主要从事高精度模拟底盘细胞重要生理过程的数据模型构建和指导细胞设计的网站工具开发等研究，在细胞模型的构建和分析，特定菌种知识库开发、途径和代谢改造靶点设计等方面取得了一系列成果。

   

071005-微生物学

细胞模型构建；知识库构建

2013-09--2020-01   中国科学院大学   博士
2008-09--2013-07   哈尔滨医科大学   学士

   

2023-09~现在, 中国科学院天津工业生物技术研究所, 副研究员
2022-07~2023-09,中国科学院天津工业生物技术研究所, 助理研究员
2020-01~2022-07,中国科学院天津工业生物技术研究所, 博士后

   

[1] 毛志涛, 马红武, 赵剑箫, 廖小平, 袁倩倩, 王若宇, 史振坤. 一种多约束代谢网络模型工具包的生成方法和应用. CN: CN119252351A, 2025-01-03.
[2] 袁倩倩, 魏凡, 蔡敬一, 马红武, 廖小平, 毛雨丰, 邓芮, 史振坤, 毛志涛. 基于BiGG数据库的定量异源途径设计方法及系统. CN: CN118098400A, 2024-05-28.
[3] 廖小平, 毛志涛, 马红武, 史振坤, 袁倩倩, 邓芮, 吴柯. 基于深度学习的同源寡聚体亚基数量预测方法. CN: CN118335182A, 2024-07-12.
[4] 史振坤, 马红武, 廖小平, 袁倩倩, 毛志涛. 一种酶号预测的系统及其应用方法. CN: CN116779024A, 2023-09-19.
[5] 廖小平, 马红武, 林嘉威, 毛志涛, 王若宇, 史振坤, 袁倩倩, 刘翠, 杨春贺. 一种转录因子和转录因子靶点的预测方法及系统. 2025105706654, 2025-05-06.
[6] 毛志涛, 马红武, 廖小平, 赵剑箫, 袁倩倩, 王若宇, 史振坤. 一个基于模块化思维构建个性化多约束代谢网络模型的工具包. 2024110596999, 2024-08-02.

   

[1] Wenyu Li, Zhitao Mao, Zhengyang Xiao, Xiaoping Liao, Mattheos Koffas, Yixin Chen, Hongwu Ma, Yinjie J Tang. Large language model for knowledge synthesis and AI-enhanced biomanufacturing. Trends in Biotechnology[J]. 2025, https://www.sciencedirect.com/science/article/pii/S0167779925000459.
[2] Jiacheng Dong, Zhitao Mao, Haoran Li, Ruoyu Wang, Yutao Wang, Haokai Jia, Jingen Li, Qian Liu, Chenglin Zhang, Xiaoping Liao, Defei Liu, Hongwu Ma, Chaoguang Tian. MTD: A cloud-based omics database and interactive platform for Myceliophthora thermophila. Synthetic and Systems Biotechnology[J]. 2025, 10(3): 783-793, http://www.sciencedirect.com/science/article/pii/S2405805X25000481.
[3] 毛志涛, 廖小平, 马红武, , , . 面向生物制造的数据库、知识库与大模型. 生物工程学报[J]. 2025, 第 1 作者41(3): 901-916, https://cjb.ijournals.cn/cjbcn/article/abstract/02240653?st=article_issue.
[4] Yan, Xiongying, Bao, Weiwei, Wu, Yalun, Zhang, Chenyue, Mao, Zhitao, Yuan, Qianqian, Hu, Zhousheng, He, Penghui, Peng, Qiqun, Hu, Mimi, Geng, Binan, Ma, Hongwu, Chen, Shouwen, Fei, Qiang, He, Qiaoning, Yang, Shihui. Paradigm of engineering recalcitrant non-model microorganism with dominant metabolic pathway as a biorefinery chassis. NATURE COMMUNICATIONS[J]. 2024, 15(1): http://dx.doi.org/10.1038/s41467-024-54897-5.
[5] Wei, Fan, Cai, Jingyi, Mao, Yufeng, Wang, Ruoyu, Li, Haoran, Mao, Zhitao, Liao, Xiaoping, Li, Aonan, Deng, Xiaogui, Li, Feiran, Yuan, Qianqian, Ma, Hongwu. Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design. ADVANCED SCIENCE[J]. 2024, 11(45): http://dx.doi.org/10.1002/advs.202404632.
[6] 毛志涛. DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes. International Journal of Molecular Sciences[J]. 2024, 第 1 作者  通讯作者  null(null): 
[7] Yutao Wang, Zhitao Mao, Jiacheng Dong, Peiji Zhang, Qiang Gao, Defei Liu, Chaoguang Tian, Hongwu Ma. Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based k cat data. MICROBIAL CELL FACTORIES[J]. 2024, 23(1): 1-16, https://doaj.org/article/ba11eb4929be419a8823cdd51613a257.
[8] Zhitao Mao, Jinhui Niu, Jianxiao Zhao, Yuanyuan Huang, Ke Wu, Liyuan Yun, Jirun Guan, Qianqian Yuan, Xiaoping Liao, Zhiwen Wang, Hongwu Ma. ECMpy 2.0:A Python package for automated construction and analysis of enzyme-constrained models. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY[J]. 2024, 9(3): 494-502, http://lib.cqvip.com/Qikan/Article/Detail?id=7113173571.
[9] Yuanyuan Huang, Zhitao Mao, Yue Zhang, Jianxiao Zhao, Xiaodi Luan, Ke Wu, Lili Yun, Jing Yu, Zhenkun Shi, Xiaoping Liao, Hongwu Ma. Omics data analysis reveals the system-level constraint on cellular amino acid composition. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY[J]. 2024, 9(2): 304-311, http://lib.cqvip.com/Qikan/Article/Detail?id=7113182459.
[10] Shi, Zhenkun, Wang, Dehang, Li, Yang, Deng, Rui, Lin, Jiawei, Liu, Cui, Li, Haoran, Wang, Ruoyu, Zhao, Muqiang, Mao, Zhitao, Yuan, Qianqian, Liao, Xiaoping, Ma, Hongwu. REME: an integrated platform for reaction enzyme mining and evaluation. NUCLEIC ACIDS RESEARCH[J]. 2024, 52(W1): W299-W305, http://dx.doi.org/10.1093/nar/gkae405.
[11] Xue Yang, Zhitao Mao, Jianfeng Huang, Ruoyu Wang, Huaming Dong, Yanfei Zhang, Hongwu Ma. Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY[J]. 2023, 8(4): 597-605, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10514394/.
[12] Wu, Ke, Mao, Zhitao, Mao, Yufeng, Niu, Jinhui, Cai, Jingyi, Yuan, Qianqian, Yun, Lili, Liao, Xiaoping, Wang, Zhiwen, Ma, Hongwu. ecBSU1: A Genome-Scale Enzyme-Constrained Model of Bacillus subtilis Based on the ECMpy Workflow. MICROORGANISMS[J]. 2023, 11(1): http://dx.doi.org/10.3390/microorganisms11010178.
[13] Wang, Pengju, Zhao, Dongdong, Li, Ju, Su, Junchang, Zhang, Chunzhi, Li, Siwei, Fan, Feiyu, Dai, Zhubo, Liao, Xiaoping, Mao, Zhitao, Bi, Changhao, Zhang, Xueli. Artificial Diploid Escherichia coli by a CRISPR Chromosome-Doubling Technique. ADVANCED SCIENCE[J]. 2023, 10(7): 
[14] Zhitao Mao, Qianqian Yuan, Haoran Li, Yue Zhang, Yuanyuan Huang, Chunhe Yang, Ruoyu Wang, Yongfu Yang, Yalun Wu, Shihui Yang, Xiaoping Liao, Hongwu Ma. CAVE: a cloud-based platform for analysis and visualization of metabolic pathways. NUCLEIC ACIDS RESEARCH[J]. 2023, 51(W1): W70-W77, 
[15] Zhang, Zhiyu, Cui, Mengfei, Chen, Panting, Li, Juxing, Mao, Zhitao, Mao, Yufeng, Li, Zhenjing, Guo, Qingbin, Wang, Changlu, Liao, Xiaoping, Liu, Huanhuan. Insight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level. FRONTIERS IN MICROBIOLOGY[J]. 2023, 14: http://dx.doi.org/10.3389/fmicb.2023.1199144.
[16] Qianqian Yuan, Fan Wei, Xiaogui Deng, Aonan Li, Zhenkun Shi, Zhitao Mao, Feiran Li, Hongwu Ma. Reconstruction and metabolic profiling of the genome-scale metabolic network model of Pseudomonas stutzeri A1501. SYNTHETIC AND SYSTEMS BIOTECHNOLOGY[J]. 2023, 8(4): 688-696, http://lib.cqvip.com/Qikan/Article/Detail?id=7111812431.
[17] Shi, Zhenkun, Deng, Rui, Yuan, Qianqian, Mao, Zhitao, Wang, Ruoyu, Li, Haoran, Liao, Xiaoping, Ma, Hongwu. Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework. RESEARCH[J]. 2023, 6(5): 117-128, http://lib.cqvip.com/Qikan/Article/Detail?id=7110871156.
[18] Jianxiao Zhao, Xi Sun, Zhitao Mao, Yangyang Zheng, Zhouxiao Geng, Yuhan Zhang, Hongwu Ma, Zhiwen Wang. Independent component analysis of Corynebacterium glutamicum transcriptomes reveals its transcriptional regulatory network. MICROBIOLOGICAL RESEARCH. 2023, 276: http://dx.doi.org/10.1016/j.micres.2023.127485.
[19] 王依婷, 李素珍, 毛志涛, 廖小平, 许慧敏, 邱艺华, 闫雪崧, 杨凤妍, 李贞景, 郭庆彬, 刘欢欢. 解淀粉芽孢杆菌群体遗传特征分析. 食品研究与开发[J]. 2023, 第 3 作者44(17): 160-170, http://lib.cqvip.com/Qikan/Article/Detail?id=7110431866.
[20] Niu, Jinhui, Mao, Zhitao, Mao, Yufeng, Wu, Ke, Shi, Zhenkun, Yuan, Qianqian, Cai, Jingyi, Ma, Hongwu. Construction and Analysis of an Enzyme-Constrained Metabolic Model of Corynebacterium glutamicum. BIOMOLECULES[J]. 2022, 12(10): http://dx.doi.org/10.3390/biom12101499.
[21] Junchang Su, Pengju Wang, Ju Li, Dongdong Zhao, Siwei Li, Feiyu Fan, Zhubo Dai, Xiaoping Liao, Zhitao Mao, Chunzhi Zhang, Changhao Bi, Xueli Zhang. A CRISPR-based chromosomal-separation technique for Escherichia coli. MICROBIAL CELL FACTORIES[J]. 2022, 21(1): 1-11, https://doaj.org/article/7f67eeb6c6344612bd842ae15295c01e.
[22] Mao, Zhitao, Zhao, Xin, Yang, Xue, Zhang, Peiji, Du, Jiawei, Yuan, Qianqian, Ma, Hongwu. ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model. BIOMOLECULES[J]. 2022, 12(1): http://dx.doi.org/10.3390/biom12010065.
[23] Zhitao Mao, Teng Huang, Qianqian Yuan, Hongwu Ma. Construction and analysis of an integrated biological network of Escherichia coli. 系统微生物学与生物制造(英文)[J]. 2022, 2(1): 165-176, http://lib.cqvip.com/Qikan/Article/Detail?id=7107117680.
[24] Zhang, Hao, Liu, Huanhuan, Shu, Lin, Xu, Huimin, Cheng, Ying, Mao, Zhitao, Liu, Bin, Liao, Xiaoping, Huang, Di. Metabolomics Analysis Coupled with Weighted Gene Co-Expression Network Analysis Unravels the Associations of Tricarboxylic Acid Cycle-Intermediates with Edible Pigments Produced by Monascus purpureus (Hong Qu). FOODS[J]. 2022, 11(14): http://dx.doi.org/10.3390/foods11142168.
[25] Mao, Zhitao, Yang, Ping, Liu, Huanhuan, Mao, Yufeng, Lei, Yu, Hou, Dongwei, Ma, Hongwu, Liao, Xiaoping, Jiang, Wenxia. 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. FRONTIERS IN MICROBIOLOGY[J]. 2022, 13: http://dx.doi.org/10.3389/fmicb.2022.880946.
[26] Shi, Zhenkun, Liu, Pi, Liao, Xiaoping, Mao, Zhitao, Zhang, Jianqi, Wang, Qinhong, Sun, Jibin, Ma, Hongwu, Ma, Yanhe. Data-Driven Synthetic Cell Factories Development for Industrial Biomanufacturing. BIODESIGN RESEARCH. 2022, 2022: http://dx.doi.org/10.34133/2022/9898461.
[27] Mao, Zhitao, Wang, Ruoyu, Li, Haoran, Huang, Yixin, Zhang, Qiang, Liao, Xiaoping, Ma, Hongwu. ERMer: a serverless platform for navigating, analyzing, and visualizing Escherichia coli regulatory landscape through graph database. NUCLEIC ACIDS RESEARCH[J]. 2022, 50(W1): W298-W304, http://dx.doi.org/10.1093/nar/gkac288.
[28] 杨雪, 张培基, 毛志涛, 赵欣, 王若宇, 蔡敬一, 王智文, 马红武, , , , , , , , . 多约束代谢网络模型的研究进展. 生物工程学报[J]. 2022, 第 3 作者38(2): 531-545, https://cjb.ijournals.cn/cjbcn/article/abstract/gc22020531?st=article_issue.
[29] 高雅杰, 袁倩倩, 杨雪, 毛志涛, 余文童, 刘浩, Igor, Goryanin, 马红武, , , , , , , . 基于图论的代谢网络中流通代谢物处理新方法. 生物工程学报[J]. 2022, 第 4 作者38(4): 1554-1564, https://cjb.ijournals.cn/cjbcn/article/abstract/gc22041554?st=article_issue.
[30] 袁倩倩, 毛志涛, 杨雪, 廖小平, 马红武, , , , , . 数字细胞模型的研究及应用. 生物工程学报[J]. 2022, 第 2 作者38(11): 4146-4161, https://cjb.ijournals.cn/cjbcn/article/abstract/gc22114146?st=article_issue.
[31] Yang, Xue, Mao, Zhitao, Zhao, Xin, Wang, Ruoyu, Zhang, Peiji, Cai, Jingyi, Xue, Chaoyou, Ma, Hongwu. Integrating thermodynamic and enzymatic constraints into genome-scale metabolic models. METABOLIC ENGINEERING[J]. 2021, 67: 133-144, http://dx.doi.org/10.1016/j.ymben.2021.06.005.
[32] Gao, Yajie, Yuan, Qianqian, Mao, Zhitao, Liu, Hao, Ma, Hongwu. Global connectivity in genome-scale metabolic networks revealed by comprehensive FBA-based pathway analysis. BMC MICROBIOLOGY[J]. 2021, 21(1): http://dx.doi.org/10.1186/s12866-021-02357-1.
[33] Ding, Dongqin, Bai, Danyang, Li, Jinlong, Mao, Zhitao, Zhu, Yaru, Liu, Pi, Lin, Jianping, Ma, Hongwu, Zhang, Dawei. Analyzing the genetic characteristics of a tryptophan-overproducing Escherichia coli. BIOPROCESS AND BIOSYSTEMS ENGINEERING[J]. 2021, 44(8): 1685-1697, http://dx.doi.org/10.1007/s00449-021-02552-4.
[34] Yun, Liyuan, Wu, Tao, Mao, Zhitao, Li, Wen, Zhang, Min, Sun, Xiaotao. A novel wheat germ polysaccharide: Structural characterization, potential antioxidant activities and mechanism. INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES[J]. 2020, 165: 1978-1987, http://dx.doi.org/10.1016/j.ijbiomac.2020.10.112.
[35] Mao, Zhitao, Ma, Hongwu. iMTBGO: An Algorithm for Integrating Metabolic Networks with Transcriptomes Based on Gene Ontology Analysis. CURRENT GENOMICS[J]. 2019, 20(4): 252-259, 
[36] 赵欣, 杨雪, 毛志涛, 马红武, , , , , . 基于酶约束的代谢网络模型研究进展及其应用. 生物工程学报[J]. 2019, 第 3 作者35(10): 1914-1924, https://cjb.ijournals.cn/cjbcn/article/abstract/gc19101914?st=article_issue.
[37] Zhang, Shuanghong, Liu, Dingyu, Mao, Zhitao, Mao, Yufeng, Ma, Hongwu, Chen, Tao, Zhao, Xueming, Wang, Zhiwen. Model-based reconstruction of synthetic promoter library in Corynebacterium glutamicum. BIOTECHNOLOGY LETTERS[J]. 2018, 40(5): 819-827, https://www.webofscience.com/wos/woscc/full-record/WOS:000430175100009.
[38] Liu, Dingyu, Mao, Zhitao, Guo, Jiaxin, Wei, Leyi, Ma, Hongwu, Tang, Yajie, Chen, Tao, Wang, Zhiwen, Zhao, Xueming. Construction, Model-Based Analysis, and Characterization of a Promoter Library for Fine-Tuned Gene Expression in Bacillus subtilis. ACS SYNTHETIC BIOLOGY[J]. 2018, 7(7): 1785-1797, https://www.webofscience.com/wos/woscc/full-record/WOS:000439761800016.
[39] Sun, Jie, Zhou, Meng, Mao, ZhiTao, Hao, DaPeng, Wang, Zhenzhen, Li, ChuanXing. Systematic analysis of genomic organization and structure of long non-coding RNAs in the human genome. FEBS LETTERS[J]. 2013, 587(7): 976-982, http://dx.doi.org/10.1016/j.febslet.2013.02.036.
[40] Jie Sun, Meng Zhou, Zhitao Mao, Chuanxing Li. Characterization and Evolution of microRNA Genes Derived from Repetitive Elements and Duplication Events in Plants. PLOS ONE[J]. 2012, 7(4): http://dx.doi.org/10.1371/journal.pone.0034092.

   

（ 1 ） 数据驱动的高精度多约束代谢网络模型构建, 负责人, 国家任务, 2024-01--2026-12
（ 2 ） 固碳酶元件数据库与智能设计, 负责人, 国家任务, 2023-02--2026-01