bioRxiv

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Machine Learning Enables Viral Genome-Agnostic Classification of RNA Virus Infections from Host Transcriptomes

bioRxiv Jan 1, 2025
Targeted PCR diagnosis of RNA viruses is sequence dependent, meaning that the accuracy of the assay depends on the identity of the viral sequence. However, sequence-targeted assays can miss novel or divergent viruses. We test whether the host transcr...
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Geno2pheno[bNAbs]: Interpretable and accurate HIV antibody resistance prediction

bioRxiv Jan 1, 2025
Antiretroviral therapy (ART) is a life saving option for people living with HIV-1 (PLWH) and is effective against many viral strains. The most common ARTs involve combinations of drugs targeting viral or cellular proteins. Most of these drugs have to...
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Distinct brain mechanisms support trust violations, belief integration, and bias in human-AI teams

bioRxiv Jan 1, 2025
This study provides an integrated electrophysiological and behavioral account of the neuro-cognitive markers underlying trust evolution during human interaction with artificial intelligence (AI). Trust is essential for effective collaboration and pla...
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Mapping Risk and Conservation Potential Across the Indo-Pacific with Reefshark Genomescapes

bioRxiv Jan 1, 2025
Overfishing has severely depleted marine populations worldwide, including within protected areas. Illegal and unreported fishing are major contributors to this decline. Large-bodied apex predators such as sharks are among the most affected, with over...
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Beyond Sequence Similarity: ML-Powered Identification of pHLA Off-Targets for TCR-Mimic Antibodies Using High Throughput Binding Kinetics

bioRxiv Jan 1, 2025
T-cell receptor mimic (TCRm) antibodies are an emerging class of tumor-targeting agents used in advanced immunother-apies such as bispecific T-cell engagers and CAR-T cells. Unlike conventional antibodies, TCRms are designed to recognize peptide–huma...
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VesiclePy: A Machine Learning Vesicle Analysis Toolbox for Volume Electron Microscopy

bioRxiv Jan 1, 2025
Vesicles are critical components of neurons that package neurotransmitters and neuropeptides for their release, in order to communicate with other neurons and cells. However, due to their small size, the reconstruction of the full vesicle endowment a...
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PhageAI: a new approach to predicting the lifestyle of bacteriophages using proteinBERT and convolutional neural networks

bioRxiv Jan 1, 2025
Bacteriophages are viruses that infect bacteria, including temperate, virulent and chronic phages. In the current times of increasing resistance to antibiotics (AMR), it is necessary to quickly find phages and determine their lifecycle, therefore com...
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Machine Learning-Driven Prediction of TLR4 Binding Affinity: A Comprehensive Molecular Feature Analysis for Drug Discovery

bioRxiv Jan 1, 2025
Toll-like receptor 4 (TLR4) represents a promising therapeutic target for inflammatory diseases and cancer, but developing selective modulators remains challenging. We present a machine learning approach for predicting TLR4 binding affinity using com...
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Estimating how Site-Level Differences in Acoustic Environments Affect Species Detection by Machine Learning Models

bioRxiv Jan 1, 2025
Machine learning models are vital in species detection from acoustic data, due to the large amount of recordings produced, especially in passive acoustic monitoring studies. However, the acoustic environment of a site can significantly impact the det...
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T-SCAPE: T-cell Immunogenicity Scoring via Cross-domain Aided Predictive Engine

bioRxiv Jan 1, 2025
T-cell immunogenicity, the ability of peptide fragments to elicit T-cell responses, is a critical determinant of the safety and efficacy of protein therapeutics and vaccines. While deep learning shows promise for in silico prediction, the scarcity of...
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