A. Simon

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A Sequence-Independent, Unstructured Internal Ribosome Entry Site Is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus

Jared P. May, Philip Z Johnson, H. Saleem, 2017, Journal of Virology.

Involvement of a stem-loop structure in the location of junction sites in viral RNA recombination.

A. Simon, C. Carpenter, J. Oh, 1995, Journal of molecular biology.

Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch

F. Gao, B. Shapiro, W. Kasprzak, 2017, eLife.

Complete Genome Sequence and Genome Analysis of Eggplant mottled dwarf virus-Iranian Isolate

A. Simon, A. Dizadji, A. Massah, 2015 .

Structural Plasticity and Rapid Evolution in a Viral RNA Revealed by In Vivo Genetic Selection

D. Kushner, A. Simon, Jiuchun Zhang, 2008, Journal of Virology.

Satellite RNA-mediated resistance to turnip crinkle virus in Arabidopsis involves a reduction in virus movement.

A. Simon, J. Wang, Q. Kong, 1997, The Plant cell.

Nucleotide sequence of a cDNA clone of Brassica napus 12S storage protein shows homology with legumin from Pisum sativum

S. Scofield, A. Simon, M. Crouch, 1985, Plant Molecular Biology.

Turnip crinkle virus defective interfering RNAs intensify viral symptoms and are generated de novo.

T. J. Morris, A. Simon, L. A. Heaton, 1989, Proceedings of the National Academy of Sciences of the United States of America.

Mechanism of mutation at the aprt locus in Chinese hamster ovary cells: analysis of heterozygotes and hemizygotes

A. Simon, W. Bradley, M. W. Taylor, 1983, Molecular and cellular biology.

Changes in locations of crossover sites over time in de novo generated RNA recombinants.

A. Simon, C. D. Carpenter, 1996, Virology.

RNA recombination in turnip crinkle virus: its role in formation of chimeric RNAs, multimers, and in 3′-end repair

P. D. Nagy, A. Simon, 1996 .

Rapid evolution of in vivo -selected sequences and structures replacing twenty percent of a subviral RNA

D. Kushner, A. Simon, Allison M Murawski, 2018 .

Targeting of viral RNAs by Upf1-mediated RNA decay pathways.

Jared P. May, A. Simon, 2020, Current opinion in virology.

Long-distance kissing loop interactions between a 3' proximal Y-shaped structure and apical loops of 5' hairpins enhance translation of Saguaro cactus virus.

A. Simon, K. Shi, Xuefeng Yuan, 2011, Virology.

The Capsid Protein of Turnip Crinkle Virus Overcomes Two Separate Defense Barriers To Facilitate Systemic Movement of the Virus in Arabidopsis

M. Redinbaugh, F. Qu, T. J. Morris, 2010, Journal of Virology.

The 3 9 proximal translational enhancer of Turnip crinkle virus binds to 60 S ribosomal subunits

Yaroslava G. Yingling, B. Shapiro, J. Dinman, 2022 .

Two new umbravirus-like associated RNAs (ulaRNAs) discovered in maize and johnsongrass from Ecuador

W. Menzel, A. Simon, D. quito-avila, 2022, Archives of Virology.

The coat protein of turnip crinkle virus is involved in subviral RNA-mediated symptom modulation and accumulation.

A. Simon, J. Oh, Q. Kong, 1997, Virology.

A novel procedure for the localization of viral RNAs in protoplasts and whole plants.

Fengli Zhang, A. Simon, 2003, The Plant journal : for cell and molecular biology.

cDNA clones for Brassica napus seed storage proteins: evidence from nucleotide sequence analysis that both subunits of napin are cleaved from a precursor polypeptide.

R. Ferl, A. Simon, M. Crouch, 1983, Journal of molecular and applied genetics.

Translation Enhancers of Plant Viruses

W. Miller, A. Simon, 2013 .

G e n es E n cod i n g G I y ci n e - Ri c h A rabidopsis thaliana Proteins with RNA-Binding Motifs Are lnfluenced by Cold Treatment and an Endogenous Circadian Rhythm'

J. Kreps, A. Simon, C. D. Carpenter, 1994 .

Model involving gene inactivation in the generation of autosomal recessive mutants in mammalian cells in culture

L. Thompson, A. Simon, W. Bradley, 1982, Molecular and cellular biology.

Analysis in vivo of turnip crinkle virus satellite RNA C variants with mutations in the 3'-terminal minus-strand promoter.

A. Simon, V. Stupina, 1997, Virology.

RNase III nucleases from diverse kingdoms serve as antiviral effectors

S. Cherry, D. Sachs, B. tenOever, 2017, Nature.

Trajectories of the ribosome as a Brownian nanomachine

Hstau Y Liao, Joachim Frank, Peter Schwander, 2014, Proceedings of the National Academy of Sciences.

Plant virus satellite and defective interfering RNAs: new paradigms for a new century.

Z. Havelda, A. Simon, M. Roossinck, 2004, Annual review of phytopathology.

Effects of Defective Interfering Viruses on Virus Replication and Pathogenesis In Vitro and In Vivo

J. Holland, L. Roux, A. Simon, 1991, Advances in Virus Research.

High-frequency mutation at the adenine phosphoribosyltransferase locus in Chinese hamster ovary cells due to deletion of the gene.

A. Simon, M. W. Taylor, 1983, Proceedings of the National Academy of Sciences of the United States of America.

Mutations in a satellite RNA of turnip crinkle virus result in addition of poly(U) in vivo.

A. Simon, C. D. Carpenter, P. J. Cascone, 1991, Virology.

In vivo, large-scale preparation of uniformly (15)N- and site-specifically (13)C-labeled homogeneous, recombinant RNA for NMR studies.

A. Simon, T. K. Dayie, M. Le, 2015, Methods in enzymology.

Symptom attenuation by a satellite RNA in vivo is dependent on reduced levels of virus coat protein.

A. Simon, J. Wang, 1999, Virology.

Sequences and structures required for recombination between virus-associated RNAs.

A. Simon, T. Haydar, P. J. Cascone, 1993, Science.

Formation of multimers of linear satellite RNAs.

A. Simon, C. D. Carpenter, P. J. Cascone, 1991, Virology.

Recombination between satellite RNAs of turnip crinkle virus.

A. Simon, X. H. Li, C. D. Carpenter, 1990, The EMBO journal.

Symptom intensification on cruciferous hosts by the virulent satellite RNA of turnip crinkle virus.

A. Simon, Xiao Hua Li, 1990 .

Simplified RNA sequencing using dideoxy chain termination.

A. Simon, C. D. Carpenter, 1990, BioTechniques.

Synthesis in vitro of infectious RNA copies of the virulent satellite of turnip crinkle virus.

S. Howell, A. Simon, 1987, Virology.

The virulent satellite RNA of turnip crinkle virus has a major domain homologous to the 3′ end of the helper virus genome

S. Howell, A. Simon, 1986, The EMBO journal.

Importance of coat protein and RNA silencing in satellite RNA/virus interactions.

A. Simon, A. Manfre, 2008, Virology.

An RNA Element That Facilitates Programmed Ribosomal Readthrough in Turnip Crinkle Virus Adopts Multiple Conformations

F. Gao, A. Simon, M. Kuhlmann, 2016, Journal of Virology.

Multiple Cis-acting elements modulate programmed -1 ribosomal frameshifting in Pea enation mosaic virus

F. Gao, A. Simon, 2015, Nucleic acids research.

Genes Encoding Glycine-Rich Arabidopsis thaliana Proteins with RNA-Binding Motifs Are Influenced by Cold Treatment and an Endogenous Circadian Rhythm

J. Kreps, A. Simon, C. D. Carpenter, 1994, Plant physiology.

Callus Cultures of Arabidopsis

A. Simon, J. C. McCormack, 2006, Current protocols in microbiology.

Satellite RNAs of plant viruses

A. Simon, 1988, Plant Molecular Biology Reporter.

3′-End Stem-Loops of the Subviral RNAs Associated with Turnip Crinkle Virus Are Involved in Symptom Modulation and Coat Protein Binding

Jianlong Wang, A. Simon, 2000, Journal of Virology.

Protein Binding Involved in Symptom Modulation and Coat Associated with Turnip Crinkle Virus Are-End Stem-Loops of the Subviral RNAs ′ 3

Jianlong Wang, A. Simon, 2000 .

The 3′ Untranslated Region of Pea Enation Mosaic Virus Contains Two T-Shaped, Ribosome-Binding, Cap-Independent Translation Enhancers

F. Gao, B. Shapiro, W. Kasprzak, 2014, Journal of Virology.

3' cap-independent translation enhancers of plant viruses.

W. Miller, A. Simon, W. Miller, 2013, Annual review of microbiology.

Importance of sequence and structural elements within a viral replication repressor.

A. Simon, Jiuchun Zhang, 2005, Virology.

Requirement for Host RNA-Silencing Components and the Virus-Silencing Suppressor when Second-Site Mutations Compensate for Structural Defects in the 3′ Untranslated Region

A. Simon, M. Kuhlmann, K. Shi, 2015, Journal of Virology.

A Local, Interactive Network of 3′ RNA Elements Supports Translation and Replication of Turnip Crinkle Virus

A. Simon, K. Shi, Xuefeng Yuan, 2012, Journal of Virology.

Opium Poppy Mosaic Virus Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3′ CITE

A. Simon, M. Ilyas, Z. Du, 2021, Journal of Virology.

3'UTRs of carmoviruses.

A. Simon, 2015, Virus research.

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

J. Dinman, A. Simon, A. Meskauskas, 2011, Journal of Virology.

Differential use of 3'CITEs by the subgenomic RNA of Pea enation mosaic virus 2.

F. Gao, A. Simon, 2017, Virology.

Preparation of RNA.

A. Simon, C. D. Carpenter, Anne E. Simon, 1998, Methods in molecular biology.

Complete Nucleotide Sequence, Genome Organization, and Comparative Genomic Analyses of Citrus Yellow-Vein Associated Virus (CYVaV)

K. Gadhave, I. Tzanetakis, A. Simon, 2021, Frontiers in Microbiology.

Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3′ UTR of turnip crinkle virus

Wojciech Kasprzak, Charles D Schwieters, Bruce A Shapiro, 2010, Proceedings of the National Academy of Sciences.

RNA virus evasion of nonsense-mediated decay

Jared P. May, A. Simon, Xuefeng Yuan, 2018, PLoS pathogens.

The Multifunctional Long-Distance Movement Protein of Pea Enation Mosaic Virus 2 Protects Viral and Host Transcripts from Nonsense-Mediated Decay

F. Gao, Jared P. May, A. Simon, 2020, mBio.

The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits.

Bruce A Shapiro, Yaroslava G Yingling, Yaroslava G. Yingling, 2008, RNA.

Novel 3′ Proximal Replication Elements in Umbravirus Genomes

F. Gao, A. Simon, S. Bera, 2022, Viruses.

Identification of Novel 5′ and 3′ Translation Enhancers in Umbravirus-Like Coat Protein-Deficient RNA Replicons

A. Simon, Jingyuan Liu, 2022, Journal of virology.

Structural Analysis and Whole Genome Mapping of a New Type of Plant Virus Subviral RNA: Umbravirus-Like Associated RNAs

F. Gao, Jared P. May, A. Simon, 2021, Viruses.

Rapid evolution of in vivo-selected sequences and structures replacing 20% of a subviral RNA.

D. Kushner, A. Simon, Allison M Murawski, 2015, Virology.

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.

A. Simon, K. Shi, Xuefeng Yuan, 2010, Virology.

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.

Anne E Simon, A. Simon, Arturas Meskauskas, 2009, RNA.

RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs

Lee Gehrke, L. Gehrke, A. Simon, 2009, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.

Structural Domains within the 3′ Untranslated Region of Turnip Crinkle Virus

Bruce A. Shapiro, Wojciech Kasprzak, Yaroslava G. Yingling, 2008, Journal of Virology.

A Pseudoknot in a Preactive Form of a Viral RNA Is Part of a Structural Switch Activating Minus-Strand Synthesis

Bruce A. Shapiro, Guohua Zhang, Jiuchun Zhang, 2006, Journal of Virology.

A cis-replication element functions in both orientations to enhance replication of Turnip crinkle virus.

Xiaoping Sun, Anne E Simon, A. Simon, 2006, Virology.

Conformational changes involved in initiation of minus-strand synthesis of a virus-associated RNA.

A. Simon, Jiuchun Zhang, Guohua Zhang, 2006, RNA.

Repression and Derepression of Minus-Strand Synthesis in a Plus-Strand RNA Virus Replicon

A. Simon, Jiuchun Zhang, Guohua Zhang, 2004, Journal of Virology.

Conserved Structure Associated with Different 3′CITEs Is Important for Translation of Umbraviruses

A. Simon, S. Bera, Muhammad Ilyas, 2023, Viruses.

Structural characterization of a new subclass of panicum mosaic virus-like 3′ cap-independent translation enhancer

B. Shapiro, W. Kasprzak, A. Simon, 2022, Nucleic acids research.

Position of the kissing-loop interaction associated with PTE-type 3'CITEs can affect enhancement of cap-independent translation.

A. Simon, M. Kuhlmann, Maitreyi Chattopadhyay, 2014, Virology.

Concerted action of two 3′ cap-independent translation enhancers increases the competitive strength of translated viral genomes

O. Alekhina, K. Vassilenko, A. Simon, 2017, Nucleic acids research.

The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin

Suna P. Gulay, F. Gao, B. Shapiro, 2013, Journal of Virology.

The kl-TSS translational enhancer of PEMV can bind simultaneously to

Suna P. Gulay, F. Gao, B. Shapiro, 2013 .

Open reading frames of turnip crinkle virus involved in satellite symptom expression and incompatibility with Arabidopsis thaliana ecotype Dijon.

A. Simon, J. Oh, C. Song, 1995, Molecular plant-microbe interactions : MPMI.

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.

Fengli Zhang, A. Simon, 2003, Virology.

Susceptibility and resistance of Arabidopsis thaliana to turnip crinkle virus

M. Polacco, A. Simon, R. Stange, 1992 .

26 Interactions between Arabidopsis thaliana and Viruses

A. Simon, 1994 .

synthesis of a virus-associated RNA Conformational changes involved in initiation of minus-strand

A. Simon, Jiuchun Zhang, Guohua Zhang, 2005 .

Biased Hypermutagenesis Associated with Mutations in an Untranslated Hairpin of an RNA Virus

A. Simon, Anne E. Simon, John C. McCormack, 2004, Journal of Virology.

RNA Virus Mutations in an Untranslated Hairpin of an Biased Hypermutagenesis Associated with

A. Simon, J. C. McCormack, 2004 .

A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional SELEX.

Guohua Zhang, Anne E Simon, A. Simon, 2003, Journal of molecular biology.

Minimal sequence and structural requirements of a subgenomic RNA promoter for turnip crinkle virus.

A. Simon, J. Wang, C. D. Carpenter, 1999, Virology.

Replication, recombination, and symptom-modulation properties of the satellite RNAs of turnip crinkle virus.

A. Simon, 1999, Current topics in microbiology and immunology.

Analysis of sequences and predicted structures required for viral satellite RNA accumulation by in vivo genetic selection.

A. Simon, C. D. Carpenter, 1998, Nucleic acids research.

Analysis of the two subgenomic RNA promoters for turnip crinkle virus in vivo and in vitro.

A. Simon, J. Wang, 1997, Virology.

In vivo restoration of biologically active 3' ends of virus-associated RNAs by nonhomologous RNA recombination and replacement of a terminal motif

A. Simon, C. D. Carpenter, C. D. Carpenter, 1996, Journal of virology.

Symptom attenuation by a normally virulent satellite RNA of turnip crinkle virus is associated with the coat protein open reading frame.

A. Simon, J. Oh, Q. Kong, 1995, The Plant cell.

terminal motif . RNA recombination and replacement of a of virus-associated RNAs by nonhomologous In vivo restoration of biologically active 3 ' ends

A. Simon, C. D. Carpenter, 1995 .

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.

F. Gao, D. Kushner, A. Simon, 2018, Virology.

Evolution of a helper virus-derived, ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus.

J. Dinman, A. Simon, A. Meskauskas, 2011, Virology.

Short Internal Sequences Involved in Replication and Virion Accumulation in a Subviral RNA of Turnip Crinkle Virus

A. Simon, Guohua Zhang, Xiaoping Sun, 2005, Journal of Virology.

Analysis of a viral replication repressor: sequence requirements for a large symmetrical internal loop.

Jiuchun Zhang, Anne E Simon, A. Simon, 2004, Virology.

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

A. Simon, Xiaoping Sun, 2003, Journal of Virology.

In situ hybridization to RNA in whole Arabidopsis plants.

A. Simon, Q. Kong, 1998, Methods in molecular biology.

Environmental and genetic effects on circadian clock-regulated gene expression in Arabidopsis.

J. Kreps, A. Simon, Anne E. Simon, 1997, The Plant cell.

RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences

Bruce A Shapiro, Wojciech K Kasprzak, Anne E Simon, 2019, RNA biology.

In vivo accumulation of a turnip crinkle virus defective interfering RNA is affected by alterations in size and sequence

A. Simon, X. H. Li, 1991, Journal of virology.

Genome characterization of fig umbra-like virus

John S. Hu, J. Suzuki, M. Melzer, 2021, Virus Genes.

Recombination between satellite and genomic RNAs of turnip crinkle virus.

A. Simon, C. Zhang, P. J. Cascone, 1991, Virology.

ADAR1 Biology Can Hinder Effective Antiviral RNA Interference

Justin J. Frere, B. tenOever, Chanyong Jang, 2023, Journal of virology.

The 3 9 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

A. Simon, K. Shi, A. Meskauskas, 2009 .

RNAcanvas: interactive drawing and exploration of nucleic acid structures

A. Simon, Philip Z. Johnson, 2023, Nucleic Acids Res..

Unusual dicistronic expression from closely spaced initiation codons in an umbravirus subgenomic RNA

F. Gao, O. Alekhina, K. Vassilenko, 2018, Nucleic acids research.

A Ribosome-Binding, 3′ Translational Enhancer Has a T-Shaped Structure and Engages in a Long-Distance RNA-RNA Interaction

F. Gao, B. Shapiro, W. Kasprzak, 2012, Journal of Virology.

Combined single molecule experimental and computational approaches for understanding the unfolding pathway of a viral translation enhancer that participates in a conformational switch

B. Shapiro, W. Kasprzak, A. Simon, 2017, RNA biology.

Evolution of virus-derived sequences for high-level replication of a subviral RNA.

A. Simon, Jiuchun Zhang, Guohua Zhang, 2006, Virology.

In vivo and in vitro characterization of an RNA replication enhancer in a satellite RNA associated with turnip crinkle virus.

P. D. Nagy, A. Simon, J. Pogány, 2001, Virology.

RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs

L. Gehrke, A. Simon, 2009, Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.

The Kissing-Loop T-Shaped Structure Translational Enhancer of Pea Enation Mosaic Virus Can Bind Simultaneously to Ribosomes and a 5′ Proximal Hairpin

Suna P. Gulay, F. Gao, B. Shapiro, 2013, Journal of Virology.

Evolution of a helper virus-derived, ribosome binding translational enhancer in an untranslated satellite RNA of Turnip crinkle virus.

J. Dinman, A. Simon, Rong Guo, 2011, Virology.

Studies on RNA Recombination in vivo and in vitro

P. D. Nagy, A. Simon, C. D. Carpenter, 1997 .

New insights into the mechanisms of RNA recombination.

P. D. Nagy, A. Simon, A. Simon, 1997, Virology.

A Sequence-Independent, Unstructured Internal Ribosome Entry Site Is Responsible for Internal Expression of the Coat Protein of Turnip Crinkle Virus

Jared P. May, H. Saleem, A. Simon, 2017, Journal of Virology.

A novel 3'-end repair mechanism in an RNA virus.

P. D. Nagy, A. Simon, C. D. Carpenter, 1997, Proceedings of the National Academy of Sciences of the United States of America.