Xiaowo Wang, Ph.D.
Associate Professor of Bioinformatics
Department of Automation, Ministry of Education Key Laboratory of Bioinformatics, Center for Synthetic and Systems Biology, Tsinghua University, Beijing 100084, China
Bioinformatics Division, Tsinghua National Laboratory for Information Science and Technology, Beijing 100084, China
Phone:86-10-6279-4294 ext.808
Fax:86-10-6278-3552
Email:xwwang@tsinghua.edu.cn


Education background

2003.9-2008.7  Ph.D. of Bioinformatics, Tsinghua University, China
1999.9-2003.7  Bachelor of Engineering, Tsinghua University, China

Experience

2016.01-present, Associate Professor (Tenure), Department of Automation, Tsinghua University
2011.12-2015.12, Associate Professor, Department of Automation, Tsinghua University
2012.03-2013.03, Tang Distinguished Scholar, QB3-UC Berkeley
2008.7-2011.11, Lecturer, Department of Automation, Tsinghua University
2007.09-2008.03  Visiting student, Michael Q. Zhang Lab., CSHL, USA

Concurrent Academic

Bioinformatics
Bio-omics Data Mining
Pattern recognition and machine learning: Methods and Application
Design principle of synthetic biological systems

Social service

Director, Youth Committee of Chinese Association of Biotechnology
Secretary-general, Committee of Bioinformatics and Artificial Life, Chinese Association of Artificial Intelligence
NSFC reviewer
Reviewer of Nature Biotechnology, PNAS, Genome Biolgy, Bioinformatics、PLoS Computational Biology, etc.

Honors And Awards

National Science fund for Excellent Young Scholars, National Science foundation of China (2013)
New Century Excellent Talent Award, Ministry of Education of China (2013)
UC Berkeley’s Tang Distinguished Scholar Fellowship (2012)
National Excellent Doctoral Dissertation, China (2010)
National Education Award, China (the 2nd Class) (2009) (Shared with Prof. Zhang XG, Prof. Li S., Prof. Li YD., Prof. Jiang R.)
Beijing Teaching Achievement Award (the 1st Class) (2008) (Shared with Prof. Zhang XG, Prof. Li S., Prof. Li YD., Prof. Jiang R.)

Academic Achievement

1.Chao He?, Guipeng Li?, Diekidel M. Nadhir, Yang Chen* , Xiaowo Wang,*  and Michael Q. Zhang*, Advances in computational ChIA-PET data analysis, Quantitative Biology 2016, 4(3): 217–225
2.Lei Wei,Ye Yuan, Xiaowo Wang*,Challenges in large-scale synthetic gene circuits design,Chinese Journal of Biotechnology,2017,33(3):372-385 (in Chinese)
3.Zhe Cao#, Chang Liu#, Jianwei Xu#, Lei You, Chunyou Wang, Wenhui Lou, Bei Sun, Yi Miao, Xubao Liu, Xiaowo Wang*, Taiping Zhang*, Yupei Zhao*, Plasma microRNA panels to diagnose pancreatic cancer: Results from a multicenter study, Oncotarget, 2016, 7(27):41575-41583
4.Ye Yuan, Xinying Ren, Zhen Xie, Xiaowo Wang*, A quantitative understanding of microRNA-mediated competing endogenous RNA regulation, Quantitative Biology 4 (1), 47-57
5.Chao He, Michael Q. Zhang*, Xiaowo Wang*, MICC: an R package for identifying chromatin interactions from ChIA-PET data, Bioinformatics, 2015, 31(23): 3832-4
6.Honglei Liu, Zheng Wei, Antonia Dominguez, Yanda Li, Xiaowo Wang*, Lei S. Qi*, CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation, Bioinformatics, 2015, 31(22):3676-8
7.Yaru Liang#, Chang Liu#, Zhuoran Wang, Qiongye Dong, Xiaowo Wang *, Zhao Wang*. Meta-analytic Insights into the Effects of Different Anti-aging Drugs on Survival Curves of Caenorhabditis elegans. SCIENTIA SINICA Vitae, 2015, 45(5): 479-487 (in Chinese)
8.Ye Yuan, Bing Liu, Peng Xie, Michael Q. Zhang, Yanda Li, Zhen Xie*, Xiaowo Wang*, Model-guided quantitative analysis of microRNA-mediated regulation on competing endogenous RNAs using a synthetic gene circuit, Proc Natl Acad Sci U S A, 2015, 112(10):3158-63
9.Honglei Liu, Yanda Li, Xiaowo Wang*, OP-Synthetic: identification of optimal genetic manipulations for the overproduction of native and non-native metabolites, Quantitative Biology 2014, 2(3): 100?109
10.Chao He, Xiaowo Wang*, Michael Q. Zhang*, Nucleosome eviction and multiple co-factor binding predict estrogen-receptor-alphaassociated long-range interactions, Nucleic Acid Research, 2014, 42(11):6935-44
11.Peng Xie, Yu Liu, Yan-da Li, Michael Zhang* and Xiaowo Wang*, MIROR: a method for cell-type specific microRNA occupancy rate prediction, Mol. BioSyst. 2014, 10 (6), 1377 - 1384
12.YingXue Li, XueNing Liu, Xiaowo Wang, XueGong Zhang, Sequence signatures of genes with accompanying antisense transcripts in Saccharomyces cerevisiae, Science China Life Sciences, 2014 Jan;57(1):52-58
13.Yong Chen, Yunfeng Ding, Yi Yang, Jinhai Yu, Guiing Liu, Xumin Wang, Shuyan Zhang, Dan Yu, Lai Song, Hangxiao Zhang, Congyan Zhang, Linhe Huo, Chaoxing Huo, Yang Wang, Yalan Du, Huina Zhang, PengZhang, Huimin Na, Shimeng Xu, Yaxin Zhu, Zhensheng Xie, Tong He, Yue Zhang, Guoliang Wang, Zhonghua Fan, Honglei Liu, Xiaowo Wang, Xuegong Zhang, Michael Q. Zhang, Yanda Li, Alexander Steinbuchel,Toyoshi Fujimoto, Simon Cichello, Jun Yu, Pingsheng Liu, Integrated omics study delineates the dynamics of lipid droplets in Rhodococcus opacus PD630, Nucleic Acids Research, 2014, 42(2):1052-64
14.Matthew H Larson, Luke A Gilbert, Xiaowo Wang, Wendell A Lim, Jonathan S Weissman & Lei S Qi, CRISPR interference (CRISPRi) for sequence-specific control of gene expression, Nature Protocols, 2013; 8, 2180?2196
15.Ruijuan Li, Weilong Guo, Jin Gu, Michael Q. Zhang, Xiaowo Wang*, Chromatin state and microRNA determine different gene expression dynamics responsive to TNF stimulation, Genomics, 2012 ;100(5):297-302
16.Ozlem Aksoy, Agustin Chicas, Tianying Zeng, Zhen Zhao, Mila McCurach, Xiaowo Wang, Scott Lowe, The atypical E2F family member E2F7 couples the p53 and Rb pathways during cellular senescence, Genes Dev.2012; 26(14):1546-57
17.Agustin Chicas#, Avnish Kapoor#, Xiaowo Wang#, Ozlem Aksoy, Adam G. Evertts, Michael Q. Zhang, Benjamin A. Garcia, Emily Bernstein*, Scott Lowe*, H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence, Proc Natl Acad Sci U S A. 2012 ;109(23):8971-6 (#equally contributed)
18.Ratnakumar K, Duarte LF, Leroy G, Hasson D, Smeets D, Vardabasso C, Bonisch 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.
19.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
20.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
21.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.
22.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
23.Xi Wang, Xiaowo Wang, Likun Wang, Zhixing Feng, Xuegong Zhang, A Review on The Processing and Analysis of Next-generation RNA-seq Data, Progress in Biochemistry and Biophysics, 37(8):834-846, 2010
24.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
25.Tingting Li, Xueya Zhou, Xiaowo Wang, Dahai Zhu, Yong Zhang, Identification and characterization of human snoRNA core promoters, Genomics, 96(1):50-6, 2010
26.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
27.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
28.Xiaowo Wang , Jin Gu, Michael Q. Zhang and Yanda Li., Identification of phylogenetically conserved microRNA cis-regulatory elements across 12 Drosophila species, Bioinformatics, 15;24(2):165-71,2008
29.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
30.Xiaowo Wang , Xuegong Zhang, Yanda Li, Complicated evolutionary patterns of miRNAs in vertebrates, Sci China Ser C-Life Sci, 51(6):552-9 2008
31.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
32.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, 2007
33.Xiaowo Wang, Jing Zhang, Fei Li , Jin Gu , Tao He , Xuegong Zhang and Yanda Li, MicroRNA identification based on sequence and structure alignment. Bioinformatics, 21 (18): 3610-4, 2005


Courses

Fundamental Pattern Recognition (Undergraduate) (2017-present)
Interdisciplinary training – synthetic biology (Undergraduate) (2012-present)
Introductory Computational Molecular Biology (graduate) (2009-present)
Elements of Information Theory (graduate) (2010-2016)