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We study the structure and function of RNA elements involved in cap-independent translation of plus-strand RNA viruses.  The goals of our research are: (1) to understand how translation of genomic and subgenomic RNAs is controlled by 3' elements using carmoviruses and umbraviruses; (2)  the process that allows ribosomes to read-through or frameshift at a specific location to synthesize the viral RNA-dependent RNA polymerase; and (3) how virus levels are controlled by nonsense mediated decay.


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 Past and Present

Listen to podcast of Anne Simon discussing women in STEM

  • Anne Simon elected to the American Academy of Microbiology.  Check out an interview with ASM on this link

  • Congratulations to My-Tra Le, (PhD 2016) now postdoc at Indiana University

  • Congratulations to Micki Kuhlmann (PhD 2016) now postdoc at the NCI

  • Congratulations to Maitreyi Chattopadhyay (PhD 2015) now research scientist at the FDA

  • Congratulations to Megan Young (PhD 2015) now research scientist, industry

  • Congratulations to Rong Guo (PhD 2011) Now a permanent regulatory officer at the FDA

  • Congratulations to Xiaoping Sun.  (PhD 2006)  Professor, Wuhan University

  • Congratulations to Xuefeng Yuan (Postdoc 2007-2012)   Professor, Shandong Agricultural University

  • Congratulations to Kerong Shi (Postdoc 2008-2010)   Associate Professor, Shandong Agricultural University

  • Congratulations to Jong-Won Oh  (PhD 1997)  Associate Professor at Yonsei University in Seoul, Korea

  • Congratulations to Qingzhong Kong  (PhD 1997)  Associate Professor at Case Western University

  • Congratulations to Hancheng Guan  (PhD 1999) Research Associate Professor, University of Pennsylvania

  • Congratulations to Jianlong Wang  (PhD 1999)  Associate Professor, Mount Sinai School of Medicine 

  • Congratulations to Peter Nagy  Postdoc (1997-1999)   Professor at University of Kentucky

  • Congratulations to Jiuchun Zhang (PhD 2006)   Postdoc at University of Wisconsin

  • Congratulations to Fengli Zhang (PhD 2007)  Senior Microbiologist, Wisconsin State Laboratory of Hygiene


Kwon, S-J, Bodaghi, S, Gadhave, KR, Tzanetakis, IE, Simon, AE, and Vidalakis, G. 2021. Complete nucleotide sequence, genome organization and comparative genomic analyses of citrus yellow-vein associated virus, an umbravirus-like associated virus-like RNA.  Front Microbiol, in press.


Liu, J., Carino, E., Bera, S., Gao, F., May, J.P., and Simon, A.E. 2021. Structural analysis and whole genome mapping of a new class of plant virus subviral RNAs:  umbravirus-Like associated RNAs. Viruses 13, 646;


May, J.P. and Simon, A.E. 2021. Targeting of viral RNAs by Upf1-mediated RNA decay pathways.  Curr Opin Virol 47, 1-8.


Ilyas, M, Du, Z. and Simon, A.E. 2021.  Opium poppy mosaic virus has an Xrn-resistant, translated subgenomic RNA and a BTE 3’ CITE.  J Virol  95 (9): e02109-20 DOI: 10.1128/JVI.02109-20 [SPOTLIGHT selection]


May, J.P., Johnson, P.Z., Ilyas, M., Gao, F., and Simon, A.E. 2020. Disruption of nonsense-mediated decay by the multifunctional long-distance movement protein of Pea enation mosaic virus 2.  Mbio 11:e00204-20.


Johnson, P.Z., Kasprzak, W.K., Shapiro, B.A., and Simon, A.E. 2019. RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences.  RNA Biol


May, J.P., Yuan, X-F., Sawicki, E., and Simon, A.E. 2018. RNA virus evasion of nonsense-mediated decay. PLoS Pathog 14(11): e1007459.  

Gao, F., Alekhina, O.M., Vassilenko, K.S., and Simon, A.E.  2018. Unusual dicistronic expression from closely-spaced initiation codons of overlapping open reading frames in Pea enation mosaic virus 2.  Nucleic Acids Res 46, 11726–11742   doi: 10.1093/nar/gky871

Gao, F. and Simon, A.E.2017. Differential use of 3’CITEs by the subgenomic RNA of Pea enation mosaic virus 2.  Virology 510, 194-204.

Du, Z., Alekhina, O.M., Vassilenko, K.S., and Simon, A.E.  2017. Concerted action of two 3’ cap-independent translation enhancers increases the competitive strength of translated viral genomes.  Nucleic Acids Res. doi: 10.1093/nar/gkx643


Aguado, L.C., Schmid, S., May, J., Sabin, L.R., Panis, M., Blanco-Melo, D., Shim, J.V., Sachs, D., Cherry, S., Simon, A.E., Levraud, J.P. and tenOever, B.R.  2017.    RNase III nucleases from diverse kingdoms serve as antiviral effectors.  Nature 547,114–117


Le, M.-T., Kasprzak, W.K., Kim, T., Gao, F., Young, M.Y.L, Yuan, X., Shapiro, B.A., Seog, J., and Simon, A.E.  2017.  Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch.  RNA Biology (Solicited Point of View), in press.


Le, M.-T., Kasprzak, W.K., Kim, T., Gao, F., Young, M.Y.L, Yuan, X., Shapiro, B.A., Seog, J., and Simon, A.E.  2017.  Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch.   eLife 6:e22883.

May, J., Johnson, P., Saleen, H., and Simon, A.E. 2017.  A sequence-independent, unstructured IRES is responsible for internal expression of the coat protein of Turnip crinkle virus.  J Virol 91, e02421 [SPOTLIGHT selection].

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