AIMC Topic: Bacteriophages
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Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.
NPJ biofilms and microbiomes
Jul 5, 2025
Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder frequently accompanied by psychological symptoms. Bacterial microbiota plays a critical role in mediating local and systemic immunity, and alterations in these microbial communities...
Discovery and affinity maturation of antibody fragments from an unfavorably enriched phage display selection by deep sequencing and machine learning.
Journal of bioscience and bioengineering
Jun 4, 2025
Phage display selection has been used for directed evolution of antibody fragments. However, variants with binding affinity cannot be always identified due to undesirable enrichment of target-unrelated variants in the biopanning process. Here, our go...
Optimizing phage therapy with artificial intelligence: a perspective.
Frontiers in cellular and infection microbiology
May 27, 2025
Phage therapy is emerging as a promising strategy against the growing threat of antimicrobial resistance, yet phage and bacteria are incredibly diverse and idiosyncratic in their interactions with one another. Clinical applications of phage therapy o...
Exploring deep learning in phage discovery and characterization.
Virology
Apr 29, 2025
Bacteriophages, or bacterial viruses, play diverse ecological roles by shaping bacterial populations and also hold significant biotechnological and medical potential, including the treatment of infections caused by multidrug-resistant bacteria. The d...
PhageDPO: A machine-learning based computational framework for identifying phage depolymerases.
Computers in biology and medicine
Feb 13, 2025
Bacteriophages (phages) are the most predominant and genetically diverse biological entities on Earth. Phages are viruses that infect bacteria and encode numerous proteins with potential biotechnological application. However, most phage-encoded prote...
Bacteriophage-Activated DNAzyme Hydrogels Combined with Machine Learning Enable Point-of-Use Colorimetric Detection of Escherichia coli.
Advanced materials (Deerfield Beach, Fla.)
Nov 26, 2024
Developing cost-effective, consumer-accessible platforms for point-of-use environmental and clinical pathogen testing is a priority, to reduce reliance on laborious, time-consuming culturing approaches. Unfortunately, a system offering ultrasensitive...
Improving viral annotation with artificial intelligence.
mBio
Sep 4, 2024
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environme...
Discovery of Antimicrobial Lysins from the "Dark Matter" of Uncharacterized Phages Using Artificial Intelligence.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Jun 20, 2024
The rapid rise of antibiotic resistance and slow discovery of new antibiotics have threatened global health. While novel phage lysins have emerged as potential antibacterial agents, experimental screening methods for novel lysins pose significant cha...
Exploring the roles of ribosomal peptides in prokaryote-phage interactions through deep learning-enabled metagenome mining.
Microbiome
May 24, 2024
BACKGROUND: Microbial secondary metabolites play a crucial role in the intricate interactions within the natural environment. Among these metabolites, ribosomally synthesized and post-translationally modified peptides (RiPPs) are becoming a promising...
Prediction of Klebsiella phage-host specificity at the strain level.
Nature communications
May 22, 2024
Phages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging to find matching phages against bacteria of interest. Current computational tools d...
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