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Integrating transcriptome-wide single-cell gene expression data with spatial context substantially enhances our understanding of tissue biology, cellular interactions, and disease progression. Although single-cell RNA sequencing (scRNA-seq) provides high-resolution gene expression data, it lacks crucial spatial …
Read PDFAdult human hearts show limited regeneration after acute myocardial infarction (AMI) despite a small subpopulation (~5%) of cardiomyocytes re-entering the cell cycle. We integrated public single-nucleus RNA-seq, spatial transcriptomics, bulk RNA-seq and ATAC-seq datasets from …
Read PDFGastric cancer (GC) is characterized by a complex tumor microenvironment (TME) with substantial cellular heterogeneity. Tumor-associated macrophages (TAMs) represent the most abundant immune cell population in the TME and exhibit remarkable functional plasticity. This study …
Read PDFAccurate cell type annotation is critical for studying cellular heterogeneity in single-cell and spatial transcriptomics. However, existing methods largely rely on static gene markers, limiting adaptability to diverse biological contexts and data types. To overcome …
Read PDFAutologous cell therapies for knee osteoarthritis, including bone marrow aspirate concentrate (BMAC) and stromal vascular fraction (SVF), have advanced clinically despite an incomplete understanding of their mechanisms. Chatterjee et al. apply single-cell transcriptomics to multicenter …
Read PDFControlled plant growth in laboratories can be achieved by cultivating plants under sterile or axenic conditions on predefined synthetic growth media, typically supplemented with sugar. In nature, plants do not receive exogenous sugar supplies, form …
Read PDFRecent advances in our understanding of the molecular landscape of meningioma have generated new insights into the biology and heterogeneity of this disease, with demonstrated clinical value. However, there remains a need to understand tumor-intrinsic …
Read PDFCancer-associated fibroblasts (CAFs) are central to the pancreatic ductal adenocarcinoma (PDAC) microenvironment, promoting tumor progression and therapeutic resistance. However, the expression landscape of CAF membrane proteins in PDAC remains poorly defined. We integrated scRNA-seq (n …
Read PDF<h4>Background</h4>Recent advances in spatial transcriptomic technologies enable in situ gene expression profiling while preserving spatial context. This capability is particularly important for studying the tumor microenvironment (TME), where diverse and admixed cell populations interact within …
Read PDFThe integration of neuroimaging and transcriptomics data has revolutionized our understanding of complex brain phenomena and holds promise for linking molecular level genetic markers to brain dynamics and function. However, the involved data differ strongly …
Read PDFThe issues of how microorganisms survive very long periods of desiccation and how they react during both drying and rehydration phases have long been topics of interest in a range of relevant fields, including desert …
Read PDF<h4>Summary</h4>Visium HD Spatial Transcriptomics Data Analysis and Visualization (VST-DAVis) is an interactive, R Shiny application and web browser designed for intuitive analysis of spatial transcriptomics data generated using the 10x Genomics Visium HD platform. This …
Read PDF<h4>Background</h4>The therapeutic response to disease-modifying antirheumatic drugs (DMARDs) remains relatively low in psoriatic arthritis (PsA), leading to delayed disease control and frequent treatment switches. Predictive biomarkers may enable personalized treatment and earlier disease control. We …
Read PDFRecent advances in spatial transcriptomics (ST) have revolutionized the understanding of cellular functions by providing gene expression profiles with rich spatial context. Effectively learning spatial representations is essential for downstream analyses and requires robust integration …
Read PDF<h4>Background</h4>Disulfidptosis is a regulated cell death program linked to redox stress, metabolism, and the actin cytoskeleton. Its organization in tissue and clinical relevance in renal cell carcinoma are not well defined.<h4>Methods</h4>We integrated spatial transcriptomics from …
Read PDFSpatial transcriptomics (ST) enables mapping gene expression in native tissue context to resolve architecture and cellular interactions, but current analytical workflows rely on separate algorithms for distinct tasks. We present RGAST (Relational Graph Attention network …
Read PDFSpatial transcriptomics (ST) enables the simultaneous measurement of gene expression and spatial localization within tissue sections, providing unprecedented opportunities to dissect tissue architecture and functional organization. As a relatively new omics technology, bioinformatics has driven …
Read PDFIntegrating single-cell and spatial multi-omics data is essential for resolving cellular identity, regulatory programs and tissue organization, yet remains challenging under realistic experimental designs. In practice, data are often incomplete, unpaired and partially overlapping across …
Read PDFThe solanaceae family includes several economically important crops. Tomato (<i>Solanum lycopersicum</i>), potato (<i>S. tuberosum</i>), eggplant (<i>S. melongena</i>), and pepper (<i>Capsicum annuum</i>) are among the most consumed vegetables worldwide. Over the past few decades, consumers have …
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