Genetics

CKLF1 Serves as a Pivotal Mediator of Blood-Brain Barrier Disruption and Neuroinflammation via PI3K/AKT/mTOR Signaling in Ischemic Stroke.

Ischemic stroke (IS) is accompanied by blood-brain barrier (BBB) disruption and neuroinflammatory activation, but the upstream regulatory mechanisms remain incompletely defined. Here, integrated single-cell RNA sequencing, regulatory network analysis, and machine-learning screening identified Chemokine-like factor 1 (CKLF1) as a candidate endothelial regulator associated with IS. Functional valida...

Integrative TWAS and multi-omics analyses prioritize HSPE1 as a candidate risk gene for bipolar disorder with immune cell-specific regulatory evidence.

BACKGROUND: Bipolar disorder (BD) is a severe psychiatric disorder associated with substantial disability. Although genome-wide association studies have identified multiple BD-associated loci, the underlying genes and mechanisms remain incompletely understood. METHODS: We integrated a European-ancestry BD genome-wide association dataset with cross-tissue and tissue-specific transcriptome-wide asso...

SPCC: Inferring Spatial Cell-Cell Interaction by Integrating Single-cell and Spatial Transcriptomics.

Study of single-cell spatial biology reveals the importance of integrating single-cell and spatial data for capturing spatial structure at individual ...

Fine-Grained Structural Classification of Biosynthetic Gene Cluster-Encoded Products.

MOTIVATION: Biosynthetic gene clusters (BGCs) are responsible the biosynthesis of many natural products, including a multitude of effective therapeuti...

MOFUN-CCC: A Multi-omics Intermediate Fusion Network for Digital White Blood Cell Count Prediction.

As the volume of omics data continues to grow exponentially, there is an increasing demand for innovative methodologies that combine multi-omics data ...

Genomic characterization of an unusual bloodstream Weissella viridescens isolate obtained from a Bulgarian intensive care unit patient.

BACKGROUND: The present study aimed to explore the genomic characteristics of an extremely rare clinical Weissella viridescens isolate (designated Wvi...

Clustering of rheumatoid arthritis patients: an unsupervised machine learning approach for characterizing the TNFi response.

This study aimed to identifydistinct profiles of response to Tumor Necrosis Factor inhibitors (TNFi) in rheumatoid arthritis (RA) patients using unsup...

The miRNA-virus Axis in RNA Virus Infections: Mechanisms, Therapeutic Targeting, and Systems Biology Approaches.

RNA viruses are a diverse and rapidly evolving group of pathogens that significantly contribute to worldwide morbidity and mortality, propelled by ele...

Structural bases of the conformational transitions of the mitochondrial choline carrier SLC25A48 captured by molecular dynamics simulations.

The mitochondrial choline carrier SLC25A48 mediates choline import into the mitochondrial matrix, supporting one‑carbon metabolism and epigenetic regu...

Comprehensive Analysis of Starvation Response-Related Genes in the Diagnosis of Ischemic Stroke: Based on Machine Learning and Single-Cell RNA Sequencing Data.

BACKGROUND: The pathogenesis of ischemic stroke (IS) involves a starvation response (SR); however, the mechanistic link between the two remains unclea...

Multi-Omics Integration Identifies a CDH3-Associated Malignant Epithelial State and Immunosuppressive Niche to Predict Prognosis in Thymic Epithelial Tumors.

Thymic epithelial tumors (TETs) are rare and heterogeneous malignancies whose aggressive epithelial states and microenvironmental organization remain ...

Integration of single-cell transcriptomics and genomic mutation analysis identifies an immunotherapy-resistant tumor subcluster and validates ARNTL2 as a malignant driver in lung adenocarcinoma.

BACKGROUND: Immunotherapy resistance in lung adenocarcinoma (LUAD) remains a critical clinical challenge, and the mechanisms underlying resistance-ass...

Diagnostic Model Development for IC/BPS and Its Subtypes Using Clinical Indicators, Urinary Biomarkers, and Single-Cell Transcriptomic Analysis.

Interstitial cystitis/bladder pain syndrome (IC/BPS) is a chronic, heterogeneous, and often debilitating condition. This condition is often misdiagnos...

CPTCs Drive Somatic-Visceral Communication via the Wnt Axis in Somatic Mechanotherapy: A Single-Cell Deep Learning Study.

Somatic mechanical stimulation (e.g., acupuncture) exerts systemic immunomodulatory effects, yet the cellular bridge translating peripheral physical f...

Integrating heterogeneity into topologically associating domain boundary prediction in large genomic context in human.

A fundamental understanding of genome organization relies on accurately annotating topologically associating domains (TADs) and their boundaries. This...

Precision Lipid Management in the Era of Biotechnology and Artificial Intelligence: From Gene Editing to Smart Drug Delivery.

BACKGROUND: Hyperlipidemia is a major modifiable contributor to atherosclerotic cardiovascular disease (ASCVD). Despite statins as first-line therapy,...

Machine Learning-Derived Sarcopenia Signature Identifies High-Risk Molecular State in T2D Skeletal Muscle.

Sarcopenia is common in type 2 diabetes (T2D), but whether sarcopenia-associated transcriptomic features can be detected in diabetic skeletal muscle r...

Multimodal MRI insights into hippocampal pathological changes across the Alzheimer's disease continuum: advances and challenges.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder, with early and progressive hippocampal pathology serving as a hallmark across th...

scKanFormer: A Transformer-KAN framework with biologically informed attention for cell type annotation in large-scale scRNA-seq data.

A key challenge in single-cell RNA sequencing (scRNA-seq) data analysis is accurately and efficiently identifying the cell type of each cell. Cell typ...

Structure-aware deep learning enhances m6A prediction and reveals cell type-associated RNA structural signatures.

N6-methyladenosine (m6A), the most abundant mRNA modification in eukaryotes, plays essential roles in gene regulation and disease pathogenesis. Comput...