5 papers
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…
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…
GiantHunter: Accurate detection of giant virus in metagenomic data using reinforcement-learning and Monte Carlo tree search
Fuchuan Qu, Cheng Peng, Jiaojiao Guan +3
Motivation: Nucleocytoplasmic large DNA viruses (NCLDVs) are notable for their large genomes and extensive gene repertoires, which contribute to their widespread environmental pres…
PhaGO: Protein function annotation for bacteriophages by integrating the genomic context
Jiaojiao Guan, Yongxin Ji, Cheng Peng +4
Bacteriophages are viruses that target bacteria, playing a crucial role in microbial ecology. Phage proteins are important in understanding phage biology, such as virus infection,…