针对重要工业微生物，开展基因组学、转录组学、蛋白质组学、代谢组学、脂质组学、通量组学、相互作用组学以及表型组学分析，解析菌株工业生产和胁迫耐受的分子机制，利用组学数据构建全细胞模型、开发仿真模拟算法，实现虚拟细胞工厂的优化设计。
利用多组学方法解析在微生物菌群结构变化以及成员间相互作用机制。构建虚拟菌群模型，开发菌群成员空间动态协作的计算方法，实现合成微生物组的最优设计。
代表论著：
1. Chung WY, Abdul Rahim N, Mahamad Maifiah MH, Hawala Shivashekaregowda NK, Zhu Y*, Wong EH*. In silico genome-scale metabolic modeling and in vitro static time-kill studies of exogenous metabolites alone and with polymyxin B against Klebsiella pneumoniae. Front Pharmacol. 2022;13:880352.
2. Jin P, Dai J, Guo Y, Wang X, Lu J, Zhu Y*, Yu F*. Genomic Analysis of Mycobacterium abscessus Complex Isolates from Patients with Pulmonary Infection in China. Microbiol Spectr. 2022;10:e0011822.
3. Guo Y, Su L, Liu Q, Zhu Y*, Dai Z*, Wang Q. Dissecting carbon metabolism of Yarrowia lipolytica type strain W29 using genome-scale metabolic modelling. Comput Struct Biotechnol J. 2022;20:2503-2511.
4. Zhu Y*, Zhao J, Li J. Genome-scale metabolic modelling in antimicrobial pharmacology. Engineering Microbiology. 2022:100021.
5. Roberts KD#, Zhu Y#, Azad MAK#, Han ML, Wang J, Wang L, Yu HH, Horne AS, Pinson JA, Rudd D, Voelcker NH, Patil NA, Zhao J, Jiang X, Lu J, Chen K, Lomovskaya O, Hecker SJ, Thompson PE, Nation RL, Dudley MN, Griffith DC, Velkov T, Li J. A synthetic lipopeptide targeting top-priority multidrug-resistant Gram-negative pathogens. Nat Commun. 2022;13:1625.
6. Bin Hafeez A, Jiang X, Bergen PJ, Zhu Y*. Antimicrobial Peptides: An Update on Classifications and Databases. Int J Mol Sci. 2021;22:11691.
7. Dai Z#, Zhu Y#, Dong H, Zhao C, Zhang Y, Li Y. Enforcing ATP hydrolysis enhanced anaerobic glycolysis and promoted solvent production in Clostridium acetobutylicum. Microb Cell Fact. 2021;20:149.
8. Zhu Y#, Lu J#, Han ML#, Jiang X#, Azad MAK, Patil NA, Lin YW, Zhao J, Hu Y, Yu HH, Chen K, Boyce JD, Dunstan RA, Lithgow T, Barlow CK, Li W, Schneider-Futschik EK, Wang J, Gong B, Sommer B, Creek DJ, Fu J, Wang L, Schreiber F, Velkov T, Li J. Polymyxins Bind to the Cell Surface of Unculturable Acinetobacter baumannii and Cause Unique Dependent Resistance. Adv Sci. 2020;7:2000704.
9. Zhao J, Zhu Y*, Han J, Lin YW, Aichem M, Wang J, Chen K, Velkov T, Schreiber F, Li J*. Genome-Scale Metabolic Modeling Reveals Metabolic Alterations of Multidrug-Resistant Acinetobacter baumannii in a Murine Bloodstream Infection Model. Microorganisms. 2020;8:1793.
10. Li M, Aye SM, Ahmed MU, Han ML, Li C, Song J, Boyce JD, Powell DR, Azad MAK, Velkov T, Zhu Y*, Li J*. Pan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments. Mol Omics. 2020;16:327-338.
11. Huang J, Chen L, Song J, Velkov T, Wang L, Zhu Y*, Li J*. Regulating Polymyxin Resistance in Gram-negative Bacteria: Roles of Two-Component Systems PhoPQ and PmrAB. Future Microbiol. 2020;15:445-459.
12. Zhu Y*, Lu J, Zhao J, Zhang X, Yu HH, Velkov T, Li J*. Complete genome sequence and genome-scale metabolic modelling of Acinetobacter baumannii type strain ATCC 19606. Int J Med Microbiol. 2020;310:151412.
13. Zhu Y#*, Zhao J#, Maifiah MHM, Velkov T, Schreiber F, Li J. Metabolic Responses to Polymyxin Treatment in Acinetobacter baumannii ATCC 19606: Integrating Transcriptomics and Metabolomics with Genome-Scale Metabolic Modeling. mSystems. 2019;4:e00157-18.
14. Zhu Y, Galani I, Karaiskos I, Lu J, Aye SM, Huang J, Yu HH, Velkov T, Giamarellou H, Li J. Multifaceted mechanisms of colistin resistance revealed by genomic analysis of multidrug-resistant Klebsiella pneumoniae isolates from individual patients before and after colistin treatment. J Infect. 2019;79:312-321.
15. Zhu Y, Czauderna T, Zhao J, Klapperstueck M, Maifiah MHM, Han ML, Lu J, Sommer B, Velkov T, Lithgow T, Song J, Schreiber F, Li J. Genome-scale metabolic modeling of responses to polymyxins in Pseudomonas aeruginosa. Gigascience. 2018;7:giy021.
16. Zhu Y#, Pham TH#, Nhiep TH#, Vu NM#, Marcellin E, Chakrabortti A, Wang Y, Waanders J, Lo R, Huston WM, Bansal N, Nielsen LK, Liang ZX, Turner MS. Cyclic-di-AMP synthesis by the diadenylate cyclase CdaA is modulated by the peptidoglycan biosynthesis enzyme GlmM in Lactococcus lactis. Mol Microbiol. 2016;99:1015-27.
17. Zhu Y#, Li D#, Bao G, Wang S, Mao S, Song J, Li Y, and Zhang Y. Metabolic changes in Klebsiella oxytoca in response to low oxidoreduction potential, as revealed by comparative proteomic profiling integrated with flux balance analysis. Appl Environ Microbiol. 2014;80:2833-41.
18. Zhu Y, Song J, Xu Z, Sun J, Zhang Y, Li Y, and Ma Y. Development of thermodynamic optimum searching (TOS) to improve the prediction accuracy of flux balance analysis. Biotechnol Bioeng. 2013;110:914-23.
19. Zhu L#, Zhu Y#, Zhang Y, and Li Y. Engineering the robustness of industrial microbes through synthetic biology. Trends Microbiol. 2012;20:94-101.
20. Zhu Y, Zhang Y, and Li Y. Understanding the industrial application potential of lactic acid bacteria through genomics. Appl Microbiol Biotechnol. 2009;83:597-610.
