Research Group of Aquatic Bioinformatics
PI: Prof. XIA Xiaoqin, PhD.
Prof. XIA Xiaoqin graduated from college of life sciences in Wuhan University in 1992, than got the PhD degree in the institute of hydrobiology, CAS, in 1997. In 2000, he started the study on systems biology and bioinformatics at Cambridge University. Prof. Xia was involved in genomics research and bioinformatics study of cancer and pathogenic microbes during 2004 to 2011. In 2011, Prof. Xia returned to China for the purpose of studying fish genomics and molecular-assisted breeding. To date, Prof. Xia has been supported by many funds, such as the National High Technology Research and Development Program ("863" Program) of China, the National Natural Science Foundation of China, the Strategic Priority Research Program of the Chinese Academy of Sciences, and the Knowledge Innovation Program of the Chinese Academy of Sciences. Prof. Xia has published more than 20 papers in specialized international academic journals, and also been invited to join the editorial board of many academic journals, such as Scientific Reports.
Assoc. Prof. Nan WU, PhD
Assis. Prof. Mijuan SHI, PhD
Experimentalists Yingyin CHENG, MA
Experimentalists Wanting ZHANG, MA
Yanxin JIANG, Xiaocui Ma, You DUAN & Qiangxiang ZHANG.
Lei XIA, Lei HUANG, Ming LI & Weidong YE.
Yulong SONG, PhD, Lecturer in Sun Yat-sen University, Guangzhou, China
Qin TANG, PhD, Post-doc in Albert Einstein College of Medicine, New York, USA
Yaxin CHEN, PhD, Post-Doc in Sun Yat-sen University, Guangzhou, China
Xiaoli HUANG, MA, Bioinformatics Analysis Engineer in MONITOR HELIX Bio-Technology Co., Ltd.
By using bioinformatics and genomics methods, and experimental techniques in molecular and cell biology, the Research Group of Aquatic Bioinformatics aims at two aspects of research on molecular genetics and breeding of fish:
* The development of fish genome breeding information platform, including the construction of genome-wide databases and omics analysis platforms for important economic fishes, and development of analytical algorithms and tools related to breeding research
* Analysis of molecular mechanisms of important economic traits and breeding research, targeting fish growth, intermuscular bones, intestinal mucosal immunity and spinal deformity and other traits.
This group is fully equipped with molecular experiment equipment and a perfect cell room. With other facilities in the Analysis & Testing Center of the institute, complex molecular cytology experiments can be completed.
This group has a complete fish culture system, including independent circulating water treatment systems and rooms for model fish and economic fish, as well as ponds and cages. Therefore, they can complete the breeding process of a variety of fish from reproduction to adult; with independent computation and storage servers, and supported by the Wuhan Branch of Supercomputing Center, Chinese Academy of Sciences, they can meet various computing needs.
In addition, they also established internal document databases, BBS, wiki encyclopedia, and file server platforms to facilitate internal communication. Some information platforms built by them can be accessed through their website (http://bioinfo.ihb.ac.cn).
1. Fish genetics and breeding. We aim to cultivate better strains or varieties of aquacultural fishes such as grass carp, loach, and ricefield eel. The research strategy to investigate the mechanism is combining genomic, cellular, genetic approaches via both cell culture for in vitro experiments and zebrafish for in vivo experiments. The research goals include 3 aspects:
1) investigate the molecular mechanisms underlying important economic traits including growth, intermuscular bone, and immunity to infection;
2) develop proceedures and techniques for molecular marker-assisted breeding and genomic breeding;
3) breed new varieties or strains of economic fishes with better straits, e.g., high-yield, disease-resistance, etc.
2. Bioinformatics study. We also develop novel methods for integrated bioinformatucs analysis for multi-omics datasets, as well as specific algorithms and platforms for either aquatic organisms or water environment are under developing. The detailed research includes 3 aspects:
1) strategy and procedures for assembly and annotation of genome or transcriptome;
2) integrative analysis of genome, transcriptome, metabonome, metagenome, etc;
3) database construction, algorithm and software develpment.
Publications with lab members as the first author or the correspondence author:
 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.
 Xia X-Q*, Huang X, Shi M, Cheng Y, Zhang W & Lu C-P. The report of a new species of Ancyrocephalid (Monogenea) from Carassius auratus in China. Acta Hydrobiological Sinica, 2018, 42(2): 369-372. [In Chinese]
 Wu N, Wang B, Cui ZW, Zhang XY, Chen YY, Xu X, Li XM, Wang ZX, Chen DD and Zhang YA. Integrative transcriptomic and microRNAomic profiling reveals immune mechanism for the resilience to soybean meal stress in fish gut and liver. Frontiers in Physiology, doi: 10.3389/fphys.2018.01154.
 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: The Journal of Biological Databases and Curation. 2017;2017:bax051.
 Shi M, Cheng Y, Zhang W & Xia X-Q*. The evolutionary mechanism of genome size. Chinese Science Bulletin, 2016, 61(30): 3188-3195. [In Chinese]
 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.
 Tang Q, Song Y, Shi M, Cheng Y, Zhang W, Xia XQ*. Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition. Scientific Reports, 2015, 5:17155.
 Wu N, Zhang XY, Huang B, Zhang N, Zhang XJ, Guo X, Chen XL, Zhang YA, Wu H, Li S, Li AH and Zhang YA. Investigating the potential immune role of fish NCAMs: Molecular cloning and expression analysis in mandarin fish. Fish and Shellfish Immunology, 2015, 46(2):765-777.
 Shi MJ, Huang R, Du FK, Pei YY, Liao LJ, Zhu ZY, Wang YP, RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses, Molecular Immunology, 2014, 61(1): 44~53.
 Wu N, LaPatra SE, Li J, Sunyer JO and Zhang YA. Complement C5a acts as molecular adjuvant in fish by enhancing antibody response to soluble antigen. Fish and Shellfish Immunology, 2014, 40(2):616-623.
 Wu N*, Rao XP, Gao YL, Wang J, and Xu FQ. Aβ deposition and olfactory dysfunction in an Alzheimer's disease model. Journal of Alzheimer’s Disease, 2013, 37(4): 699-712.
 Wu N, Guo J, Xiong L & Zhang YA. Research progress on vaccine of streptococcosis in tilapia. South China Fisheries Science, 2013, 9(6): 85-90. [In Chinese]
 Wu N & Zhang YA. Research advances in fish NK-like cells. Acta Hydrobiologica Sinica, 2012, 36(6): 1176-1183. [In Chinese]
 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.
 Xia X-Q*, McClelland M*, Wang Y*. TabSQL - a MySQL tools to facilitate data queries with public databases. BMC Bioinformatics, 2010, 11: 342.
 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.
 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.
 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.
 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.
 Wang Y, McClelland M & Xia X-Q*. Analyzing microarray data using WebArray. Cold Spring Harbor Protocols, 2009, 4(8), doi:10.1101/pdb.prot5260.
 Wu N, Yue HM, Chen B and Gui JF. Histone H2A has a novel variant in fish oocytes. Biology of Reproduction, 2009, 81: 275-83.
 Wu N, Li CJ and Gui JF. Molecular Characterization and functional commonality of nucleophosmin/nucleoplasmin in two cyprinid fish. Biochemical Genetics, 2009, 47: 749-762.
 Wu N and Gui JF. Histone variants and histone exchange. Hereditas（Beijing), 2006, 28: 493-500. [In Chinese]
 Xia X, McClelland M & Wang Y. WebArray: an online platform for microarray data analysis. BMC Bioinformatics, 2005, 6(1): 306.
 Xia X-Q & Wise M. DiMSim: a discrete-event simulator of metabolic networks. Journal of Chemical Information and Computer Science, 2003, 43:1011-1019.
 Xia X-Q. Protection and Conservation of Aquatic Animals. In Animal Protection, the 1st edtion in 2000 and the 2nd edition in 2002. Ed. by Lu C-P, China Higher Education Press.
 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.
 Xia X-Q*, Wang W-J & Yao W-J. Study on host-specificity of monogeneans in China. Acta Ecologica Sinica, 2000, 20(4): 594-597. [In Chinese]
 Xia X-Q*, Wang W-J & Yao W-J. The seasonal dynamics of D. vaginulatus (Monogenea). Acta Hydrobiological Sinica, 1999, 23(3): 235-239. [In Chinese]
 Xia X-Q*, Wang W-J & Yao W-J. The composition of Monogenea in inland water of China. Journal of Hunan Agricultural University, 1999,25(1): 423-427. [In Chinese]
 Xia X-Q*, Wang W-J & Yao W-J. Study on the aggregation of the population of Dactylogyrus vaginulatus Zhang et Niu, 1966 (Monogenea) on Hypophthalmichthys molitrix. Zoological Research, 1999, 20(6): 426-430. [In Chinese]
 Xia X-Q*, Wang W-J & Yao W-J. The life span of Dactylogyrus vaginulatus (Monogenea). Journal of Nanjing Agricultural University, 1999, 2(1): 95-98. [In Chinese]
 Xia X-Q*, & Wang W-J. A new report of Gyrodactylus sp. (Monogenea) on Pelteobagrus fulvidraco in China. Journal of Nanjing Agricultural University, 1998, 21(2): 127. [In Chinese]
 Xia X-Q* & Wang W-J, Studies on the behaviors of three species of monogeneans. Journal of Chongqing Teachers College (Natural Science Edition), 1998, 13(3): 18-21. [In Chinese]
 Xia X-Q & Wang W-J. The biology and ecology of Monogenea. Acta Hydrobiologica Sinica, 1997, 21(1): 75-84. [In Chinese]
 Xia X-Q, Nie P, & Yao W-J. Effects of light, temperature and host mucus on the egg hatching of Ancyrocephalus mogurndae (Monogenea). Acta Hydrobiologica Sinica, 1996, 20(2): 195-196. [In Chinese]
 Xia X-Q*. Enhancement of WBZX, a method for inputting Chinese characters. Microcomputer Application, 1995, 16(4): 55-59 [In Chinese]
 Lu XB, Chen YX, Cui ZW, Zhang XY, Lu LF, Li S, Xia X-Q, Nie P, Zhang YA. Characterization of grass carp CD40 and CD154 genes and the association between their polymorphisms and resistance to grass carp reovirus. Fish & Shellfish Immunology, 2018, 81:304-308.
 Chen DD, Yao YY, Cui ZW, Zhang XY, Peng KS, Guo X, Wang B, Zhou YY, Li S, Wu N and Zhang YA. Comparative study of the immunoprotective effect of two DNA vaccines against grass carp reovirus. Fish and Shellfish Immunology, 2018, 75: 66-73.
 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.
 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.
 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.
 Yu D, Xia M, Zhang L, Song Y, Duan Y, Yuan T, Yao M, Wu L, Tian C, Wu Z, Li X, Zhou J, Qiu D. RpoN (sigma(54)) Is Required for Floc Formation but Not for Extracellular Polysaccharide Biosynthesis in a Floc-Forming Aquincola tertiaricarbonis Strain. Applied and Environmental Microbiology, 2017, 83(14): e00709-17.
 An W, Guo F, Song Y, Gao N, Bai S, Dai J, Wei H, Zhang L, Yu D, Xia M, Yu Y, Qi M, Tian C, Chen H, Wu Z, Zhang T, Qiu D. Comparative Genomics Analyses on EPS Biosynthesis Genes Required for Floc Formation of Zoogloea Resiniphila and Other Activated Sludge Bacteria. Water Research, 2016, 102: 494–504.
 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.
 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.
 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, et al, 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.
 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 XYDMY？ sex reversal female medaka (Oryzias latipes) by embryo microinjection of TALENs. Scientific Reports, 2015, 5:14057.
 Li S, Guo X, Lu LF, Lu XB, Wu N and Zhang YA. Regulation pattern of fish irf4 (the gene encoding IFN regulatory factor 4) by STAT6, c-Rel and IRF4. Developmental and Comparative Immunology, 2015, 51(1):65-73.
 Zhang XJ, Zhang XY, Zhang N, Guo X, Peng KS, Wu H, Lu LF, Wu N, Chen DD, S Li et al. Distinctive structural hallmarks and biological activities of the multiple cathelicidin antimicrobial peptides in a primitive teleost fish. Journal of Immunology, 2015, 194(10):4974-4987.
 Xia S, Cheng YY, Zhu H, Liu GX, Hu ZY. Distribution and population dynamics of cryptomonads in a Chinese lake with three basins varying in their trophic state, Phycological Reaserch, 2015, 2:93-101.
 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.
 Jiang XB, Yu T, Wu N, Meng HC and Shi L. Detection of qnr, aac(6 ')-Ib-cr and qepA genes in Escherichia coli isolated from cooked meat products in Henan, China. International Journal of Food Microbiology, 2014, 187:22-25.
 Li S, Lu LF, Feng H, Wu N, Chen DD, Zhang YB, Gui JF, Nie P and Zhang YA. IFN regulatory factor 10 is a negative regulator of the IFN responses in fish. Journal of Immunology, 2014, 193(3):1100-1109.
 Tian JY, Qi ZT, Wu N, Chang MX and Nie P. Complementary DNA sequences of the constant regions of T-cell antigen receptors alpha, beta and gamma in mandarin fish, Siniperca chuatsi Basilewsky, and their transcriptional changes after stimulation with Flavobacterium columnare. Journal of Fish Disease, 2014, 37(2):89-101.
 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.
 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.
 Wang WW, Wu SG, Zheng YZ, Cheng YY, Li WX, Zou H, Wang GT, Characterization of the bacterial community associated with early-developmental stages of grass carp(Ctenopharyngodon idella), Aquaculture Research, 2014, DOI: 10.1111/are, 12428, 1-8.
 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.
 Yue HM, Li Z, Wu N, Liu Z, Wang Y and Gui JF. Oocyte-specific H2A variant H2af1o is required for cell synchrony before midblastula transition in early zebrafish embryos. Biology of Reproduction, 2013, 89(4):82, 1–13.
 Liu Q, Li A, Gong L, Zhang L, Wu N, Xu FQ. Decreased coherence between the two olfactory bulbs in Alzheimer's disease model mice. Neurosci Lett, 2013, 545:81-85.
 Xia S, Zhu H, Cheng YY, Liu GX, Hu ZY. Phylogenetic position of Ecballocystis and Ecballocystopsis (Chlorophyta), Fottea, 2013, 13(1), 65-75.
 Xia S, Zhang Q, Zhu H, Cheng YY, Liu GX, Hu ZY. Systematics of a kleptoplastidal dinoflagellate, Gymnodinium eucyaneum Hu (Dinophyceae), and its cryptomonad endosymbiont, PLoS ONE, 2013, 8: e53820.
 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.
 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.
 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 Genus Drosophila. PLoS Genetics, 2012, 8(2): e1002475.
 Lian H, Shi M, Du F, Jiang Y, Huang R, Liao L, Wang Y & Zhu Z. Cloning and characterization of (AG)-microsatellites in grass carp (Ctenopharyngodon idella). Acta Hydrobiologica Sinica, 2012, 36(1): 29-34. [In Chinese]
 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.
 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.
 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.
 Zhu J-Z, Xia X-Q & Lu C-P. Dynamics of Shrimp White Spot Syndrome Virus (WSSV) in crawfish by dot-blot DNA hybridization. Virologica Sinica, 2001, 16(1):92. [In Chinese]
 Guo A-Z & Xia X-Q. Protection and Pets. In Animal Protection, Ed. By Lu C-P, China Higher Education Press. (the first edition in 2000 and the second edition in 2002) . [In Chinese]
 Chen Y, Xia X-Q & Lu C-P. Construction of mobilizable vector plasmid containing green fluorescent protein (GFP) and its expression in Aeromonas hydrophila. Journal of Agricultural Biotechnology, 1999, 70(4): 329-332. [In Chinese]
 Ma X, Ouyan Z-M, Chen H-Q, Lu C-P & Xia X-Q. Internalization and replication of E. tarda in HEp-2 cells. Acta Microbiological Sinica, 1998, 38(5): 336-340. [In Chinese]
 Gao M, Li R, Feng P, Dai X & Xia X-Q. Identification of genes for insect-killing proteins in Bacillus thuringiensis spp. nov. by PCR with specific primers. Journal of Wuhan University (Natural Science Edition), 1998, 10: 21-23. [In Chinese]
 Yao W-J, Wang W-J, Xia X-Q & Chen W-Z. Four new species of Ancyrocephalidae of marine fishes from Nanao Island, Guangdong. Acta Hydrobiologica Sinica, 1998, 22(Supplement): 120-125. [In Chinese]
 Wang W-J, Yao W-J, Liu J-X, Xiao W-H, Wang J-G & Xia X-Q. Parasite composition of the fishes in Honghu Lake. In: Hydrobiology and Resources Exploitation in Honghu Lake. (Ed. by Chen Yiyu), 1995, p322-333. Beijing, Science Press. [In Chinese]