Genetics

Rectifying Stress into Structural Memory Drives Specialization in Cells and Adaptive Computational Systems

Functional specialization in continuous systems requires balancing adaptation to environmental stress with the preservation of encoded information. Yet, the physical constraints governing how living systems reconcile selective information retention with energetic structural reorganization remain unclear, a trade-off that may offer transferable design rules for adaptive computing. Here we present a...

Ab initio prediction of RNA structure ensembles with RNAnneal

RNA utilizes three-dimensional structure in addition to sequence to carry out diverse functions in gene expression and disease. Much like well-folded proteins, RNAs adopt specific three-dimensional structures to carry out their function. Yet comparatively few RNA structures have been solved by atomic resolution structural techniques, in part because unlike structured proteins, RNAs fold into heter...

An AI-Native Biofoundry for Autonomous Enzyme Engineering: Integrating Active Learning with Automated Experimentation

The engineering of enzymes with novel functions is a cornerstone of synthetic biology but remains bottlenecked by the fragmentation between computatio...

An AI-Integrated Framework for Precision Genomics in Coronary Artery Disease Using Whole Exome and Phenotypic Data

Coronary artery disease (CAD) is a multifactorial condition influenced by genetic, phenotypic, and environmental factors. Traditional risk prediction ...

Integrating multi-omic QTLs and predictive models reveals regulatory architectures at immune-related GWAS loci in CD4+ T cells

Functional interpretation is essential for understanding how genetic variants contribute to complex traits. Here, we identified and characterized regu...

Diversity of antibiotic resistance genes increases in urbanized lakes: a multi-tool screening

Antimicrobial resistance (AMR) is a growing global public health threat projected to cause up to 10 million deaths annually by 2050 if no immediate ac...

Zero-shot biological reasoning with open-weights large language models reproduces CRISPR screen based prediction of synthetic lethal interactions.

Identifying clinically relevant synthetic lethal interactions has great potential for uncovering novel therapeutic vulnerabilities in cancer. Current ...

DVPNet: A New XAI-Based Interpretable Genetic Profiling Framework Using Nucleotide Transformer and Probabilistic Circuits

This research provides an XAI-driven genetic profiling approach that may contribute to scientific discoveries in genetic research. We propose a new ex...

A systematic assessment of machine learning for structural variant filtering

Background: Accurate discrimination of true structural variants (SVs) from artifacts in long-read sequencing data remains a critical bottleneck. Numer...

Longevity Bench: Are SotA LLMs ready for aging research?

Aging is a core biological process observed in most species and tissues, which is studied with a vast array of technologies. We argue that the abiliti...

Synthetic Abundance Maps for Unsupervised Super-Resolution of Hyperspectral Remote Sensing Images

Hyperspectral single image super-resolution (HS-SISR) aims to enhance the spatial resolution of hyperspectral images to fully exploit their spectral i...

Classification of SARS-CoV-2 Variants through The Epistatical Circos Plots with Convolutional Neural Networks

The COVID-19 pandemic has profoundly affected global health, driven by the remarkable transmissibility and mutational adaptability of the SARS-CoV-2 v...

HistoPrism: Unlocking Functional Pathway Analysis from Pan-Cancer Histology via Gene Expression Prediction

Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical im...

Multi-omic deep learning identifies exercise-responsive ageing pathways in humans

Genome-wide association studies of physical activity traits have mapped numerous loci, yet the molecular mechanisms through which exercise influences ...

Gene-centered representation of coding and regulatory variation enables outcome prediction

Integrating coding and regulatory variation into unified, interpretable representations remains a challenge in functional genomics. Current approaches...

Functional In-Context Learning in Genomic Language Models with Nucleotide-Level Supervision and Genome Compression

Genomic foundation models aim to learn general-purpose representations directly from DNA sequence, enabling sequence understanding, generation, and pr...

Spatial mapping of RNA turnover kinetics and regulatory landscapes of mRNA stability in the mammalian brain

Spatial and activity-dependent gene regulation in the mammalian brain requires coordinated control of RNA synthesis and degradation, yet spatially res...

Machine Learning Ensemble Reveals Distinct Molecular Pathways of Retinal Damage in Spaceflown Mice

Spaceflight-associated neuro-ocular syndrome (SANS) threatens astronaut health during long-duration missions, yet its molecular pathology remains uncl...

Adversarial Vulnerability Transcends Computational Paradigms: Feature Engineering Provides No Defense Against Neural Adversarial Transfer

Deep neural networks are vulnerable to adversarial examples--inputs with imperceptible perturbations causing misclassification. While adversarial tran...

HistoPrism: Unlocking Functional Pathway Analysis from Pan-Cancer Histology via Gene Expression Prediction

Predicting spatial gene expression from H&E histology offers a scalable and clinically accessible alternative to sequencing, but realizing clinical im...