Genetics

Prognostic Significance and Therapeutic Implications of Migrasome-related genes in Sorafenib Treatment for Primary Liver Cancer.

PURPOSE: This study aimed to reveal the mechanism and prognostic significance of migrasome-related genes (MGs) in primary liver cancer (PLC) treated with Sorafenib (Sor) treatment. METHODS: Datasets were extracted from an online database, and differentially expressed genes (DEGs) were explored. WGCNA was used to detect co-expressed gene modules. Next, MGs and differentially expressed MGs were inte...

Exploration and validation of potential diagnostic biomarkers of PANoptosis in periodontitis using bioinformatics approaches.

BACKGROUND: Periodontitis represents a chronic inflammatory disease resulting from the interaction between plaque-associated microorganisms and the host immune response. PANoptosis, a newly recognized programmed cell death, is linked to multiple inflammatory disorders. However, its role in periodontitis pathogenesis and diagnostic potential remains unclear. This study aimed to identify key PANopto...

Identification of diagnostic senescence-associated marker genes in asthma based on machine learning and experimental validation.

BACKGROUND AND AIMS: Asthma imposes a significant global health burden; however, the mechanistic role of cellular senescence in its pathogenesis remai...

Stable maintenance of MERVL-positive embryonic stem cells reveals sustained transcriptional programs and enhancer remodeling.

Mouse embryonic stem cells (ESCs) occasionally transit into a rare two-cell-like (2C) state characterized by transient activation of endogenous retrov...

Cross-Platform Comparative Spatial Transcriptomics in High-Grade Serous Carcinoma.

PURPOSE: High-grade serous carcinoma (HGSC) is a remarkably heterogeneous tumor. The purpose of this study was to directly compare the reproducibility...

The role of whole genome sequencing in antimicrobial susceptibility prediction of bacteria: 2025 update from the EUCAST Subcommittee.

SCOPE: The 2017 European Committee on Antimicrobial Susceptibility Testing (EUCAST) subcommittee report on the role of Whole Genome Sequencing (WGS) i...

Artificial intelligence in the differential diagnosis of hypertrophic cardiomyopathy and physiological hypertrophy: a scoping review.

BACKGROUND: Hypertrophic cardiomyopathy (HCM) is the most common inherited myocardial disorder and a major cause of sudden cardiac death in young adul...

Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data.

MOTIVATION: Analysis of single cell ATAC-seq and RNA-seq data has allowed to gain unprecedented insights into gene regulation by allowing to define ce...

PythiaStudio: a one-stop protein engineering platform powered by Pythia model suite.

Predicting how mutations affect protein stability and protein-protein binding affinity is crucial for protein engineering and drug development. Althou...

Integrating spatial and single-cell transcriptomics via machine learning to characterize efferocytosis in hepatocellular carcinoma prognosis and immunotherapy.

BACKGROUND: The intratumoral heterogeneity and immunosuppressive microenvironment of hepatocellular carcinoma (HCC) significantly limit therapeutic ef...

NucVerse3D: generalizable 3D nuclear instance segmentation across heterogeneous microscopy modalities.

Accurate three-dimensional (3D) nuclear instance segmentation is a prerequisite for quantitative phenotyping in volumetric microscopy, yet remains cha...

Network clustering algorithms and preprocessing pipelines for robust cell type identification in single-cell RNA sequencing data.

Single cell RNA-seq (scRNA-seq) technologies provide unprecedented resolution representing transcriptomics at the level of single cell. One of the big...

Osteoarthritis phenotypes: advancing precision medicine through clinical, structural, and molecular stratification.

PURPOSE: Osteoarthritis (OA) is now understood as a heterogeneous syndrome driven by diverse biological, biomechanical, metabolic, genetic, and molecu...

HESpotEx: a dual-stream deep learning framework for spot-level gene expression prediction from histological images.

Whole-slide histopathological images (WSIs) constitute a fundamental approach in disease diagnosis and prognosis. Recently emerging spatial transcript...

Metabolomics at the Crossroads of Forensic Toxicology and Precision Diagnostics: Analytical Innovations and Translational Opportunities.

Metabolomics is the comprehensive analysis of small-molecule metabolites in living systems and is increasingly being applied in forensic science and h...

Structure-aware retinal disentanglement reveals the genetic architecture of ocular and systemic diseases.

Deep learning effectively extracts retinal phenotypes but often functions as an entangled black box, obscuring specific genetic mechanisms and hinderi...

Co-application of pan-genomics and machine learning uncovers novel insights into the maintenance and evolution of microcystins production trait in Microcystis.

Microcystins (MCs), the potent hepatotoxins produced by toxic strains of Microcystis and other cyanobacteria, pose a major threat to freshwater ecosys...

Sequence determinant and functional relevance of 8-oxoguanine RNA modification unveiled from foundation-model-based predictor.

8-Oxoguanine (o8G) is an oxidative RNA modification that plays critical roles in cellular processes including stress responses and RNA integrity regul...

Identification and validation of lactylation-related genes signature and immune infiltration landscape of rheumatoid arthritis based on machine learning.

BACKGROUND: The pathogenic mechanisms underlying rheumatoid arthritis (RA) remain elusive. Lactylation, a novel post-translational modification, may r...

Crotonylation: A Novel Layer of the Epigenetic Landscape in Disease.

Crotonylation is a lysine acylation modification that links cellular metabolism to epigenetic regulation. Its rigid planar crotonyl group is specifica...