Publications (18)
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…
CHERRY: a Computational metHod for accuratE pRediction of virus-pRokarYotic interactions using a graph encoder-decoder model
Jiayu Shang, Yanni Sun
Prokaryotic viruses, which infect bacteria and archaea, are key players in microbial communities. Predicting the hosts of prokaryotic viruses helps decipher the dynamic relationshi…
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…
PhaTYP: Predicting the lifestyle for bacteriophages using BERT
Jiayu Shang, Xubo Tang, Yanni Sun
Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with t…
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…
PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data
Jiayu Shang, Cheng Peng, Herui Liao +2
Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an e…
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…
Bacteriophage classification for assembled contigs using Graph Convolutional Network
Jiayu Shang, Jingzhe Jiang, Yanni Sun
Motivation: Bacteriophages (aka phages), which mainly infect bacteria, play key roles in the biology of microbes. As the most abundant biological entities on the planet, the number…
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…
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…
Phage family classification under Caudoviricetes: a review of current tools using the latest ICTV classification framework
Yilin Zhu, Jiayu Shang, Cheng Peng +1
Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles…
Accurate identification of bacteriophages from metagenomic data using Transformer
Jiayu Shang, Xubo Tang, Ruocheng Guo +1
Motivation: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their b…
Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning
Jiayu Shang, Yanni Sun
Background: Prokaryotic viruses, which infect bacteria and archaea, are the most abundant and diverse biological entities in the biosphere. To understand their regulatory roles in…
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,…
SmoothGNN: Smoothing-aware GNN for Unsupervised Node Anomaly Detection
Xiangyu Dong, Xingyi Zhang, Yanni Sun +3
The smoothing issue in graph learning leads to indistinguishable node representations, posing significant challenges for graph-related tasks. However, our experiments reveal that t…
ProDOMA: improve PROtein DOMAin classification for third-generation sequencing reads using deep learning
Du Nan, Jiayu Shang, Yanni Sun
Motivation: With the development of third-generation sequencing technologies, people are able to obtain DNA sequences with lengths from 10s to 100s of kb. These long reads allow pr…
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…