主要以草鱼和泥鳅等经济鱼类为研究对象，以斑马鱼等模式鱼类和细胞培养为辅助，以细胞操作技术、基因组学等组学技术和生物信息学分析手段来开展如下研究： 

（1）鱼类重要经济性状分子机制的解析及育种研究 

ü 解析鱼类生长、肌间刺等性状的分子网络及分子模块耦合作用 

ü 研发鱼类分子辅助育种与基因组育种的相关技术与流程 

ü 培育具有高产、优质等优良性状的鱼类新品种或新品系 

（2）重要经济鱼类基因组育种信息平台的研发 

ü 开发基因组与转录组的测序策略、组装与注释流程的优化及多组学数据分析技术 

ü 探索新类型数据的分析算法，开发相关软件工具 

ü 建立重要经济鱼类的基因组数据库系统及多组学数据分析平台 

发明专利 ： 

[1] 夏晓勤, 夏雷, 石米娟, 段攸, 张婉婷  程莹寅, 吴南。一种直接从全基因组重测序数据中得到微单体型及其分型的方法。中国，申请号：201811248346.8，公开号： CN109346130A 

[2] 夏晓勤，吴南，黎明，石米娟，程莹寅，张婉婷，青藤碱在防治豆粕饲料引起的鱼类肠肝炎症中的应用。中国，申请号：201910847367 

[3] 夏晓勤，吴南，黎明，石米娟，程莹寅，张婉婷，沙棘在防治豆粕饲料引起的鱼类肠肝炎症中的应用。中国，申请号：201910846893.4 

开发软件：（全部软件基于GPL开源协议发布） 

denovo_assembly_abyss_pe.sh, 一个基于二代测序数据的分析程序，用于混合感染的病毒种群的基因组组装，已成功地应用于检测猪蓝耳病的混合感染病毒分析。（2017） 

GCCD (http://bioinfo.ihb.ac.cn/gcgd), 草鱼基因组数据库，可视化草鱼的基因组数据，提供草鱼基因组相关的检索与分析功能，基于LAMP系统部署（Linux / Apache / MySQL / PHP）。(2017) 

FVD (http://bioinfo.ihb.ac.cn/fvd), 鱼类病毒数据库，通过鱼类或病毒来检索相关病毒的信息以及各种分布与统计数据。基于EXT库建站，用Python编写CGI。(2017) 

Seq2Hosts (http://bioinfo.ihb.ac.cn/seq2hosts/), 一个通过冠状病毒的spike蛋白基因序列预测其潜在宿主的网站，基于马氏距离判别与支持向量机算法。(2015) 

markers_4_unique_parents.py / markers_sources.py，二倍体生物个体间亲缘关系相关分子标记的筛选以及亲子鉴定。(2014) 

SingleArm (http://mercola.hs.uci.edu/singlearm/)，通过计算手段为前列腺癌的单臂辅助实验产生虚拟控制组的网站，用 Python / R 编写后台。(2013) 

ReadContigs，一个命令行程序，允许用户通过各种规则非常灵活地从大型序列文件中提取所需要的序列片段。(2012) 

CellPred (http://www.webarray.org/cellpred), 一个癌症组织细胞成分预测网站。通过对生物芯片数据的多元回归分析，来预测癌症组织中不同细胞成分的比例。允许用户自定义影响因子 。提供有前列腺癌和乳腺癌的训练模型。(2010) 

TabSQL (http://tabsql.sourceforge.net), 一个基于MySQL的基因组注解软件。能自动下载多种数据库，并允许整合用户数据进行查询。提供查询的图形用户界面和命令行界面，后者支持完整的SQL SELECT语法。用Python编写，可运行于多种操作系统。(2010) 

PypeR (http://pypi.python.org/pypi/PypeR), Python与R语言的接口软件包。通过该软件包中面向对象的封装接口，用户可以方便地在Python中调用本地或远程机器上R统计语言，并进行双向数据交流。用Python和R编写，可运行于多种操作系统。该软件已被“软件百科”(http://www.softpedia.com)、WareSeeker (http://www.wareseeker.com) 等多个数据库收录。(2009) 

PVConcord (http://www.webarray.org/softwares/pvconcord), 一个寻找Biomarker的软件包。通过对异源的生物芯片分析结果进行整合分析，来发现高可重复性的标记基因。用R和C语言编写。(2009) 

SeqInfo (http://www.webarray.org/softwares/seqinfo/seqInfo.zip), 一组计算核酸序列特征参数的Python程序，可用于序列分析和辅助基因芯片设计。运行于SMP及Linux机群。(2008) 

WebArrayDB (http://www.webarraydb.org), 一个生物芯片数据库及跨平台数据分析网站。可管理多个数据库，可存贮任意多通道的微阵列数据，可作差异分析 ，Meta分析，CGH分析，转座子分析。允许用户自定义数据特征，自定义方差分析模型等。(2007) 

WebArray (http://www.webarray.org), 一个基于用户数据文件的生物芯片数据分析网站。可处理Affymetrix基因芯片数据和各类双色微阵列数据。(2005) 

DiMSim, 一个离散事件过程模拟器。可模拟各类酶促反应、非酶促的生物化学反应，膜通道，以及容器等。不仅可以模拟细胞内生化网络的动态，还可模型各类生态学过程，如Lotka-Voltera种群竞争模型。用户可方便的监控模拟过程。用Python编写，可运行于多种操作系统。(2003) 

RAMARRAY, 一个微阵列的辅助设计软件。用Python编写，可运行于多种操作系统。(2002) 

TAXONOMY (http://www.webarray.org/softwares/Taxonomy.exe), 一个支持核酸序列编辑的系统分类学软件。用C++编写。(1999) 

中国内陆水体单殖吸虫的生态学数据库。用Foxpro构建。(1997) 

DATACHK / NB, 统计数据预处理、概率分布拟合软件。用C/C++编写。(1994 - 1996) 

WBZC, WBBM和PYZC, 汉字输入法造词与学习的DOS软件。用宏汇编语言MASM编写。(1995) 

BACID, 一个用于芽孢杆菌鉴定的小型专家系统。用人工智能语言Prolog编写。(1992) 

研究论文：（# 并列第一作者；* 通讯作者） 

[1] Ma X, Wei H*, Zhang Y, Duan Y, Zhang W, Cheng Y, Xia X-Q, Shi M*. Glutathione peroxidase 5 deficiency induces lipid metabolism regulated by reactive oxygen species in Chlamydomonas reinhardtii. Microbial Pathogenesis, 2020, doi: 10.1016/j.micpath.2020.104358. 

[2] 夏雷, 石米娟, 张婉婷, 段攸, 程莹寅, 吴南, 夏晓勤*. 基于微单体型分子标记的草鱼亲子鉴定方法. 水生生物学报, 2020, 44(3):509-517. 

[3] Ma X, Zhang B, Miao R, Deng X, Duan Y, Cheng Y, Zhang W, Shi M, Huang K*, Xia X-Q*. Transcriptomic and physiological responses to oxidative stress in a Chlamydomonas reinhardtii glutathione peroxidase mutant. Genes, 2020, 11:463. doi: 10.3390/genes11040463. 

[4] Huang X#, Jiang Y#, Zhang W, Cheng Y, Wang Y, Ma X, Duan Y, Xia L, Chen Y, Wu N, Shi M*, Xia X-Q*. Construction of a high-density genetic map and mapping of growth related QTLs in the grass carp (Ctenopharyngodon idellus). BMC Genomics, 2020, 21:313. doi: 10.1186/s12864-020-6730-x. 

[5] Wu N*, Xu X, Wang B, Li X-M, Cheng Y-Y, Li M, Xia X-Q, Zhang Y-A. Anti-foodborne enteritis effect of galantamine potentially via acetylcholine anti-inflammatory pathway in fish. Fish and Shellfish Immunology, 2020, 97:204-215. doi: 10.1016/j.fsi.2019.12.028. 

[6] Chen Y#, Shi M#, Cheng Y, Zhang W, Tang Q*, Xia X-Q*. FVD: The fish-associated virus database. Infection, Genetics and Evolution, 2018, 58:23-26. 

[7] 夏晓勤*, 黄晓丽, 石米娟, 程莹寅, 张婉婷, 陆承平. 寄生于鲫的锚首虫一新种. 水生生物学报, 2018, 42(2): 369-372. 

[8] Lu X-B, Chen Y-X, Cui Z-W, Zhang X-Y, Lu L-F, Li S, Xia X-Q, Nie P*, Zhang Y-A*. Characterization of grass carp CD40 and CD154 genes and the association between their polymorphisms and resistance to grass carp reovirus. Fish and Shellfish Immunology, 2018, 81:304-308. 

[9] Xia H#, Zhong C#, Wu X, Chen J, Tao B, Xia X, Shi M, Zhu Z, Trudeau VL, Hu W*. Mettl3 mutation disrupts gamete maturation and reduces fertility in zebrafish. Genetics, 2017, doi: 10.1534/genetics.117.300574. 

[10] Chen Y, Shi M, Zhang W, Cheng Y, Wang Y, Xia X-Q*. The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. Database, 2017, 2017:bax051. doi: 10.1093/database/bax051. 

[11] Zhang J*, Zheng Y, Xia X-Q, Chen Q, Bade SA, Yoon K-J, Harmon KM, Gauger PC, Main RG, Li G*. High-throughput whole genome sequencing of Porcine reproductive and respiratory syndrome virus from cell culture materials and clinical specimens using next-generation sequencing technology. Journal of Veterinary Diagnostic Investigation, 2017, 29(1):41-50. ("2018" JVDI Best Full Manuscript Award by AAVLD – The American Association of Veterinary Laboratory Diagnosticians) 

[12] Clifton BD, Librado P, Yeh S-D, Solares E, Real D, Jayasekera S, Zhang W, Shi M, Park R, Magie R, Ma H-C, Xia X-Q, Marco A, Rozas J, Ranz JM*. Rapid Functional And Sequence Differentiation of a Tandemly-Repeated Species-Specific Multigene Family in Drosophila. Molecular Biology and Evolution, 2017, 34:51-65. 

[13] Wu N, Song Y-L, Wang B, Zhang X-Y, Zhang X-J, Wang Y-L, Cheng Y-Y, Chen D-D, Xia X-Q, Lu Y-S, Zhang Y-A*. Fish gut-liver immunity during homeostasis or inflammation revealed by integrative transcriptome and proteome studies. Scientific Reports, 2016, 6:36048. 

[14] Zhang N, Zhang X-J, Song Y-L, Lu X-B, Chen D-D, Xia X-Q, Sunyer JO Zhang Y-A*. Preferential combination between the light and heavy chain isotypes of fish immunoglobulins. Developmental and Comparative Immunology, 2016, 61:169-179. 

[15] 石米娟, 程莹寅, 张婉婷, 夏晓勤*. 浅析基因组大小的进化机制. 科学通报, 2016, 61(30): 3188-3195. 

[16] Yang H-J, Bogomolnaya LM, Elfenbein JR, Endicott-Yazdani T, Reynolds MM, Porwollik S, Cheng P, Xia X-Q, McClelland M*, Andrews-Polymenis H*. Novel two-step hierarchical screening of mutant pools reveals mutants under selection in chicks. Infection and Immunity, 2016, 84:1226-1238. 

[17] Tang Q, Song Y, Shi M, Cheng Y, Zhang W, Xia X-Q*. Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition. Scientific Reports, 2015, 5:17155.  

[18] Luo D, Liu Y, Chen J, Xia X, Cao M, Cheng B, Wang X, Gong W, Qiu C, Zhang Y, Cheng CHK, Zhu Z, Hu W*. Direct production of XY^DMY？ sex reversal female medaka (Oryzias latipes) by embryo microinjection of TALENs. Scientific Reports, 2015, 5:14057. 

[19] Wang Y#*, Lu Y#, Zhang Y#, Ning Z#, Li Y, Zhao Q, Lu H, Huang R, Xia X, Feng Q, Liang X, Liu K, Zhang L, Lu T, Huang T, Fan D, Weng Q, Zhu C, Lu Y, Li W, Wen Z, Zhou C, Tian Q, Kang X, Shi M, Zhang W, Jang S, Du K, He S, Liao L, Li Y, Gui B, He H, Ning Z, Yang C, He L, Luo L, Yang R, Luo Q, Liu X, Li S, Huang W, Xiao L, Lin H*, Han B*, Zhu Z*. The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation. Nature Genetics, 2015, 47:625-631. 

[20] Datta S, Xia X-Q, Bhattacharjee S, Jia Z*. Advances in statistical medicine. Computational and Mathematical Methods in Medicine, 2014, 2014:1-2 , doi:10.1155/2014/316153. 

[21] Yeh SD, von Grotthuss M, Gandasetiawan KA, Jayasekera S, Xia X-Q, Chan C, Jayaswal V, Ranz JM*. Functional Divergence of the miRNA Transcriptome at the Onset of Drosophila Metamorphosis. Molecular Biology and Evolution, 2014, 31(10): 2557-2572. doi:10.1093/molbev/msu195. 

[22] Jia Z*, Lilly MB, Koziol JA, Chen X, Xia X-Q, Wang Y, Skarecky D, Sutton M, Sawyers A, Ruckle H, Carpenter PM, Wang-Rodriguez J, Jiang J, Deng M, Pan C, Zhu J, McLaren CE, Gurley MJ, Lee C, McClelland M, Ahlering T, Kattan MW, Mercola D. Generation of “Virtual” Control Groups for Single Arm Prostate Cancer Adjuvant Trials. PLoS ONE. 2014, 9(1): e85010. 

[23] Jia Z#*, Wang Y#, Hu Y, McLaren C, Yu Y, Ye K, Xia X-Q, Koziol, Lernhardt W, McClelland M, Mercola D. A Sample Selection Strategy to Boost the Statistical Power of Signature Detection in Cancer Expression Profile Studies. Anti-Cancer Agents in Medicinal Chemistry. 2013, 13(2):203-211. 

[24] Jia Z*, Rahmatpanah F, Chen X, Lernhardt W, Wang Y, Xia X-Q, Sawyers A, McClelland M*, Mercola D*. Expression changes in the stroma of prostate cancer predict subsequent relapse. PLoS ONE. 2012, 7(8):e41371. 

[25] Canals R, Xia X-Q, Fronick C, Clifton SW, Ahmer B, Andrews-Polymenis HL, Porwollik S, McClelland M*. High-throughput comparison of gene fitness among related bacteria. BMC Genomics, 2012, 13:212. 

[26] Díaz-Castillo C, Xia X-Q, Ranz JM. Evaluation of the Role of Functional Constraints on the Integrity of an Ultra-conserved Region in the GenusDrosophila. PLoS Genetics, 2012, 8(2): e1002475.  

[27] Bie, L, Zhao G, Cheng P, Rondeau G, Porwollik S, Ju Y, Xia X-Q*, McClelland M*. The Accuracy of Survival Time Prediction for Patients with Glioma Is Improved by Measuring Mitotic Spindle Checkpoint Gene Expression. PLoS ONE, 2011, 6(10): e25631. 

[28] Jia Z#, Wang Y#, Sawyers A, Yao H, Rahmatpanah F, Xia X-Q, Xu Q, Pio R, Turan T, Koziol J, Goodison S, Carpenter P, Wang-Rodriguez J, Simoneau A, Meyskens F, Sutton M, Lernhardt W, Beach T, McClelland M*, Mercola D*. Diagnosis of prostate cancer using differentially expressed genes in stroma. Cancer Research, 2011, 71(14):2476-2487. 

[29] Xia X-Q*, McClelland M*, Wang Y*. TabSQL - a MySQL tools to facilitate data queries with public databases. BMC Bioinformatics, 2010, 11: 342. 

[30] Wang Y#, Xia X-Q#, Jia Z#, Sawyers A, Yao H, Wang-Rodriquez J, Mercola D*, McClelland M*. In silico estimates of tissue components in surgical samples based on expression profiling data. Cancer Research, 2010, 70(16): 6448-6455. 

[31] Xia X-Q*, McClelland M*, Wang Y*. PypeR, a Python package for using R in Python. Journal of Statistical Software, 2010, 35(Code Snippets 2): 1-8. 

[32] Kucerova E, Clifton SW, Xia X-Q, Long F, Porwollik S, Fulton L, Fronick C, Minx P, Kyung K, Warren W, Fulton R, Feng D, Wollam A, Shah N, Bhonagiri V, Nash WE, Hallsworth-Pepin K, Wilson RK, McClelland M*, Forsythe SJ. Genome sequence of Cronobacter sakazakii BAA-894 and Comparative Genomic Hybridization Analysis with Other Cronobacter Species. PLoS ONE, 2010, 5(3):e9556. 

[33] Xia X-Q#*, Jia Z#, Porwollik S, Long F, H？mme C, Ye K, Müller-Tidow C, McClelland M*, Wang Y*. Evaluating Oligonucleotide Probe Properties for DNA Microarray Probe Design. Nucleic Acid Research, 2010, 38(11): e121. doi: 10.1093/nar/gkq039. 

[34] Xia X-Q*, McClelland M*, Porwollik S, Song W, Cong X, Wang Y*. WebArrayDB: cross-platform microarray data analysis and public data repository. Bioinformatics, 2009, 25(18): 2425 – 2429. 

[35] Wang Y, McClelland M, Xia X-Q*. Analyzing microarray data using WebArray. Cold Spring Harbor Protocols, 2009, 4(8), doi:10.1101/pdb.prot5260. 

[36] Tang Y#, Akbulut H#, Maynard J, Petersen L, Fang X, Zhang WW, Xia X, Koziol J, Linton PJ, Deisseroth A*. Vector Prime/Protein Boost Vaccine That Overcomes Defects Acquired during Aging and Cancer. Journal of Immunology, 2006, 177: 5697 - 5707. 

[37] Xia X, McClelland M, Wang Y. WebArray: an online platform for microarray data analysis. BMC Bioinformatics, 2005, 6(1): 306.  

[38] Xia X-Q, Wise M*. DiMSim: a discrete-event simulator of metabolic networks. Journal of Chemical Information and Computer Science, 2003, 43:1011-1019. 

[39] 朱建中, 夏晓勤, 陆承平, 郭福生. 斑点杂交检测对虾白斑综合征病毒青岛株在螯虾体内的动态分布. 中国病毒学, 2001, 16(1): 92-95. 

[40] 夏晓勤. 水生动物的保护. 动物保护概论（陆承平主编, 1999年第一版, 2002年第二版）, 高等教育出版社. (教育部面向21世纪优秀教材一等奖) 

[41] 郭爱珍, 夏晓勤. 家庭动物的保护. 动物保护概论（陆承平主编, 1999年第一版, 2002年第二版）, 高等教育出版社. (教育部面向21世纪优秀教材一等奖) 

[42] Xia X-Q*, Wang WJ, Lu CP. The distribution of monogenean parasites on aquatic vertebrates inhabiting Chinese inland waters. Systematic Parasitology, 2000, 46: 151-155. 

[43] 夏晓勤, 王伟俊, 姚卫建. 我国内陆水体单殖吸虫的宿主特异性分析. 生态学报, 2000, 20(4):594-597. 

[44] 陈营, 夏晓勤, 陆承平. 绿色荧光蛋白标记可移动载体质粒的构建及其在嗜水气单胞菌的表达. 农业生物技术学报, 1999, 7(4): 329-332. 

[45] 夏晓勤, 王伟俊, 姚卫建. 小鞘指环虫种群的季节动态. 水生生物学报, 1999, 23(3): 235-239. 

[46] 夏晓勤, 王伟俊, 姚卫建. 中国内陆水体单殖吸虫的种类组成. 湖南农业大学学报, 1999, 25(1): 423-427. 

[47] 夏晓勤, 王伟俊, 姚卫建. 小鞘指环虫种群的聚集性研究. 动物学研究, 1999, 20(6): 426-430. 

[48] 夏晓勤, 王伟俊. 鲢指环虫病病原小鞘指环虫的存活时间. 南京农业大学学报, 1999, 2(1): 95-98. 

[49] 马勋, 欧阳志明, 陈怀青, 陆承平, 夏晓勤. 迟缓爱德华氏菌对HEp-2细胞的侵袭特性. 微生物学报, 1998, 38(5): 336-340. 

[50] 夏晓勤, 王伟俊. 黄颡鱼寄生三代虫的新发现. 南京农业大学学报, 1998, 21(2): 127. 

[51] 高梅影, 李荣森, 冯平辉, 戴顺英, 夏晓勤. 特异性引物PCR法鉴定苏云金芽孢杆菌的杀虫蛋白质基因. 武汉大学学报(自然科学版), 1998, 10：21-23. 

[52] 夏晓勤, 王伟俊. 三种单殖吸虫个体行为的研究. 重庆师范大学学报(自然科学), 1998, 13(3): 18-21. 

[53] 姚卫建, 王伟俊, 夏晓勤, 陈伟洲. 南澳岛鱼类寄生锚首科四新种的描述. 水生生物学报, 1998, 22（增刊）: 120-125. 

[54] 夏晓勤, 王伟俊. 单殖吸虫生物学及生态学. 水生生物学报, 1997, 21(1): 75-84. 

[55] 夏晓勤, 聂品, 姚卫建. 光照、温度及宿主粘液对河鲈锚首吸虫虫卵卿化的影响. 水生生物学报, 1996, 20(2): 195-196. 

[56] 王伟俊, 姚卫建, 刘建雄, 肖武汉, 汪建国, 夏晓勤. 洪湖鱼类寄生虫种类的组成. 洪湖水生生物及其资源开发（陈宜瑜主编）, 北京, 科学出版社. 1995, pp 322-333. 

[57] 夏晓勤. 实现五笔字型的即时造词功能. 微计算机应用, 1995, 16(4): 55-59.