Chase Holdener

High-resolution spatial transcriptomics maps viral tropism and reveals spatially organized immune modules in viral encephalitis

Chase Holdener, Shaowen Jiang, Kira A. Griswold, K. A. Kimble et autres

Viral encephalitis is a debilitating disease that most commonly affects vulnerable populations, including the very young and elderly. Despite its severity, few countermeasures exist due to the structural and immunological complexities of the central nervous system (CNS). To better understand the spatial …

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Smoothie: efficient inference and integration of spatial co-expression networks from denoised spatial transcriptomics data

Chase Holdener, Iwijn De Vlaminck

Finding correlations in spatial gene expression is fundamental in spatial transcriptomics, as co-expressed genes within a tissue are linked by regulation, function, pathway, or cell type. Yet, sparsity and noise in spatial transcriptomics data pose significant analytical challenges. Here, we introduce Smoothie, …

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Spatial transcriptomics maps host–gut microbiome biogeography at high resolution

Ioannis Ntekas, Lena Takayasu, David W. McKellar, Benjamin Grodner et autres

Intermicrobial and host-microbial interactions are critical for the functioning of the gut microbiome, but few tools are available to measure these interactions in situ. Here we report a method for broad spatial sampling of microbiome-host interactions in the gut at high resolution …

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A temporal and spatial atlas of adaptive immune responses in the lymph node following viral infection

Shaowen Jiang, Jahanara Freedman, Madhav Mantri, Viviana I. Maymí et autres

The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell …

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Analyses and Scripts for "Smoothie: Efficient inference of spatial co-expression networks from denoised spatial transcriptomics data"

Chase Holdener, Iwijn De Vlaminck

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Analyses and Scripts for "Smoothie: Efficient inference of spatial co-expression networks from denoised spatial transcriptomics data"

Chase Holdener, Iwijn De Vlaminck

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Spatial Transcriptomics to Study Virus-Host Interactions

Chase Holdener, Shaowen Jiang, Danica M. Sutherland, Kira A. Griswold et autres

The morbidity and mortality associated with viral diseases in plants, animals, and humans are significant concerns. Understanding how viruses cause disease and identifying the viral and host factors that determine the outcome of infection are essential to develop new antiviral therapeutics and …

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Smoothie: Efficient Inference of Spatial Co-expression Networks from Denoised Spatial Transcriptomics Data

Chase Holdener, Iwijn De Vlaminck

Finding correlations in spatial gene expression is fundamental in spatial transcriptomics, as co-expressed genes within a tissue are linked by regulation, function, pathway, or cell type. Yet, sparsity and noise in spatial transcriptomics data pose significant analytical challenges. Here, we introduce Smoothie, …

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A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection

Shaowen Jiang, Madhav Mantri, Viviana I. Maymí, Scott A. Leddon et autres

The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial transcriptomics with paired, high-fidelity long-read sequencing of T and B cell …

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High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing

Ioannis Ntekas, Lena Takayasu, David W. McKellar, Benjamin Grodner et autres

ABSTRACT Inter-microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few tools are available to measure these interactions. Here, we report a method for unbiased spatial sampling of microbiome-host interactions in the gut at …

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Functional Ball Dropping: A superfast hypergraph generation scheme

Lilith Orion Hafner, Chase Holdener, Nicole Eikmeier

We present a straightforward paradigm for designing simple, efficient generators for a wide variety of hypergraph models. This approach yields asymptotically optimal algorithms and concise implementations that outperform existing implementations by multiple orders of magnitude. Our generalization of ball dropping, called functional …

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Acid Experimental Evolution of the Haloarchaeon Halobacterium sp. NRC-1 Selects Mutations Affecting Arginine Transport and Catabolism

Karina S. Kunka, Jessie M. Griffith, Chase Holdener, Katarina M. Bischof et autres

Halobacterium sp. NRC-1 (NRC-1) is an extremely halophilic archaeon that is adapted to multiple stressors such as UV, ionizing radiation and arsenic exposure; it is considered a model organism for the feasibility of microbial life in iron-rich brine on Mars. We conducted …

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