bioRxiv

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Discovery and performance of DNA methylation panels for cancer detection and classification in blood

bioRxiv Jan 1, 2025
Examining DNA in a liquid biopsy for non-invasive cancer detection relies on identifying dilute signal in a high background. This study aims to identify DNA methylation biomarkers for multi-cancer detection. Utilizing large tissue datasets, we apply ...
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Hollow-fibre biomanufacturing and cell-free engineering of HEK293 extracellular vesicles

bioRxiv Jan 1, 2025
Extracellular vesicles (EVs) are lipid-delineated nanoparticles that are produced by most cell types. EVs contain complex molecular cargoes that can have useful therapeutic or vaccine immunological effects. Cell-free gene expression systems can be us...
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A Biosecurity Agent for Lifecycle LLM Biosecurity Alignment

bioRxiv Jan 1, 2025
Large language models (LLMs) are increasingly integrated into biomedical re-search workflows-from literature triage and hypothesis generation to experimental design-yet this expanded utility also heightens dual-use concerns, including the potential m...
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Interpretable Machine Learning Identifies an Emergent Absence Seizure Mechanism

bioRxiv Jan 1, 2025
Absence epilepsy is a generalized seizure disorder marked by widespread spike-and-wave oscillations and sudden lapses in consciousness. Although no consensus exists on mechanisms of consciousness, several frameworks highlight dynamic processes relyin...
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MicroNucML: A machine learning approach for micronuclei segmentation and the refinement of nuclei-micronuclei relationships

bioRxiv Jan 1, 2025
Micronuclei (MN) are structures containing small fragments of DNA, arising from mitotic errors or failed DNA repair attempts. Therefore, MN serve as markers of genomic instability and are typically quantified either manually or through threshold-base...
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Recovery of human upper airway epithelium after smoking cessation is driven by a slow-cycling stem cell population and immune surveillance

bioRxiv Jan 1, 2025
The upper airway epithelium in humans is maintained in homeostasis by a resident population of basal stem cells. In the presence of tobacco smoke these gain mutations that significantly increase their risk of transformation to lung squamous cell carc...
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How many crystal structures do you need to trust your docking results?

bioRxiv Jan 1, 2025
Structure-based drug discovery technologies generally require the prediction of putative bound poses of protein:small molecule complexes to prioritize them for synthesis. The predicted structures are used for a variety of downstream tasks such as pos...
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Determination of Aedes mosquito mating success by a rapidly-evolving female-controlled lock-and-key mechanism

bioRxiv Jan 1, 2025
Mosquitoes, the world’s deadliest animal, exemplify single-mating systems where females mate only once in their lifetime, making mate choice critically important for reproductive success and mosquito control. Despite this importance, the mechanisms o...
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qcMol: a large-scale dataset of 1.2 million molecules with high-quality quantum chemical annotations for molecular representation learning

bioRxiv Jan 1, 2025
Recent advancements in deep learning have greatly prompted the de novo design of drugs and materials. Previous studies have shown that a well-designed molecular representation is critical for improving the accuracy of deep-learning-based molecular pr...
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Molecular Contrastive Learning with Graph Attention Network (MoCL-GAT) for Enhanced Molecular Representation

bioRxiv Jan 1, 2025
Learning the representation of molecules is crucial for drug discovery but is often hindered by the scarcity of labeled experimental data, which limits the performance of supervised machine learning models. While self-supervised learning (SSL) offers...
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