- Assistant Professor of Biology
- Email: firstname.lastname@example.org
- Office: (434) 982-5481
- Lab: (434) 982-5774
- Office: 214 PLSB
- B.A., Peking University, 1997
- Ph.D., Michigan State University, 2003
The long-term research interest of my laboratory is to understand how gene expression is regulated in response to internal signals and external stimuli. We use combined high throughput experimental and bioinformatic approaches to address this question at the genome scale in model plant systems. We have been using genomic tiling microarrays and next-generation sequencing technologies to measure a suit of molecular parameters associated with global transcriptional regulation, including profiles of mRNA and non-coding RNAs, epigenetic markings and genome architecture. Results from these experimental approaches entail a hierarchy of information that is processed in living cells through complex regulatory networks. We integrate these experimental data with computational modeling to identify the underlying transcriptional regulatory networks that define biological processes such as endosperm development, hybrid vigor, and phenotypic variation between closely related species. Our results provide insights at the genome level to the u nderstanding of these processes that are important to meet the global challenges of changing climate and ever-increasing demand for food and energy.
For more information about research interests, visit my lab website.
Yang X, Li L.(2012) Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. Biology.1:297-310
Yang X, Zhang H, Li L.(2012) Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.Plant J.70(3):421-431
Wu N, Yang X, Li L.(2011) Identification of feed forward loops composed of microRNAs and transcription factors in Arabidopsis.Journal of Biochemistry and Molecular Biology in the Post Genomic Era.1:79-86
Yang X, Li L.(2011) miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics.27(18):2614-2615
Yang X, Zhang H, Li L.(2011) Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data. Genomics.98(1):40-46.
Zhang H, He H, Wang X, Wang X, Yang X, Li L*, Deng XW.(2011) Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation. Plant J.65(3):346-58. *Co-corresponding authors.
He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW, Li L.(2010) Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression. Genomics.96(5):308-315
Wang X, Yu Z, Yang X, Deng XW, Li L. (2009) Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome. Bioinformatics. 25:1215-1218.
Peng ZY, Zhang H, Liu T, Dzikiewicz KM, Li S, Wang X, Hu G, Zhu Z, Wei X, Zhu QH, Sun Z, Ge S, Ma L, Li L*, Deng XW* (2009)Characterization of the genome expression trends in the heading-stage panicle of six rice lineages. Genomics.93:169-178. *Co-corresponding authors.
Zhang HY, He H, Chen LB, Li L, Liang MZ, Wang XF, Liu XG, He GM, Chen RS, Ma LG, and Deng XW (2008) A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol Plant. 1,720-731.
Li L, He H, Zhang J, Wang X, Bai S, Stolc V, Tongprasit W, Young ND, Yu O, Deng XW (2008) Transcriptional analysis of highly syntenic regions between Medicago truncatula and Glycine max using tiling microarrays. Genome Biol.9,R57.