Xiaowo Wang, Ph.D.

Assist Prof. of Bioinformatics

MOE Key Laboratory of Bioinformatics and Bioinformatics Div, TNLIST / Dpartment of Automation, Tsinghua University (Link)

 

Address: Room 1-112, FIT Building, Tsinghua University, Beijing 100084, China

Phone: 86-10-6279-4294 ext.808

Fax:     86-10-6278-3552

Email: xwwang    tsinghua.edu.cn

 

说明: 说明: 说明: 说明: 说明: 说明: 说明: 说明: Xiaowo_Wang

Chinese version

 

Postdoc Positions Open in Bioinformatics and Synthetic Biology

Call for Applications: 2012 PhD and MS program in Bioinformatics

    For students graduating in 2012 from the following majors: Automation, Computer Science, Biology, Mathematics, Statistics, Physics, etc.

 

Work Experience

·       2008.7-present            Lecturer of Bioinformatics, MOE Key  Laboratory of Bioinformatics and Bioinformatics Div, TNLIST / Department of Automation, Tsinghua University

 

Education

·       2003.9-2008.7 Ph.D. of Bioinformatics, Tsinghua University, China (link)

Thesis: Computational studies on recognition, evolution and transcriptional regulation of microRNAs

·       2007.9-2008.3 Visiting student, Cold Spring Harbor Laboratory, USA (link)

·       1999.9-2003.7 Bachelor of Engineering, Tsinghua University, China

 

Research Interest

Computational Systems Biology and Synthetic biology

·       Gene regulation analysis: Transcription regulation, epigenomic regulation, RNA regulation, post-translational regulation

·       Computational analysis of microRNA regulatory networks

·       Next generation sequencing data analysis

·       Design of synthetic biological systems

 

Courses Given

·       Introductory Computational Molecular Biology (graduate)

·       Elements of Information Theory (graduate)

 

Publications

  • Ratnakumar K, Duarte LF, Leroy G, Hasson D, Smeets D, Vardabasso C, B?nisch C, Zeng T, Xiang B, Zhang DY, Li H, Wang X, Hake SB, Schermelleh L, Garcia BA, Bernstein E., ATRX-mediated chromatin association of histone variant macroH2A1 regulates α-globin expression, Genes Dev. 2012 Mar 1;26(5):433-8.
  • Miao He, Yu Liu, Xiaowo Wang, Michael Q. Zhang, Gregory Hannon, Z. Josh Huang, Cell-type based analysis of microRNA profiles in the mouse brain, Neuron, 2012, 73(1):35-48
  • Chien Y, Scuoppo C, Wang X, Fang X, Balgley B, Bolden JE, Premsrirut P, Luo W, Chicas A, Lee CS, Kogan SC, Lowe SW, Control of the senescence-associated secretory phenotype by NF-κB promotes senescence and enhances chemosensitivity, Genes Dev.;25(20):2125-36, 2011
  • Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 2011 Dec 1;6(12):1505-12.
  • Likun Wang, Xiaowo Wang, Xi Wang, Xuegong Zhang, Yanchun Liang, Observations on novel splice junctions from RNA sequencing data, Biochemical and Biophysical Research Communications, 409(2):299-303, 2011
  • Xi Wang, Xiaowo Wang, Likun Wang, Zhixing Feng, Xuegong Zhang, A review on the processing and analysis of next-generation RNA-seq data，Prog. Biochem. Biophys., 37(8):834-846, 2010 (In Chinese)
  • Agustin Chicas, Xiaowo Wang, Chaolin Zhang, Mila McCurrach, Zhen Zhao, Ozlem Mert, Ross A. Dickins, Masashi Narita, Michael Zhang and Scott W. Lowe, Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence, Cancer Cell, 17(4): 376-387, 2010 Comments on Cancer Cell
  • Tingting Li, Xueya Zhou, Xiaowo Wang, Dahai Zhu, Yong Zhang, Identification and characterization of human snoRNA core promoters, Genomics, 96(1):50-6, 2010
  • Likun Wang, Zhixing Feng, Xi Wang, Xiaowo Wang*, Xuegong Zhang*, DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, 26(1):136-138 2010 (*co-corresponding Author) Comments on SCIENCE WATCH
  • Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang, High-resolution Human Core-promoter prediction with CoreBoost_HM, Genome Research, 19(2):266-75, 2009
  • Tao Peng, Chenghai Xue, Jianning Bi, Tingting Li, Xiaowo Wang, Xuegong Zhang and Yanda Li, Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse, BMC Genomics, 26;9:191, 2008
  • Xiaowo Wang, Jin Gu, Michael Q. Zhang and Yanda Li., Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species, Bioinformatics, 2008, 15;24(2):165-71
  • Xiaowo Wang , Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of microRNAs in vertebrates, Sci China Ser C-Life Sci, 51(6):552-9 2008
  • Jian Huang, Pei Hao, Yun-Li Zhang, Fu-Xing Deng, Qing Deng, Yi Hong, Xiaowo Wang, Yun Wang, Ting-Ting Li, Xue-Gong Zhang, Yi-Xue Li, Peng-Yuan Yang, Hong-Yang Wang and Ze-Guang Han. Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS), BMC Genomics, 8:207,2007
  • Jin Gu, Tao He, Yunfei Pei, Fei Li, Xiaowo Wang, Jing Zhang, Xuegong Zhang and Yanda Li, Primary Transcripts and Expressions of Mammal Intergenic MicroRNAs Detected by Mapping ESTs to Their Flanking Sequences. Mamm Genome, 17(10):1033-1041, 2006
  • Xiaowo Wang, Jing Zhang, Fei Li , Jin Gu , Tao He , Xuegong Zhang and Yanda Li, MicroRNA identification based on sequence and structure alignment. Bioinformatics, 2005, 21 (18): 3610-4

 

Bioinformatics Software：

  • SeqSaw：Short Spliced Sequence Mapping Tool. A package for mapping of spliced reads and unbiased detection of novel splice junctions from RNA-seq data.
  • DEGseq: An R package for Identifying Differentially Expressed Genes from RNA-seq data.
  • CoreBoost_HM:  High resolution human Pol II core-promoter prediction method, which integrate the information from DNA sequence and histone modification signal.
  • Perl scripts to perform two-step phylogenetic footprinting
  • miRAlign: a tool for prediction of homologous microRNAs.