部分研究论文（*通讯作者）

1. Bian C.*, Huang Y., Li R., Xu P., You X., Lv Y., Ruan Z., Chen J., Xu J., Shi Q.* Genomics comparisons of three chromosome-level mudskipper genome assemblies reveal molecular clues for water-to-land evolution and adaptation. Journal of Advanced Research. https://doi.org/10.1016/j.jare.2023.05.005。

2. Bian C., Liu C., Zhang G., Tao M., Huang D., Wang C., Lou S., Li H., Shi Q.*, Hu Z.* A chromosome-level genome assembly for the astaxanthin-producing microalga Haematococcus pluvialis. Scientific Data, 2023, 10:511.

3. Zhang K., Huang Y., Zhang Y, Liang R, Li Q., Li R, Zhao X., Bian C., Chen Y., Wu J., Shi Q.*, Lin L.* A chromosome-level reference genome assembly of the Reeve's moray eel (Gymnothorax reevesii). Scientific Data, 2023, 10:501.

4. Guo S., Gao W., Zeng M., Liu F., Yang Q., Chen L., Wang Z., Jin Y., Xiang P., Chen H., Wen Z.*, Shi Q.*, Song Z.* Characterization of TLR1 and expression profiling of TLR signaling pathway related genes in response to Aeromonas hydrophila challenge in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × P. vachelli ♂). Frontiers in Immunology, 2023, 14:1163781.

5. Sun C., Zhang X., Dong J., You X., Tian Y., Shi Q.*, Ye X.* Whole-genome resequencing reveals recent signatures of selection in five populations of farmed large-mouth bass (Micropterus salmoides). Zoological Research, 2023, 44(1):78-89.

6. Li R., Huang Y., Peng C., Gao Z., Liu J., Ying X., Gao B., Ovchinnikova T.V., Qiu L.*, Bian C.*, Shi Q.* High-throughput prediction and characterization of antimicrobial peptides from multi-omics datasets of Chinese tubular cone snail (Conus betulinus). Frontiers in Marine Science, 2022, 9:1092731.

7. Zhao X., Huang Y., Bian C., You X., Zhang X., Chen J., Wang M., Hu C., Xu Y., Xu J., Shi Q.* Whole genome sequencing of the fast-swimming Southern bluefin tuna (Thunnus maccoyii). Frontiers in Genetics, 2022, 13:1020017.

8. Huang Y., Chen X., Shu H., Xiao P., Lin X., Xu J., Bian C., You X., Yang J.*, Shi Q.* High-throughput identification of antihypertensive peptides (AHTPs) and characterization of AHTP-derived genes in the lined seahorse (Hippocampus erectus). Frontiers in Marine Science, 2022, 9:863310.

9. Huang Y.*, Li J., Bian C., Li R., You X., Shi Q.* Evolutionary genomics reveals multiple functions of arylalkylamine N-acetyltransferase in fish. Frontiers in Genetics, 2022, 13:820442.

10. Mu Y., Bian C., Liu R., Wang Y., Shao G., Li J., Qiu Y., He T., Li W., Ao J., Shi Q.*, Chen X.* Whole genome sequencing of a snailfish from Yap Trench (~7000 m) reveals molecular evolution in hadal environments. PLoS Genetics, 2021, 17(5):e1009530.

11. Chen P., Huang Y., Lv Y., Du H., Raun Z., Li C., Ye H., Zhang H., Wu J., Wang C., Ruan R., Li Y., Bian C., You X., Shi C., Han K., Xu J., Shi Q.*, Wei Q.* The American paddlefish genome provides novel insights into chromosomal evolution and bone mineralization in early vertebrates. Molecular Biology and Evolution, 2021, 38(4):1595-1607.

12. Peng C., Huang Y., Bian C., Li J., Liu J., Zhang K., You X., Lin Z., He Y., Chen J., Lv Y., Ruan Z., Zhang X., Yi Y., Li Y., Lin X., Gu R., Xu J., Yang J., Fan C., Yao G., Chen J.-S., Jiang H., Gao B.*, Shi Q.* The first Conus genome assembly reveals a primary genetic central dogma of conopeptides in C. betulinus. Cell Discovery, 2021, 7(1):11.

13. Sun C., Li J., Dong J., Niu Y., Hu J., Lian J., Li W., Li J., Tian Y., Shi Q.*, Ye X.* Chromosome-level genome assembly for the largemouth bass Micropterus salmoides provides insights into adaptation to fresh and brackish water. Molecular Ecology Resources, 2021, 21(1):301-315.

14. Hughes L.C.*, Orti G.*, Huang Y., Sun Y., Baldwin C., Thompson A.W., Arcila D.K., Betancurr-R R., Li C., Becker L., Bellora N., Zhao X., Li X., Wang M., Fang C., Xie B., Zhou Z., Huang H., Chen S., Venkatesh B.*, Shi Q.* Comprehensive phylogeny of ray-finned fishes (Actinopterygii) based on transcriptomic and genomic data. Proceedings of the National Academy of Sciences of the United States of America, 2018, 115(24):6249-6254.

15. Lin Q., Fan S., Zhang Y., Xu M., Zhang H., Yang Y., Lee A.P., Woltering J.M., Ravi V., Gunter H.M., Luo W., Gao Z., Lim Z.W., Qin G., Schneider R.F., Wang X., Xiong P., Li G., Wang K., Min J., Zhang C., Qiu Y., Bai J., He W., Bian C., Zhang X., Shan D., Qu H., Sun Y., Gao Q., Huang L., Shi Q.*, Meyer A.*, Venkatesh B.* The seahorse genome and the evolution of its specialized morphology. Nature, 2016, 540(7633):395-399.（封面文章）。

16. Peng C., Yao G., Gao B., Fan C., Wang J., Cao Y., Wen B., Zhu Y., Ruan Z., You X., Bian C., Li J., Lin Z., Zou S., Zhang X., Qiu Y., Chen J., Coon S.L., Yang J., Chen J.-S.*, Shi Q.* High-throughput identification of novel conotoxins from the Chinese tubular cone snail (Conus betulinus) by multi-transcriptome sequencing. GigaScience, 2016, 5:17.

17. Yang J.*, Chen X., Bai J., Fang D., Qiu Y., Jiang W., Yuan H., Bian C., Lu J., He S., Pan X., Zhang Y., Wang X., You X., Wang Y., Sun Y., Mao D., Liu Y., Fan G., Zhang H., Chen X., Zhang X., Zheng L., Wang J., Cheng L., Chen J., Ruan Z., Li J., Yu H., Peng C., Ma X., Xu J., He Y., Xu Z., Xu P., Wang J., Yang H., Wang J., Whitten T.*, Xu X.*, Shi Q.* The Sinocyclocheilus cavefish genome provides insights into cave adaptation. BMC Biology, 2016, 14:1.

18. You X., Bian C.*, Zan Q., Xu X., Liu X., Chen J., Wang J., Qiu Y., Li W., Zhang X., Sun Y., Chen S., Hong W., Li Y., Cheng S., Fan G., Shi C., Liang J., Tang Y.T., Yang C., Ruan Z., Bai J., Peng C., Mu Q., Lu J., Fan M., Yang S., Huang Z., Jiang X., Fang X., Zhang G., Zhang Y., Yu H., Li W., Liu Z., Zhang G., Ravi V., Coon S. L., Wang J., Yang H., Venkatesh B., Wang J.*, Shi Q.* Mudskipper genomes provide insights into the terrestrial adaptation of amphibious fishes. Nature Communications, 2014, 5:5594.

 

部分专著

1. 石 琼（参编）。Encyclopedia of Marine Biotechnology. Kim S.-K. (ed.). John Wiley & Sons Inc., UK. 2020年。

2. 石 琼、高炳淼、彭超（主编）。海洋芋螺资源图鉴。广州：中山大学出版社。2018年。

3. 石 琼（参编）。鱼类基因组学与基因组育种技术，陈松林主编。北京：科学出版社。2017年。

4. 孙颖、石 琼（主编）。后基因组时代的鱼类样本库建设与实践。北京：科学出版社。2017年。

5. 宋林生、石 琼（主编）。海洋生物功能基因开发与利用。北京：科学出版社。2016年。

6. 石 琼（参编）。Marine Omics: Principles and Applications. Kim S.-K. (Ed.), CRC Press. 2016年。

7. 孙颖（主编）、黄玉、石 琼（副主编）。基因组学及其应用专业英语。广州：中山大学出版社。2015年。

8. 石 琼、孙颖（主编）。海洋生物基因组学概论。广州：中山大学出版社。2015年。