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公衍海                                                博士/副研究员    

2014年获清华大学硕士学位，2024年获中国科学院大学博士学位。2014年7月加入中国科学院青岛生物能源与过程所，现任单细胞中心生物信息研究组副研究员。曾获国家自然科学基金面上项目（2024）、科技部重点研发计划子课题（2021）、国家自然科学基金青年项目（2020）和山东省自然科学基金青年项目（2019）资助。已在Innovation、Plant Commun、Plant J、iMeta、PNAS、Small、Anal Chem 等期刊发表论文10余篇，专利和软件著作权申请5项。目前担任Appl Environ Microbiol、mSystems、mLife、Sci Data 等学术期刊的审稿人。


研究方向

  • 生物信息学与系统生物学


承担的科研项目

  1. 国家自然科学基金面上项目，宏基因组生物标志物驱动的菌群单细胞基因组-表型组关联分析方法研究（32370097），50万，2024.1-2027.12，主持

  2. 国家重点研发计划子课题，微拟球藻抗逆性的表观遗传机制及调控策略（课题号2021YFA0909703），40万，2021.12-2026.11，主持

  3. 国家自然科学基金青年项目，基于深度迁移学习的微拟球藻蛋白质亚细胞定位预测方法研究（31900071），24万，2020.1-2022.12，主持

  4. 山东省自然科学基金青年项目，微拟球藻蛋白质亚细胞定位预测与特性分析（ZR2019QC012），15万，2019.7-2022.6，主持


代表性论文

  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


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