Jie Zheng
Associate Professor
Graduated School:Ph.D., University of California, Riverside, USA
Tel: (021) 20684861
Office:Room 1A-504D, SIST Building
Research Interests
Biography
Selected Publications

RESEARCH INTERESTS

  • Data Science

  • Bioinformatics

  • Healthcare Big Data

  • Artificial Intelligence


BIOGRAPHY

Jie Zheng is currently the SMIRC Director and the Recruitment and Admissions Committee Director.

Jie Zheng received his B.Eng degree (honors) in Computer Science from Zhejiang University in 2000, and Ph.D. in Computer Science from the University of California, Riverside in 2006. From Aug. 2006 to Feb. 2011, he was a postdoctoral visiting fellow and research scientist at National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), USA. After that, he worked as an Assistant Professor at the School of Computer Science and Engineering, Nanyang Technological University (NTU), Singapore. From Oct. 2012, he was also an Adjunct Senior Research Scientist at Genome Institute of Singapore (GIS), A*STAR, Singapore. In June 2018, Dr. Zheng joined ShanghaiTech University as an Associate Professor.
Dr. Zheng has published more than 50 journal papers (14 of which have impact factors higher than 5) and over 40 conference papers. He has served as PC member and reviewer for a number of international conferences, and as Program Co-Chair for two conferences. Moreover, he reviews many papers for top-tier journals (e.g. Bioinformatics, Nucleic Acids Research) each year. In Singapore, Dr. Zheng was PI of 3 competitive external research grants at national level (with total funding more than 2 millions Singapore dollars), and he participated in more than 10 other projects as Co-PI or collaborator. In the iGEM (International Genetically Engineered Machine Competition) 2015, Dr. Zheng was the coach of mathematical modeling for the NTU team of students, who won a gold medal. At InCoB (International Conference on Bioinformatics) 2017, he won a best paper award (gold medal) in BMC track. In 2016 and 2017, Dr. Zheng was nominated for the Nanyang Education Award at NTU.


SELECTED PUBLICATIONS

  1. Shike Wang#, Fan Xu# (joint first authors), Yunyang Li, Jie Wang, Ke Zhang, Yong Liu, Min Wu*, Jie Zheng*. KG4SL: Knowledge graph neural network for synthetic lethality prediction in human cancers. Bioinformatics, Vol. 37, pp. i418-i425 (ISMB/ECCB 2021 special issue, , acceptance rate 19%), 2021 (IF = 7.14).

  2. Fan Xu#, Shike Wang# (joint first authors), Xinnan Dai, Piyushkumar A. Mundra, Jie Zheng*. Ensemble learning models that predict surface protein abundance from single-cell multimodal omics data. Methods, Vol. 189, pp. 65-73, 2021 (IF = 3.812).

  3. Yong Liu, Min Wu*, Chenghao Liu, Xiao-Li Li, Jie Zheng* (joint corresponding authors). SL2MF: Predicting synthetic lethality in human cancers via logistic matrix factorization. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 17(3): 748-757, 2020 (IF = 3.03).

  4. Jing Guo, Jie Zheng*. HopLand: Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddington’s epigenetic landscape. Bioinformatics, 33(14): i102 – i109 (special issue of ISMB/ECCB 2017, acceptance rate 16.5%), 2017 (IF = 7.14).

  5. Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng*. NetLand: quantitative modeling and visualization of Waddington’s epigenetic landscape using probabilistic potential. Bioinformatics, 33(10), pp. 1583 – 1585, 2017 (IF = 7.14).

  6. Jing Guo, Hui Liu*, Jie Zheng*. SynLethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. Nucleic Acids Research, 44 (D1): D1011 – D1017, 2016 (IF = 16.48).

  7. Haifen Chen, Jing Guo, Shital K Mishra, Paul Robson, Mahesan Niranjan, Jie Zheng*. Single-cell transcriptional analysis to uncover regulatory circuits driving cell fate decisions in early mouse development. Bioinformatics, 31(7), pp. 1060 – 1066, 2015 (IF = 7.14).

  8. Fan Zhang, Min Wu, Xuejuan Li, Xiaoli Li, Chee Keong Kwoh, Jie Zheng*. Predicting essential genes and synthetic lethality via influence propagation in signaling pathways of cancer cell fates. Journal of Bioinformatics and Computational Biology (JBCB), 13(03), 1541002, 2015 (IF = 1.08).

  9. Min Wu, Xuejuan Li, Fan Zhang, Xiaoli Li, Chee-Keong Kwoh, Jie Zheng*. In Silico Prediction of Synthetic Lethality by Meta-Analysis of Genetic Interactions, Functions, and Pathways in Yeast and Human Cancer. Cancer Informatics, 13(Suppl. 3), pp. 71-80, 2014 (IF = 2.06).

  10. J. Mei*, C-K Kwoh, P. Yang, X-L Li, J. Zheng. Drug-Target Interaction Prediction by Learning from Local Information and Neighbors. Bioinformatics, 29(2): 238-245, 2013 (IF = 7.14).