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BACKGROUND: 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 PDFDistinct regional functionality of the human cortex is orchestrated by diverse cellular and molecular processes, yet the underlying regulatory mechanisms remain poorly understood. We performed multiomic single-cell and spatial characterization of nine regions of the …
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 …
Read PDFEstablishing a cell type-specific chromatin landscape is crucial for the maintenance of cell identity during embryonic development. However, our knowledge of how this landscape is set during vertebrate embryogenesis has been limited, due to the …
Read PDF<h4>Background</h4>Natural killer (NK) cells are core components of innate antitumor immunity, the dysfunction of NK cells in the tumor microenvironment is a major obstacle to the antitumor efficacy. Runt-related transcription factor 3 (RUNX3) acts as …
Read PDF<h4>Background</h4>Previous studies have integrated genome-wide association studies with expression quantitative trait locus (eQTL) data from bulk tissues to identify stroke susceptibility genes. However, eQTL data exhibit high cell-type specificity, and genetic variants may have distinct …
Read PDF<h4>Background</h4>Developmental dysplasia of the hip (DDH) is a common pediatric orthopedic disorder that predisposes affected children to early-onset osteoarthritis (OA), yet the cellular heterogeneity and fibrotic remodeling of acetabular cartilage are poorly understood.<h4>Methods</h4>We performed single-cell …
Read PDF<h4>Background</h4>Cirrhosis is a severe liver disease characterized by inflammation, fibrosis, and immune dysregulation. This study exploits publicly available single-cell sequencing datasets to decipher disease-relevant specific immune cell subtypes, their gene expression profiles and altered transcription …
Read PDF<h4>Background</h4>Clear cell renal cell carcinoma (ccRCC) is the most common histological subtype of kidney cancer and shows marked heterogeneity in progression, metastasis, and therapeutic response. Sphingolipid metabolism has emerged as an important regulator of tumor …
Read PDF<h4>Background</h4>Endometriosis is a chronic estrogen-dependent inflammatory disease that shares epidemiological and pathological features with endometrial cancer. However, the cellular and genetic mechanisms underlying this association remain unclear.<h4>Aim</h4>To investigate the immunological mechanisms underlying endometriosis and endometrial …
Read PDF<h4>Introduction</h4>Population aging is a global demographic shift closely associated with immune dysregulation, which significantly increases the risk of chronic liver diseases. As a crucial immune and metabolic organ, the liver relies on a complex immune …
Read PDFLung cancer in smokers (LCIS) and lung cancer in never-smokers (LCINS) are different entities with distinct molecular features. However, their cellular heterogeneity still requires further investigation. Through an integrated analysis of single-cell RNA sequencing and …
Read PDFClustering is commonly used in single-cell RNA sequencing (scRNA-seq) to assess cellular heterogeneity, but standard methods often require user-specified heuristics and rely on post-selective differential expression analyses, which often lead to inflated false discovery rates. …
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