bioRxiv

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Large vision model framework for automated C. elegans analysis: From static morphometry to dynamic neural activity

bioRxiv Jan 1, 2025
Quantitative phenotyping of Caenorhabditis elegans is essential across numerous fields, yet data extraction remains a significant analytical bottleneck. Traditional segmentation methods, typically reliant on pixel-intensity thresholding, are highly s...
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Benchmarking large language models for cell-free RNA diagnostic biomarker discovery

bioRxiv Jan 1, 2025
Large-language models (LLMs) can parse vast amounts of data and generate executable code, positioning them as promising tools for the development of biomarkers and classifiers from high-throughput omics data. Here, we benchmarked six LLMs, OpenAI’s o...
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C3PI: Component Puzzle Protein-Protein Interaction Prediction

bioRxiv Jan 1, 2025
Proteins primarily perform their functions through interactions with other proteins, making the accurate prediction of protein-protein interactions (PPIs) a fundamental problem. Experimental methods for determining PPIs are often slow and expensive, ...
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MiGenPro: A linked data workflow for phenotype-genotype prediction of microbial traits using machine learning

bioRxiv Jan 1, 2025
Availability of microbial genomic data and development of machine learning methods create a unique opportunity to establish associations between genetic information and phenotypes. Here we present a computational workflow for Microbial Genome Prospec...
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Bat anthropogenic roosting ecology influences taxonomic and geographic predictions of zoonotic risk

bioRxiv Jan 1, 2025
The ability of wildlife to live in anthropogenic structures is widely observed across many animal species. As proximity to humans is an important risk factor for pathogen transmission, anthropogenic roosting may have important consequences for predic...
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How good is Generative Diffusion Model for Enhanced Sampling of Protein Conformations Across Scales and in All-atom Resolution?

bioRxiv Jan 1, 2025
Molecular dynamics (MD) simulations are fundamental for probing the structural dynamics of biomolecules, yet their efficiency is limited by the high computational cost of exploring long-timescale events. Generative machine learning (ML) models, parti...
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Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues

bioRxiv Jan 1, 2025
The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from nine new donors, doubles the number of cells in Tabu...
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Active learning-guided optimization of cell-free biosensors for lead testing in drinking water

bioRxiv Jan 1, 2025
Point-of-use diagnostics based on allosteric transcription factors (aTFs) are promising tools for environmental monitoring and human health. However, biosensors relying on natural aTFs rarely exhibit the sensitivity and selectivity needed for real-wo...
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Uncertainty and reward histories have distinct effects on decisions after wins and losses

bioRxiv Jan 1, 2025
Intelligent behavior necessitates an adaptive integration of feedback. It is well-known that animals asymmetrically learn from positive and negative feedback. While asymmetrical learning is a robust behavioral effect, the latent computations behind h...
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BOLD-GPCRs: A Transformer-Powered App for Predicting Ligand Bioactivity and Mutational Effects Across Class A GPCRs

bioRxiv Jan 1, 2025
G protein-coupled receptors (GPCRs) are important targets for drug discovery owing to their ability to respond to a broad range of stimuli and their involvement in numerous pathologies. Although traditional ligand-based and structure-based approaches...
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