CV
From Jie Wu Home Page
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''(* Co-first author, ** major contribution)'' | ''(* 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, In press. ** | *'''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, In press. ** | ||
| − | *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 | + | *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. [http://www.sciencedirect.com/science/article/pii/S2211124712001635] |
*'''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. ** | *'''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. ** | ||
*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. | *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. | ||
Revision as of 21:13, 8 April 2013
This is a short version, click here to see my detailed CV.
Contents |
Education
| 2008~Present | Ph.D. Program (Major: Computational Biology)
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
|
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, In press. **
- 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. [1]
- 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. **
- 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.
- 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 **
- 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.
- 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.