Research Geneticist
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Influence of Vaccines, Host Genetics and Pathogen Mutation Rates on the Evolutionary Dynamics of Infectious Diseases - Purdue Cooperative Agreement (A) Accession Number:439583 
Elucidation of Molecular Determinants of Avian Herpesviruses Virulence and Evolution to Inform the Development of Safe and Effective Vaccines In-House Appropriated (D) Accession Number:441124 Enhancing Genetic Resistance and Vaccinal Response to Control Marek's Disease, Infectious Laryngotracheitis, and Infectious Bursal Disease in Chicken In-House Appropriated (D) Accession Number:443180 Influence of Vaccines, Host Genetics, and Pathogen Mutation Rates on the Evolutionary Dynamics of Infectious Diseases - Berlin Non-Assistance Cooperative Agreement (S) Accession Number:439572
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-(Peer Reviewed Journal)
Pan, Z., Wang, Y., Wang, M., Wang, Z., Zhu, X., Gu, S., Zhong, C., An, L., Damas, J., Halsted, M., Cheng, H.H., Zhou, H. 2023. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. Science Advances. 9:eade1204. https://www.science.org/doi/10.1126/sciadv.ade1204. -(Peer Reviewed Journal)
Warren, W.C., Rice, E.S., Meyer, A., Hearn, C.J., Steep, A., Hunt, H.D., Monson, M.S., Lamont, S.J., Cheng, H.H. 2023. The immune cell landscape and response of Marek's disease resistant and susceptible chickens infected with Marek's disease virus . Scientific Reports. 13. Article 5355. https://doi.org/10.1038/s41598-023-32308-x. -(Peer Reviewed Journal)
Hearn, C.J., Cheng, H.H. 2023. Contribution of the TCR beta repertoire to Marek's disease genetic resistance in chicken. Viruses. 15(3):607. https://doi.org/10.3390/v15030607. -(Peer Reviewed Journal)
Fiddaman, S., Klopp, C., Charles, M., Bardou, P., Lebrasseur, O., Derks, M., Schauer, J., Reimer, C., Geibel, J., Gheyas, A., Smith, A., Schnabel, R., Martin Cerezo, M., Nishibori, M., Godinez, C.P., Layos, J.N., Larson, G., Ng'Ang'A, I., Muir, W., Lange, M., Wright, D., Simianer, H., Cheng, H.H., Weigend, S., Warren, W., Crooijmans, R., Hanotte, O., Smith, J., Tixier-Boichard, M., Frantz, L. 2023. Chicken genomic diversity consortium: large-scale genomics to unravel the origins and adaptations of chickens. Cytogenetics and Genome Research. 90-94. https://doi.org/10.1159/000529376. -(Peer Reviewed Journal)
Warren, W.C., Fedrigo, O., Tracey, A., Mason, A.S., Formenti, G., Perini, F., Wu, Z., Murphy, T., Schneider, V., Stiers, K., Rice, E.S., Coghill, L., Anthony, N., Okimoto, R., Carroll, R., Mountecastle, J., Balacco, J., Haase, B., Yang, C., Zhang, G., Smith, J., Dreschler, Y., Cheng, H.H., Howe, K., Jarvis, E. 2023. Multiple chicken (Gallus gallus) genome references to advance genetic variation studies. Cytogenetics and Genome Research. 3-12. https://doi.org/10.1159/000529376. -(Peer Reviewed Journal)
Xing, N., Hofler, T., Hearn, C.J., Nascimento, M., Camps Paradell, G., Mcmahon, D.P., Kunec, D., Cheng, H.H., Trimpert, J., Osterrieder, N. 2022. Fast forwarding evolution – accelerated adaptation in a proofreading deficient hypermutator herpesvirus. Virus Evolution. 8(2):veac099. https://doi.org/10.1093/ve/veac099. -(Peer Reviewed Journal)
Guan, D., Halsted, M.M., Islas-Trejo, A.D., Goszczynski, D.E., Cheng, H.H., Ross, P.J., Zhou, H. 2022. Prediction of transcript isoforms in 19 chicken tissues by Oxford Nanopore long-read sequencing. Frontiers in Genetics. 13:997460. https://doi.org/10.3389/fgene.2022.997460. -(Peer Reviewed Journal)
Steep, A., Hildebrandt, E.C., Xu, H., Hearn, C.J., Frishman, D., Niikura, M., Dunn, J.R., Kim, T.N., Conrad, S.J., Muir, W.M., Cheng, H.H. 2022. Identification and validation of Ikaros (IKZF1) as a cancer driver gene for Marek’s disease virus-induced lymphomas. Microorganisms. 10(2):401. https://doi.org/10.3390/microorganisms10020401. -(Peer Reviewed Journal)
Stephan, T., Burgess, S.M., Cheng, H.H., Danko, C., Gill, C.A., Jarvis, E.D., Koepfli, K., Koltes, J.E., Lyons, E., Ronald, P., Ryder, O.A., Schriml, L.M., Soltis, P., Vandewoude, S., Zhou, H., Ostrander, E.A., Karlsson, E.K. 2022. Darwinian genomics and diversity in the tree of life. Proceedings of the National Academy of Sciences(PNAS). 119:4. https://doi.org/10.1073/pnas.2115644119. -(Book / Chapter)
Cheng, H.H., Warren, W.C., Zhou, H. 2021. Avian genomics. Book Chapter. In: Scanes, Collin G., Dridi, Sami, editors. Sturkie's Avian Physiology. 7th edition. San Diego, CA: Academic Press. p. 7-16. https://doi.org/10.1016/B978-0-12-819770-7.00047-5. -(Peer Reviewed Journal)
Glass, M.C., Smith, J.M., Cheng, H.H., Delany, M.E. 2021. Marek’s disease virus telomeric integration profiles of neoplastic host tissues reveal unbiased chromosomal selection and loss of cellular diversity during tumorigenesis. Genes. 12(10):1630. https://doi.org/10.3390/genes12101630. -(Peer Reviewed Journal)
Hoencamp, C., Dudchenko, O., Elbatsh, A.M., Brahmachari, S., Raaijmakers, J.A., Van Schaik, T., Sedeño Cacciatore, A., Contessoto, V., Hildebrandt, E.C., Cheng, H.H., Lieberman Aiden, E., Rowland, B.D. 2021. 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. Science. 372(6545):984-989. https://doi.org/10.1126/science.abe2218. -(Peer Reviewed Journal)
Tixier-Boichard, M., Fabre, S., Dhorne-Pollet, S., Goubil, A., Acloque, H., Vincent-Naulleau, S., Ross, P., Wang, Y., Chanthavixay, G., Cheng, H.H., Catherine, E., Leesburg, V.L., Giuffra, E., Zhou, H. 2021. Tissue resources for the functional annotation of animal genomes. Frontiers in Genetics. 12:666265. https://doi.org/10.3389/fgene.2021.666265. -(Peer Reviewed Journal)
Kern, C., Ying, W., Xu, X., Pan, Z., Halstead, M., Chanthavixay, G., Saelao, P., Waters, S., Xiang, R., Chamberlain, A., Korf, I., Delany, M.E., Cheng, H.H., Medrano, J.F., Van Eenennaam, A.L., Tuggle, C.K., Ernst, C., Flicek, P., Quon, G., Ross, P., Zhou, H. 2021. Functional annotations of three domestic animal genomes provide vital resources for comparative and agricultural research. Nature Communications. 12:1821. https://doi.org/10.1038/s41467-021-22100-8. -(Peer Reviewed Journal)
Umthong, S., Dunn, J.R., Cheng, H.H. 2020. Depletion of CD8aß+ T cells in chickens demonstrates their involvement in protective immunity towards Marek’s disease with respect to tumor incidence and vaccinal protection. Vaccines. 8(4):557. https://doi.org/10.3390/vaccines8040557. -(Peer Reviewed Journal)
Bai, H., He, Y., Ding, Y., Chu, Q., Lian, L., Heifetz, E.M., Yang, N., Cheng, H.H., Zhang, H., Chen, J., Song, J. 2020. Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek's disease using next generation sequencing. BMC Genetics. 21:77. https://doi.org/10.1186/s12863-020-00884-w. -(Peer Reviewed Journal)
Bailey, R.I., Cheng, H.H., Chase-Topping, M., Mays, J.K., Anacleto, O., Dunn, J.R., Doeschl-Wilson, A. 2020. Pathogen transmission from vaccinated hosts can cause dose-dependent reduction in virulence. PLoS Biology. 18(3):e3000619. https://doi.org/10.1371/journal.pbio.3000619. -(Peer Reviewed Journal)
Umthong, S., Dunn, J.R., Cheng, H.H. 2019. Towards a mechanistic understanding of the synergistic response induced by bivalent Marek’s disease vaccines to prevent lymphomas. Vaccine. 37(43):6397-6404. https://doi.org/10.1016/j.vaccine.2019.09.003. -(Peer Reviewed Journal)
Dunn, J.R., Black Pyrkosz, A., Steep, A., Cheng, H.H. 2019. Identification of Marek’s disease virus genes associated with virulence of US strains. Journal of General Virology. 100(7):1132-1139. https://doi.org/10.1099/jgv.0.001288. -(Peer Reviewed Journal)
Rexroad III, C.E., Vallet, J.L., Matukumalli, L.K., Ernst, C., Van Tassell, C.P., Cheng, H.H., Reecy, J., Fulton, J., Taylor, J., Lunney, J.K., Liu, J., Cockett, N., Smith, T.P., Van Eenennaam, A., Clutter, A., Telugu, B., Purcell, C., Bickhart, D.M., Blackburn, H.D., Neibergs, H., Wells, K., Boggess, M.V., Sonstegard, T. 2019. Genome to phenome: improving animal health, production, and well-being: a new USDA blueprint for animal genome research 2018–2027. Frontiers in Genetics. 10:327. https://doi.org/10.3389/fgene.2019.00327. -(Peer Reviewed Journal)
Kern, C., Wang, Y., Chitwood, J., Korf, I., DeLany, M., Cheng, H.H., Medrano, J.F., Van Eenennaam, A.L., Ernst, C., Ross, P., Zhou, H. 2018. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics. 19:684. https://doi.org/10.1186/s12864-018-5037-7. -(Peer Reviewed Journal)
Xu, L., He, Y., Ding, Y., Liu, G., Zhang, H., Cheng, H.H., Taylor, R.L., Song, J. 2018. Genetic assessment of inbred chicken lines indicates genomic signatures of resistance to Marek’s disease. Journal of Animal Science and Biotechnology. 9:65. https://doi.org/10.1186/s40104-018-0281-x. -(Peer Reviewed Journal)
McPherson, M.C., Cheng, H.H., Smith, J.M., Delany, M.E. 2018. Vaccination and host Marek's disease-resistance genotype significantly reduce oncogenic gallid alphaherpesvirus 2 telomere integration in host birds. Cytogenetics and Genome Research. 156(4):204-214. https://doi.org/10.1159/000495174. -(Peer Reviewed Journal)
Webb, A.E., Youngworth, I.A., Kaya, M., Gitter, C.L., O’Hare, E.A., May, B.P., Cheng, H.H., Delany, M.E. 2018. Narrowing the wingless-2 mutation to a 227 Kb candidate region on chicken chromosome 12. Poultry Science. 97(6):1872–1880. https://dx.doi.org/10.3382/ps/pey073. -(Peer Reviewed Journal)
Tai, S., Hearn, C.J., Umthong, S., Agafitei, O., Cheng, H.H., Dunn, J.R., Niikura, M. 2017. Expression of Marek's disease virus oncoprotein Meq during infection in the natural host. Virology. 503:103-113. doi:10.1016/j.virol.2017.01.011. -(Peer Reviewed Journal)
Dunn, J.R., Reddy, S., Niikura, M., Nair, V., Fulton, J.E., Cheng, H.H. 2017. Evaluation and identification of Marek’s disease virus BAC clones as standardized reagents for research. Avian Diseases. 61(1):107-114. doi: 10.1637/0005-2086-61.1.107. -(Peer Reviewed Journal)
Teague, K.D., Graham, L.E., Dunn, J.R., Cheng, H.H., Anthony, N., Latorre, J.D., Meconi, A., Wolfeden, R.E., Wolfeden, A.D., Mahaffey, B.D., Baxter, M., Hernandez-Velasco, X., Merino-Guzman, R., Bielke, L.R., Hargis, B.M., Tellez, G. 2017. In ovo evaluation of FloraMax®-B11 on Marek´s disease HVT vaccine protective efficacy, hatchability, microbiota composition, morphometric analysis, and Salmonella Enteritidis infection in broiler chickens. Poultry Science. 96(7):2074-2082. doi:10.3382/ps/pew494. -(Peer Reviewed Journal)
Warren, W.C., Hillier, L.W., Tomlinson, C., Minx, P., Kremitzki, M., Graves, T., Markovic, C., Bourk, N., Pruitt, K.D., Thibaud-Nissen, F., Schneider, V., Mansour, T.A., Brown, C.T., Zimin, A., Hawken, R., Abrahamsen, M., Black Pyrkosz, A.A., Morrison, M., Fillon, V., Vignal, A., Chow, W., Howe, K., Fulton, J.E., Miller, M.M., Lovell, P., Mello, C.V., Cheng, H.H. 2017. A new chicken genome assembly provides insight into avian genome structure. G3, Genes/Genomes/Genetics. 7(1):109-117. https://doi.org/10.1534/g3.116.035923. -(Peer Reviewed Journal)
McPherson, M.C., Cheng, H.H., Delany, M.E. 2016. Marek’s disease herpesvirus vaccines integrate into chicken host chromosomes yet lack a virus-host phenotype associated with oncogenic transformation. Vaccine. 34(46):5554-5561. doi:10.1016/j.vaccine.2016.09.051.
Perumbakkam, S., Hunt, H.D., Cheng, H.H. 2016. Differences in CD8 alpha alpha and cecal microbiome community during proliferation and late cytolytic phases of Marek's disease virus (MDV) infection are associated with genetic resistance to Marek's disease. Environmental Microbiology. 92:1-11. doi:10.1093/femsec/fiw188. -(Review Article)
Tuggle, C.K., Giuffra, E., White, S.N., Clarke, L., Zhou, H., Ross, P.J., Acloque, H., Reecy, J.M., Archibald, A., Boichard, M., Chamberlain, A., Cheng, H.H., Crooijmans, R., Delany, M., Groenen, M.A., Hayes, B., Lunney, J.K., Plastow, G.S., Silverstein, J., Song, J., Watson, M. 2016. GO-FAANG meeting: A gathering on functional annotation of animal genomes. Animal Genetics. 47(5):528-533. -(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. -(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.
Yan, Y., Yang, N., Cheng, H.H., Song, J., Qu, L. 2015. Genome-wide identification of copy number variations between two chicken lines that differ in genetic resistance to Marek’s disease. Biomed Central (BMC) Genomics. 16(843):1-10.
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. -(Peer Reviewed Journal)
Hildebrandt, E., Dunn, J.R., Cheng, H.H. 2015. Characterizing in vivo stability and potential interactions of a UL5 helicase-primase mutation previously shown to reduce virulence and in vivo replication of Marek's disease virus. Virus Research. 203(2015):1-3. doi: 10.1016/j.virusres.2015.03.011. -(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. -(Peer Reviewed Journal)
Hildebrandt, E., Dunn, J.R., Cheng, H.H. 2015. Addition of a UL5 helicase-primase subunit point mutation eliminates bursal-thymic atrophy of Marek’s disease virus delta-Meq recombinant virus but reduces vaccinal protection. Avian Pathology. 44(4):254-258. -(Review Article)
Andersson, L., Archibald, A.L., Bottema, C.D., Brauning, R., Burgess, S.C., Burt, D.W., Casas, E., Cheng, H.H., Clarke, L., Couldrey, C., Dalrymple, B.P., Elski, C.G., Foissac, S., Giuffra, E., Groenen, M.A., Hayes, B.J., Huang, L.S., Khatib, H., Kijas, J.W., Kim, H., Lunney, J.K., McCarthy, F.M., McEwan, J.C., Moore, S., Nanduri, B., Notredame, C., Palti, Y., Plastow, G.S., Reecy, J.M., Rohrer, G.A., Sarrapoulou, E., Schmidt, C.J., Silverstein, J., Tellam, R.L., Tixier-Biochard, M., Tosser-Klopp, G., Tuggle, C.K., Vilkki, J., White, S.N., Zhao, S., Zhou, H. 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. -(Peer Reviewed Journal)
Hildebrandt, E., Dunn, J.R., Niikura, M., Cheng, H.H. 2014. Mutations within ICP4 acquired during in vitro attenuation do not alter virulence of recombinant Marek’s disease viruses in vivo. Virology Reports. 5:10-18. -(Peer Reviewed Journal)
Hildebrandt, E., Dunn, J.R., Cheng, H.H. 2014. The Mut UL5-I682R Marek’s disease virus with a single nucleotide mutation within the UL5 helicase-primase subunit gene not only reduces virulence, but also provides partial vaccinal protection against Marek's disease. Avian Diseases. 59(1):94-97. -(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.
Dunn, J.R., Cheng, H.H., Fadly, A.M., Heidari, M., Hunt, H.D., Zhang, H. 2014. Avian Disease & Oncology Lab (ADOL) Research Update. Proceedings of the One Hundred and Eighteenth Annual Meeting of the United States Animal Health Association. p. 411-413. -(Peer Reviewed Journal)
Kim, D., Lillehoj, H.S., Jang, S.I., Lee, S.H., Hong, Y.H., Cheng, H.H. 2014. Transcriptional analysis of host-pathogen interaction in genetically disparate chicken lines showing different levels of disease susceptibility to necrotic enteritis. PLoS One. 9(12):e114960.
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.
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.
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.
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. -(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.
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. -(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. -(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. -(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. -(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. -(Peer Reviewed Journal)
Hildebrandt, E.C., Dunn, J.R., Perumbakkam, S., Niikura, M., Cheng, H.H. 2014. Characterizing the molecular basis of attenuation of Marek’s disease virus via in vitro serial passage. Journal of Virology. 88(11):6232. Available: http://jvi.asm.org/content/88/11/6232#ref-list-1.
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.
Dunn, J.R., Cheng, H.H. 2014. Use of BAC clones as standardized reagents for Marek’s disease virus research. American Veterinary Medical Association Convention, July 25-29, 2014, Denver, Colorado. Abstract No. 16755. -(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.
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. -(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.
Crooijmans, R.P., Fife, M.S., Fitzgerald, T.W., Strickland, S., Cheng, H.H., Kaiser, P., Redon, R., Groenen, M.A. 2013. Large scale variation in DNA copy number in chicken breeds. Biomed Central (BMC) Genomics. 2013(14):398. Available: http://www.biomedcentral.com/1471-2164/14/398. -(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. -(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.
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.
Perumbakkam, S., Muir, W.M., Black Pyrkosz, A.A., Okimoto, R., Cheng, H.H. 2013. Comparison and contrast of genes and biological pathways responding to Marek’s disease virus infection using allele-specific expression and differential expression in broiler and layer chickens. Biomed Central (BMC) Genomics. 14:64. Available: http://www.biomedcentral.com/content/pdf/1471-2164-14-64.pdf.
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.
Fadly, A.M., Cheng, H.H., Dunn, J.R., Heidari, M., Hunt, H.D., Lee, L.F., Silva, R.F., Zhang, H. 2012. Research update: Avian Disease and Oncology Laboratory avian tumor viruses. United States Animal Health Association Proceedings. 513-516.
Kumar, S., Kunec, D., Buza, J.J., Chiang, H.I., Zhou, H., Subramaniam, S., Pendarvis, K., Cheng, H.H., Burgess, S.C. 2012. Nuclear Factor kappa B is central to Marek’s Disease herpesvirus induced neoplastic transformation of CD30 expressing lymphocytes in-vivo. BMC Systems Biology. 6(123). Available: http://www.biomedcentral.com/1752-0509/6/123.
Subramaniam, S., Brown, C., Niikura, M., Cheng, H.H. 2012. Genome-wide identification of host genes directly regulated by Marek’s disease virus (MDV) oncoprotein Meq. Meeting Abstract. American Society for Virology 31st Annual Meeting July 21-25, 2012, Madison, Wisconsin. Workshop No. 19-4
Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A.A., Subramaniam, S., Muir, W.M. 2012. Identification of genes conferring genetic resistance to Marek’s disease [abstract]. 9th International Symposium on Marek's Disease and Avian Herpesviruses, June 24-28, 2012, Freie Universitat Berlin. p. 25.
Hildebrandt, E., Niikura, M., Cheng, H.H. 2012. Uncovering the genetic basis of attenuation in Marek’s disease virus [abstract]. 9th International Symposium on Marek's Disease and Avian Herpesviruses, June 24-28, 2012, Freie Universitat Berlin. p.23.
Cheng, H.H., Maceachern, S., Subramaniam, S., Muir, W.M. 2012. Chicks and single-nucleotide polymorphisms: an entree into identifying genes conferring disease resistance in chicken. Animal Production Science. 52(3). Available: http://dx.doi.org/10.1071/AN11099.
Maceachern, S., Muir, W.M., Crosby, S.D., Cheng, H.H. 2012. Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek's disease virus infection via analysis of allele-specific expression. Frontiers in Genetics. 2(113):1-11.
Fadly, A.M., Cheng, H.H., Dunn, J.R., Heidari, M., Hunt, H.D., Lee, L.F., Silva, R.F., Zhang, H. 2012. Research update: Avian Disease and Oncology Laboratory avian tumor viruses. In: Proceedings for the 115th Annual Meeting of the United States Animal Health Association, September 29-October 5, 2011, Buffalo, New York. 462-464.
Groenen, M., Megens, H., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R., Vereijken, A., Okimoto, R., Muir, W., Cheng, H.H. 2011. The development and characterization of a 60K SNP chip for chicken. Biomed Central (BMC) Genomics. 12:274. Available: http://www.biomedcentral.com/1471-2164/12/274.
Cheng, H.H., MacEachern, S., Subramaniam, S., Muir, W.M. 2011. Chicks and SNPs--an entree into identifying genes conferring disease resistance in chicken [abstract]. Applied Genomics for Sustainable Livestock Breeding Conference Handbook, May 2-5, 2011, Melbourne, Australia. p. 3.
Hildebrandt, E., Niikura, M., Cheng, H.H. 2011. Identifying the genetic basis of attenuation in Marek's disease virus [abstract]. American Society for Virology 30th Annual Meeting Scientific Program and Abstracts, University of Minnesota, July 16-20, 2011. P5-3 p. 258.
Subramaniam, S., Brown, C.T., Niikura, M., Cheng, H.H. 2011. Genome-wide identification of host genes directly regulated by Marek's disease virus (MDV) oncoprotein Meq [abstract]. American Society for Virology 30th Annual Meeting Scientific Program and Abstracts, University of Minnesota, July 16-20, 2011. P8-3 p. 273.
Meydan, H., Yildiz, M.A., Dodgson, J.B., Cheng, H.H. 2011. Allele-specific expression analysis reveals CD79B has a cis-acting regulatory element that responds to Marek's disease virus infection in chicken. Poultry Science. 90(6):1206-1211.
Dodgson, J.B., Delany, M.E., Cheng, H.H. 2011. Poultry genome sequences: progress and outstanding challenges. Cytogenetics and Genome Research. p. 1-8. Available: http://content.karger.com/ProdukteDB/produkte.asp?Aktion=ShowAbstract&ArtikelNr=324413&Ausgabe=255102&ProduktNr=224037.
Luo, J., Mitra, A., Tian, F., Zhang, H., Chang, S., Cui, K., Zhao, K., Krause, M., Cheng, H.H., Song, J. 2011. Genome-wide histone modification profile induced by MDV in MD-resistant and -susceptible chickens. Plant and Animal Genome XIX Conference, January 15-19, 2011, San Diego, California. Paper No. 578.
Robinson, C.M., Hunt, H.D., Cheng, H.H., Delany, M.E. 2010. Chromosomal integration of an avian oncogenic herpesvirus reveals telomeric preferences and evidence for lymphoma clonality. BioMed Central (BMC) Herpesviridae. 1:5. http://www.herpesviridae.org/content/1/1/5.
Cheng, H.H. 2010. Viral diseases in chickens. In: Bishop S.C., Axford, R.F.E., Nicholas, F.W., Owen, J.B., editors. Breeding for Disease Resistance in Farm Animals. 3rd edition. Oxfordshire, United Kingdom: CAB International. p. 70-87.
Niikura, M., Kim, T., Silva, R.F., Dodgson, J., Cheng, H.H. 2011. Virulent Marek's disease virus generated from infectious bacterial artificial chromosome clones with complete DNA sequence and implication of viral genetic homogeneity in pathogenesis. Journal of General Virology. 92:598-607.
Fadly, A.M., Cheng, H.H., Dunn, J.R., Heidari, M., Hunt, H.D., Lee, L.F., Silva, R.F., Zhang, H. 2011. Avian Disease and Oncology Laboratory (ADOL) research update. Proceedings One Hundred and Fourteenth Annual Meeting of the United States Animal Health Association (USAHA), November 11-17, 2010, Minneapolis, Minnesota. p. 528-530.
Robb, E.A., Gitter, C.L., Cheng, H.H., Delany, M.E. 2011. Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics. Journal of Heredity. 102(2):141-156.
Luo, J., Yu, Y., Zhang, H., Tian, F., Chang, S., Cheng, H.H., Song, J. 2011. Down-regulation of promoter methylation level of CD4 gene after MDV infection in MD-susceptible chicken line. BioMed Central (BMC) Proceedings. 5(Suppl 4):57. Available: http://www.biomedcentral.com/1753-6561/5/S4/S7
Hildebrandt, E., Silva, R.F., Cheng, H.H. 2010. Progress on identifying specific genetic changes in the Marek's disease virus genome associated with attenuation induced by repeated in vitro passages [abstract]. In: 5th International Workshop on the Molecular Pathogenesis of Marek's Disease Virus and 1st Symposium on Avian Herpesviruses, October 17-20, 2010, Athens, Georgia, p. 65.
Subramaniam, S., Brown, T.C., Cheng, H.H. 2010. Genome-wide identification of host genes directly and indirectly regulated by Marek's disease virus (MDV) oncoprotein Meq [abstract]. In: 5th International Workshop on the Molecular Pathogenesis of Marek's Disease Virus and 1st Symposium on Avian Herpesviruses, October 17-20, 2010, Athens, Georgia, p.93.
MacEachern, S., Muir, W.M., Crosby, S., Cheng, H.H. 2010. Comprehensive genome-wide screen for genes with cis-acting regulatory elements that respond to Marek's disease virus infection [abstract]. In: 5th International Workshop on the Molecular Pathogenesis of Marek's Disease Virus and 1st Symposium on Avian Herpesviruses, October 17-20, 2010, Athens, Georgia, p. 87.
MacEachern, S., Muir, W.M., Crosby, S., Cheng, H.H. 2010. Comprehensive Identification Of Specific Genes Controlling Complex Traits Through A Genome-Wide Screen for Cis-Acting Regulatory Elements - An Example Using Marek's Disease [abstract]. In: Proceedings of World Congress of Genetics Applied in Livestock Production. Lecture on Functional genomics and systems biology, August 1-6, 2010, Leipzig, Germany. Paper No. 0213. available at http://www.kongressband.de/wcgalp2010/assets/pdf/0213.pdf.
Subramaniam, S., Brown, C.T., Cheng, H.H. 2010. Genome-wide identification of host genes directly and indirectly regulated by Marek's disease virus (MDV) oncoprotein Meq [abstract]. In: 35th Annual International Herpesvirus Workshop, July 24-29, 2010, Salt Lake City, Utah. Paper No. 7.26.
MacEachern, S., Muir, W.M., Crosby, S., Cheng, H.H. 2011. Genome-wide identification of allele-specific expression (ASE) in response to Marek's disease virus infection using next generation sequencing. Biomed Central (BMC) Proceedings. 5(Suppl 4):S14. Available on-line at: http://www.biomedcentral.com/1753-6561/5/S4/S14.
Kim, T., Hunt, H.D., Cheng, H.H. 2010. Marek's Disease Viruses Lacking Either R-LORF10 or LORF4 Have Altered Virulence in Chickens. Virus Genes. 40(3):410-420.
Tai, S.H., Niikura, M., Cheng, H.H., Kruger, J.M., Wise, A.G., Maes, R.K. 2010. Complete Genomic Sequence and an Infectious BAC Clone of Feline Herpesvirus-1 (FHV-1). Virology. 401(2):215-227.
Silva, R.F., Dunn, J.R., Cheng, H.H., Niikura, M. 2010. A MEQ-Deleted Marek's Disease Virus Cloned as a Bacterial Artificial Chromosome Is a Highly Efficacious Vaccine. Avian Diseases. 54(2):862-869.
MacEachern, S.A., Muir, W.M., Crosby, S., Cheng, H.H. 2010. Identifying Specific Genes Controlling Complex Traits Through A Genome-Wide Screen For cis-Acting Regulatory Elements - An Example Using Marek's Disease [abstract]. International Plant and Animal Genome XVIII Conference, January 9-13, 2010, San Diego, California. p. 169.
Megens, H., Crooijmans, R., Bastiaansen, J., Kerstens, H., Coster, A., Jalving, R., Vereijken, A., Silva, P., Muir, W., Cheng, H.H., Hanotte, O., Groenen, M. 2009. Comparison of Linkage Disequilibrium and Haplotype Diversity on Macro- and Microchromosomes in Chicken. BioMed Central (BMC) Genetics. Available: http://www.biomedcentral.com/1471-2156/10/86.
Subramaniam, S., Burgess, S., Cheng, H.H. 2009. Interaction of Marek's Disease Virus (MDV) Oncoprotein Meq with Host Proteins: A Proteomic Approach [abstract]. Systems Biology Symposium at the University of Michigan, Ann Arbor, Michigan, December 1, 2009. Poster #32.
Mao,W., Hunt, H.D., Cheng, H.H. 2010. Cloning and Functional Characterization of Chicken Stem Cell Antigen 2. Developmental and Comparative Immunology. 34(3):360-368.
Mao, W., Hunt, H.D., Kim, T., Cheng, H.H. 2009. Characterization of Chicken Stem Cell Antigen 2 and Initial Investigation of Its Role in Marek's Disease Virus Infection [abstract]. 34th International Herpesvirus Workshop, Ithaca, New York, July 25-30, 2009. Paper No. 2.15.
Heifetz, E.M., Fulton, J.E., O'Sullivan, N.P., Arthur, J.A., Cheng, H.H., Wang, J., Soller, M., Dekkers, J.C. 2009. Mapping QTL Affecting Resistance to Marek's Disease in an F6 Advanced Intercross Population of Commercial Layer Chickens. Biomed Central (BMC) Genomics. Available: http://www.biomedcentral.com/1471-2164/10/20.
Groenen, M.A., Wahlberg, P., Foglio, M., Cheng, H.H., Megens, H.J., Crooijmans, R.P., Besnier, F., Lathrop, M., Muir, W.M., Wong, G.K., Gut, I., Andersson, L. 2009. A High-Density SNP-Based Linkage Map of the Chicken Genome Reveals Sequence Features Correlated With Recombination Rate. Genome Research. 19(3):510-519.
Muir, W.M., Wong, G., Zhang, Y., Wang, J., Groenen, M., Crooijmans, R., Megens, H., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G., Taylor Lawley, C., Delany, M.E., Maceachern, S.A., Cheng, H.H. 2008. Genome-Wide Assessment of Worldwide Chicken SNP Genetic Diversity Indicates Significant Absence of Rare Alleles in Commercial Breeds. Proceedings of the National Academy of Sciences. 105(45):17312-17317.
Cheng, H., Niikura, M., Kim, T., Mao, W., MacLea, K., Hunt, H., Dodgson, J., Burnside, J., Morgan, R., Ouyang, M., Lamont, S., Dekkers, J., Fulton, J., Soller, M., Muir, W. 2008. Using integrative genomics to elucidate genetic resistance to Marek's disease in chicken. In: Pinard M-H, Gay, C., Pastoret, P-P, Dodet, B., editors. Integrative Genomics for Disease Resistance: Animal Genomics for Animal Health. Developments in Biologicals. Basel, Switzerland: Karger. p. 365-372.
Cheng, H.H. 2008. Integrating genomics to understand the Marek's disease virus-chicken host-pathogen interaction. In: Gustafson, P., Stacey, G., Taylor, J., editors. Genomics of Disease. Stadler Genetics Symposium. New York, NY: Springer. p. 115-126.
Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A., Crooijmans, R.P., Megens, H.J., Zhang, H.M., McKay, J.C., McLeod, S., Okimoto, R., Fulton, J.E., Settar, P., O'Sullivan, N.P., Vereijken, A., Jungerius-Rattink, A., Albers, G.A., Lawley, C.T., Delany, M.E., Cheng, H.H. 2008. Review of the initial validation and characterization of a 3K chicken SNP array. World Poultry Science Journal. 64:219-225.
Mao, W., Niikura, M., Silva, R.F., Cheng, H.H. 2008. Quantitative evaluation of viral fitness due to a single nucleotide polymorphism in the Marek's disease virus UL41 gene via an in vitro competition assay. Journal of Virological Methods. 148:125-131.
Cogburn, L.A., Porter, T.E., Duclos, M.J., Simon, J., Burgess, S.C., Zhu, J., Cheng, H.H., Dodgson, J.B., Burnside, J. 2007. Functional genomics of the chicken - a model organism. Poultry Science. 86:2059-2094.
Maclea, K.S., Cheng, H.H. 2007. The threat of Marek's disease virus is expanding. Microbe Magazine. Volume 2:238-243.
Zhang, H.M., Bacon, L.D., Heidari, M., Muir, W.M., Groenen, M.A.M., Zhang, Y., Wong, G.K.S., Fulton, J.E., O'Sullivan, N.P., Albers, G.A.A., Vereijken, A.L.J., Rattink, A.P., Okimoto, R., McKay, J.C., McLeod, S., Cheng, H.H. 2007. Genetic variation at the tumour virus B locus in commercial and laboratory chicken populations assessed by a medium-throughput or a high-throughput assay. Avian Pathology. p. 283-291.
Muir, W., Cheng, H.H. 2007. A World Wide and Genome Wide Assessment of Biodiversity in Commercial Poultry Populations. Proceedings of the 56th National Breeders Roundtable. p. 1-8.
Granevitze, Z., Blum, S., Cheng, H.H., Vignal, A., Morisson, M., Ben-Ari, G., David, L., Feldman, M.W., Weigend, S., Hillel, J. 2007. Female-specific DNA sequences in the chicken genome. Journal of Heredity. 98:238-242.
Cheng, H.H., Lamont, S.J. 2008. Genetics of disease resistance. In: Saif, Y.M., Fadly, A.M., Glisson, J.R., McDougald, L.R., Nolan, L.K., Swayne, D.E., editors. Diseases of Poultry. 12th edition. Ames, IA: Iowa State University Press. p. 59-72.
Zhang, H.M., Dunn, J.R., Witter, R.L., Heidari, M., Bacon, L.D., Cui, Y., Song, J., Cheng, H.H. 2007. Putative evidence that genes outside the MHC have a significant influence on efficacy of Marek's disease vaccine [abstract]. Plant and Animal Genome VX Conference Abstracts. Paper #107. p. 128.
Cheng, H.H., Zhang, Y., Muir, W. 2007. Evidence for widespread epistatic interactions influencing Marek's disease virus viremia levels in chicken. Cytogenetics and Genome Research. 117:313-318.
Niikura, M., Kim, T., Hunt, H.D., Burnside, J., Morgan, R., Dodgson, J., Cheng, H.H. 2007. Marek's disease virus up-regulates major histocompatibility complex class II cell surface expression in infected cells. Virology. 359(1): 212-219.
Cheng, H.H., Hunt, H.D., Delany, M.E. 2006. Molecular characterization of MD tumors with respect to clonality, loss of heterozygosity, and MDV integration [abstract]. 4th International Workshop on Molecular Pathogenesis of Marek's Disease Virus. p. 6.
Kim, T., Hunt, H.D., Cheng, H.H. 2006. Characterization of MDV LORF4 and R-LORF10 in MDV-infected cells and chicken [abstract]. 4th International Workshop on Molecular Pathogenesis of Marek's Disease Virus. p. 38.
MacLea, K.S., Cheng, H.H. 2006. Purification of MDV-chicken protein complexes using molecularly cloned and tagged MDV-BACS [abstract]. 4th International Workshop on Molecular Pathogenesis of Marek's Disease Virus. p. 38.
Niikura, M., Dodgson, J., Silva, R.F., Cheng, H.H. 2006. Infectious bacterial artificial chromosome clones of Marek's disease virus possessing the complete viral genome derived from Md5 cosmid clones [abstract]. 4th International Workshop on Molecular Pathogenesis of Marek's Disease Virus. p. 37.
Backstrom, N., Brandstrom, M., Gustafsson, L., Qvarnstrom, A., Cheng, H.H., Ellegren, H. 2006. Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics. Paper no. 106.058917(1). Available: http://www.genetics.org/cgi/content/abstract/genetics.
Hillel, J., Granevitze, Z., Twito, T., Ben-Avraham, D., Blum, S., Lavi, U., David, L., Feldman, M.W., Cheng, H.H., Weigend, S. 2007. Molecular markers for the assessment of chicken biodiversity. World's Poultry Science Journal. 63(01):33-45.
Hunt, H.D., Kim, T., Niikura, M., Cheng, H.H., Parcells, M., Ewald, S., Osterrieder, K. 2006. Marek's disease virus immune escape mechanisms. American Association of Avian Pathologists. In: American Association of Avian Pathologists Symposium Program. Impact of Subclinical Immunosuppression on Poultry Production, July 2006, Honolulu, Hawaii. p. 61-66.
Cheng, H.H., Kim, T.J., Niikura, M., Hunt, H.D. 2006. Using recombinant viruses to query the functional significance of the protein-protein interactions between chicken MHC class II and Marek's disease virus LORF4 and R-LORF10 [abstract]. International Symposium on Animal Functional Genomics. p. 8.
Atzmon, G., Ronin, Y.I., Korol, A., Yonash, N., Cheng, H.H., Hillel, J. 2006. QTLs associated with growth traits and abdominal fat weight and their interactions with gender and hatch in commercial meat-type chickens. Animal Genetics. 37(4):352-358.
Niikura, M., Dodgson, J., Cheng, H.H. 2006. Direct evidence of host genome acquisition by the alphaherpesvirus Marek's disease virus (MDV)[Abstract]. Keystone Symposia: Cell Biology of Virus Entry, Replication and Pathogenesis. p. 69
MacLea, K.S., Cheng, H.H. 2006. Cloning and expression of deoxyribonuclease II from chicken. Gene. 373:44-51. Available: http://www.sciencedirect.com.
Niikura, M., Dodgson, J.B., Cheng, H.H. 2006. Stability of Marek's disease virus 132bp repeats during serial in vitro passages. Archives of Virology. 151:1431-1438.
Ben-Avraham, D., Blum, S., Granevitze, Z., Weigend, S., Cheng, H.H., Hillel, J. 2006. W-specific microsatellite loci detected by in silico analysis, map to chromosome Z of the chicken genome. Animal Genetics. 37:179-188.
Cheng, H.H., Zhang, H.M., Muir, W.M., Groenen, M.A., Wong, G.K. 2006. Preliminary results on the validation and application of 3,072 chicken SNPs by genotyping 2,576 commercial and experimental birds [abstract]. Plant and Animal Genome XIV. p. 143.
Niikura, M., Dodgson, J., Cheng, H.H. 2006. Direct evidence of host genome acquisition by the alphaherpesvirus Marek's disease virus. Archives of Virology. 151:537-549. Available online. DOI 10.1007/S00705-005-0633-7.
Zhang, H.M., Bacon, L.D., Cheng, H.H., Hunt, H.D. 2005. Development and validation of a PCR-RFLP assay to evaluate TVB haplotypes coding receptors for subgroup B and subgroup E avian leukosis viruses in White Leghorns. Avian Pathology. 34(4):324-331.
Cheng, H.H. 2005. Integrated genomic approaches to understanding resistance to Marek's disease. In: Proceedings of the 3rd International Symposium on Genetics of Animal Health, July 13-15, 2005, Ames, Iowa. p. 24-33.
McElroy, J.P., Dekkers, J.C., Fulton, J.E., O'Sullivan, N.P., Soller, M., Lipkin, E., Zhang, W., Koehler, K.J., Lamont, S.J., Cheng, H.H. 2005. Microsatellite markers associated with resistance to Marek's disease in commercial layer chickens. Poultry Science. 84:1678-1688.
Cheng, H.H., Niikura, M., Kim, T., MacLea, K.S., Hunt, H.D., Morgan, R., Burnside, J. 2005. Integrating genomic and immunological approaches to understand Marek's disease [abstract]. Keystone Symposia: Systems and Biology (X4), p. 101.
Cheng, H.H. 2005. Marek's disease: an evolving problem. Poultry Science. p. 173.
Hansen, C., Yi, N., Zhang, Y.M., Xu, S., Gavora, J., Cheng, H.H. 2005. Identification of QTL for production traits in chickens. Animal Biotechnology. 16:67-79.
Wong, G., Liu, B., Andersson, L., Groenen, M., Hunt, H.D., Cheng, H.H. 2004. A genetic variation map for chicken with 2.8 million single nucleotide polymorphisms. Nature Magazine. 432:717-722.
Zhang, H.M., Hunt, H.D., Cheng, H.H., Dodgson, J.B., Romanov, M., Bacon, L.D. 2005. Identification and evaluation of SNPs at the 3' end of the tva gene segregating among ALSV resistance and susceptible lines of chickens [abstract]. Plant & Animal Genome XIII Conference. p. 197:123.
Okumura, F., Shimogiri, T., Shinbo, Y., Yoshizawa, K., Kawabe, K., Mannen, H., Okamoto, S., Cheng, H.H., Maeda, Y. 2005. Linkage mapping of four chicken calpain genes. Animal Science Journal. 76:121-127.
Wallis, J.W., Aerts, J., Groenen, M., Crooijmans, R., Layman, D., Graves, T.A., Scheer, D., Kremitzki, C., Fedele, M., Mudd, N., Cardenas, M., Higginbotham, J., Carter, J., McGrane, R., Gaige, T., Mead, K., Walker, J., Albracht, D., Davito, J., Yang, S., Leong, S., Chinwalla, A., Sekhon, M., Wylie, K., Dodgson, J., Romanov, M., Cheng, H.H., deJong, P., Osoegawa, K., Nefedov, M., Zhang, H., McPherson, J., Krzywinski, M., Schein, J., Hillier, L., Mardis, E., Wilson, R., Warren, W. 2004. A physical map of the chicken genome. Nature Magazine. 432:761-764.
Niikura, M., Dodgson, J., Cheng, H.H. 2004. Characterization and complete sequence of an infectious Marek's disease virus bacterial artificial chromosome clone generated from a virulent strain [abstract]. International Marek's Disease Symposium Abstracts and Proceedings. Paper No. P.17.
Cheng, H.H., Niikura, M., Hunt, H.D. 2004. Identification of novel genes involved in resistance to Marek's disease [abstract]. International Marek's Disease Symposium Abstracts and Proceedings. Paper No. II-5.
Cheng, H.H., Niikura, M., Hunt, H.D. 2004. Identification of novel genes involved in resistance to Marek's disease. International Marek's Disease Symposium Abstracts and Proceedings. Paper II.5.
Cheng, H.H., Niikura, M., Hunt, H.D. 2004. Identifying Marek's disease resistance gene and pathways through integrative genomic approaches. World Veterinary Poultry Association Congress Proceedings, June 8-13, 2004, Istanbul, Turkey. 2004 CD ROM.
Kinoshita, K., Shimogiri, T., Okamoto, S., Yoshizawa, K., Mannen, H., Ibrahim, H.R., Cheng, H.H., Maeda, Y. 2004. Linkage mapping of chicken ovoinhibitor and ovomucoid genes to chromosome 13. Animal Genetics. 35:356-358.
Zhang, H.M., Cheng, H.H. 2004. Chicken tubby-like protein 1 (tulp1) gene maps to chromosome 26. Animal Genetics. 35:165-166.
Zhang, H.M., Cheng, H.H. 2004. SNP identification and genetic mapping of chicken ephrin type-B receptor 2 gene to linkage group E54. Animal Genetics. 35:162-163.
Niikura, M., Liu, H.C., Dodgson, J.B., Cheng, H.H. 2004. A comprehensive screen for chicken proteins that interact with proteins unique to virulent strains of Marek's disease virus. Poultry Science. 83:1117-1123.
Cheng, H.H., Liu, H., Niikura, M. 2004. A comprehensive screen for Marek's disease virus-chicken protein interactions to identify disease resistance genes. Plant and Animal Genome Conference Proceedings. p. 293.
Cheng, H.H. 2003. Integrating genomic and functional genomic approaches to identify Marek's disease resistance genes [abstract]. Chicken Genome Sequence: Impact and Applications. p. 13.
Cheng, H.H. 2003. Molecular genetics and Marek's disease resistance. Feedinfo.com. Available From: http://www.feedinfo.com.
Liu, H., Niikura, M., Fulton, J.E., Cheng, H.H. 2003. Identification of chicken lymphocyte antigen 6 complex, locus e (LY6E, alias SCA2) as a putative Marek's disease resistance gene via a virus-host protein interaction screen. Cytogenetics and Genome Research. 102:304-308. (DOI:10.1159/000075767).
Zhang, H.M., Hunt, H.D., Cheng, H.H., Bacon, L.D. 2003. A PCR based SNP analysis of the chicken TVB receptor gene [abstract]. Poultry Science. 82(1):49.
Zhu, J.J., Lillehoj, H.S., Allen, P.C., Van Tassell, C.P., Sonstegard, T.S., Cheng, H.H., Pollock, D., Sadjadi, M., Min, W., Emara, M.G. 2003. Mapping quantitative trait locus associated with resistance to avian coccidiosis and growth. Poultry Science 82:9-16.
Liu, H., Niikura, M., Cheng, H.H. 2003. Screening for candidate genes that confer marek's disease resistance by combining two-hybrid assays and QTL linkage analysis [abstract]. Plant and Animal Genome Conference Proceedings. p. 108.
Cheng, H.H., Liu, H. 2003. Identifying disease resistance genes and pathways through host-pathogen protein interactions [abstract]. Plant and Animal Genome Conference Proceedings. p. 40.
Liu, H., Cheng, H.H. 2003. Genetic mapping of the chicken stem cell antigen 2 (SCA2) gene to chromosome 2 via PCR primer mutagenesis. Animal Genetics. 34:146-160.
Cheng, H.H. 2003. Selection for disease resistance: molecular genetic techniques. In: Muir, W.M., Aggrey, S.E., editors. Poultry Genetics Breeding and Biotechnology. Cambridge, MA: CABI Publishing. p. 385-398.
Liu, H., Cheng, H.H. 2002. Integrating molecular approaches with QTL to identify positional candidate genes. World Congress of Genetics Applied in Livestock Production. p. 40-49.
Ambady, S., Cheng, H.H., Ponce De Leon, F.A. 2002. Development and mapping of microsatellite markers derived from chicken chromosome-specific libraries. Poultry Science. 81:1644-1646.
Lipkin, E., Fulton, J., Cheng, H.H., Yonash, N., Soller, M. 2002. Quantitative trait locus mapping in chicken by selective DNA pooling with dinucleotide microsatellite markers using purified DNA and fresh or frozen red blood cells as applied to marker-assisted selection. Poultry Science. 81:283-292.
MARIANI, P., BARROW, P., CHENG, H.H., GROENEN, M.A., NEGRINI, R., BUMSTEAD, N. LOCALIZATION OF A LOCUS DETERMINING SALMONELLOSIS RESISTANCE TO CHICKEN CHROMOSOME. IMMUNOGENETICS. 2001. V. 53. P. 786-791.
CHENG, H.H., HUNT, H.D. GENE MANIPULATION AND GENETIC RESISTANCE TO DISEASE IN POULTRY. WORLD VETERINARY POULTRY ASSOCIATION. 2001. P. 40-49.
CHENG, H.H. TAPPING THE CENTRAL DOGMA FOR DISEASE RESISTANCE GENES IN POULTRY. ANIMAL GENOMICS SYMPOSIUM NORTH CAROLINA STATE UNIVERSITY RALEIGH. 2001. NO PAGE NUMBERS.
Research Interests
My lab is one of five groups in the Avian Disease and Oncology Laboratory, and we all share a common research goal. Thus, with our unique collection of inbred chickens lines and virus strains, we have a well-equipped multidisciplinary effort with expertise in molecular virology, pathology, immunology, and genetics to understand viral-induced cancers of the chicken.
My laboratory uses genomic and functional genomic approaches to identify and functionally characterize genes of agricultural importance in chicken, especially with regard to resistance to Marek’s disease (a herpesvirus-induced T cell cancer). Current projects include:
- Chicken genetic map - I lead the US effort, which forms the framework for the chicken genome assembly lead by Wes Warren (Genome Institute, Wash. U. in St. Louis)
- Molecular genetics and genomic selection for Marek’s disease resistance – Using an integrated genomics strategy (e.g., GWAS, RNA seq), we are identifying genes that confer genetic resistance to Marek’s disease. In addition, linked SNP markers, mainly based on allele-specific expression, are being used in genomic selection strategies in both experimental and commercial poultry flocks. Hi-C is also being employed to identify promoter-enhancer interactions with the hope of revealing causative polymorphisms that account for genetic resistance.
- Driver mutations for Marek’s disease – Hypothesizing that somatic mutations are required for transformation, various genomic strategies (e.g., DNA seq, RNA seq, cytogenetics) are being employed and integrated to identify driver genes.
- Vaccine synergy – Marek’s disease vaccines form the primary control method, however, very little information in known as to how they actually protect birds.
Education and Employment
1983 B.S., Michigan State University
1988 Ph.D., University of California at Berkeley
1988-90 Postdoctoal Fellow, University of California at Davis
1990-92 Molecular Geneticist, Petoseed, Woodland, CA
1992-date USDA, ARS
Key publications
Warren, W.C., Hillier, L.W. Tomlinson, C., Minx, P., Kremitzki, M., Graves, T., Markovic, C., Bouk, N., Pruitt, K.D., Thibaud-Nissen, F., Schneider, V., Mansour, T.A., Brown, C.T., Zimin, A., Hawken, R., Abrahamsen, M., Pyrkosz, A.B., Morisson, M., Fillon, V., Vignal, A., Chow, W., Howe, K., Fulton, J.E., Miller, M.M., Lovell, P., Mello, C.V., Wirthlin, M., Mason, A.S., Kuo, R., Burt, D.W., Dodgson, J.B., and Cheng, H.H. 2017. A new chicken genome assembly provides insight into avian genome structure. G3 7:109-117.
Cheng, H.H., Perumbakkam, S., Black Pyrkosz, A., Dunn, J.R., Legarra, A., and 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. BMC Genomics 16:816.
Perumbakkam, S., Hunt, H.D., and 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 Microbiol. Ecol. 90:300-312.
Hildebrandt, E., Dunn, J.R., Perumbakkam, S., Niikura, M, and Cheng, H.H. 2014. Characterizing the molecular basis of attenuation of Marek’s disease virus via in vitro serial passage identifies de novo mutations in the helicase-primase subunit gene UL5 and other candidates associated with reduced virulence. J. Virology 88:6232-6242.
Subramaniam, S., Johnston, J., Preeyanon, L., Brown, C.T., Kung, H.J., and Cheng, H.H. 2013. Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by Marek's disease oncoprotein, Meq. J. Virology 87:9016-9029.
Groenen, M.A.M., Megens, H.-J., Zare, Y., Warren, W.C., Hillier, L.W., Crooijmans, R.P.M.A., Vereijken, A., Okimoto, R., Muir, W.M., and Cheng, H.H. 2011. The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12:274.
Robinson, C.M., Hunt, H.D., Cheng, H., and Delany, M. 2010. Mapping of Marek’s disease herpesvirus integrations into chicken chromosomes indicates positional preference for telomeres and clonal relationships among tumors. Herpesviridae 1:5.
Niikura, M., Kim, T., Silva, R.F., Dodgson, J., and Cheng, H.H. 2011. Virulent Marek’s disease virus generated from infectious bacterial artificial chromosome clones with complete DNA sequence and implication of viral genetic homogeneity in pathogenesis. J. Gen. Virol. 92:598-607.
Silva, R.F., Dunn, J.R., Cheng, H.H., and Niikura, M. 2010. A MEQ deleted Marek’s disease virus cloned as a bacterial artificial chromosome is a highly efficacious vaccine. Avian Diseases 54:862-869.
Tai, S.H.S., Niikura, M., Cheng, H.H., Kruger, J.M., Wise, A.G., and Maes, R.K. 2010. Complete genomic sequence and an infectious BAC clone of feline herpesvirus-1 (FHV-1). Virology 401:215-227.
Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A. M, Crooijmans, R.P.M.A., Megens, H.-J., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G.A.A., Taylor Lawley, C., Delany, M.E., MacEachern, S., and Cheng, H.H. 2008. Genome-wide assessment of world-wide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. PNAS 105:17312-17317.
Cheng, H.H., Zhang, Y., and Muir, W.M. 2007. Evidence for widespread epistatic interactions influencing Marek’s disease virus viremia levels in chicken. Cytogen. Genome Res. 117:313-318.
Niikura, M., Kim, T., Hunt, H.D., Burnside, J., Morgan, R.W., Dodgson, J.B., and Cheng, H.H. 2007. Marek's disease virus up-regulates major histocompatibility complex class II cell surface expression in infected cells. Virology 359:212-219.
Wong, G.K., Liu, B., Wang, J., Zhang, Y., Yang, X., Zhang, Z., Meng, Q., Zhou, J., Li, D., Zhang, J., Ni, P., Li, S., Ran, L., Li, H., Zhang, J., Li, R., Li, S., Zheng, H., Lin, W., Li, G., Wang, X., Zhao, W., Li, J., Ye, C., Dai, M., Ruan, J., Zhou, Y., Li, Y., He, X., Zhang, Y., Wang, J., Huang, X., Tong, W., Chen, J., Ye, J., Chen, C., Wei, N., Li, G., Dong, L., Lan, F., Sun, Y., Zhang, Z., Yang, Z., Yu, Y., Huang, Y., He, D., Xi, Y., Wei, D., Qi, Q., Li, W., Shi, J., Wang, M., Xie, F., Wang, J., Zhang, X., Wang, P., Zhao, Y., Li, N., Yang, N., Dong, W., Hu, S., Zeng, C., Zheng, W., Hao, B., Hillier, LW., Yang, SP., Warren, W.C., Wilson, R.K., Brandstrom, M., Ellegren, H., Crooijmans, R.P., van der Poel, J.J., Bovenhuis, H., Groenen, M.A., Ovcharenko, I., Gordon, L., Stubbs, L., Lucas, S., Glavina, T., Aerts, A., Kaiser, P., Rothwell, L., Young, J.R., Rogers, S., Walker, B.A., van Hateren, A., Kaufman, J., Bumstead, N., Lamont, S.J., Zhou, H., Hocking, P.M., Morrice, D., de Koning, D.J., Law, A., Bartley, N., Burt, D.W., Hunt, H., Cheng, H.H., Gunnarsson, U., Wahlberg, P., Andersson, L., Kindlund, E., Tammi, M.T., Andersson, B., Webber, C., Ponting, C.P., Overton, I.M., Boardman, P.E., Tang, H., Hubbard, S.J., Wilson, S.A., Yu, J., Wang, J., Yang, H; International Chicken Polymorphism Map Consortium. 2004. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432:717-722.
Wallis, J.W., Aerts, J., Groenen, M.A., Crooijmans, R.P., Layman, D., Graves, T.A., Scheer, D.E., Kremitzki, C., Fedele, M.J., Mudd, N.K., Cardenas, M., Higginbotham, J., Carter, J., McGrane, R., Gaige, T., Mead, K., Walker, J., Albracht, D., Davito, J., Yang, S.P., Leong, S., Chinwalla, A., Sekhon, M., Wylie, K., Dodgson, J., Romanov, M.N., Cheng, H., de Jong, P.J., Osoegawa, K., Nefedov, M., Zhang, H., McPherson, J.D., Krzywinski, M., Schein, J., Hillier, L., Mardis, E.R., Wilson, R.K., and Warren, W.C. 2004. A physical map of the chicken genome. Nature 432:761-764.
Niikura, M., Liu, H.-C., Dodgson, J.B., and Cheng, H.H. 2004. A comprehensive screen for chicken proteins that interact with proteins unique to virulent strains of Marek’s disease virus. Poultry Science 83:1117-1123.
Liu, H.-C., Cheng, H.H., Softer, L. and Burnside, J. 2001. A strategy to identify positional candidate genes conferring Marek’s disease resistant by integrating DNA microarrays and genetic mapping. Anim. Genet. 32:351-359.
Liu, H.-C., Kung, H.-J., Fulton, J.E., Morgan, R.W. and Cheng, H.H. 2001. Growth hormone interacts with the Marek’s disease virus SORF2 protein and is associated with disease resistance in chicken. PNAS 98:9203-9208.
Bacon, L.D., Hunt, H.D. and Cheng, H.H. 2000. A review of the development of chicken lines to resolve genes determining resistance to diseases. Poultry Sci. 79:1082-1093.
Groenen, M.A.M., Crooijmans, R.P.M.A., Veenendall, A., Cheng, H.H., Siwek, M. and van der Poel, J.J. 1998. A comprehensive microsatellite linkage map of the chicken genome. Genomics 49:265-274.
Liu, W.-T., Marsh. T.L., Cheng, H. and Forney, L.J. 1997. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of 16S ribosomal DNA. Appl. Environ. Microbiol. 63:4516-4522.
Cheng, H.H. and Crittenden, L.B. 1994. Microsatellite markers for genetic mapping in the chicken. Poultry Sci. 73:539-546.
Cheng, H.H., Muhlrad, P.J., Hoyt, M.A., Crowl, R. and Echols, H. 1988. Cleavage of the cII protein of phage l by purified HflA protease: control of the switch between lysis or lysogeny. PNAS 85:7882-7886.
Current Personnel
Postdoctoral Associates
- Alexis Black Pyrkosz
Graduate Students
- Cari Hearn – CMIB
- Alec Steep – Genetics Program
- Sudawapee Umthong – Microbiology
Undergraduate Student
- Kalee Rumfelt
Technician
- Laurie Molitor
Additional External Funding Beyond ARS Support
- USDA AFRI, Enhancing genetic resistance to Marek’s disease in chicken via allele-specific expression screens and genome-wide selection; PI
- USDA AFRI, Genome biology of Marek’s disease: Viral integration and genome alterations in genetically resistant and susceptible stocks: PI
- USDA AFRI, The role of host genetic resistance and vaccination on transmission of Marek’s disease virus in poultry; co-PI.
- USDA National Needs Graduate Fellowship Grants; co-PI
