Anne E. Simon - Publications

Affiliations: 
CBMG University of Maryland, College Park, College Park, MD 

60 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 May JP, Johnson PZ, Ilyas M, Gao F, Simon AE. The Multifunctional Long-Distance Movement Protein of Protects Viral and Host Transcripts from Nonsense-Mediated Decay. Mbio. 11. PMID 32156817 DOI: 10.1128/mBio.00204-20  0.64
2019 Johnson PZ, Kasprzak WK, Shapiro BA, Simon AE. RNA2Drawer: Geometrically Strict Drawing of Nucleic Acid Structures with Graphical Structure Editing and Highlighting of Complementary Subsequences. Rna Biology. PMID 31441369 DOI: 10.1080/15476286.2019.1659081  0.8
2018 May JP, Yuan X, Sawicki E, Simon AE. RNA virus evasion of nonsense-mediated decay. Plos Pathogens. 14: e1007459. PMID 30452463 DOI: 10.1371/journal.ppat.1007459  0.68
2018 Gao F, Alekhina OM, Vassilenko KS, Simon AE. Unusual dicistronic expression from closely spaced initiation codons in an umbravirus subgenomic RNA. Nucleic Acids Research. PMID 30272199 DOI: 10.1093/nar/gky871  0.64
2018 Bayne CF, Widawski ME, Gao F, Masab MH, Chattopadhyay M, Murawski AM, Sansevere RM, Lerner BD, Castillo RJ, Griesman T, Fu J, Hibben JK, Garcia-Perez AD, Simon AE, Kushner DB. SELEX and SHAPE reveal that sequence motifs and an extended hairpin in the 5' portion of Turnip crinkle virus satellite RNA C mediate fitness in plants. Virology. 520: 137-152. PMID 29864677 DOI: 10.1016/j.virol.2018.05.010  0.68
2017 Gao F, Simon AE. Differential use of 3'CITEs by the subgenomic RNA of Pea enation mosaic virus 2. Virology. 510: 194-204. PMID 28750323 DOI: 10.1016/j.virol.2017.07.021  0.64
2017 Le MT, Kasprzak WK, Shapiro BA, Simon AE. 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. 0. PMID 28548627 DOI: 10.1080/15476286.2017.1325069  0.8
2017 Le MT, Kasprzak WK, Kim T, Gao F, Young MY, Yuan X, Shapiro BA, Seog J, Simon AE. Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch. Elife. 6. PMID 28186489 DOI: 10.7554/eLife.22883  0.8
2016 Kuhlmann MM, Chattopadhyay M, Stupina VA, Gao F, Simon AE. An RNA Element that Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations. Journal of Virology. PMID 27440887 DOI: 10.1128/JVI.01129-16  0.68
2015 Weaver SC, Simon AE. Editorial overview: Virus-vector interactions. Current Opinion in Virology. PMID 26616158 DOI: 10.1016/j.coviro.2015.11.001  1
2015 Gao F, Simon AE. Multiple Cis-acting elements modulate programmed -1 ribosomal frameshifting in Pea enation mosaic virus. Nucleic Acids Research. PMID 26578603 DOI: 10.1093/nar/gkv1241  0.64
2015 Chattopadhyay M, Stupina VA, Gao F, Szarko CR, Kuhlmann MM, Yuan X, Shi K, Simon AE. Requirement for Host RNA Silencing Components and the Virus Silencing Suppressor when Second-Site Mutations Compensate For Structural Defects in the 3' UTR. Journal of Virology. PMID 26355083 DOI: 10.1128/JVI.01566-15  0.68
2015 Murawski AM, Nieves JL, Chattopadhyay M, Young MY, Szarko C, Tajalli HF, Azad T, Jean-Jacques NB, Simon AE, Kushner DB. Rapid evolution of in vivo-selected sequences and structures replacing 20% of a subviral RNA. Virology. 483: 149-162. PMID 25974866 DOI: 10.1016/j.virol.2015.04.002  1
2014 Dashti A, Schwander P, Langlois R, Fung R, Li W, Hosseinizadeh A, Liao HY, Pallesen J, Sharma G, Stupina VA, Simon AE, Dinman JD, Frank J, Ourmazd A. Trajectories of the ribosome as a Brownian nanomachine. Proceedings of the National Academy of Sciences of the United States of America. 111: 17492-7. PMID 25422471 DOI: 10.1073/pnas.1419276111  1
2014 Gao F, Kasprzak WK, Szarko C, Shapiro BA, Simon AE. The 3' untranslated region of Pea Enation Mosaic Virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers. Journal of Virology. 88: 11696-712. PMID 25100834 DOI: 10.1128/JVI.01433-14  0.8
2014 Chattopadhyay M, Kuhlmann MM, Kumar K, Simon AE. Position of the kissing-loop interaction associated with PTE-type 3'CITEs can affect enhancement of cap-independent translation. Virology. 458: 43-52. PMID 24928038 DOI: 10.1016/j.virol.2014.03.027  0.4
2013 Gao F, Gulay SP, Kasprzak W, Dinman JD, Shapiro BA, Simon AE. The kissing-loop T-shaped structure translational enhancer of Pea enation mosaic virus can bind simultaneously to ribosomes and a 5' proximal hairpin. Journal of Virology. 87: 11987-2002. PMID 23986599 DOI: 10.1128/JVI.02005-13  1
2013 Stupina VA, Simon AE. Preparation of biologically active Arabidopsis ribosomes and comparison with yeast ribosomes for binding to a tRNA-mimic that enhances translation of plant plus-strand RNA viruses. Frontiers in Plant Science. 4: 271. PMID 23885260 DOI: 10.3389/fpls.2013.00271  0.68
2012 Gao F, Kasprzak W, Stupina VA, Shapiro BA, Simon AE. A ribosome-binding, 3' translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction. Journal of Virology. 86: 9828-42. PMID 22761367 DOI: 10.1128/JVI.00677-12  0.8
2012 Yuan X, Shi K, Simon AE. A local, interactive network of 3' RNA elements supports translation and replication of Turnip crinkle virus. Journal of Virology. 86: 4065-81. PMID 22345459 DOI: 10.1128/JVI.07019-11  0.68
2011 McFadden G, Simon AE. Building bridges between plant and animal viruses. Current Opinion in Virology. 1: 319-21. PMID 22440834 DOI: 10.1016/j.coviro.2011.10.004  1
2011 Guo R, Meskauskas A, Dinman JD, Simon AE. Evolution of a helper virus-derived, ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus. Virology. 419: 10-6. PMID 21862095 DOI: 10.1016/j.virol.2011.07.019  1
2011 Chattopadhyay M, Shi K, Yuan X, Simon AE. Long-distance kissing loop interactions between a 3' proximal Y-shaped structure and apical loops of 5' hairpins enhance translation of Saguaro cactus virus. Virology. 417: 113-25. PMID 21664637 DOI: 10.1016/j.virol.2011.05.007  0.68
2011 Stupina VA, Yuan X, Meskauskas A, Dinman JD, Simon AE. Ribosome binding to a 5' translational enhancer is altered in the presence of the 3' untranslated region in cap-independent translation of turnip crinkle virus. Journal of Virology. 85: 4638-53. PMID 21389125 DOI: 10.1128/JVI.00005-11  1
2010 Cao M, Ye X, Willie K, Lin J, Zhang X, Redinbaugh MG, Simon AE, Morris TJ, Qu F. The capsid protein of Turnip crinkle virus overcomes two separate defense barriers to facilitate systemic movement of the virus in Arabidopsis. Journal of Virology. 84: 7793-802. PMID 20504923 DOI: 10.1128/JVI.02643-09  1
2010 Yuan X, Shi K, Young MY, Simon AE. The terminal loop of a 3' proximal hairpin plays a critical role in replication and the structure of the 3' region of Turnip crinkle virus. Virology. 402: 271-80. PMID 20403628 DOI: 10.1016/j.virol.2010.03.036  0.68
2010 Zuo X, Wang J, Yu P, Eyler D, Xu H, Starich MR, Tiede DM, Simon AE, Kasprzak W, Schwieters CD, Shapiro BA, Wang YX. Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3' UTR of turnip crinkle virus. Proceedings of the National Academy of Sciences of the United States of America. 107: 1385-90. PMID 20080629 DOI: 10.1073/pnas.0908140107  1
2009 Yuan X, Shi K, Meskauskas A, Simon AE. The 3' end of Turnip crinkle virus contains a highly interactive structure including a translational enhancer that is disrupted by binding to the RNA-dependent RNA polymerase. Rna (New York, N.Y.). 15: 1849-64. PMID 19656866 DOI: 10.1261/rna.1708709  1
2009 Simon AE, Gehrke L. RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs. Biochimica Et Biophysica Acta. 1789: 571-83. PMID 19501200 DOI: 10.1016/j.bbagrm.2009.05.005  1
2009 Guo R, Lin W, Zhang J, Simon AE, Kushner DB. Structural plasticity and rapid evolution in a viral RNA revealed by in vivo genetic selection. Journal of Virology. 83: 927-39. PMID 19004956 DOI: 10.1128/JVI.02060-08  1
2008 Stupina VA, Meskauskas A, McCormack JC, Yingling YG, Shapiro BA, Dinman JD, Simon AE. The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits. Rna (New York, N.Y.). 14: 2379-93. PMID 18824512 DOI: 10.1261/rna.1227808  1
2008 McCormack JC, Yuan X, Yingling YG, Kasprzak W, Zamora RE, Shapiro BA, Simon AE. Structural domains within the 3' untranslated region of Turnip crinkle virus. Journal of Virology. 82: 8706-20. PMID 18579599 DOI: 10.1128/JVI.00416-08  1
2006 McCormack JC, Simon AE. Callus cultures of Arabidopsis. Current Protocols in Microbiology. Unit16D.1. PMID 18770584 DOI: 10.1002/9780471729259.mc16d01s00  0.52
2006 Zhang J, Zhang G, Guo R, Shapiro BA, Simon AE. A pseudoknot in a preactive form of a viral RNA is part of a structural switch activating minus-strand synthesis. Journal of Virology. 80: 9181-91. PMID 16940529 DOI: 10.1128/JVI.00295-06  1
2006 Sun X, Simon AE. A cis-replication element functions in both orientations to enhance replication of Turnip crinkle virus. Virology. 352: 39-51. PMID 16757010 DOI: 10.1016/j.virol.2006.03.051  1
2006 Zhang J, Zhang G, McCormack JC, Simon AE. Evolution of virus-derived sequences for high-level replication of a subviral RNA. Virology. 351: 476-88. PMID 16682064 DOI: 10.1016/j.virol.2006.03.011  1
2006 Zhang G, Zhang J, George AT, Baumstark T, Simon AE. Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA. Rna (New York, N.Y.). 12: 147-62. PMID 16301603 DOI: 10.1261/rna.2166706  1
2005 Zhang J, Simon AE. Importance of sequence and structural elements within a viral replication repressor. Virology. 333: 301-15. PMID 15721364 DOI: 10.1016/j.virol.2004.12.015  1
2005 Sun X, Zhang G, Simon AE. Short internal sequences involved in replication and virion accumulation in a subviral RNA of turnip crinkle virus. Journal of Virology. 79: 512-24. PMID 15596844 DOI: 10.1128/JVI.79.1.512-524.2005  1
2004 Zhang J, Stuntz RM, Simon AE. Analysis of a viral replication repressor: sequence requirements for a large symmetrical internal loop. Virology. 326: 90-102. PMID 15262498 DOI: 10.1016/j.virol.2004.05.006  1
2004 McCormack JC, Simon AE. Biased hypermutagenesis associated with mutations in an untranslated hairpin of an RNA virus. Journal of Virology. 78: 7813-7. PMID 15220455 DOI: 10.1128/JVI.78.14.7813-7817.2004  0.52
2004 Zhang G, Zhang J, Simon AE. Repression and derepression of minus-strand synthesis in a plus-strand RNA virus replicon. Journal of Virology. 78: 7619-33. PMID 15220437 DOI: 10.1128/JVI.78.14.7619-7633.2004  1
2003 Zhang F, Simon AE. A novel procedure for the localization of viral RNAs in protoplasts and whole plants. The Plant Journal : For Cell and Molecular Biology. 35: 665-73. PMID 12940959  0.96
2003 Zhang F, Simon AE. Enhanced viral pathogenesis associated with a virulent mutant virus or a virulent satellite RNA correlates with reduced virion accumulation and abundance of free coat protein. Virology. 312: 8-13. PMID 12890616  0.96
2003 Sun X, Simon AE. Fitness of a turnip crinkle virus satellite RNA correlates with a sequence-nonspecific hairpin and flanking sequences that enhance replication and repress the accumulation of virions. Journal of Virology. 77: 7880-9. PMID 12829828  1
2003 Zhang G, Simon AE. A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional SELEX. Journal of Molecular Biology. 326: 35-48. PMID 12547189  0.84
2000 Guan H, Simon AE. Polymerization of nontemplate bases before transcription initiation at the 3' ends of templates by an RNA-dependent RNA polymerase: An activity involved in 3' end repair of viral RNAs Proceedings of the National Academy of Sciences of the United States of America. 97: 12451-12456. PMID 11070075 DOI: 10.1073/pnas.97.23.12451  1
2000 Wang J, Simon AE. 3'-End stem-loops of the subviral RNAs associated with turnip crinkle virus are involved in symptom modulation and coat protein binding. Journal of Virology. 74: 6528-37. PMID 10864666 DOI: 10.1128/JVI.74.14.6528-6537.2000  0.32
2000 Yoshinari S, Nagy PD, Simon AE, Dreher TW. CCA initiation boxes without unique promoter elements support in vitro transcription by three viral RNA-dependent RNA polymerases Rna. 6: 698-707. PMID 10836791 DOI: 10.1017/S1355838200992410  1
1999 Wang J, Simon AE. Symptom attenuation by a satellite RNA in vivo is dependent on reduced levels of virus coat protein. Virology. 259: 234-45. PMID 10364508 DOI: 10.1006/viro.1999.9781  0.52
1998 Kong Q, Simon AE. In situ hybridization to RNA in whole Arabidopsis plants Methods in Molecular Biology (Clifton, N.J.). 82: 409-415. PMID 9664442 DOI: 10.1385/0-89603-391-0:409  1
1997 Kong Q, Wang J, Simon AE. Satellite RNA-mediated resistance to turnip crinkle virus in Arabidopsis involves a reduction in virus movement Plant Cell. 9: 2051-2063. PMID 9401127 DOI: 10.1105/tpc.9.11.2051  1
1997 Kong Q, Oh JW, Carpenter CD, Simon AE. The coat protein of turnip crinkle virus is involved in subviral RNA- mediated symptom modulation and accumulation Virology. 238: 478-485. PMID 9400620 DOI: 10.1006/viro.1997.8853  1
1997 Wang J, Simon AE. Analysis of the two subgenomic RNA promoters for turnip crinkle virus in vivo and in vitro. Virology. 232: 174-86. PMID 9185601 DOI: 10.1006/viro.1997.8550  0.4
1995 Kong Q, Oh JW, Simon AE. Symptom attenuation by a normally virulent satellite RNA of turnip crinkle virus is associated with the coat protein open reading frame Plant Cell. 7: 1625-1634. PMID 9750054 DOI: 10.1105/tpc.7.10.1625  1
1993 Cascone PJ, Haydar TF, Simon AE. Sequences and structures required for recombination between virus-associated RNAs. Science (New York, N.Y.). 260: 801-5. PMID 8484119  1
1991 Li XH, Simon AE. In vivo accumulation of a turnip crinkle virus defective interfering RNA is affected by alterations in size and sequence. Journal of Virology. 65: 4582-90. PMID 1870188 DOI: 10.1128/JVI.65.9.4582-4590.1991  0.56
1989 Li XH, Heaton LA, Morris TJ, Simon AE. Turnip crinkle virus defective interfering RNAs intensify viral symptoms and are generated de novo. Proceedings of the National Academy of Sciences of the United States of America. 86: 9173-7. PMID 2594759 DOI: 10.1073/PNAS.86.23.9173  0.48
1987 Simon AE, Howell SH. Synthesis in vitro of infectious RNA copies of the virulent satellite of turnip crinkle virus. Virology. 156: 146-52. PMID 3811230 DOI: 10.1016/0042-6822(87)90445-4  1
1985 Simon AE, Tenbarge KM, Scofield SR, Finkelstein RR, Crouch ML. Nucleotide sequence of a cDNA clone of Brassica napus 12S storage protein shows homology with legumin from Pisum sativum. Plant Molecular Biology. 5: 191-201. PMID 24306655 DOI: 10.1007/BF00015683  1
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