2004年本科毕业于中国农业大学生物学院，2014年博士毕业于美国弗吉尼亚大学生物系。博士毕业后先后在美国陶氏化学和北京市农林科学院工作。2023年底到植物多样性与特色经济作物重点实验室工作。主要从事菊科植物和植物小RNA研究。发表学术论文40余篇，获批多项发明专利和软件著作权。主持国家自然基金委创新人才项目、面上项目和多项北京市及北京市农林科学院重点项目。国家人才计划入选者、北京市特聘专家。

主要研究领域

1. 植物microRNA（miRNA）鉴定及演化研究

植物miRNA是植物中一类重要的转录后调控因子，在生长发育和响应环境刺激等生命活动中扮演重要的角色。实验室关注利用生物大数据的方法精准鉴定和注释不同植物中miRNA、数据库构建、起源演化和功能研究。

2. 生菜、菊苣、橡胶草等菊科植物资源收集评价和挖掘利用

生菜、菊苣、橡胶草等菊科植物具有重要的经济价值。生菜是全球范围内重要的蔬菜，菊苣是果聚糖-菊粉-的重要来源，橡胶草被认为是一种理想的新型产胶植物。通过对这些植物全球范围内种质资源的收集评价，利用生物技术达到改良这些植物特定性状的目的，满足育种和产业需求。

3. 菊科植物多样性和适应性研究

菊科植物是被子植物中物种数量最丰富的科之一（约占被子植物总数10%），在全球范围内广泛分布，具有极好的适应性。通过基因组学等手段，实验室关注菊科植物物种丰富多样性和良好环境适应性的成因，以期为作物改良、物种保护、防范外来物种入侵等提供理论基础。

主持的科研项目

国家人才计划2022-2024（主持）

国家自然科学基金委面上项目植物miRNA及其靶基因研究2021-2024（主持）

北京市设施农业新种质创制和品种选育联合攻关项目生菜育种2021-2024（子课题主持）

北京市农林科学院杰出科学家培育计划植物miRNA进化研究2022-2026 （主持）

北京市农林科学院重点项目基因编辑II期2020-2022（主持）

北京市农林科学院重点项目基因编辑I期2018-2019 （主持）

北京市农林科学院重点项目精准育种技术体系开发2018 （主持）

北京市财政项目高通量测序平台构建2018（主持）

研究论文（注：*通讯作者；#第一作者）

2024

1. Zhao J, Guo Z, Yang X. sRNAminer, a swiss army knife in small RNA research. Science China Life Sciences.2024.

2023

2. Kuang Z, Zhao Y, Yang X*. The use of artificial intelligence to assist in the prediction of microRNAs in plants. Agriculture Communications. 2023.
3. Shen F#, Hu C#, Huang X, He H, Deng Y, Zhao J*, Yang X*. Advances in alternative splicing identification: integration of deep learning and pan-genomics studies. Frontiers in Plant Science. 2023.
4. Shen F#, Qin Y#, Wang R#, Huang X, Wang Y, Gao T, He J, Zhou Y, Jiao Y, Wei J*, Li L*, and Yang X*. Comparative Genomics Reveals a Unique Nitrogen-Carbon Balance System in Asteraceae. Nature Communications.2023.
5. Yu S#, Fan J#, Lu X, Wen W, Shao S, Liang D, Yang X*, Guo X*, Zhao C*. Deep learning models based on hyperspectral data and time-series phenotypes for predicting quality attributes in lettuces under water stress. Computers and Electronics in Agriculture. 2023.
6. Guo Z#, Wei J#, Xu Z, Lin C, Peng Y, Wang Q, Wang D, Yang X*, Xu K*. HollyGTD: an integrated database for holly (Aquifoliaceae) genome and taxonomy. Frontiers in Plant Science. 2023.
7. Shen 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.

2022

8. Guo 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. 2022.
9. Guo 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.
10. Yang 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.
11. Guo 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.
12. Deng 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.
13. Du 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.
14. Guo 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. 2022.

2021

15. Deng 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.
16. Yang 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.
17. Du 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.
18. Zhao Y# , Kuang Z#, Wang Y, Li L*, Yang X*. MicroRNA annotation in plants: current status and challenges. Briefings in Bioinformatics. 2021.
19. Yang 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.
20. Yin 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.

2020

21. Du 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.
22. Fromm B*, Keller A, Yang X, Friedlander MR, Peterson KJ, Griffiths-Jones S. Quo vadis microRNAs? Trends in Genetics. 2020.
23. Yang 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.
24. Yang 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.
25. Wang Y#, Kuang Z#, Li L*, Yang X*. A Bioinformatics Pipeline to Accurately and Efficiently Analyze the MicroRNA Transcriptomes in Plants.JoVE. 2020.
26. Guo 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.
27. 杨攀, 杨诗雯, 李磊, 杨效曾*. 生菜研究进展综述. 现代园艺. 2020.

2019及以前

28. Kuang Z#, Wang Y#, Li L*, Yang X*. miRDeep-P2: accurate and fast analysis of the microRNA transcriptome in plants.Bioinformatics. 2019.
29. 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.
30. 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.
31. 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.
32. Aryal 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.
33. Yang X#, Zhang H#, Li L*. Alternative mRNA processing increases the complexity of microRNA-based gene regulation in Arabidopsis. The Plant Journal. 2012.
34. Yang X, Li L*. Analyzing the microRNA Transcriptome in Plants Using Deep Sequencing Data. Biology (Basel). 2012.
35. Yang X, Li L*. miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants. Bioinformatics. 2011.
36. Yang X, Zhang H, Li L*. Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data. Genomics. 2011.
37. Zhang 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.
38. Wu 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.
39. He 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.
40. Wang 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.

发表专著（章节）

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

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

发明专利

1. 一种来源于生菜的叶绿体转运肽Lsa3084及其应用，中国，2022，ZL202210035813.9

2. Lsa25711转运肽在叶绿体遗传转化中的应用，中国，2022，ZL202210062843.9

3. 一种将目的蛋白定位于叶绿体的方法及其应用，中国，2022，ZL202210057679.2

4. 一种用于鉴定莴苣杂交种真实性的方法及其使用的KASP引物组合，中国，2021，ZL202110233141.5

5. Short/Small Hairpin RNA Molecules，国际专利，WO2019161449

6. Extension Sequences for RNA Inhibitory Molecules，国际专利，WO2020112736

软件著作权

1. 2018SR1090606，miRDeep-P2 软件

2. 2019SR0343185，Plant microRNA Encyclopedia软件[简称：PmiREN] V1.0

3. 2021SR0375359，miRDeep-AP软件

4. 2021SR1514924，Plant microRNA Encyclopedia平台[简称：PmiREN] V2.0

5. 2022SR0253720，Lettuce Genome Database平台[简称：LettuceGDB]