Murawski, A.M., Nieves, J.L., Chattopadhyay, M., Young, M.Y., Szarko, C., Tajalli, H.F., Azad, T., Jean-Jacques, N.B., Simon, A.E., andKushner, D.B. 2015. Rapid evolution of in vivo-selected sequences and structures replacing 20% of a subviral RNA. Virology 483, 149-162.
Yuan, X., Shi, K., and Simon, A.E. 2012. A local interactive network of 3' RNA elements supports translation and replication in Turnip crinkle virus. J. Virol. 86, 4065-4081.
Yuan, X., Shi, K., Young, M. Y. L., and Simon, A. E. 2010. The terminal loop of a 3’ proximal hairpin plays a critical role in the structure of the 3’ region of Turnip crinkle virus and the RdRp-mediated conformational switch. Virology 402, 271-280.
Yuan, X., Shi, K., Meskauskas, A. and Simon, A.E. 2009. The 3’ End of Turnip crinkle virus contains a highly interactive structure with a translational enhancer that is disrupted by binding to the RNA-dependent RNA polymerase. RNA 15, 1849-1864.
McCormack, J. C., Yuan, X., Yingling, Y. G., Zamora, R. E., Shapiro, B. A., and Simon, A. E. 2008. Structural domains within the 3' UTR of Turnip crinkle virus. J. Virol. 82, 8706-8720.
Zhang, J., Zhang, G., Guo, R., Shapiro, B. and Simon, A. E. 2006. A pseudoknot in a pre-active form of a viral RNA is part of a structural switch activating minus-strand synthesis. J. Virol 80, 9181-9191.
Zhang, J., Zhang, G., McCormack, J. and Simon, A. E. 2006. Evolution of virus-derived sequences for high level replication of a subviral RNA. Virology 351, 476-488.
Sun, X., and Simon, A. E. 2006 A cis-replication element functions in both orientations to enhance replication of Turnip crinkle virus. Virology 352, 39-51.
Zhang, G., Zhang, J., George, A. T., Baumstark, T., and Simon, A. E. 2006. Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA. RNA 12, 147-162.
Zhang, J. and Simon, A. E. 2005. Importance of sequence and structural elements within A viral replication repressor. Virology 333, 301-315.
Sun, X., Zhang, G., and Simon, A. E. 2005. Short internal sequences involved in RNA replication and virion accumulation in a subviral RNA of Turnip crinkle virus. J. Virol. 79, 512-524.
Zhang, J., Stuntz, R. M., and Simon, A. E. 2004. Analysis of a viral replication repressor: Sequence requirements in the large symmetrical loop. Virology 326,90-102.
Zhang G, Zhang J, and Simon AE. 2004. Repression and derepression of minus-strand synthesis in a plus-strand RNA virus replicon. J. Virol. 78, 7619-7633.
McCormack, J. and Simon, A. E. 2004. Biased hypermutagensis associated with mutations in an untranslated hairpin of an RNA virus. J. Virol. 78, 7813-7817.
Sun, X., and Simon, A.E 2003. Fitness of a Turnip crinkle virus satellite RNA correlates with a sequence-nonspecific hairpin and flanking sequences that enhance replication and repress accumulation of virions. J. Virol. 77, 7880-7889.
Zhang, G. and Simon, A. E. 2003. A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional selex. J. Mol. Biol. 326, 35-48.
Nagy, P. D., Pogany, J., and Simon, A. E. 2001. In vivo and in vitro characterization of an RNA replication enhancer in a satellite RNA associated with Turnip crinkle virus: comparison of sequences and structures stimulating primer-dependent and primer-independent RNA synthesis. Virology 288, 315-324.
Guan, H., Carpenter, C. D., and Simon, A. E. 2000. Requirement of a 5’-proximal linear sequence on minus strands for plus-strand synthesis of a satellite RNA associated with TCV. Virology 268, 355-363.
Guan, H and Simon, A. E. 2000. Polymerization of non-template bases prior to transcription initiation by an RNA-dependent RNA polymerase: A novel activity involved in 3’-end repair of viral RNAs. Proc. Natl. Acad. Sci. 97, 12451-12456.
Guan, H., Carpenter, C. D., and Simon, A. E. 2000. Analysis of cis-acting sequences involved in plus-strand synthesis of a TCV-associated satellite RNA identifies a new carmovirus replication element. Virology 268, 345-354.
Wang, J.L., and Simon, A.E. 2000. 3'-end stem-loops of the subviral RNAs associated with turnip crinkle virus are involved in symptom modulation and coat protein binding. J Virol 74, 6528-6537.
Wang, J., Carpenter, C.D. and Simon, A. E. 1999. Minimal Sequence and Structural Requirements of A Subgenomic RNA Promoter for Turnip Crinkle Virus Virology 253, 327-336.
Carpenter, C.D. and Simon, A. E. (1998) Analysis of sequences and predicted structures required for viral satellite RNA accumulation by in vivo genetic selection Nucleic Acids Research, 1998, Vol. 26, 2426 - 2432
Nagy, P. D., Carpenter, C. D., and Simon, A. E. 1997. A novel 3' end repair mechanism in an RNA virus. Proc. Natl. Acad. Sci. USA. 94, 1113-1118. PMid: 9037015
Guan, H., Song, C., and Simon, A. E. 1997. RNA promoters located on (-)-strands of a subviral RNA associated with turnip crinkle virus RNA 3:1401-1412
Stupina, V., and Simon, A. E. 1997. Analysis in vivo of trunip crinkle virus satellite RNA C variants with mutations in the 3' terminal minus strand promoter. Virology, 238, 470-477.
Wang, J. and Simon, A. E. 1997. Analysis of the two subgenomic RNA promoters for turnip crinkle virus in vivo and in vitro. Virology 232, 174-186.
Song, C. and Simon, A. E. 1995. Requirement of a 3'-terminal stem-loop in in vitro transcription by an RNA-dependent RNA polymerase. J. Mol. Biol. 254, 6-14.
Song, C., and Simon, A. E. 1995. Synthesis of novel products in vitro by an RNA-dependent RNA polymerase. J. Virol. 69. 4020-4028.
Carpenter, C.D., Oh, J.-W., Zhang, C., and Simon, A. E. 1995. Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination. J. Mol. Biol. 245, 608-622.
Zhang, C., and Simon, A. E. 1994. Effect of template size on replication of defective interfering RNAs. J. Virol. 68, 8466-8469.
Song, C., and Simon, A.E. 1994. RNA-dependent RNA polymerase from plants infected with turnip crinkle virus can transcribe (+)- and (-)-strands of virus-associated RNAs. Proc. Natl. Acad Sci.USA. 91, 8792-8796.
