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Periodontitis is one of the most common oral inflammatory diseases. Baiyaojian decoction, known for its prominent immunomodulatory and anti-inflammatory properties, shows significant potential in treating periodontitis, though its molecular mechanisms remain unknown. The active ingredients …
Read PDFSingle-cell profiling of histone post-translational modifications (scHPTMs) offers a powerful lens for dissecting epigenetic regulation and cellular identity, yet low read depth and inherent noise in these datasets pose significant analytical challenges. Here, we introduce …
Read PDFSingle-cell multimodal assays measure multiple layers of molecular information. Existing single-cell tools have limited capability to analyze nuclear proteins and genomic DNA from the same originating single cell. To address this gap, we designed and …
Read PDFFate-mapping studies have challenged the longstanding view of the adult mammalian heart as a post-mitotic organ, suggesting limited cardiomyocyte renewal. This has spurred efforts to determine whether selected cardiac stromal cells have regenerative potential; however, …
Read PDF<h4>Key message</h4>CRaman imaging combined with a multi-layer perceptron neural network enables non-destructive, label-freeclassifi cation of tobacco BY-2 cells based on carotenoid composition. Carotenoids are natural tetraterpenoid pigments with important nutritional properties and broad industrial applications. …
Read PDFUnderstanding the mechanisms that drive chimeric antigen receptor (CAR) T-cell function and persistence in multiple myeloma (MM) remains a critical challenge for improving therapeutic outcomes. In this study, we applied single-cell multiomics and gene regulatory …
Read PDFAccording to the 2024 World Health Organization (WHO)Global Tuberculosis (TB)Report, tuberculosis remains the leading cause of death from a single infectious agent, with 10.8 million new cases and 1.25 million deaths in 2023. Early and …
Read PDFAccurately annotating cell types is essential for extracting biological insight from single-cell RNA sequencing data. Although cell types are naturally organized into hierarchical ontologies, most computational models do not explicitly incorporate this structure into their …
Read PDFIdentifying cancer driver genes (CDGs) remains a central challenge in cancer genomics, as frequency-based mutation approaches often miss rare but functionally important regulators. We present PICDGI, a computational framework that predicts driver-like regulatory genes by …
Read PDFCutaneous T-cell lymphoma (CTCL) is a type of lymphoma that affects the skin and has various subtypes with different features. It can be either slow-growing or aggressive and currently has limited treatment options, causing a …
Read PDFSingle-cell multiomics (scMultiomics) technologies and methods encompassing transcriptomics, genomics, epigenomics, proteomics, and metabolomics, together with associated computational tools have profoundly revolutionized disease research, enabling unprecedented dissection of cellular heterogeneity and dynamic biological responses. The use …
Read PDF<h4>Summary</h4>Recent advances in single-cell analysis have introduced new computational challenges. Researchers often need to use multiple analysis tools written in different programming languages while managing version conflicts between related packages within a single workflow. For …
Read PDFCancer remains one of the leading causes of mortality worldwide, accounting for ≈10 million deaths annually. Critically, it is metastasis and not the primary tumour that causes most of these deaths. Understanding the mechanisms behind …
Read PDFMass spectrometry imaging enables spatially resolved, label-free detection of metabolites in tissue and culture systems, providing insight into their metabolic landscapes and spatial distribution. However, conventional approaches often lack the spatial resolution and specificity needed …
Read PDFThe single-cell sequencing revolution enables simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues. Among all the analysis steps, assigning individual cells to …
Read PDFFetal skeletal muscle development involves coordinated interactions among myogenic, stromal, vascular, and immune compartments, yet the cellular and molecular programs guiding tissue maturation remain incompletely understood. To address this, we generated a high-resolution single-cell atlas …
Read PDFSingle-cell transcriptomics is reshaping the study of cellular physiology and pathology by revealing fine-grained cell functions and states. Interpreting these signals across cell types, organs, and species benefits from curated gene sets and tools for …
Read PDFNumerous studies have identified a large number of miRNA editing sites via deep sRNA sequencing profiling of tissue samples. However, the single-cell landscape of miRNA editing patterns has remained largely unknown to date. To investigate …
Read PDFOver the past 2 to 3 years, mass-spectrometry-based single-cell proteomics (SCP) has experienced transformative improvements in microfluidic and robotic sample preparation, innovative MS1- and MS2-based multiplexing strategies, and specialized hardware (e.g., timsTOF Ultra 2, Astral), …
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