自2013年以来，已发表学术论文40余篇，其中以第一作者（共一）和通讯（共同通讯）身份在Nature Ecology and Evolution、Molecular Ecology Resources、Science Bulletin、Journal of Environmental Management、Ecological indicators、水生生物学报等期刊发表文章30余篇，部分论文如下：

2024年 (持续更新）

[1] Shen Yanjun, Zhou Xinxin, Zhang Yufeng, Zhang Jiaming, Li Qinghua, Chen Qiliang, Liu Zhihao, Li Yingwen, Cheng Ruli, Luo Yang*(2024). Important fish diversity maintenance status of the tributaries in a hotspot fish conservation area in the upper Yangtze River revealed by eDNA metabarcoding. Scientific Reports, 14, 24128. https://doi.org/10.1038/s41598-024-75176-9.

[2]张玉凤, 周鑫鑫，李清华, 张家铭, & 沈彦君* (2024). 基于eDNA的长江流域重庆段鱼类多样性格局研究. 水产学报, 接受.

[3]Cheng, R., Zhou, X., Zhang, Y., Li, Q., Zhang, J., Luo, Y., Chen, Q., Liu, Z., Li, Y., Shen, Y.,*(2024). eDNA reveals spatial homogenization of fish diversity in a mountain river affected by a reservoir cascade. Journal of Environmental Management, 361 (2024) 121248.

[4]Shen, Y., Zhou, X., Li, Q., Zhang, J., Zhang, Y., Dong X., Huang J., Chen, R., Luo, Y.*(2024). Spatiotemporal Dynamics of Plankton Communities in the Chongqing Section of the National Nature Reserve for Rare and Endemic Fishes in the Upper Yangtze River. Sustainability, 16,6732.

[5]Shen, Y., Zhang, Y.,  Zhou, X., Li, Q., Zhang, J., Chen, R., Zuo, Q.*(2024). Environmental DNA metabarcoding revealing the distinct responses of phytoplankton and zooplankton to cascade dams along a river-way. Ecological Indicators, 166,112545.

[6]罗杨, 杨鑫, 程如丽, 王梦, 李清华, 张玉凤, 李英文, 沈彦君* (2024). 基于eDNA的长江流域重庆段鱼类多样性格局研究. 水生态学杂志, https://doi.org/10.15928/j.1674-3075.202212260513.

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2023年

[1]程如丽, 罗杨, 张玉凤, 李清华, 刘智皓, 王梦, 张钰, 李英文, & 沈彦君* (2023). 基于环境DNA 技术的乌江干流梯级水电库区的鱼类多样性. 水产学报, 接受.

[2]Shen, Y., Li, Q., Cheng, R., Luo, Y., Zhang, Y., & Zuo, Q.*(2023). Mitochondrial genomic characterization of two endemic Chinese freshwater crabs of the genus Sinopotamon (Brachyura: Potamidae) and implications for biogeography analysis of Potamidae. Ecology and Evolution, 13(3), https://doi.org/10.1002/ece3.9858.

[3]Luo, Y., Zhang, Y., Cheng, R., Li, Q., Li, Y., & Shen, Y.*(2023). Genetic Diversity of Jinshaia sinensis (Cypriniformes, Balitoridae) Distributed Upstream of the Yangtze River. Fishes, 8(2),  https://doi.org/10.3390/fishes8020075.

[4]Cheng, R., Luo, Y., Li, Q., Zhang, Y., Liu, Z., Chen, Q., Li, Y., & Shen, Y.*(2023). Application of eDNA metabarcoding for monitoring the fish diversity of the Jiangjin to Fuling section of the upper reaches of the Yangtze River. Hydrobiologia. https://doi.org/10.1007/s10750-023-05297-1.

[5]Cheng, R., Luo, Y., Zhang, Y., Li, Q., Li, Y., & Shen, Y.*(2023). eDNA metabarcoding reveals differences in fish diversity and community structure in heterogeneous habitat areas shaped by cascade hydropower. Ecology and Evolution, https://doi.org/10.1002/ece3.10275.

[6]Shen, Y., Zhang, Y., Cheng, R., Wang, W., Duan, C., Liu, Z., Chen, Q., Li, Y., Wang, M., & Luo, Y.*(2023).Diversity and spatiotemporal dynamics of fish communities in the Chongqing section of the upper Yangtze River based on eDNA metabarcoding. Ecology and Evolution, https://doi.org/10.1002/ece3.10681.

2022年

[1]Zhang, Y., Wang, M., Cheng, R., Luo, Y., Li, Y., Liu, Z., Chen, Q., & Shen, Y.* (2022). Mitochondrial characteristics of Pseudohynobius flavomaculatus a protected salamander in China, and biogeographical implications for the family Hynobiidae (Amphibia, Caudata). Zoosystematics and Evolution, 98(2), 263-274.

[2]Chen, Q., Lian, X., Li, Y., Liu, Z., & Shen, Y.*(2022). Complete mitochondrial genome of Acrossocheilus yunnanensis (Cypriniformes: Cyprinidae: Acrossocheilus) and its phylogenetic analysis. Mitochondrial DNA Part B, 7(10), 1764-1765.

[3]Zuo, Q., Zhang, Z.*, & Shen, Y.*(2022). Novel mitochondrial gene rearrangements pattern in the millipede Polydesmus sp. GZCS- 2019 and phylogenetic analysis of the Myriapoda. Ecology and Evolution, 12(3),  e8764.

[4]王梦, 杨鑫, 王维, 段聪, 刘智皓, 陈启亮,李英文*, & 沈彦君* (2022). 基于 eDNA 技术的长江上游珍稀特有鱼类国家级自然保护区重庆段鱼类多样性研究. 水生生物学报, 46(1) 1-15.

2021年

[1]Yang, N., Li, Y., Liu, Z., Chen, Q., & Shen, Y.* (2021). Molecular phylogenetics and evolutionary history of Sinocyclocheilus (Cypriniformes: Cyprinidae) species within Barbinae in China. Environmental Biology of Fishes, 104(9), 1149-1162.

2020年

[1]Shen, Y., Yang, N., Liu, Z., Chen, Q., & Li, Y. (2020). Phylogenetic perspective on the relationships and evolutionary history of the Acipenseriformes. Genomics, 112(5), 3511-3517.

[2]Shen, Y., Wang, J., & Zhang, F. (2020). Complete mitochondrial genome of Parabotia bimaculata (Cypriniformes: Cobitidae: Botiinae), an endemic riverine loach in China and phylogenetic analysis for Botiinae. Thalassas: An International Journal of Marine Sciences, 36(2), 387-393.

[3]Yang, N., Li, Y., Liu, Z., Chen, Q., & Shen, Y.* (2020). The complete mitochondrial genome of Cobitis macrostigma (Cypriniformes: Cobitidae: Cobitinae) and a phylogenetic implication for its closely related species. Biologia, 75, 393-399.

2019年

[1]Shen, Y., Hubert, N., Huang, Y., Wang, X., Gan, X., Peng, Z., & He, S. (2019). DNA barcoding the ichthyofauna of the Yangtze River: Insights from the molecular inventory of a mega‐diverse temperate fauna. Molecular Ecology Resources, 19(5), 1278-1291.

[2]Wang, K.#, Shen, Y.#, Yang, Y.#, Gan, X.#, Liu, G., Hu, K., ... & He, S*. (2019). Morphology and genome of a snailfish from the Mariana Trench provide insights into deep-sea adaptation. Nature Ecology & Evolution, 3(5), 823-833.

[3]Li, Y., Li, C., Chen, Q., Liu, Z., & Shen, Y.*(2019). The mitochondrial genome for tadpole of Emei moustache toad (Leptobrachium boringii: Anura: Megophryidae) from the Southwest China and its phylogenetic analysis. Mitochondrial DNA Part B, 4(1), 265-266.

[4]Yang, N., Li, Y., Liu, Z., Chen, Q., & Shen, Y.* (2019). The complete mitochondrial genome of Silurus asotus (Siluriformes: Siluridae: Silurus) and its phylogenetic analysis. Mitochondrial DNA Part B, 4(2), 2377-2378.

[5]Zhang, F., & Shen, Y.* (2019). Characterization of the complete mitochondrial genome of Rhinogobius leavelli (Perciformes: Gobiidae: Gobionellinae) and its phylogenetic analysis for Gobionellinae. Biologia, 74, 493-499.

2017年

[1]Shen, Y., Dai, W., Gao, Z., Yan, G., Gan, X., & He, S. (2017). Molecular phylogeny and divergence time estimates using the mitochondrial genome for the hadal snailfish from the Mariana trench. Science Bulletin, 62(16), 1106-1108.

[2]Shen, Y., Kou, Q., Zhong, Z., Li, X., He, L., He, S., & Gan, X. (2017). The first complete mitogenome of the South China deep‐sea giant isopod Bathynomus sp.(Crustacea: Isopoda: Cirolanidae) allows insights into the early mitogenomic evolution of isopods. Ecology and Evolution, 7(6), 1869-1881.

2016年

[1]Shen, Y., Kang, J., Chen, W., & He, S. (2016). DNA barcoding for the identification of common economic aquatic products in Central China and its application for the supervision of the market trade. Food Control, 61, 79-91.

[2]Shen, Y., Guan, L., Wang, D., & Gan, X. (2016). DNA barcoding and evaluation of genetic diversity in Cyprinidae fish in the midstream of the Yangtze River. Ecology and Evolution, 6(9), 2702-2713.

[3]Shen, Y.^#, Kou, Q.^#, Chen, W., He, S., Yang, M., Li, X., & Gan, X. (2016). Comparative population structure of two dominant species, Shinkaia crosnieri (Munidopsidae: Shinkaia) and Bathymodiolus platifrons (Mytilidae: Bathymodiolus), inhabiting both deep‐sea vent and cold seep inferred from mitochondrial multi‐genes. Ecology and Evolution, 6(11), 3571-3582.