CV

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This is a short version, please click here to see my detailed CV in pdf format.

Contents

Education

2008~2013 Ph.D. (Major: Computational Biology)

Cold Spring Harbor Laboratory & Applied Mathematics and Statistics Department, Stony Brook University

2004~2007 M.Sc (Major: Bioinformatics)

College of Life Sciences, Nankai University, China

2000~2004 B.Sc (Major: Biophysics)

Department of Biophysics, College of Physics, Nankai University, China

Recent Experience

2013.9~Present Bioinformatics Scientist

BioMicro Center, Massachusetts Institute of Technology

2013.1~2013.8 Visiting Graduate Student

Center for Motor Neuron Biology and Disease, Columbia University, Prof. Chaolin Zhang

2009.2~2013.8 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)

Selected Publications

To see a full list, please click here to see my google scholar page.

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

  • Kristin A Knouse, Jie Wu and Angelika Amon. Assessment of megabase-scale somatic copy number variation using single cell sequencing, Genome Research, 2016. gr. 198937.115. **[1]
  • Kristin A Knouse, Jie Wu, Charles A Whittaker and Angelika Amon. Single cell sequencing reveals low levels of aneuploidy across mammalian tissues. Proceedings of the National Academy of Sciences, 2014. 111(37):13409-13414.**[2]
  • Wangzhi Li, Jie Wu, Sang-Yong Kim, Ming Zhao, Stephen A Hearn, Michael Q Zhang, Marvin L Meistrich and Alea A Mills. Chd5 orchestrates chromatin remodelling during sperm development. Nature communications, 2014. 5. [3]
  • 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, 41(10):5149-5163. ** [4]
  • 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. [5]
  • 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. ** [6]
  • 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. [7]
  • 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 ** [8]
  • 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. [9]
  • 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

  • Extensive experience on RNA-Seq data analysis (quality control, alignment, gene expression, isoform discovery, splicing detection, splicing quantification, differential gene expression and splicing)
  • Analysis of ChIP-Seq, Copy Number Variations, Mutation calling, Pathway analysis, Gene set enrichment, Assembly, Motif analysis
  • 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

×Cloud computing experience on AWS/Google Cloud/Azure

  • Statistical analysis (hypothesis test, linear regression, Bayesian inference, etc.)
  • Signal processing (Fourier transformation, wavelet methods)
  • Webserver techniques (MySQL, HTML, ASP, JSP and PHP)

×Software for data analysis (IPA, Spotfire, GSEA, etc.)

Wet Lab

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