Genetics

Bioinformatics applications in pharmacogenomics: towards personalized medicine.

Pharmacogenomics investigates how genetic variation influences individual responses to drug therapy and aims to optimize treatment outcomes through personalized approaches. Bioinformatics plays a foundational role in this field, enabling the processing, annotation, and interpretation of complex genomic and multi-omics datasets. This review explores the current landscape of bioinformatics in pharma...

Advancing CNS tumor diagnostics with expanded DNA methylation-based classification.

DNA methylation-based classification is now central to contemporary neuro-oncology, as highlighted by the World Health Organization (WHO) classification of central nervous system (CNS) tumors. We present the Heidelberg CNS Tumor Methylation Classifier version 12.8 (v12.8), trained on 7,495 methylation profiles, which expands recognized entities from 91 classes in version 11 (v11) to 184 subclasses...

Integrated m6A reader network in acute myeloid leukemia: prognostic modeling, immune modulation, and functional validation of YTHDF3.

Emerging evidence highlights RNA N6-methyladenosine (m6A) modifications as pivotal regulators of tumorigenesis, yet the synergistic roles of m6A reade...

Genomic assessment of reproduction traits in Holstein dairy cattle across 3 lactations using additive genetic models and post hoc random forest analysis.

The typical objective of genomic analyses is to assess additive genetic variance in traits. However, the nonadditive component of genetic variation is...

Prediction of IDH-mutation and 1p19q-codeletion status in adult-type diffuse gliomas using three-class radiomics models.

PURPOSE: To predict the genetic subtypes of adult-type diffuse gliomas with three-class MRI radiomics. MATERIAL AND METHODS: Four hundred and eighty p...

From macroscopic clearance to molecular eradication: paradigm shift and future perspectives in the detecting of residual lesions after transurethral resection of bladder tumors.

INTRODUCTION: Residual lesions after transurethral resection of bladder tumor (TURBT) are a major contributor to recurrence in bladder cancer. Advance...

Machine learning-assisted photoelectrochemical biosensor based on DNA-AgNCs nanowires for exosomal lncRNA intelligent diagnosis.

BACKGROUND: Exosomal long non-coding RNA (lncRNA) as a burgeoning biomarker, its abnormal expression is closely related to the progression of cancer. ...

Biological multi-omics approaches to next-generation biomarkers in immune-related disorders and malignancies: An overview.

Cancer and autoimmune diseases are major global health challenges characterized by molecular and clinical heterogeneity. Traditional single-analyte bi...

Graph-based deep learning approach for high-throughput protein-DNA interaction scoring.

Accurately quantifying protein-DNA interactions (PDIs) is critical for understanding biological processes and facilitating drug design. However, the i...

Unveiling CDKN1A and RELA: Machine learning-driven aging biomarkers for precision diagnosis and therapy in knee osteoarthritis.

BACKGROUND: Knee Osteoarthritis (KOA) is a degenerative joint disease marked by progressive cartilage deterioration, closely tied to cellular senescen...

Pathway-Informed Machine Learning Identifies Genetic Predictors of High-Dose Methotrexate-Induced Mucositis in Pediatric Acute Lymphoblastic Leukemia.

High-dose methotrexate for pediatric cancer treatment is frequently associated with mucositis, which can lead to delayed or discontinued treatment and...

Impact of disease-modifying therapy on [99mTc]Tc-DPD SPECT/CT markers in transthyretin cardiac amyloidosis enabled by artificial intelligence.

PURPOSE: Transthyretin cardiac amyloidosis (ATTR-CM) is a progressive, underdiagnosed disease with high morbidity and mortality. While disease-modifyi...

Integrating pan-genome analysis, GWAS, and interpretable machine learning to prioritize trait-associated structural variations in Setaria italica.

Structural variations (SVs), especially presence-absence variations (PAVs), are crucial in crop domestication and trait improvement. Although pan-geno...

Engineering lignin pathway, plant cell wall modification, and genome editing for advanced renewable bioenergy and material applications.

Lignin biosynthesis and plant cell wall engineering are central to plant structural integrity and biomass utility. Recent advances in molecular and sy...

Forensic geolocation of Norwegian soil samples using random forest analysis of microbiomes.

Soil is a substrate easily picked up during everyday activities due to its ubiquity and adhesiveness. A method to determine the origin of soil precise...

Viral traits from deep mutational scanning and socio-demographic context predict SARS-CoV-2 lineage fitness across diverse countries.

OBJECTIVES: To assess the joint effects of SARS-CoV-2 viral traits (ACE2 binding, immune escape, and cell entry) and socio-demographic context on vira...

An Explainable Deep Model for Risk Scoring and Accurate Radionecrosis Identification Following Brain Metastasis Stereotactic Radiosurgery.

PURPOSE: As survival improves for patients with brain metastases (BM), distinguishing local recurrence (LR) from radionecrosis (RN) is a growing neuro...

Recent advances in the management of skin and soft tissue infections.

PURPOSE OF REVIEW: Skin and soft tissue infections (SSTIs) are one of the most frequent infections that need management either in outpatient setting o...

High-throughput sequencing reveals microbial transitions in refrigerated sturgeon meat: Implications for quality assurance.

This study investigated the microbially driven spoilage mechanism of sturgeon (Acipenser baerii) under refrigerated (4 °C) aerobic storage. High-throu...

EIOFX-DT: Leveraging graph centrality metrics for feature extraction and classification of viral genetic sequences.

Many diseases have a genetic origin, and analyzing intracellular structures through genetic data yields specific features for the diagnosis and classi...