Genetics

Advancing sarcoma diagnostics with expanded DNA methylation-based classification

Sarcomas pose a severe diagnostic challenge. A wide variety of these distinct entities need to be distinguished from each other and from less aggressive types of mesenchymal tumors, to ensure correct clinical management. A machine learning based classifier for sarcomas utilizing DNA methylation data from 1077 tumors recognizing 62 sarcoma types has already been developed and termed the sarcoma cla...

Omics Integration Uncovers Mechanisms Associated with HIV Viral Load and Potential Therapeutic Insights

While antiretroviral therapy (ART) has significantly improved disease prognosis in people with HIV (PWH), understanding the biological mechanisms underlying plasma HIV-1 RNA viral load (VL) can inform additional strategies to slow HIV/AIDS disease progression. Here, we integrated multi-omic datasets and used two machine learning network biology tools (GRIN and MENTOR) to identify biological mechan...

Transcriptomic age prediction using mixture-of-experts models reveals tissue-specific aging signatures in large-scale human RNA-sequencing data

Transcriptomic age prediction has emerged as a powerful approach for understanding biological aging processes, yet systematic comparisons of large-sca...

MOKA: A pipeline for multi-omics bridged SNP-set kernel association test

The explosion of genomic and multi-omics data has created a need for scalable, reproducible tools that integrate functional annotations into genome-wi...

Genetic Profiling and Early Detection of Type 2 Diabetes Subtypes through Sex-Stratified GWAS and Explainable AI

Type 2 diabetes (T2D) is a complex and clinically heterogeneous disease. Although clustering approaches have defined clinical subtypes, their genetic ...

Genomics reveals eleven obesity endotypes with distinct biological and phenotypic signatures

Obesity, a leading global risk factor for cardiometabolic conditions, arises from multifaceted and biologically complex mechanisms1,2. To elucidate th...

Multimodal Integration of Alzheimer’s Plasma Biomarkers, MRI, and Genetic Risk for Individual Prediction of Cerebral Amyloid Burden

Alzheimer’s disease (AD), the most prevalent neurodegenerative disorder, is marked by the accumulation of amyloid-β (Aβ) plaques. Although cerebral Aβ...

Prematurity and Genetic Liability for Autism Spectrum Disorder

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by diverse presentations and a strong genetic component. Environmental ...

Quantification of Optical Coherence Tomography Features in >3500 Patients with Inherited Retinal Disease Reveals Novel Genotype-Phenotype Associations

To quantify spectral-domain optical coherence tomography (SD-OCT) images cross-sectionally and longitudinally in a large cohort of molecularly charact...

Network-Based Stratification Refines Stratification of Intermediate-Risk Acute Myeloid Leukemia Samples

The European LeukemiaNet (ELN) risk stratification of acute myeloid leukemia (AML) uses genetic and molecular markers to categorize patients. However,...

Polygenic prediction of phenotypes with a neural empirical Bayes approach

Polygenic risk scores (PRS) estimate the expected value of a phenotype based on individual genotypes. Although statistical approaches for calculating ...

Explainable AI for Precision Oncology: A Task-Specific Approach Using Imaging, Multi-omics, and Clinical Data

Despite continued advances in oncology, cancer remains a leading cause of global mortality, highlighting the need for diagnostic and prognostic tools ...

Artificial Intelligence Agent: AI-HOPE-TP53 Enables Pathway-Centric Analysis of TP53-Driven Molecular Alterations in Colorectal Cancer Precision Oncology

Early-onset colorectal cancer (EOCRC) is rising rapidly, especially among populations at risk who experience disproportionate incidence and mortality....

Translation of miRNA blood-based discovery to molecular testing for clinical diagnosis of endometriosis

Endometriosis is a common yet often underdiagnosed condition, partly due to the lack of reliable diagnostics. This study examines the clinical feasibi...

A clinically relevant morpho-molecular classification of lung neuroendocrine tumours

Lung neuroendocrine tumours (NETs, also known as carcinoids) are rapidly rising in incidence worldwide but have unknown aetiology and limited therapeu...

Genetic regulation of cell type–specific chromatin accessibility shapes immune function and disease risk

Understanding how genetic variation influences gene regulation at the single-cell level is crucial for elucidating the mechanisms underlying complex d...

Unveiling genetic architecture of white matter microstructure through unsupervised deep representation learning of fractional anisotropy maps

Fractional anisotropy (FA) derived from diffusion MRI is a widely used marker of white matter (WM) integrity. However, conventional FA-based genetic s...

Complex pathways to ceftolozane-tazobactam resistance in clinical Pseudomonas aeruginosa isolates: a genomic epidemiology study

We aimed to conduct a comprehensive genomic analysis of ceftolozane/tazobactam (C/T) resistance mechanisms in Pseudomonas aeruginosa by combining nove...

Convolutional neural networks quantify antibiotic resistance in Mycobacterium tuberculosis with diagnostic grade accuracy and predict treatment response

There is considerable interest in training machine learning (ML) models on genomic data that achieve clinical grade diagnostic accuracy. Many successf...

Sample Size Requirements for Machine Learning Classification of Binary Outcomes in Bulk RNA-Seq Data

Bulk RNA sequencing data is often leveraged to build machine learning (ML)-based predictive models for classification of disease groups or subtypes, b...