Genetics

WGCNA and machine learning identify mitochondria programmed cell death-related genes as diagnostic biomarkers for septic shock.

Septic shock (SS), the most severe stage of sepsis, has a high mortality rate. Mitochondria-mediated programmed cell death (MPCD) plays a key role in SS pathogenesis, but its diagnostic value remains unclear. This study integrated the GEO public dataset and used the WGCNA method to identify gene modules significantly associated with SS, and intersected them with MPCD-related genes to obtain the SS...

PTBP1 knockdown reprograms glioma stem cells into neuronal-like cells and suppresses tumorigenesis via the DUSP5-ERK1/2 signaling pathway.

BACKGROUND: Glioblastoma (GBM), the most prevalent and aggressive primary brain tumor in adults, has a median survival of merely 14 months. Current therapeutic approaches, including maximal safe resection, radiotherapy, and temozolomide-based chemotherapy, have limited efficacy owing to resistance and the high rate of recurrence. METHODS: We analyzed H&E-stained specimens from 65 patients with gli...

Machine learning-predicted chromatin organization landscape across pediatric tumors.

Structural variants (SVs) are increasingly recognized as important contributors to oncogenesis through their effects on 3D genome folding. Recent adva...

Investigating Phase Separation in Genome Folding via Multiscale Computational Modeling.

The 3D organization of the genome is central to gene regulation, and phase separation has emerged as an important physical principle for this architec...

DoTT-ML: Condition-aware detection of transcriptional readthrough from RNA-seq with optional ML-based prioritization.

Disruption of transcription termination (DoTT) occurs when RNA polymerase II reads past a gene's normal 3' end, generating downstream "readthrough" RN...

Endothelial cells recruit pro-inflammatory macrophage clusters via app-Cd74 exacerbating ICI-associated myocarditis.

Immune checkpoint inhibitor-related myocarditis (ICI-myocarditis) is a rare but highly threatening adverse reaction, and its pathogenesis is still unc...

OMICS Data in the Diagnosis of Diabetic Retinopathy: A Comparison between Transcriptome Data and DNA Methylation Data.

PURPOSE: Diabetic retinopathy is a serious complication of diabetes that can damage the retina of the eye. It potentially leads to vision impairment o...

Hypergraph Representations of Single-Cell RNA Sequencing Data for Improved Cell Clustering.

MOTIVATION: Single-cell RNA sequencing (scRNA-seq) data analysis is often performed using network projections that produce co-expression networks. The...

Advancing plant DNA barcoding: integrating chloroplast genome sequencing, cryptic diversity discovery and machine learning.

Accurate plant species identification underpins taxonomy, conservation, ecological monitoring, and the authentication of medicinal and food resources....

IGH::FENDRR and specific KRAS mutations define a novel B-ALL molecular subtype with poor chemotherapy response.

Large scale sequencing efforts have defined up to 27 diagnostic entities in B-ALL, leaving few samples without subtype assignment. Extended genomic an...

Beyond Percutaneous Coronary Intervention - Targeted Molecular Therapies for the Next Era of Coronary Care.

Coronary artery disease (CAD) remains the leading global cause of cardiovascular morbidity and mortality, driven by dysregulated lipid metabolism, chr...

Leveraging weighted embedding and Transformer architecture to improve phenotype prediction of complex traits for crops.

Understanding the relationship between genomic variation and phenotype is fundamental to deciphering the genetic architecture underlying complex trait...

What does it take to learn the rules of RNA base pairing? A lot less than you may think.

Amidst the fast-developing trend of RNA large language models with millions of parameters, we asked what would be minimally required to rediscover the...

CRISPR/Cas12a: A Comprehensive Review from Structural Foundations to Applications in Nucleic Acid Precision Detection.

CRISPR/Cas12a technology, characterized by its distinctive trans-cleavage activity, has evolved beyond its gene-editing function to emerge as a powerf...

Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution.

Bulk RNA sequencing (RNA-seq) deconvolution typically uses single-cell RNA sequencing (scRNA-seq) references, but some cells are only detectable throu...

CT Radiomic Features Are Associated with DNA Copy Number Alterations of Head and Neck Squamous Cell Carcinomas.

BACKGROUND AND PURPOSE: While a larger fraction of head and neck squamous cell carcinoma (HNSCC) genomes is characterized by a high prevalence of copy...

Deep learning-based precision phenotyping of spine curvature identifies novel genetic risk loci for scoliosis in the UK Biobank.

Scoliosis is the most common developmental spinal deformity, but its genetic underpinnings remain only partially understood. To identify scoliosis-rel...

Molecularly Engineered SERS Platform with Microturbulence-Enhanced Electrohydrodynamics for Multiplexed Profiling of Lung Cancer ctDNA.

Precise profiling of multiple circulating tumor DNA (ctDNA) is hindered by the challenge of resolving single-nucleotide variants (SNVs) and their trac...

Development and validation of a highly accurate multigene gene expression biomarker to predict chemotherapy response in primary triple-negative breast cancer.

PURPOSE: Triple-negative breast cancer (TNBC) is an aggressive subtype lacking estrogen and progesterone receptors and HER2 amplification. Representin...

DeepLMI: Deep Feature Mining with a Globally Enhanced Graph Convolutional Network for Robust lncRNA-miRNA Interaction Prediction.

MOTIVATION: Interactions between long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) play pivotal roles in gene regulation and disease progression, ...