Genetics

Melody: Decoding the Sequence Determinants of Locus-Specific DNA Methylation Across Human Tissues

DNA methylation is a fundamental epigenetic modification that plays crucial roles in transcriptional regulation, cellular differentiation, and genome stability. However, how locus-specific DNA methylation is determined by intrinsic DNA sequence features remains poorly understood. Here, we introduce Melody, a deep learning framework designed to elucidate the sequence determinants underlying human D...

Assessing the feasibility of machine learning for ancient DNA age prediction: limitations and insights

We investigated the possibility of estimating the age of ancient biological samples directly from their DNA damage profiles using supervised machine learning. Traditional dating methods such as radiocarbon dating, dendrochronology rely on either material context or isotope composition, while our approach exploits intrinsic molecular degradation signatures. Using damage statistics obtained from anc...

ARCLID: Accurate and Robust Characterization of Long Insertions and Deletions in Genome

Structural variants (SVs) play crucial roles in genome diversity and disease, yet their accurate detection remains challenging, particularly under low...

Clair-Mosaic: A deep-learning method for long-read mosaic small variant calling

Mosaic variants, defined as postzygotic mutations occurring during an organism’s development from zygote to adult, play critical roles in developmenta...

Toward Accurate RNA Non-Canonical Structure Prediction: The NC-Bench Benchmark and the NCfold Framework

Accurate prediction of non-canonical (NC) base pairs is a pivotal step toward un-raveling the full functional landscape of RNA. This goal requires bot...

Predicting RNA:DNA Triplex Structures from Sequence Features Using Deep Learning Architecture

Long non-coding RNAs (lncRNAs) can perform their regulatory roles by forming triple helices through RNA–DNA interactions. Although this has been verif...

VariantFormer: A hierarchical transformer integrating DNA sequences with genetic variations and regulatory landscapes for personalized gene expression prediction

Accurately predicting gene expression from DNA sequence remains a central challenge in human genetics. Current sequence-based models overlook natural ...

Scalable and systematic hierarchical virus taxonomy with vConTACT3

Viruses are key players in diverse ecosystems, but studying their impacts is technically and taxonomically challenging. Taxonomic complexities derive ...

Predicting Future SARS-CoV-2 Mutations using Deep Learning

SARS-CoV-2 continues to spread over the world steadily as opposed to many earlier estimations that it would disappear in less than two years. Even tho...

ATHENA: A deep learning–based AI for functional prediction of genomic mutations and synergistic vulnerabilities in prostate cancer

Identifying functional mutations that drive therapy resistance remains a major challenge in prostate cancer. Large-scale sequencing often produces ext...

Nona: A unifying multimodal masking framework for functional genomics

The non-coding genome encodes complex regulatory logic that orchestrates gene expression and cell identity. While machine learning models for function...

Harnessing Interpretable Deep Learning to Predict Meropenem Resistance in Klebsiella pneumoniae

Antimicrobial resistance represents an escalating global healthcare threat, complicating treatment and increasing both morbidity and mortality. Deep l...

The blood proteome predicts the impact of circulating factors on age-related mitochondrial health

Circulating non-cellular factors, such as plasma proteins, contribute to various features of aging. To determine the impacts of endogenous circulating...

BioToken and BioFM – Biologically-Informed Tokenization Enables Accurate and Efficient Genomic Foundation Models

Genomic variation underlies human phenotypic diversity, disease susceptibility, and evolutionary adaptation. Although large-scale genomic sequencing h...

Evo2HiC: a multimodal foundation model for integrative analysis of genome sequence and architecture

Understanding how genomic sequences shape three-dimensional (3D) genome architecture is funda-mental to interpreting diverse biological processes. Alt...

Machine Learning Identifies Common Risk Variants and Implicates Abnormal Vision Physiology in ASD

Genomic technology advancements have facilitated associations between genetic variants and disease risk. Rare deleterious variants can independently i...

The Macroevolution of Filamentation Morphology Across the Saccharomycotina Yeast Subphylum

Saccharomycotina yeasts are a highly diverse and widely distributed subphylum of ascomycete fungi that exhibit diversity in their asexual growth morph...

Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods

The diverse regulatory functions, protein production capacity, and stability of natural and synthetic RNAs are closely tied to their ability to fold i...

cfOncoXpress: Tumor gene expression prediction from cell-free DNA whole-genome sequences

Cell-free DNA (cfDNA) fragments in the plasma capture cellular nucleosomal profiles since nucleosome-protected regions escape enzymatic degradation wh...

ProAffinity++

Proteins are essential biological macromolecules that play a crucial role in living organisms. Protein-protein interactions, which govern various biol...