Jie Zheng, Associate Professor

Jie Zheng, Associate Professor

Tel:  (021) 20684861
Email: zhengjie@@shanghaitech.edu.cn
Office: Room 1A-504D, SIST Building
Major: CS
Website: https://shanghaitechzhengjielab.github.io/Zhenglab.github.io/index.htm

RESEARCH INTERESTS

Data Science

Bioinformatics

Healthcare Big Data

Artificial Intelligence


BIOGRAPHY

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.Lichun Ma,Jie Zheng*. Single-cell gene expression data analysis reveals beta-cell dysfunction and deficit mechanisms in type 2 diabetes.BMC Bioinformatics, 19(Suppl 19):515, 2018 (special issue of GIW 2018) (IF=2.213).

2.Haifen Chen, Devamuni A.K. Maduranga, Piyushkumar Mundra,Jie Zheng*. Bayesian data fusion of gene expression and histone modification profiles for inference of gene regulatory network.IEEE/ACM Transactions on Computational Biology and Bioinformatics(TCBB), Early Access, 2018 (IF= 2.428)

3.Jing Guo, Jie Zheng*. HopLand: Single-cell pseudotime recovery using continuous Hopfield network based modeling of Waddingtons epigenetic landscape, Bioinformatics, 33(14): i102  i109 (special issue of flagship conference ISMB/ECCB 2017, acceptance rate 16.5%), 2017 (IF= 7.307). 

4.Lichun Ma, Jie Zheng*. A polynomial based model for cell fate prediction in human diseases. BMC Systems Biology, 11(Suppl 7):126, 2017 (Best Paper Award, Gold Medal, the 16th International Conference on Bioinformatics (InCoB 2017)). 

5.Jing Guo, Feng Lin, Xiaomeng Zhang, Vivek Tanavde, Jie Zheng*. NetLand: quantitative modeling and visualization of Waddingtons epigenetic landscape using probabilistic potential. Bioinformatics, 33(10), pp. 1583  1585, 2017 (IF = 7.307).

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 = 10.162).

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 = 7.307).

8.Jian-Ping Mei, Chee-Keong Kwoh, Peng Yang, Xiao-Li Li, Jie Zheng. Drug-Target Interaction Prediction by Learning from Local Information and Neighbors. Bioinformatics, 29(2): 238-245, 2013 (IF = 7.307).

9.Jie Zheng, Pavel P. Khil, R. Daniel Camerini-Otero, Teresa M. Przytycka. Detecting sequence polymorphisms associated with meiotic recombination hotspots in the human genome. Genome Biology, 11:R103. 2010 (Highly accessed) (IF = 11.313).

10.Jie Zheng*, David Zhang, Pawel F. Przytycki, Rafal Zielinski, Jacek Capala, Teresa M. Przytycka* (co-corresponding authors). SimBoolNet - A Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics, 26(1): 141-142, 2010 (IF = 7.307).