代表性论文（更新至2025年）：

1.Cai, J.^#*; Liu, J.; Wei, F.; Wu, W.; Xu, W.; Wang, Y.; Yuan, Q.*; Ma, H*. Exploring Biomass Precursor Synthesis as a Determinant in Microbial Adaptation to Unadapted Carbon Sources. Research 2025,8

2.Xu, W.^#; Cai, J.^#*; Wu, W.; Yuan, Q.; Mao, Z.; Ma, H*. Improving Metabolic Engineering Design with Enzyme-Thermo Optimization. Metab Eng 2025, 91, 356–365.

3.Wei, F.^#; Cai, J.^#; Mao, Y.; Wang, R.; Li, H.; Mao, Z.; Liao, X.; Li, A.; Deng, X.; Li, F.; Yuan, Q.*; Ma, H*. Unveiling Metabolic Engineering Strategies by Quantitative Heterologous Pathway Design. Advanced Science 2024, 11 (45) 

4.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, 18 (9)

5.Cai, J.^#; Tan, T.*; Chan, S. H. J*. Predicting Nash Equilibria for Microbial Metabolic Interactions. Bioinformatics 2020, 36 (24), 5649–5655.

授权专利： 

1、蔡敬一，马红武，袁倩倩，刘嘉钰，以单独依赖某种唯一碳源为目的自适应实验室进化起始菌株设计方法；ZL202411319497.3；

2、蔡敬一，许雯淇，马红武，袁倩倩，武文君，一种基于参考型-高产型蛋白浓度范围比较的代谢工程靶点预测方法；ZL202411481455.X

3、蔡敬一，马红武，一种基于贪婪算法的菌株构建排程设计方法；ZL202310143252.9

4、蔡敬一，马红武，一种用于设计目标菌株平行构建最小化总基因操作数的方法；ZL202310071082.8

5、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；ZL202410250567.8