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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…
Accurate and efficient protein embedding using multi-teacher distillation learning
Jiayu Shang, Cheng Peng, Yongxin Ji +4
Motivation: Protein embedding, which represents proteins as numerical vectors, is a crucial step in various learning-based protein annotation/classification problems, including gen…
PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer
Jiayu Shang, Cheng Peng, Xubo Tang +1
Motivation: As viruses that mainly infect bacteria, phages are key players across a wide range of ecosystems. Analyzing phage proteins is indispensable for understanding phages' fu…