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Vizgen is developing the next generation of genomics tools to expand on the capabilities of spatially resolved transcriptomics. Our technology will aide the acceleration of biological research and discovery to advance human health. Access supporting resources by selecting the category below.
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Publications
Accurate single-molecule spot detection for image-based spatial transcriptomics with weakly supervised deep learning
Abstract Image-based spatial transcriptomics methods enable transcriptome-scale gene expression measurements with spatial information but require complex, manually-tuned analysis pipelines. We present Polaris, an analysis pipeline for image-based spatial transcriptomics that combines deep learning models for…
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Altered Fhod3 Expression Involved in Progressive High-Frequency Hearing Loss via Dysregulation of Actin Polymerization Stoichiometry in The Cuticular Plate
Abstract Age-related hearing loss (ARHL) is a common sensory impairment with complex underlying mechanisms. In our previous study, we performed a meta-analysis of genome-wide association studies (GWAS) in mice and identified a novel locus on…
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Spatiotemporal molecular dynamics of the developing human thalamus
Abstract The thalamus plays a central coordinating role in the brain. Thalamic neurons are organized into spatially-distinct nuclei, but the molecular architecture of thalamic development is poorly understood, especially in humans. To begin to delineate…
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Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization
Abstract In situ transcriptomic techniques promise a holistic view of tissue organization and cell-cell interactions. Recently there has been a surge of multiplexed RNA in situ techniques but their application to human tissues and clinical…
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Optimal transport for mapping senescent cells in spatial transcriptomics
Abstract Spatial transcriptomics (ST) provides a unique opportunity to study cellular organization and cell-cell interactions at the molecular level. However, due to the low resolution of the sequencing data additional information is required to utilize…
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Subcytoplasmic location of translation controls protein output
Summary The cytoplasm is highly compartmentalized, but the extent and consequences of subcytopIasmic mRNA localization in non-polarized cells are largely unknown. We determined mRNA enrichment in TIS granules (TGs) and the rough endopIasmic reticuIum (ER)…
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Search and Match across Spatial Omics Samples at Single-cell Resolution
Abstract Spatial omics technologies characterize tissue molecular properties with spatial information, but integrating and comparing spatial data across different technologies and modalities is challenging. A comparative analysis tool that can search, match, and visualize both…
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HEARTSVG: a fast and accurate method for spatially variable gene identification in large-scale spatial transcriptomic data
Abstract Identifying spatially variable genes (SVGs) is crucial for understanding the spatiotemporal characteristics of diseases and tissue structures, posing a distinctive challenge in spatial transcriptomics research. We propose HEARTSVG, a distribution-free, test-based method for fast…
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