1、参与构建了华大基因第一个转录组测序标准分析流程，完成了一系列基于 RNA-seq 的转录组数据分析项目；
2、开发新的转录组学生物信息分析方法，工具和流程。包括已经发表的 SOAPsplice 和 SOAPfusion 等分析工具，以及内部使用未发表的 RNA 编辑检测、等位基因不平衡性表达、基于 RNA-seq的 eQTL mapping、长非编码 RNA 鉴定等方法和流程；
3、开发了一套基于全基因组测序和 RNA-seq测序鉴定 RNA 编辑的方法，并首次分析了人类全基因组 RNA 编辑的特点。以并列第一作者在 Nature Biotechnology 上发表文章。
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2. Li H, Peng Z, Yang X, et al. Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels[J]. Nature Genetics, 2013, 45(1): 43-50.
3. Fu J, Cheng Y, Linghu J, et al. RNA sequencing reveals the complex regulatory network in the maize kernel[J]. Nature communications, 2013, 4.
4. Wu J, Zhang W, Huang S, et al. SOAPfusion: a robust and effective computational fusion discovery tool for RNA-seq reads[J]. Bioinformatics, 2013: btt522.
5. Peng X, Sova P, Green R R, et al. Deep sequencing of HIV-infected cells: insights into nascent transcription and host-directed therapy[J]. Journal of virology, 2014, 88(16): 8768-8782.
6. Wu S, Chen J, Dong P, et al. Global gene expression profiling identifies ALDH2, CCNE1 and SMAD3 as potential prognostic markers in upper tract urothelial carcinoma[J]. BMC cancer, 2014, 14(1): 1.
7. Zhang Z, Peng Z Y, Yi K, et al. Identification of representative genes of the central nervous system of the locust, Locusta migratoria manilensis by deep sequencing[J]. Journal of insect science, 2012, 12(1): 86.
8. Xue J, Bao Y Y, Li B, et al. Transcriptome analysis of the brown planthopper Nilaparvata lugens[J]. PloS one, 2010, 5(12): e14233.
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