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United States Department of Agriculture

Agricultural Research Service

Research Project: Employing Genomics, Epigenetics, and Immunogenetics to Control Diseases Induced by Avian Tumor Viruses Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Isolation, identification and evolution analysis of a novel subgroup of avian leukosis virus isolated from a local Chinese yellow broiler in South China - (Peer Reviewed Journal)
(01-Jul-16)
Transcriptional analyses of response to vaccines in two highly inbred lines of White Leghorns resistant or susceptible to Marek’s disease - (Abstract Only)
Dong, K., Chang, S., Xie, O., Zhang, H. 2016. Transcriptional analyses of response to vaccines in two highly inbred lines of White Leghorns resistant or susceptible to Marek’s disease [abstract]. In: Proceeding for the 11th International Symposium on Marek's Disease and Avian Herpesviruses, July 6-9, 2016, Tours, France. p. 69.
In vitro characterization of felid herpesvirus 1 (FHV-1) mutants generated by recombineering in a recombinant BAC vector - (Peer Reviewed Journal)
Tai, S., Holz, C., Engstrom, M.D., Cheng, H.H., Maes, R.K. 2016. In vitro characterization of felid herpesvirus 1 (FHV-1) mutants generated by recombineering in a recombinant BAC vector. Virus Research. 221(2016):15-22. doi: 10.1016/j.virusres.2016.05.001.
Validation of alternative transcript splicing in chicken lines that differ in genetic resistance to Marek’s disease - (Peer Reviewed Journal)
Kaya, M., Preeyanon, L., Dodgson, J., Cheng, H.H. 2016. Validation of alternative transcript splicing in chicken lines that differ in genetic resistance to Marek’s disease. Animal Biotechnology. 27(4):238-244 doi: 10.1080/10495398.2016.1178139.
Molecular characterization, phylogeny analysis and pathogenicity of a Muscovy duck adenovirus strain isolated in China in 2014 - (Peer Reviewed Journal)
Zhang, X., Zhong, Y., Zhou, Z., Liu, Y., Zhang, H., Chen, F., Chen, W., Xie, Q. 2016. Molecular characterization, phylogeny analysis and pathogenicity of a Muscovy duck adenovirus strain isolated in China in 2014. Virology. 493(2016):12-21. doi: 10.1016/j.virol.2016.03.004.
Differential expression profiles of miRNAs induced by vaccination followed by Marek’s disease virus challenge at cytolytic stage in chickens resistant or susceptible to Marek’s disease - (Abstract Only)
Zhang, H., Chang, S., Xie, Q., He, Y., Dong, K., Ernst, C.W., Song, J. 2016. Differential expression profiles of miRNAs induced by vaccination followed by Marek’s disease virus challenge at cytolytic stage in chickens resistant or susceptible to Marek’s disease. In Proceedings of: International Conference of Plant and Animal Genome, January 8-13, 2016, San Diego, California. W776.
The conservation and signatures of lincRNAs in Marek’s disease of chicken - (Abstract Only)
Song, J., He, Y., Zhang, H., Yang, N. 2016. The conservation and signatures of lincRNAs in Marek’s disease of chicken. In Proceedings of: International Conference of Plant and Animal Genome, January 8-13, 2016, San Diego, California. P0664.
Genetic susceptibility to and presence of endogenous avian leukosis viruses impose no significant impact on survival days of chickens challenged with very virulent plus Marek's disease virus - (Peer Reviewed Journal)
Chang, S., Xie, Q., Wang, C., Heidari, M., Ernst, C.W., Dunn, J.R., Zhang, H. 2015. Genetic susceptibility to and presence of endogenous avian leukosis viruses impose no significant impact on survival days of chickens challenged with very virulent plus Marek's disease virus. Annals of Virology and Research. 1(2):1007.
Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek’s disease is predominantly determined by transcriptional regulation - (Peer Reviewed Journal)
Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A.A., Dunn, J.R., Muir, W.M. 2015. Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek’s disease is predominantly determined by transcriptional regulation. Biomed Central (BMC) Genomics. DOI: 10.1186/s12864-015-2016-0.
The conservation and signatures of lincRNAs in Marek’s disease of chicken - (Peer Reviewed Journal)
He, Y., Ding, Y., Zhan, F., Zhang, H., Han, B., Hu, G., Zhao, K., Yang, N., Yu, Y., Mao, L., Song, J. 2015. The conservation and signatures of lincRNAs in Marek’s disease of chicken. Scientific Reports. DOI: 10.1038/srep15184.
Reproductive Characteristics Differed in a Series of B-Congenic Lines of White Leghorns Evidently Indicating Significant Influence of Major Histocompatibility Complex in Chickens - (Peer Reviewed Journal)
Wang, C., Kulkarni, G., Zhang, H. 2015. Reproductive Characteristics Differed in a Series of B-Congenic Lines of White Leghorns Evidently Indicating Significant Influence of Major Histocompatibility Complex in Chickens. International Journal of Poultry Science. 14(8):441-448.
Histone modifications induced by MDV infection at early cytolytic and latency phases     Reprint Icon - (Peer Reviewed Journal)
Mitra, A., Luo, J., He, Y., Gu, Y., Zhang, H., Zhao, K., Cui, K., Song, J. 2015. Histone modifications induced by MDV infection at early cytolytic and latency phases. Biomed Central (BMC) Genomics. 16:311. doi:10.1186/s12864-015-1492-6.
Transcriptome variation in response to Marek’s disease virus acute infection     Reprint Icon - (Peer Reviewed Journal)
Preeyanon, L., Brown, C., Cheng, H.H. 2015. Transcriptome variation in response to Marek’s disease virus acute infection. Cytogenetics and Genome Research. 145:154-163.
Intronic deletions of tva receptor gene decrease the susceptibility to infection by subgroup A avian sarcoma and leukosis virus subgroup A     Reprint Icon - (Peer Reviewed Journal)
Chen, W., Yang, L., Li, H., Chang, S., Shu, D., Zhang, H., Chen, F., Xie, Q. 2015. Intronic deletions of tva receptor gene decrease the susceptibility to infection by subgroup A avian sarcoma and leukosis virus subgroup A. Scientific Reports. 5:9900. doi: 10.1038/srep09900.
Biological characterization of a serotype 1 Marek’s disease virus-vectored Bi-valent 4 vaccine for infectious laryngotracheitis and Marek’s disease - (Peer Reviewed Journal)
(10-Feb-15)
The influence of major histocompatibility complex and vaccination with turkey herpesvirus on Marek's disease virus evolution     Reprint Icon - (Peer Reviewed Journal)
Hunt, H.D., Dunn, J.R. 2015. The influence of major histocompatibility complex and vaccination with turkey herpesvirus on Marek's disease virus evolution. Avian Diseases. 59(1):122-129.
Evaluation of reproductive characteristics of 21 highly inbred lines of White Leghorns divergently selected for or segregating in tumor resistance     Reprint Icon - (Peer Reviewed Journal)
Kulkarni, G., Zhang, H. 2015. Evaluation of reproductive characteristics of 21 highly inbred lines of White Leghorns divergently selected for or segregating in tumor resistance. Open Journal of Animal Sciences. 5:59-70. doi: 10.4236/ojas.2015.51008.
Vaccine induced differential expressions of miRNAs at cytolytic stage in chickens resistant or susceptible to Marek’s disease - (Abstract Only)
Zhang, H., Xie, Q., Chang, S., He, Y., Ernst, C., Song, J. 2015. Vaccine induced differential expressions of miRNAs at cytolytic stage in chickens resistant or susceptible to Marek’s disease. Meeting Abstract. Plant & Animal Genome XXIII, January 10-14, 2015. Paper No. W643.
Prior genetic architecture impacting genomic regions under selection: An example using genomic selection in two poultry breeds     Reprint Icon - (Peer Reviewed Journal)
Zhang, X., Misztal, I., Heidaritabar, M., Bastiaansen, J.W., Hawken, R.R., Okimoto, R., Sapp, R.L., Cheng, H.H., Muir, W.M. 2015. Prior genetic architecture impacting genomic regions under selection: An example using genomic selection in two poultry breeds. Livestock Science. 171(2015):1-11. doi:10.1016/j.livsci.2014.11.003.
AN MHC class I immune evasion gene of Marek's disease virus     Reprint Icon - (Peer Reviewed Journal)
Hearn, C., Preeyanon, L., Hunt, H.D., York, I.A. 2014. AN MHC class I immune evasion gene of Marek's disease virus. Virology. 475:88-95. doi:10.1016/j.virol.2014.11.008.
Genomic selection for genetic resistance to Marek's disease - (Abstract Only)
Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A.A., Dunn, J.R., Muir, W.M. 2014. Genomic selection for genetic resistance to Marek's disease [abstract]. In: Proceeding of 10th International Symposium on Marek's Disease and Avian Herpesviruses, July 20-23, 2014, East Lansing, Michigan. p. 45.
Characterizing a point mutation within the UL5 gene that reduces in vivo replication and MD incidence - (Abstract Only)
Hildebrandt, E., Dunn, J.R., Cheng, H.H. 2014. Characterizing a point mutation within the UL5 gene that reduces in vivo replication and MD incidence [abstract]. In: Proceeding for 10th International Symposium on Marek's Disease and Avian Herpesviruses, July 20-23, 2014, East Lansing, Michigan. p. 58.
Influence of Marek’s disease virus on the core-gut microbiome of chickens resistant or susceptible to Marek’s disease - (Abstract Only)
Perumbakkam, S., Hunt, H.D., Cheng, H.H. 2014. Influence of Marek’s disease virus on the core-gut microbiome of chickens resistant or susceptible to Marek’s disease [abstract]. In: Proceeding of 10th International Symposium on Marek's Disease and Avian Herpesviruses, July 20-23, 2014, East Lansing, Michigan. p. 51.
Differential expression profiling of miRNAs between Marek’s disease resistant and susceptible chickens - (Abstract Only)
Zhang, H., Xie, Q., Chang, S., He, Y., Ernst, C., Heidari, M., Black Pyrkosz, A.A., Song, J. 2014. Differential expression profiling of miRNAs between Marek’s disease resistant and susceptible chickens [abstract]. In: Proceeding of 10th International Symposium on Marek's Disease and Avian Herpesviruses, July 20-23, 2014, East Lansing, Michigan. p.47.
LincRNAs in CD4+ T cells and Marek’s disease - (Abstract Only)
He, Y., Ding, Y., Zhang, H., Cheng, H.H., Zhao, K., Song, J. 2014. LincRNAs in CD4+ T cells and Marek’s disease [abstract]. In: Proceeding of 10th International Symposium on Marek's Disease and Avian Herpesviruses, July 20-23, 2014, East Lansing, Michigan. p. 46.
Marek’s Disease Virus influences the core gut microbiome of the chicken during the early and late phases of viral replication     Reprint Icon - (Peer Reviewed Journal)
Perumbakkam, S., Hunt, H.D., Cheng, H.H. 2014. Marek’s Disease Virus influences the core gut microbiome of the chicken during the early and late phases of viral replication. FEMS Microbiology Ecology. 90(1):300-312. doi: 10.1111/1574-6941.12392.
Infection with Marek’s disease virus induces high levels of CD8a/a cells in chickens resistant to Marek’s disease - (Abstract Only)
Hunt, H.D., Hearn, C., Perumbakkam, S., Cheng, H.H. 2014. Infection with Marek’s disease virus induces high levels of CD8a/a cells in chickens resistant to Marek’s disease. Meeting Abstract. Guelph, Canada, July 16, 2014.
Single nucleotide polymorphism variants within tva and tvb receptor genes in Chinese chickens - (Peer Reviewed Journal)
Lao, C., Chen, S., Chen, W., Liu, Y., Sun, B., Li, H., Zhang, H., Qu, H., Wang, J., Shu, D., Xie, Q. 2014. Single nucleotide polymorphism variants within tva and tvb receptor genes in Chinese chickens. Poultry Science. 93(10): 2482-2489. DOI: 10.3382/PS.2014-04077.
Temporal kinetics of Marek's disease herpesvirus: integration occurs early after infection in both B and T cells     Reprint Icon - (Peer Reviewed Journal)
Robinson, C.M., Cheng, H.H., Delany, M.E. 2014. Temporal kinetics of Marek's disease herpesvirus: integration occurs early after infection in both B and T cells. Cytogenetics and Genome Research. 144(2):142-154. doi: 10.1159/000368379.
The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant talpid2     Reprint Icon - (Peer Reviewed Journal)
Chang, C., Schock, E.N., O'Hare, E.A., Dodgson, J.B., Cheng, H.H., Muir, W.M., Edelmann, R.E., Delany, M.E., Brugmann, S.A. 2014. The cellular and molecular etiology of the craniofacial defects in the avian ciliopathic mutant talpid2. Development. 141:3003-3012. Available: http://dev.biologists.org/content/141/15/3003.long.
Mapping and genotypic analysis of NK-lysin gene in chicken     Reprint Icon - (Peer Reviewed Journal)
Lee, M., Yang, E., Morrison, M., Vignal, A., Huang, Y., Cheng, H.H., Muir, W.M., Lamont, S.J., Lillehoj, H.S., Lee, S.H., Womack, J.E. 2014. Mapping and genotypic analysis of NK-lysin gene in chicken. Genetic Selection Evolution. 46:43. Available: http://www.gsejournal.org/content/46/1/43.
Systematic Differences in the Response of Genetic Variation to Pedigree and Genome Based Selection Methods     Reprint Icon - (Peer Reviewed Journal)
Heidaritabar, M., Vereijken, A., Muir, W.M., Meuwissen, T., Cheng, H.H., Megens, H., Groenen, M.A., Bastiaansen, J.W. 2014. Systematic Differences in the Response of Genetic Variation to Pedigree and Genome Based Selection Methods. Heredity. 55:1-11. Available: http://www.nature.com/hdy/journal/vaop/ncurrent/full/hdy201455a.html.
Allele-Specific Expression Screening Demonstrates that Variation in Genetic Resistance to Marek’s Disease in Chicken is Mainly Controlled at the Transcriptional Level - (Proceedings)
Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A.A., Dunn, J.R., Muir, W.M. 2014. Mapping and genotypic analysis of NK-lysin gene in chicken. Proceedings of World Congress of Genetics Applied in Livestock Production. Vancouver, BC Canada, August 17, 2014.
gga-miR-375 plays a key role in tumorigenesis post subgroup J Avian Leukosis Virus infection     Reprint Icon - (Peer Reviewed Journal)
Li, H., Shang, H., Shu, D., Zhang, H., Ji, J., Sun, B., Li, H., Xie, Q. 2014. gga-miR-375 plays a key role in tumorigenesis post subgroup J Avian Leukosis Virus infection. PLoS One. 9(4):e90878. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0090878.
Host genetic resistance to Marek’s disease sustains protective efficacy of herpesvirus of turkey in both experimental and commercial lines of chickens     Reprint Icon - (Peer Reviewed Journal)
Chang, S., Xie, Q., Dunn, J.R., Ernst, C.W., Song, J., Zhang, H. 2014. Host genetic resistance to Marek’s disease sustains protective efficacy of herpesvirus of turkey in both experimental and commercial lines of chickens. Vaccine. 32(16):1820-1827. Available: http://www.sciencedirect.com/science/article/pii/S0264410X14001558.
Preliminary analysis of microRNA transcriptome altered by vaccine and Marek’s disease virus in chickens - (Abstract Only)
Zhang, H., Xie, Q., Chang, S., Ernst, C.W., Song, J. 2014. Preliminary Analysis of MicroRNA Transcriptome Altered by Vaccine and Marek’s Disease Virus in Chickens. Plant and Animal Genome Conference. Paper No. 9952. Available: https://pag.confex.com/pag/xxii/webprogram/Paper9952.html.
Differential expression of Toll-like receptor pathway genes in chicken embryo fibroblasts from chickens resistant and susceptible to Marek’s disease     Reprint Icon - (Peer Reviewed Journal)
Haunshi, S., Cheng, H.H. 2014. Differential expression of Toll-like receptor pathway genes in chicken embryo fibroblasts from chickens resistant and susceptible to Marek’s disease. Poultry Science. 93:550-555. Available: http://dx.doi.org/10.3382/ps.2013-03597.
The Genetic Architecture of Genetic Resistance to Marek's Disease - (Proceedings)
Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A.A., Subramaniam, S., Preeyanon, L., Dunn, J.R., Van Sambeek, F., Ansah, G., Muir, W.M. 2013. The Genetic Architecture of Genetic Resistance to Marek's Disease. In: Proceedings of the 8th European Symposium on Poultry Genetics, September 25-27, 2013, Venice, Italy. p. 12-13.
Transcriptional profiling of Meq-dependent genes in Marek’s disease resistant and susceptible inbred chicken lines     Reprint Icon - (Peer Reviewed Journal)
Subramaniam, S., Preeyanon, L., Cheng, H.H. 2013. Transcriptional profiling of Meq-dependent genes in Marek’s disease resistant and susceptible inbred chicken lines. PLoS One. 8(10):e78171. Available: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0078171.
Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by the Marek's disease virus oncoprotein Meq     Reprint Icon - (Peer Reviewed Journal)
Subramaniam, S., Johnston, J., Preeyanon, L., Brown, C., Kung, H., Cheng, H.H. 2013. Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by the Marek's disease virus oncoprotein Meq. Journal of Virology. 87(16):9016-9029. Available at: http://jvi.asm.org/content/87/16/9016.full.
Visualization of Marek’s disease virus in vitro using enhanced green fluorescent protein fused with US10     Reprint Icon - (Peer Reviewed Journal)
Mao, W., Kim, T., Cheng, H.H. 2013. Visualization of Marek’s disease virus in vitro using enhanced green fluorescent protein fused with US10. Virus Genes. 47(1):181-183. Available: http://link.springer.com/journal/11262/47/1/page/2.
DNMT gene expression and methylome in Marek’s disease resistant and susceptible chickens prior to and following infection by MDV     Reprint Icon - (Peer Reviewed Journal)
Tian, F., Zhan, F., Vanderkraats, N.D., Hiken, J.F., Edwards, J.R., Zhang, H., Zhao, K., Song, J. 2013. DNMT gene expression and methylome in Marek’s disease resistant and susceptible chickens prior to and following infection by MDV. Epigenetics. 8(4):431-444.
Does resistance to Marek’s disease select for specific gut microflora that play a role in influencing the host immune response - (Abstract Only)
Sudeep, P., Hunt, H.D., Cheng, H.H. 2013. Does resistance to Marek’s disease select for specific gut microflora that play a role in influencing the host immune response. Meeting Abstract. Keystone Symposia Conference, The Gut Microbiome: The Effector/Regulator Immune Network, February 10-15, 2013, Taos, New Mexico.
Reproducible Bioinformatics Research for Biologists - (Book / Chapter)
(09-Feb-13)
DNA methylation down-regulates EGFR expression in chicken     Reprint Icon - (Peer Reviewed Journal)
Luo, J., Chang, S., Zhang, H., Li, B., Song, J. 2013. DNA methylation down-regulates EGFR expression in chicken. Avian Diseases. 57(2):366-371.
Identification of direct gene targets that the MDV oncoprotein Meq regulates via ChIP and expression analyses - (Abstract Only)
Subramaniam, S., Preeyanon, L., C. Titus, B., Cheng, H.H. 2013. Identification of direct gene targets that the MDV oncoprotein Meq regulates via ChIP and expression analyses [abstract]. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. A-W638. Available: https://pag.confex.com/pag/xxi/webprogram/Paper5456.html.
Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek's disease - (Abstract Only)
Luo, J., Yu, Y., Mitra, A., Zhang, H., Liu, G., Song, J. 2013. Genome-wide copy number variant analysis in inbred chickens lines with different susceptibility to Marek's disease [abstract]. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. A-P0649. Avaliable: https://pag.confex.com/pag/xxi/webprogram/Paper5185.html.
Identification of specific long noncoding RNA profiles in chicken with different susceptibility to Marek's disease - (Abstract Only)
Luo, J., Zhang, H., Zhao, K., Song, J. 2013. Identification of specific long noncoding RNA profiles in chicken with different susceptibility to Marek's disease [abstract]. Plant and Animal Genome XXI Conference, January 12-16, San Diego, California. A-P0651. Available:https://pag.confex.com/pag/xxi/webprogram/Paper5186.html.
Marek's Disease Virus Infection Induces Widespread Differential Chromatin Marks in Inbred Chicken Lines - (Abstract Only)
Mitra, A., Luo, J., Zhang, H., Zhao, K., Song, J. 2013. Marek's Disease Virus Infection Induces Widespread Differential Chromatin Marks in Inbred Chicken Lines [abstract]. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. A-P0650. Available:https://pag.confex.com/pag/xxi/webprogram/Paper5688.html.
Host Genetics and Vaccine Efficacy: Global gene expression differentiation induced by vaccine and MDV in MD resistant and susceptible chickens based on Next-Gen RNA-Seq reads - (Abstract Only)
Zhang, H., Chang, S., Xie, Q., Song, J., Ernst, C. 2013. Host Genetics and Vaccine Efficacy: Global gene expression differentiation induced by vaccine and MDV in MD resistant and susceptible chickens based on Next-Gen RNA-Seq reads [abstract]. Plant and Animal Genome XXI Conference, January 12-16, 2013, San Diego, California. A-W640. Available: https://pag.confex.com/pag/xxi/webprogram/Paper5459.html.
Last Modified: 8/25/2016
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