bioRxiv

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MARISMa: a routine MALDI-TOF MS dataset from 2018 to 2024 from Spain

bioRxiv Jan 1, 2025
Clinical microbiology laboratories play a crucial role in identifying pathogens, guiding antibiotic treatment, and managing antimicrobial resistance (AMR). Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) ha...
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Can a history of crop rotations improve the prediction of soil organic carbon in the Andes? integrating machine learning multi-annual crop classification as a proxy of soil management

bioRxiv Jan 1, 2025
Soil organic carbon (SOC) is a crucial component related to various processes that ensure soil health and function. Its modeling is vital for assessing and monitoring soil degradation caused by the potential impact of agricultural activities. This st...
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Exploring Stress-Induced Neural Circuit Remodeling through Data-Driven Analysis and Artificial Neural Network Simulation

bioRxiv Jan 1, 2025
Chronic stress induces behavioral rigidity and neural circuit remodeling, yet the underlying computational mechanisms remain unclear. In this study, we analyze in vivo GCaMP8s recordings from the amygdala-striatal circuits (Giovanniello et al.) and i...
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A Context-Specific, Literature-Supported Framework for Validating Stress Response Models in Mammals

bioRxiv Jan 1, 2025
Computational models of stress responses can highlight candidate genes underlying physiological adaptation, but their utility depends on rigorous validation. Using existing biological databases, we tested a novel approach to identify and group differ...
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Discovery of Electron Hole-hopping Redox Mutations in Myoglobin by Deep Mutational Learning

bioRxiv Jan 1, 2025
In addition to storing molecular oxygen, myoglobin catalyzes peroxidase-like reactions involving high valency iron(IV)-oxo species that support oxidation of a range of substrates at an open active site. Until now, it was unclear whether long-range el...
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EMCF ecosystem: Towards pretrained foundation model for electron microscopy image analysis

bioRxiv Jan 1, 2025
Volume electron microscopy (vEM) enables nanoscale visualization of three-dimensional (3D) cellular ultrastructure, providing critical insights into physiological processes and pathological alterations. However, its application to large-scale biologi...
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DeepCAST-GWAS: Improving the Discovery of Genetic Associations Using Deep Learning-Based Regulatory SNP Prioritization

bioRxiv Jan 1, 2025
Genome-wide association studies (GWAS) have uncovered numerous variants linked to complex traits, yet power remains limited by the large multiple testing burden and the inclusion of many variants with minimal regulatory impact. We present Deep learni...
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Single-cell co-mapping reveals relationship between chromatin state and gene expression in early zebrafish development

bioRxiv Jan 1, 2025
Establishing a cell-type-specific chromatin landscape is crucial for the maintenance of cell identity during embryonic development. However, our knowledge of how this landscape is set during vertebrate embryogenesis has been limited, due to the lack ...
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A dataset of differentiable biologically-derived single neuron models

bioRxiv Jan 1, 2025
Biological neural networks contain diverse cell types with heterogeneous electrophysiological properties. Artificial neural networks (ANNs) model computational aspects of biology but use homogeneous neurons, limiting realism. A key obstacle to buildi...
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Can We Extract Physics-like Energies from Generative Protein Diffusion Models?

bioRxiv Jan 1, 2025
Diffusion models have emerged as the state-of-the-art method in generative artificial intelligence (AI) and have shown great success in image synthesis, video generation, molecular design, and protein structure prediction. For biophysical problems, s...
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