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Single-cell studies rely on advanced integration methods for complex datasets affected by batch effects from technical factors alongside meaningful biological variation. Silhouette is an established metric for assessing unsupervised clustering results, comparing within-cluster cohesion to …
Read PDFEmbedding is the key step in single-cell Hi-C (scHi-C) analysis which relies on capturing biological meaningful heterogeneity at various levels of genome architecture. To understand the strength and limitations of existing tools in various applications, …
Read PDFCannabis use is prevalent among individuals living with HIV in the United States, but the impact of cannabis exposure on the reservoir of latently infected cells that persists during antiretroviral therapy (ART) remains unclear. To …
Read PDF<h4>Background</h4>The study of three-dimensional (3D) genome structures at the single-cell level is crucial for understanding cell-to-cell variability. However, it is challenging to reconstruct the 3D structures of the whole genome based on single-cell Hi-C data …
Read PDFAtherosclerosis, a major cause of cardiovascular diseases, is characterized by the buildup of lipids and chronic inflammation in the arteries, leading to plaque formation and potential rupture. Despite recent advances in single-cell transcriptomics (scRNA-seq), the …
Read PDFGraves' disease (GD) is an autoimmune disorder primarily targeting the thyroid tissue. While major histocompatibility complex (MHC)-dependent B cell activation and thyroid-stimulating hormone receptor (TSHR) autoantibody production are central to GD, the intrathyroidal immune landscape …
Read PDF<h4>Background</h4>The transformation of non-small cell lung cancer (NSCLC) into small cell lung cancer (SCLC) is a recognized treatment resistance mechanism, most often arising from EGFR-mutant lung adenocarcinoma (LUAD). However, the underlying mechanisms of transformation remain …
Read PDFIschemic stroke (IS) remains a leading cause of death and disability, with limited effective treatments in the acute phase. Mitophagy, the selective degradation of damaged mitochondria, plays a crucial role in cellular homeostasis and survival …
Read PDF<h4>Background</h4>Notch1 exhibits a high mutation rate in head and neck squamous cell carcinoma (HNSCC), but its functional role in nasopharyngeal carcinoma (NPC) invasion and metastasis remains incompletely understood. This study systematically investigates the function and …
Read PDF<h4>Background</h4>Osteoporosis is characterized by reduced bone mineral density and disrupted bone microstructure, leading to an increased risk of fractures. This study aimed to investigate the role of B cell subpopulations in osteoporosis and their effects …
Read PDFAnimals can provide meaningful context for human single-cell data. To transfer information between species, we propose a deep learning approach that pre-trains a conditional variational autoencoder on animal data and transfers its final encoder layers …
Read PDFSevere skin injury in humans typically heals through fibrotic remodelling rather than true regeneration, resulting in permanent loss of appendages, sensory function, and tissue architecture. Over the past decades, advances in bulk, single-cell, and spatial …
Read PDFSingle-cell multimodal omics technologies have empowered the profiling of complex biological systems at a resolution and scale that were previously unattainable. These biotechnologies have propelled the fast-paced innovation and development of data integration methods, leading …
Read PDFThe cerebellar rhombic lip neurogenic niche is critical for glutamatergic neurogenesis, and dysregulated differentiation of rhombic lip lineage cells is hypothesized to cause medulloblastoma (MB), a malignant pediatric cancer lacking targeted therapies. Humans have structural …
Read PDFOral squamous cell carcinoma (OSCC) is a highly aggressive head and neck malignancy with a poor prognosis associated with its complex tumor microenvironment. Cancer-associated fibroblasts (CAFs) contribute to tumor progression by secreting various signaling molecules. …
Read PDFMultiple myeloma (MM) is a heterogeneous hematologic cancer marked by clonal plasma cell expansion in the bone marrow. Although treatments have improved, relapse remains common due to clonal evolution, tumor microenvironment changes, ultimately leading to …
Read PDFDrug-induced liver injury remains a major obstacle in pharmaceutical development and a leading cause of acute liver failure, underscoring the need for predictive and human-relevant in vitro models. Acetaminophen, a widely used analgesic with well-characterized …
Read PDFAlthough microsatellite instability (MSI) is traditionally regarded as a binary trait, growing evidence indicates that it exists on a continuum, with higher intensity of MSI correlating with better prognosis. However, accurate quantification of MSI intensity …
Read PDFFever elevates body temperature to enhance immune response; however, intracellular temperature can fluctuate by up to 15 °C, suggesting a previously unrecognized layer of thermal regulation. While hyperthermia has long been exploited in medicine, how …
Read PDFSingle-cell multiomics technologies provide unprecedented opportunities to dissect cellular heterogeneity by capturing multidimensional information on complex cellular states and regulatory networks. However, challenges such as high dimensionality, extreme data sparsity, and modality-specific discrepancies hinder the …
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