CV

This is a short version, click here to see my detailed CV.

Education

2008~Present	Ph.D. Candidate (Major: Computational Biology) Cold Spring Harbor Laboratory & Applied Mathematics and Statistics Department, Stony Brook University
2004~2007	Master of Science (Major: Bioinformatics) College of Life Sciences, Nankai University, China
2000~2004	Bachelor of Science (Major: Biophysics) Department of Biophysics, College of Physics, Nankai University, China

Current Research

2013.1~Present	Visiting Graduate Student Center for Motor Neuron Biology and Disease, Columbia University, Prof. Chaolin Zhang
2009.2~Present	Graduate Student Computational Biology and Bioinformatics Lab, Cold Spring Harbor Laboratory, Prof. Michael Q. Zhang & Prof. Adrian R. Krainer Second generation sequencing data analysis Alternative splicing detection and quantification from mRNA-seq data and differential splicing analysis (SpliceTrap) Fast, accurate and sensitive splice mapping of mRNA-seq reads (OLego)

Recent Publications

(* Co-first author, ** major contribution)

• Jie Wu, Olga Anczuków, Adrian R. Krainer, Michael Q. Zhang, Chaolin Zhang, OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acid Research, 2013, Published online. ** [1]
• Bin Zhang, Gayatri Arun, Yuntao S. Mao, Zsolt Lazar, Gene Hung, Gourab Bhattacharjee, Xiaokun Xiao, Carmen J. Booth, Jie Wu, Chaolin Zhang, and David L.Spector, The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Reports, 2012.2(1):111-123. [2]
• Jie Wu*, Martin Akerman*, Shuying Sun, W. Richard McCombie, Adrian R. Krainer, Michael Q. Zhang, SpliceTrap: a method to quantify alternative splicing under single cellular conditions, Bioinformatics, 2011.27(21): 3010-3016. ** [3]
• Manli Shen, Eduardo Eyras, Jie Wu, Amit Khanna, Serene Josiah, Mathieu Rederstorff, Michael Q. Zhang and Stefan Stamm, Direct cloning of double-stranded RNAs from RNase protection analysis reveals processing patterns of C/D box snoRNAs and provides evidence for widespread antisense transcript expression. Nucleic Acid Research, 2011.39(22): 9720–9730. [4]
• Bing Xiong*, Jie Wu*, David L. Burk, Mengzhu Xue, Hualiang Jiang, Jingkang Shen, BSSF: a fingerprint based ultrafast binding site similarity search and function analysis server, BMC Bioinformatics, 2010, 11:47 ** [5]
• Bing Xiong, Ke Liu, Jie Wu, David L. Burk, Hualiang Jiang, Jingkang Shen, DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks, Bioinformatics, 2008. 24(18):2117-2118. [6]
• Jie Wu, Ning Zhang, Zhuo Yang, Tao Zhang, Wavelet coherence and its application in analyzing auditory and motor task event-related potentials. ACTA BIOPYSICA SINICA, 2007, 23(6): 482-487. **

Skills

Bioinformatics Skills

• mRNA-seq data analysis pipeline ( quality control, alignment, gene expression, isoform discovery, splicing detection, splicing quantification, differential gene expression and splicing )
• Motif analysis; clustering; molecular dynamics; protein-ligand docking, optimization algorithms

Computer Skills and Data Analysis Skills

• Programming in Perl, C++, Shell, R and MATLAB
• Parallel computing experience on clusters with QSUB and MPI
• Statistical analysis (hypothesis test, linear regression, Bayesian inference, etc.)
• Signal processing (Fourier transformation, wavelet methods)
• Webserver techniques (MySQL, HTML, ASP, JSP and PHP)

Wet Lab

• RNA purification, reverse transcription, RT-PCR, PAGE.