研究领域
1. Pathway design based on metabolic network analysis: finding optimal pathways for converting a substrate to useful bioproducts; designing metabolic Engineering strategies to redirect the metabolic flux toward the optimal pathways.
2. kinetic models of biosystems: building kinetic models based on experimental measurement or literature data, model simulation and control analysis.
3. Whole cell models for model organisms that integrate enzyme kinetics, regulatory information and thermodynamics information with stoichiometric network models.
4. Web/cloud based tools and software for computational analysis of biosystems.
近期论文
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Construction and application of high-quality genome-scale metabolic model of Zymomonas mobilis to guide rational design of microbial cell factories
Synthetic and Systems Biotechnology
2023-09 | Journal article
DOI: 10.1016/j.synbio.2023.07.001
CONTRIBUTORS: Yalun Wu; Qianqian Yuan; Yongfu Yang; Defei Liu; Shihui Yang; Hongwu Ma
Protein engineering and iterative multimodule optimization for vitamin B6 production in Escherichia coli
Nature Communications
2023-08-31 | Journal article
DOI: 10.1038/s41467-023-40928-0
CONTRIBUTORS: Linxia Liu; Jinlong Li; Yuanming Gai; Zhizhong Tian; Yanyan Wang; Tenghe Wang; Pi Liu; Qianqian Yuan; Hongwu Ma; Sang Yup Lee et al.
Engineering Escherichia coli for Poly-β-hydroxybutyrate Production from Methanol
Bioengineering
2023-03-26 | Journal article
DOI: 10.3390/bioengineering10040415
CONTRIBUTORS: Jiaying Wang; Zhiqiang Chen; Xiaogui Deng; Qianqian Yuan; Hongwu Ma
SCP4ssd: A Serverless Platform for Nucleotide Sequence Synthesis Difficulty Prediction Using an AutoML Model
Genes
2023-02-28 | Journal article
DOI: 10.3390/genes14030605
CONTRIBUTORS: Jianqi Zhang; Shuai Ren; Zhenkui Shi; Ruoyu Wang; Haoran Li; Huijuan Tian; Miao Feng; Xiaoping Liao; Hongwu Ma
ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow
Microorganisms
2023-01-11 | Journal article
DOI: 10.3390/microorganisms11010178
CONTRIBUTORS: Ke Wu; Zhitao Mao; Yufeng Mao; Jinhui Niu; Jingyi Cai; Qianqian Yuan; Lili Yun; Xiaoping Liao; Zhiwen Wang; Hongwu Ma
ecBSU1: A Genome-scale Enzyme-constrained Model of Bacillus subtilis based on the ECMpy Workflow
2022-11-18 | Preprint
DOI: 10.20944/preprints202211.0351.v1
CONTRIBUTORS: Ke Wu; Zhitao Mao; Yufeng Mao; Jinhui Niu; Jingyi Cai; Qianqian Yuan; Lili Yun; Xiaoping Liao; Zhiwen Wang; Hongwu Ma
Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum
Biomolecules
2022-10-17 | Journal article
DOI: 10.3390/biom12101499
CONTRIBUTORS: Jinhui Niu; Zhitao Mao; Yufeng Mao; Ke Wu; Zhenkun Shi; Qianqian Yuan; Jingyi Cai; Hongwu Ma
Base editor enables rational genome-scale functional screening for enhanced industrial phenotypes in Corynebacterium glutamicum
Science Advances
2022-09-02 | Journal article
DOI: 10.1126/sciadv.abq2157
CONTRIBUTORS: Ye Liu; Ruoyu Wang; Jiahui Liu; Hui Lu; Haoran Li; Yu Wang; Xiaomeng Ni; Junwei Li; Yanmei Guo; Hongwu Ma et al.
Construction and Analysis of an Enzyme‐constrained Metabolic Model of Corynebacterium glutamicum
2022-09-01 | Preprint
DOI: 10.20944/preprints202209.0019.v1
CONTRIBUTORS: Jinhui Niu; Zhitao Mao; Yufeng Mao; Ke Wu; Zhenkun Shi; Qianqian Yuan; Jingyi Cai; Hongwu Ma
Engineering substrate specificity of HAD phosphatases and multienzyme systems development for the thermodynamic-driven manufacturing sugars
Nature Communications
2022-06-23 | Journal article
DOI: 10.1038/s41467-022-31371-8
CONTRIBUTORS: Chaoyu Tian; Jiangang Yang; Cui Liu; Peng Chen; Tong Zhang; Yan Men; Hongwu Ma; Yuanxia Sun; Yanhe Ma
Construction and analysis of an integrated biological network of Escherichia coli
Systems Microbiology and Biomanufacturing
2022-01 | Journal article
DOI: 10.1007/s43393-021-00051-x
CONTRIBUTORS: Zhitao Mao; Teng Huang; Qianqian Yuan; Hongwu Ma
Data-Driven Synthetic Cell Factories Development for Industrial Biomanufacturing
BioDesign Research
2022-01 | Journal article
DOI: 10.34133/2022/9898461
CONTRIBUTORS: Zhenkun Shi; Pi Liu; Xiaoping Liao; Zhitao Mao; Jianqi Zhang; Qinhong Wang; Jibin Sun; Hongwu Ma; Yanhe Ma
ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
Biomolecules
2022-01-02 | Journal article
DOI: 10.3390/biom12010065
CONTRIBUTORS: Zhitao Mao; Xin Zhao; Xue Yang; Peiji Zhang; Jiawei Du; Qianqian Yuan; Hongwu Ma
ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model
2021-12-03 | Preprint
DOI: 10.20944/preprints202112.0048.v1
CONTRIBUTORS: Zhitao Mao; Xin Zhao; Xue Yang; Peiji Zhang; Jiawei Du; Qianqian Yuan; Hongwu Ma
Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea
AMB Express
2018-12 | Journal article
DOI: 10.1186/s13568-018-0635-y
CONTRIBUTORS: Feiran Li; Wei Xie; Qianqian Yuan; Hao Luo; Peishun Li; Tao Chen; Xueming Zhao; Zhiwen Wang; Hongwu Ma
Yang, X.; Yuan, Q.; Luo, H.; Li, F.; Mao, Y.; Zhao, X.; Du, J.; Li, P.; Ju, X.; Zheng, Y.; Chen, Y.; Liu, Y.; Jiang, H.; Yao, Y.; Ma, H.; Ma, Y., Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metabolic engineering 2019.
Wang, Y.; Liu, Y.; Li, J.; Yang, Y.; Ni, X.; Cheng, H.; Huang, T.; Guo, Y.; Ma, H.; Zheng, P.; Wang, M.; Sun, J.; Ma, Y., Expanding targeting scope, editing window, and base transition capability of base editing in Corynebacterium glutamicum. Biotechnology and bioengineering 2019.
Lu, X.; Liu, Y.; Yang, Y.; Wang, S.; Wang, Q.; Wang, X.; Yan, Z.; Cheng, J.; Liu, C.; Yang, X.; Luo, H.; Yang, S.; Gou, J.; Ye, L.; Lu, L.; Zhang, Z.; Guo, Y.; Nie, Y.; Lin, J.; Li, S.; Tian, C.; Cai, T.; Zhuo, B.; Ma, H.; Wang, W.; Ma, Y.; Liu, Y.; Li, Y.; Jiang, H., Constructing a synthetic pathway for acetyl-coenzyme A from one-carbon through enzyme design. Nature communications 2019, 10 (1), 1378.
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.
Cui, Z., Zhao, Y. , Mao, Y. , Shi, T. , Lu, L. , Ma, H. , Wang, Z. and Chen, T. , In vitro biosynthesis of optically pure d‐(？)‐acetoin from meso‐2,3‐butanediol using 2,3‐butanediol dehydrogenase and NADH oxidase. J. Chem. Technol. Biotechnol. 2019, 94, 8.
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), 209-213.
Zhang, S.; Liu, D.; Mao, Z.; Mao, Y.; Ma, H.; Chen, T.; Zhao, X.; Wang, Z., Model-based reconstruction of synthetic promoter library in Corynebacterium glutamicum. Biotechnology letters 2018, 40 (5), 819-827.
Liu, D.; Mao, Z.; Guo, J.; Wei, L.; Ma, H.; Tang, Y.; Chen, T.; Wang, Z.; Zhao, X., Construction, Model-Based Analysis, and Characterization of a Promoter Library for Fine-Tuned Gene Expression in Bacillus subtilis. ACS synthetic biology 2018, 7 (7), 1785-1797.
Li, F.; Xie, W.; Yuan, Q.; Luo, H.; Li, P.; Chen, T.; Zhao, X.; Wang, Z.; Ma, H., Genome-scale metabolic model analysis indicates low energy production efficiency in marine ammonia-oxidizing archaea. AMB Express 2018, 8 (1), 106.
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, 60-66.
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