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Integrating single-cell omics data at an atlas scale enhances our understanding of cell types and disease mechanisms. However, the integration of data processed by different normalization methods can lead to biases, such as unexpected batch …
Read PDF<b>Background</b>: Virtual cells are embedded in widely used single-cell generative models. Nonetheless, the models' implicit knowledge of perturbations remains unclear. <b>Methods</b>: We train variational autoencoders on three gene expression datasets spanning genetic, chemical, and temporal …
Read PDFThe discovery of novel cell types and their marker genes is a fundamental goal of single-cell RNA sequencing (scRNA-seq). Nevertheless, most conventional methods rely on cell clustering, a process in which parameter selection is often …
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Read PDFSkeletal muscle satellite cells (SMSCs) are essential for embryonic myogenesis and postnatal muscle regeneration; however, their cellular heterogeneity and transcriptional dynamics during avian development remain largely unexplored. Here, we performed single-cell RNA sequencing (scRNA-seq) on …
Read PDFNeural crest cells (NCCs) are a key component of the vertebrate body plan and contribute to a variety of different traits. Recent advances in single-cell transcriptomics (scRNA-seq) have significantly improved our understanding of NCC biology. …
Read PDFExtracting biologically interpretable insights from single-cell RNA sequencing (scRNA-seq) data remains a major challenge. While deep learning approaches have demonstrated strong predictive performance for dimensionality reduction and representation learning, their latent representations often lack clear …
Read PDFIn this study, we developed an integrated single-cell transcriptomic (scRNAseq) atlas of human breast cancer (BC), the largest resource of its kind, totaling >600 000 cells across 138 patients. Rigorous integration and annotation of publicly …
Read PDFHuman milk is a bioactive fluid containing maternal leukocytes that support infant immune protection and development. Prior work has demonstrated the presence of atypical, non-granulocyte milk myeloid cells that do not conform to previously-defined cell …
Read PDFcrocketa (single-Cell Repertoire Organization & Combined Kinetics Exploration for Transcriptomic Analysis) is an automated and adaptable Snakemake pipeline designed to perform fundamental initial stages of single-cell analysis for both transcriptomic and immune repertoire data, with …
Read PDF<h4>Objective</h4>Irinotecan, a standard therapeutic agent for metastatic colorectal cancer (mCRC), often faces significant limitations due to drug resistance, with treatment failure observed in approximately 30%-50% of patients, leading to poor clinical outcomes. This study aims …
Read PDFBACKGROUND: Gastric intestinal metaplasia (GIM) is a precancerous lesion closely associated with gastric cancer (GC) risk. A systematic characterization of the molecular profiles across distinct cell types during GIM progression is crucial for devising new …
Read PDFThe exponential growth of single-cell transcriptomics datasets has made it essential to integrate heterogeneous datasets for constructing large-scale single-cell reference atlases and mapping query datasets onto these references. However, this integration process is significantly hampered …
Read PDFImmune ageing impairs adaptive and innate responses, yet the spleen remains underexplored by cross-cohort single-cell studies. We profiled splenocytes from young, old and chronically stressed old mice with natural microbiota using single-cell RNA sequencing. Ageing …
Read PDF<b>Objective:</b> To elucidate the role of cytoskeleton-associated protein 2 (CKAP2) in gastric cancer (GC) progression and evaluate its prognostic and potential protective significance. <b>Methods:</b> The candidate genes for GC were identified using differential expression and …
Read PDF<h4>Background</h4>Cancer-associated fibroblasts (CAFs) are a major stromal component of high-grade serous ovarian carcinoma (HGSOC), yet their functional programs and spatial organization remain incompletely defined and inconsistently reported across studies.<h4>Methods</h4>We analyzed single-cell RNA-seq data from 7 …
Read PDFThis study integrates single-cell RNA sequencing with Mendelian randomization to elucidate the role of nuclear factor of activated T cells (NFAT)-related genes in the progression of hepatocellular carcinoma (HCC). The GSE162616 dataset was analyzed to …
Read PDFThe advent of single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore cellular heterogeneity and developmental processes at the single-cell level. Despite its transformative potential, challenges such as technical limitations, high costs, and sample …
Read PDFBACKGROUND: Migraine and Meniere’s disease (MD) show high clinical comorbidity, shared symptoms such as vertigo and overlapping mechanisms like neurogenic inflammation suggest common pathophysiology. However, the core immunogenetic drivers underlying this comorbidity, particularly at cellular …
Read PDF<h4>Purpose</h4>Psoriasis is a chronic inflammatory skin disease that is characterized by abnormal keratinocyte proliferation and differentiation. This study aimed to explore potential regulatory mechanisms and key genes related to autophagy in the pathogenesis of psoriasis.<h4>Patients …
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