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.
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.
no code implementations • 5 Sep 2022 • Yilin Zhu, Jiayu Shang, Cheng Peng, Yanni Sun
Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art.
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.
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\%.
1 code implementation • 4 Jan 2022 • Jiayu Shang, Yanni Sun
Experimental methods for host prediction cannot keep pace with the fast accumulation of sequenced phages.
1 code implementation • 28 May 2021 • Jiayu Shang, Yanni Sun
High-throughput sequencing and its application to the microbiome have offered new opportunities for computational approaches for predicting which hosts particular viruses can infect.
1 code implementation • 7 Feb 2021 • Jiayu Shang, Jingzhe Jiang, Yanni Sun
Results: In this work, we present a novel semi-supervised learning model, named PhaGCN, to conduct taxonomic classification for phage contigs.
1 code implementation • 26 Sep 2020 • Du Nan, Jiayu Shang, Yanni Sun
In summary, ProDOMA is a useful end-to-end protein domain analysis tool for long noisy reads without relying on error correction.