Genetics

Eukaryotic MAGs recovered from deep metagenomic sequencing of the seagrass, Zostera marina, include a novel chytrid in the order Lobulomycetales

Fungi play pivotal roles in terrestrial ecosystems as decomposers, pathogens, and endophytes, yet their significance in marine environments is often understudied. Seagrasses, as globally distributed marine flowering plants, have critical ecological functions, but knowledge about their associated fungal communities remains relatively limited. Previous amplicon surveys of the fungal community associ...

A Multi-Label Temporal Convolutional Framework for Transcription Factor Binding Characterization

Transcription factors (TFs) regulate gene expression through complex and co-operative mechanisms. While many TFs act together, the logic underlying TFs binding and their interactions is not fully understood yet. Most current approaches for TF binding site prediction focus on individual TFs and binary classification tasks, without a full analysis of the possible interactions among various TFs. In t...

A Standardized Framework For Evaluating Gene Expression Generative Models

The rapid development of generative models for single-cell gene expression data has created an urgent need for standardised evaluation frameworks. Cur...

HAETAE: A highly accurate and efficient epigenome transformer for tissue-specific histone modification prediction

While genomic models trained on four bases often fail to capture cell-type specificity, we introduce HAETAE, which integrates 5-methylcytosine from lo...

Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders

Noncoding genetic variation contributes to brain disorder risk, but the mechanisms through which it acts in specific brain cell types remain unclear. ...

mRNA-Protein Coordination is Contextualized by Metastatic Biological Phenotypes

A central goal of conducting omics measurements is to understand how molecular features inform higher-order cell- and tissue-level phenotypes. In part...

Continuous Diffusion Transformers for Designing Synthetic Regulatory Elements

We present a parameter-efficient Diffusion Transformer (DiT) for generating 200bp cell-type-specific regulatory DNA sequences. By replacing the U-Net ...

Improving Causal Gene Identification Using Large Language Models

Genome-Wide Association Studies (GWAS) have successfully identified numerous loci associated with complex traits and diseases, yet pinpointing causal ...

Bacterial proteome foundation model enhances functional prediction from enzymes to ecological interactions

Bacteria play fundamental roles in ecosystems, human health, and biotechnology. Although bacterial genome sequencing data have accumulated rapidly ove...

Fine-scale environmental, genetic, and temporal factors can drive the coral, sediment, and water column metagenome on reefs

Understanding the stability of microbial community assembly on coral reefs is crucial for determining their response to changing environments. Here, w...

Streaming Autoregressive Video Generation via Diagonal Distillation

Large pretrained diffusion models have significantly enhanced the quality of generated videos, and yet their use in real-time streaming remains limite...

Conversational Artificial Intelligence-Enabled Molecular Characterization of Sezary Syndrome Reveals Distinct Pathway-Level Alterations Compared with Non-Sezary Cutaneous T-Cell Lymphoma

ABSTRACT Background: Sezary syndrome (SS) represents an aggressive leukemic variant of cutaneous T-cell lymphoma (CTCL) with distinct clinical behavio...

Identification and Developmental Analysis of the Facial Characteristics Associated with Sickle Cell Disease using Machine Learning

Background Sickle cell disease (SCD) is a common inherited genetic disorder and contributor to global childhood mortality and morbidity. In the Democr...

Streaming Autoregressive Video Generation via Diagonal Distillation

Large pretrained diffusion models have significantly enhanced the quality of generated videos, and yet their use in real-time streaming remains limite...

Quantifying Memorization and Privacy Risks in Genomic Language Models

Genomic language models (GLMs) have emerged as powerful tools for learning representations of DNA sequences, enabling advances in variant prediction, ...

Geometric Brain Signatures for Diagnosing Rare Hereditary Ataxias and Predicting Function

Hereditary cerebellar ataxias (HCAs) are rare neurodegenerative disorders characterised by progressive motor impairment and overlapping clinical pheno...

Uncovering genetic mechanisms underlying trait variation in switchgrass using explainable artificial intelligence

Uncovering the genetic architecture of quantitative traits is challenging because polygenic control yields small individual gene effects and because g...

Benchmarking 80 binary phenotypes from the openSNP dataset using deep learning algorithms and polygenic risk score tools

Genotype-phenotype prediction plays a crucial role in identifying disease-causing single nucleotide polymorphisms and precision medicine. In this manu...

A minimal transcriptomic signature predicts intravascular tumor extension in renal cell carcinoma

Renal cell carcinoma (RCC) with venous tumor thrombus, termed renal intravascular tumor extension (RITE), is associated with aggressive behavior and p...

Adversarial Domain Adaptation Enables Knowledge Transfer Across Heterogeneous RNA-Seq Datasets

Accurate phenotype prediction from RNA sequencing (RNA-seq) data is essential for diagnosis, biomarker discovery, and personalized medicine. Deep lear...