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Single-cell RNA sequencing has transformed immunological research by enabling high-resolution transcriptional profiling of individual immune cells. Despite its transformative impact, annotating immune cells based solely on transcriptomic data remains challenging. These difficulties arise from biological …
Read PDFBreast cancer remains the leading cause of cancer-related mortality among women worldwide, primarily due to metastatic complications. The immune components of the tumor microenvironment (TME) significantly influence metastatic progression. The objective of this study was …
Read PDF<h4>Introduction</h4>This study constructs a high-resolution multi-omics map of Diffuse Large B-Cell Lymphoma (DLBCL) by integrating single-cell, single-nucleus, and spatial transcriptomics.<h4>Methods</h4>We identified a previously unrecognized, recurrent subset of malignant B cells that unexpectedly express CD3, a …
Read PDFThe skin is the largest human organ and a site of substantial disease burden, yet its cellular and molecular organization across the body is largely undefined. Here we construct an organ-wide single-cell spatial atlas of …
Read PDFSpatial transcriptomics (ST) enables in situ analysis of gene expression patterns and spatial microenvironments. However, current ST technologies are limited by detection sensitivity and gene coverage, posing significant challenges for precise cell type annotation at …
Read PDFThe generation of complex traits involves the coordinated interplay of multiple gene networks. Elucidating the function of transcriptional cis-regulatory elements (CREs) in regulating gene expression is crucial for understanding complex regulatory pathways and improving our …
Read PDFTelmisartan, an angiotensin II type 1 receptor blocker with established anti-inflammatory and antihypertensive properties, has been reported to inhibit tumor cell proliferation, yet its impact on the tumor immune microenvironment remains poorly understood. In this …
Read PDFAfrican swine fever virus (ASFV) infection leads to severe lung lesions in the host, yet detailed insights into the <i>in vivo</i> immune response of the lung microenvironment to ASFV infection at the single-cell level remain …
Read PDFTumor-associated macrophages (TAMs) constitute a critical immune cell population within the tumor microenvironment (TME) and exhibit high functional heterogeneity. In this study, a pan-cancer atlas comprising 28 TAM subtypes was systematically constructed by integrating single-cell …
Read PDFAmpullary carcinoma (AC) is a rare epithelial cancer, representing around 0.2% of all gastrointestinal malignancies worldwide, with an estimated incidence of 0.73 per 100,000 people. The rarity of AC, combined with the intricate anatomy of …
Read PDFWe present SCITE-RNA, a novel phylogenetic tree inference method designed for single-cell RNA sequencing data which takes reference and alternative read counts of single-nucleotide variants as input. Our approach uses a maximum-likelihood random-scan greedy search …
Read PDFAt the transcriptomic level, several molecular subtyping schemes have been established to elucidate the intrinsic heterogeneity of urothelial carcinoma and to inform prognostic assessment and therapeutic guidance. However, a unified molecular classification scheme characterizing genomic …
Read PDF<h4>Background</h4>Congenital anomalies of the kidney and urinary tract (CAKUT) comprise a heterogeneous group of developmental disorders with diverse genetic etiologies. However, it remains unclear whether these genetic factors converge on shared cellular programs across development …
Read PDFAlternative splicing expands transcriptomic and proteomic diversity and contributes to cell identity and function. Advances in single-cell RNA sequencing enable transcriptome profiling at cellular resolution, yet their performance across biologically relevant tasks has not been …
Read PDFReference-based annotation tools have become standard for cell type assignment in single-cell RNA sequencing, leveraging large-scale atlases to transfer labels to new datasets. However, a substantial fraction of cells often receive uncertain or ambiguous annotations-low …
Read PDF<h4>Motivation</h4>Throughout the years, single-cell RNA sequencing (scRNA-seq) has become a standard approach for characterising transcriptomic changes associated with diseases and other biological conditions. However, the rapid expansion of tools and algorithms developed in various programming …
Read PDFThis study investigates the role and mechanism of ergothioneine (EGT) in mitigating the progression of acute kidney injury (AKI) to chronic kidney disease (CKD). Using a cisplatin-induced mouse model of the AKI-to-CKD transition with EGT …
Read PDFAlternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism that diversifies transcript isoforms and modulates mRNA stability, localization, and translation. Although single-cell RNA sequencing (scRNA-seq) provides an unprecedented opportunity to study cell-type-specific APA dynamics, existing …
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