Dr. SUN Yanni (孫燕妮)

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Research Output

  1. 2023
  2. Accepted/In press/Filed

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

    Shang, J., Peng, C., Tang, X. & Sun, Y., Jul 2023, (Accepted/In press/Filed) ISMB/ECCB 2023 Proceedings.

    Research output: Chapters, Conference Papers, Creative and Literary Works (RGC: 12, 32, 41, 45) › 32_Refereed conference paper (with ISBN/ISSN) › peer-review

    Check@CityULib
  3. Published

    Global prevalence of SARS-CoV-2 3CL protease mutations associated with nirmatrelvir or ensitrelvir resistance

    Ip, J. D., Chu, A. W., Chan, W., Leung, R. C., Abdullah, S. M. U., Sun, Y. & To, K. K., May 2023, In: eBioMedicine. 91, 104559.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  4. Published

    HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer

    Ji, Y., Shang, J., Tang, X. & Sun, Y., May 2023, In: Bioinformatics. 39, 5, btad283.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  5. Published

    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, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  6. Published

    AccuVIR: an ACCUrate VIRal genome assembly tool for third-generation sequencing data

    Yu, R., Cai, D. & Sun, Y., Jan 2023, In: Bioinformatics. 39, 1, 8 p., btac827.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  7. Published

    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., & 4 othersTang, X., Sun, Y., El-Omar, E. & Jiang, X., Jan 2023, In: Viruses. 15, 1, 13 p.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  8. Published

    PhaTYP: predicting the lifestyle for bacteriophages using BERT

    Shang, J., Tang, X. & Sun, Y., Jan 2023, In: Briefings in Bioinformatics. 24, 1, bbac487.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 2
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  9. Published

    Virus classification for viral genomic fragments using PhaGCN2

    Jiang, J., Yuan, W., Shang, J., Shi, Y., Yang, L., Liu, M., Zhu, P., & 3 othersJin, T., Sun, Y. & Yuan, L., Jan 2023, In: Briefings in Bioinformatics. 24, 1, bbac505.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  10. 2022
  11. Published

    HaploDMF: viral Haplotype reconstruction from long reads via Deep Matrix Factorization

    Cai, D., Shang, J. & Sun, Y., 15 Dec 2022, In: Bioinformatics. 38, 24, p. 5360–5367

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  12. Published

    SEISMIC HAZARD DETERMINATION METHOD AND SYSTEM

    ZUKERMAN, M., Wang, Gang, WANG, Z., MORAN, W., SUN, Y., WANG, Q., WANG, X., & 1 othersWANG, Y., 15 Nov 2022, Patent No. US11,500,125, Priority No. 16/889,663

    Research output: Patents, Agreements and Assignments (RGC: 51, 52, 53) › 51_Patents granted (CityU only, data source from KTO)

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  13. Published

    Artificial Intelligence in Meta-optics

    Chen, M. K., Liu, X., Sun, Y. & Tsai, D. P., 12 Oct 2022, In: Chemical Reviews. 122, 19, p. 15356–15413 58 p.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 20
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  14. Published

    Distinct composition and amplification dynamics of transposable elements in sacred lotus (Nelumbo nucifera Gaertn.)

    Cerbin, S., Ou, S., Li, Y., Sun, Y. & Jiang, N., Oct 2022, In: Plant Journal. 112, 1, p. 172-192

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Check@CityULib
  15. Published

    CHERRY: a Computational metHod for accuratE pRediction of virus–pRokarYotic interactions using a graph encoder–decoder model

    Shang, J. & Sun, Y., Sep 2022, In: Briefings in Bioinformatics. 23, 5, bbac182.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 3
    Check@CityULib
  16. Published

    Accurate identification of bacteriophages from metagenomic data using Transformer

    Shang, J., Tang, X., Guo, R. & Sun, Y., Jul 2022, In: Briefings in Bioinformatics. 23, 4, bbac258.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 3
    Check@CityULib
  17. Published

    Reconstructing viral haplotypes using long reads

    Cai, D. & Sun, Y., 15 Apr 2022, In: Bioinformatics. 38, 8, p. 2127–2134 8 p.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 1
    Check@CityULib
  18. Published

    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, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 1
    Check@CityULib
  19. Published

    AnnoSINE: a short interspersed nuclear elements annotation tool for plant genomes

    Li, Y., Jiang, N. & Sun, Y., Feb 2022, In: Plant Physiology. 188, 2, p. 955-970

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 1
    Check@CityULib
  20. Published

    Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework

    Zhu, Y., Shang, J., Peng, C. & Sun, Y., 2022, In: Frontiers in Microbiology. 13, 1032186.

    Research output: Journal Publications and Reviews (RGC: 21, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 1
    Check@CityULib
  21. Published

    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, 22, 62) › 21_Publication in refereed journal › peer-review

    Scopus citations: 3
    Check@CityULib
  22. 2021
  23. Published

    Bacteriophage classification for assembled contigs using Graph Convolutional Network

    Shang, J., Jiang, J. & Sun, Y., Jul 2021, ISMB/ECCB 2021 Proceedings. Oxford University Press, p. i25-i33 9 p. (Bioinformatics; vol. 37, no. Suppl. 1).

    Research output: Chapters, Conference Papers, Creative and Literary Works (RGC: 12, 32, 41, 45) › 32_Refereed conference paper (with ISBN/ISSN) › peer-review

    Scopus citations: 13
    Check@CityULib
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