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Spatial transcriptomics in neuroscience
Experimental and Molecular Medicine, 2023 The brain is one of the most complex living tissue types and is composed of an exceptional diversity of cell types displaying unique functional connectivity.
Namyoung Jung, Tae-Kyung Kim
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Advanced Science, 2023 Spatial transcriptomics is a newly emerging field that enables high‐throughput investigation of the spatial localization of transcripts and related analyses in various applications for biological systems.
Han‐Eol Park +8 more
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Museum of Spatial Transcriptomics [PDF]
Nature Methods, 2020 Abstract The function of many biological systems, such as embryos, liver lobules, intestinal villi, and tumors depends on the spatial organization of their cells. In the past decade high-throughput technologies have been developed to quantify gene expression in space, and computational methods have been developed that
Lambda Moses, Lior Pachter
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Spatially Aware Dimension Reduction for Spatial Transcriptomics [PDF]
Nature Communications, 2022 Abstract Spatial transcriptomics are a collection of genomic technologies that have enabled transcriptomic profiling on tissues with spatial localization information. Analyzing spatial transcriptomic data is computationally challenging, as the data collected from various spatial transcriptomic technologies are often noisy and display ...
Lulu Shang, Xiang Zhou
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Spatial Transcriptomic Technologies
Cells, 2023 Spatial transcriptomic technologies enable measurement of expression levels of genes systematically throughout tissue space, deepening our understanding of cellular organizations and interactions within tissues as well as illuminating biological insights in neuroscience, developmental biology and a range of diseases, including cancer.
Tsai-Ying Chen +3 more
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Modeling zero inflation is not necessary for spatial transcriptomics
Genome Biology, 2022 Background Spatial transcriptomics are a set of new technologies that profile gene expression on tissues with spatial localization information. With technological advances, recent spatial transcriptomics data are often in the form of sparse counts with ...
Peiyao Zhao +3 more
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Spatial transcriptomics in development and disease
Molecular Biomedicine, 2023 AbstractThe proper functioning of diverse biological systems depends on the spatial organization of their cells, a critical factor for biological processes like shaping intricate tissue functions and precisely determining cell fate. Nonetheless, conventional bulk or single-cell RNA sequencing methods were incapable of simultaneously capturing both gene
Ran Zhou +3 more
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Single-cell spatial explorer: easy exploration of spatial and multimodal transcriptomics
BMC Bioinformatics, 2023 Background: The development of single-cell technologies yields large datasets of information as diverse and multimodal as transcriptomes, immunophenotypes, and spatial position from tissue sections in the so-called ’spatial transcriptomics’.
Frédéric Pont +10 more
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Opportunities and challenges in the application of single-cell and spatial transcriptomics in plants
Frontiers in Plant Science, 2023 Single-cell and spatial transcriptomics have diverted researchers’ attention from the multicellular level to the single-cell level and spatial information.
Ce Chen, Yining Ge, Lingli Lu, Lingli Lu
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Computational solutions for spatial transcriptomics
Computational and Structural Biotechnology Journal, 2022 Transcriptome level expression data connected to the spatial organization of the cells and molecules would allow a comprehensive understanding of how gene expression is connected to the structure and function in the biological systems. The spatial transcriptomics platforms may soon provide such information.
Iivari Kleino +3 more
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