1. Genome scale metabolic model reconstruction and quality control; computational design of optimal/heterogenous/non-natural metabolic pathways; metabolic engineering strategies design.

2. Development of cellular models for model organisms that integrate enzyme kinetics, regulatory information and thermodynamics information with stoichiometric network models.

3. Data driven biodiscovery, development of AI algorithms/methods for qualitative and quantitative function prediction of bioparts; AI assisted strain design.

4. Development of databases/knowledge graphs for model organisms; Development of Web/cloud based tools for computational design of biosystems.

1. Zhao J, Sun X, Mao Z, Zheng Y, Geng Z, Zhang Y, et al. Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network. Microbiol Res. 2023;276:127485.

2. Yang X, Mao Z, Huang J, Wang R, Dong H, Zhang Y, et al. Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. Synth Syst Biotechnol. 2023;8(4):597-605.

3. Wu Y, Yuan Q, Yang Y, Liu D, Yang S, Ma H. Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories. Synth Syst Biotechnol. 2023;8(3):498-508.

4. Wu K, Mao Z, Mao Y, Niu J, Cai J, Yuan Q, et al. ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow. Microorganisms. 2023;11(1).

5. Wang J, Chen Z, Deng X, Yuan Q, Ma H. Engineering Escherichia coli for Poly-β-hydroxybutyrate Production from Methanol. Bioengineering (Basel). 2023;10(4).

6. Shi Z, Deng R, Yuan Q, Mao Z, Wang R, Li H, et al. Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework. Research (Wash D C). 2023;6:0153.

7. Naz S, Liu P, Liu C, Cui M, Ma H. In silico prediction of mutation sites for anthranilate synthase from Serratia marcesens to deregulate tryptophan feedback inhibition. Journal of biomolecular structure & dynamics. 2023:1-11.

8. Naz S, Liu P, Farooq U, Ma H. Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microbial cell factories. 2023;22(1):161.

9. Mao Z, Yuan Q, Li H, Zhang Y, Huang Y, Yang C, et al. CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. Nucleic acids research. 2023;51(W1):W70-w7.

10. Cai J, Liao X, Mao Y, Wang R, Li H, Ma H. Designing gene manipulation schedules for high throughput parallel construction of objective strains. Biotechnol J. 2023:e2200578.

11. Zhang T, Liu P, Wei H, Sun X, Zeng Y, Zhang X, et al. Protein Engineering of Glucosylglycerol Phosphorylase Facilitating Efficient and Highly Regio- and Stereoselective Glycosylation of Polyols in a Synthetic System. ACS Catalysis. 2022;12(24):15715-27.

12. Yang Y, Mao Y, Wang R, Li H, Liu Y, Cheng H, et al. AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. Nucleic acids research. 2022;50(W1):W75-82.

13. Tian C, Yang J, Liu C, Chen P, Zhang T, Men Y, et al. Engineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars. Nature communications. 2022;13(1):3582.

14. Niu J, Mao Z, Mao Y, Wu K, Shi Z, Yuan Q, et al. Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum. Biomolecules. 2022;12(10).

15. Mao Z, Zhao X, Yang X, Zhang P, Du J, Yuan Q, et al. ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model. Biomolecules. 2022;12(1).

16. Mao Z, Wang R, Li H, Huang Y, Zhang Q, Liao X, et al. ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. Nucleic acids research. 2022;50(W1):W298-304.

17. Luo J, Yuan Q, Mao Y, Wei F, Zhao J, Yu W, et al. Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems. Frontiers in bioengineering and biotechnology. 2022;10:913077.

18. Liao X, Ma H, Tang YJ. Artificial intelligence: a solution to involution of design-build-test-learn cycle. Current opinion in biotechnology. 2022;75:102712.

19. Yang Y, Mao Y, Liu Y, Wang R, Lu H, Li H, et al. GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum. Frontiers in bioengineering and biotechnology. 2021;9:768289.

20. Yang X, Mao Z, Zhao X, Wang R, Zhang P, Cai J, et al. Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models. Metabolic engineering. 2021;67:133-44.

21. Mao Y, Yuan Q, Yang X, Liu P, Cheng Y, Luo J, et al. Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro. Frontiers in microbiology. 2021;12:677596.

22. Gao Y, Yuan Q, Mao Z, Liu H, Ma H. Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis. BMC microbiology. 2021;21(1):292.

23. Cai T, Sun H, Qiao J, Zhu L, Zhang F, Zhang J, et al. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science (New York, NY). 2021;373(6562):1523-7.

24. Lieven C, Beber ME, Olivier BG, Bergmann FT, Ataman M, Babaei P, et al. MEMOTE for standardized genome-scale metabolic model testing. Nature biotechnology. 2020;38(3):272-6.

25. Yang X, Yuan Q, Luo H, Li F, Mao Y, Zhao X, et al. Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metabolic engineering. 2019;56:142-53.

26. Mao Z, Ma H. iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis. Current Genomics. 2019;20(4):252-9.

27. Liu D, Sun H, Ma H. Deciphering Microbiome Related to Rusty Roots of Panax ginseng and Evaluation of Antagonists Against Pathogenic Ilyonectria. Frontiers in microbiology. 2019;10:1350.

28. Zheng Y, Yuan Q, Luo H, Yang X, Ma H. Engineering NOG-pathway in Escherichia coli for poly-(3-hydroxybutyrate) production from low cost carbon sources. Bioengineered. 2018;9(1):209-13.

29. Li F, Xie W, Yuan Q, Luo H, Li P, Chen T, et al. Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea. AMB Express. 2018;8(1):106.

30. Zheng Y, Yuan Q, Yang X, Ma H. Engineering Escherichia coli for poly-(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis. Enzyme and microbial technology. 2017;106:60-6.

31. Yuan Q, Huang T, Li P, Hao T, Li F, Ma H, et al. Pathway-Consensus Approach to Metabolic Network Reconstruction for Pseudomonas putida KT2440 by Systematic Comparison of Published Models. PloS one. 2017;12(1):e0169437.

32. Yang X, Yuan Q, Zheng Y, Ma H, Chen T, Zhao X. An engineered non-oxidative glycolysis pathway for acetone production in Escherichia coli. Biotechnology letters. 2016;38(8):1359-65.

33. Meng Q, Zhang Y, Ju X, Ma C, Ma H, Chen J, et al. Production of 5-aminolevulinic acid by cell free multi-enzyme catalysis. Journal of biotechnology. 2016;226:8-13.

34. Zhang Y, Meng Q, Ma H, Liu Y, Cao G, Zhang X, et al. Determination of key enzymes for threonine synthesis through in vitro metabolic pathway analysis. Microbial cell factories. 2015;14:86.

Leading or participating in dozens of projects supported by Ministry of Science & Technology(MOST), National natural science Foundation (NSFC), Tianjin local government and Chinese academy of Sciences.

1. National Key Research and Development Program of China：high version chassis for model organisms，2019-2023

2. Tianjin Synthetic Biotechnology Innovation Capacity Improvement Project: platform for biocomputing and biodesign,2019-2022

3. Strategic Priority Research Program of the Chinese Academy of Sciences: Synthetic of single cell life, 2023-2026

4. International Partnership Program  of  Chinese Academy of Sciences：Artificial cell factories for natural product synthesis. 2018-2022

5. National Key Basic Research Program of China：Construction of novel pathways for biomaterial synthesis using synthetic biology methods, 2012-2016