-
1
-
-
80052788094
-
An RNA G-quadruplex in the 3′ UTR of the proto-oncogene PIM1 represses translation
-
Arora, A., Suess, B.: An RNA G-quadruplex in the 3′ UTR of the proto-oncogene PIM1 represses translation. RNA Biology 8, 802-805 (2011)
-
(2011)
RNA Biology
, vol.8
, pp. 802-805
-
-
Arora, A.1
Suess, B.2
-
2
-
-
84861416464
-
Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals
-
Baral, A., Kumar, P., Halder, R., Mani, P., Yadav, V.K., Singh, A., Das, S.K., Chowdhury, S.: Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals. Nucleic Acids Res. (2012)
-
(2012)
Nucleic Acids Res.
-
-
Baral, A.1
Kumar, P.2
Halder, R.3
Mani, P.4
Yadav, V.K.5
Singh, A.6
Das, S.K.7
Chowdhury, S.8
-
3
-
-
77957058196
-
5′-UTR G-quadruplex structures acting as translational repressors
-
Beaudoin, J.D., Perreault, J.P.: 5′-UTR G-quadruplex structures acting as translational repressors. Nucleic Acids Res. 38, 7022-7036 (2010)
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 7022-7036
-
-
Beaudoin, J.D.1
Perreault, J.P.2
-
4
-
-
62549119174
-
FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure
-
Bensaid, M., Melko, M., Bechara, E.G., Davidovic, L., Berretta, A., Catania, M.V., Gecz, J., Lalli, E., Bardoni, B.: FRAXE-associated mental retardation protein (FMR2) is an RNA-binding protein with high affinity for G-quartet RNA forming structure. Nucleic Acids Res. 37, 1269-1279 (2009)
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 1269-1279
-
-
Bensaid, M.1
Melko, M.2
Bechara, E.G.3
Davidovic, L.4
Berretta, A.5
Catania, M.V.6
Gecz, J.7
Lalli, E.8
Bardoni, B.9
-
5
-
-
58249121729
-
RNAalifold: Improved consensus structure prediction for RNA alignments
-
Bernhart, S.H., Hofacker, I.L., Will, S., Gruber, A.R., Stadler, P.F.: RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9, 474 (2008)
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474
-
-
Bernhart, S.H.1
Hofacker, I.L.2
Will, S.3
Gruber, A.R.4
Stadler, P.F.5
-
6
-
-
0023984838
-
An improved algorithm for nucleic acid secondary structure display
-
Bruccoleri, R.E., Heinrich, G.: An improved algorithm for nucleic acid secondary structure display. Computer Appl. Biosci. 4, 167-173 (1988)
-
(1988)
Computer Appl. Biosci.
, vol.4
, pp. 167-173
-
-
Bruccoleri, R.E.1
Heinrich, G.2
-
7
-
-
38849085810
-
A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA Gquadruplexes
-
Bugaut, A., Balasubramanian, S.: A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA Gquadruplexes. Biochemistry 47, 689-697 (2008)
-
(2008)
Biochemistry
, vol.47
, pp. 689-697
-
-
Bugaut, A.1
Balasubramanian, S.2
-
8
-
-
84862229118
-
5'-UTR RNA G-quadruplexes: Translation regulation and targeting
-
doi: 10.1093/nar/gks068
-
Bugaut, A., Balasubramanian, S.: 5'-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res. (2012), doi: 10.1093/nar/gks068
-
(2012)
Nucleic Acids Res.
-
-
Bugaut, A.1
Balasubramanian, S.2
-
9
-
-
33747874580
-
CONTRAfold: RNA secondary structure prediction without physics-based models
-
Do, C.B., Woods, D.A., Batzoglou, S.: CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22(14), e90-e98 (2006)
-
(2006)
Bioinformatics
, vol.22
, Issue.14
-
-
Do, C.B.1
Woods, D.A.2
Batzoglou, S.3
-
10
-
-
33748519569
-
Gene function correlates with potential for G4 DNA formation in the human genome
-
Eddy, J., Maizels, N.: Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res. 34, 3887-3896 (2006)
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3887-3896
-
-
Eddy, J.1
Maizels, N.2
-
12
-
-
77957082956
-
A G-quadruplex structure within the 5'-UTR of TRF2 mRNA represses translation in human cells
-
Gomez, D., Guédin, A., Mergny, J.L., Salles, B., Riou, J.F., Teulade-Fichou, M.P., Calsou, P.: A G-quadruplex structure within the 5'-UTR of TRF2 mRNA represses translation in human cells. Nucleic Acids Res. 38, 7187-7198 (2010)
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 7187-7198
-
-
Gomez, D.1
Guédin, A.2
Mergny, J.L.3
Salles, B.4
Riou, J.F.5
Teulade-Fichou, M.P.6
Calsou, P.7
-
13
-
-
54349124117
-
G-Quadruplex formation interferes with P1 helix formation in the RNA component of telomerase hTERC
-
Gros, J., Guédin, A., Mergny, J.L., Lacroix, L.: G-Quadruplex formation interferes with P1 helix formation in the RNA component of telomerase hTERC. Chem-BioChem 9, 2075-2079 (2008)
-
(2008)
Chem-BioChem
, vol.9
, pp. 2075-2079
-
-
Gros, J.1
Guédin, A.2
Mergny, J.L.3
Lacroix, L.4
-
14
-
-
43049132871
-
Sequence effects in single-base loops for quadruplexes
-
Guédin, A., De Cian, A., Gros, J., Lacroix, L., Mergny, J.L.: Sequence effects in single-base loops for quadruplexes. Biochimie 90, 686-696 (2008)
-
(2008)
Biochimie
, vol.90
, pp. 686-696
-
-
Guédin, A.1
De Cian, A.2
Gros, J.3
Lacroix, L.4
Mergny, J.L.5
-
15
-
-
78649850820
-
How long is too long? Effects of loop size on G-quadruplex stability
-
Guédin, A., Gros, J., Patrizia, A., Mergny, J.L.: How long is too long? Effects of loop size on G-quadruplex stability. Nucleic Acids Res. 38, 7858-7868 (2010)
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 7858-7868
-
-
Guédin, A.1
Gros, J.2
Patrizia, A.3
Mergny, J.L.4
-
16
-
-
0036301332
-
Secondary structure prediction for aligned RNA sequences
-
Hofacker, I.L., Fekete, M., Stadler, P.F.: Secondary structure prediction for aligned RNA sequences. J. Mol. Biol. 319, 1059-1066 (2002)
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1059-1066
-
-
Hofacker, I.L.1
Fekete, M.2
Stadler, P.F.3
-
17
-
-
1042304206
-
Prediction of locally stable RNA secondary structures for genome-wide surveys
-
Hofacker, I.L., Priwitzer, B., Stadler, P.F.: Prediction of locally stable RNA secondary structures for genome-wide surveys. Bioinformatics 20, 191-198 (2004)
-
(2004)
Bioinformatics
, vol.20
, pp. 191-198
-
-
Hofacker, I.L.1
Priwitzer, B.2
Stadler, P.F.3
-
18
-
-
20144364292
-
Prevalence of quadruplexes in the human genome
-
Huppert, J.L., Balasubramanian, S.: Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908-2916 (2005)
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2908-2916
-
-
Huppert, J.L.1
Balasubramanian, S.2
-
19
-
-
56049121180
-
G-quadruplexes: The beginning and end of UTRs
-
Huppert, J.L., Bugaut, A., Kumari, S., Balasubramanian, S.: G-quadruplexes: the beginning and end of UTRs. Nucleic Acids Res. 36, 6260-6268 (2008)
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 6260-6268
-
-
Huppert, J.L.1
Bugaut, A.2
Kumari, S.3
Balasubramanian, S.4
-
20
-
-
81855190848
-
Inhibition of translation by small RNA-stabilized mRNA structures in human cells
-
Ito, K., Go, S., Komiyama, M., Xu, Y.: Inhibition of translation by small RNA-stabilized mRNA structures in human cells. J. Am. Chem. Soc. 133, 19153-19159 (2011)
-
(2011)
J. Am. Chem. Soc.
, vol.133
, pp. 19153-19159
-
-
Ito, K.1
Go, S.2
Komiyama, M.3
Xu, Y.4
-
21
-
-
84856801825
-
Potential G-quadruplexes in the human long non-coding transcriptome
-
Jayaraj, G.G., Pandey, S., Scaria, V., Maiti, S.: Potential G-quadruplexes in the human long non-coding transcriptome. RNA Biolog. 9, 81-86 (2012)
-
(2012)
RNA Biolog.
, vol.9
, pp. 81-86
-
-
Jayaraj, G.G.1
Pandey, S.2
Scaria, V.3
Maiti, S.4
-
22
-
-
69949186768
-
A comparison of DNA and RNA quadruplex structures and stabilities
-
Joachimi, A., Benz, A., Hartig, J.S.: A comparison of DNA and RNA quadruplex structures and stabilities. Bioorg. Med. Chem. 17, 6811-6815 (2009)
-
(2009)
Bioorg. Med. Chem.
, vol.17
, pp. 6811-6815
-
-
Joachimi, A.1
Benz, A.2
Hartig, J.S.3
-
23
-
-
47649105111
-
In vivo veritas: Using yeast to probe the biological functions of G-quadruplexes
-
Johnson, J.E., Smith, J.S., Kozak, M.L., Johnson, F.B.: In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie 90, 1250-1263 (2008)
-
(2008)
Biochimie
, vol.90
, pp. 1250-1263
-
-
Johnson, J.E.1
Smith, J.S.2
Kozak, M.L.3
Johnson, F.B.4
-
24
-
-
33747860882
-
QGRS mapper: A web-based server for predicting G-quadruplexes in nucleotide sequences
-
Kikin, O., D'Antonio, L., Bagga, P.S.: QGRS mapper: a web-based server for predicting G-quadruplexes in nucleotide sequences. Nucleic Acids Res. 34, W676-W682 (2006)
-
(2006)
Nucleic Acids Res.
, vol.34
-
-
Kikin, O.1
D'Antonio, L.2
Bagga, P.S.3
-
25
-
-
33947310727
-
An RNA Gquadruplex in the 5′UTR of the NRAS proto-oncogene modulates translation
-
Kumari, S., Bugaut, A., Huppert, J.L., Balasubramanian, S.: An RNA Gquadruplex in the 5′UTR of the NRAS proto-oncogene modulates translation. Nat. Chem. Biol. 3, 218-221 (2007)
-
(2007)
Nat. Chem. Biol.
, vol.3
, pp. 218-221
-
-
Kumari, S.1
Bugaut, A.2
Huppert, J.L.3
Balasubramanian, S.4
-
26
-
-
0029138009
-
RNA aptamers that bind flavin and nicotinamide redox cofactors
-
Lauhon, C.T., Szostak, J.W.: RNA aptamers that bind flavin and nicotinamide redox cofactors. J. Am. Chem. Soc. 117, 1246-1257 (1995)
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 1246-1257
-
-
Lauhon, C.T.1
Szostak, J.W.2
-
27
-
-
82055164092
-
ViennaRNA Package 2.0
-
Lorenz, R., Bernhart, S.H., Höner zu Siederdissen, C., Tafer, H., Flamm, C., Stadler, P.F., Hofacker, I.L.: ViennaRNA Package 2.0. Alg. Mol. Biol. 6, 26 (2011)
-
(2011)
Alg. Mol. Biol.
, vol.6
, pp. 26
-
-
Lorenz, R.1
Bernhart, S.H.2
Höner Zu Siederdissen, C.3
Tafer, H.4
Flamm, C.5
Stadler, P.F.6
Hofacker, I.L.7
-
28
-
-
69849104275
-
TERRA: Telomeric repeat-containing RNA
-
Luke, B., Lingner, J.: TERRA: telomeric repeat-containing RNA. EMBO J. 28, 2503-2510 (2009)
-
(2009)
EMBO J.
, vol.28
, pp. 2503-2510
-
-
Luke, B.1
Lingner, J.2
-
29
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
Mathews, D.H., Disney, M.D., Childs, J.L., Schroeder, S.J., Zuker, M., Turner, D.H.: Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101, 7287-7292 (2004)
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
30
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill, J.S.: The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29, 1105-1119 (1990)
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
31
-
-
34548726219
-
Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family
-
Menon, L., Mihailescu, M.R.: Interactions of the G quartet forming semaphorin 3F RNA with the RGG box domain of the fragile X protein family. Nucleic Acids Res. 35, 5379-5392 (2007)
-
(2007)
Nucleic Acids Res.
, vol.35
, pp. 5379-5392
-
-
Menon, L.1
Mihailescu, M.R.2
-
33
-
-
67049134254
-
An unusually stable G-quadruplex within the 5′-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells
-
Morris, M.J., Basu, S.: An unusually stable G-quadruplex within the 5′-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells. Biochemistry 48, 5313-5319 (2009)
-
(2009)
Biochemistry
, vol.48
, pp. 5313-5319
-
-
Morris, M.J.1
Basu, S.2
-
34
-
-
33646877072
-
Thermodynamics of RNA-RNA binding
-
Mückstein, U., Tafer, H., Hackermüller, J., Bernhard, S.B., Stadler, P.F., Hofacker, I.L.: Thermodynamics of RNA-RNA binding. Bioinformatics 22, 1177-1182 (2006)
-
(2006)
Bioinformatics
, vol.22
, pp. 1177-1182
-
-
Mückstein, U.1
Tafer, H.2
Hackermüller, J.3
Bernhard, S.B.4
Stadler, P.F.5
Hofacker, I.L.6
-
35
-
-
27144451010
-
Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo
-
Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D., Lipps, H.J.: Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nature Struct. Mol. Biol. 12, 847-854 (2005)
-
(2005)
Nature Struct. Mol. Biol.
, vol.12
, pp. 847-854
-
-
Paeschke, K.1
Simonsson, T.2
Postberg, J.3
Rhodes, D.4
Lipps, H.J.5
-
36
-
-
0028196714
-
From sequences to shapes and back: A case study in RNA secondary structures
-
Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L.: From sequences to shapes and back: A case study in RNA secondary structures. Proc. Roy. Soc. Lond. B 255, 279-284 (1994)
-
(1994)
Proc. Roy. Soc. Lond. B
, vol.255
, pp. 279-284
-
-
Schuster, P.1
Fontana, W.2
Stadler, P.F.3
Hofacker, I.L.4
-
37
-
-
37249066753
-
Geometric formalism for DNA quadruplex folding
-
Webba da Silva, M.: Geometric formalism for DNA quadruplex folding. Chemistry 13, 9738-9745 (2007)
-
(2007)
Chemistry
, vol.13
, pp. 9738-9745
-
-
Webba Da Silva, M.1
-
38
-
-
66349125451
-
Predicting and understanding the stability of G-quadruplexes
-
Stegle, O., Payet, L., Mergny, J.L., MacKay, D.J.C., Huppert, J.L.: Predicting and understanding the stability of G-quadruplexes. Bioinformatics 25, i374-i382 (2009)
-
(2009)
Bioinformatics
, vol.25
-
-
Stegle, O.1
Payet, L.2
Mergny, J.L.3
MacKay, D.J.C.4
Huppert, J.L.5
-
39
-
-
35448996964
-
Bioinformatics approaches to quadruplex sequence location
-
Todd, A.K.: Bioinformatics approaches to quadruplex sequence location. Methods 43, 246-251 (2007)
-
(2007)
Methods
, vol.43
, pp. 246-251
-
-
Todd, A.K.1
-
40
-
-
52449093394
-
G-quadruplex DNA motifs as conserved cis-regulatory elements
-
Verma, A., Halder, K., Halder, R., Yadav, V.K., Rawal, P., Thakur, R.K., Mohd, F., Sharma, A., Chowdhury, S.: G-quadruplex DNA motifs as conserved cis-regulatory elements. J. Med. Chem. 51, 5641-5649 (2008)
-
(2008)
J. Med. Chem.
, vol.51
, pp. 5641-5649
-
-
Verma, A.1
Halder, K.2
Halder, R.3
Yadav, V.K.4
Rawal, P.5
Thakur, R.K.6
Mohd, F.7
Sharma, A.8
Chowdhury, S.9
-
41
-
-
34447541999
-
RNA quadruplex-based modulation of gene expression
-
Wieland, M., Hartig, J.S.: RNA quadruplex-based modulation of gene expression. Chem. Biol. 14, 757-763 (2007)
-
(2007)
Chem. Biol.
, vol.14
, pp. 757-763
-
-
Wieland, M.1
Hartig, J.S.2
-
42
-
-
63849156605
-
Function and targeting of G-quadruplexes
-
Wong, H.M., Payet, L., Huppert, J.L.: Function and targeting of G-quadruplexes. Curr. Opin. Mol. Ther. 11, 146-155 (2009)
-
(2009)
Curr. Opin. Mol. Ther.
, vol.11
, pp. 146-155
-
-
Wong, H.M.1
Payet, L.2
Huppert, J.L.3
-
43
-
-
80051739988
-
A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology
-
Zhang, A.Y., Bugaut, A., Balasubramanian, S.: A sequence-independent analysis of the loop length dependence of intramolecular RNA G-quadruplex stability and topology. Biochemistry 50, 7251-7258 (2011)
-
(2011)
Biochemistry
, vol.50
, pp. 7251-7258
-
-
Zhang, A.Y.1
Bugaut, A.2
Balasubramanian, S.3
-
44
-
-
77952870567
-
Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors
-
Zhang, D.H., Fujimoto, T., Saxena, S., Yu, H.Q., Miyoshi, D., Sugimoto, N.: Monomorphic RNA G-quadruplex and polymorphic DNA G-quadruplex structures responding to cellular environmental factors. Biochemistry 49, 4554-4563 (2010)
-
(2010)
Biochemistry
, vol.49
, pp. 4554-4563
-
-
Zhang, D.H.1
Fujimoto, T.2
Saxena, S.3
Yu, H.Q.4
Miyoshi, D.5
Sugimoto, N.6
-
45
-
-
77957334049
-
Structure monomorphism of RNA G-quadruplex that is independent of surrounding condition
-
Zhang, D.H., Zhi, G.Y.: Structure monomorphism of RNA G-quadruplex that is independent of surrounding condition. J. Biotechnol. 150, 6-10 (2010)
-
(2010)
J. Biotechnol.
, vol.150
, pp. 6-10
-
-
Zhang, D.H.1
Zhi, G.Y.2
-
46
-
-
34247645020
-
Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals
-
Zhao, Y., Du, Z., Li, N.: Extensive selection for the enrichment of G4 DNA motifs in transcriptional regulatory regions of warm blooded animals. FEBS Letters 581, 1951-1956 (2007)
-
(2007)
FEBS Letters
, vol.581
, pp. 1951-1956
-
-
Zhao, Y.1
Du, Z.2
Li, N.3
-
47
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker, M., Stiegler, P.: Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 9, 133-148 (1981)
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|