Innovation through Validation: The Case for Cross-Species Approaches
No abstract available.
Read PDFBrowse Papers
Search the literature by keyword, topic, or author. Filter to articles with full text available.
3689 results
Single-cell and spatial transcriptomic profiling of POU5F1 in Lung Adenocarcinoma: Dynamics, spatial niche, and prognosis via multi-algorithm ML
<h4>Background</h4>POU5F1 (OCT4), a core regulator of pluripotency, plays an important role in tumor stemness and immune microenvironment remodeling, yet its systematic function and mechanisms in lung adenocarcinoma (LUAD) remain incompletely elucidated.<h4>Methods</h4>This study integrated genetic causality …
Read PDFResearch progress in single‑cell omics technologies for kidney disease (Review)
The kidney is a vital organ for maintaining metabolic balance within the body and facilitating excretion. Its complex tissue structure comprises diverse cell types, including glomerular, tubular, interstitial and immune cells. The highly differentiated nature …
Read PDFThe translational paradox of AI in hepatocellular carcinoma: from algorithmic over-engineering to real-world clinical utility
Synthesizing recent literature from 2025 to 2026, this mini-review critically evaluates the methodological evolution of artificial intelligence (AI) in hepatocellular carcinoma (HCC) from static pattern recognition to mechanism-driven spatial and imaging diagnostics. We expose a …
Read PDFHarveST uses a heterogeneous graph learning framework to reveal spatial transcriptomics patterns
Spatial transcriptomics enables in situ gene expression profiling, yet precise spatial domain identification and marker gene detection remain challenging. We present HarveST, a heterogeneous graph-based framework that integrates spatial, transcriptomic, and gene-gene interaction data through …
Read PDFPrediction of clinical outcomes of advanced cutaneous squamous cell carcinoma to PD-1 inhibition directly from histopathology slides using inferred transcriptomics
<h4>Introduction</h4>Metastatic or locally advanced cutaneous squamous cell carcinoma (cSCC) that is not amenable to local therapy is treated with programmed death-1 (PD-1) inhibitors. Although response rates are relatively high, there are no validated predictive biomarkers …
Read PDFSingle-Cell and Spatial Omics: Methods and Applications
Single-cell and spatial omics have revolutionized biomedical research by enabling high-resolution molecular profiling across cells and tissues, thereby overcoming key limitations of bulk sequencing and revealing unprecedented cellular heterogeneity and spatial organization central to development, …
Read PDFIntegrative Molecular Analyses of Inflammatory and Autoimmune Signals in Cardiac Sarcoidosis
<h4>Background</h4>Cardiac sarcoidosis (CS) is an enigmatic disorder characterized by unexplained patchy, sterile granulomas intermixed with preserved myocardium and fibrotic regions without granuloma. CS causes arrhythmias, sudden cardiac death, and heart failure. The mechanisms producing this …
Read PDFComparative review of artificial intelligence for transcriptomic biomarker discovery in coronavirus disease 2019 (COVID-19)
The Coronavirus Disease 2019 (COVID-19) pandemic has highlighted the significance of reliable molecular biomarkers in clinical use. Despite the popularity of traditional statistical approaches, the high dimensionality of transcriptomic data presents challenges for these conventional …
Read PDFSpatial single-cell omics: new insights into liver diseases
The liver is a highly multifunctional organ that can perform many metabolic and immunological functions due to a highly complex spatially organised microarchitecture that is disturbed in many liver diseases. Recent methodological advances in spatial …
Read PDFAdvancing human ovarian biology in tandem with clinical care: considerations for collecting ovarian tissue for research after oophorectomy for tissue cryopreservation
Increased access to OTC has enabled the collection, with patient consent, of research tissue samples from healthy premenopausal patients. These samples are a critical resource to advance our understanding of fundamental ovarian biology. When choosing …
Read PDFTranscriptomics and AI-driven approaches to the diagnosis and treatment of rheumatoid arthritis
Rheumatoid arthritis (RA) is a chronic autoimmune inflammatory disorder marked by joint swelling, pain, and progressive tissue destruction. Increasing evidence suggests that dysregulated RNA expression critically drives RA progression by perturbing immune, inflammatory, and stromal …
Read PDFBenchmarking Spatial Clustering Methods for Mass Spectrometry-Based Spatial Metabolomics
<b>Background:</b> Mass spectrometry imaging (MSI) enables in situ mapping of metabolite distributions within tissues, and spatial clustering is a key step for delineating metabolically distinct regions. Nevertheless, spatial clustering methods have not been systematically benchmarked …
Read PDFImaging-Based Spatial Transcriptomics: Data Interpretation Methods and Biomedical Applications
Imaging-based spatial transcriptomics has advanced from low-plex single-molecule fluorescence in situ hybridization to a diverse set of highly multiplexed platforms, with recent multimodal and pathology-compatible capabilities. Despite major differences in chemistry, coding, and imaging strategies …
Read PDFThe "oral-gut axis" transmission of microorganisms in colorectal cancer: Insights from <i>Peptostreptococcus'</i> perspective
Colorectal cancer (CRC) is linked to gut microecological imbalances, and increasing evidence suggests that oral-gut microecosystem aberrant interactions also significantly contribute to CRC pathogenesis. The emerging "oral-gut axis" offers novel perspectives into the cross-organ microbial …
Read PDF