刘士凯 教授

发布者：吕敏发布时间：2017-05-11浏览次数：5523

基本信息

刘士凯，博士，教授、博士生导师，海水养殖教育部重点实验室副主任

主要研究领域：水产动物基因组学、生物信息学、分子遗传育种。

联系方式：liushk@ouc.edu.cn

网页：https://www.researchgate.net/profile/Shikai-Liu-6

学习/工作经历

        2014年获美国奥本大学博士学位，2014-2017美国奥本大学从事博士后研究工作；2017年获聘中国海洋大学“青年英才工程”第一层次教授、博士生导师，2023年中国海洋大学“筑峰人才工程”三岗特聘教授；曾获世界牡蛎学会青年学者奖、海洋工程科学技术奖，入选国家高层次人才计划青年项目。

科研/教学情况

  从事水产动物基因组学、生物信息学、分子遗传育种等领域的教学与科研工作。在水产动物基因组、转录组测序分析、分子标记开发、高密度芯片构建、重要经济性状精细遗传解析和基因组选择育种等领域系统开展工作。已在国际知名学术刊物发表SCI论文150余篇，申请/授权国家专利15项。参编学术专著4部。

主要研究方向

1）水产动物基因组学、进化发育基因组生物学

2）牡蛎分子遗传学、基因组辅助育种技术

3）牡蛎高产抗病抗逆分子育种

***与国外多所高校、研究所保持密切合作关系，硕士期间表现优异者，有机会推荐至美国雪城大学（Syracuse University）、奥本大学（Auburn University）、马里兰大学（University of Maryland）、英国爱丁堡大学（The University of Edinburgh）等高校攻读博士学位或进行联合培养。

科研项目

      主持/承担国家自然科学基金、科技部重点研发计划、山东省重点研发计划等国家与省部级项目10余项，累计经费600余万元。

主要科研项目：

1. 国家自然科学基金“生物育种研究”青年专项，2024.01-2028.12，主持，在研。

2. 国家自然科学基金面上项目，2023.01-2026.12，主持，在研。

3. 国家高层次人才特殊支持计划青年项目，2023.01-2025.12，主持，在研。

4. 国家自然科学基金面上项目，2020.01-2023.12，主持，在研。

5. 国家自然科学基金青年科学基金项目，2019.01-2021.12，主持，结题。

6. 国家自然科学基金应急管理项目，2018.01-2018.12，主持，结题。

学术兼职

目前担任国际知名杂志Reviews in Aquaculture, Marine Biotechnology编委（Editorial Board），Frontiers in Genetics副编辑（Associate Editor）及十多个领域知名学术刊物审稿人。

主讲课程

1）本科生课程：

  《生物信息学》，32课时，2学分，春季学期

2）研究生课程：

  《水产生物信息学》，32课时，2学分，秋季学期

  《水产动物遗传育种》，32课时，2学分，英文授课，秋季学期


主要学术成果（论文及专利）

一. 代表性论文（*第一作者，#通讯作者）：

Full list of publications can be accessed at Researchgate or Google Scholar

  1. Yang B, Li Y, Li Q, Liu S#. Development of high-throughput genotyping method by low-coverage whole genome sequencing with genotype imputation in Pacific oyster, Crassostrea gigas. Aquaculture, 2024, 591:741134.

  2. Yang B, Zhi C, Li P, Xu C, Li Q, Liu S#. Genomic selection accelerates genetic improvement of resistance to Vibriosis in the Pacific oyster, Crassostrea gigas. Aquaculture, 2024, 584:740679.

  3. Wang H, Yang B, Li Q, Liu S#. Low-dose of formalin-inactivated Vibrio alginolyticus protects Crassostrea gigas from secondary infection and confers broad-spectrum Vibrio resistance on offspring. Developmental and Comparative Immunology, 2024, 152:105122.

  4. Wang H, Shi C, Yang B, Li Q, Liu S#.  Characterization of the genome and cell invasive phenotype of Vibrio diabolicus Cg5 isolated from mass mortality of Pacific oyster, Crassostrea gigas. Microbial Pathogenesis, 2024, 186:106466.

  5. Mokrani A, Liu S#. Harnessing CRISPR/Cas9 system to improve economic traits in aquaculture species. Aquaculture, 2024, 579:740279.

  6. Tan Y, Li Y, Ren Li, Fu H, Li Q, Liu S#. Integrative proteome and metabolome analyses reveal molecular basis underlying growth and nutrient composition in the Pacific oyster, Crassostrea gigas. Journal of Proteomics, 2024, 290:105021.

  7. Bai Y*, Liu S*, Hu Y, Yu H, Kong L, Xu C, Li Q.  Multi-omic insights into the formation and evolution of a novel shell microstructure in oysters. BMC Biology, 2023, 21:204.

  8. Li Y, Mokrani A, Fu H, Shi C, Li Q, Liu S#. Development of Nanopore sequencing-based full-length transcriptome database toward functional genome annotation of the Pacific oyster, Crassostrea gigas. Genomics, 2023, 115(5):110697.

  9. Li Y, Yang B, Shi C, Yan Y, Ren L, Mokrani A, Li Q, Liu S#. Integrated analysis of mRNAs and lncRNAs reveals candidate marker genes and potential hub lncRNAs associated with growth regulation of the Pacific oyster, Crassostrea gigas. BMC Genomics, 2023, 24:453.

  10. Li Y, Tan Y, Ren L, Li Q, Liu S#. Structural and expression analysis of the dopamine receptors reveals their crucial roles in regulating the insulin signaling pathway in oysters. International Journal of Biological Macromolecules, 2023, 247:125703.

  11. Fu H, Li Y, Tian J, Yang B, Li Y, Li Q, Liu S#. Contribution of HIF-1α to heat shock response by transcriptional regulation of HSF1/HSP70 signaling pathway in Pacific oyster, Crassostrea gigas. Marine Biotechnology, 2023, 25(5):691-700.

  12. Waldbieser G*, Liu S*, Yuan Z*, Older C, Gao D, Shi C, Bosworth B, Li N, Bao L, Kirby M, Jin Y, Wood M, Scheffler B, Simpson S, Youngblood R, Duke M, Ballard L, Phillippy A, Koren S, Liu Z. Reference genomes of channel catfish and blue catfish reveal multiple pericentric chromosome inversions. BMC Biology, 2023, 21(1):67.

  13. Wu D, Yang B, Li Q, Liu S#. Estimation of genetic parameters for female reproduction traits in the Pacific oyster, Crassostrea gigas. Aquaculture, 2023, 569, 739387.

  14. Li X, Shi C, Yang B, Li Q, Liu S#. High temperature aggravates mortalities of oysters infected with Vibrio: a perspective from homeostasis of digestive microbiota and immune response. Aquaculture, 2023, 568:739309.

  15. Wang K, Yang B, Li Q, Liu S#. Systematic evaluation of genomic prediction algorithms for genomic prediction and breeding of aquatic animals. Genes, 2022, 13(12), 2247.

  16. Fu H, Tian J, Shi C, Li Q, Liu S#. Ecological significance of G protein-coupled receptors in the Pacific oyster (Crassostrea gigas): pervasive gene duplication and distinct transcriptional response to marine environmental stresses. Marine Pollution Bulletin, 2022, 185, 114269.

  17. Li F, Fan M, Wang S, Gu Z, Wang A, Liu C, Yang Y#, Liu S#. The complete mitochondrial genome of Hyotissa hyotis (Bivalvia: Gryphaeidae) reveals a unique gene order within Ostreoidea. Fishes, 2022, 7(6), 317.

  18. Tan C, Shi C, Li Y, Teng W, Li Y, Fu H, Ren L, Yu H, Li Q, Liu S#. Comparative methylome analysis reveals epigenetic signatures associated with growth and shell color in the Pacific oyster, Crassostrea gigas. Marine Biotechnology, 2022, 24, 911-926. 

  19. Somrup S, Sangsawang A, McMillan N, Winitchai S, Inthoncharoen J, Liu S#, Muangmai N#. Pinctada phuketensis sp. nov. (Bivalvia, Ostreida, Margaritidae), a new pearl oyster species from Phuket, western coast of Thailand. ZooKeys, 2022, 1119:181-195.

  20. Wang W, Yang Y, Tan S, Zhou T, Liu Y, Tian C, Bao L, Xing D, Su B, Wang J, Zhang Y, Liu S, Shi H, Gao D, Dunham R, Liu Z. Genomic imprinting-like monoallelic paternal expression determines sex of channel catfish. Science advances, 2022, 8(51):eadc8786.

  21. Jang D*, Liu Q*, Sun J*, Liu S*, Fan G*, Wang L, Zhang Y, Seim I, An S, Liu X, Li Q, Zheng X. The gold-ringed octopus (Amphioctopus fangsiao) genome and cerebral single-nucleus transcriptomes provide insights into the evolution of karyotype and neural novelties. BMC Biology, 2022, 20(1):289.

  22. He Y, Li X, Shi C, Li Y, Li Q, Liu S#. Transcriptome profiling of the Pacific oyster (Crassostrea gigas) suggests distinct host immune strategy in response to Vibrio alginoticus infection. Aquaculture, 2022, 560:738563.

  23. Li X, Yang B, Shi C, Wang H, Yu R, Li Q, Liu S#. Synergistic interaction of low salinity stress with Vibrio infection causes mass mortalities in the oyster by inducing host microflora imbalance and immune dysregulation. Frontiers in Immunology, 2022, 13:859975.

  24. Yang B, Zhai S, Zhang F, Wang H, Ren L, Li Y, Li Q, Liu S#. Genome-wide association study toward efficient selection breeding of resistance to Vibrio alginolyticus in Pacific oyster, Crassostrea gigas. Aquaculture, 2022, 548:737592.

  25. Li Y, Ren L, Fu H, Yang B, Tian J, Li Q, Liu Z, Liu S#. Crosstalk between dopamine and insulin signaling in growth control of the oyster. General and Comparative Endocrinology, 2021, 313:113895.

  26. Jiao Z, Tian Y, Hu B, Li Q, Liu S#. Genome structural variation landscape and its selection signatures in the fast-growing strains of the Pacific oyster, Crassostrea gigas. Marine Biotechnology, 2021, 23:736-748.

  27. Hu B, Tian Y, Li Q#, Liu S#. Genomic signatures of artificial selection in the Pacific oyster, Crassostrea gigas. Evolutionary Applications, 2022, 15(4):618-630.

  28. Tian J, Li Y, Fu H, Ren L, He Y, Zhai S, Yang B, Li Q, Liu N, Liu S#. Physiological role of CYP17A1-like in cadmium detoxification and its transcriptional regulation in the Pacific oyster, Crassostrea gigas. Science of the Total Environment, 2021, 796:149039.

  29. Li Y, Fu H, Zhang F, Ren L, Tian J, Li Q, Liu S#. Insulin-like peptide receptor-mediated signaling pathways orchestrate regulation of growth in the Pacific oyster (Crassostrea gigas), as revealed by gene expression profiles. International Journal of Molecular Sciences, 2021, 22:5259.

  30. Ren L, Li Y, Fu H, Zhang F, Yang B, Tan C, Li Q, Liu S#. A regulatory variant of tryptophan hydroxylase gene modulates transcription activity and biases growth rate in the Pacific oyster, Crassostrea gigas. Aquaculture, 2021, 542: 736906.

  31. Fu H, Jiao Z, Li Y, Tiang J, Ren L, Zhang F, Li Q, Liu S#. Transient receptor potential (TRP) channels in the Pacific oyster (Crassostrea gigas): genome-wide identification and expression profiling after heat stress between C. gigas and C. angulata. International Journal of Molecular Sciences, 2021, 22(6):3222.

  32. Wang H, Yang B, Li X, Li Q, Liu S#. Screening of bacterial pathogens associated with mass summer mortality of the Pacific Oyster, Crassostrea gigas, in China. Aquaculture Reports, 2021, 20:100672

  33. Yang B, Zhai S, Li X, Li Q, Shan H, Liu S#. Identification of Vibrio alginolyticus as a causative pathogen associated with mass summer mortality of the Pacific oyster (Crassostrea gigas) in China. Aquaculture, 2021, 535: 736363.

  34. Zhai S, Yang B, Zhang F, Li Q, Liu S#. Estimation of genetic parameters for resistance to Vibrio alginolyticus infection in the Pacific oyster (Crassostrea gigas). Aquaculture, 2021, 736545.

  35. Tian J, Jiao Z, Fu H, Qi L, Li Q, Liu N, Liu S#. Identification of cytochrome P450s and their expression profiles following cadmium exposure in the Pacific oyster, Crassostrea gigas. Aquaculture Reports, 2021, 19:100582.

  36. Li Y, Fu H, Zhang F, Ren L, Tiang J, Li Q, Liu S#. Identification, characterization, and expression profiles of insulin-like peptides suggest their critical roles in growth regulation of the Pacific oyster, Crassostrea gigas. Gene, 2021, 769: 145244.

  37. Zhang F, Hu B, Fu H, Jiao Z, Li Q#, Liu S#. Comparative transcriptome analysis reveals molecular basis underlying fast-growth of the selectively bred Pacific oyster, Crassostrea gigas. Frontiers in Genetics, 2019, 10:610.

  38. Liu S and Liu Z. 2017. Analysis of microRNAs and their target genes. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch13: 200-227.

  39. Liu S and Liu Z. 2017. Introduction to Linux and command line tools for bioinformatics.  In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch1: 3-29.

  40. Liu S, Zeng P and Liu Z. 2017. Gene set analysis of SNP data from genome-wide association studies. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch24: 434-459.

  41. Liu S, Zeng Q, Wang X and Liu Z. 2017. SNP array development, genotyping, data analysis, and applications. In: Bioinformatics in Aquaculture: Principles and Methods, Wiley and Blackwell Publishing, Ames, IA (Ed. Liu Z). Ch18: 308-337.

  42. Liu S*, Li Y*, Qin Z, Geng X, Bao L, Kaltenboeck L, Kucuktas H, Dunham R, Liu Z. High-density interspecific genetic linkage mapping provides insights into genomic incompatibility between channel catfish and blue catfish. Animal Genetics, 2016, 47:81-90.

  43. Liu Z*, Liu S*, Yao J*, Bao L*, Zhang J*, Li Y*, Jiang C, Sun L, Zhang Y, Zhou T, Zeng Q, Fu Q, Gao S, Li N, Wang R, Koren S, Jiang Y, Zimin A, Xu P, Phillippy A, Geng X, Song L, Sun F, Li C, Wang X, Chen A, Jin Y, Yuan Z, Yang Y, Tan S, Peatman E, Lu J, Qin Z, Dunham R, Li Z, Sonstegard T, Feng J, Danzmann R, Schroeder S, Scheffler B, Duke M, Ballard L, Kucuktas H, Kaltenboeck L, Liu H, Armbruster J, Xie Y, Kirby M, Tian Y, Flanagan M, Mu W, Waldbieser G. The channel catfish genome sequence provides insights into evolution of scale formation in teleosts. Nature Communications, 2016, 7:11757.

  44. Zeng Q*, Liu S*, Yao J*, Zhang Y, Yuan Z, Jiang C, Chen A, Fu Q, Sun B, Dunham R, Liu Z. Transcriptome Display during Testicular Differentiation of Channel Catfish (Ictalurus punctatus) as Revealed by RNA-Seq Analysis. Biology of Reproduction, 2016, 95:19, 1-17.

  45. Liu S, Yao J, Zhang J, LiuZ. Next generation sequencing yields the complete mitochondrial genome of the striped raphael catfish, Platydoras armatulus (Siluriformes: Doradidae). Mitochondrial DNA, 2016, 27(3):1963-4.

  46. Liu S, Zhang J, Yao J, LiuZ. The complete mitochondrial genome of the armored catfish, Hypostomus plecostomus (Siluriformes: Loricariidae). Mitochondrial DNA, 2016, 27(3):1908-9.

  47. Zhou Z*, Liu S*, Dong Y, Gao S, Chen Z, Jiang J, Yang A, Guan X, Jiang B, Wang B, Sun H. High-density genetic mapping with interspecific hybrids of two sea urchins, Strongylocentrotus nudus and S. intermedius, by RAD sequencing. PLoS ONE, 2015, 10(9):e0138585.

  48. Wang H*, Liu S*, Cui J*, Li C, Hu Y, Zhou W, Chang Y, Qiu X, Liu Z, Wang X. Identification and characterization of microRNAs from longitudinal muscle and respiratory tree in sea cucumber (Apostichopus japonicus) using high-throughput sequencing. Plos One, 2015, 10(8): e0134899.

  49. Tian Y*, Yao J*, Liu S*, Jiang C, Zhang J, Li Y, Liu Z. Identification and expression analysis of 26 oncogenes of the receptor tyrosine kinase family in channel catfish after hypoxic stress and bacterial infection. Comparative Biochemistry and Physiology - Part D: Genomics & Proteomics, 2015, 14:16-25.

  50. Li Y*, Liu S*, Qin Z, Waldbieser G, Wang R, Sun L, Bao L, Danzmann R, Dunham R, Liu Z. Construction of high-density SNP-based genetic map and its integration with BAC-based physical map in channel catfish. DNA Research, 2015, 22 (1): 39-52.

  51. Li Y*, Liu S*, Qin Z, Yao J, Jiang C, Song L, Dunham R, Liu Z. The serpin superfamily in channel catfish: Identification, phylogenetic analysis and expression profiling in mucosal tissues after bacterial infection. Developmental and Comparative Immunology, 2015, 49(2), 267-277.

  52. Liu S, Sun L, Li Y, Sun F, Jiang Y, Zhang Y, Zhang J, Feng J, Kaltenboeck L, Kucuktas H and Liu Z. Development of the catfish 250K SNP array for genome-wide association studies. BMC Research Notes, 2014, 7:135.

  53. Liu S*, Wang X*, Sun F, Zhang J, Feng J, Liu H, Rajendran KV, Sun L, Zhang Y, Jiang Y, Peatman E, Kaltenboeck L, Kucuktas H and Liu Z. RNA-Seq reveals expression signatures of genes involved in oxygen transport, protein synthesis, folding and degradation in response to heat stress in catfish. Physiological Genomics, 2013, 45 (12):462-476.

  54. Liu S, Li Q, Liu Z. Genome-wide identification and evolutionary analysis of the ATP-binding cassette (ABC) transporter superfamily in catfish. PLoS ONE, 2013, 8(5): e63895.

  55. Liu S, Zhang Y, Sun F, Jiang Y, Wang R, Li C, Zhang J, Liu Z. 2012. Functional genomics research in aquaculture: principles and general approaches. In: Functional Genomics in Aquaculture, Wiley and Blackwell Publishing, Ames, IA (Eds. Saroglia M and Liu Z). Ch1: 1-40.

  56. Liu S, Zhang Y, Zhou Z, Waldbieser G, Sun F, Lu J, Zhang J, Jiang Y, Zhang H, Wang X, Rajendran KV, Kucuktas H, Peatman E, Liu Z. Efficient assembly and annotation of the transcriptome of catfish by RNA-Seq analysis of a doubled haploid homozygote. BMC Genomics. 2012, 13:595.

  57. Liu S, Zhou Z, Lu J, Sun F, Wang S, Liu H, Jiang Y, Kucuktas H, Kaltenboeck L, Peatman E, Liu Z. Generation of genome-scale gene-associated SNPs in catfish for the construction of a high-density SNP array. BMC Genomics. 2011, 12:53.

二. 国家专利（代表性专利，授权/申请）：

  1. 刘士凯，杨奔，李琪。 一种基因组预测方法、预测系统及应用。国家发明专利，申请号：202111620265.8，申请日：2021.12.28.

  2. 刘士凯，杨奔，支承均，李琪，于瑞海。基于全基因组选择的牡蛎抗弧菌优良品系的选育方法。国家发明专利，申请号：202311264954.9，申请日期：2023.9.27。

  3. 刘士凯，汪贺冰，杨奔，鲁林基，支承均。一种提高长牡蛎及其幼虫弧菌抗性的方法。国家发明专利，申请号：202211549079.4，申请日期：2022.12.5。

  4. 刘士凯，支承均，鲁林基，李寅，李琪，李鹏飞，李忠玉。一种牡蛎养殖装置。实用新型专利，专利号：ZL202221059236.9，授权公告日：2022.8.9。

  5. 李忠玉，李琪，刘士凯，于瑞海，徐成勋，李鹏飞。一种可筛选的长牡蛎群体选育方法。国家发明专利，专利号：ZL202110630329.6，授权公告日：2022.6.2。