Genetics

Identification of exosome-related genes signature based on bioinformatics and machine learning for prognostic prediction in colorectal cancer.

BACKGROUND: Colorectal cancer (CRC) is a prevalent malignant tumor with increasing incidence and mortality rates worldwide. Exosomes are secretory vesicles generated by the endosomal system within cells. Previous studies have reported that exosome-related genes (ERGs) are associated with the progression of malignancies. This study investigates the role of ERGs in CRC, evaluates their impact on CRC...

Positional interpretation of cis-regulatory code and nucleosome organization with deep learning models.

Sequence-to-function neural networks learn cis-regulatory sequence rules driving many types of genomic data. Interpreting these models to relate the sequence rules to underlying biological processes remains challenging, especially for complex genomic readouts such as MNase-seq, which maps nucleosome occupancy but is confounded by experimental bias. Here, we introduce pairwise influence by sequence...

GLORIF1, a global river flow dataset created by integrating process-based modelling and machine learning.

Accurate streamflow data are essential for managing water resources and enhancing climate resilience worldwide. Yet, existing global streamflow datase...

RankVar: machine learning-based variant ranking and reinterpretation for rare genetic diseases.

BACKGROUND: Prior biological knowledge and phenotype information can help identify disease genes from whole genome/exome sequencing studies, but how b...

Multi-omics integration identifies macrophage senescence driven by the RUNX1-P53 axis as a key mechanism in diabetic foot ulcer.

Diabetic foot ulcer (DFU) is a severe complication of diabetes, characterized by chronic inflammation and impaired healing. Although cellular and immu...

ELMERF: A deep-learning-assisted hydroponic RGB phenotyping framework for rice seedling salt-stress evaluation and genetic mapping.

Rice seedling salt-tolerance evaluation commonly relies on visual scoring or destructive assays, which are subjective, labor-intensive, and difficult ...

Evolving role of biomarkers beyond prostate‑specific antigen in refining prostate cancer screening: From blood‑based tests to urinary and genetic markers (Review).

Prostate‑specific antigen (PSA) screening reduces prostate cancer (PCa) mortality but is limited by overdiagnosis and poor specificity for clinically ...

Unlocking the Regulatory Genome: Interpreting the Clinical Impact of Noncoding Variants in Genetic Cardiomyopathies.

Clinical genetic testing is now the standard of care for cardiomyopathy, guiding risk stratification, clinical management, and earlier diagnosis in fa...

Artificial intelligence in molecular diagnostics for pandemic preparedness.

INTRODUCTION: Molecular diagnostics focusing on the detection and analysis of nucleic acids, are indispensable tools for early pathogen identification...

Identification and validation of novel diagnostic biomarkers across multiple tissues in osteoarthritis.

BACKGROUND: Osteoarthritis (OA) is a degenerative joint disease characterized by synovial inflammation, cartilage degradation, and subchondral bone re...

Machine learning models using 18F-FDG PET/CT radiomics for RAS mutation prediction and prognostic stratification in colorectal cancer.

OBJECTIVE: To evaluate a machine learning (ML) model that integrates clinical data and 2-deoxy-2-[18F]fluoro-D-glucose (18F-FDG)-PET radiomic features...

Recent advances in the detection and functional analysis of circRNAs with short-read RNA sequencing-based methods.

Circular RNAs (circRNAs) were first identified approximately 50 years ago in pathogenic viroids as single-stranded, covalently closed RNA molecules. I...

Network toxicology and multi-omics identify potential interactions between between air pollutants and interferon-related signaling in tuberculosis.

BACKGROUND: Air pollution increases tuberculosis (TB) susceptibility, yet the underlying molecular mechanisms remain elusive. METHODS: We integrated h...

Comprehensive identification of three key genes and three key DNA methylation CpG sites associated with prognosis and prediction in colon adenocarcinoma.

Colon adenocarcinoma (COAD) is a common cancer with high incidence and mortality rates worldwide. DNA methylation has a significant impact on the occu...

EssTFNet: integration of adaptive time-frequency and DNA language models for interpretable human essential gene prediction.

Essential genes are defined as indispensable for an organism's survival. The loss of function of these genes results in cell death or an inability to ...

Bridging local-global transmembrane protein contexts with contrastive pretraining for alignment-free pathogenicity prediction.

Predicting the pathogenic consequences of protein mutations is a cornerstone of precision medicine, yet it remains a formidable challenge for transmem...

Machine Learning-Based Drug Susceptibility Prediction from Candida Genomic Data.

Invasive Candida infection is an increasing clinical concern, with antifungal resistance rising across multiple species. However, rapid and accurate a...

Face/off: phase-specific modeling of lineage plasticity using near-patient models in genitourinary cancers.

Lineage plasticity has emerged as a fundamental mechanism of adaptive therapy resistance in prostate and bladder cancers, enabling malignant cells to ...

Urinary Volatile Organic Compound Metabolites and Depressive Symptoms Among U.S. Adults With Cardiovascular-Kidney-Metabolic Syndrome Stages 0-3: NHANES-Based Associations and In Silico Multi-Omics Insights.

BACKGROUND: Depression is a major global public health burden, and environmental pollutants are increasingly associated with depressive symptoms. Vola...

Integrating DNA methylation biomarkers for breast cancer risk prediction using artificial intelligence.

Breast cancer remains a major cause of morbidity and mortality among women worldwide, highlighting the necessity for predictive tools to identify at-r...