Genetics

Machine learning and burden analyses highlight novel genes in Parkinson's Disease

Background Genome-wide association studies (GWAS) have identified numerous risk loci for Parkinson's disease, yet identifying causal genes and mechanisms remains challenging due to non-coding associations and complex linkage disequilibrium. Methods We prioritized genes within 147 GWAS loci using an XGBoost machine-learning model trained on 285 multi-omic features, including brain-specific eQTLs an...

AlphaGenome -enabled analysis of non-coding regulatory variants underlying RHD Expression

Systematic identification of functional non-coding regulatory variants remains a major challenge in human genetics. Conventional approaches such as large-scale CRISPR screening and genome-wide association studies (GWAS) are powerful but often prohibitively expensive, time-consuming, and experimentally intensive, limiting their scalability for locus-specific mechanistic studies. Recent advances in ...

Ensemble Machine Learning Approaches Predict Survival in Lower-Grade Glioma Based on Glycosphingolipid Gene Expression and Metabolic Modelling

Glycosphingolipids (GSLs) are essential components of biological membranes with important roles in cell signalling. Disrupted GSL metabolism is associ...

Predicting Gene Mutations in Colon Cancer Using Long-Term Temporal Dependency Learning on a Directed Co-Occurrence Asymmetry Graph

Accurate prediction of mutational dependencies to model tumor evolution can improve our understanding of cancer progression and is crucial for early d...

Clinical and Cross-Domain Validation of an LLM-Guided, Literature-Based Gene Prioritization Framework

Background: We previously published a literature based pipeline for sepsis gene prioritization (PS3 and candidate genes) using an LLM enabled retrieva...

Noise-immune and AI-enhanced DNA storage via adaptive partition mapping of digital data

Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and...

FASTR: Reimagining FASTQ via Compact Image-inspired Representation

Motivation: High-throughput sequencing (HTS) enables population-scale genomics but generates massive datasets, creating bottlenecks in storage, transf...

Gene-exposure interactions regulate cytokine-mediated chronic inflammation and cardiac remodeling

Background: Chronic inflammation predicts adverse cardiovascular outcomes, but mechanisms linking systemic inflammation to cardiac remodeling remain i...

EpiTADformer: A Transformer-Based Model for High-Resolution TAD Boundary Detection Using Epigenomic Signal Embeddings

The human genome is partitioned at different levels of 3D genome organization, with topologically associating domains (TADs) being among the most well...

Evolving Without Ending: Unifying Multimodal Incremental Learning for Continual Panoptic Perception

Continual learning (CL) is a great endeavour in developing intelligent perception AI systems. However, the pioneer research has predominantly focus on...

VAETracer: Mutation-Guided Lineage Reconstruction and Generational State Inference from scRNA-seq

Somatic mutations accumulate with cell division and are key to understanding tumor evolution. While single-cell RNA sequencing (scRNA-seq) can effecti...

Searching the Druggable Genome using Large Language Models

The druggable genome encompasses the genes that are known or predicted to interact with drugs. The Drug-Gene Interaction Database (DGIdb) provides an ...

TPCAV: Interpreting deep learning genomics models via concept attribution

Interpreting genomics deep learning models remains challenging. Existing feature attribution methods largely focus on scoring individual bases or extr...

SigFormer: an Attention-Based Framework for Robust Single-Sample Mutational Signature Decomposition

Somatic mutational signatures imprint the history of exogenous exposures and endogenous processes on the genome, offering critical insights into patho...

Computational Discovery of CRISPR-Cas13b Guide RNAs for Broad-Spectrum Dengue Virus Targeting

Dengue (DENV), an RNA virus, remains a significant global health threat, particularly in developing regions, with no widely effective antiviral therap...

Robust Machine Learning for Regulatory Sequence Modeling under Biological and Technical Distribution Shifts

Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and atte...

DiSPA: Differential Substructure-Pathway Attention for Drug Response Prediction

Accurate prediction of drug response in precision medicine requires models that capture how specific chemical substructures interact with cellular pat...

Characterizing Highly Conserved Fragments in 3'UTRs via Computational and Transfer Learning Approaches

3' untranslated regions (3' UTRs) serve as regulatory platforms that modulate translation, mRNA localization, and stability through the binding of reg...

Extracting useful information about reversible evolutionary processes from irreversible evolutionary accumulation models

Evolutionary accumulation models (EvAMs) are an emerging class of machine learning methods designed to infer the evolutionary pathways by which featur...

Pharmacogenomic Determinants of Post-Liver Transplant Diabetes Mellitus: A Systematic Review and In Silico Pharmacogenomic Analysis

Introduction: Tacrolimus remains central to liver transplantation, yet its narrow therapeutic index and pharmacokinetic variability are associated wit...