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A recent technology breakthrough in spatial molecular profiling has enabled the comprehensive molecular characterizations of single cells while preserving spatial information. It provides new opportunities to delineate how cells from…
The location, timing, and abundance of gene expression (both mRNA and proteins) within a tissue define the molecular mechanisms of cell functions. Recent technology breakthroughs in spatial molecular profiling, including imaging-based…
Identifying genes that display spatial patterns is critical to investigating expression interactions within a spatial context and further dissecting biological understanding of complex mechanistic functionality. Despite the increase in…
The advent of next-generation sequencing-based spatially resolved transcriptomics (SRT) techniques has reshaped genomic studies by enabling high-throughput gene expression profiling while preserving spatial and morphological context.…
Spatially resolved transcriptomics is a fast-developing set of technologies that enables the measurement of localized gene expression across spatial locations in a sample. Detecting spatially varying genes is critical for analyzing such…
Identifying disease-indicative genes is critical for deciphering disease mechanisms and has attracted significant interest in biomedical research. Spatial transcriptomics offers unprecedented insights for the detection of disease-specific…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
Spatial transcriptomics technologies enable the measurement of gene expression with spatial context, providing opportunities to understand how gene regulatory networks vary across tissue regions. However, existing graphical models focus…
With the emergence of advanced spatial transcriptomic technologies, there has been a surge in research papers dedicated to analyzing spatial transcriptomics data, resulting in significant contributions to our understanding of biology. The…
Advances in spatial transcriptomics (ST) technologies enable systematic molecular characterization of tumor microenvironment, tumor gradients and gene regulatory networks. Cancer progression is known to vary along pathological gradients,…
Spatial transcriptomics measures the expression of thousands of genes in a tissue sample while preserving its spatial structure. This class of technologies has enabled the investigation of the spatial variation of gene expressions and their…
Spatial variable genes (SVGs) reveal critical information about tissue architecture, cellular interactions, and disease microenvironments. As spatial transcriptomics (ST) technologies proliferate, accurately identifying SVGs across diverse…
Recent advancements in spatial transcriptomics technologies allow researchers to simultaneously measure RNA expression levels for hundreds to thousands of genes while preserving spatial information within tissues, providing critical…
Spatial Transcriptomics is a novel technology that aligns histology images with spatially resolved gene expression profiles. Although groundbreaking, it struggles with gene capture yielding high corruption in acquired data. Given potential…
Spatial transcriptomics studies are becoming increasingly large and commonplace, necessitating simultaneous analysis of a large number of spatially resolved variables. Correspondingly, a diverse range of methodologies have been proposed to…
Spatial transcriptomics is a modern sequencing technology that allows the measurement of the activity of thousands of genes in a tissue sample and map where the activity is occurring. This technology has enabled the study of the so-called…
In the analysis of spatially resolved transcriptomics data, detecting spatially variable genes (SVGs) is crucial. Numerous computational methods exist, but varying SVG definitions and methodologies lead to incomparable results. We review 33…
Spatial transcriptomics is a technology that captures gene expression levels at different spatial locations, widely used in tumor microenvironment analysis and molecular profiling of histopathology, providing valuable insights into…
Spatial transcriptomics (ST) technologies enable transcriptome-wide gene expression profiling while preserving spatial resolution, offering unprecedented opportunities to uncover complex spatial structures. Due to the ultra-high…
Spatial transcriptomics allows researchers to visualize and analyze gene expression within the precise location of tissues or cells. It provides spatially resolved gene expression data but often lacks cellular resolution, necessitating cell…