| Year |
Citation |
Score |
| 2011 |
Yu CH, Noteborn MH, Pleij CW, Olsthoorn RC. Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting. Nucleic Acids Research. 39: 8952-9. PMID 21803791 DOI: 10.1093/nar/gkr579 |
0.36 |
|
| 2010 |
Olsthoorn RC, Reumerman R, Hilbers CW, Pleij CW, Heus HA. Functional analysis of the SRV-1 RNA frameshifting pseudoknot. Nucleic Acids Research. 38: 7665-72. PMID 20639537 DOI: 10.1093/nar/gkq629 |
0.394 |
|
| 2009 |
de Smit MH, Verlaan PW, van Duin J, Pleij CW. In vivo dynamics of intracistronic transcriptional polarity. Journal of Molecular Biology. 385: 733-47. PMID 19059415 DOI: 10.1016/j.jmb.2008.11.020 |
0.356 |
|
| 2006 |
Nagel JH, Flamm C, Hofacker IL, Franke K, de Smit MH, Schuster P, Pleij CW. Structural parameters affecting the kinetics of RNA hairpin formation. Nucleic Acids Research. 34: 3568-76. PMID 16855293 DOI: 10.1093/Nar/Gkl445 |
0.478 |
|
| 2005 |
Koenig R, Pleij CW, Lesemann DE, Loss S, Vetten HJ. Molecular characterization of isolates of anagyris vein yellowing virus, plantago mottle virus and scrophularia mottle virus -- comparison of various approaches for tymovirus classification. Archives of Virology. 150: 2325-38. PMID 15883655 DOI: 10.1007/s00705-005-0545-6 |
0.345 |
|
| 2004 |
Giro A, Bergia A, Zuccheri G, Bink HH, Pleij CW, Samorì B. Single molecule studies of RNA secondary structure: AFM of TYMV viral RNA. Microscopy Research and Technique. 65: 235-45. PMID 15630685 DOI: 10.1002/Jemt.20123 |
0.55 |
|
| 2004 |
Olsthoorn RC, Laurs M, Sohet F, Hilbers CW, Heus HA, Pleij CW. Novel application of sRNA: stimulation of ribosomal frameshifting. Rna (New York, N.Y.). 10: 1702-3. PMID 15496520 DOI: 10.1261/rna.7139704 |
0.435 |
|
| 2004 |
van Roon AM, Bink HH, Plaisier JR, Pleij CW, Abrahams JP, Pannu NS. Crystal structure of an empty capsid of turnip yellow mosaic virus. Journal of Molecular Biology. 341: 1205-14. PMID 15321716 DOI: 10.1016/j.jmb.2004.06.085 |
0.679 |
|
| 2004 |
Koenig R, Pleij CW, Loss S, Burgermeister W, Aust H, Schiemann J. Molecular characterisation of potexviruses isolated from three different genera in the family Cactaceae. Archives of Virology. 149: 903-14. PMID 15098106 DOI: 10.1007/s00705-003-0268-5 |
0.474 |
|
| 2004 |
Bink HH, Roepan SK, Pleij CW. Two histidines of the coat protein of turnip yellow mosaic virus at the capsid interior are crucial for viability. Proteins. 55: 236-44. PMID 15048817 DOI: 10.1002/prot.10600 |
0.488 |
|
| 2004 |
Barends S, Rudinger-Thirion J, Florentz C, Giegé R, Pleij CW, Kraal B. tRNA-like structure regulates translation of Brome mosaic virus RNA. Journal of Virology. 78: 4003-10. PMID 15047816 DOI: 10.1128/JVI.78.8.4003-4010.2004 |
0.664 |
|
| 2004 |
Meulewaeter F, van Lipzig R, Gultyaev AP, Pleij CW, Van Damme D, Cornelissen M, van Eldik G. Conservation of RNA structures enables TNV and BYDV 5' and 3' elements to cooperate synergistically in cap-independent translation. Nucleic Acids Research. 32: 1721-30. PMID 15020708 DOI: 10.1093/nar/gkh338 |
0.458 |
|
| 2003 |
Bink HH, Schirawski J, Haenni AL, Pleij CW. The 5'-proximal hairpin of turnip yellow mosaic virus RNA: its role in translation and encapsidation. Journal of Virology. 77: 7452-8. PMID 12805444 |
0.576 |
|
| 2003 |
Barends S, Bink HH, van den Worm SH, Pleij CW, Kraal B. Entrapping ribosomes for viral translation: tRNA mimicry as a molecular Trojan horse. Cell. 112: 123-9. PMID 12526799 |
0.586 |
|
| 2002 |
Bink HH, Pleij CW. RNA-protein interactions in spherical viruses. Archives of Virology. 147: 2261-79. PMID 12491096 DOI: 10.1007/s00705-002-0891-6 |
0.656 |
|
| 2002 |
Nagel JH, Pleij CW. Self-induced structural switches in RNA. Biochimie. 84: 913-23. PMID 12458084 DOI: 10.1016/s0300-9084(02)01448-7 |
0.495 |
|
| 2002 |
de Smit MH, Gultyaev AP, Hilge M, Bink HH, Barends S, Kraal B, Pleij CW. Structural variation and functional importance of a D-loop-T-loop interaction in valine-accepting tRNA-like structures of plant viral RNAs. Nucleic Acids Research. 30: 4232-40. PMID 12364602 |
0.343 |
|
| 2002 |
Bink HH, Hellendoorn K, van der Meulen J, Pleij CW. Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA. Proceedings of the National Academy of Sciences of the United States of America. 99: 13465-70. PMID 12361978 DOI: 10.1073/pnas.202287499 |
0.474 |
|
| 2002 |
Nagel JH, Gultyaev AP, Oistämö KJ, Gerdes K, Pleij CW. A pH-jump approach for investigating secondary structure refolding kinetics in RNA. Nucleic Acids Research. 30: e63. PMID 12087188 DOI: 10.1093/nar/gnf057 |
0.528 |
|
| 2002 |
van Lipzig R, Gultyaev AP, Pleij CW, van Montagu M, Cornelissen M, Meulewaeter F. The 5' and 3' extremities of the satellite tobacco necrosis virus translational enhancer domain contribute differentially to stimulation of translation. Rna (New York, N.Y.). 8: 229-36. PMID 11924567 DOI: 10.1017/s1355838202018071 |
0.401 |
|
| 2002 |
Gultyaev AP, van Batenburg FH, Pleij CW. Selective pressures on RNA hairpins in vivo and in vitro. Journal of Molecular Evolution. 54: 1-8. PMID 11734892 DOI: 10.1007/s00239-001-0010-4 |
0.504 |
|
| 2001 |
Michiels PJ, Versleijen AA, Verlaan PW, Pleij CW, Hilbers CW, Heus HA. Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. Journal of Molecular Biology. 310: 1109-23. PMID 11501999 DOI: 10.1006/jmbi.2001.4823 |
0.361 |
|
| 2001 |
van Batenburg FH, Gultyaev AP, Pleij CW. PseudoBase: structural information on RNA pseudoknots. Nucleic Acids Research. 29: 194-5. PMID 11125088 DOI: 10.1093/nar/29.1.194 |
0.344 |
|
| 2000 |
Koenig R, Pleij CW, Büttner G. Structure and variability of the 3' end of RNA 3 of Beet soil-borne pomovirus--a virus with uncertain pathogenic effects. Archives of Virology. 145: 1173-81. PMID 10948990 DOI: 10.1007/s007050070117 |
0.434 |
|
| 2000 |
Koenig R, Pleij CW, Huth W. Molecular characterization of a new furovirus mainly infecting rye. Archives of Virology. 144: 2125-40. PMID 10603167 DOI: 10.1007/s007050050627 |
0.457 |
|
| 2000 |
van Batenburg FH, Gultyaev AP, Pleij CW, Ng J, Oliehoek J. PseudoBase: a database with RNA pseudoknots. Nucleic Acids Research. 28: 201-4. PMID 10592225 DOI: 10.1093/nar/28.1.201 |
0.356 |
|
| 2000 |
Deiman BA, Verlaan PW, Pleij CW. In vitro transcription by the turnip yellow mosaic virus RNA polymerase: a comparison with the alfalfa mosaic virus and brome mosaic virus replicases. Journal of Virology. 74: 264-71. PMID 10590114 DOI: 10.1128/jvi.74.1.264-271.2000 |
0.6 |
|
| 1999 |
Bringloe DH, Pleij CW, Coutts RH. Mutation analysis of cis-elements in the 3'- and 5'-untranslated regions of satellite tobacco necrosis virus strain C RNA. Virology. 264: 76-84. PMID 10544131 DOI: 10.1006/VIRO.1999.9994 |
0.608 |
|
| 1999 |
Gultyaev AP, van Batenburg FH, Pleij CW. An approximation of loop free energy values of RNA H-pseudoknots. Rna (New York, N.Y.). 5: 609-17. PMID 10334330 DOI: 10.1017/S135583829998189X |
0.466 |
|
| 1998 |
Kolk MH, van der Graaf M, Fransen CT, Wijmenga SS, Pleij CW, Heus HA, Hilbers CW. Structure of the 3'-hairpin of the TYMV pseudoknot: preformation in RNA folding. The Embo Journal. 17: 7498-504. PMID 9857204 DOI: 10.1093/emboj/17.24.7498 |
0.615 |
|
| 1998 |
Koenig R, Pleij CW, Beier C, Commandeur U. Genome properties of beet virus Q, a new furo-like virus from sugarbeet, determined from unpurified virus. The Journal of General Virology. 2027-36. PMID 9714254 DOI: 10.1099/0022-1317-79-8-2027 |
0.672 |
|
| 1998 |
Bringloe DH, Gultyaev AP, Pelpel M, Pleij CW, Coutts RH. The nucleotide sequence of satellite tobacco necrosis virus strain C and helper-assisted replication of wild-type and mutant clones of the virus. The Journal of General Virology. 1539-46. PMID 9634099 DOI: 10.1099/0022-1317-79-6-1539 |
0.439 |
|
| 1998 |
Deiman BA, Koenen AK, Verlaan PW, Pleij CW. Minimal template requirements for initiation of minus-strand synthesis in vitro by the RNA-dependent RNA polymerase of turnip yellow mosaic virus. Journal of Virology. 72: 3965-72. PMID 9557683 DOI: 10.1128/JVI.72.5.3965-3972.1998 |
0.625 |
|
| 1998 |
Kolk MH, van der Graaf M, Wijmenga SS, Pleij CW, Heus HA, Hilbers CW. NMR structure of a classical pseudoknot: interplay of single- and double-stranded RNA. Science (New York, N.Y.). 280: 434-8. PMID 9545221 DOI: 10.1126/science.280.5362.434 |
0.647 |
|
| 1998 |
Gultyaev AP, van Batenburg FH, Pleij CW. Dynamic competition between alternative structures in viroid RNAs simulated by an RNA folding algorithm. Journal of Molecular Biology. 276: 43-55. PMID 9514713 DOI: 10.1006/jmbi.1997.1384 |
0.577 |
|
| 1997 |
Hellendoorn K, Verlaan PW, Pleij CW. A functional role for the conserved protonatable hairpins in the 5' untranslated region of turnip yellow mosaic virus RNA. Journal of Virology. 71: 8774-9. PMID 9343237 DOI: 10.1128/JVI.71.11.8774-8779.1997 |
0.489 |
|
| 1997 |
Deiman BA, Kortlever RM, Pleij CW. The role of the pseudoknot at the 3' end of turnip yellow mosaic virus RNA in minus-strand synthesis by the viral RNA-dependent RNA polymerase. Journal of Virology. 71: 5990-6. PMID 9223489 DOI: 10.1128/JVI.71.8.5990-5996.1997 |
0.61 |
|
| 1997 |
Deiman BA, Séron K, Jaspars EM, Pleij CW. Efficient transcription of the tRNA-like structure of turnip yellow mosaic virus by a template-dependent and specific viral RNA polymerase obtained by a new procedure [corrected]. Journal of Virological Methods. 64: 181-95. PMID 9079764 DOI: 10.1016/S0166-0934(96)02166-0 |
0.631 |
|
| 1997 |
Melchers WJ, Hoenderop JG, Bruins Slot HJ, Pleij CW, Pilipenko EV, Agol VI, Galama JM. Kissing of the two predominant hairpin loops in the coxsackie B virus 3' untranslated region is the essential structural feature of the origin of replication required for negative-strand RNA synthesis. Journal of Virology. 71: 686-96. PMID 8985400 DOI: 10.1128/jvi.71.1.686-696.1997 |
0.576 |
|
| 1997 |
Deiman BA, Pleij CW. Pseudoknots: A Vital Feature in Viral RNA Seminars in Virology. 8: 166-175. DOI: 10.1006/SMVY.1997.0119 |
0.595 |
|
| 1996 |
Hellendoorn K, Michiels PJ, Buitenhuis R, Pleij CW. Protonatable hairpins are conserved in the 5'-untranslated region of tymovirus RNAs. Nucleic Acids Research. 24: 4910-7. PMID 9016660 DOI: 10.1093/nar/24.24.4910 |
0.531 |
|
| 1996 |
Hellendoorn K, Mat AW, Gultyaev AP, Pleij CW. Secondary structure model of the coat protein gene of turnip yellow mosaic virus RNA: long, C-rich, single-stranded regions. Virology. 224: 43-54. PMID 8862398 DOI: 10.1006/viro.1996.0505 |
0.626 |
|
| 1995 |
van Batenburg FH, Gultyaev AP, Pleij CW. An APL-programmed genetic algorithm for the prediction of RNA secondary structure. Journal of Theoretical Biology. 174: 269-80. PMID 7545258 DOI: 10.1006/jtbi.1995.0098 |
0.433 |
|
| 1995 |
Gultyaev AP, van Batenburg FH, Pleij CW. The computer simulation of RNA folding pathways using a genetic algorithm. Journal of Molecular Biology. 250: 37-51. PMID 7541471 DOI: 10.1006/jmbi.1995.0356 |
0.542 |
|
| 1995 |
Pleij CW. Structure and function of RNA pseudoknots. Genetic Engineering. 17: 67-80. PMID 7540028 |
0.58 |
|
| 1995 |
Gultyaev AP, van Batenburg FH, Pleij CW. The influence of a metastable structure in plasmid primer RNA on antisense RNA binding kinetics. Nucleic Acids Research. 23: 3718-25. PMID 7479002 DOI: 10.1093/nar/23.18.3718 |
0.586 |
|
| 1994 |
ten Dam E, Brierley I, Inglis S, Pleij C. Identification and analysis of the pseudoknot-containing gag-pro ribosomal frameshift signal of simian retrovirus-1. Nucleic Acids Research. 22: 2304-10. PMID 8036158 DOI: 10.1093/nar/22.12.2304 |
0.384 |
|
| 1994 |
Gultyaev AP, van Batenburg E, Pleij CW. Similarities between the secondary structure of satellite tobacco mosaic virus and tobamovirus RNAs. The Journal of General Virology. 75: 2851-6. PMID 7931178 DOI: 10.1099/0022-1317-75-10-2851 |
0.675 |
|
| 1994 |
Pleij CW. RNA pseudoknots Current Opinion in Structural Biology. 4: 337-344. DOI: 10.1016/S0959-440X(94)90101-5 |
0.62 |
|
| 1993 |
Ringquist S, Cunningham P, Weitzmann C, Formenoy L, Pleij C, Ofengand J, Gold L. Translation initiation complex formation with 30 S ribosomal particles mutated at conserved positions in the 3'-minor domain of 16 S RNA. Journal of Molecular Biology. 234: 14-27. PMID 8230193 DOI: 10.1006/Jmbi.1993.1560 |
0.384 |
|
| 1993 |
Garcia A, van Duin J, Pleij CW. Differential response to frameshift signals in eukaryotic and prokaryotic translational systems. Nucleic Acids Research. 21: 401-6. PMID 7680118 DOI: 10.1093/nar/21.3.401 |
0.31 |
|
| 1992 |
Danthinne X, Seurinck J, Van Montagu M, Pleij CW, van Emmelo J. Structural similarities between the RNAs of two satellites of tobacco necrosis virus. Virology. 185: 605-14. PMID 1962441 DOI: 10.1016/0042-6822(91)90531-F |
0.6 |
|
| 1990 |
Dumas P, Moras D, Florentz C, Giegé R, Verlaan P, Van Belkum A, Pleij CW. 3-D graphics modelling of the tRNA-like 3'-end of turnip yellow mosaic virus RNA: structural and functional implications. Journal of Biomolecular Structure & Dynamics. 4: 707-28. PMID 3270524 DOI: 10.1080/07391102.1987.10507674 |
0.618 |
|
| 1990 |
Jupin I, Richards K, Jonard G, Guilley H, Pleij CW. Mapping sequences required for productive replication of beet necrotic yellow vein virus RNA 3. Virology. 178: 273-80. PMID 2389553 DOI: 10.1016/0042-6822(90)90403-E |
0.6 |
|
| 1990 |
Mans RM, Guerrier-Takada C, Altman S, Pleij CW. Interaction of RNase P from Escherichia coli with pseudoknotted structures in viral RNAs. Nucleic Acids Research. 18: 3479-87. PMID 2194161 DOI: 10.1093/Nar/18.12.3479 |
0.541 |
|
| 1990 |
Steen MT, Kaper JM, Pleij CW, Hansen JN. In-vitro translation of cucumoviral satellites. III. Translational efficiencies of cucumber mosaic virus-associated RNA 5 sequence variants can be related to the predicted secondary structures of their first 55 nucleotides. Virus Genes. 4: 41-52. PMID 1697436 DOI: 10.1007/BF00308564 |
0.381 |
|
| 1990 |
Abrahams JP, van den Berg M, van Batenburg E, Pleij C. Prediction of RNA secondary structure, including pseudoknotting, by computer simulation. Nucleic Acids Research. 18: 3035-44. PMID 1693421 DOI: 10.1093/nar/18.10.3035 |
0.683 |
|
| 1990 |
Pleij CW. Pseudoknots: a new motif in the RNA game. Trends in Biochemical Sciences. 15: 143-7. PMID 1692647 DOI: 10.1016/0968-0004(90)90214-v |
0.62 |
|
| 1989 |
van Belkum A, Wiersema PJ, Joordens J, Pleij C, Hilbers CW, Bosch L. Biochemical and biophysical analysis of pseudoknot-containing RNA fragments. Melting studies and NMR spectroscopy. European Journal of Biochemistry / Febs. 183: 591-601. PMID 2776753 DOI: 10.1111/J.1432-1033.1989.Tb21088.X |
0.774 |
|
| 1988 |
van Belkum A, Verlaan P, Kun JB, Pleij C, Bosch L. Temperature dependent chemical and enzymatic probing of the tRNA-like structure of TYMV RNA. Nucleic Acids Research. 16: 1931-50. PMID 2833723 DOI: 10.1093/nar/16.5.1931 |
0.744 |
|
| 1988 |
van Belkum A, Verlaan P, Kun JB, Pleij C, Bosch L. Temperature dependent chemical and enzymatic probing of the tRNA-like structure of TYMV RNA Nucleic Acids Research. 16: 1931-1950. DOI: 10.1093/Nar/16.5.1931 |
0.744 |
|
| 1985 |
Pleij CW, Rietveld K, Bosch L. A new principle of RNA folding based on pseudoknotting. Nucleic Acids Research. 13: 1717-31. PMID 4000943 DOI: 10.1093/nar/13.5.1717 |
0.629 |
|
| 1985 |
van Belkum A, Abrahams JP, Pleij CW, Bosch L. Five pseudoknots are present at the 204 nucleotides long 3' noncoding region of tobacco mosaic virus RNA. Nucleic Acids Research. 13: 7673-86. PMID 3934645 DOI: 10.1093/Nar/13.21.7673 |
0.778 |
|
| 1984 |
Joshi S, Neeleman L, Pleij CW, Haenni AL, Chapeville F, Bosch L, Van Vloten-Doting L. Nonstructural alfalfa mosaic virus RNA-coded proteins present in tobacco leaf tissue. Virology. 139: 231-42. PMID 18639831 DOI: 10.1016/0042-6822(84)90370-2 |
0.645 |
|
| 1984 |
Rietveld K, Linschooten K, Pleij CW, Bosch L. The three-dimensional folding of the tRNA-like structure of tobacco mosaic virus RNA. A new building principle applied twice. The Embo Journal. 3: 2613-9. PMID 16453568 |
0.793 |
|
| 1984 |
Rietveld K, Linschooten K, Pleij CW, Bosch L. The three-dimensional folding of the tRNA-like structure of tobacco mosaic virus RNA. A new building principle applied twice The Embo Journal. 3: 2613-2619. DOI: 10.1002/J.1460-2075.1984.Tb02182.X |
0.793 |
|
| 1983 |
Joshi S, Pleij CW, Haenni AL, Bosch L. Age dependence of cowpea protoplasts for uptake of spermidine and infectibility by alfalfa mosaic virus. Plant Molecular Biology. 2: 89-94. PMID 24318141 DOI: 10.1007/BF01595170 |
0.584 |
|
| 1983 |
Joshi S, Pleij CW, Haenni AL, Chapeville F, Bosch L. Properties of the tobacco mosaic virus intermediate length RNA-2 and its translation. Virology. 127: 100-11. PMID 18638998 DOI: 10.1016/0042-6822(83)90375-6 |
0.757 |
|
| 1983 |
Rietveld K, Pleij CW, Bosch L. Three-dimensional models of the tRNA-like 3' termini of some plant viral RNAs Embo Journal. 2: 1079-1085. PMID 6628363 DOI: 10.1002/J.1460-2075.1983.Tb01549.X |
0.797 |
|
| 1982 |
Noort A, van den Dries CL, Pleij CW, Jaspars EM, Bosch L. Properties of turnip yellow mosaic virus in cesium chloride solutions: the formation of high-density components. Virology. 120: 412-21. PMID 18638730 DOI: 10.1016/0042-6822(82)90041-1 |
0.646 |
|
| 1982 |
Rietveld K, Van Poelgeest R, Pleij CW, Van Boom JH, Bosch L. The tRNA-like structure at the 3' terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Research. 10: 1929-46. PMID 7079175 DOI: 10.1093/nar/10.6.1929 |
0.665 |
|
| 1979 |
Mellema JR, Benicourt C, Haenni AL, Noort A, Pleij CW, Bosch L. Translational studies with turnip yellow mosaic virus RNAs isolated from major and minor virus particles. Virology. 96: 38-46. PMID 18631590 DOI: 10.1016/0042-6822(79)90170-3 |
0.773 |
|
| 1977 |
Pleij CW, Eecen HG, Bosch L, Mandel M. The formation of fast-sedimenting turnip yellow mosaic virus RNA: structural rearrangement inside the capsid. Virology. 76: 781-6. PMID 14439 DOI: 10.1016/0042-6822(77)90258-6 |
0.766 |
|
| 1976 |
Pleij CW, Neeleman A, van Vloten-Doting L, Bosch L. Translation of turnip yellow mosaic virus RNA in vitro: a closed and an open coat protein cistron. Proceedings of the National Academy of Sciences of the United States of America. 73: 4437-41. PMID 1069996 DOI: 10.1073/Pnas.73.12.4437 |
0.751 |
|
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