Prof. SUN Yanni (孫燕妮)

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Research Output

  1. 2025
  2. Published

    MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction

    Zou, W., Ji, Y., Guan, J. & Sun, Y., Mar 2025, In: Bioinformatics. 41, 3, btaf075.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  3. Accepted/In press/Filed

    ​RTTAP: 基於短讀長的全感染組分類分析流程​

    JIANG, W. (Inventor), LIAO, H. (Inventor), Shi, Mang (Inventor), Chen, Liangjun (Inventor) & SUN, Y. (Inventor), 12 Feb 2025, (Accepted/In press/Filed) Priority No. 2025101558418

    Research output: Patents, Agreements and Assignments › RGC 51 - Patents (CityUHK)

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  4. Published

    GOPhage: protein function annotation for bacteriophages by integrating the genomic context

    Guan, J., Ji, Y., Peng, C., Zou, W., Tang, X., Shang, J. & Sun, Y., Jan 2025, In: Briefings in Bioinformatics. 26, 1, bbaf014.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  5. 2024
  6. Published

    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

    Scopus citations: 1
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  7. Published

    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. & 13 others, 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

    Check@CityULib
  8. Published

    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

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  9. Published

    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

    Scopus citations: 1
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  10. Published

    SegVir: Reconstruction of Complete Segmented RNA Viral Genomes from Metatranscriptomes

    Tang, X., Shang, J., Chen, G., Chan, K. H. K., Shi, M. & Sun, Y., Aug 2024, In: Molecular Biology and Evolution. 41, 8, msae171.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 1
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  11. Published

    Towards more accurate microbial source tracking via non-negative matrix factorization (NMF)

    Huang, Z. (Co-first Author), Cai, D. (Co-first Author) & Sun, Y., Jul 2024, ISMB 2024 Proceedings. Oxford University Press, p. i68-i78 (Bioinformatics; vol. 40, no. Supplement_1).

    Research output: Chapters, Conference Papers, Creative and Literary Works › RGC 32 - Refereed conference paper (with host publication) › peer-review

    Scopus citations: 2
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  12. Published

    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

    Scopus citations: 2
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  13. Published

    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. & 13 others, 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

    Scopus citations: 2
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  14. Published

    Identifying ARG-carrying bacteriophages in a lake replenished by reclaimed water using deep learning techniques

    Wang, D., Shang, J., Lin, H., Liang, J., Wang, C., Sun, Y. & Bai, Y. & 1 others, Qu, J., 1 Jan 2024, In: Water Research. 248, 120859.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 8
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  15. Published

    Accelerating de novo SINE annotation in plant and animal genomes

    Liao, H., Sun, Y. & Ou, S., 2024, In: Mobile DNA. 15, 24.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  16. Published

    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. & 40 others, 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., 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

    Scopus citations: 4
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  17. Published

    PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure

    Ji, Y., Shang, J., Guan, J., Zou, W., Liao, H., Tang, X. & Sun, Y., 2024, In: GigaScience. 13, 17 p., giae104.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  18. Presented

    Quantum Modeling for Simulating Biological Stochastic Processes

    Ho, L. Y. L., PAN, L., MENG, F., Ho, K. T. M., LIU, F., Wu, M.-T. & Lei, P. & 5 others, Bhachu, G., Dahlsten, O., SUN, Y., Lee, P.-H. & TAN, G. Y. A., 2024, (Presented).

    Research output: Conference Papers › Poster › peer-review

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  19. Published

    Quantum modeling simulates nutrient effect of bioplastic polyhydroxyalkanoate (PHA) production in Pseudomonas putida

    Ho, L. Y. L., Pan, L., Meng, F., Ho, K. T. M., Liu, F., Wu, M.-T. & Lei, H. I. & 6 others, Bhachu, G., Wang, X., Dahlsten, O., Sun, Y., Lee, P.-H. & Tan, G. Y. A., 2024, In: Scientific Reports. 14, 18255.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 1
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  20. Published

    RNAVirHost: a machine learning–based method for predicting hosts of RNA viruses through viral genomes

    Chen, G., Jiang, J. & Sun, Y., 2024, In: GigaScience. 13, giae059.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

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  21. 2023
  22. Published

    GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data

    Liao, H., Shang, J. & Sun, Y., Dec 2023, In: Bioinformatics. 39, 12, btad747.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Scopus citations: 2
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  23. Published

    LncRNA-Top: Controlled Deep Learning Approaches for LncRNA Gene Regulatory Relationship Annotations across Different Platforms

    Xie, W., Chen, X., Zheng, Z., Wang, F., Zhu, X., Lin, Q. & Sun, Y. & 1 others, Wong, K.-C., 17 Nov 2023, In: iScience. 26, 11, 108197.

    Research output: Journal Publications and Reviews › RGC 21 - Publication in refereed journal › peer-review

    Check@CityULib
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