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Unraveling the significance of decorin in endometriosis development through single cell sequencing and experimental approaches
<h4>Background</h4>A link exists between decorin (DCN) and endometriosis, nevertheless, the role of DCN in this condition remains unclear. This study aims to bioinformatically characterize DCN expression, diagnostic value, and related signaling in endometriosis using single-cell …
Read PDFGenomic evolution of pancreatic cancer at single-cell resolution
Most evolutionary studies on pancreatic cancer rely on bulk sequencing, yet clonal evolution happens at the single-cell level. We used single-nucleus DNA sequencing to study 137,491 single nuclei from 24 pancreatic neoplasms reflecting various clinical …
Read PDFscComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution
Cell-cell communication regulates complex biological processes in multicellular systems. Existing scRNA-seq-based methods typically aggregate gene expression by clusters, overlooking within-cluster heterogeneity. We present scComm, a computational framework that infers cell-cell communications between individual cells using …
Read PDFIdentification of non-cardiomyocytes marker genes in patients with diabetes and cardiomyopathy through single-cell analysis
<h4>Background</h4>Diabetic cardiomyopathy (DCM) is a diabetes-related myocardial disorder causing fibrosis, hypertrophy, and progressive diastolic and systolic dysfunction. This study aims to explore how metabolic, inflammatory, and fibrotic mechanisms in non-cardiomyocytes drive DCM to reveal new …
Read PDFAssessment of dispersion metrics for estimating single-cell transcriptional variability
Single-cell RNA sequencing data enables analysis of transcript levels of single cells across different cell types and conditions. Recent work has highlighted the value of measuring gene-specific transcriptional variability, or noise, within a genetically identical …
Read PDFTranscriptomic profile of embryoid bodies under hypoxia at single cell level
Oxygen availability is a key regulator of cellular physiology and hypoxia plays a central role driving vasculogenesis and angiogenesis during development. Although bulk transcriptomics has revealed important oxygen-regulated gene networks, such approaches cannot resolve the …
Read PDFA Mouthful of Genomic Data: Single-Cell Insights into Salivary Gland Biology and Disease
Single-cell RNA-sequencing (scRNA-seq) studies over the past several years have provided unprecedented resolution into the transcriptomic landscape of both major and minor salivary glands. This technology enables the identification of diverse and functionally specialized cell …
Read PDFIdentification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data
<h4>Background</h4>Bladder cancer (BLCA) exhibits a poor prognosis, highlighting the urgent need for reliable prognostic genes. Although succinylation is linked to tumor progression, its role in BLCA remains understudied. This study aimed to identify and validate …
Read PDFSingle-Cell Profiling Reveals Distinct Immune Communication Networks in Centenarians and Elderly Controls
Aberrant cell-cell communication (CCC) is a recognized hallmark of aging, yet comprehensive analyses of immune CCC-particularly in the context of healthy aging-remain limited. Using single-cell transcriptomics of PBMCs from centenarians (CEN), their offspring (CO), and …
Read PDFMEAST: a novel framework for analyzing gene set stability in single cell transcriptomics
Biological processes rely on the coordinated activity of multiple genes, forming biological pathways that regulate specific cellular functions. Gene set activity analysis tools are essential for understanding how groups of genes regulate these processes. However, …
Read PDFA longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma
Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities with adult glioma, it comprises distinct disease entities. In this …
Read PDFNavigating the Landscape of Cytometry-Based Single-Cell Proteomics: Quantification, Annotation, and Resources
Cytometry-based single-cell proteomics (CySCP) has emerged as a powerful tool for analyzing cellular heterogeneity at the protein level because of its ability to reveal dynamic cell states and response patterns through high-dimensional protein expression profiling …
Read PDFiAODE for benchmarking and continuum modeling of single-cell chromatin accessibility
Single-cell chromatin accessibility profiles are extremely sparse but reflect continuous developmental trajectories. Most existing methods for dimensionality reduction and trajectory analysis optimize reconstruction error or cluster separation, without encoding temporal continuity in the model or …
Read PDFMultiplexed single-cell transcriptomics reveals diverse phenotypic outcomes for pathogenic SHP2 variants
The protein tyrosine phosphatase SHP2, encoded by <i>PTPN11</i>, is an important regulator of Ras/mitogen-activated protein kinase signaling that acts downstream of receptor tyrosine kinases and other transmembrane receptors. Germline <i>PTPN11</i> mutations cause developmental disorders such …
Read PDFSingle-cell transcriptomic analysis reveals APOE genotype-dependent sex differences in Alzheimer's disease
<h4>Introduction</h4>Alzheimer's disease (AD) is the most common form of dementia, with approximately two-thirds of AD patients being female. Basic and clinical research studies provide strong evidence that sex-specific differences contribute to AD complexity. Additionally, sex-specific …
Read PDFProtocol for single-cell optimization objective and trade-off inference
Single-cell optimization objective and trade-off inference (SCOOTI) is a computational framework that integrates bulk and single-cell omics data with genome-scale metabolic modeling to infer metabolic objectives and trade-offs in biological systems. Here, we present a …
Read PDFRedefining the immune microenvironment of gliomas in the era of single-cell genomics
Infiltrating gliomas are the most common primary malignant brain tumor and remain universally fatal. Over the past decade, advances in single-cell technologies, including single-cell RNA sequencing, have significantly advanced our understanding of malignant cells in …
Read PDFSingle-cell trajectory inference for detecting transient events in biological processes
Transient changes in gene or protein expression often mark the key regulatory checkpoints that propel cells from one functional state to the next, yet they are easy to miss in sparse, noisy single-cell omics data. …
Read PDFScalable data harmonization for single-cell image-based profiling with CytoTable
High-content imaging (HCI) involves the automated acquisition and quantitative analysis of cell phenotypes from microscopy images. These studies often rely on screening, which can involve thousands of chemical or genetic perturbations that produce terabytes of …
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