bioRxiv

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AI-discovered tuning laws explain neuronal population code geometry

bioRxiv Jan 1, 2025
The activity of visual cortical neurons forms a population code representing image stimuli. There is, however, a discrepancy between our understanding of this code at the single-cell and population levels: direct measurements indicate the population ...
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Satellite microglia gate neuronal excitability by shielding inhibitory synapses in adult brain

bioRxiv Jan 1, 2025
Microglia, the primary immune cells of the central nervous system, are known for sculpting excitatory neural circuits via dynamic processes. However, their role in modulating inhibitory synaptic connections in adulthood remains largely unexplored. In...
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GENET: AI-Powered Interactive Visualization Workflows to Explore Biomedical Entity Networks

bioRxiv Jan 1, 2025
Formulating hypotheses about gene-disease associations requires logical inference from prior data, followed by a laborious literature review. AI models trained on curated datasets (e.g., GWAS Catalog) can suggest SNP–disease links, but validating the...
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Excellent agreement between automated deep learning-based and manual DWI infarct volume measurements in hyperacute stroke

bioRxiv Jan 1, 2025
Diffusion-weighted imaging (DWI) lesion volume and infarct growth are important imaging markers in acute ischemic stroke, but manual volume measurement is time-consuming and resource-intensive. Deep learning (DL)-based automated segmentation may faci...
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Exploiting pair correlation function to describe biological tissue structure

bioRxiv Jan 1, 2025
Multiplexed imaging technologies now enable the simultaneous profiling of hundreds to thousands of molecular targets in intact tissues, providing unprecedented insight into cellular heterogeneity and spatial organization. While data generation has ra...
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A novel NLP-based method and algorithm to discover RNA-binding protein (RBP) motifs, contexts, binding preferences, and interactions

bioRxiv Jan 1, 2025
RNA-binding proteins (RBPs) are essential modulators in the regulation of mRNA processing. The binding patterns, interactions, and functions of most RBPs are not well-characterized. Previous studies have shown that motif context is an important contr...
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Resolving phenotyping discordance with SPACEMAP, an integrated machine learning framework

bioRxiv Jan 1, 2025
Multiplex imaging technologies have revolutionized our ability to study cellular behavior within the tissue microenvironment. Translating this complex data into meaningful biological insights requires a unified analytical framework. To address this, ...
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Protein Diffusion Models as Statistical Potentials

bioRxiv Jan 1, 2025
Machine learning has driven rapid progress in protein structure prediction and design, but key challenges remain such as predicting protein structures when evolutionary information is unavailable, modeling full conformational landscapes, and capturin...
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Ω-Loop mutations control dynamics of the active site by modulating the hydrogen-bonding network in PDC-3 β-lactamase

bioRxiv Jan 1, 2025
The expression of antibiotic-inactivating enzymes, such as Pseudomonas-derived cephalosporinase-3 (PDC-3), is a major mechanism of intrinsic resistance in bacteria. Using reinforcement learning-driven molecular dynamics simulations and constant pH MD...
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A Comparative Review of Deep Learning Methods for RNA Tertiary Structure Prediction

bioRxiv Jan 1, 2025
Several deep learning-based tools for RNA 3D structure prediction have recently emerged, including DRfold, DeepFoldRNA, RhoFold, RoseTTAFoldNA, trRosettaRNA, and AlphaFold 3. In this study, we systematically evaluate these six models on three dataset...
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