Genetics

PPGL-Swarm: Integrated Multimodal Risk Stratification and Hereditary Syndrome Detection in Pheochromocytoma and Paraganglioma

Pheochromocytomas and paragangliomas (PPGLs) are rare neuroendocrine tumors, of which 15-25% develop metastatic disease with 5-year survival rates reported as low as 34%. PPGL may indicate hereditary syndromes requiring stricter, syndrome-specific treatment and surveillance, but clinicians often fail to recognize these associations in routine care. Clinical practice uses GAPP score for PPGL gradin...

Novel 4D tensor decomposition-based approach integrating tri-omics profiling data can identify functionally relevant gene clusters

Integrating transcriptome, translatome, and proteome data remains challenging because changes in mRNA, ribosome occupancy, and protein abundance do not always occur simultaneously. To address this, we applied tensor-decomposition-based unsupervised feature extraction to a tri-omics dataset generated under branched-chain amino acid starvation. The three layers were organized into a tensor and analy...

Hidden Diversity in Yeast tRNAs: Comparative Genomics and Modification Mapping in a Eukaryotic Subphylum

tRNA are adapter molecules with an integral role in translation and further roles in stress adaptation. Processing of tRNA is tightly regulated and in...

Evolution as Active Geometry: The Geometric State Equation of the Tree of Life

Any process that generates information at a constant rate into a branching hierarchy faces a geometric packing problem: the number of distinguishable ...

A comprehensive CRISPR screen of the Drosophila glutamate receptome reveals Ekar as a selective regulator of presynaptic homeostatic plasticity

Homeostatic mechanisms protect synapses from destabilizing challenges throughout an organism's lifespan, ensuring stable yet flexible neural network a...

Improving genomic language model reliability under distribution shift

Transformer-based Genomic Language Models (GLMs) have achieved strong performance across diverse genomic prediction tasks. However, their tendency tow...

Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA

mRNA coding sequence design is a critical component in the development of mRNA vaccines, nucleic acid therapeutics, and heterologous gene expression s...

Systematic assessment of machine learning-based variant annotation methods for rare variant association testing

Machine learning-based annotation methods are increasingly used to assess the pathogenicity of genetic variants, but their performance at prioritizing...

Evolutionary and Deep Learning Models Highlight Deleterious Mutations Behind the History of Sugar Beet Breeding

Sugar beet (Beta vulgaris ssp. vulgaris) is a major global source of sucrose. Domestication and a history of breeding have shaped the distribution of ...

RNAGAN: Train One and Get Four, Multipurpose Human RNA-Seq Analysis Tool with Enhanced Interpretability and Small Data Size Capability

The advent of artificial intelligence (AI) has brought revolutionary tools for biomedical transcriptomic (RNA-level) research. However, there are pers...

X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

Causal models of cellular systems hold the promise to empower broad biological discovery, including the systematic identification of novel targets for...

Machine Learning Enabled Smartphone CRISPR-Cas12a Lateral Flow Platform for Sensitive Detection of Circulating HPV DNA

Persistent infection with high-risk human papillomavirus (HPV) is the primary cause of cervical cancer and other HPV-related malignancies. Effective s...

The results of Transcriptome-wide Mendelian Randomization (TWMR) in large-scale populations can directly validate, across scales, the results of causal inference from deep learning combined with double machine learning on single-cell transcriptomes of human samples.

Objective Aiming at the core problems prevalent in biomedical research, including the "translational distance", the difficulty in aligning cross-scale...

Spatio-temporal mapping of immune cell dynamics during human sequential lymph node metastasis

Regional lymph node (LN) metastasis critically influences distant metastatic progression, anti-tumour immunity, and patient prognosis. While tumour-in...

Enabling high-plex spectral imaging via DNA-barcoded signal tuning and panel optimization

High-plex spectral imaging has the potential to transform the analysis of spatial organization in cells and tissues, yet its practical implementation ...

Coupled Solvent and Protein Dynamics Confer Differences in Exon-19 Deletion Mutants of the Epidermal Growth Factor Receptor Kinase

Deletions in Exon-19 of the epidermal growth factor receptor (EGFR) play a pivotal role in the pathogenesis of non-small cell lung cancer (NSCLC), inf...

Cell-Type Prototype-Informed Neural Network for Gene Expression Estimation from Pathology Images

Estimating slide- and patch-level gene expression profiles from pathology images enables rapid and low-cost molecular analysis with broad clinical imp...

Unpaired TCRα + TCRβ sequencing is sufficient for training machine learning TCR-epitope recognition predictors

T-cell recognition of infected and malignant cells is elicited by the binding of heterodimeric T-Cell Receptors (TCRs) to epitopes and both the TCR an...

A Long-Context Generative Foundation Model Deciphers RNA Design Principles

Programmable design of RNA sequences with defined functions remains a central challenge in biology. Despite recent advances, existing RNA generative m...

rSDNet: Unified Robust Neural Learning against Label Noise and Adversarial Attacks

Neural networks are central to modern artificial intelligence, yet their training remains highly sensitive to data contamination. Standard neural clas...