bioRxiv

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Cytoplasmic dynamics are overlooked in single nuclei RNA-seq but can be rescued by CytoRescue, a generative AI model to recover cytoplasm enriched gene

bioRxiv Jan 1, 2025
Single-nucleus RNA sequencing (snRNA-seq) generates single cell data from nuclei. It provides valuable compatibility with frozen or difficult-to-dissociate tissues while avoiding stress responses in fresh samples. However, cytoplasmic depletion inher...
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Passive acoustic monitoring of Tasmanian masked owls and swift parrots: an effective tool for conservation actions

bioRxiv Jan 1, 2025
The Tasmanian masked owl (Tyto novaehollandiae subsp. castanops) and swift parrot (Lathamus discolor), both endangered species, rely on old forest features that are declining across their ranges in Tasmania, Australia. Their elusive behavior and high...
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Rapid Liquid Chromatography-Mass Spectrometry (rLC-MS) for Deep Metabolomics Analysis of Population Scale Studies

bioRxiv Jan 1, 2025
Mass spectrometry (MS)-based metabolomics is a key technology for the interrogation of exogenous and endogenous small molecule mediators that influence human health and disease. To date, however, low throughput of MS systems have largely precluded la...
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Accelerating Biomolecular Modeling with AtomWorks and RF3

bioRxiv Jan 1, 2025
Deep learning methods trained on protein structure databases have revolutionized biomolecular structure prediction, but developing and training new models remains a considerable challenge. To facilitate the development of new models, we present AtomW...
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DiffBreed: Automatic differentiation enables efficient gradient-based optimization of breeding strategies

bioRxiv Jan 1, 2025
Differentiable programming frameworks like PyTorch and JAX revolutionized biological modeling. A foremost merit is that multiple components programmed separately can be put together so that the parameters are jointly optimized. Despite its proven val...
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Uncovering Cas9 PAM diversity through metagenomic mining and machine learning

bioRxiv Jan 1, 2025
Recognition of protospacer adjacent motifs (PAMs) is crucial for target site recognition by CRISPR–Cas systems. In genome editing applications, the requirement for specific PAM sequences at the target locus imposes substantial constraints, driving ef...
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Modeling hidden cognitive states reveals acute and chronic effects of fentanyl on decision-making

bioRxiv Jan 1, 2025
The cognitive mechanisms underlying behavior are often dynamic, shifting gradually or abruptly over time scales spanning years, to weeks, to minutes. Whether drug-induced changes in learning and decision-making follow similarly dynamic patterns remai...
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Tripleknock: predicting lethal effect of three-gene knockout in bacteria by deep learning

bioRxiv Jan 1, 2025
Investigating the lethal effect of multi-gene knockout is essential for discovering novel antibiotics targets and metabolic engineering. Unlike single genes or gene pairs, three-gene combinations involve more intricate interactions, making experiment...
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Deep Learning Reveals Endogenous Sterols as Allosteric Modulators of the GPCR-Gα Interface

bioRxiv Jan 1, 2025
Endogenous intracellular allosteric modulators of GPCRs remain largely unexplored, with limited binding and phenotype data available. This gap arises from the lack of robust computational methods for unbiased cavity identification, cavity-specific li...
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SXTractor: A Self-Supervised Feature Extractor of Soft X-Ray Images That Enables Few-Shot Tomogram Segmentation

bioRxiv Jan 1, 2025
Soft X-ray tomography (SXT) is a powerful, non-invasive bio-imaging technique that enables visualization of cellular structures in near-native states. Despite its potential, the development of dedicated image analysis tools — particularly deep-learni...
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