Contact

+86 15050535286, hcui@nnu.edu.cn
College of Life Science, Nanjing Normal University
No.1, Wenyuan Road, Xingzhi Building, Room 619, 2100462, Nanjing, China

EDUCATION

RWTH-Aachen University                                       Aachen, Germany
PhD, Biotechnology (Summa Cum Laude)                                     Nov. 2020
University of Chinese Academy of Sciences                                      Beijing, China
M.En, Structural Biology                                                     Jul. 2016
Ludong University                                                    Yantai, China
B.En, Bioengineering                                              Jun. 2013

WORKING EXPERIENCE

Nanjing Normal University, College of Life Science                        Nanjing, China
Full professor                                                 Jan. 2024-present
•    Applied machine learning and computational biology into protein engineering
University of Illinois at Urbana-Champaign, Carl R. Woese Institute for Genomic Biology              Urbana, U.S.
Postdoc Researcher; Supervisor: Prof. Dr. Huimin Zhao                     March. 2021-Jan.2024
•    Applied deep learning into halogenase 
DWI – Leibniz-Institute for Interactive Materials                             Aachen, Germany
Postdoc Researcher; Supervisor: Prof. Dr. Ulrich Schwaneberg                    Dec. 2020-Mar.2021
•    Engineered the non-conventional media and thermal resistant enzyme

PUBLICATIONS 

In total 50 papers, including 22 (co-)first/corresponding author papers (e.g., Science, Angew. Chemi., Nat. Comm et al.). See later page.

PATENTS 

•    Cheng, S, Cui, H.; A Method of liquid fermentation for producing cellulase by beneficial bacteria that can be used for the feed industry. CN 103960483 A (China)
•    Li, X., Wang, M., Cui, H., Li, A., Qiao, J., Wei, J.; The mutagenesis, coding genes, recombination vectors, recombination variant, enzyme preparations and applications of
exoglucanase. Applying, 202211543049.2 (China)
•    Li, X., Li, A., Wu, L., Son, Y., Cui, H., Hu, J., Hou, L., Tang, J., Liu, F., The mutagenesis, coding genes, recombination vectors, recombination variant, enzyme preparations and
applications of BHETase. CN 116555222 A (China)
•    Hu, J., Hou, L., Li, A., Tang, J., Liu, F., Cui, H., Wu, L., Li, X., A method, electronic device, medium for recommending mutation sites for plastic degrading enzymes 202310724842.0
(China)

CONFERENCE TALK, ABSTRACT, POSTER

•    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

JOINT PROJECTS

•    Science Fund Program for Excellent Young Scientists (Overseas), Principal Investigator
•    Jiangsu outstanding professor project, Principal Investigator
•    Using Machine Learning Guided Directed Evolution to Accelerate Optimization of Enzymes, Thrust 2, Molecule Maker Lab Institute (MMLI), National Science Foundation (NSF), Participant
•    Halogenation mechanism understanding towards halogenase by the molecular dynamics simulation and QM/MM. DELTA, National Center for Supercomputing Applications, Principal
Investigator

TEACHING

University of Illinois at Urbana-Champaign                                            Urbana, USA
Course instructor, Taught middle and high school student about enzyme engineering                May. 2023
RWTH-Aachen University                                         Aachen, Germany
Teaching Assistant, Computational Biology Practical Course                         2019

MENTORING

University of Illinois at Urbana-Champaign                                            Urbana, USA
Mentored seven undergraduate who served as interns (principal supervisor/co-supervisor)            2021-2023
•    Yoon Lee (2023), Chemical Engineering, Current Work: Bachler in UIUC
•    Max Jing (2023), Computer Science, Current Work: Bachler in UIUC
•    Dylan Hendrixson (2023), Biochemical Engineering, Bachler in UIUC
•    Amie Patel (2022), Chemical Engineering, Bachler in UIUC
•    Claudia Molnar (2022), Chemical Engineering, Bachler in UIUC 
•    Ansh Sharma (2021), Computer Science, Current Work: Bachler in UIUC
•    Gurevich, Juliana (2021), Chemical Engineering, Bachler in UIUC
RWTH-Aachen University                                         Aachen, Germany
Thesis supervisor for three Master’s students (co-supervisor)                                     2019-2020
•    Markus Vedder (2020), Molecule and Applied biotechnology, Current work: Scientific Officer, Charles River Laboratories, Germany
•    Lobna Eltoukhy (2020), Microbiology/Chemistry, Current work: PhD fellow, Dresden University of Technology, Germany
•    Qianjia Jiang (2019), Biology, Current work: Data Governance Consultant in Zeiss, Germany
Mentored one undergraduate who served as intern                             2019-2020
•    Seval Kübra Korkunç (2019), Molecular biology and genetics, Current work: PhD fellow,  Max Planck Institute for Heart and Lung Research, Germany

SERVICE AND ASSOCIATION / LEADERSHIP EXPERIENCE

MMLI Student Post Doc Council                        Advocacy Chair        2023
US. DOE Small Business Innovation Research (SBIR/STTR) program    Reviewer        2023
Asian Journal of Pharmaceutical Sciences                Editorial board member        2023-present
Frontiers in Microbiology                        Review Editor        2022-present
Frontiers in Bioengineering and Biotechnology                 Review Editor        2022-present
Liquid                                Topical Advisory Panel member    2022-present
BMC Biotechnology                        Editorial board member        2021-present
Wiley, Frontiers, MDPI, BMC Journal                    Reviewer        2020-present
Chinese-German Chemical Association    (CGCA)                Board Member        2019-2021
Institute of Biotechnology, RWTH-Aachen University         Research Council Member    2019-2020
Chinese-German Chemical Association-West (CGCA-West)            Chairman         2018-2019
Chinese Scholarship Students and Scholars Union in NRW             Chairman        2018-2019
Chinese Scholarship Students and Scholars Union in Aachen        Chairman        2016 –2018

SELECTED GRANTS AND AWARDS

Graduate College Mentoring Certificate, UIUC, USA                            2022
Borchers-plaketter award, RWTH-Aachen University, Germany                        2021
Honorary Chairman, Chinese Scholarship Students and Scholars Union in North                2019
Rhine-Westphalia, Germany
Honorary Chairman, Chinese Scholarship Students and Scholars Union in Aachen, Germany               2018
National Scholarship of China Scholarship Council                                 2016-2020
Outstanding Thesis of Bachelor, Shandong Province, China                        2014
Outstanding Graduates, Shandong Province, China                            2013
Bronze, 8th CHALLENGE CUP National College Students Business Plan Competition                2012
Outstanding Award, 8th CHALLENGE CUP Shandong Province College Students Business Plan Competition    2012

PUBLICATIONS   ORCID: 0000-0001-8360-0447   Google scholar

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
---------------------------------Top 10 papers above this line---------------------------------
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
46.    Cui, H., Cheng, S.*, Huang, T., Li, X., Yang, L., Chen, G., Screening and identifying of Bacillus Amyloliquefaciens for cellulase production and its enzymatic characters. Journal of
Food Science and Technology 2014, 32 (3), 43-47.
47.    Cheng, S.*, Cui, H., Huang, T., Ma, Y., Liu, J., Identification of the cellulase-producing bacteria and optimization of its culture conditions. Journal of Xihua University (Natural
Science Edition) 2013, 3, 94-97+104.
48.    Cheng, S.*, Liang, H., Cui, H., Study on the preparation of cross-linking cellulase aggregation and its catalytic properties. Journal of Xihua University (Natural Science Edition)
2012, 02, 81-83+96.
49.    Cheng, S.*, Zhang, Y., Ni, P., Cui, H., Yang, L., Ma, Y., Isolation, Identification and culture characters of Enterobacter sp. for the chitosanase production. Journal of Ludong
University (Natural Science Edition) 2014, 30 (1), 43-47. 
50.    Miao, J.*, Li, T., Cheng, S., Liang, H., Cui, H., Isolation, Identification and Culture Characteristics of Cellulase-Producing Exiguobacterium sp. Yt9. Food Science 2013, 17, 210-
214.