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Deciphering normal and cancer stem cell niches by spatial transcriptomics: opportunities and challenges
Cancer stem cells (CSCs) often exhibit stem-like attributes that depend on an intricate
stemness-promoting cellular ecosystem within their niche. The interplay between CSCs and …
stemness-promoting cellular ecosystem within their niche. The interplay between CSCs and …
Statistical identification of cell type-specific spatially variable genes in spatial transcriptomics
An essential task in spatial transcriptomics is identifying spatially variable genes (SVGs).
Here, we present Celina, a statistical method for systematically detecting cell type-specific …
Here, we present Celina, a statistical method for systematically detecting cell type-specific …
spVC for the detection and interpretation of spatial gene expression variation
Spatially resolved transcriptomics technologies have opened new avenues for
understanding gene expression heterogeneity in spatial contexts. However, existing …
understanding gene expression heterogeneity in spatial contexts. However, existing …
A count-based model for delineating cell–cell interactions in spatial transcriptomics data
Abstract Motivation Cell–cell interactions (CCIs) consist of cells exchanging signals with
themselves and neighboring cells by expressing ligand and receptor molecules and play a …
themselves and neighboring cells by expressing ligand and receptor molecules and play a …
Interpretable Spatial Gradient Analysis for Spatial Transcriptomics Data
Cellular anatomy and signaling vary across niches, which can induce gradated gene
expressions in subpopulations of cells. Such spatial transcriptomic gradient (STG) makes a …
expressions in subpopulations of cells. Such spatial transcriptomic gradient (STG) makes a …
Investigating spatial dynamics in spatial omics data with StarTrail
Spatial omics technologies revolutionize our view of biological processes within tissues.
However, existing methods fail to capture localized, sharp changes characteristic of critical …
However, existing methods fail to capture localized, sharp changes characteristic of critical …
[HTML][HTML] The indispensable role of time in autonomous development
W Letsou - BioSystems, 2024 - Elsevier
Advances in single-cell analysis have led to a picture of development largely in agreement
with Waddington's eponymous epigenetic landscape, in which a cell's fate is determined by …
with Waddington's eponymous epigenetic landscape, in which a cell's fate is determined by …
Quantitative assessment of single-cell RNA-seq clustering with CONCORDEX
Many single cell RNA-sequencing (scRNA-seq) data analysis workflows rely on methods
that embed and visualize the properties of a k-nearest neighbor (kNN) graph in two …
that embed and visualize the properties of a k-nearest neighbor (kNN) graph in two …
SpottedPy quantifies relationships between spatial transcriptomic hotspots and uncovers new environmental cues of epithelial-mesenchymal plasticity in cancer
Spatial transcriptomics is revolutionising our ability to explore intratissue heterogeneity in
cancer, but methods that can effectively capture cancer cell niches and explore their …
cancer, but methods that can effectively capture cancer cell niches and explore their …
[HTML][HTML] Identification of spatial homogeneous regions in tissues with concordex
Spatial homogeneous regions (SHRs) in tissues are domains that are homogeneous with
respect to cell type composition. We present a method for identifying SHRs using spatial …
respect to cell type composition. We present a method for identifying SHRs using spatial …