Viral Metagenomic Sequencing As A road-spectrum Pathogen Detection Technology For Viral Diseases

SUN, Yanni (Principal Investigator / Project Coordinator)
Shi, Mang (Co-Investigator)
Wang, Sibo (Co-Investigator)

Department of Electrical Engineering

Project: Research

11 RGC 21 - Publication in refereed journal
1 RGC 32 - Refereed conference paper (with host publication)

12 results

2025
SmoothGNN: Smoothing-aware GNN for Unsupervised Node Anomaly Detection
Dong, X., Zhang, X., Sun, Y., Chen, L., Yuan, M. & Wang, S., 2025, WWW ’25: Proceedings of the ACM Web Conference 2025. Association for Computing Machinery, p. 1225-1236 (WWW - Proceedings of the ACM Web Conference).
Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

Open Access
File
1 Downloads (CityUHK Scholars)
2024
Accurate and efficient protein embedding using multi-teacher distillation learning
Shang, J., Peng, C., Ji, Y., Guan, J., Cai, D., Tang, X. & Sun, Y., Sept 2024, In: Bioinformatics. 40, 9, btae567.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
1 Citation (Scopus)

10 Downloads (CityUHK Scholars)
Consensus statement from the first RdRp Summit: advancing RNA virus discovery at scale across communities
Charon, J., Olendraite, I., Forgia, M., Chong, L. C., Hillary, L. S., Roux, S., Kupczok, A., Debat, H., Sakaguchi, S., Tahzima, R., Nakagawa, S., Babaian, A., Abroi, A., Bejerman, N., Ben Mansour, K., Brown, K., Butkovic, A., Cervera, A., Charriat, F. & Chen, G. & 27 others, Chiba, Y., De Coninck, L., Demina, T., Dominguez-Huerta, G., Dubrulle, J., Gutierrez, S., Harvey, E., Jayaraj Mallika, F. R., Karapliafis, D., Lim, S. J., Kasibhatla, S. M., Mifsud, J. C. O., Nishimura, Y., Ortiz-Baez, A. S., Raco, M., Rivero, R., Sadiq, S., Saghaei, S., San, J. E., Shaikh, H. M., Sieradzki, E. T., Sullivan, M. B., Sun, Y., Wille, M., Wolf, Y. I., Zrelovs, N. & Neri, U., 2024, In: Frontiers in Virology. 4, 1371958.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
4 Citations (Scopus)

24 Downloads (CityUHK Scholars)
The clinical outcome of COVID-19 is strongly associated with microbiome dynamics in the upper respiratory tract
Xie, L. (Co-first Author), Luo, G. (Co-first Author), Yang, Z., Wu, W.-C., Chen, J., Ren, Y., Zeng, Z., Ye, G., Pan, Y., Zhao, W.-J., Chen, Y.-Q., Hou, W., Sun, Y., Guo, D., Yang, Z., Li, J., Holmes, E. C., Li, Y., Chen, L. & Shi, M., Mar 2024, In: Journal of Infection. 88, 3, 106118.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
5 Citations (Scopus)

43 Downloads (CityUHK Scholars)
Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review
Yu, R., Huang, Z., Lam, T. Y. C. & Sun, Y., Jul 2024, In: Briefings in Bioinformatics. 25, 4, bbae292.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
2 Citations (Scopus)

26 Downloads (CityUHK Scholars)
ViraLM: empowering virus discovery through the genome foundation model
Peng, C. (Co-first Author), Shang, J. (Co-first Author), Guan, J., Wang, D. & Sun, Y., Dec 2024, In: Bioinformatics. 40, 12, btae704.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
3 Citations (Scopus)

12 Downloads (CityUHK Scholars)
VirID: Beyond Virus Discovery — An Integrated Platform for Comprehensive RNA Virus Characterization
Yang, Z. (Co-first Author), Shan, Y. (Co-first Author), Liu, X., Chen, G., Pan, Y., Gou, Q., Zou, J., Chang, Z., Zeng, Q., Yang, C., Kong, J., Sun, Y., Li, S., Zhang, X., Wu, W.-C., Li, C., Peng, H., Holmes, E. C., Guo, D. & Shi, M., Oct 2024, In: Molecular Biology and Evolution. 41, 10, msae202.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
26 Downloads (CityUHK Scholars)
VirTAXA: Enhancing RNA virus taxonomic classification with remote homology search and tree-based validation
Zhu, Y., Chen, G. & Sun, Y., Oct 2024, In: Bioinformatics. 40, 10, btae575.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
18 Downloads (CityUHK Scholars)
2023
Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients
Zhang, F., Gia, A., Chen, G., Gong, L., Behary, J., Hold, G. L., Zekry, A., Tang, X., Sun, Y., El-Omar, E. & Jiang, X.-T., Jan 2023, In: Viruses. 15, 1, 13 p.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
1 Citation (Scopus)

64 Downloads (CityUHK Scholars)
VirBot: an RNA viral contig detector for metagenomic data
Chen, G., Tang, X., Shi, M. & Sun, Y., Mar 2023, In: Bioinformatics. 39, 3, btad093.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
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11 Citations (Scopus)

68 Downloads (CityUHK Scholars)
2022
RdRp-based sensitive taxonomic classification of RNA viruses for metagenomic data
Tang, X., Shang, J. & Sun, Y., Mar 2022, In: Briefings in Bioinformatics. 23, 2, bbac011.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
3 Citations (Scopus)

66 Downloads (CityUHK Scholars)
VirStrain: a strain identification tool for RNA viruses
Liao, H., Cai, D. & Sun, Y., 2022, In: Genome Biology. 23, 1, 38.
Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

Open Access
File
10 Citations (Scopus)

77 Downloads (CityUHK Scholars)

Viral Metagenomic Sequencing As A road-spectrum Pathogen Detection Technology For Viral Diseases

Research output

Search results