bioRxiv

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Predicting emergent phenotypes from single cell populations using CELLECTION

bioRxiv Jan 1, 2025
Biological systems exhibit emergent phenotypes that arise from the collective behavior of individual components, such as whole-organ functions that arise from the coordinated activity of its individual cells, or organism-level phenotypes that result ...
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Digit-Tracking Reveals Curiosity-Driven Visual Attention in Macaque Monkeys

bioRxiv Jan 1, 2025
We used digit-tracking, a touch-based method for assessing visual attention, to investigate spontaneous exploration in macaque monkeys. By engaging with degraded images on a touch-sensitive display, monkeys could uncover high-resolution portions thro...
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Small Molecule Approach to RNA Targeting Binder Discovery (SMARTBind) Using Deep Learning Without Structural Input

bioRxiv Jan 1, 2025
Accurate identification of small molecule binders to RNA is critical for chemical probes and therapeutics. Computational approaches offer a cost-effective strategy to identify small molecules targeting RNA but are often limited by poor predictive acc...
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PathPCNet: Pathway Principal Component-Based Interpretable Framework for Drug Sensitivity Prediction

bioRxiv Jan 1, 2025
Precision medicine aims to identify significant biomarkers and effective drugs tailored to individual genomic profiles, thereby enabling personalized treatment strategies. Drug efficacy is often attributed to drug response, commonly measured as the c...
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Data-efficient protein mutational effect prediction with weak supervision by molecular simulation and protein language models

bioRxiv Jan 1, 2025
Machine learning-based protein mutational effect prediction is widely used in protein engineering and pathogenicity prediction, but training data scarcity remains a major challenge due to high costs of experimental measurements. A previous study prop...
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Single-cell transcriptomics and machine learning reveal RNF144B and C5AR1 as immune-related biomarkers and therapeutic targets in myocardial infarction

bioRxiv Jan 1, 2025
Myocardial infarction (MI) is a life-threatening cardiovascular disease characterized by high morbidity and mortality. Although advances in clinical management have improved patient outcomes, early diagnosis and effective immunomodulatory therapies r...
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Benchmarking large language models for genomic knowledge with GeneTuring

bioRxiv Jan 1, 2025
Large language models (LLMs) show promise in biomedical research, but their effectiveness for genomic inquiry remains unclear. We developed GeneTuring, a benchmark consisting of 16 genomics tasks with 1,600 curated questions, and manually evaluated 4...
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T-cell receptor specificity landscape revealed through de novo peptide design

bioRxiv Jan 1, 2025
T-cells play a key role in adaptive immunity by mounting specific responses against diverse pathogens. An effective binding between T-cell receptors (TCRs) and pathogen-derived peptides presented on Major Histocompatibility Complexes (MHCs) mediate a...
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An Open-Source Deep Learning-Based Toolbox for Automated Auditory Brainstem Response Analyses (ABRA)

bioRxiv Jan 1, 2025
Hearing loss is a pervasive global health challenge with profound impacts on communication, cognitive function, and quality of life. Recent studies have established age-related hearing loss as a significant risk factor for dementia, highlighting the ...
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High-throughput virus quantification using cytopathic effect area analysis by deep learning

bioRxiv Jan 1, 2025
Traditional infectivity-based virion quantification methods, such as 50% tissue culture infectious dose (TCID50) and plaque assays, are typically performed in 6-, 12-, 24-, or 48-well cell culture plates and require manual work and analysis based on ...
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