#Co-first authors; *Co-corresponding authors; Yang Lab member names are bolded.

36Shen F#, He H#, Huang X, Deng Y, Yang X. Insights into the convergent evolution of fructan biosynthesis in angiosperms from the highly characteristic chicory genome. New Phytologist. 2023. Full article link.

35Kuang Z#, Zhao Y#, Yang X. Plant microRNA identification and annotation using deep sequencing data. Methods in Molecular Biology. 2023. Full article link.

34Guo Z, Kuang Z, Deng Y, Li L*, Yang X*. Identification of species-specific microRNAs provides insights into dynamic evolution of microRNAs in plants. International Journal of Molecular Sciences. 2023. Full article link.


33Guo Z, Kuang Z, Tao Y, Wang H, Wan M, Hao C,Shen F, Yang X*, Li L*. Miniature inverted-repeat transposable elements drive rapid microRNA diversification in angiosperms. Molecular Biology and Evolution. 2022. Full article link.

32Yang X*,Unver T, Zhang X, Li L. Editorial: Regulatory roles and mechanisms of microRNAs in plant development, evolution, and adaptation. Frontiers in Plant Science. 2022. Full article link.

31Guo Z#, Li B#,Du J#, Shen F, Zhao Y, Deng Y, Kuang Z, Tao Y, Wan M, Lu X, Wang D, Wang Y, Han Y, Wei J, Li L, Guo X*, Zhao C*, Yang X*. LettuceGDB: the community database for lettuce genetics and omics. Plant Communications. 2022. Full article link.

30Deng Y#,Zhang H#, Wang H, Xing G, Lei B, Kuang Z, Zhao Y, Li C, Dai S, Yang X*, Wei J*, Zhang J*. The construction and exploration of a comprehensive microRNA centered regulatory network in foxtail millet (Setaria italica L.) Frontiers in Plant Science. 2022. Full article link.

29Du J, Li B, Lu X, Yang X*, Guo X*, Zhao C*. Quantitative phenotyping and evaluation for lettuce leaves of multiple semantic components. Plant Methods. 2022. Full article link.

28Guo Z#, Kuang Z#, Zhao Y#, Deng Y#, He H, Wan M, Tao Y, Wang D, Wei J, Li L*, Yang X*. PmiREN2.0: from data annotation to functional exploration of plant microRNAs. Nucleic Acids Research. Full article link.


27Deng Y#, Qin Y#, Yang P#, Du J#, Kuang Z, Zhao Y, Wang Y, Li D, Wei J, Guo X*, Li L*, Yang X*. Comprehensive annotation and functional exploration of microRNAs in lettuce. Frontiers in Plant Science. 2021. Full article link.

26Yang J, Guo Z, Wang W, Cao X*, Yang X*. Genome-Wide Characterization of SPL Gene Family in Codonopsis pilosula Reveals the Functions of CpSPL2 and CpSPL10 in Promoting the Accumulation of Secondary Metabolites and Growth of C. pilosula Hairy Root. Genes (Basel). 2021. Full article link.

25Du J, Fan J, Wang C, Lu X, Zhang Y, Wen W, Liao S, Yang X*, Guo X*, Zhao C*. Greenhouse-based vegetable high-throughput phenotyping platform and trait evaluation for large-scale lettuces.Computers and Electronics in Agriculture.. 2021. Full article link.

24Zhao Y# , Kuang Z#, Wang Y, Li L*, Yang X*. MicroRNA annotation in plants: current status and challenges. Briefings in Bioinformatics.. 2021. Full article link.

23Yang X*, Fishilevich E, German MA, Gandra P, McEwan ER, Billion A, Knorr E, Vilcinskas A, Narva KE*. Elucidation of the microRNA Transcriptome in Western Corn Rootworm Reveals Its Dynamic and Evolutionary Complexity. Genomics Proteomics Bioinformatics. 2021. Full article link.

22Yin X, Romero-Campero FJ, de Los Reyes P, Yan P, Yang J, Tian G, Yang X, Mo X, Zhao S, Calonje M, Zhou Y. H2AK121ub in Arabidopsis associates with a less accessible chromatin state at transcriptional regulation hotspots. Nature Communications.. 2021. Full article link.


21Du J, Lu X, Fan J, Qin Y, Yang X*, Guo X*. Image-Based High-Throughput Detection and Phenotype Evaluation Method for Multiple Lettuce Varieties. Frontiers in Plant Science.. 2020. Full article link.

20Fromm B, Keller A, Yang X, Friedlander MR, Peterson KJ, Griffiths-Jones S. Quo vadis microRNAs? Trends in Genetics.. 2020. Full article link.

19Yang J, Yang X, Kuang Z, Li B, Lu X, Cao X, Kang J. Selection of suitable reference genes for qRT-PCR expression analysis of Codonopsis pilosula under different experimental conditions. Molecular Biology Reports.. 2020. Full article link.

18Yang J, Yang X, Li B, Lu X, Kang J, Cao X. Establishment of in vitro culture system for Codonopsis pilosula transgenic hairy roots.3 Biotech. . 2020. Full article link.

17Wang Y#, Kuang Z#, Li L*, Yang X*. A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants.JoVE. 2020. Full article link.

16Guo Z#, Kuang Z#, Wang Y#, Zhao Y#, Tao Y, Cheng C, Yang J, Lu X, Hao C, Wang T, Cao X, Wei J, Li L*, and Yang X*. PmiREN: a comprehensive encyclopedia of plant miRNAs.Nucleic Acids Research.. 2020. Full article link.

15杨攀, 杨诗雯, 李磊, 杨效曾. 生菜研究进展综述.现代园艺. 2020. Full article link.


14Kuang Z#, Wang Y#, Li L*, Yang X*. miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.Bioinformatics. 2019. Full article link.

2017 and Before

13 Sidorenko LV, Lee TF, Woosley A, Moskal WA, Bevan SA, Merlo PAO, Walsh TA, Wang X, Weaver S, Glancy TP, Wang P, Yang X, Sriram S, Meyers BC. GC-rich coding sequences reduce transposon-like, small RNA-mediated transgene silencing. Nature Plants.. 2017. Full article link.

12 Chennareddy S, Cicak T, Clark L, Russell S, Skokut M, Beringer J, Yang X, Jia Y, Gupta M. Expression of a novel bi-directional Brassica napus promoter in soybean.Transgenic Research. 2017. Full article link.

11 Su C, Yang X, Gao S, Tang Y, Zhao C, Li L. Identification and characterization of a subset of microRNAs in wheat (Triticum aestivum L.).Genomics.2014. Full article link.

10 Yang X, Li L. Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. The Role of Bioinformatics in Agriculture. 2014. Full article link.

09Aryal R, Yang X, Yu Q, Sunkar R, Li L, Ming R. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya.BMC Genomics.2012. Full article link.

08Yang X#, Zhang H#, Li L. Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis.The Plant Journal.2012. Full article link.

07Yang X, Li L. Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data.Biology (Basel).2012. Full article link.

06Yang X,Li L. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants.Bioinformatics. 2011. Full article link.

05Yang X,Zhang H, Li L. Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data. Genomics. 2011. Full article link.

04Zhang H, He H, Wang X, Wang X, Yang X, Li L, Deng XW. Genome-wide mapping of the HY5-mediated gene networks in Arabidopsis that involve both transcriptional and post-transcriptional regulation.The Plant Journal.2011. Full article link.

03Wu N, Yang X, Li L. Identification of Feed Forward Loops Composed of MicroRNAs and Transcription Factors in Arabidopsis.Journal of Biochemistry and Molecular Biology in the Post Genomic Era. 2011.

02He H, Zhang H, Wang X, Wu N, Yang X, Chen R, Li Y, Deng XW, Li L. Development of a versatile, target-oriented tiling microarray assay for measuring allele-specific gene expression.Genomics.2010. Full article link.

01Wang X, Yu Z, Yang X, Deng XW, Li L. Transcriptionally active gene fragments derived from potentially fast-evolving donor genes in the rice genome.Bioinformatics.2009. Full article link.