bioRxiv

Showing 4931 to 4940 of 5021 articles

Multi-cohort, cross-species urinary proteomics reveals signatures of LRRK2 dysfunction in Parkinson’s disease

bioRxiv Jan 1, 2025
Pathogenic mutations in Leucine-rich repeat kinase 2 (LRRK2) are the predominant genetic cause of Parkinson’s disease (PD) and often increase kinase activity, making LRRK2 inhibitors promising treatment options. Although LRRK2 kinase inhibitors are a...
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ProCyon: A multimodal foundation model for protein phenotypes

bioRxiv Jan 1, 2025
Characterizing human proteins remains a major challenge: approximately 29% of human proteins lack experimentally validated functions and even well-annotated proteins often lack context-specific phenotypic insights. To enable universal modeling of pro...
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A neural circuit framework for economic choice: from building blocks of valuation to compositionality in multitasking

bioRxiv Jan 1, 2025
Value-guided decisions are a cornerstone of cognition, yet the underlying circuit-level mechanisms remain elusive. We used reinforcement learning to train recurrent neural network models endowed with Dale’s law on a battery of economic choice tasks, ...
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Dynamics-enhanced Molecular Property Prediction Guided by Deep Learning

bioRxiv Jan 1, 2025
Molecular property prediction (MPP) is a key challenge in computational biology and drug discovery. Traditional approaches mostly rely on feature representations yielded from static structures of molecules, ignoring their dynamic nature. The scarcity...
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Puget predicts gene expression across cell types using sequence and 3D chromatin organization data

bioRxiv Jan 1, 2025
Gene expression is governed by both linear DNA sequence and three-dimensional (3D) chromatin architecture. Most gene expression prediction models rely on sequence alone, thereby failing to capture structural context and to generalize to unseen cell t...
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BioPrediction-PPI: Simplifying the Prediction of Protein-Protein actions through Artificial Intelligence

bioRxiv Jan 1, 2025
Proteins are essential in biological processes, primarily through their interactions with other molecules, including proteins. These interactions are crucial for cellular functions and maintaining life. Predicting Protein-Protein Interactions (PPIs) ...
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Zygosity-Aware DNA Language Modeling Improves Ancestry and Gene Expression Prediction

bioRxiv Jan 1, 2025
DNA language models (DNA-LMs) are transforming how genomic sequence information is represented and interpreted. Yet most current approaches treat DNA as a single sequence, overlooking the diploid structure and zygosity information that distinguish th...
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Machine Learning Driven Simulations of the SARS-CoV-2 Fitness Landscape from Deep Mutational Scanning Experiments

bioRxiv Jan 1, 2025
Predicting protein variant effects is a key challenge in preparing for pathogenic viral strains, understanding mutation-linked diseases, and designing new proteins. Protein sequence-structure-function relationships are difficult to model due to compl...
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Local differences in baseline sodium shape astrocytic potassium uptake by the NKA

bioRxiv Jan 1, 2025
Astrocytes are vital for the maintenance of ion and transmitter homeostasis in the extracellular space, with the inward Na⁺ gradient playing a pivotal role in these processes. Earlier studies not only reported a low baseline Na+ concentration ([Na+])...
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TP53 and RB1 are predictive genetic biomarkers for sensitivity to cytarabine in gliomas

bioRxiv Jan 1, 2025
Therapeutic progress in glioma, one of the most lethal human cancers, has been limited by molecular heterogeneity and lack of biomarker-driven drug deployment. Here we used a proprietary large-scale CRISPRi screening in primary patient-derived glioma...
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