Education and working experiences:

2024.1-Present: Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Single-Cell Center, Associate Professor

2017.1-2023.12: Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Single-Cell Center, Research Associate

2014.7-2016.12: Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Single-Cell Center, Research Assistant

Education

2021.9-2024.6: University of Chinese Academy of Sciences, Biochemistry and Molecular Biology, Ph.D.

2011.8-2014.7: Tsinghua University, Control Science and Engineering, M.S.

2005.9-2009.7: China University of Petroleum (East China), Automation, B.S.

Grants

National Natural Science Foundation of China (32370097 and 31900071)

Subproject of the Key Research and Development Program of the Ministry of Science and Technology (2021YFA0909703)

Shandong Provincial Natural Science Foundation (ZR2019QC012)

Publications

1. Gong, Y.#, Wang, Q.#, Wei, L., Wang, L., Lv, N., Du, X., Shen, C., Xin, Y., Sun, L., Xu, J. (2025). Multi-dimensional epigenomic dynamics converge on H3K4-mediated regulation of low-CO2 adaptation in Nannochloropsis oceanica. Plant Communications 6(12):101534. https://doi.org/10.1016/j.xplc.2025.101534

2. Jing, X., Gong, Y., Ren, Y., Wang, L., Mu, R., Sun, P., Diao, Z., Meng, Y., Huang, L., Wang, X., et al. (2025). Mining robust in situ phosphorus-accumulating organisms via single-cell RACS-Culture for rational ecosystem engineering. Water Research 284: 124025. https://doi.org/10.1016/j.watres.2025.124025

3. Wang, X.#, Wang, S.#, Diao, Z.#, Hou, X.#, Gong, Y., Sun, Q., Zhang, J., Ren, L., Li, Y., Ji, Y., et al. (2025). Label-free high-throughput live-cell sorting of genome-wide random mutagenesis libraries for metabolic traits by Raman flow cytometry. PNAS 122(22): e2503641122. https://doi.org/10.1073/pnas.2503641122

4. Jing, X.#, Gong, Y.#, Diao, Z.#, Ma, Y.#, Meng, Y., Chen, J., Ren, Y., Liang, Y., Li, Y., Sun, W., et al. (2025). Phylogeny-metabolism dual-directed single-cell genomics for dissecting and mining ecosystem function by FISH-scRACS-seq. The Innovation 6(3):100759. https://doi.org/10.1016/j.xinn.2024.100759

5. Gong, Y.#, Wang, Q.#, Wei, L., Liang, W., Wang, L., Lv, N., Du, X., Zhang, J., Shen, C., Xin, Y., et al. (2024). Genome-wide adenine N6-methylation map reveals epigenomic regulation of lipid accumulation in Nannochloropsis. Plant Communications 5(3):100773. https://doi.org/10.1016/j.xplc.2023.100773

6. Zhang, J.#, Ren, L.#, Zhang, L.#, Gong, Y.#, Xu, T., Wang, X., Guo, C., Zhai, L., Yu, X., Li, Y., et al. (2023). Single-cell rapid identification, in situ viability and vitality profiling, and genome-based source-tracking for probiotics products. iMeta 2(3):e117. https://doi.org/10.1002/imt2.117

7. Jing, X.#, Gong, Y.#, Pan, H., Meng, Y., Ren, Y., Diao, Z., Mu, R., Xu, T., Zhang, J., Ji, Y., et al. (2022). Single-cell Raman-activated sorting and cultivation (scRACS-Culture) for assessing and mining in situ phosphate-solubilizing microbes from nature. ISME Communications 2:106. https://doi.org/10.1038/s43705-022-00188-3

8. Jing, X.#, Gong, Y.#, Xu, T.#, Davison, P.A., MacGregor-Chatwin, C., Hunter, C.N., Xu, L., Meng, Y., Ji, Y., Ma, B., et al. (2022). Revealing CO2-fixing SAR11 bacteria in the ocean by Raman-based single-cell metabolic profiling and genomics. BioDesign Research 2022:9782712. https://doi.org/10.34133/2022/9782712

9. Chen, G.E., Hitchcock, A., Mareš, J., Gong, Y., Tichý, M., Pilný, J., Kovářová, L., Zdvihalová, B., Xu, J., Hunter, C.N., et al. (2021). Evolution of Ycf54-independent chlorophyll biosynthesis in cyanobacteria. PNAS 118(10):e2024633118. https://doi.org/10.1073/pnas.2024633118

10. Jing, X.#, Gong, Y.#, Xu, T.#, Meng, Y., Han, X., Su, X., Wang, J., Ji, Y., Li, Y., Jia, Z., et al. (2021). One-cell metabolic phenotyping and sequencing of soil microbiome by Raman-activated gravity-driven encapsulation (RAGE). mSystems 6(3):10.1128/msystems.00181-00121. https://doi.org/10.1128/msystems.00181-21

11. Gong, Y.#, Kang, N.K.#, Kim, Y.U., Wang, Z., Wei, L., Xin, Y., Shen, C., Wang, Q., You, W., Lim, J.-M., et al. (2020). The NanDeSyn database for Nannochloropsis systems and synthetic biology. The Plant Journal 104(6):1736-1745. https://doi.org/10.1111/tpj.15025

12. Xu, T.#, Gong, Y.#, Su, X.#, Zhu, P., Dai, J., Xu, J., and Ma, B. (2020). Phenome–genome profiling of single bacterial cell by Raman-activated gravity-driven encapsulation and sequencing. Small 16(30):2001172. https://doi.org/10.1002/smll.202001172

13. Su, X.#, Gong, Y.#, Gou, H., Jing, X., Xu, T., Zheng, X., Chen, R., Li, Y., Ji, Y., Ma, B., et al. (2020). Rational optimization of Raman-activated cell ejection and sequencing for bacteria. Analytical Chemistry 92(12):8081-8089. https://doi.org/10.1021/acs.analchem.9b05345

14. Jing, X.#, Gou, H.#, Gong, Y.#, Su, X., Xu, L., Ji, Y., Song, Y., Thompson, I.P., Xu, J., and Huang, W.E. (2018). Raman-activated cell sorting and metagenomic sequencing revealing carbon-fixing bacteria in the ocean. Environmental Microbiology 20(6):2241-2255. https://doi.org/10.1111/1462-2920.14268

15. Sturme, M.H.J.#, Gong, Y.#, Heinrich, J.M., Klok, A.J., Eggink, G., Wang, D., Xu, J., and Wijffels, R.H. (2018). Transcriptome analysis reveals the genetic foundation for the dynamics of starch and lipid production in Ettlia oleoabundans. Algal Research 33:142-155. https://doi.org/10.1016/j.algal.2018.05.004