AIMC Journal:
bioRxiv

Showing 2871 to 2880 of 4993 articles

Deep Evolutionary Fitness Inference for Variant Nomination from Directed Evolution

bioRxiv Jan 1, 2025
Iterative screening techniques, such as directed evolution, enable high-throughput affinity maturation to optimize binders to molecular interfaces. However, the decision problem of selecting variants from rich, evolved populations to enter low-throug...
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ATOMIC: A graph attention neural network for ATOpic dermatitis prediction on human gut MICrobiome

bioRxiv Jan 1, 2025
Atopic dermatitis (AD) is a chronic inflammatory skin disease driven by complex interactions among genetic, environmental, and microbial factors; however, its etiology remains unclear. Recent studies have reported the role of gut microbiota dysbiosis...
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Accelerating protein engineering with fitness landscape modeling and reinforcement learning

bioRxiv Jan 1, 2025
Protein engineering holds significant promise for designing proteins with customized functions, yet the vast landscape of potential mutations versus limited lab capacity constrains the discovery of optimal sequences. To address this, we present the µ...
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AI becomes a masterbrain scientist

bioRxiv Jan 1, 2025
Recent rapid and unexpected advancements in Artificial Intelligence (AI) have dramatically shocked the world. Large language models, such as ChatGPT and GPT-4, have demonstrated remarkable potential in aggregating and organizing knowledge while provi...
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Starvation transforms signal encoding in C. elegans thermoresponsive neurons and suppresses heat avoidance via bidirectional glutamatergic and peptidergic signaling

bioRxiv Jan 1, 2025
Animals must continuously adapt their behavioral outputs in response to changes in internal state, including nutritional state. Here, we show that starvation induces a profound and progressive suppression of thermonociceptive behavior in Caenorhabdit...
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BAGEL: Protein Engineering via Exploration of an Energy Landscape

bioRxiv Jan 1, 2025
Despite recent breakthroughs in deep learning methods for protein design, existing computational pipelines remain rigid, highly specific, and ill-suited for tasks requiring non-differentiable or multi-objective design goals. In this report, we introd...
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Listening Beyond The Labels

bioRxiv Jan 1, 2025
Alzheimer’s Disease (AD), a progressive neurodegenerative condition of cognitive decline, presents formidable challenges to patients, caregivers, and healthcare systems. Early identification is essential for successful intervention, but traditional d...
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Fully Automated and Scalable Pipeline for Macaque Brain Registration

bioRxiv Jan 1, 2025
With the rapid development of various whole-brain ex vivo imaging technologies, there is a growing need to develop cross-modal 3D image registration methods to integrate multimodal imaging datasets. While comprehensive cross-modality registration too...
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Deep-learning-assisted SICM for enhanced real-time imaging of nanoscale biological dynamics

bioRxiv Jan 1, 2025
Scanning Ion Conductance Microscopy (SICM) provides high-resolution, nanoscale imaging of living cells, but it is generally limited by a slow scan rate, making it challenging to capture dynamic processes in real time. To tackle this challenge, we pro...
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XL-Ranker: A Computational Workflow for Prioritizing Protein-Protein Interactions from Cross-Linking Mass Spectrometry Data

bioRxiv Jan 1, 2025
Protein-protein interactions (PPIs) are central to virtually all biological processes, and their disruption can lead to a wide spectrum of human diseases. Cross-linking mass spectrometry (XL-MS) enables proteome-scale detection of interacting peptide...
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