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BMC Bioinformatics|November 6, 2019
A binning tool to reconstruct viral haplotypes from assembled contigsJiao Chen, Jiayu Shang, Jianrong Wang, et al.
Bioinformatics (Oxford, England)|April 22, 2023
HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformerYongxin Ji, Jiayu Shang, Xubo Tang, et al.
Frontiers in Microbiology|January 2, 2023
Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification frameworkYilin Zhu, Jiayu Shang, Cheng Peng, et al.
Briefings in Bioinformatics|June 30, 2022
Accurate identification of bacteriophages from metagenomic data using TransformerJiayu Shang, Xubo Tang, Ruocheng Guo, et al.
Nucleic Acids Research|July 10, 2023
PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformerXubo Tang, Jiayu Shang, Yongxin Ji, et al.
Bioinformatics (Oxford, England)|November 23, 2024
ViraLM: empowering virus discovery through the genome foundation modelCheng Peng, Jiayu Shang, Jiaojiao Guan, et al.
Briefings in Bioinformatics|November 15, 2023
PhaGenus: genus-level classification of bacteriophages using a Transformer modelJiaojiao Guan, Cheng Peng, Jiayu Shang, et al.
Bioinformatics Advances|August 29, 2023
PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic dataJiayu Shang, Cheng Peng, Herui Liao, et al.
Genome Biology|February 7, 2026
PlasRAG: comprehensive plasmid characterization and retrieval through sequence-text alignmentYongxin Ji, Jiaojiao Guan, Herui Liao, et al.
Nucleic Acids Research|March 26, 2026
Fast and accurate identification of emerging viral reassortment from genome sequencesDehan Cai, Jiayu Shang, Cheng Peng, et al.
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