bioRxiv

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Comparative analysis of sequential and thermodynamic features of pre-miRNA in insects with various organisms and applying XGBoost for one-vs-rest binary classification

bioRxiv Jan 1, 2025
MicroRNAs are found to regulate various biological processes which are produced from precursor microRNA. As the length of such microRNA are small, homology-based searching is not very useful. Hence, various machine learning based tools have been desi...
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Efficacy and safety evaluation of artificial intelligence-identified antimicrobial peptides for use against avian pathogenic Escherichia coli in the poultry industry

bioRxiv Jan 1, 2025
The overuse of antibiotics in both veterinary and human medicine has resulted in the emergence of antibiotic-resistant bacteria, prompting a search for effective alternatives. Antimicrobial peptides (AMP) are short, often cationic, peptide-based mole...
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Instruction-tuned extraction of virus-host interactions from integrated scientific evidence

bioRxiv Jan 1, 2025
Viral infectious diseases continue to pose a major threat to global health. Understanding protein-protein interactions (PPIs) and RNA-protein interactions (RPIs) between viruses and hosts is essential for elucidating infection mechanisms. However, ma...
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Unveiling the Human Nasopharyngeal Microbiome Compendium: Systematic Characterization of Community Architecture and Function Through a Comprehensive Meta-Analysis

bioRxiv Jan 1, 2025
The nasopharyngeal microbiome acts as a dynamic interface between the human body and environmental exposures, modulating immune responses and helping to maintain respiratory health. Despite its clinical significance, the nasopharyngeal microbiome rem...
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Efficient Search of Ultra-Large Synthesis On-Demand Libraries with Chemical Language Models

bioRxiv Jan 1, 2025
Ultra-large ‘building block’ catalogs provide inexpensive access to billions of synthesis-on-demand molecules, but the combinatorial scale renders conventional virtual screening impractical. We present Vector Virtual Screen (VVS), a score-function-ag...
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Iterative improvement of deep learning models using synthetic regulatory genomics

bioRxiv Jan 1, 2025
Deep learning models can accurately reconstruct genome-wide epigenetic tracks from the reference genome sequence alone. But it is unclear what predictive power they have on sequence diverging from the reference, such as disease- and trait-associated ...
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A deep reinforcement learning platform for antibiotic discovery

bioRxiv Jan 1, 2025
Antimicrobial resistance (AMR) is projected to cause up to 10 million deaths annually by 2050, underscoring the urgent need for new antibiotics. Here we present ApexAmphion, a deep-learning framework for de novo design of antibiotics that couples a 6...
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High-level Prediction of Continuous Speech During Mind-Wandering

bioRxiv Jan 1, 2025
Abundant evidence shows that when listening to speech or reading text, we continuously make predictions about upcoming words. Does this process stop when our mind wanders away and subjective experience becomes decoupled from the content of the speech...
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Breaking the culture habit: metagenomic diagnosis of companion animal skin infections

bioRxiv Jan 1, 2025
Skin infections have been described as the primary cause for presentation in veterinary small animal practices and they frequently result in prescription of both topical and systemic antibiotics. Because such infections are often secondary complicati...
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Machine learning based lineage prediction from AMR phenotypes for Escherichia coli ST131 clade C surveillance across infection types

bioRxiv Jan 1, 2025
Rising antimicrobial resistance (AMR) in Escherichia coli bloodstream infections (BSIs) in high-income settings has typically been dominated by one clone, the sequence type (ST) 131. More specifically, ST131 clade C (ST131-C) is associated with fluor...
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