bioRxiv

Showing 4521 to 4530 of 5021 articles

Design of Allosteric Inhibitors for Mutant EGFR by Combined use of Machine Learning and Molecular Dynamics Simulations

bioRxiv Jan 1, 2025
The non-small cell lung cancer (NSCLC)-associated Epidermal Growth Factor Receptor (EGFR) mutant L858R/T790M confers resistance to first- and second-generation tyrosine kinase inhibitors (TKIs). Allosteric inhibitors, binding outside the ATP-binding ...
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Towards automatic derivation of geometry-based descriptors as surrogates for complex computational approaches in enzyme-substrate prediction

bioRxiv Jan 1, 2025
Accurate prediction of enzyme-substrate interactions remains a fundamental challenge in biocatalysis and drug discovery. While machine learning approaches have shown promise, they require extensive training data and often lack mechanistic interpretab...
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Foundation model reveals the shared organization of transcription and topologically associating domains

bioRxiv Jan 1, 2025
The three-dimensional organization of chromatin into topologically associating domains (TADs) may impact gene regulation by bringing distant genes into contact. However, studies of TADs’ function and their influence on transcription have been constra...
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Beyond one-size-fits-all: single-cell transcriptomic signatures predict drug efficacy and reveal responder subgroups in endometriosis

bioRxiv Jan 1, 2025
Endometriosis affects ∼10% of reproductive-age women, yet targeted non-hormonal therapies remain unavailable, and treatment response is highly variable. Here, we apply a single-cell framework to resolve therapeutic heterogeneity at a resolution previ...
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A Theory of Thalamocortical Loops in Evidence Accumulation and Decision-Making

bioRxiv Jan 1, 2025
A prominent property of the neocortex is that it forms reciprocal excitatory loops with the thalamus. Here, we propose a function for the loops between layer 5 pyramidal tract neurons in the cortex and matrix-type relay cells in the thalamus, which i...
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TRIO-AI: Hybrid temporal graph, ODE, and VAE modeling for high-resolution cellular trajectory inference in liver injury

bioRxiv Jan 1, 2025
Resolving dynamic cellular transitions at single-cell resolution is essential for understanding complex biological processes in development, disease, and regeneration. However, existing trajectory inference methods struggle to capture heterogeneous t...
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ORANGE: A Machine Learning Approach for Modeling Tissue-Specific Aging from Transcriptomic Data

bioRxiv Jan 1, 2025
Despite aging being a fundamental biological process which profoundly influences health and disease, the interplay between tissue-specific aging and mortality remains underexplored. This study applies machine learning on GTEx transcriptomic data to m...
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Large extracellular vesicles subsets and contents discrimination: the potential of morpho mechanical approaches at single vesicle level

bioRxiv Jan 1, 2025
Extracellular vesicles (EVs) are heterogenous lipid bound membranous structures released by different cells, showing a great potential to be used as biomarkers. They have also been explored for their role in the context of environmental toxicity. Whe...
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GenVS-TBDB: A Target-Aware AI-Generated and Virtual-Screened Small-Molecule Library for Tuberculosis Drug Discovery

bioRxiv Jan 1, 2025
Tuberculosis (TB) remains a leading global health threat, with over 10 million new cases and 1.25 million deaths reported in 2023. Current TB therapies rely on a limited drug repertoire and prolonged treatment courses that have changed little in four...
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Inter- and intra-individual differences in brain sex map to neuroendocrine profiles

bioRxiv Jan 1, 2025
Sex hormone fluctuations modulate structural and functional brain dynamics, yet little is known how sex steroid levels map onto the expression of sex differences in the brain. Here, we trained machine learning models for brain sex classification base...
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