7 papers
SeekRBP: Leveraging Sequence-Structure Integration with Reinforcement Learning for Receptor-Binding Protein Identification
Xiling Luo, Le Ou-Yang, Yang Shen +6
Motivation: Receptor-binding proteins (RBPs) initiate viral infection and determine host specificity, serving as key targets for phage engineering and therapy. However, the identif…
TPMM: Three-component Posterior Mixture Model Enables Robust Inverton Detection in Low-Depth Metagenomes and Suggests Potential Viral Invertons
Yi Lu, Jiaojiao Guan, Yang Shen +2
Bacterial phase variation enables reversible, locus-specific phenotypic switching, often driven by DNA inversion (invertons). To identify these events, researchers commonly rely on…
PhageMind: Generalized Strain-level Phage Host Range Prediction via Meta-learning
Yang Shen, Keming Shi, Chen Yu +3
Bacteriophages (phages) are key regulators of bacterial populations and hold great promise for applications such as phage therapy, biocontrol, and industrial fermentation. The succ…
AI Agents in Drug Discovery
Srijit Seal, Dinh Long Huynh, Moudather Chelbi +17
Artificial intelligence (AI) agents are emerging as transformative tools in drug discovery, with the ability to autonomously reason, act, and learn through complicated research wor…
Computational approaches for virus host prediction: A review of methods and applications
Jiayu Shang, Cheng Peng, Jiaojiao Guan +3
Accurate prediction of virus-host interactions is critical for understanding viral ecology and developing applications like phage therapy. However, the growing number of computatio…
ViralQC: A Tool for Assessing Completeness and Contamination of Predicted Viral Contigs
Cheng Peng, Jiayu Shang, Jiaojiao Guan +1
Motivation: Viruses represent the most abundant biological entities on the planet and play vital roles in diverse ecosystems. Cataloging viruses across various environments is esse…