bioRxiv

Showing 4301 to 4310 of 5016 articles

Biophysical validation of explainable AI for functional brain imaging: bridging cellular mechanisms and network dynamics

bioRxiv Jan 1, 2025
Deep neural networks have revolutionized functional neuroimaging analysis but remain “black boxes,” concealing which brain mechanisms and regions drive their predictions—a critical limitation for clinical neuroscience. Here we develop and validate an...
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MARRVEL-MCP: A Context-Engineered Natural-Language Query-to-Response Interface for Mendelian Disease Discovery

bioRxiv Jan 1, 2025
Rare disease variant interpretation requires navigating multiple genomic databases with strict input formats and synthesizing heterogeneous evidence, creating barriers for non-experts and cognitive burdens even for specialists. MARRVEL exemplifies th...
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Cardiac myofibril networks induce shear stress

bioRxiv Jan 1, 2025
Myofibril arrangement is critical to cardiac muscle function in health and disease. Historically, analysis of the impact of myofibril organisation on force and cell contraction has relied on the assumption of uniaxial arrays. However, improvements in...
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Model-based EEG phenotyping uncovers distinct neurocomputational mechanisms underlying learning impairments across psychopathologies

bioRxiv Jan 1, 2025
Major depressive disorder (MDD), bipolar disorder (BP), and schizophrenia (SCZ) involve learning impairments with poorly understood mechanisms. Understanding both the similarities and differences in these mechanisms is important to guide the developm...
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Can Lightweight LLM Agents Improve Spatial Transcriptomics Annotation?

bioRxiv Jan 1, 2025
Spatial transcriptomics (ST) links gene expression to tissue organization, yet automated annotation of spatial regions remains a persistent challenge. Recent studies have explored large language models (LLMs) for biological reasoning, but their appli...
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SignalGen: A Protein Language Model Based AI Agent For Optimal Signal Peptide Prediction

bioRxiv Jan 1, 2025
Signal peptides are short amino acid sequences attached to the N-termini of mature proteins. They play determinant roles in protein expression as well as localization of mature proteins. While sequence-based machine learning (ML) models have been dev...
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Robust Deep Learning-based 3D Segmentation and Morphological Analysis of Mitochondria using Soft X-ray Tomography

bioRxiv Jan 1, 2025
Mitochondrial morphology is crucial for cellular function, but large-scale analysis is limited by challenges in high-resolution imaging and segmentation. MitoXRNet, a compact 3D deep-learning model, efficiently segments mitochondria and nuclei from S...
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intDesc-AbMut: Describing and understanding how antibody mutations impact their environmental interactions1

bioRxiv Jan 1, 2025
Previously, we proposed a double-point mutation (DPM) strategy involving the simultaneous substitution of two amino acids to optimize antibodies. By selecting mutants based on the criterion that favorable interactions between mutated residues and the...
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Design of multimodal antibiotics using deep learning

bioRxiv Jan 1, 2025
The rise of antimicrobial resistance has rendered many treatments ineffective, posing serious public health challenges. Intracellular infections are particularly difficult to treat since conventional antibiotics fail to neutralize pathogens hidden wi...
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CPIExtract: A software package to collect and harmonize small molecule and protein interactions

bioRxiv Jan 1, 2025
The binding interactions between small molecules and proteins are the basis of cellular functions. Yet, experimental data available regarding compound-protein interactions (CPIs) are not harmonized into a single entity but rather scattered across mul...
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