Protein function annotation; enzymatic reaction mechanism analysis; bioinformatics software development; high-performance computing; AI for biology; data mining; artificial intelligence.

Education

 Ph.D., Computer Application Technology, College of Computer Science and Technology, Jilin University, China — Sep 2016 – Dec 2020

CSC-funded Joint Ph.D. Student (Medical Data Mining), The University of Queensland, Australia — Nov 2017 – Dec 2019

•M.Eng., Computer Technology, College of Computer Science and Technology, Jilin University, China — Jun 2014 – Sep 2016

B.Eng., Software Engineering, College of Information Science and Technology, Hebei Agricultural University, China — Sep 2009 – Jul 2013

Professional Experience

Associate Professor, Master’s Supervisor, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences — Nov 2023 – Present

Postdoctoral Researcher, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences — Dec 2020 – Oct 2023

1. Zhenkun Shi, Dehang Wang, Yang Li, Rui Deng, Jiawei Lin, Cui Liu, Haoran Li, Ruoyu Wang, Muqiang Zhao, Zhitao Mao, Qianqian Yuan, Xiaoping Liao✉, Hongwu Ma✉. REME: an integrated platform for reaction enzyme mining and evaluation [J]. Nucleic Acids Research (2024): gkae405. (SCI Q1, IF:16.6)

2. Zhenkun Shi, Rui Deng, Qianqian Yuan, Zhitao Mao, Ruoyu Wang, Haoran Li, Xiaoping Liao*, Hongwu Ma*. Enzyme Commission Number Prediction and Benchmarking with Hierarchical Dual-core Multitask Learning Framework[J]. Research, 2023. (SCI Q1, IF:11.04).

3. Zhenkun Shi, Sen Wang, Lin Yue, Yijia Zhang*, Binod Kumar Adhikari, Shuai Xue, Wanli Zuo, Xue Li. Dual-Core Mutual Learning Between Scoring Systems and Clinical Features for ICU Mortality Prediction[J]. Information Sciences, 2023: 118984. (CCF B, SCI Q1, IF:8.23).

4. Zhenkun Shi, Pi Liu, Xiaoping Liao, Zhitao Mao, Jianqi Zhang, Qinhong Wang, Jibin Sun, Hongwu Ma, Yanhe Ma. Data-driven synthetic cell factories development for industrial biomanufacturing [J]. BioDesign Research, 2022.

5. Shining Liang, Wanli Zuo, Zhenkun Shi*, Sen Wang, Junhu Wang, Xianglin Zuo. A multi-level neural network for implicit causality detection in web texts [J]. Neurocomputing, 2022, 481: 121-132. (CCF C， SCI Q2, WOS:000761785300011, IF:5.78 ).

6. Yijia Zhang, Wanli Zuo, Zhenkun Shi*, Binod Kumar Adhikari. Journal of Ambient Intelligence and Humanized Computing [J]. , 2022: 1-21. (SCI Q2，WOS:000760720900001, IF:3.66).

7. Yi Yang, Yufeng Mao, Ruoyu Wang, Haoran Li, Ye Liu, Haijiao Cheng, Zhenkun Shi, Yu Wang, Meng Wang, Ping Zheng, Xiaoping Liao, Hongwu Ma. AutoESD: a web tool for automatic editing sequence design for genetic manipulation of microorganisms [J]. Nucleic Acids Research, 2022, 50(W1): W75-W82. (SCI Q1, WOS:000805210700001, IF:19.16)

8. Zhenkun Shi, Sen Wang, Lin Yue, Lixin Pang, Xianglin Zuo, Wanli Zuo*, Xue Li. Deep dynamic imputation of clinical time series for mortality prediction[J]. Information Sciences, 2021, 579: 607-622 (CCF B, SCI Q1， WOS:000701122700013, IF:8.23).

9. Zhenkun Shi, Wanli Zuo, Shining Liang, Xianglin Zuo*, Lin Yue, Xue Li. IDDSAM: An Integrated Disease Diagnosis and Severity Assessment Model for Intensive Care Units [J]. IEEE Access, 2020, 15423-15435:1-1. (SCI Q2, IF: 4.098, WOS: 000524741300012).

10. Yijia Zhang, Zhenkun Shi*, Wanli Zuo, Lin Yue, Shining Liang, Xue Li. Joint Personalized Markov Chains with Social Network Embedding for Cold-Start Recommendation[J]. Neurocomputing, 2020, 386: 208-220. (SCI Q2, IF: 4.072)

11. Suresh Pokharel, Zhenkun Shi*., Guido Zuccon, & Yu Li. (2020, November). Discriminative Features Generation for Mortality Prediction in ICU. In International Conference on Advanced Data Mining and Applications (pp. 324-338). Foshan, Cham (CCF C, WOS: 000723588900025).

12. Zhenkun Shi, Wanli Zuo, Weitong Chen, Lin Yue, Yuwei Hao, Shining Liang*. DMMAM: Deep Multi-Source Multi-Task Attention Model for Intensive Care Unit Diagnosis [C]. Lecture Notes In International Conference on Database Systems for Advanced Applications, 53-69. Springer, Cham, 2019. (SCI, WOS:000485172700004, CCF B).

13. Zhenkun Shi, Weitong Chen, Shining Liang, Wanli Zuo*, Lin Yue, Sen Wang. Deep Interpretable Mortality Model for Intensive Care Unit Risk Prediction [C]. International Conference on Advanced Data Mining and Applications. Springer, Dalian, 2019: 617-631. (CCF C, WOS: 000582483200045).