1998.09 – 2002.06 于上海师范大学 生物教育专业攻读学士学位

2002.09 – 2005.06 于上海师范大学 水生生物学专业攻读硕士学位

2005.08 – 2009.12 于美国迈阿密大学 植物学专业攻读博士学位

2010.01 – 2013.05 就职于美国德克萨斯州立大学化学和生物化学系，担任博士后

2013.06 – 2014.06 就职于美国圣路易斯华盛顿大学基因组研究所，担任研究助理教授

2014.08 – 2015.07 就职于厦门大学 环境与生态学院，担任副教授

2015.08 – 至今 就职于厦门大学 环境与生态学院，担任教授

2026.04 - 至今 就职于宁夏大学生态环境学院 ， 担任教授

分子生态学、人工智能、生物的环境适应机制（利用组学和人工智能技术研究动植物对环境响应的分子机制）

1. 滨海湿地生态系统中关键物种的环境适应性机制的研究，中组部海外高层次人才引进计划青年计划，2015-2018，主持

2. 海洋青鱂鱼基因组结构其对盐度适应的分子机理的研究，国家自然科学基金面上项目，2017-2020，主持

3. 红树林生态系统适应性研究，厦门市杰出青年，厦门市，2018-2020，主持

4. 福建省科技特派员项目，福建省科技厅，2019-2020，主持

5. 闽三角城市群生态安全保障海岸带生态修复技术，科技部重点研发计划，2016-2020，参与

6. 通过调控RNA加工因子表达促进作物再生技术研究，国家重点研发计划"政府间国际科技创新合作"重点专项，2016-2019，参与

7. 创新引智基地，滨海湿地生态系统与全球变化学科创新引智基地，B20012，科技部/教育部，2019-2024，参与

8. 冷链物流新冠病毒羟基自由基快速绿色消杀的新技术设备，科技部，2022-2025，参与

9. 重点研发项目大型海藻重要经济性状遗传解析与复合性状良种培育之良种评价测试与示范推广课题，2023-2026，子课题负责人

一、英文图书章节

1. Shen Y, Garcia T, Walter RB. De novo Transcriptome Assembly and Gene Expression Analysis using RNA-Seq from Organisms Lacking Substantial Genomic Resources. Systems and Computational Biology - Molecular and Cellular Experimental Systems. ISBN 978-953-307-280-7

2. Lu Y, Shen Y, Warren WC, Walter RB. Next Generation Sequencing in Aquatic Models. Next Generation Sequencing - Advances, Applications and Challenges. InTech

二、英文期刊论文（代表性论文，共49篇）

1. Li HQ, Wang WL, Shen Y, Su JQ. Mangrove plastisphere as a hotspot for high-risk antibiotic resistance genes and pathogens. Environ Res. 2025;274:121282.

2. Zheng R, ..., Feng M*, Shen Y*. Sunlight-mediated environmental risks of tinidazole in seawater. J Hazard Mater. 2025;487:137217.

3. Yi Y, ..., Shen Y*. Genome-wide identification of the bZIP family in Kandelia obovata and its role in response to stress. BMC Plant Biol. 2025;25(1):161.

4. Li HQ, Wang WL, Shen Y, Su JQ. Vegetation, salinity, and tides drive nitrogen cycling in Mangrove plastispheres. Sci Rep. 2025;15(1):28792.

5. Qiao H, ..., Ye C*, Li QQ*, Shen Y*. Molecular mechanism of vivipary as revealed by the genomes of viviparous mangroves. Curr Biol. 2024;34(16):3707-3721.

6. Xu X, Hou C, Shen Y*. The complete mitochondrial genome of Kandelia obovata. Mitochondrial DNA B Resour. 2023;8(12):1440-1444.

7. Xu X#, Shen Y#, ..., Zhu X. A comparison of 25 complete chloroplast genomes between sister mangrove species. Front Plant Sci. 2023;13:1075353.

8. He S, ..., Zhang YY*, Shen Y*. Physiological and transcriptomic responses to cold waves of Kandelia obovata. Front Plant Sci. 2023;14:1069055.

9. Guo Z, ..., Shen Y*, Li QQ*, Zheng HL*. Genome-wide identification of aquaporins in mangrove plant Kandelia obovata. Plant Cell Environ. 2022;45(6):1698-1718.

10. Ni X, Shen Y*. Transgenerational Effects of Hexavalent Chromium on Marine Medaka. Biomolecules. 2021;11(2):138.

11. Li HQ, ..., Shen Y*, Su JQ*. Distinct patterns of abundant and rare subcommunities in paddy soil. Sci Total Environ. 2021;785:147298.

12. Zhao Y, ..., Zhang Y*, Shen Y*. Multi-omics analyses on Kandelia obovata. BMC Plant Biol. 2021;21(1):341.

13. Liang P, ..., Shen Y*. RNA-seq analyses of Marine Medaka reveals salinity responsive transcriptomes. Aquatic Toxicology. 2021;240:105970.

14. Liang P, ..., Shen Y*. Long-read sequencing and de novo genome assembly of marine medaka. BMC Genomics. 2020;21(1):640.

15. Fu H, ..., Shen Y, Li QQ*, Liang J*. Distinct genome-wide alternative polyadenylation in Thalassiosira pseudonana. Plant J. 2019;99(1):67-80.

16. Hong L, ..., Shen Y, Li QQ*. Transcriptome profiling during mangrove viviparity in response to abscisic acid. Sci Rep. 2018;8(1):770.

17. Wu M, ..., Shen Y*, Yang M*. Global transcriptomic analysis of zebrafish in response to three antidepressants. Aquat Toxicol. 2017;192:274-283.

18. Cui Z, Shen Y, ..., Zhang G. KANK1 inhibits cell growth by inducing apoptosis in malignant peripheral nerve sheath tumors. Sci Rep. 2017;7:40325.

19. Fu H, ..., Shen Y, ..., Li QQ. Genome-wide dynamics of alternative polyadenylation in rice. Genome Res. 2016;26:1753-1760.

20. Shen Y, ..., Warren WC, Walter RB. X. couchianus and X. hellerii genome models provide genomic variation insight. BMC Genomics. 2016;17:37.

21. Schartl M, Shen Y, ..., Warren WC. Whole Body Melanoma Transcriptome Response in Medaka. PLoS One. 2015;10:e0143057.

22. Badenhorst D, ..., Shen Y, ..., Valenzuela N. Physical Mapping and Refinement of the Painted Turtle Genome. Genome Biol Evol. 2015;7:2038-50.

23. Yang K, ..., Shen Y, ..., Walter RB. UVB-induced Gene Expression in the Skin of Xiphophorus maculatus. Comp Biochem Physiol C. 2014;163:86-94.

24. Garcia TI, ..., Shen Y, ..., Walter RB. Novel method for analysis of allele specific expression in triploid Oryzias latipes. PLoS One. 2014;9:6.

25. Schartl M*+, Walter RB*+, Shen Y, ..., Warren CW. The genome of the platyfish, Xiphophorus maculatus. Nature Genetics. 2013. (共同第一作者)

26. Pabuwal V, ..., Shen Y, ..., Walter RB. Transcriptomic analysis of cultured whale skin cells exposed to Cr(VI). Aquat Toxicol. 2013;134-135C:74-81.

27. Shen Y, ..., Walter RB. Alternative strategies for development of a reference transcriptome. Comp Biochem Physiol Part D. 2012;8:11-16.

28. Garcia T, Shen Y, ..., Walter RB. RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis. BMC Genomics. 2012;13:474.

29. Shen Y, ..., Walter RB. Identification of SNPs between Xiphophorus Lines and Species. Comp Biochem Physiol Part C. 2012;155:102-108.

30. Downs KP, Shen Y, ..., Walter RB. Characterization of telomeres and telomerase expression in Xiphophorus. Comp Biochem Physiol Part C. 2012;155:89-94.

31. Garcia T, Shen Y, ..., Walter RB. Effects of short read quality and quantity on a de novo vertebrate Transcriptome assembly. Comp Biochem Physiol Part C. 2012;155:95-101.

32. Zheng J, ..., Shen Y, ..., Li QQ. Ratio-based Analysis of Differential mRNA Processing using Arabidopsis Genomic Tiling Microarray. PLoS ONE. 2011;6:e14719.

33. Ji G, ..., Shen Y, ..., Li QQ. Classification-Based Prediction Models of Messenger RNA Polyadenylation Sites. J Theor Biol. 2010;265:287-96.

34. Shen Y, ..., Li QQ. Transcriptome Dynamics Through Alternative Polyadenylation in Plants. Genome Research. 2011;21:1478-1486.

35. Shen Y, ..., Li QQ. Genome level analysis of rice mRNA 3'-end processing signals. Nucleic Acids Research. 2008;36:3150-3161.

36. Shen Y, ..., Li QQ. Distinct genome-wide alternative polyadenylation in Thalassiosira pseudonana. Genetics. 2008;179:167-176.

37. Liang C, ..., Shen Y, Li QQ. Expressed sequence tags in Chlamydomonas reinhardtii. Genetics. 2008;179:83-93.

38. Ji G, ..., Shen Y, ..., Li QQ. Predictive modeling of plant messenger RNA polyadenylation sites. BMC Bioinformatics. 2007;7:43.

39. Ji G, ..., Shen Y, Li QQ. Modeling Plant mRNA Poly(A) sites. J Comput Theor Nanoscience. 2007;4:1365-1368.

40. Zhong X, ..., Shen Y, ..., Yang Z. Isolation and Analysis of a High Expression Promoter in Rice. Chinese J Biotechnology. 2007;23:836-840.

41. Shen Y, Chen DH. Effect of Different Light Cycle on Growth of Microcystis aeruginosa and Microcystis viridis. J Lake Sci. 2005;16:285-288.

42. Shen Y, ..., Yang ZN. Development of Genome-Wide DNA Polymorphism Database for Map-Based Cloning of Rice Genes. Plant Physiol. 2004;135:1198-1205.

2014-2015年 厦门大学环境与生态学学院菁英班（与中国科学院城市环境研究所合办）班主任

2015年至今 厦门大学环境与生态学学院国际化班班主任

2015-2024年 厦门大学环境与生态学学院教授委员会副主任

2016年至今 厦门大学环境与生态学学院学术委员会成员

2019年至今 担任《CABI Agriculture and Bioscience》杂志编辑

2021年 第一届海岸带生态系统与全球变化国际研讨会筹备委员会成员

2015年至今 《Nature Communication》、《Gene》、《Scientific Data》等杂志审稿人