• Applications of artificial intelligence in medicine
• Mechanisms of antibiotic resistance and novel antimicrobial therapies

Nancy Zhang’s research focuses on developing AI-assisted computational frameworks to advance phage therapy, precision diagnostics, and antimicrobial stewardship. Her work applies deep learning across several complementary areas of microbial multi-omics. In proteomics, she contributes to the development of de novo peptide sequencing methods to identify novel drug targets and vaccine candidates. In metagenomics, she develops computational tools to characterize microbial community diversity and functional potential in complex clinical samples. A major area of her research is antimicrobial resistance, where she integrates phage genomics, resistance gene profiling, and phenotype-genotype association analyses to support precision therapeutics and the development of phage-based therapeutics. She has also co-developed integrated platforms for rapid microbial identification that combine sample preprocessing optimization, on-site sequencing workflows, and automated bioinformatics pipelines to support precision diagnostics and antimicrobial stewardship.

Nancy Zhang is an Assistant Professor in the Department of Anaesthesia and Intensive Care and the Li Ka Shing Institute of Health Sciences, Faculty of Medicine, at The Chinese University of Hong Kong (CUHK). Her research focuses on developing AI-assisted computational frameworks for microbial multi-omics, with particular interests in antimicrobial resistance, phage therapy, and clinical diagnostics. She applies deep learning approaches across microbial genomics, proteomics, metagenomics, and population genetics to support microbial identification, resistance profiling, transmission tracking, and precision therapeutics. She has also developed integrated diagnostic platforms for rapid microbial detection, including systems for strain-level traceability, workflow optimization, and automated bioinformatics analysis. Her work contributes to the advancement of precision diagnostics and antimicrobial stewardship.

1. Expert Member, Beijing Expert Database for Medical and Health Technology Innovation and Translation, Beijing Medical and Health Science and Technology Promotion Center (2025)
2. Student Travel Award, International Conference on Computational Advances in Bio and Medical Sciences (ICCABS) (2017)
3. Postdoctoral Research Fellowship, University of Waterloo
4. Trainee Travel Award, Ontario Consortium for Regeneration inducing Therapeutics (OCRiT) (2012)
5. 2nd China Open Source Software Competition Merit Award, China Software Industry Association (2006)

1. Jiang Y, Wang Y, Che L, Yang S, Zhang X, Lin Y, Shi Y, Zou N, Wang S, Zhang Y, Zhao Z, Li SC. GutMetaNet: An integrated database for exploring horizontal gene transfer and functional redundancy in the human gut microbiome. Nucleic Acids Research. 2025;53(D1):D772-D782. doi:10.1093/nar/gkae1007.
2. Wang RH, Ng YK, Zhang X, Wang J, Li SC. Coding genomes with gapped pattern graph convolutional network. Bioinformatics. 2024;40(4):1-8. doi:10.1093/bioinformatics/btae188.
3. Zheng L, Yang C, Chen P, Zhu L, Wen H, Liu M, Guan J, Lu G, Jing J, Sun S, Wang Y, Song Y, Yang R, Zhang X, Cui Y, Guo X. Vibrio parahaemolyticus from migratory birds in China carries an extra copy of tRNA-Gly and plasmid-mediated quinolone resistance gene qnrD. Microbiology Spectrum. 2023;11(4):1-12. doi:10.1128/spectrum.02170-22.
4. Sun S, Zhang X. Genetic characteristics and integration specificity of Salmonella enterica temperate phages. Frontiers in Microbiology. 2023;14(August):1-14. doi:10.3389/fmicb.2023.1199843.
5. Zhang JX, Xu JH, Yuan B, Wang XD, Mao XH, Wang JL, Zhang XLL, Yuan Y. Detection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags. Frontiers in Public Health. 2023;11:1-11. doi:10.3389/fpubh.2023.1153352.
6. Ji B, Pi W, Liu W, Liu Y, Cui Y, Zhang X, Peng S. HyperVR: A hybrid deep ensemble learning approach for simultaneously predicting virulence factors and antibiotic resistance genes. NAR Genomics and Bioinformatics. 2023;5(1):1-17. doi:10.1093/nargab/lqad012.
7. Zhang X, Wang R, Xie X, Hu Y, Wang J, Sun Q, Feng X, Lin W, Tong S, Yan W, Wen H, Wang M, Zhai S, Sun C, Wang F, Niu Q, Kropinski AM, Cui Y, Jiang X, Peng S, Li S, Tong Y. Mining bacterial NGS data vastly expands the complete genomes of temperate phages. NAR Genomics and Bioinformatics. 2022;4(3). doi:10.1093/nargab/lqac057.
8. Chen J, Ng YK, Lin L, Zhang X, Li S. On triangle inequalities of correlation-based distances for gene expression profiles. BMC Bioinformatics. 2023;24(1):1-16. doi:10.1186/s12859-023-05161-y.
9. Wang R, Zhang X, Wang J, Li SC. DeepHost: Phage host prediction with convolutional neural network. Briefings in Bioinformatics. 2022;23(1):1-10. doi:10.1093/bib/bbab385.
10. Tran NH, Qiao R, Xin L, Chen X, Liu C, Zhang X, Shan B, Ghodsi A, Li M. Deep learning enables de novo peptide sequencing from data-independent-acquisition mass spectrometry. Nature Methods. 2019;16(1):63-66. doi:10.1038/s41592-018-0260-3.
11. Dong D, Li M, Liu Z, Feng J, Jia N, Zhao H, Zhao B, Zhou T, Zhang X, Tong Y, Zhu Y. Characterization of a NDM-1-encoding plasmid pHFK418-NDM from a clinical Proteus mirabilis isolate harboring two novel transposons, Tn6624 and Tn6625. Frontiers in Microbiology. 2019;10:1-10. doi:10.3389/fmicb.2019.02030.
12. Tran NH, Zhang X, Li M. Deep omics. Proteomics. 2018;18(2):1-5. doi:10.1002/pmic.201700319.
13. Zhou P, Fan H, Lan T, Yang X Lou, Shi WF, Zhang W, Zhu Y, Zhang YW, Xie QM, Mani S, Zheng XS, Li B, Li JM, Guo H, Pei GQ, An XP, Chen JW, Zhou L, Mai KJ, Wu ZX, Li D, Anderson DE, Zhang LB, Li SY, Mi ZQ, He TT, Cong F, Guo PJ, Huang R, Luo Y, Liu XL, Chen J, Huang Y, Sun Q, Zhang XLL, Wang YY, Xing SZ, Chen YS, Sun Y, Li J, Daszak P, Wang LF, Shi ZL, Tong YG, Ma JY. Fatal swine acute diarrhoea syndrome caused by an HKU2-related coronavirus of bat origin. Nature. 2018;556(7700):255-259. doi:10.1038/s41586-018-0010-9.
14. Zhang X, Wang Y, Tong Y. Analyzing genome termini of bacteriophage through high-throughput sequencing. Methods in Molecular Biology. 2018;1681:139-163. doi:10.1007/978-1-4939-7343-9_11.
15. Tran NH, Zhang X, Xin L, Shan B, Li M. De novo peptide sequencing by deep learning. Proceedings of the National Academy of Sciences of the United States of America. 2017;114(31):8247-8252. doi:10.1073/pnas.1705691114.
16. Zhang Q, Xing S, Sun Q, Pei G, Cheng S, Liu Y, An X, Zhang X, Qu Y, Tong Y. Characterization and complete genome sequence analysis of a novel virulent Siphoviridae phage against Staphylococcus aureus isolated from bovine mastitis in Xinjiang, China. Virus Genes. 2017;53(3):464-476. doi:10.1007/s11262-017-1445-z.
17. Zhang X, Guo X, Fan H, Zhao Q, Zuo S, Sun Q, Pei G, Cheng S, An X, Wang Y, Mi Z, Huang Y, Zhang Z, Tong Y, Zhou H, Zhang J. Complete genome sequence of Menghai flavivirus, a novel insect-specific flavivirus from China. Archives of Virology. 2017;162(5):1435-1439. doi:10.1007/s00705-017-3232-5.
18. Tong YG, Shi WF, Liu D, Qian J, Liang L, Bo XC, Liu J, Ren HG, Fan H, Ni M, Sun Y, Jin Y, Teng Y, Li Z, Kargbo D, Dafae F, Kanu A, Chen CC, Lan ZH, Jiang H, Cao WC, et al. Genetic diversity and evolutionary dynamics of Ebola virus in Sierra Leone. Nature. 2015;524(7563):93-96. doi:10.1038/nature14490.
19. Zhang X, Kang H, Li Y, Liu X, Yang Y, Li S, Pei G, Sun Q, Shu P, Mi Z, Huang Y, Zhang Z, Liu Y, An X, Xu X, Tong Y. Conserved termini and adjacent variable region of Twortlikevirus Staphylococcus. Virologica Sinica. 2015;30(6):433-440. doi:10.1007/s12250-015-3643-y.
20. Zhang X, Wang Y, Li S, An X, Pei G, Huang Y, Fan H, Mi Z, Zhang Z, Wang W, Chen Y, Tong Y. A novel termini analysis theory using HTS data alone for the identification of Enterococcus phage EF4-like genome termini. BMC Genomics. 2015;16(1):414-. doi:10.1186/s12864-015-1612-3.