Genetics

Machine learning-based prediction of multi-level antimicrobial resistance in Klebsiella pneumoniae using whole-genome sequencing data.

OBJECTIVES: In this study, we developed an integrated approach for accurate and comprehensive prediction of anti-microbial resistance (AMR) using whole-genome sequencing (WGS) data. METHODS: We developed machine learning (ML) models using WGS data from 5239 strains, spanning three independent, geographically and temporally diverse cohorts. The models were designed for multi-level AMR prediction, i...

Decoupling lactylation-associated metabolic remodelling in Asthma: Integrated multi-omics and machine learning identify RCC2 as a potential therapeutic target.

BACKGROUND: Aerobic glycolysis promotes lactate accumulation and histone lactylation (Kla), yet the cell-type-specific distribution of this axis and its link to metabolically stratified intercellular signalling in asthma remain poorly defined. We aimed to map lactate/Kla-associated metabolic states across airway lineages and develop an interpretable Lactate Metabolic Biomarker Diagnosis (LMBD) fra...

MRI-driven multimodal deep learning approach for predicting pathological complete response after neoadjuvant chemoradiotherapy in locally advanced rectal cancer: A multicenter study.

OBJECTIVES: Achieving a pathological complete response (pCR) following neoadjuvant chemoradiotherapy (nCRT) in patients with locally advanced rectal c...

From pathogenesis to precision medicine in systemic lupus erythematosus: Emerging biomarkers and targeted interventions.

Systemic lupus erythematosus (SLE) is a chronic, systemic autoimmune disease characterized by immune dysregulation, autoantibody production, and chron...

Integrated multi-omics analysis identifies TBC1D10C as an NK- and T cell-associated diagnostic biomarker in childhood obesity.

Childhood obesity is a growing global health crisis associated with an increased risk of metabolic and cardiovascular diseases in adulthood. While acc...

Epigenetic Instability-Based Metrics in Cell-Free DNA for Early Cancer Detection.

PURPOSE: Cancers present significant DNA methylation changes, which arise in a stochastic manner, marked by extensive epigenetic variation, indicative...

Recent Advances in Analytical Techniques for Cancer Diagnostics and Therapeutics: Combining State-of-the-Art Technologies for Precision Oncology.

Cancer remains a leading global health challenge, necessitating continuous advancements in diagnostics and therapeutics to enhance patient outcomes. A...

Machine learning-based multi-omic analysis identifies CEP55, DLGAP5, and EZH2 as regulated cell death biomarkers linked to immunotherapy resistance in hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) often exhibits limited responsiveness to immune checkpoint inhibitors (ICIs), largely due to an immunosuppressive tumor...

Integrating Next-Generation Sequencing into von Willebrand Disease Diagnostics: Insights from the PCM-EVW-ES Multicenter Project.

Von Willebrand disease (VWD) is the most common inherited bleeding disorder, caused by quantitative or qualitative defects in von Willebrand factor (V...

Cytoplasmic lattices are megadalton storage complexes in mammalian oocytes.

Mammalian oocytes store proteins for embryonic development on abundant structures known as cytoplasmic lattices (CPLs)1; however, the mechanisms by wh...

Unveiling gene perturbation effects through gene regulatory networks inference from single-cell transcriptomic data.

Physiological and pathological processes are governed by networks of genes called gene regulatory networks (GRNs). By reconstructing GRNs, we can accu...

Bioinformatics analysis and qRT-PCR validation of iron metabolism-related genes in pediatric asthma.

Pediatric asthma (PA) is a chronic airway disease with a complex etiology, and iron metabolism disorder is believed to be involved in its pathogenesis...

Filtering of artificial chimeric reads generated by ligation preparation method of nanopore sequencing.

Nanopore sequencing provides long and ultra-long reads that are valuable for structural variation (SV) detection and genome assembly. However, false-p...

TargetGAN: A generative AI framework for the design of plant core promoters with targeted activity.

Plant core promoters (PCPs) are key genetic elements that control gene expression and have significant value for crop breeding and plant synthetic bio...

Identification and Validation of Transcriptomic Signatures in Inflammatory Bowel Disease with Metabolic Syndrome via Bioinformatics and Machine Learning.

BACKGROUND: Inflammatory bowel disease (IBD) is a chronic, nonspecific inflammatory disorder affecting the gastrointestinal tract. The condition's pat...

STC2-mediated calcium homeostasis dysregulation in the osteosarcoma microenvironment: Insights from single-cell sequencing and machine learning.

BACKGROUND: Osteosarcoma (OS) is an aggressive bone malignancy with a poor prognosis. Dysregulated calcium homeostasis may contribute to OS progressio...

Cross-task interpretability through unified modeling reveals a universal shortcut bias in neoantigen prediction.

Accurate neoantigen prediction is central to the design of personalized cancer immunotherapy. The immune recognition of neoantigens is a multi-step pr...

A sequence knowledge-guided deep learning method for single-cell multi-omics translation.

BACKGROUND: Analysis of proteins is key to understanding biological processes, disease pathogenesis, and advancing therapeutic development. However, p...

Integrated multi-omics and machine learning identify Casp8 and Pycard as central regulators of pyroptosis and necroptosis in spinal cord injury.

Programmed cell death pathways exacerbate secondary damage after spinal cord injury, yet their shared regulators and tractable therapeutic points rema...

The AudioGene Translational Dashboard for Diagnosing Autosomal Dominant Nonsyndromic Hearing Loss: Phenotypic Data Visualization and Analysis Study.

BACKGROUND: Autosomal dominant nonsyndromic hearing loss (ADNSHL) is highly heterogeneous, with more than 64 genes implicated in its etiology. This co...