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Autologous 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 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>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 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 PDFImaging-based spatial transcriptomic (ST) assays now profile targeted gene panels for hundreds of thousands of cells while preserving tissue context, yet most downstream analyses still need a compact, interpretable subset. We introduce CiCLoDS (Clustering in …
Read PDFGastric cancer (GC) shows marked heterogeneity driven by the tumor microenvironment, leading to therapeutic resistance and poor prognosis. Using spatial transcriptomics of invasive murine tumors and human GC samples, we identified a distinct stromal-immune-vascular core …
Read PDF<h4>Background</h4>Invasive plants pose a major threat to global biodiversity, yet the molecular and genomic mechanisms underlying their success remain poorly understood. Here, we investigate the invasion of the common reed Phragmites australis, a grass species …
Read PDFBACKGROUND: Inflammatory bowel disease (IBD) represents a group of chronic and relapsing inflammatory disorders of the gastrointestinal tract, primarily encompassing Crohn’s disease (CD) and ulcerative colitis (UC). To elucidate immune heterogeneity and molecular mechanisms underlying …
Read PDFIn vivo evaluation of biomaterials largely relies on histology to assess biocompatibility and foreign body responses. While effective for capturing end-stage outcomes, these methods offer limited insight into the cellular mechanisms driving tissue remodeling, hindering …
Read PDFHuman atherosclerosis is increasingly recognized as a spatially organized inflammatory disease in which macrophages act as central regulators of lesion evolution rather than as a uniform foam-cell population. Recent single-cell and spatial profiling studies have …
Read PDFThe global prevalence of gastrointestinal tumours and the bottlenecks in their diagnosis and treatment are being systematically overcome by the multi-omics revolution: high-throughput technologies are driving the multidimensional integration of genomics-transcriptomics-proteomics-metabolomics to comprehensively decode the …
Read PDFDeciphering the cellular composition of spatial spots in spatial transcriptomics (ST) data is fundamental for elucidating the heterogeneity of tissue spatial structures. However, existing models often require retraining for each new deconvolution task, reflecting limitations …
Read PDFSpatial transcriptomics (ST) and spatial proteomics (SP) have revolutionised our ability to map RNA and protein distributions within intact tissues, shedding new light on the dynamic interactions that drive physiological processes in healthy and diseased …
Read PDF<h4>Background/purpose</h4>Multi-omics integration linking genomic, transcriptomic, epigenomic, proteomic, metabolomic, single-cell, and spatial data has transformed the interpretation of human genetic variation by capturing molecular processes that extend beyond DNA sequence alone. Although these approaches substantially improve …
Read PDFDeconvolution algorithms estimate cell-type abundances from tissue-level data, enabling systematic cellular analysis of large cohorts. However, most deconvolution algorithms are specifically designed for single-omics data, thereby limiting their generalizability and scalability for various omics data …
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