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Single-cell RNA sequencing (scRNA-seq) has revolutionized transcriptomic research, enabling the creation of detailed tissue, organ, and species-level atlases for model organisms. In Hydractinia, a cnidarian model for stem cell and regeneration studies, recent atlases have …
Read PDF<h4>Introduction</h4>Intra-tumoural heterogeneity contributes to treatment resistance and disease progression in cancer. Single-cell RNA sequencing (scRNA-seq) enables profiling of cellular diversity in the tumour microenvironment. However, current protocols for generating single-cell 3'gene expression data require intact …
Read PDF<h4>Background</h4>Hepatocellular carcinoma (HCC) is one of the most prevalent malignant tumors globally, with liver cirrhosis (LC) recognized as a significant precursor. Xenobiotic metabolism plays a pivotal role in liver diseases, where the liver's primary function …
Read PDFFollowing thymic egress, CD8<sup>+</sup> T cells undergo post-thymic maturation to transition from recent thymic emigrants (RTEs) to mature naive T cells. Although RTEs are phenotypically and functionally distinct from mature naive CD8<sup>+</sup> T cells, most …
Read PDFThe pons and medulla, key regions of the hindbrain within the brainstem, regulate a wide range of complex behaviors, ranging from motor control to autonomic regulation and reflexes. As the central hub of neural projections …
Read PDFBACKGROUND: Breast cancer is one of the most prevalent malignant tumors among women, with its metastasis serving as a leading cause of mortality in affected patients. Recent studies have increasingly highlighted the significant role of …
Read PDFSingle-cell RNA sequencing (scRNA-seq) provides an instantaneous snapshot of the transcriptional state of a cell, which results from the simultaneous activity of many cellular processes. In this issue of Cell Genomics, Chen et al.<sup>1</sup> describe …
Read PDFAdeno-associated viral (AAV) vectors are rapidly advancing as gene therapies for retinal diseases, but gene therapy-associated uveitis (GTAU) limits their broader application. We assessed the ocular immune response to subretinal AAV gene therapy in two …
Read PDFSystematic whole-protein screening and comprehensive profiling of antigen-specific CD4<sup>+</sup> T cells are crucial for advancing vaccine design and cancer immunotherapies, yet remain technically challenging. Here, we present a high-throughput platform that utilizes large-scale class II …
Read PDF<h4>Background</h4>Microvascular invasion (MVI) is a critical determinant of early recurrence and poor prognosis in hepatocellular carcinoma (HCC). The cellular and molecular mechanisms driving MVI, particularly the role of endothelial heterogeneity, remain incompletely understood.<h4>Methods</h4>We integrated single-cell …
Read PDFImmune checkpoint blockade has shown benefit in some Triple-negative breast cancer (TNBC) patients, but responses are variable. BRCA1-mutated TNBC represents a biologically distinct subgroup, potentially differing in immunogenicity and immunotherapy responsiveness. However, immune microenvironment differences …
Read PDF<h4>Introduction</h4>The formation and homeostatic maintenance of cranial sutures rely on cellular activities within the suture mesenchyme. However, how mesenchymal stem/stromal cells (MSCs) rapidly and extensively contribute to suture and cranial development remains insufficiently explored.<h4>Methods</h4>We integrated …
Read PDF<h4>Background</h4>Atopic dermatitis (AD), a common chronic inflammatory skin disease, has been extensively studied using single-cell genomics. However, keratinocytes, as key effector cells in AD, have underlying mechanisms remain incompletely understood and require further investigation.<h4>Methods</h4>We integrated …
Read PDFBACKGROUND: Leaves require the coordinated regulation of multiple types of cells to accumulate energy for plants. Transcriptome analysis at the tissue level cannot analyze the heterogeneity of cells or reveal the molecular regulatory mechanisms of …
Read PDF<h4>Background</h4>The tumor immune microenvironment, containing a variety of immune cells with both tumor-promoting and anti-tumoral functions, plays a significant role in tumor immune surveillance and immunological evasion. Characterizing the landscape of the tumor immune microenvironment …
Read PDF<b>Background</b>: Standard single-cell RNA sequencing (scRNA-seq) analysis workflows face significant limitations, particularly the rigidity of clustering-dependent methods that can obscure subtle cellular heterogeneity and the potential loss of biologically meaningful cells during stringent quality control …
Read PDFTumor-associated B (TAB) cells and plasma cells are increasingly recognized as key components of the tumor microenvironment; however, their heterogeneity and functional roles in breast cancer remain incompletely understood. Here, by integrating publicly available single-cell …
Read PDFSingle-cell RNA-seq data from F1 hybrids provide a unique framework for dissecting complex regulatory mechanisms, but allelic measurements are limited by technical noise due to low counts. Here, we present ASPEN, a statistical method for …
Read PDFPrecise prediction of perturbation responses is essential in systems biology research, as it plays a pivotal role in characterizing cellular identities and elucidating the regulatory mechanisms of biological pathways. Existing perturbation-responses prediction approaches are predominantly …
Read PDFOmics research is changing the way medicine develops new strategies for diagnosis, prevention, and treatment. With the surge of advanced machine learning models tailored for omicss analysis, recent research has shown improved results and pushed …
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