About Citation

If you find our work useful for your research work, please cite the corresponding subprogram listed below.

  • PhaBOX

Jiayu Shang, Cheng Peng, Herui Liao, Xubo Tang, and Yanni Sun. "PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data." arXiv preprint arXiv:2303.15707 (2023).

  • PhaMer (phage identification)

Jiayu Shang, Xubo Tang, Ruocheng Guo, Yanni Sun, Accurate identification of bacteriophages from metagenomic data using Transformer, Briefings in Bioinformatics, Volume 23, Issue 4, July 2022, bbac258,

  • PhaGCN (taxonomy classification)

Jiayu Shang, Jingzhe Jiang, Yanni Sun, Bacteriophage classification for assembled contigs using graph convolutional network, Bioinformatics, Volume 37, Issue Supplement_1, July 2021, Pages i25–i33,

  • Cherry (host prediction)

Jiayu Shang, Yanni Sun, CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model, Briefings in Bioinformatics, Volume 23, Issue 5, September 2022, bbac182,

  • PhaTYP (Lifestyle prediction)

Jiayu Shang, Xubo Tang, Yanni Sun, PhaTYP: predicting the lifestyle for bacteriophages using BERT, Briefings in Bioinformatics, 2022, bbac487,

  • PhaVIP (Protein annotation)

Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun. (2023). PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer. arXiv preprint arXiv:2301.12422,