Previously, my research mainly focused on developing new methods to analyze high-throughput genomic data, and using computational approaches to understand gene regulation. For example, we developed a microRNA prediction method to find distantly related microRNA homologs; proposed comparative genomic approaches to identify microRNA cis-regulatory elements; provided a high-resolution human gene core promoter prediction method by combining genetic and epigenetic features; and developed popular software used to analyze differentially expressed genes from RNA-seq experiments and a highly sensitive alignment algorithm to detect novo RNA splice junctions. I also collaborated closely with biologists to study the regulatory mechanisms of important biological processes like cellular senescence using integrative systems approaches.
I am currently drawn to the emerging field of synthetic biology, and welcome the opportunity provided by Tang Scholars program to work on synthetic and systems biology at UC Berkeley. Drawing on my knowledge in computational biology, I would like to design efficient and predictable synthetic circuits, and use synthetic biology approaches to analyze gene regulatory networks by perturbing natural systems or by building synthetic alternatives.
Impacts in China
Synthetic biology provides an opportunity to combine biology and engineering, to build new biological system with functions that address our needs, and gain a deeper understanding of how biological systems work. It shows great potential to provide new solutions to the energy, environment and health problems in the future. Synthetic biology is still in an early developmental stage in China. Taking the opportunity to study and work with the world’s leading synthetic biologists at UC Berkeley, I hope I can contribute to the development of the synthetic biology field in China.
Ratnakumar K, Duarte LF, Leroy G, Hasson D, Smeets D, Vardabasso C, Bönisch 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.
Lily Yan Wang, Panwen Wang, Mulin Jun Li, Jing Qin, Xiaowo Wang, Michael Q. Zhang, Junwen Wang, EpiRegNet: Constructing epigenetic regulatory network from high throughput gene expression data for humans, Epigenetics, Volume 6, Issue 12:1505-1512, 2011.
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.
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.
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.
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.
Xiaowo Wang, Zhenyu Xuan, Xiaoyue Zhao, Yanda Li, Michael Q. Zhang, High-resolution Human Core-promoter prediction with CoreBoost_HM, Genome Research,19: 266-275, 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 miRNAs 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.