电子邮件： ma_hw@tib.cas.cn
通信地址： 天津市空港经济区西七道32号
邮政编码： 300308
研究领域
我的研究方向包括系统生物学、合成生物学和计算生物学，重点是数据和模型指导下的细胞系统设计。主要研究领域包括：
1. 细胞模型的构建与分析
代谢网络的快速半自动构建，代谢网络的标准化、质量控制及途径比较分析方法，通量平衡分析计算与可视化软件工具包的开发，基于复合代谢网络的途径设计。开发了半自动化的代谢网络构建和质控流程，基于相关流程完成了包括真核原核生物近10个不同物种的高质量代谢网络模型的构建。在代谢网络计量学模型基础上开发了整合酶约束、热力学约束等的多约束细胞模型构建分析框架，针对大肠杆菌、谷氨酸棒杆菌等多种模式生物构建了多约束细胞模型，显著提高细胞模型的准确度。
2. 代谢途径与菌种改造靶点设计
基于细胞模型开发了最优途径、异源途径和非天然途径设计算法及工具，指导菌种代谢工程改造中强化、弱化敲除和插入靶点的设计，为所内外多个团队的菌种改造提供了技术支持，其中设计的二氧化碳及一碳化合物非天然利用途径得率均超过天然途径的得率，相关成果在Science， Metabolic Engineering等期刊发表。
3. 基于人工智能的蛋白功能预测设计
开发了基于深度学习的酶定性定量功能预测算法和相应的网站工具，预测准确度和召回率与其它方法相比显著提高，为酶新催化功能的发现和更完整细胞模型的构建提供了支撑。开发了人工智能与酶结构机理相结合的酶设计新方法，成功应用于多种不同类型酶的设计改造。
招生信息
欢迎具有生物化工、生物工程、微生物学方面以及计算机科学和数学科学教育背景的学生报考，特别欢迎受到生物学方面教育，同时对计算机编程又非常感兴趣的学生
招生专业
071021-生物信息学
071023-计算生物学
招生方向
代谢工程
生物信息学
教育背景
1993-09--1996-03 天津大学化工学院 硕士研究生
1989-09--1993-07 天津大学 本科学士学位
教授课程
工业生物技术导论
工业生物技术——生物技术的第三次浪潮系列讲座
计算系统生物学
专利与奖励
2023年 天津市自然科学奖特等奖
2014年 汤森路透高被引科学家奖
科研活动
科研项目
（ 2 ） 二氧化碳的人工生物转化, 参与, 中国科学院计划, 2016-01--2018-12
（ 3 ） 面向天然产物生物合成的人工细胞, 负责人, 中国科学院计划, 2018-01--2022-01
（ 4 ） 高版本模式微生物底盘细胞, 负责人, 国家任务, 2019-09--2024-06
（ 5 ） 大肠杆菌新一代网络模型和多菌体系代谢网络模型的构建与优化, 负责人, 国家任务, 2021-10--2024-09
（ 6 ） 生物大分子合成单细胞生命, 参与, 中国科学院计划, 2023-01--2026-12
发表论文
1. Wang, Y.; Mao, Z.; Dong, J.; Zhang, P.; Gao, Q.; Liu, D.; Tian, C.; Ma, H., Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based k(cat) data. Microb Cell Fact 2024, 23 (1), 138.
2. Shi, Z.; Wang, D.; Li, Y.; Deng, R.; Lin, J.; Liu, C.; Li, H.; Wang, R.; Zhao, M.; Mao, Z.; Yuan, Q.; Liao, X.; Ma, H., REME: an integrated platform for reaction enzyme mining and evaluation. Nucleic Acids Res 2024.
3. Mao, Z.; Niu, J.; Zhao, J.; Huang, Y.; Wu, K.; Yun, L.; Guan, J.; Yuan, Q.; Liao, X.; Wang, Z.; Ma, H., ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models. Synth Syst Biotechnol 2024, 9 (3), 494-502.
4. Huang, Y.; Mao, Z.; Zhang, Y.; Zhao, J.; Luan, X.; Wu, K.; Yun, L.; Yu, J.; Shi, Z.; Liao, X.; Ma, H., Omics data analysis reveals the system-level constraint on cellular amino acid composition. Synth Syst Biotechnol 2024, 9 (2), 304-311.
5. Deng, R.; Wu, K.; Lin, J.; Wang, D.; Huang, Y.; Li, Y.; Shi, Z.; Zhang, Z.; Wang, Z.; Mao, Z.; Liao, X.; Ma, H., DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes. Int J Mol Sci 2024, 25 (9).
6. Wu, P.; Yuan, Q.; Cheng, T.; Han, Y.; Zhao, W.; Liao, X.; Wang, L.; Cai, J.; He, Q.; Guo, Y.; Zhang, X.; Lu, F.; Wang, J.; Ma, H.; Huang, Z., Genome sequencing and metabolic network reconstruction of a novel sulfur-oxidizing bacterium Acidithiobacillus Ameehan. Front Microbiol 2023, 14, 1277847.
7. Yuan, Q.; Wei, F.; Deng, X.; Li, A.; Shi, Z.; Mao, Z.; Li, F.; Ma, H., Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501. Synth Syst Biotechnol 2023, 8 (4), 688-696.
8. Yu, J.; Wang, X.; Yuan, Q.; Shi, J.; Cai, J.; Li, Z.; Ma, H., Elucidating the impact of in vitro cultivation on Nicotiana tabacum metabolism through combined in silico modeling and multiomics analysis. Front Plant Sci 2023, 14, 1281348.
9. Zhao, J.; Sun, X.; Mao, Z.; Zheng, Y.; Geng, Z.; Zhang, Y.; Ma, H.; Wang, Z., Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network. Microbiol Res 2023, 276, 127485.
10. Yang, X.; Mao, Z.; Huang, J.; Wang, R.; Dong, H.; Zhang, Y.; Ma, H., Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. Synth Syst Biotechnol 2023, 8 (4), 597-605.
11. 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. J Biomol Struct Dyn 2023, 1-11.
12. Liu, Y.; Chen, L.; Liu, P.; Yuan, Q.; Ma, C.; Wang, W.; Zhang, C.; Ma, H.; Zeng, A., Design, Evaluation, and Implementation of Synthetic Isopentyldiol Pathways in Escherichia coli. ACS Synth Biol 2023.
13. Liu, L.; Li, J.; Gai, Y.; Tian, Z.; Wang, Y.; Wang, T.; Liu, P.; Yuan, Q.; Ma, H.; Lee, S. Y.; Zhang, D., Protein engineering and iterative multimodule optimization for vitamin B(6) production in Escherichia coli. Nat Commun 2023, 14 (1), 5304.
14. Zhang, Z.; Cui, M.; Chen, P.; Li, J.; Mao, Z.; Mao, Y.; Li, Z.; Guo, Q.; Wang, C.; Liao, X.; Liu, H., Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level. Front Microbiol 2023, 14, 1199144.
15. Liu, Y.; Wang, Q.; Liu, X.; Cheng, J.; Zhang, L.; Chu, H.; Wang, R.; Li, H.; Chang, H.; Ahmed, N.; Wang, Z.; Liao, X.; Jiang, H., pUGTdb: A comprehensive database of plant UDP-dependent glycosyltransferases. Mol Plant 2023, 16 (4), 643-646.
16. 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.
17. Naz, S.; Liu, P.; Farooq, U.; Ma, H., Insight into de-regulation of amino acid feedback inhibition: a focus on structure analysis method. Microb Cell Fact 2023, 22 (1), 161.
18. Mao, Z.; Yuan, Q.; Li, H.; Zhang, Y.; Huang, Y.; Yang, C.; Wang, R.; Yang, Y.; Wu, Y.; Yang, S.; Liao, X.; Ma, H., CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. Nucleic Acids Res 2023, 51 (W1), W70-w77.
19. 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).
20. Shi, Z.; Deng, R.; Yuan, Q.; Mao, Z.; Wang, R.; Li, H.; Liao, X.; Ma, H., Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework. Research (Wash D C) 2023, 6, 0153.
21. 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.
22. Zhang, J.; Ren, S.; Shi, Z.; Wang, R.; Li, H.; Tian, H.; Feng, M.; Liao, X.; Ma, H., SCP4ssd: A Serverless Platform for Nucleotide Sequence Synthesis Difficulty Prediction Using an AutoML Model. Genes (Basel) 2023, 14 (3).
23. Wu, K.; Mao, Z.; Mao, Y.; Niu, J.; Cai, J.; Yuan, Q.; Yun, L.; Liao, X.; Wang, Z.; Ma, H., ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow. Microorganisms 2023, 11 (1).
24. Shi, L.; Liu, P.; Tan, Z.; Zhao, W.; Gao, J.; Gu, Q.; Ma, H.; Liu, H.; Zhu, L., Complete Depolymerization of PET Wastes by an Evolved PET Hydrolase from Directed Evolution. Angew Chem Int Ed Engl 2023, 62 (14), e202218390.
25. Pu, W.; Chen, J.; Liu, P.; Shen, J.; Cai, N.; Liu, B.; Lei, Y.; Wang, L.; Ni, X.; Zhang, J.; Liu, J.; Zhou, Y.; Zhou, W.; Ma, H.; Wang, Y.; Zheng, P.; Sun, J., Directed evolution of linker helix as an efficient strategy for engineering LysR-type transcriptional regulators as whole-cell biosensors. Biosens Bioelectron 2023, 222, 115004.
26. Mao, Z.; Huang, T.; Yuan, Q.; Ma, H., Construction and analysis of an integrated biological network of Escherichia coli. Systems Microbiology and Biomanufacturing 2022, 2 (1), 165-176.
27. Liu, J.; Liu, M.; Shi, T.; Sun, G.; Gao, N.; Zhao, X.; Guo, X.; Ni, X.; Yuan, Q.; Feng, J.; Liu, Z.; Guo, Y.; Chen, J.; Wang, Y.; Zheng, P.; Sun, J., CRISPR-assisted rational flux-tuning and arrayed CRISPRi screening of an l-proline exporter for l-proline hyperproduction. Nature Communications 2022, 13 (1), 891.
28. Zhang, T.; Liu, P.; Wei, H.; Sun, X.; Zeng, Y.; Zhang, X.; Cai, Y.; Cui, M.; Ma, H.; Liu, W.; Sun, Y.; Yang, J., Protein Engineering of Glucosylglycerol Phosphorylase Facilitating Efficient and Highly Regio- and Stereoselective Glycosylation of Polyols in a Synthetic System. ACS Catalysis 2022, 12 (24), 15715-15727.
29. Li, J.; Yang, J.; Mu, S.; Shang, N.; Liu, C.; Zhu, Y.; Cai, Y.; Liu, P.; Lin, J.; Liu, W.; Sun, Y.; Ma, Y., Efficient O-Glycosylation of Triterpenes Enabled by Protein Engineering of Plant Glycosyltransferase UGT74AC1. ACS Catalysis 2020, 10 (6), 3629-3639.
30. Li, J.; Wang, S.; Liu, C.; Li, Y.; Wei, Y.; Fu, G.; Liu, P.; Ma, H.; Huang, D.; Lin, J.; Zhang, D., Going Beyond the Local Catalytic Activity Space of Chitinase Using a Simulation-Based Iterative Saturation Mutagenesis Strategy. ACS Catalysis 2022, 12 (16), 10235-10244.
31. Lu, X.; Li, J.; Li, C.; Lou, Q.; Peng, K.; Cai, B.; Liu, Y.; Yao, Y.; Lu, L.; Tian, Z.; Ma, H.; Wang, W.; Cheng, J.; Guo, X.; Jiang, H.; Ma, Y., Enzymatic DNA Synthesis by Engineering Terminal Deoxynucleotidyl Transferase. ACS Catalysis 2022, 12 (5), 2988-2997.
32. Yuan, X. J.; Chen, W. J.; Ma, Z. X.; Yuan, Q. Q.; Zhang, M.; He, L.; Mo, X. H.; Zhang, C.; Zhang, C. T.; Wang, M. Y.; Xing, X. H.; Yang, S., Rewiring the native methanol assimilation metabolism by incorporating the heterologous ribulose monophosphate cycle into Methylorubrum extorquens. Metab Eng 2021, 64, 95-110.
33. Tian, C.; Yang, J.; Liu, C.; Chen, P.; Zhang, T.; Men, Y.; Ma, H.; Sun, Y.; Ma, Y., Engineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars. Nat Commun 2022, 13 (1), 3582.
34. Liu, Y.; Wang, R.; Liu, J.; Lu, H.; Li, H.; Wang, Y.; Ni, X.; Li, J.; Guo, Y.; Ma, H.; Liao, X.; Wang, M., Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum. Sci Adv 2022, 8 (35), eabq2157.
35. Liu, D.; Xu, Z.; Li, J.; Liu, Q.; Yuan, Q.; Guo, Y.; Ma, H.; Tian, C., Reconstruction and analysis of genome-scale metabolic model for thermophilic fungus Myceliophthora thermophila. Biotechnol Bioeng 2022, 119 (7), 1926-1937.
36. Liao, X.; Ma, H.; Tang, Y. J., Artificial intelligence: a solution to involution of design-build-test-learn cycle. Curr Opin Biotechnol 2022, 75, 102712.
37. Jiang, M.; Hong, K.; Mao, Y.; Ma, H.; Chen, T.; Wang, Z., Natural 5-Aminolevulinic Acid: Sources, Biosynthesis, Detection and Applications. Front Bioeng Biotechnol 2022, 10, 841443.
38. Jiang, G.; Wang, J.; Zhao, D.; Chen, X.; Pu, S.; Zhang, C.; Li, J.; Li, Y.; Yang, J.; Li, S.; Liao, X.; Ma, H.; Ma, Y.; Zhou, Z.; Bi, C.; Zhang, X., Molecular Mechanism of the Cytosine CRISPR Base Editing Process and the Roles of Translesion DNA Polymerases. ACS Synth Biol 2021, 10 (12), 3353-3358.
39. Chang, Z.; Dai, W.; Mao, Y.; Cui, Z.; Zhang, Z.; Wang, Z.; Ma, H.; Chen, T., Enhanced 3-Hydroxypropionic Acid Production From Acetate via the Malonyl-CoA Pathway in Corynebacterium glutamicum. Front Bioeng Biotechnol 2021, 9, 808258.
40. Cai, T.; Sun, H.; Qiao, J.; Zhu, L.; Zhang, F.; Zhang, J.; Tang, Z.; Wei, X.; Yang, J.; Yuan, Q.; Wang, W.; Yang, X.; Chu, H.; Wang, Q.; You, C.; Ma, H.; Sun, Y.; Li, Y.; Li, C.; Jiang, H.; Wang, Q.; Ma, Y., Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 2021, 373 (6562), 1523-1527.
41. Zhang, P.; Liu, X.; Liu, P.; Wang, F.; Ariyama, H.; Ando, T.; Lin, J.; Wang, L.; Hu, J.; Li, B.; Fan, C., Capturing transient antibody conformations with DNA origami epitopes. Nat Commun 2020, 11 (1), 3114.
42. Yang, Y.; Mao, Y.; Liu, Y.; Wang, R.; Lu, H.; Li, H.; Luo, J.; Wang, M.; Liao, X.; Ma, H., GEDpm-cg: Genome Editing Automated Design Platform for Point Mutation Construction in Corynebacterium glutamicum. Front Bioeng Biotechnol 2021, 9, 768289.
43. Yang, X.; Mao, Z.; Zhao, X.; Wang, R.; Zhang, P.; Cai, J.; Xue, C.; Ma, H., Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models. Metab Eng 2021, 67, 133-144.
44. Wang, S.; Fu, G.; Li, J.; Wei, X.; Fang, H.; Huang, D.; Lin, J.; Zhang, D., High-Efficiency Secretion and Directed Evolution of Chitinase BcChiA1 in Bacillus subtilis for the Conversion of Chitinaceous Wastes Into Chitooligosaccharides. Front Bioeng Biotechnol 2020, 8, 432.
45. Mao, Y.; Yuan, Q.; Yang, X.; Liu, P.; Cheng, Y.; Luo, J.; Liu, H.; Yao, Y.; Sun, H.; Cai, T.; Ma, H., Non-natural Aldol Reactions Enable the Design and Construction of Novel One-Carbon Assimilation Pathways in vitro. Front Microbiol 2021, 12, 677596.
46. 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 Microbiol 2021, 21 (1), 292.
47. Ding, D.; Bai, D.; Li, J.; Mao, Z.; Zhu, Y.; Liu, P.; Lin, J.; Ma, H.; Zhang, D., Analyzing the genetic characteristics of a tryptophan-overproducing Escherichia coli. Bioprocess Biosyst Eng 2021, 44 (8), 1685-1697.
48. Yang, Y.; Mao, Y.; Wang, R.; Li, H.; Liu, Y.; Cheng, H.; Shi, Z.; Wang, Y.; Wang, M.; Zheng, P.; Liao, X.; Ma, H., AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms. Nucleic Acids Res 2022, 50 (W1), W75-82.
49. Niu, J.; Mao, Z.; Mao, Y.; Wu, K.; Shi, Z.; Yuan, Q.; Cai, J.; Ma, H., Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum. Biomolecules 2022, 12 (10).
50. Mao, Z.; Zhao, X.; Yang, X.; Zhang, P.; Du, J.; Yuan, Q.; Ma, H., ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model. Biomolecules 2022, 12 (1).
51. Mao, Z.; Yang, P.; Liu, H.; Mao, Y.; Lei, Y.; Hou, D.; Ma, H.; Liao, X.; Jiang, W., Whole-Genome Sequencing and Analysis of the White-Rot Fungus Ceriporia lacerata Reveals Its Phylogenetic Status and the Genetic Basis of Lignocellulose Degradation and Terpenoid Synthesis. Front Microbiol 2022, 13, 880946.
52. Mao, Z.; Wang, R.; Li, H.; Huang, Y.; Zhang, Q.; Liao, X.; Ma, H., ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. Nucleic Acids Res 2022, 50 (W1), W298-304.
53. Luo, J.; Yuan, Q.; Mao, Y.; Wei, F.; Zhao, J.; Yu, W.; Kong, S.; Guo, Y.; Cai, J.; Liao, X.; Wang, Z.; Ma, H., Reconstruction of a Genome-Scale Metabolic Network for Shewanella oneidensis MR-1 and Analysis of its Metabolic Potential for Bioelectrochemical Systems. Front Bioeng Biotechnol 2022, 10, 913077.