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Single-cell spatial transcriptomes have demonstrated molecular and cellular diversity in the brain, but gene regulatory mechanisms underlying transcriptomic profiles and disease pathogenesis remain largely unknown in primates. Here we performed single-nucleus Assay for Transposase-Accessible Chromatin …
Read PDFSingle-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular heterogeneity in complex biological systems. However, analyzing and integrating scRNA-seq data poses unique computational challenges due to sparsity, high variability, and technical batch effects. Here, …
Read PDFSingle-cell multiomics technologies generate paired measurements of different cellular modalities, such as gene expression and chromatin accessibility. However, multiomics technologies are more expensive than their unimodal counterparts, resulting in smaller and fewer available multiomics datasets. …
Read PDFSubtalar arthrodesis (SA) is a widely used salvage procedure for posttraumatic subtalar arthritis (PSA), but its underlying healing mechanisms remain poorly understood. The immune system plays a critical role in the union process after arthrodesis; …
Read PDFSingle-cell RNA-seq (scRNA-seq) data from multiple species present remarkable opportunities to explore cellular origins and evolution. However, integrating and annotating scRNA-seq data across different species remains challenging due to the variations in sequencing techniques, ambiguity …
Read PDFThe development of skeletal muscle is a biological process of great complexity and high regulation whereby there is a spatiotemporal coordination of interactions amongst various cell and molecular events. Recent advances in scRNA-seq and ST …
Read PDFGene regulatory networks (GRNs) are essential models for understanding gene expression, cell differentiation, and cellular function. Existing GRN resources primarily focus on transcriptomic data and often overlook the epigenetic mechanisms of gene regulation, limiting evaluation …
Read PDFRapid technological progress now enables large-scale generation of single-cell data. Many laboratories can produce single-cell transcriptomic profiles from diverse tissues. A key step in single-cell analysis is unsupervised clustering followed by cell-type annotation, yet there …
Read PDFEndometriosis (EMS) is a common gynecological disease that seriously affects women's health and quality of life. However, the detailed dynamic cellular and molecular mechanisms underlying EMS pathogenesis remain largely unknown. This study establishes a novel …
Read PDFChondrosarcoma (CHS) is a malignant bone tumor resistant to adjuvant treatment, with high-grade patients suffering an unfavorable prognosis. Therefore, a deeper insight into the tumor microenvironment is essential for developing effective treatments for advanced CHS. …
Read PDF<h4>Background</h4>Lung adenocarcinoma (LUAD) is a leading cause of cancer-related mortality worldwide. The tumor microenvironment (TME) plays a pivotal role in LUAD progression, but the specific molecular mechanisms driving malignancy and immune evasion remain incompletely understood. …
Read PDFTo enhance the understanding of cellular heterogeneity within the pediatric thyroid, single-nuclei RNA sequencing was used to recover 38,069 non-pathogenic cells from thyroid tissue of three female pediatric/young adult patients. The recovered cells were analyzed …
Read PDFZ-DNA binding protein 1 (ZBP1) is a critical factor that induces various forms of cell death and inflammatory responses. However, it has not been comprehensively analyzed in malignancies. The present study aimed to elucidate the …
Read PDFSingle-cell transcriptomics enables precise characterization of cellular heterogeneity, but current pre-trained models relying solely on expression data fail to capture gene associations. We present scKGBERT, a knowledge-enhanced foundation model integrating 41 M single-cell RNA-seq profiles …
Read PDF<h4>Background</h4>The immune microenvironment of the three most common gynaecological malignancies-tubo-ovarian cancer, endometrial cancer and cervical cancer-has not been systematically studied, limiting clinical application.<h4>Methods</h4>This study analyses 272 389 CD45+ immune cells by integrating publicly available single-cell …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) carries a dismal prognosis, yet the contribution of deubiquitination-an essential posttranslational regulator-to its progression remains poorly defined.<h4>Methods</h4>Single-cell RNA-seq profiles of 13 treatment-naïve HCC tumors were integrated with 374 TCGA and 243 ICGC …
Read PDFThe relationship between melanogenesis, pigmentation, and melanocyte behavior is complex. In melanocytes, pigmentation is often associated with differentiation, yet mature melanocytes vary in pigment content. In melanoma, pigmentation-linked transcriptional programs may have prognostic value, but …
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