崔海洋，教授，博士生导师，南京师范大学生命科学学院-副院长，微生物改造技术全国重点实验室固定成员，煤炭重大专项-青年首席，国家级青年人才，江苏省特聘教授。2016年硕士毕业于中科院天津工业生物技术研究所（导师：郭瑞庭 教授）；2020年，博士毕业于德国亚琛工业大学（导师：Ulrich Schwaneberg教授）；同年，进入德国DWI-莱布尼茨互动材料研究所进行博士后研究；2021-2023年于美国伊利诺伊大学厄巴纳-香槟分校继续进行博士后研究（导师：Huimin Zhao教授）。2024年加入南京师范大学，组建“人工智能与工程生物学”研究团队，搭建超算平台Infinity（无穷生物超算集群）。已发表SCI论文52篇，其中一作通讯（含共同）27篇（Top 22篇，包括Nature, Science, Angew. Chemi., Nat. Commun.等; 封面文章7篇; Hot Paper 4篇）;申请专利7项, 授权2项;并应邀在国际权威丛书 Methods in Molecular Biology 分别撰写独立章节3章。ABLab课题组网站：http://www.oceancuilab.com
教育背景
2016.10-2020.11 德国亚琛工业大学 (RWTH-Aachen University) 生物技术 博士
2013.09-2016.07 中国科学院大学 结构生物学 硕士
2009.09-2013.06 鲁东大学 生物工程 学士
工作经历
2024.02-至今 南京师范大学 教授（博导）
2021.03-2024.01 美国伊利诺伊大学厄巴纳-香槟分校 博士后（导师Huimin Zhao赵惠民 教授）
2020.12-2021.03 德国DWI-莱布尼茨互动材料研究所 博士后（导师Ulrich Schwaneberg教授）
研究兴趣
深度融合蛋白质工程、人工智能、计算机模拟技术，理解探索序列-结构-功能的相互关系。
1.利用前沿的深度学习模型，发展全新的深度新酶挖掘和智能改造方案
2.基于微观计算模拟，高效理解设计酶的多种催化性能
3.采用体外固化修饰和体内级联催化双驱动，结合深度学习优化，推进高鲁棒性酶的工业应用
关键词：蛋白质工程 定向进化 计算模拟 机器学习 生物催化 自动化生物铸造厂
获奖及荣誉
江苏省特聘教授 2023
南京师范大学鱼跃学者 2023
研究生院教学指导证书, 美国伊利诺伊大学厄巴纳-香槟分校 2022
德国亚琛工业大学 Borchers-plaketter奖章（博士论文获最高等级拉丁文学位荣誉“Summa Cum Laude”）2021
德国北莱茵-威斯特法伦州中国公派学生学者联合会名誉主席 2019
德国亚琛中国公派学生学者联合会名誉主席 2018
学术成果
已发表SCI论文45篇，其中一作通讯(含共一)文章论著22篇，其中Top 21篇（包括Science, Angew. Chemi., Nat. Comm等; 封面文章4篇; Hot Paper 3篇）; 申请专利4项, 授权2项; 邀请口头报告3次; 会议海报3次; 成果清单见后文。
项目主持参与
· 优秀青年基金（海外） 课题负责人
· 江苏省特聘教授项目 课题负责人
· Using Machine Learning Guided Directed Evolution to Accelerate Optimization of Enzymes, Thrust 2, Molecule Maker Lab Institute (MMLI), National Science Foundation (NSF) 主要参与人
· Halogenation mechanism understanding towards halogenase by the molecular dynamics simulation and QM/MM. DELTA, National Center for Supercomputing Applications 课题负责人
教学与指导
2021-2023 美国伊利诺伊大学厄巴纳-香槟分校 协助指导博士研究生 2名; 指导本科生课程实习 5名
2019-2020 德国亚琛工业大学 指导联培博士生1名, 硕士研究生3名, 本科生1名
2019 德国亚琛工业大学 计算生物学实践课程教学助教
学术兼职与社会服务
2023 MMLI分子制造实验室研究所学生博士后委员会 倡导主席
2023 美国能源部小企业创新研究 和技术转让计划 评审人
2023-至今 Asian Journal of Pharmaceutical Sciences 青年编委
2023-至今 Frontiers in Microbiology 审查编辑
2022-至今 Frontiers in Bioengineering and Biotechnology 审查编辑
2021-至今 BMC Biotechnology学术期刊 编委
2021-至今 Angewandte Chemie International Edition学术期刊 审稿人
2020-至今 Wiley, MDPI, BMC等杂志社系列学术期刊 审稿人
2019.05-2021.03 留德华人化学化工学会(CGCA)理事会 理事
2019.12-2020.10 亚琛工业大学生物技术研究所研究管理理事会 常任理事
2018.09-2019.07 留德华人化学化工学会-西部分会 (CGCA-West) 主席
2018.06-2019.11 德国北莱茵-威斯特法伦州中国公派学生学者联合会 主席，创始人2016.11-2018.06 亚琛中国公派学生学者联合会 主席，创始人
研究经历
2021.03-2024.01美国伊利诺伊大学厄巴纳-香槟分校Carl R. Woese基因组生物学研究所（师从赵惠民教授）
研究内容: 面向酶工程领域开发人工智能驱动的“设计-构建-测试-学习(DBTL)” 全自动封闭式循环
2016-2021 亚琛工业大学生物技术研究所; DWI-莱布尼茨互动材料研究所（师从Ulrich Schwaneberg教授）
研究内容: 开发了基于ΔΔG能量和水化层为基础的蛋白质工程策略以高效改造目标酶
2013- 2016 中国科学院天津工业生物技术研究所（师从郭瑞庭教授）
研究内容: 锚定膜蛋白锥虫单体氧化烯环化酶（TcOC）的纯化、结晶和定点突变研究
会议报告
· Cui, H., Predicting the Substrate Specificity and Regioselectivity of Halogenases Using Deep Learning2023 AIChE Annual Meeting Invited Talk
· Cui, H., Machine learning-guided directed evolution of halogenases for biocatalysis, Molecule Maker Lab Institute Symposium 2022, Invited Talk
· Cui, H., How to engineer an organic solvent tolerant lipase: Insights from directed evolution and molecular dynamics simulation, 33rd Chinese-German Chemical Association (CGCA) Annual Conference, 2021, Invited Talk
· Cui, H., et al. Using machine learning guided directed evolution to accelerate optimization of enzymes, Molecule Maker Lab Institute Retreat 2021, Poster Winner
· Cui, H., Markel U., Frauenkron-Machedjou V. J., Zhao J., Mehdi D. Davari et al. Engineering a lipase for organic cosolvent resistance – how do current directed evolution approaches compete with the potential that nature offers? Aachen Protein Engineering Symposium (AcES), Germany, 2018, Abstract, Poster
· Dommaraju S, Ren H, Huang C, Cui, H., Pan Y, Nesic M, Zhu L, Sarlah D, Mitchell D, Zhao H. Genome mining unveils class of ribosomal peptides with two amino termini. In4th International Conference on Natural Product Discovery and Development in the Genomic Era 2023 Jan 8. SIMB, Abstract
· Cui, H., Su, Y., Dean, TJ., Shukla, D., Zhao, H., Predicting the Substrate Specificity and Regioselectivity of Halogenases Using Deep Learning2023 AIChE Annual Meeting Abstract, Poster
· H Ren, SR Dommaraju, C Huang, H Cui, Y Pan, M Nesic, L Zhu, D Sarlah, Genome Mining Unveils Class of Ribosomal Peptides with Two Amino Termini, 2022 AIChE Annual meeting, 648191, Abstract
· H Ren, C Huang, H Cui, Y Pan, H Zhao, Ribosomal Peptides Containing Fatty Acyl Moieties Synthesized By Noncannonical Kas III Enzymes, 2022 AIChE Annual meeting, 648447 Abstract
· T Yu, H Cui, N Singh, H Zhao, In Vitro Continuous Evolution of Proteins Via Bioautomata, 2022 AIChE Annual Meeting, 645800 Abstract
论文著作
1. Yu, T.,# Cui, H.,# Li J. C., Luo, Y., Zhao, H.*, Enzyme function prediction using contrastive learning. Science 2023 379(6639), 1358-1363. IF= 63.714, Top
2. Cui, H., Eltoukhy, L., Zhang, L., Markel, U., Jaeger, K. E., Davari, M. D.*, Schwaneberg, U. *, Less unfavorable salt bridges on the enzyme surface result in more organic cosolvent resistance. Angewandte Chemie International Edition 2021, 60, 11448. (Hot paper) IF=16.823, Top
3. Cui, H., Zhang, L. *, Söder, D., Tang, X. M., Davari, M. D., Schwaneberg, U.*, Rapid and oriented immobilization of laccases on electrodes via a methionine-rich peptide. ACS Catalysis 2021, 11 (4), 2445–2453. IF= 13.700, Top
4. Cui, H., Zhang, L., Eltoukhy, L., Jiang, Q. J., Korkunç, S. K., Schwaneberg, U.*, Davari, M. D.*, Enzyme hydration determines resistance in organic cosolvents. ACS Catalysis 2020, 10, 14847–14856. IF= 13.700, Top
5. Wang, X.#, Sheng, Y.#, Cui, H.#, Qiao, J., Song, Y., Li, X.*, Huang, H.*, Corner engineering: Tailoring enzymes for enhanced resistance and thermostability in deep eutectic solvents. Angewandte Chemie International Edition. 2023, e202315125. IF=16.823, Top
6. Cui, H., Pramanik, S., Jaeger, K. E., Davari, M. D.*, Schwaneberg, U.*, CompassR-guided recombination unlocks design principles to stabilize lipases in ILs with minimal experimental efforts. Green Chemistry 2021,23, 3474-3486. IF=11.034, Top
7. Li, A.#, Sheng, Y.#, Cui, H.#; Wang, M., Wu, L., Song, Y., Yang, R., Li, X.*, Huang, H.* Discovery and mechanism-guided engineering of BHET hydrolases for improved PET recycling and upcycling. Nature Communication. 2023, 14, 4169 IF= 17.690, Top
8. Li, X.#, Cui, H.#, Qiao, J., Wang, M., Yue, G.*, An integrative approach enables high bioresource utilization and bioethanol production from whole stillage. Bioresource Technology 2022, 343, 126153. IF=11.889, Top
9. Cui, H., Vedder, M., Zhang, L., Jaeger, K. E., Schwaneberg, U.*, Davari, M. D.* Polar substitutions on the surface of a lipase substantially improve tolerance in organic solvents. ChemSusChem 2022, 15(9): e202102551. IF=9.140, Top
10. Cui, H., Zhang, L., Yildiz, C. B., Eltoukhy, L., Cheng, L., Jaeger, K. E., Schwaneberg, U.*, Davari, M. D.* Enzyme hydration: How to retain resistance in ionic liquids. ACS Sustainable Chemistry & Engineering 2022 10, 46, 15104–15114 IF=9.224, Top
---------------------------------以上为十篇代表作---------------------------------
11. Li, A.,# Wu, L.,# Cui, H.,# Song, Y., Zhang, X. and Li, X., 2024. Unlocking a sustainable future for plastics: a chemical‐enzymatic pathway for efficient conversion of mixed waste to MHET and energy-saving pet recycling. ChemSusChem, p.e202301612. IF=9.140, Top
12. Wang, X.#, Li, A.#,, Li, X.* and Cui, H.*, 2024. Empowering protein engineering through recombination of beneficial substitutions. Chemistry–A European Journal, p.e202303889. IF=5.020, Top, Cover feature.
13. Liu, M., Zhang, L., Wang, M., Wang X., Cui, H.*, Wei J.*, Li X.* The role of metal-organic frameworks in removing emerging contaminants in wastewater. Journal of Cleaner Production, IF=11.1, Top
14. Pramanik, S.#, Cui, H.#, Dhoke, G. V., Yildiz, C. B. Vedder, M., Jaeger, K. E., Schwaneberg, U.*, Davari, M. D.*, How does surface charge engineering of Bacillus subtilis lipase A improve ionic liquids resistance? Lessons learned from molecular dynamics simulations. ACS Sustainable Chemistry & Engineering 2022 10(8): 2689-2698. IF=9.224, Top
15. Wang, M., Qiao, J., Sheng, Y., Wei, J., Cui, H.*, Li, X.*, & Yue, G. Bioconversion of corn fiber to bioethanol: Status and perspectives. Waste Management, 2023, 157, 256-268. IF=8.816, Top
16. Wang, M.#; Cui, H.#; Gu, C.; Li, A.; Qiao, J.; Schwaneberg, U.; Zhang, L.; Wei, J.; Li, X.; Huang, H.., Engineering all-round cellulase for bioethanol production. ACS Synthetic Biology 2023, 12(7), 2187-2197. IF= 5.249, Top
17. Cui, H., Jaeger, K. E., Davari, M. D.*, Schwaneberg, U.*, CompassR yields highly organic solvent-tolerant enzymes through recombination of compatible substitutions. Chemistry-A European Journal 2021, 27, 2789. (Hot paper) IF=5.236, Top
18. Cui, H., Cao, H., Cai, H., Karl-Erich, J., Davari, M. D., Schwaneberg, U.*, Computer-assisted recombination (CompassR) teaches us how to recombine beneficial substitutions from directed evolution campaigns. Chemistry-A European Journal 2020, 26 (3), 643-649. (Cover Feature) IF=5.236, Top
19. Cui, H., Stadtmüller, T. H., Jiang, Q., Jaeger, K. E., Schwaneberg, U.*, Davari, M. D.*, How to engineer organic solvent resistant enzymes: insights from combined molecular dynamics and directed evolution study. ChemCatChem 2020, 12, 4073. IF=5.497
20. Cui, H., Davari, M. D.*, Schwaneberg, U.*, Recombination of compatible substitutions by 2GenReP and InSiReP. Methods in Molecular Biology 2022;2397:71-81. (Book Chapter)
21. Cui, H., Vedder, M., Schwaneberg, U.*, Davari, M. D.*, Using molecular simulation to guide protein engineering for biocatalysis in organic solvents. Methods in Molecular Biology 2022;2397:179-202. (Book Chapter)
22. Cui, H., Davari, M. D., Schwaneberg, U.*, Recombination of single beneficial substitutions obtained from directed evolution by Computer-assisted Recombination (CompassR). Methods in Molecular Biology 2022;2461:9-18. (Book Chapter)
23. Sheng, Y., Cui, H., Wang, X., Wang, M., Song, P., Huang, H. and Li, X., Harnessing Solvation-Guided Engineering to Enhance Deep Eutectic Solvent Resistance and Thermostability in Enzymes. Green Chemistry. 2024, DOI: 10.1039/D3GC04933G
24. Pourhassan N, Z., Cui, H., Davari, M. D.,... & Schmitt, L*. A step forward to the optimized HlyA type 1 secretion system through directed evolution. Applied Microbiology and Biotechnology doi.org/10.1007/s00253-023-12653-7. 2023 IF= 5.560, Top
25. Zhang, L., Cui, H., Zou, Z., Garakani, T. M., Novoa‐Henriquez, C., Jooyeh, B., Schwaneberg, U.*, Directed evolution of a bacterial laccase (CueO) for enzymatic biofuel cells. Angewandte Chemie International Edition 2019, 131 (14), 4610-4613. IF=16.823, Top
26. Huang, C., Cui, H., Ren, H., Zhao, H.*, Investigation of the biosynthetic mechanism of bipentaromycin featuring an unprecedented cyclic head-to-tail dimeric scaffold JACS Au 2023, 3 (1), 195–203
27. Qiao, J, Cui, H., Wang, M., Fu, X., Wang, X., Li, X.*, Huang, H.*, Integrated biorefinery approaches for the industrialization of cellulosic ethanol fuel. Bioresource Technology 2022. 360, 127516. IF=11.889, Top
28. Zhang, L., Cui, H., Liu, M., Wang, W., Li, X.*, Huang, H.*, The role of multi-low molecular weight organic acids on phenanthrene biodegradation: Insight from cellular characteristics and proteomics, Chemosphere 2023, 326,138406 IF= 8.943, Top
29. Li, A., Cui, H., Sheng Y., Qiao J., Li, X*, Huang H.*, Global plastic upcycling during and after the COVID-19 pandemic: the status and perspective, Journal of Environmental Chemical Engineering, 2023, 110092., IF= 7.968 Top
30. Zhang, L., Cui, H., Dhoke, G. V., Zou, Z., Sauer, D. F., Davari, M. D., Schwaneberg, U.*, Engineering of laccase CueO for improved electron transfer in bioelectrocatalysis by semi-rational design. Chemistry-A European Journal 2020, 26 (22), 4974. (Front Cover) IF=5.236, Top
31. Pourhassan N, Z., Cui, H., Khosa, S., Davari, M. D., Jaeger, K. E., Smits, S. H., ... & Schmitt, L.* Optimized Hemolysin type 1 secretion system in Escherichia coli by directed evolution of the Hly enhancer fragment and including a terminator region. ChemBioChem 2022 IF=3.461
32. Zhang, L., Wang M., Cui, H., Qiao J., Guo D., Wang B., Li X.*, Huang H.*, How humic acid and Tween80 improve the phenanthrene biodegradation efficiency: Insight from cellular characteristics and quantitative proteomics, Journal of Hazardous Materials 2022, 421, 126685 IF=14.224, Top
33. Cheng, L., Zhang, H., Cui, H., Wei, B., Davari, M. D., Wang, W.*, & Yuan, Q.* Efficient Enzyme-catalyzed Production of Diosgenin: Inspired by the Biotransformation Mechanisms of Steroid Saponins in Talaromyces Stollii CLY-6. Green Chemistry 2021, 23 (16), 5896-5910. IF=11.034, Top
34. Cheng, L., Zhang, H., Cui, H., Cheng, J., Wang, W., Wei, B., ... & Yuan, Q.* A novel α-L-Rhamnosidase renders efficient and clean production of icaritin. Journal of Cleaner Production 2022, 130903. IF=11.072, Top
35. Wang, M., Sheng, Y., Cui, H., Li, A., Li, X.*, Huang, H.* The role of glycerol in preserving proteins needs to be reconsidered. ACS Sustainable Chemistry & Engineering 2022 IF=9.224, Top
36. Ji, Y., Islam, S., Cui, H., Dhoke, G. V., Davari, M. D., Mertens, A., Schwaneberg, U.*, Loop engineering of aryl sulfotransferase b for improving catalytic performance in regioselective sulfation. Catalysis Science & Technology 2020, 10, 2369-2377. IF= 6.177, Top
37. Cheng, L., Zhang, H., Cui, H., Wang, W.*, Yuan, Q.*. Efficient production of the anti-aging drug Cycloastragenol: insight from two Glycosidases by enzyme mining. Applied Microbiology and Biotechnology 2020, 104, 9991-10004 IF= 5.556, Top
38. Zhang, L., Qiao J., Cui, H., Wang M., Li X.*, Using Low Molecular Weight Organic Acids to Enhance Microbial Degradation of Polycyclic Aromatic Hydrocarbons: Current Understanding and Future Perspectives, Water 13(4):446, IF= 3.530
39. Zhang, Z#, Feng J.#, Yang, C., Cui, H., Harrison, W., Zhong D., Wang, B, Zhao, H*. Photoenzymatic Enantioselective Intermolecular Radical Hydroamination. Nature Catalysis Accepted. IF= 47.253, Top
40. Liu, M., Zhang, L., Yang, R., Cui, H., Li X.* Integrating metal-organic framework ZIF-8 with green modifier empowered bacteria with improved bioremediation. Journal of Hazardous Materials, Accepted.
41. Ren, H., Dommaraju, S.R., Huang C., Cui, H., Pan Y., Nesic, M., Zhu, L., Sarlah, D., Mitchell, D. A., Zhao, H., Genome mining unveils class of ribosomal peptides with two amino termini. Nature Communication 2023, 14, 1624. IF= 17.690, Top
42. Yu, T., Boob, A. G., Volk M. J., Liu, X., Cui, H., Zhao, H.*, Machine learning-enabled retrobiosynthesis of molecules. Nature Catalysis, 2023, 6, 137–151. IF= 47.253, Top
43. Markel, U., Sauer, D. F., Wittwer, M., Schiffels, J., Cui, H., Davari, M. D., Kröckert, K.W., Herres-Pawlis, S., Okuda, J.* and Schwaneberg, U.* Chemogenetic evolution of a peroxidase-like artificial metalloenzyme. ACS Catalysis 2021, 11, 5079-5087. IF= 13.700, Top
44. Feng, L., Gao, L., Sauer, D.F., Ji, Y., Cui, H., Schwaneberg, U.*, Fe (iii)-complex mediated bacterial cell surface immobilization of eGFP and enzymes. Chemical Communications 2021. IF= 6.222, Top
45. Zhang, K., Li, H., Chen, W., Zhao, M., Cui, H., Min, Q., Wang, H., Chen, S., Li, D.*, Regulation of The Docosapentaenoic Acid/Docosahexaenoic Acid Ratio (DPA/DHA Ratio) in Schizochytrium Limacinum B4D1. Applied Biochemistry and Biotechnology 2017, 182 (1), 67-81. IF= 3.094
专利
1. 程仕伟, 崔海洋 等; 一种主产纤维素酶饲用益生菌制剂的液体发酵生产方法CN 103960483 A
2. 李秀娟, 王明慧, 崔海洋, 李安妮, 乔杰, 魏珺楠。外切葡聚糖酶突变体及其编码基因、重组载体、重组菌体和酶制剂以及它们的应用 申请号: 202211543049.
3. 李秀娟, 李安妮, 吴璐璇, 宋艺博, 崔海洋, 胡捷, 侯丽亚, 唐进, 刘扶芮。 2-羟乙基对苯二甲酸二酯水解酶突变体及编码基因、重组载体、重组菌株、酶制剂和应用 CN 116555222 A
4. 胡捷,侯丽亚,李安妮,唐进,刘扶芮,崔海洋,吴丽娜,李秀娟。 一种推荐塑料降解酶突变位点的方法、电子设备、介质 申请号: 202310724842.0
