ... See more keywords
Single-cell and spatially resolved transcriptomics for liver biology.
Sign Up to like & getrecommendations! Published in 2023 at "Hepatology"
DOI: 10.1097/hep.0000000000000387
Abstract: Single-cell transcriptomics enables the identification of rare cell types and the inference of state transitions, and spatially resolved transcriptomics allows the quantification of cells and genes in the context of tissues. The recent progress in… read more here.
Keywords: cell; biology; single cell; spatially resolved ... See more keywords
Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics
Sign Up to like & getrecommendations! Published in 2017 at "Proceedings of the IEEE"
DOI: 10.1109/jproc.2016.2538562
Abstract: It is well known that cells in tissue display a large heterogeneity in gene expression due to differences in cell lineage origin and variation in the local environment. Traditional methods that analyze gene expression from… read more here.
Keywords: information; resolved transcriptomics; bridging histology; analysis ... See more keywords
Abstract 6766: Pan-cancer characterization of tumor-immune interactions using spatially resolved transcriptomics
Sign Up to like & getrecommendations! Published in 2023 at "Cancer Research"
DOI: 10.1158/1538-7445.am2023-6766
Abstract: The development of immunotherapy drugs, such as immune checkpoint inhibitors (ICIs) has changed the environment of cancer treatment tremendously by providing efficacious therapeutic options for many cancer patients. However, only a minority of patients experience… read more here.
Keywords: resolved transcriptomics; tumor immune; spatially resolved; immune interactions ... See more keywords
Abstract 1205: Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics
Sign Up to like & getrecommendations! Published in 2024 at "Cancer Research"
DOI: 10.1158/1538-7445.am2024-1205
Abstract: Tumors evolve through the acquisition of somatic mutations over time and across space. While the temporal aspects of tumor evolution can be inferred by applying phylogenetic techniques to bulk or single-cell DNA sequencing data, the… read more here.
Keywords: copy; spatially resolved; resolved transcriptomics; copy number ... See more keywords
Bayesian hidden mark interaction model for detecting spatially variable genes in imaging-based spatially resolved transcriptomics data
Sign Up to like & getrecommendations! Published in 2024 at "Frontiers in Genetics"
DOI: 10.3389/fgene.2024.1356709
Abstract: Recent technology breakthroughs in spatially resolved transcriptomics (SRT) have enabled the comprehensive molecular characterization of cells whilst preserving their spatial and gene expression contexts. One of the fundamental questions in analyzing SRT data is the… read more here.
Keywords: spatially resolved; spatially variable; model; resolved transcriptomics ... See more keywords