Huaijun Zhou

Huaijun Zhou

Position Title

Department of Animal Science, College of Agricultural and Environmental Sciences

2247 Meyer Hall, One Shields Ave

Research Interests

Research in immunogenetics, molecular genetics, functional genomics, and bioinformatics. My group is focused on elucidating the molecular and cellular mechanisms of host-pathogen interaction including disease resistance, immune response, and pathogenesis of infection. The overall goals are to understand genetic regulation of host response and basic mechanisms of pathogen virulence in animals, to identify host and pathogen genes that are involved in the host-pathogen interplay. The pathogens of interest include avian influenza virus, Newcastle disease virus, Salmonella and Campylobacter.

Another area of my research is to functionally annotate regulatory elements of livestock species by integrating RNA-seq, ChIP-seq, DNA methylation and DNase-seq to identify conserved regulatory elements across different tissues and differenct species.

Grad Group Affiliations

  • Animal Biology
  • Avian Sciences
  • Immunology
  • Integrative Genetics and Genomics
  • Microbiology

Specialties / Focus

  • Animal Genomics
  • Computational Biology
  • Epigenomics
  • Integrated Genetics and Genomics


  • ANS 150 Animal Health and Disease, Spring
  • AVS 100 Avian Biology, Spring


  • Zhou lab
    • Colin Kern, Postdoctoral scholar
    • Ying Wang, Postdoctoral scholar
    • Perot Saelao, Ph.D. student
    • Tae-Hyun Kim, Ph.D. student
    • Khine Mon, Ph.D student
    • Karen Tracy, Ph.D. student
    • Kelly Chanthavixay, Lab Manager
    • ,Junjun Wang, Visiting Professor
    • James Mushi, USAID Borlaug LEAP fellow
    • Vivian Yu, Undergraduate intern
    • Catherine Lopez, Undergraduate intern
    • Shannon Chee, Undergraduate Intern
    • Ryan Liang, Undergraduate Intern
    • Hiu Ling Mak, Undergraduate Intern

Honors and Awards

  • 2016 - Evonik Degussa Award for Achievement in Poultry Science
  • 2014 - Chancellor’s Fellow
  • 2013 - The American Association of Immunologists Early Career Faculty Travel Award
  • 2011 - PSA Early Achievement Award for Research
  • 2010 - Hy-Line International Research Award
  • 2009 - Outstanding Overseas Young Investigator Award, NSF China
  • 2004 - Natural Sciences and Engineering Research Council of Canada (NSERC) Fellowship
  • 2002 - Research Excellence Award, Iowa State University

    Professional Societies

    • Poultry Science Association
    • International Society of Animal Genetics


    • 2002 Ph.D. Immunogenetics and Molecular Genetics Iowa State University
    • 2003 M.S. Bioinformatics and Computational Biology Iowa State University
    • 1988 B.S. Animal Science Yangzhou University


    Kim, T.H, H. Zhou. 2015. Functional Analysis of Chicken IRF7 in Response to dsRNA Analog Poly(I:C) by Integrating Overexpression and Knockdown: PLoS One 10.1371/journal.pone.0133450

    Zar Mon, K. K., P. Saelao, M. M. Halstead, G. Chanthavixay, H.-C. Chang, L. Garas, E. A Maga and H. Zhou. 2016. Salmonella enterica serovars Enteritidis infection alters the indigenous microbiota diversity in young layer chicks. Front. Vet. Sci. - Veterinary Infectious Diseases. 2:61. doi: 10.3389/fvets.2015.00061.

    Andersson  Leif, Archibald L Alan, Bottema D Cynthia, Brauning  Rudiger, Burgess C Shane, Burt W Dave, Casas  Eduardo, Cheng H Hans, Clarke  Laura, Couldrey  Christine, Dalrymple P Brian, Elsik G Christine, Foissac  Sylvain, Giuffra  Elisabetta, Groenen A Martien, Hayes J Ben, Huang S LuSheng, Khatib  Hassan, Kijas W James, Kim  Heebal, Lunney K Joan, McCarthy M Fiona, McEwan C John, Moore  Stephen, Nanduri  Bindu, Notredame  Cedric, Palti  Yniv, Plastow S Graham, Reecy M James, Rohrer A Gary, Sarropoulou  Elena, Schmidt J Carl, Silverstein  Jeffrey, Tellam L Ross, Tixier-Boichard  Michele, Tosser-Klopp  Gwenola, Tuggle K Christopher, Vilkki  Johanna, White N Stephen, Zhao  Shuhong, Zhou  Huaijun, The FAANG Consortium.  2015. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project. Genome Biology 16:57. DOI: 10.1186/s13059-015-0622-4

    Tuggle, C., E. Giuffra, S. N. White, L. Clarke, H. Zhou, P. J. Ross, H. Acloque, J. M. Reecy, A. Archibald, R. R. Bellone, M. Boichard, A. Chamberlain, H. Cheng, R. P.M.A. Crooijmans, M. E. Delany, C. J. Finno, M. A. M. Groenen, B. Hayes, J. K. Lunney, J. L. Petersen, G. S. Plastow, C. J. Schmidt, J. Song, M. Watson. 2016. “GO-FAANG meeting: a Gathering On Functional Annotation of ANimal Genomes” Animal Genetics DOI: 10.1111/age.12466.

    Schmid M. et al. H. Zhou. 2015. Third Report on Chicken Genes and Chromosomes.  Cytogenet Genome Res 145:78-179 (DOI:10.1159/000430927)

    Abernathy, J., Li, X., Jia, X., Chou, W., Lamont, S.J., Crooijmans, R., and Zhou, H. 2014. Copy number variation in Fayoumi and Leghorn chickens analyzed using array comparative genomic hybridization. Animal Genetics. doi: 10.1111/age.12141.

    Li J, Li R, Wang Y, Hu X, Zhao Y, Li L, Feng C, Gu X, Liang F, Lamont S, Hu S, Zhou H*, Li N. 2015. Genome-wide DNA methylome variation in two genetically distinct chicken lines using MethylC-seq. BMC Genomics, 16 :851

    Wang Y, Lupiani B, Reddy S, S. J. Lamont, Zhou H. 2014. RNA-seq analysis revealed novel genes and signaling pathway associated with disease resistance to avian influenza virus infection in chickens. Poultry Science. 93(2):485-93. doi: 10.3382/ps.2013-03557.

    Wang Y, N. Ghaffari, C. D. Johnson, U. M. Braga-Neto, H. Wang, R. Chen, H. Zhou. 2011 Evaluation of the coverage and depth of transcriptome by RNA-Seq in chickens. BMC Bioinformatics 12: Suppl 10, doi:10.1186/1471-2105-12-S10-S5.

    Sandford E, M. Orr , E. Balfanz , N. Bowerman , X. Li , H. Zhou , T. J Johnson , S. Kariyawasam , P. Liu , L K Nolan and S. J Lamont. 2011. Spleen transcriptome response to infection with avian pathogenic Escherichia coli in broiler chickens. BMC Genomics 12:469

    Yu Y, J. Luo, A. Mitra, S. Chang, F. Tian, H. Zhang, P. Yuan, H. Zhou, J. Song. 2011 Temporal Transcriptome Changes Induced by MDV in Marek's Disease-Resistant and -Susceptible Inbred Chickens BMC Genomics 12:501

    Wang X., F. Yang, C. Liu, H. Zhou, G. Wu, S. Qiao, D. Li, J. Wang. 2011. Dietary Supplementation with Probiotic L. fermentum I5007 and Antibiotic Aureomycin Differentially Affects the Small-Intestinal Proteomes of Weanling Piglets. Journal of Nutrition in press.

    Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, F. McCarthy, S. Burgess, Y. Pevzner,H. Zhou. 2011. Systemic Response to Campylobacter jejuni Infection by Profiling Gene Transcription in the Spleens of Two Genetic Lines of Chickens. Immunogenetics in press.

    Gang Lin, Chuang Liu, Huaijun Zhou, Shuo Feng, Yiqiang Chen, Luoyun Fang, Guoyao Wu, Jing Zhang, Shiyan Qiao and Junjun Wang*. Progresses on Personalized Nutritional Evaluation and ecommendation. Journal of Animal Science and Biotechnology. 2010, 1(3): 182-193.

    Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, H. Zhou. 2011. Cecal transcriptome analysis of colonized and non-colonized chickens within two genetic lines that differ in cecal colonization by Campylobacter jejuni. Animal Genetics 42, 491–500.

    Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, H. Zhou. 2010. Gene expression profiling of the local cecal response of genetic chicken lines that differ in their susceptibility to Campylobacter jejuni colonization. PLoS ONE 5(7): e11827. doi:10.1371/journal.pone.0011827

    Lee JY, Song JJ, Wooming A. Li XY, HJ Zhou, Bottje W. Kong BW. 2010 Transcriptional profiling of host gene expression in chicken embryo lung cells infected with laryngotracheitis virus. BMC Genomics 2010, 11:445.

    Heidari M., A. Lopes, M. Huebner, S. Sharif, D. Kireev and H. Zhou. 2010. Marek’s disease virus-induced immunosuppression: array analysis of chicken immune response genes expression profiling. Viral Immunology 23(3):309-19.

    Huo Y, X. Guo, H. Li, H. Wang, W. Zhang, Y. Wang, H. Zhou, Z. Gao, J. Ye, Y. E. Chen, R. Chapkin, and C. Wu. 2010. Disruption of PFKFB3/iPFK2 Increases Diet-induced Adipose Tissue Inflammatory Response and Systemic Insulin Resistance. Journal of Biological Chemistry. 285(6):3713-21.

    Wang Y., V. Brahmakshatriya, B. Lupiani, S. Reddy, B. Yoon, H. Zhu, P. Gunaratne, R. Chen, J. Wang, H. Zhou. 2009. Identification of differentially expressed microRNAs In chicken lung and trachea with avian influenza virus infection by Solexa Sequencer. BMC Genomics 10:512. (Highly assessed)

    Lu Y, Lopes A, S. Sharif, K. Zhu, H. Zhou, H. Yu, and J. Gong. 2009. Expression profiles of genes in Toll-like receptor-mediated signaling of broilers infected with Clostridium perfringens. Clinical and Vaccine Immunology 16:1639-1647.

    Kong, X., YZ Zhang, YL Yin, GY Wu, HJ Zhou, ZL Tan, F Yang, MJ Bo, RL Huang, TJ Li, MM Geng. 2009. Chinese yam polysaccharide enhances growth performance and cellular immune response in weanling rats. J. Sci. Food Agric. DOI 10.1002/jsfa.3688.

    Chiang HI, LR. Berghman, H. Zhou. 2009. Inhibition of NF-kB 1 (NF-kBp50) by RNA interference in chicken macrophage HD11 cell line challenged with Salmonella enteritidis. Genetics and Molecular Biology 32:507-515.

    Sarson, AJ. Wang Y*, Kang Z, Dowd SE, Lu Y., Yu H., Han Y, Zhou H. and J. Gong. 2009. Gene expression profiling within the spleen of Clostridium perfringens-challenged Broilers fed antibiotic-medicated and non-medicated diets. BMC Genomics 10:260.

    Satterfield, C. G. Song, K. Kochan, PK Riggs, R. Simmons, C. Elsik, D. Adelson, F. Bazer, H. Zhou, T. Spencer. 2009. Discovery of candidate genes in the endometrium regulating ovine blastocyst growth and conceptus elongation. Physiological Genomics 39:85-99.

    Zhou H, J. Gong, J. Brisbin, H. Yu, A. Sarson, W. Si, S. Sharif, and Y. Han. 2009. Transcriptional Profiling Analysis of Host response to Clostridium perfringens Infection in Broilers. Poult. Sci. 88:1023-1032.

    Wang J. G. Wu. H. Zhou. F. Wang. 2009. Emerging technologies for amino acid nutrition research in the post-genome era. Amino Acids. 37:177-186.

    E. Koren, H. Zhou, A. Cahaner, E.D. Heller, J. Pitcovski, S.J. Lamont. 2008 . Unique Co-expression of Immune Cell-related Genes in IBDV Resistant Chickens Indicates the Activation of Specific Cellular Host-response Mechanisms. In : Pinard M-H, Gay C, Pastoret P-P, Dodet B (eds): Animal Genomics for Animal Health. Dev Biol (Basel). Basel, Karger, 2008, vol 132, p 153-159.

    H.I. Chiang,, C. Swaggerty, M. Kogut, S. Dowd, X. Li, I. Pevzner, and H. Zhou. 2008. Gene expression profiling in chicken heterophils with Salmonella enteritidis stimulation using a chicken 44K Agilent microarray BMC Genomics 9:526.

    Li X., C. L. Swaggerty, M. H. Kogut, H. Chiang, Y. Wang, K. J. Genovese, H. He, N. J. Stern, I. Y. Pevzner, H. Zhou. 2008. The Paternal Effect of Campylobacter jejuni Colonization in Ceca in Broilers. Poult. Sci. 87:1742-1747.

    Wang J, L. Chen, P. Li, X. Li, H. Zhou, F. Wang, D. Li, Y. Yin, and G. Wu. 2008. Gene expression is altered in piglet small intestine by weaning and dietary glutamine supplementation. J. Nutrition 138:1025-1032.

    X.Y. Li, H.I. Chiang, J. Zhu, S. Dowd and H. Zhou. 2008. Characterization of newly developed chicken 44K Agilent microarray. BMC Genomics 9:60. (Highly assessed)