Selected Publications:
• Shen F, Qin Y, Wang R, Huang X, Wang Y, Gao T, He J, Zhou Y, Jiao Y, Wei J, Li L, Yang X. Comparative genomics reveals a unique nitrogen-carbon balance system in Asteraceae. Nat Commun. 2023 Jul 20;14(1):4334. doi: 10.1038/s41467-023-40002-9.
• Shen F#, Xu SX, Shen Q, Bi CW, Martin A. Lysak. The allotetraploid horseradish genome provides insights into subgenome diversification and formation of critical traits. Nat Commun. 2023 (In Press) https://doi.org/10.1038/s41467-023-39800-y. (Corresponding author)
• 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 Phytol. 2023 May;238(3):1245-1262. doi: 10.1111/nph.18796.
• Ma Q, Wang Y, Li S, Wen J, Zhu L, Yan K, Du Y, Li S, Yan L, Xie Z, Lyu Y, Shen F, Li Q. Ribosome footprint profiling enables elucidating the systemic regulation of fatty acid accumulation in Acer truncatum. BMC Biol. 2023 Apr 3;21(1):68. doi: 10.1186/s12915-023-01564-8. (Corresponding author)
• Shen F, Hu C, Huang X, Wu R, Luo S, Xu C, Zhang H, Wang X, Zhao J. Characterization of the genetic and regulatory networks associated with sugar and acid metabolism in apples via an integrated strategy. Front Plant Sci. 2022 Nov 17;13:1066592. doi: 10.3389/fpls.2022.1066592.
• Shen,F, Luca Bianco, Bei Wu, Zhendong Tian, Ting Wu, Yi Wang, Xuefeng Xue, Zhenhai Han, Riccardo velasco, Paolo Fontana, Xinzhong Zhang (2022). A bulked segregant analysis tool for out-crossing species (BSATOS) and QTL-based genomics-assisted prediction of complex traits in apple. Journal of Advanced Research IF=10.47
• Shen, F., Huang, Z., Zhang, B., Wang, Y., Zhang, X., Wu, T., Xu, X., Zhang, X., & Han, Z. (2019). Mapping gene markers for apple fruit ring rot disease resistance using a multi-omics approach. G3: Genes, Genomes, Genetics, 9(5), 1663–1678.
• Shixiao Xu, Yongle Ding, Juntao Sun, Zhiqiang Zhang, Zhaoyun Wu, Tiezhao Yang, Fei Shen# and Gang Xue# A high-quality genome assembly of Jasminum sambac provides insight into floral trait formation and Oleaceae genome evolution. (2021). Molecular Ecology Resource. 22(2):724-739 (Corresponding author) (IF=7.09) DOI: 10.1111/1755-0998.13497
• Li X#, Shen F#, Xu X, Zheng Q, Wang Y, Wu T, Li W, Qiu C, Xu X, Han Z, Zhang X (2021). An HD-ZIP transcription factor, MxHB13, integrates auxin-regulated and juvenility-determined control of adventitious rooting in Malus xiaojinensis. The Plant Journal. 2021 Jul 4. (doi: 10.1111/tpj.15406) (IF=6.14) (co-first author)
• Zhenyu Huang#, Fei Shen#, Yuling Chen, Ke Cao, Lirong Wang (2021). Chromosome scale Genome Assembly and Population Genomic Analysis Provide Insights into the Adaptation, Domestication, and Flavonoid Metabolism of Chinese Plum (Prunus salicina Lindl.). The Plant Journal. 108(4):1174-1192. doi: 10.1111/tpj.15482. (IF=6.14) (co-first author)
• Zhao, J.#, Shen, F# , Gao, Y., Wang, D., & Wang, K. (2019). Parallel Bud Mutation Sequencing Reveals that Fruit Sugar and Acid Metabolism Potentially Influence Stress in Malus. International Journal of Molecular Sciences, 20(23), 5988. (IF=5.9)
• Huang, Z# ., Shen, F.# , Chen, Y., Cao, K., & Wang, L. (2021). Preliminary Identification of Key Genes Controlling Peach Pollen Fertility Using Genome-Wide Association Study. Plants, 10(2), 242. (IF=3.18)
• Xiao Wei#, Fei Shen#, Qiuping Zhang, Ning Liu, Yuping Zhang, Ming Xu, Shuo Liu, Yujun Zhang, Xiaoxue Ma, Weisheng Liu (2021). Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing. Tree Genetics & Genomes 17 (3), 1-10 (IF=2.01)
• Wensheng Wang, Ramil Mauleon, …, Fei Shen, et al., (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 7703(557): 43-49. (IF=42.0)
• Zheng, W., Shen, F., Wang, W., Wu, B., Wang, X., Xiao, C., Tian, Z., Yang, X., Yang, J., Wang, Y., & others. (2020). Quantitative trait loci-based genomics-assisted prediction for the degree of apple fruit cover color. The Plant Genome, 13(3), e20047. (IF=4.06)
• Wu, B., Shen, F., Chen, C. J., Liu, L., Wang, X., Zheng, W. Y., Deng, Y., Wang, T., Huang, Z. Y., Xiao, C., & others. (2021). Natural variations in a pectin acetylesterase gene, MdPAE10, contribute to prolonged apple fruit shelf life. The Plant Genome, e20084. (IF=4.06)
• Liu, J., Shen, F., Xiao, Y., Fang, H., Qiu, C., Li, W., Wu, T., Xu, X., Wang, Y., Zhang, X., & others. (2020). Genomics-assisted prediction of salt and alkali tolerances and functional marker development in apple rootstocks. BMC Genomics, 21(1), 1–16. (IF=3.59)
• Zheng, C., Shen, F., Wang, Y., Wu, T., Xu, X., Zhang, X., & Han, Z. (2020). Intricate genetic variation networks control the adventitious root growth angle in apple. BMC Genomics, 21(1), 1–18 (IF=3.59)
• Wang, X., Shen, F., Gao, Y., Wang, K., Chen, R., Luo, J., Yang, L., Zhang, X., Qiu, C., Li, W., & others. (2020). Application of genome-wide insertion/deletion markers on genetic structure analysis and identity signature of Malus accessions. BMC Plant Biology, 20(1), 1–13
• Wu, B., Shen, F., Wang, X., Zheng, W. Y., Xiao, C., Deng, Y., Wang, T., Huang, Z. Y., Zhou, Q., Wang, Y., & others. (2020). Role of MdERF3 and MdERF118 natural variations in apple flesh firmness/crispness retainability and development of QTL-based genomics-assisted prediction. Plant Biotechnology Journal. 19 (5), 1022-1037. (IF=9.1)
• Jia, D., Shen, F., Wang, Y., Wu, T., Xu, X., Zhang, X., & Han, Z. (2018). Apple fruit acidity is genetically diversified by natural variations in three hierarchical epistatic genes: MdSAUR37, MdPP2CH and MdALMTII. The Plant Journal, 95(3), 427–443. （IF=6.14）
• Cui, M., Zhuang, Y., Shen, F., Yang, L., Wang, Y., Wu, T., Zhao, Y., Li, C., Han, Y., Chen, D., & others. (2014). QTL mapping for susceptibility to apple fruit ring rot and candidate gene predicting. Journal of Fruit Science, 31(5), 793–800.
• Tan, Y., Shen, F., Chen, R., Wang, Y., Wu, T., Li, T., Xu, X., Han, Z., & Zhang, X. (2017). Candidate genes associated with resistance to Valsa canker identified via quantitative trait loci in apple. Journal of Phytopathology, 165(11–12), 848–857.
• Huang, Z., Hu, H., Shen, F., Wu, B., Wang, X., Zhang, B., Wang, W., Liu, L., Liu, J., Chen, C., & others. (2018). Relatively high acidity is an important breeding objective for fresh juice-specific apple cultivars. Scientia Horticulturae, 233, 29–37.
• Jia, X. L., Chen, Y. K., Xu, X. Z., Shen, F., Zheng, Q. B., Du, Z., Wang, Y., Wu, T., Xu, X. F., Han, Z. H., & others. (2017). miR156 switches on vegetative phase change under the regulation of redox signals in apple seedlings. Scientific Reports, 7(1), 1–13.
• Zhang, M., Lv, Y., Wang, Y., Rose, J. K. C., Shen, F., Han, Z., Zhang, X., Xu, X., Wu, T., & Han, Z. (2016). TATA box insertion provide a selected mechanism for enhancing gene expression to adapt Fe deficiency. Plant Physiology, pp–01504.
• Zhao, J., Liu, G., Chang, R., Cao, K., Shen, F., Wu, T., Wang, Y., Han, Z., & Zhang, X. (2015). Diversity of flesh polyphenols and their progressive dilution during fruit expansion in Malus germplasm. Scientia Horticulturae, 197, 461–469.
• Han, Z., Hu, Y., Lv, Y., Rose, J. K. C., Sun, Y., Shen, F., Wang, Y., Zhang, X., Xu, X., Wu, T., & others. (2018). Natural variation underlies differences in ETHYLENE RESPONSE FACTOR17 activity in fruit peel degreening. Plant Physiology, 176(3), 2292–2304.
• Zhang, M., Lv, Y., Wang, Y., Rose, J. K. C., Shen, F., Han, Z., Zhang, X., Xu, X., Wu, T., & Han, Z. (2017). TATA box insertion provides a selection mechanism underpinning adaptations to Fe deficiency. Plant Physiology, 173(1), 715–727.
• Wang, W., Mauleon, R., Hu, Z., …, Fei Shen…,Zhang, F., & others. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557(7703), 43–49.
• Cao, K., Chang, Y., Sun, R., Shen, F., Wu, T., Wang, Y., Zhang, X., & Han, Z. (2015). Candidate gene prediction via quantitative trait locus analysis of fruit shape index traits in apple. Euphytica, 206(2), 381–391.