Citation

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). https://arxiv.org/abs/2303.15707

• 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, https://doi.org/10.1093/bib/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, https://doi.org/10.1093/bioinformatics/btab293

• 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, https://doi.org/10.1093/bib/bbac182

• PhaTYP (Lifestyle prediction)

Jiayu Shang, Xubo Tang, Yanni Sun, PhaTYP: predicting the lifestyle for bacteriophages using BERT, Briefings in Bioinformatics, 2022, bbac487, https://doi.org/10.1093/bib/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, https://arxiv.org/pdf/2301.12422.pdf