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View article: Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors
Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors Open
A central challenge in cancer research is to identify the secreted factors that sustain tumor cell survival. This is best exemplified in Hodgkin lymphoma, where malignant cells constitute a minor fraction of the tumor and rely on signals f…
View article: Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors
Genome-scale spatial mapping of the Hodgkin lymphoma microenvironment identifies tumor cell survival factors Open
A key challenge in cancer research is to identify the secreted factors that contribute to tumor cell survival. Nowhere is this more evident than in Hodgkin lymphoma, where malignant Hodgkin Reed Sternberg (HRS) cells comprise only 1-5% of …
View article: Genome-Scale High-Resolution Spatial Mapping of the Pro-Tumorigenic Cellular Niche in Classic Hodgkin Lymphoma
Genome-Scale High-Resolution Spatial Mapping of the Pro-Tumorigenic Cellular Niche in Classic Hodgkin Lymphoma Open
Introduction: A fundamental hallmark of cancer is that tumor cells repurpose the tissue microenvironment to promote their own survival. An increased understanding of these mechanisms may lead to improved microenvironment-directed therapies…
View article: Rare penetrant mutations confer severe risk of common diseases
Rare penetrant mutations confer severe risk of common diseases Open
We examined 454,712 exomes for genes associated with a wide spectrum of complex traits and common diseases and observed that rare, penetrant mutations in genes implicated by genome-wide association studies confer ∼10-fold larger effects th…
View article: The cell type composition of the adult mouse brain revealed by single cell and spatial genomics
The cell type composition of the adult mouse brain revealed by single cell and spatial genomics Open
The function of the mammalian brain relies upon the specification and spatial positioning of diversely specialized cell types. Yet, the molecular identities of the cell types, and their positions within individual anatomical structures, re…
View article: Cell type-specific inference of differential expression in spatial transcriptomics
Cell type-specific inference of differential expression in spatial transcriptomics Open
Spatial transcriptomics enables spatially resolved gene expression measurements at near single-cell resolution. There is a pressing need for computational tools to enable the detection of genes that are differentially expressed (DE) within…
View article: Detection of allele-specific expression in spatial transcriptomics with spASE
Detection of allele-specific expression in spatial transcriptomics with spASE Open
Allele-specific expression (ASE), or the preferential expression of one allele, can be observed in transcriptomics data from early development throughout the lifespan. However, the prevalence of spatial and cell type-specific ASE variation…
View article: Robust decomposition of cell type mixtures in spatial transcriptomics
Robust decomposition of cell type mixtures in spatial transcriptomics Open
Spatial transcriptomic technologies measure gene expression at increasing spatial resolution, approaching individual cells. However, a limitation of current technologies is that spatial measurements may contain contributions from multiple …
View article: Inverted Encoding Models of Human Population Response Conflate Noise and Neural Tuning Width
Inverted Encoding Models of Human Population Response Conflate Noise and Neural Tuning Width Open
Channel-encoding models offer the ability to bridge different scales of neuronal measurement by interpreting population responses, typically measured with BOLD imaging in humans, as linear sums of groups of neurons (channels) tuned for vis…
View article: Pemantle's min-plus binary tree
Pemantle's min-plus binary tree Open
We consider a stochastic process that describes several particles interacting by either merging or annihilation. When two particles merge, they combine their masses; when annihilation occurs, only the particle of smallest mass survives. Pa…