Selected Publications:

C. S. Sullivan, A. T. Grundhoff, S. Tevethia, J. M. Pipas, and D. Ganem. 2005. SV40-encoded microRNAs regulate viral gene expression and reduce susceptibility to cytotoxic T cells. Nature. 435: 682-6. click here

C. S. Sullivan, and D. Ganem. 2005. microRNAs and viral infection. Mol. Cell. 20: 3-7. click here

C. S. Sullivan*, and D. Ganem. 2005. A virus-encoded inhibitor that blocks RNA interference in Mammalian cells. J. Virol. 79: 7371-9 *corresponding author. click here

A. T. Grundoff*, C. S. Sullivan*, and Ganem D. 2006. Identification of microRNAs encoded by Kaposi’s Sarcoma-Associated Herpesvirus and Epstein-Barr Virus by a combined computational/microarray approach. RNA. Published in March *co-first author. click here

C. S. Sullivan. 2007. High conservation of KSHV microRNAs implies important function (invited review). Journal of Infectious Disease. 195: 618-20. click here

C. S. Sullivan, and A. T. Grundhoff. 2007. Identification of viral miRNAs. Methods Enzymol. 427:1-23. click here

L. V. McClure, and C. S. Sullivan. 2008. Kaposi’s Sarcoma Herpes Virus taps into a host microRNA regulatory network. (invited review) Cell Host and Microbe. 3(1):1-3. click here

C. S. Sullivan. 2008. New roles for large and small viral RNAs in evading host defenses. (invited review) Nature Reviews Genetics. 9(7):503-7. click here

G. J. Seo, L. H. Fink, B. O’Hara, W. J. Atwood, and C. S. Sullivan. 2008. Evolutionarily conserved function of a viral microRNA. J. Virol. 82(20):9823-8. click here

C. S. Sullivan, and B. R. Cullen. 2009. Non-coding regulatory RNAs of the DNA Tumor viruses. in “DNA Tumor Viruses”, B. Damania and J. M. Pipas, Editors. Springer Science and Media: New York. p. 645-682. (invited book chapter) click here

J. M. Ziegelbauer, C. S. Sullivan, and D. Ganem. 2009. Tandem array-based expression screens identify host mRNA targets of virus -encoded microRNAs. Nature Genetics. 41(1): 130-4. Article selected by “Faculty of 1000”. click here

G. J. Seo, C. J. Chen, and C. S. Sullivan. 2009. Merkel Cell Polyomavirus encodes a microRNA with the ability to autoregulate viral gene expression. Virology. 383(2): 183-7. click here

C. S. Sullivan, C. K. Sung, C. D. Pack, A. T. Grundhoff, A. E. Lukacher, T. Benjamin, and D. Ganem. 2009. Murine Polyomavirus encodes a microRNA that cleaves early RNA transcripts but is not essential for experimental infection. Virology. 387(1): 157-167. click here

L. V. McClure, G. J. Seo, and C. S. Sullivan. 2010. Reporter-based assays for analyzing RNA interference in mammalian cells. In Methods in Molecular Biology: “Argonaute Proteins: Methods and Protocols”, T. C. Hobman and T. Duchaine, Editors. Humana Press. (invited book chapter).

S. Asgari, and C. S. Sullivan. 2010. Role of microRNAs as regulators of host-virus interactions. In “Insect Virology”, S. Asgari and K Johnson, Editors. Horizon Scientific Press. (invited book chapter).

Y. T. Lin, R .P. Kincaid, D. Arasappan, S. E. Dowd, S. P. Hunicke-Smith, and C. S. Sullivan. 2010.   Small RNA profiling reveals antisense transcription throughout the KSHV genome and novel small RNAs. RNA. 16(8): 1540-58. click here

A. Swarbrick, S. L. Woods, A. Shaw, A. Balakrishnan, Y. Phua, A. Nguyen, Y. Chanthery, L. Lim, L. J. Ashton, R. L. Judson, N. Huskey, R. Blelloch, M. Haber, M. D. Norris, P. Lengyel, C. S. Hackett, T. Preiss, A. Chetcuti, C. S. Sullivan, E. G. Marcusson, W. Weiss, N. L’Etoile, and A. Goga. 2010. miR-380-5p represses p53 to control cellular survival and is associated with poor outcome in MYCN amplified neuroblastoma. Nature Med. 16(10): 1134-40. Article selected by “Faculty of 1000”. click here

L. V. McClure, Y. T. Lin, and C. S. Sullivan. 2011. Detection of viral microRNAs by Northern blot analysis. In Methods in Molecular Biology: “Antiviral RNAi – immune defense and therapy”, R. Van Rij, Editor. Humana Press. (invited book chapter).

C. J. Chen, R. P. Kincaid, G. J. Seo, M. D. Bennett, and C. S. Sullivan. 2011. Insights into Polyomaviridae microRNA function derived from the study of the bandicoot papillomatosis carcinomatosis viruses. J. Virol. 85(9): 4487-500. click here

A. Grundhoff, and C. S. Sullivan. Virus-encoded microRNAs. 2011. Virology. 411(2): 325-43. click here

Y. T. Lin, and C. S. Sullivan. 2011. Expanding the role of Drosha to the regulation of viral gene expression. PNAS. 108(27): 11229-34. click here

R. P. Kincaid, J. M. Burke, and C. S. Sullivan. 2012. RNA virus microRNA that mimics a B-cell oncomiR, PNAS 109 (8) 3077-82. Subject of commentary article: Cullen BR. 2012. MicroRNA expression by an oncogene retrovirus. PNAS. 109 (8) 2695-2696. Article selected by “Faculty of  1000”. click here

R. P. Kincaid, and C. S. Sullivan. 2012. Virus- encoded microRNAs: An overview and a look to the future. PLoS Pathogens. 8(12): e1003018. click here

P. I. Wang, S. Hwang, R. P. Kincaid, C. S. Sullivan, I. Lee, and E. M. Marcotte. 2012. RIDDLE: Reflective diffusion and local extension reveal functional associations for unannotated gene sets via proximity in a gene network. Genome Biology. 13:R125. click here

C. J. Chen, J. E. Cox, R. P. Kincaid, A. Martinez, and C. S. Sullivan. 2013. Divergent microRNA targetomes of closely related circulating strains of polyomavirus. J. Virol. 87(20):11135-47. Selected by the Editors as an article of significant interest. Article selected by “Faculty of 1000”. click here

L. V. McClure, R. P. Kincaid, J. M. Burke, A. Grundhoff, and C. S. Sullivan. 2013. Comprehensive mapping and analysis of KSHV 3‘UTRs identifies differential post-transcriptional control of gene expression in lytic versus latent infection. Selected by the Editors as an article of significant interest. J. Virol. 87(23):12838-49. click here

G. J. Seo, R. P. Kincaid, T. Phanaksri, J. M. Burke, J. M. Pare, J. E. Cox, T. Y. Hsiang, R. M. Krug, and C. S. Sullivan. 2013. Reciprocal regulation of intracellular antiviral signaling and RNAi in mammalian cells. Cell Host Microbe, 14(4): 435-45. Covered in a preview article in the same issue of CHM, highlighted in Nature and Nature Reviews Microbiology, included in the Cell Host Microbe “Best of 2013” reprint collection. click here

R. P. Kincaid, J. M. Burke, E. M. DeVillers, and C. S. Sullivan. 2013. A human Torque Teno Virus encodes a microRNA that inhibits interferon signaling. PLoS Pathogens. 9(12): e1003818. click here

J. M. Pare, and C. S. Sullivan. 2014. Distinct Antiviral Responses in Pluripotent versus Differentiated Cells. PLoS Pathogens. 10(2): e1003865 click here

S. Zhang, V. Sroller, P. Zanwar, C. J. Chen, S. J. Halvorson, N. J. Ajami, C. W. Hecksel, J. L. Swain, C. Wong, C. S. Sullivan, and J. S. Butel. 2014. Viral MicroRNA Effects on Pathogenesis of Polyomavirus SV40 Infections in Syrian Golden Hamsters. PLoS Pathogens. 10(2): e1003912. click here

P. J. Goodrum, J. Pfeiffer, S. Schultz-Cherry, C. S. Sullivan, and B. Tsai. 2014. Welcome from the Gems Associate Editors. J. Virol. 88(10): 5207. click here

R. P. Kincaid, Y. Chen, J. E. Cox, A. Rethwilm, and C. S. Sullivan. 2014. Non-canonical miRNA biogenesis gives rise to retroviral mimics of lymphoproliferative and immunosuppressive host miRNAs. mBio. 5(2): e00074-14. click here

J. M. Pare, and C. S. Sullivan. 2014. A Host MicroRNA Brokers Truce with HSV-1. Cell Host Microbe. 15(4):
446-456. click here

J. M. Burke, D. P. Kelenis, R. P. Kincaid, and C. S. Sullivan. 2014. A central role for the primary microRNA stem in guiding the position and efficiency of Drosha processing of a viral pri-miRNA. RNA. 20(7): 1-10. click here

J. E. Cox, and C. S. Sullivan. 2014. Balance and Stealth: The Role of Noncoding RNAs in the Regulation of Virus Gene Expression. Annual Review of Virology. 1(1): 1-21.  click here

C. J. Chen, J. M. Burke, R. P. Kincaid, K. D. Azarm, N. Mireles, J. S. Butel, and C. S. Sullivan. 2014. Naturally arising strains of polyomaviruses with severely attenuated microRNA expression. J. Virol, ePub Aug 20. In press. click here

J. M. Burke, C. R. Bass, R. P. Kincaid, and C. S. Sullivan. 2014. Identification of tri-phosphatase activity in the biogenesis of retroviral microRNAs and RNAP III-generated shRNAs. Nucleic Acids Research. 42(22):13949-62. click here

C. J. Chen, J. E. Cox, K. D. Azarm, K. N. Wylie, K. D. Woolard, P. A. Pesavento, and C. S. Sullivan. 2015. Identification of a polyomavirus microRNA highly expressed in tumors. Virology, ePub Dec 12. In press. Selected by the Editors for a highlight. click here

100. C.S. Sullivan. 2015. Viral Virtuosos: New understanding of noncoding RNAs may solve a long-standing puzzle
     

about how viruses orchestrate lifelong infections. TheScientist. click here

10. J.M. Burke, C. V. Kuny, R. P. Kincaid, and C. S. Sullivan. 2015. Identification, validation, and characterization
    

of noncanonical miRNAs. Methods. click here

C. V. Kuny, C. S. Sullivan. 2016. Virus-Host Interactions and the ARTD/PARP family of enzymes. PLOS Pathogens. click here

R. P. Kincaid and C. S. Sullivan. 2016. Lessons Learned from In Vivo Studies of a Viral Noncoding RNA. mSphere. click here

10. J.M. Burke, R. P. Kincaid, R. M. Nottingham, A. M. Lambowitz and C. S. Sullivan. 2016. DUSP11 activity on
    

tri-phosphorylated transcripts promotes Argonaute association with noncanonical viral microRNAs and regulates steady state levels of cellular non-coding RNAs. Genes & Dev. click here

10. J.M. Burke and C. S. Sullivan. 2017. DUSP11 - An RNA phosphatase that regulates host and viral non-coding
    

RNAs in mammalian cells. RNA Biology.  click here

J. M. Burke, R.P. Kincaid, F. Aloisio, N. Welch, and C. S. Sullivan. 2017. Expression of short hairpin RNAs using the compact architecture of retroviral microRNA genes. Nucleic Acids Res. click here

R. P. Kincaid, N. G. Panicker, M. M. Lozano, C.S. Sullivan, J. P. Dudley and F. Mustafa. 2018. MMTV does not encode viral microRNAs but alters the levels of cancer-associated host microRNAs. Virology. 513: 180-187. click here

J. M. Burke, C. R. Bass, E. T. Ulug, C. S. Sullivan. 2018. Murine polyomavirus microRNAs promote viruria during the acute phase of infection. Bioarchives. click here, published in J Virol, in press.

R. P. Kincaid, V. L. Lam, R. P. Chirayil, G. Randall, and C. S. Sullivan. 2018. RNA triphosphatase DUSP11 enables exonuclease XRN-mediated restriction of hepatitis C virus. PNAS. click here

R. Chirayil , R. P. Kincaid , C. Dahlke , C. V. Kuny , N Dälken, M. Spohn, B. Lawson, A. Grundhoff  and C. S. Sullivan. 2018. Identification of virus-encoded microRNAs in divergent Papillomaviruses. PLOS Pathogens, in press July 2018. Highlighted by Virology Research Services: “Papilloma virus won’t give up its weapons easily” click here