AIMC Journal:
bioRxiv

Showing 1961 to 1970 of 4956 articles

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

bioRxiv Mar 20, 2026
Machine learning-based annotation methods are increasingly used to assess the pathogenicity of genetic variants, but their performance at prioritizing variants for gene-level association testing remains poorly characterized. Here, we systematically b...
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Designing mRNA coding sequence via multimodal reverse translation language modeling with Pro2RNA

bioRxiv Mar 20, 2026
mRNA coding sequence design is a critical component in the development of mRNA vaccines, nucleic acid therapeutics, and heterologous gene expression systems. While large language models have recently been successfully applied to protein design and RN...
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HViLM: A Foundation Model for Viral Genomics Enables Multi-Task Prediction of Pathogenicity, Transmissibility, and Host Tropism

bioRxiv Mar 20, 2026
Motivation: The emergence of novel viral pathogens poses critical threats to global health, yet current computational approaches for viral risk assessment are predominantly virus-specific and require extensive retraining for each new threat. Computat...
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Comparative cross-species transcriptomic analysis identifies new candidates of Pooideae nitrate response

bioRxiv Mar 20, 2026
Nitrogen fertilizers are essential for crop productivity but cause environmental harm, necessitating the development of cultivars that thrive under limited nitrogen. This study investigates the transcriptomic response to nitrate in Arabidopsis thalia...
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Improving genomic language model reliability under distribution shift

bioRxiv Mar 20, 2026
Transformer-based Genomic Language Models (GLMs) have achieved strong performance across diverse genomic prediction tasks. However, their tendency toward overconfident predictions---particularly on noisy or unfamiliar data---limits reliability. In ge...
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A comprehensive CRISPR screen of the Drosophila glutamate receptome reveals Ekar as a selective regulator of presynaptic homeostatic plasticity

bioRxiv Mar 20, 2026
Homeostatic mechanisms protect synapses from destabilizing challenges throughout an organism's lifespan, ensuring stable yet flexible neural network activity. To delineate the molecular basis of presynaptic homeostatic potentiation (PHP), we conducte...
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Causal differential expression analysis under unmeasured confounders with causarray

bioRxiv Mar 20, 2026
Advances in single-cell sequencing and CRISPR technologies have enabled detailed case-control comparisons and experimental perturbations at single-cell resolution. However, uncovering causal relationships in observational genomic data remains challen...
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X-Cell: Scaling Causal Perturbation Prediction Across Diverse Cellular Contexts via Diffusion Language Models

bioRxiv Mar 20, 2026
Causal models of cellular systems hold the promise to empower broad biological discovery, including the systematic identification of novel targets for drug discovery. Predicting how genetic and pathway perturbations reshape gene expression across div...
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Serotonergic axons signal reward, sensory stimulation, and prepare for movement in primary somatosensory cortex

bioRxiv Mar 20, 2026
Serotonin is one of the main neuromodulators in the brain, involved in regulating mood, complex behaviors and sensory input. Serotonin reaches primary somatosensory cortex (S1) via axons of neurons located in the dorsal raphe nucleus (DRN). DRN neuro...
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BioReason-Pro: Advancing Protein Function Prediction with Multimodal Biological Reasoning

bioRxiv Mar 20, 2026
Protein function annotation is fundamental to understanding biological mechanisms, designing therapeutics, and advancing biomedical research. Current computational methods either rely on shallow sequence similarity or treat function prediction as iso...
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