Jie Zheng, Ph.D.
Research Associate
Computational Biology Branch
NCBI, NLM, NIH
Bethesda, MD 20894-0001
Tel: (301)-479-3713
Email: zhengj AT ncbi DOT nlm DOT nih DOT gov

Welcome to my homepage! I am a Research Associate with Dr. Teresa M. Przytycka at NCBI. I received my Ph.D. degree under the joint supervision of Prof. Stefano Lonardi and Prof. Tao Jiang in Department of Computer Science and Engineering at University of California, Riverside (UCR). I also worked in Plant Genomics Project led by Prof. Timothy J. Close in the Department of Botany and Plant Sciences at UCR.

Research Interests

Computational Biology and Bioinformatics
Computational Genomics, Systems Biology
Algorithm Design, Biological Data Mining,

Education

Ph.D. Computer Science, University of California, Riverside (Sept. 2006)
B.E. Computer Science, Zhejiang University, China (June 2000)

Publications

J. Zheng, PP Khil, RD Camerini-Otero, TM Przytycka. Detecting sequence polymorphisms associated with meiotic recombination hotspots in human genome. Submitted, 2009

J. Zheng*, D. Zhang, PF Przytycki, R. Zielinski, J. Capala, TM Przytycka* (co-corresponding author). SimBoolNet - A Cytoscape plugin for dynamic simulation of signaling networks. Bioinformatics, advanced access online, 2009

R. Zielinski, PF Przytycki, J. Zheng, D. Zhang, TM Przytycka, J. Capala. The crosstalk between EGF, IGF, and Insulin cell signaling pathways – computational and experimental analysis. BMC Systems Biology, 3(88), 2009 (highly accessed)

Y. Huang*, J. Zheng*, Teresa M. Przytycka (*co-first author). Discovery of regulatory mechanisms from gene expression variation by eQTL analysis. Biological Data Mining, Chapman and Hall/CRC Press, 2009

J. Zheng, IB Rogozin, EV Koonin, TM Przytycka. Support for the Coelomata Clade of animals from a rigorous analysis of the pattern of intron conservation. Molecular Biology and Evolution, 24(11):2583-92,2007
Conference version: RECOMB Comparative Genomics, LNCS 4751, pp. 177-92, 2007

J. Zheng, J. Svensson, K. Madishetty, T. Close, T. Jiang, S. Lonardi. OligoSpawn: a software tool for the design of overgo probes from large unigene databases. BMC Bioinformatics, 7:7, 2006

X. Chen, J. Zheng, Z. Fu, P. Nan, Y. Zhong, S. Lonardi and T. Jiang. Assignment of orthologous genes via genome rearrangement. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(4), 302-315, 2005
Conference version (invited): Proc. of Asia-Pacific Bioinformatics Conference (APBC), pp. 363-378, 2005

J. Zheng, S. Lonardi. Discovery of repetitive patterns in DNA with accurate boundaries. Proc. of IEEE International Symposium on BioInformatics and BioEngineering (BIBE), pp. 105-112, 2005

A. Goldstein, P. Kolman, J. Zheng (authors alphabetized). Minimum common string partition problem: hardness and approximation. Electronic Journal of Combinatorics, 12(1), 2005
Conference version: Proc. of International Symposium on Algorithms and Computation (ISAAC), pp. 484-495, LNCS 3341, 2004

J. Zheng, T. Close, T. Jiang, S. Lonardi. Efficient Selection of Unique and Popular Oligos for Large EST Databases. Bioinformatics, 20(13), 2101-2112, 2004
Conference version: Proc. of Symposium on Combinatorial Pattern Matching (CPM), pp. 384-401, LNCS 2676, 2003

Software

OligoSpawn

SimBoolNet