Publication (listed by time)

The following works have been done during my Ph.D. study.

• Shang, J., Peng, C., Liao, H., Tang, X., & Sun, Y. “PhaBOX: A web server for identifying and characterizing phage contigs in metagenomic data.” Accepted by Bioinformatics Advance. vbad101. Link
• Shang, J., Peng, C., Tang, X., & Sun, Y. “PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer.” ISMB/ECCB 2023 (proceeding paper, 17% acceptance rate)
• Tang, X., Shang, J., Ji, Y., & Sun, Y. (2023). PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer. Nucleic Acids Research, gkad578. Link
• Shang, J., Tang, X., & Sun, Y. (2023). PhaTYP: predicting the lifestyle for bacteriophages using BERT, Briefings in Bioinformatics, Volume 24. Link
• Ji, Y., Shang, J., Tang, X., & Sun, Y. (2023). HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer. Bioinformatics, 39(5), btad283.Link
• Jiang, J. Z., Yuan, W. G., Shang, J., Shi, Y. H., Yang, L. L., Liu, M., … & Yuan, L. H. (2023). Virus classification for viral genomic fragments using PhaGCN2. Briefings in Bioinformatics, Volume 24 (co-first author). Link
• Zhu Y., Shang, J., Peng, C., & Sun, Y. (2022). Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework. Frontiers in Microbiology, Volume 13 (co-first author). Link
• Cai, D., Shang, J., & Sun, Y. (2022). HaploDMF: viral haplotype reconstruction from long reads via deep matrix factorization. Bioinformatics, Volume 38. Link
• Tang, X., Shang, J., & Sun, Y. (2022). RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data. Briefings in Bioinformatics, Volume 23. Link
• Shang, J., Tang, X., Guo, R., & Sun, Y. (2022). Accurate identification of bacteriophages from metagenomic data using Transformer. Briefings in Bioinformatics, Volume 23. Link
• Shang, J., & Sun, Y. (2022). CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model. Briefings in Bioinformatics, Volume 23. Link
• Du, N., Shang, J., & Sun, Y. (2021). Improving protein domain classification for third-generation sequencing reads using deep learning. BMC genomics, Volume 22 (co-first author). Link
• Shang, J., Jiang jinzhe, & Sun, Y. (2021) “Bacteriophage classification for assembled contigs using Graph Convolutional Network.” ISMB/ECCB 2021 (proceeding paper, 18% acceptance rate) Link
• Shang, J., & Sun, Y. (2021). Predicting the hosts of prokaryotic viruses using GCN-based semi-supervised learning. BMC biology, Volume 19. Link
• Shang, J., & Sun, Y. (2021). CHEER: HierarCHical taxonomic classification for viral mEtagEnomic data via deep leaRning. Methods, Volume 189. Link
• Chen, J., Shang, J., Wang, J., & Sun, Y. (2019). A binning tool to reconstruct viral haplotypes from assembled contigs. BMC bioinformatics, Volume 20. Link

The following works have been done during my undergraduate study.

• Li, S., Shang, J., Duan, Z., & Huang, J. (2018). Fast detection method of quick response code based on run‐length coding. IET Image Processing, Volume 12. Link