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Dual spatial transcriptomics analysis offers profiling of host- and pathogen-specific transcriptional patterns in infected tissues to establish pathoadaptation signatures and predict infection outcomes. Here, we present a protocol for tissue processing, imaging, selection of regions …
Read PDFA recent study by R. Cheng, T. Lv, P. Ji, B. Ma, et al. (Appl Environ Microbiol 91:e01685-25, 2025, https://doi.org/10.1128/aem.01685-25) used multi-omics analysis to reveal the molecular map of pathogen virulence differentiation driven by natural …
Read PDFHypertrophic cardiomyopathy (HCM) is an inherited cardiac disorder most commonly caused by pathogenic variants in sarcomeric genes, yet many patients remain genotype-negative and the mechanisms linking genetic alterations to disease pathology are not fully understood. …
Read PDFSpatial transcriptomics technology represents a groundbreaking advancement in the life sciences, enabling the analysis of gene expression patterns within their native spatial context. However, inefficiencies in RNA capture from tissue samples have historically limited its …
Read PDFAccurately inferring cell-cell interactions from spatial transcriptomics data remains challenging due to tissue complexity and spatial heterogeneity. Recent deep learning models have started to combine different types of cellular information, such as spatial proximity, gene …
Read PDFThe lack of validated stage-specific biomarkers hampers the understanding of Alzheimer's disease (AD) progression and clinical translation. Current transcriptomic methods often produce unstable results with limited stage discrimination. We aimed to develop an explainable machine …
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Read PDFNeutrophils are the most abundant innate immune cells and are pivotal first responders in host defense, playing an important role in maintaining body homeostasis and regulating pathological conditions. Growing evidence indicates that neutrophils exhibit functional …
Read PDFCellular identity emerges from the dynamic coordination of context-aware gene programs that encode biological functions across molecular layers. To decode this complexity, we present SSpMosaic, a computational framework that establishes metaprograms (higher-order, cross-dataset aligned gene …
Read PDFMethods for identifying complex multicellular spatial neighborhoods do not scale to existing spatial transcriptomics data, and often divide tissues into distinct neighborhoods with hard borders. We develop neighborhood NMF (NNMF) that identifies functionally coherent neighborhoods …
Read PDF<h4>Background</h4>Helicobacter pylori (HP) infection is the strongest environmental driver of gastric cancer, yet the epithelial programs that are progressively disrupted during infection and are associated with malignant transformation remain unclear.<h4>Methods</h4>Trend-associated genes across HP-infection datasets (GSE60662, …
Read PDFBACKGROUND: The neuroactive ligand–receptor signaling pathway is increasingly recognized as a regulator of tumor–immune interactions, yet its contribution to lung adenocarcinoma (LUAD) progression and immune evasion remains poorly defined. METHODS: We integrated multi‑cohort transcriptomic datasets, …
Read PDFDespite extensive research on Saccharomyces cerevisiae functional genomics, approximately 880 out of ~6,000 open reading frames (ORFs) remain uncharacterised. In this study we propose a method for characterising genes with limited prior functional knowledge using …
Read PDF<h4>Background</h4>For over a century, the dominant hypothesis has maintained that meningiomas arise exclusively from arachnoid cap cells. However, emerging evidence from single-cell transcriptomics, spatial sequencing, developmental biology, and transgenic animal models suggests a significantly more …
Read PDFPlant bioactive compounds, particularly carotenoids, anthocyanins and flavonoids, plays a pivotal role in the pigmentation of plant tissues. In the current study, two distinct cambial meristematic cell (CMC) lines named REG-CMC-1 and REG-CMC-2 were derived …
Read PDFMicrovascular rarefaction is a predominant pathological hallmark of chronic kidney disease (CKD), functioning simultaneously as a catalyst and consequence of progressive renal compromise. Although endothelial senescence constitutes a cardinal mediator of microvascular attrition in CKD, …
Read PDFRecent advances underscore the potential of integrating multiomics, such as genomics, transcriptomics, proteomics, and metabolomics, and artificial intelligence to overcome limitations regarding early diagnosis and treatment of Parkinson's disease. Developing a comprehensive view of the …
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