Genetics

Physics-based prediction of protein folding and unfolding rates: Examining the roles of fold topology and core packing.

The (un)folding rates of natural proteins determine their native stability and functional homeostasis, making them important targets for protein engineering and design. From a prediction standpoint, the rates have been a long-standing puzzle. We have known for decades that folding rates empirically correlate with properties of the native three dimensional (3D) structures and that both, folding and...

Multiomics Profiling Identifies Blood-Based Diagnostic Markers for Sepsis.

Sepsis, characterized by a rapid transition to systemic immune dysregulation and multiorgan failure, poses a formidable clinical challenge. The lack of spatiotemporally stable biomarkers severely impedes early diagnosis and risk stratification. By integrating large-scale transcriptomic profiling with machine learning algorithms, this study identified a robust three-gene diagnostic signature (TLR5,...

Single-frame super-resolution sequencing method based on lattice prior.

High-throughput sequencing requires breaking the resolution limit to support higher-density DNA Nanoball (DNB) arrays, thereby reducing cost and incre...

Mycoplasma infection drives EGFR-TKI resistance through convergent transcriptomic reprogramming in non-small cell lung cancer.

Epidermal growth factor receptor (EGFR) mutations are an oncogenic driver in non-small cell lung cancer (NSCLC), but resistance to EGFR tyrosine kinas...

Recent advances in biomarkers, artificial intelligence, and targeted therapeutic strategies in breast cancer: Current progress and future perspectives.

Breast cancer is a complex and heterogeneous disease that remains a major global health challenge. Recent progress in molecular biology, artificial in...

Genome-wide association analysis reveals specialization to hosts and niches in multiple species of the Lactobacillaceae.

The Lactobacillaceae inhabit diverse environments, but the extent of their habitat adaptation remains unclear and the colonization factors unknown. Fi...

A module-based approach for post-omics, post-GWAS network-based gene classification.

MOTIVATION: Complex traits and diseases are highly polygenic and understanding the full set of genes involved is a central challenge in biomedicine. H...

Modular RNA-seq Analytics for Exploratory Biomarker Discovery using Public Data.

Publicly available RNA sequencing (RNA-seq) data provide a cost-effective springboard for biomarker discovery. However, heterogeneity across studies o...

VAERNAGen: A variational autoencoder-based framework for de novo generation of RNA family sequences.

RNA plays a pivotal role in diverse cellular processes, and the rational design of functional RNA sequences is central to advancing RNA engineering. W...

Classification of Inherited Retinal Diseases Using Artificial Intelligence Models for Fundus Autofluorescence and Ultrawide Retinal Images.

BACKGROUND/OBJECTIVES: Inherited retinal diseases (IRDs) are a leading cause of blindness in working-age adults. Although artificial intelligence (AI)...

Integrative multi-omics and machine learning identify CHRNA1 putative circadian-immune hub in COPD.

BACKGROUND: Circadian rhythm disruption is increasingly recognized as a contributor to chronic inflammatory disorders; however, its specific significa...

Deep learning architectures for EEG-based classification of Dravet syndrome: A comparative study of pre-trained and non-pretrained hybrid CNN-LSTM models.

OBJECTIVE: This study explores the potential of artificial intelligence (AI) using a hybrid deep learning Convolutional Neural Network-Long Short-Term...

Whole genome sequencing in cerebral palsy: a UK paediatric pilot study.

BACKGROUND: Prior international studies indicate that 9-36% of people with cerebral palsy (CP) have a monogenic condition. However, the utility of who...

Engineering autoimmune disease models using organoids: Harnessing microenvironmental engineering for precision medicine and immunological recapitulation.

Autoimmune diseases-including systemic sclerosis (SSc), systemic lupus erythematosus (SLE), and rheumatoid arthritis (RA)-are increasingly understood ...

Toxic effects and mechanisms of methyl 4-hydroxybenzoate in allergic rhinitis: a multi-omics and toxicology study.

PURPOSE: Exogenous chemical exposure is closely associated with allergic rhinitis (AR). Methyl 4-hydroxybenzoate (MeP), a widely used preservative, po...

Interferon-Associated Antiviral Programs Define LAG-3+ Exhaustion-Like CD8+ T-Cell Remodeling in Influenza a Virus Infection: An Integrative Single-Cell and Multi-Cohort Analysis.

BACKGROUND: Influenza A virus (IAV) infection induces complex antiviral immune responses, yet how innate sensing, host genetic susceptibility, and ada...

Emerging biomarkers in breast fibroadenoma: implications for differential diagnosis, malignant transformation, and precision medicine.

Fibroadenoma is the most common benign fibroepithelial lesion of the breast; it occurs most frequently in adolescents and women of reproductive age. W...

Three-class obstructive sleep apnea severity assessment: a parallel AHI and ODI explainable artificial intelligence framework using craniofacial-enriched clinical data.

BACKGROUND: Machine learning models for Obstructive Sleep Apnea (OSA) diagnosis have largely inherited some structural limitations: reliance on generi...

Enterococcus faecium MMX derived from traditional fermented mare's milk alleviates colitis by modulating the LCN2-NLRP3 pyroptosis axis.

Ulcerative colitis (UC) is a relapsing inflammatory disorder of the intestine for which safe and effective therapeutic strategies are urgently needed....

A Multi-omics Regulated Cell Death Framework Defines Immune Phenotypes and Guides Precision Therapy in Colorectal Cancer.

Colorectal cancer (CRC) is molecularly and immunologically heterogeneous, contributing to variable treatment response. Because regulated cell death (R...