bioRxiv

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FlexRibbon: Joint Sequence and Structure Pretraining for Protein Modeling

bioRxiv Jan 1, 2025
Protein foundation models have advanced rapidly, with most approaches falling into two dominant paradigms. Sequence-only language models (e.g., ESM-2) capture sequence semantics at scale but lack structural grounding. MSA-based predictors (e.g., Alph...
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Active Sampling and Sex Differences in Perceptual Decision Making in Rats

bioRxiv Jan 1, 2025
Decisions are typically viewed as arising from a sequential process: perception, decision, and then action. However, an alternative perspective, drawing from ecological psychology and embodied cognition, suggests that perception, decision, and action...
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Systems biology framework for rational design of operational conditions for in vitro / in vivo translation of microphysiological systems

bioRxiv Jan 1, 2025
Preclinical models are used extensively to study diseases and potential therapeutic treatments. Complex in vitro platforms incorporating human cellular components, known as microphysiological systems (MPS), can model cellular and microenvironmental f...
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Neuronal activity triggers widespread changes in RNA stability

bioRxiv Jan 1, 2025
Neuronal activity shapes brain development and refines synaptic connectivity in part through dynamic changes in gene expression. While activity-regulated transcriptional programs have been extensively characterized, the holistic effects of neuronal a...
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Systematic Review of Artificial Intelligence use in behavioral analysis of invertebrate and larval model organisms: Methods, Applications and Future Recommendations

bioRxiv Jan 1, 2025
Invertebrate and larval model organisms such as Drosophila melanogaster, Caenorhabditis elegans, Danio rerio larvae, and Galleria mellonella are increasingly employed in biomedical, toxicological, and ecological research. Their behavioral responses s...
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Biologically Inspired Deep Neural Network Models for Visual Emotion Processing

bioRxiv Jan 1, 2025
The perception of opportunities and threats in complex visual scenes represents one of the main functions of the human visual system. The underlying neurophysiology is often studied by having observers view pictures varying in affective content. Whil...
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Leveraging Deep Learning and MD Simulations to Decipher the Molecular Basis of Attenuated Activity in Glycocin F

bioRxiv Jan 1, 2025
The escalating crisis of multi-drug resistant bacteria demand a new generation of antibiotics. Glycocin F (GccF), a potent bacteriocin, is a promising candidate, but its function hinges on unique post-translational glycosylation. Intriguingly, a seem...
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Probe-Based Identification of Metal-Binding Sites Using Deep Learning Representations

bioRxiv Jan 1, 2025
Metalloproteins play indispensable roles in a multitude of cellular processes. They incorporate metal ions as vital cofactors to catalyze biochemical reactions, stabilize protein structures, and mediate electron transfer. Given their prevalence and i...
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GeneJepa: A Predictive World Model of the Transcriptome

bioRxiv Jan 1, 2025
We introduce GeneJepa, a self-supervised foundation model that learns a predictive world model of single-cell transcriptomes. Based on the Joint-Embedding Predictive Architecture, GeneJepa predicts latent representations of masked gene sets from visi...
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Neural field patient-specific super resolution for enhanced 1.5 Tesla brain MRI visualization

bioRxiv Jan 1, 2025
Brain magnetic resonance imaging serves as a cornerstone of preoperative neurosurgical assessment. Neural fields represent an emerging machine learning approach capable of super-resolution reconstruction and novel view synthesis without requiring lar...
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