PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data

1 code implementation • 28 Mar 2023 • Jiayu Shang, Cheng Peng, Herui Liao, Xubo Tang, Yanni Sun

Motivation: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome.

PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer

1 code implementation • 29 Jan 2023 • Jiayu Shang, Cheng Peng, Xubo Tang, Yanni Sun

Thus, there is a great demand to develop a computational method for fast and accurate phage virion protein classification.

Classification Image Classification

PhaTYP: Predicting the lifestyle for bacteriophages using BERT

1 code implementation • 20 Jun 2022 • Jiayu Shang, Xubo Tang, Yanni Sun

In this work, we develop PhaTYP (Phage TYPe prediction tool) to improve the accuracy of lifestyle prediction on short contigs.

Type prediction

Accurate identification of bacteriophages from metagenomic data using Transformer

1 code implementation • 13 Jan 2022 • Jiayu Shang, Xubo Tang, Ruocheng Guo, Yanni Sun

In the real metagenomic data experiment, PhaMer improves the F1-score of phage detection by 27\%.

Language Modelling