|Director, Bioinformatics GPB Home Area|
|Professor, Microbiology, Immunology & Molecular Genetics|
|Member, Gene Regulation GPB Home Area, Genetics & Genomics GPB Home Area|
The long-term goal of our research is to elucidate how genomic and environmental variation of RNA regulatory networks impacts phenotypic traits and diseases. We are a hybrid computational and experimental lab. We combine genomic, bioinformatic, molecular, and network approaches to study mRNA processing and post-transcriptional gene regulation in mammalian cells. We develop novel computational and statistical methods for analysis of massive genome and transcriptome data. We integrate computational studies with high-throughput and experimental research to systematically investigate the variation and dynamics of RNA regulatory networks between species, within human populations, and in response to developmental and disease signals.
Molinie Benoit, Wang Jinkai, Lim Kok Seong, Hillebrand Roman, Lu Zhi-Xiang, Van Wittenberghe Nicholas, Howard Benjamin D, Daneshvar Kaveh, Mullen Alan C, Dedon Peter, Xing Yi, Giallourakis Cosmas C m(6)A-LAIC-seq reveals the census and complexity of the m(6)A epitranscriptome. Nature methods. 2016; 13(8): 692-8.
Shen Shihao, Wang Yuanyuan, Wang Chengyang, Wu Ying Nian, Xing Yi SURVIV for survival analysis of mRNA isoform variation. Nature communications. 2016; 7(8): 11548.
Lin Lan, Jiang Peng, Park Juw Won, Wang Jinkai, Lu Zhi-Xiang, Lam Maggie P Y, Ping Peipei, Xing Yi The contribution of Alu exons to the human proteome. Genome biology. 2016; 17: 15.
Batista Pedro J, Molinie Benoit, Wang Jinkai, Qu Kun, Zhang Jiajing, Li Lingjie, Bouley Donna M, Lujan Ernesto, Haddad Bahareh, Daneshvar Kaveh, Carter Ava C, Flynn Ryan A, Zhou Chan, Lim Kok-Seong, Dedon Peter, Wernig Marius, Mullen Alan C, Xing Yi, Giallourakis Cosmas C, Chang Howard Y m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells. Cell stem cell. 2014; 15(6): 707-19.
Shen Shihao, Park Juw Won, Lu Zhi-xiang, Lin Lan, Henry Michael D, Wu Ying Nian, Zhou Qing, Xing Yi rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data. Proceedings of the National Academy of Sciences of the United States of America. 2014; 111(51): E5593-601.
Guo Rui, Zheng Lijuan, Park Juw Won, Lv Ruitu, Chen Hao, Jiao Fangfang, Xu Wenqi, Mu Shirong, Wen Hong, Qiu Jinsong, Wang Zhentian, Yang Pengyuan, Wu Feizhen, Hui Jingyi, Fu Xiangdong, Shi Xiaobing, Shi Yujiang Geno, Xing Yi, Lan Fei, Shi Yang BS69/ZMYND11 reads and connects histone H3.3 lysine 36 trimethylation-decorated chromatin to regulated pre-mRNA processing. Molecular cell. 2014; 56(2): 298-310.
Boudreau Ryan L, Jiang Peng, Gilmore Brian L, Spengler Ryan M, Tirabassi Rebecca, Nelson Jay A, Ross Christopher A, Xing Yi, Davidson Beverly L Transcriptome-wide discovery of microRNA binding sites in human brain. Neuron. 2014; 81(2): 294-305.
Zhao Keyan, Lu Zhi-xiang, Park Juw Won, Zhou Qing, Xing Yi GLiMMPS: robust statistical model for regulatory variation of alternative splicing using RNA-seq data. Genome biology. 2013; 14(7): R74.
Shen Shihao, Lin Lan, Cai James J, Jiang Peng, Kenkel Elizabeth J, Stroik Mallory R, Sato Seiko, Davidson Beverly L, Xing Yi Widespread establishment and regulatory impact of Alu exons in human genes. Proceedings of the National Academy of Sciences of the United States of America. 2011; 108(7): 2837-42.