bioRxiv

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Fine-Grained Structural Classification of Biosynthetic Gene Cluster-Encoded Products

bioRxiv Jan 1, 2025
Biosynthetic gene clusters (BGCs) are responsible the biosynthesis of many natural products, including a multitude of effective therapeutics and their precursors. Advances in genomic data collection as well as computational techniques have made it po...
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Benchmarking Chemical, Genetic, and Cell Line Encodings for Cancer Perturbation Response Prediction

bioRxiv Jan 1, 2025
Estimating the response of tumor cells to specific perturbations is crucial for identifying effective treatments that selectively target cancer cells while sparing healthy ones, enabling personalized medicine approaches. Large-scale initiatives, such...
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Image-Based Profiling of Induced Trophoblast Stem Cells Identifies Signatures Associated with Sex, Schizophrenia Genomic Risk and Placental Stress

bioRxiv Jan 1, 2025
Schizophrenia (SCZ) is a neurodevelopmental disorder where both genetic and environmental risks converge during pregnancy. Recent studies have highlighted the importance of placental biology in influencing risk of developing SCZ. However, the pathway...
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The eXplainable Artificial Intelligence (XAI) Triad: Models, Importances, and Significance at Scale

bioRxiv Jan 1, 2025
In this study, we present a comprehensive evaluation framework for comparing various combinations of artificial intelligence (AI) methods in the context of explainable AI (XAI) for variable selection in experimental biological and biomedical data. Ou...
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VaxjoGNN: A Graph Neural Network for Ontology-Grounded Vaccine Adjuvant Recommendation

bioRxiv Jan 1, 2025
The selection of an effective adjuvant is a critical bottleneck in vaccine development, particularly for emerging diseases where experimental data is sparse. While computational methods exist for antigen discovery, the task of directly ranking adjuva...
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Integrating NMR restraints into coarse-grained simulations: toward accurate conformational ensembles of complex protein systems

bioRxiv Jan 1, 2025
Structural dynamics play critical roles for the biological activity of protein molecules. Characterising the inherent conformational landscapes of these macromolecules remains a major experimental and computational challenge, particularly for heterog...
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Plant Face: Machine learning decodes genetic, environmental and developmental imprints in leaf appearance

bioRxiv Jan 1, 2025
Leaf appearance is a crucial plant phenotype. However, traditional methods for extracting this information are inefficient, limiting its full utilization. Deep learning based on convolutional neural networks (CNNs) enables us to capture previously in...
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Temporal Dynamics of High-Frequency Oscillations in Alzheimer’s Disease: A Longitudinal Study in hAPP-J20 Mice

bioRxiv Jan 1, 2025
Alzheimer’s disease (AD) is characterized by progressive cognitive decline and increased seizure susceptibility; yet both the mechanistic and temporal links between AD and epileptogenesis remain poorly defined. In this study, we conducted a longitudi...
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Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes

bioRxiv Jan 1, 2025
AlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without coevolutionary signals, such as host-pathogen and antibody-antigen interactions. Two strategies have been develope...
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Modeling patient tissues at molecular resolution with Eva

bioRxiv Jan 1, 2025
Tissue structure is essential to function and homeostasis in all organs, and disruptions to structure usually indicate disease. Modeling relationships between structural, molecular, and clinical aspects of tissues could advance new diagnostics and tr...
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