研究方向为生物信息学和进化基因组学，主要研究对象为陆地植物、药用植物和观赏植物，利用多组学大数据针对（1）植物从水生环境向陆生环境的登陆；（2）被子植物的起源和早期分化；（3）药用植物代谢通路解析与演化；（4）花器官建成的网络调控等方向开展研究工作。致力于用基因组学数据来研究陆地植物类群间的系统发育关系、基因组进化和结构变异、植物代谢与观赏特征的演化，希望通过对基因组数据的分析，建立与宏观表型特征之间的联系，发掘表型背后的分子机制。

以第一作者或通讯作者（含共同）在Cell Genomics、Nature Communications、Nature Genetics、The Innovation、Trends in Plant Science、The Plant Journal、Plant Communications、Plant Biotechnology Journal、Plant Physiology、Engineering等期刊发表研究论文40余篇，详细信息请见ORCID: 0000-0002-7128-9935。

代表性成果

科研论文：（共同第一作者^#，通讯作者*）

1.     Xue JY*^,#, Yang CA^#, Hu S, Fan HY, Zhang YM, Shao ZQ, Li L, Wang S, Wei T, Dong S, Liu Y, Li Z*, Van de Peer Y*. 2025. Evolution of protein domains and protein domain combinations provides insights into the origin and diversification of land plants. Cell Genomics ACCEPTED.

2.     Xue JY^#, Liu SJ ^#, Wang J^#, Huang XC, Xu Z, Fang X*, Li Z*, Van de Peer Y*. 2025. Multi-Omics Roadmap to Plant-Derived Medicines. Engineering https://doi.org/10.1016/j.eng.2025.10.019.

3.     Dong S^#, Wang S^#, Li L^#, Yu J^#, Zhang Y^#, Xue JY^#, Chen H, Ma J, Zeng Y, Cai Y, Huang W, Zhou X, Wu J, Li J, Yao Y, Hu R, Zhao T, Villarreal A JC, Dirick L, Liu L, Ignatov M, Jin M, Ruan J, He Y, Wang H, Xu B, Rozzi R, Wegrzyn J, Stevenson DW, Renzaglia KS, Chen H, Zhang L, Zhang S, Mackenzie R, Moreno JE, Melkonian M, Wei T, Gu Y, Xu X, Rensing SA, Huang J, Long M, Goffinet B, Bowman JL*, Van de Peer Y*, Liu H*, Liu Y*. 2025. Bryophytes hold a larger gene family space than vascular plants. Nature Genetics 57(10):2562–2569.

4.     Hu SY, Shi G, Yang CA, Van de Peer Y*, Li Z*, Xue JY*.2025. Comprehensive sampling from mitochondrial genomes substantiates the Neoproterozoic origin of land plants. Plant Communications 6(11), 101497.

5.     Wu JY, Zhou GC, Li Z*, Xue JY*. 2025. Tuning Plant Defenses in a Changing World. Trends in Plant Science. 30(10):1069-1071.

6.     Zhou X^#, Fan HY^#, Feng XY^#, Ruan Z^#, Yuan J, Han Q, He Z, You Y, Chao H; Chen M, Shao ZQ*, Xue JY*, Chen D*. 2025. PGCP: A Comprehensive Database of Plant Genomes for Comparative Phylogenomics. Plant Biotechnology Journal. 23(7):2928-2930.

7.     Guo Z^#, Guo JF^#, Wei ZY^#, Zhang RG, McMahan S, Nie S, Yan XM, Zhou SS, Yun QZ, Wu JY, Ge J, Yang Y*, Xue JY*, Mao JF*. 2025. Near-gapless telomere-to-telomere reference nuclear genome and variable mitochondrial genome of Amborella trichopoda. Journal of Genetics and Genomics. 52(9):1151-1154.

8.     Zhang YM^#, Wei ZY^#, Yang CA, Feng XY, Wang Y, Li SX, Sun XQ*, Shao ZQ*, Xue JY*. 2025. A telomere-to-telomere genome assembly for greater yam (Dioscorea alata). Plant Communications. 6, 101326.

9.     Liu SJ^#, Liu Z^#, Shao BY, Li T, Zhu X, Wang R, Shi L*, Xu S*, Van de Peer Y*, Xue JY*. 2025. Deciphering the biosynthetic pathway of triterpene saponins in Prunella vulgaris. The Plant Journal. 121(2): e17220.

10.  Xu S^#, Chen R^#, Zhang X^#, Wu Y^#, Yang L^#, Sun Z, Zhu Z, Song A, Wu Z, Li T, Jin B, Niu S, Huang XC, Liu SJ, Yang CA, Jia G, He Y, Du F, Chen M, Chen F, Wang W, Sun H, Fu Y, Liao W, Pei H, Wu X, Zheng S, Xue JY*, Ning G*, Ming R*, Teng N*. 2024. The evolutionary tale of lilies: Giant genomes derived from transposon insertions and polyploidization. The Innovation. 5(6): 100726.

11.  Huang XC^#, Tang H^#, Wei X^#, He Y, Hu S, Wu JY, Xu D, Qiao F*, Xue JY*, Zhao Y*. 2024. The gradual establishment of complex coumarin biosynthetic pathway in Apiaceae. Nature Communications. 15, 6864.

12.  Zhu S^#, Wei XF ^#, Lu YX^#, Zhang DW, Wang ZF, Ge J, Li SL, Song YF, Yang Y, Yi XG, Zhang M, Xue JY*, Duan YF*. 2024. The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants. Horticulture Research. 11(8):uhae166.

13.  Yang CA^#, Hu SY^#, Ge J, Wang H, Wang Y*, Gu C*, Xue JY*. 2024. Frequent polyploidization events in Hibiscus shaped its karyotype and species diversity. Journal of Genetics and Genomics. 52(6), 864-867.

14.  Li Q^#, Dai Y^#, Huang XC^#, Sun L, Wang K, Guo X, Xu D, Wan D, An L, Wang Z, Tang H, Qi Q, Zeng H, Qin M*, Xue JY*, Zhao Y*. 2024. The chromosome-scale assembly of the Notopterygium incisum genome provides insight into the structural diversity of coumarins. Acta Pharmaceutica Sinica B. 14(8), 3760-3773.

15.  Zhao W^#, Wu J^#, Tian M, Xu S, Hu S, Wei Z, Lin G, Tang L, Wang R, Feng B, Wang B, Lyu H, Paetz C, Feng X, Xue JY*, Li P*, Chen Y*. 2024. Characterization of O-Methyltransferases in the Biosynthesis of Phenylphenalenone Phytoalexins Based on the Telomere-to-Telomere Gap-less Genome of Musella lasiocarpa. Horticulture Research. 11(4), uhae042

16.  Xue JY^#, Fan HY ^#, Zeng Z ^#, Zhou YH, Hu SY, Li SX, Cheng YJ, Meng XR, Chen F*, Shao ZQ*, Van de Peer Y*. 2023. Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato. Horticulture Research. 10(9):uhad147.

17.  Xue JY^#, Li Z^#, Hu SY^#, Kao SM^#, Zhao T^#, Wang JY^#, Wang Y, Chen M, Qiu Y, Fan HY, Liu Y*, Shao ZQ*, Van de Peer Y*. 2023. The Saururus chinensis genome provides insights into the evolution of pollination strategies and herbaceousness in magnoliids. The Plant Journal. 113(5):1021-1034.

18.  Shao ZQ^#, Xue JY^#, Wang Q, Wang B, Chen JQ*. 2019. Revisiting the Origin of Plant NBS-LRR Genes. Trends in Plant Science. 24(1):9-12.

19.  Shao ZQ^#, Xue JY^#, Wu P, Zhang YM, Wu Y, Hang YY, Wang B*, Chen JQ*. 2016. Large-Scale Analyses of Angiosperm Nucleotide-Binding Site-Leucine-Rich Repeat Genes Reveal Three Anciently Diverged Classes with Distinct Evolutionary Patterns. Plant Physiology. 170(4): 2095-2109.

20.  Amborella Genome Project. 2013. The Amborella Genome and the Evolution of Flowering Plants. Science 342 (6165): p. 1241089

专著:

1.       Chen F & Xue JY, Eds. 2023. Genomic Analyses and New Breeding Technologies for the Enhancement of Horticultural Plants.

2.       Shao ZQ, Xue JY, Takken FLW, Maekawa T, Nepal MP, Eds. 2020. Evolution and Functional Mechanisms of Plant Disease Resistance. Lausanne: Frontiers Media SA. doi: 10.3389/978-2-88966-199-2

3.     Liu Y, Wang B, Li L, Qiu YL, Xue JY. 2012. Conservative and dynamic evolution of mitochondrial genomes in early land plants. In: Bock R, Knoop V, eds. Genomics of Chloroplasts and Mitochondria. Netherlands: Springer. p. 159-174.

发明专利：

1.     薛佳宇、刘思杰。夏枯草细胞色素氧化酶CYP蛋白及其编码基因与应用。2025-2-14。中国。CN202410470331.5

2.     薛佳宇、周广灿、王元涛、张艳梅。抗癌、抗炎多肽Lunasin在哺乳动物细胞CHO-S中的表达、纯化方法。2020-3-31。中国。ZL201710417823.8

3.     周广灿、王宜磊、薛佳宇、李稳、陈晓、吴雨含。一种旱金莲调控芥酸合成基因及其应用。2020-06-30。中国。CN2019112017877

4.     薛佳宇、张艳梅、周广灿、雷照、石磊、吴婷婷、王智。6,7-二甲氧基-喹唑啉-4-胺衍生物、其制备方法及医药用途。2017-09-15。中国。ZL201510116327.x