-
1
-
-
71849111461
-
Structure and function of regulatory RNA elements: Ribozymes that regulate gene expression
-
doi:10.1016/j.bbagrm.2009.09.006
-
Scott, W.G., Martick, M., & Chi, Y.I. Structure and function of regulatory RNA elements: ribozymes that regulate gene expression. Biochim. Biophys. Acta. 1789, 634-641, doi:10.1016/j.bbagrm.2009.09.006 (2009).
-
(1789)
Biochim. Biophys. Acta
, pp. 634-641
-
-
Scott, W.G.1
Martick, M.2
Chi, Y.I.3
-
2
-
-
84859295308
-
The roles of RNA in the synthesis of protein
-
doi:10.1101/cshperspect.a003780
-
Moore, P.B. & Steitz, T.A. The roles of RNA in the synthesis of protein. Cold Spring Harb. Perspect. Biol. 3, a003780, doi:10.1101/cshperspect.a003780 (2011).
-
(2011)
Cold Spring Harb. Perspect. Biol
, vol.3
-
-
Moore, P.B.1
Steitz, T.A.2
-
3
-
-
40849123031
-
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
-
doi:10.1371/journal.pbio.0060096
-
Wilkinson, K.A., et al. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. Plos Biol. 6, 883-899, doi:10.1371/journal.pbio.0060096 (2008).
-
(2008)
Plos Biol
, vol.6
, pp. 883-899
-
-
Wilkinson, K.A.1
-
4
-
-
16244412610
-
RNA structure analysis at single nucleotide resolution by selective 2 '-hydroxyl acylation and primer extension (SHAPE)
-
doi:10.1021/Ja043822v
-
Merino, E.J., Wilkinson, K.A., Coughlan, J.L., & Weeks, K.M. RNA structure analysis at single nucleotide resolution by selective 2 '-hydroxyl acylation and primer extension (SHAPE). J. Am. Chem. Soc. 127, 4223-4231, doi:10.1021/Ja043822v (2005).
-
(2005)
J. Am. Chem. Soc
, vol.127
, pp. 4223-4231
-
-
Merino, E.J.1
Wilkinson, K.A.2
Coughlan, J.L.3
Weeks, K.M.4
-
5
-
-
68449092202
-
Architecture and secondary structure of an entire HIV-1 RNA genome
-
doi:10.1038/nature08237
-
Watts, J.M., et al. Architecture and secondary structure of an entire HIV-1 RNA genome. Nature. 460, 711-716, doi:10.1038/nature08237 (2009).
-
(2009)
Nature
, vol.460
, pp. 711-716
-
-
Watts, J.M.1
-
6
-
-
84864377848
-
The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids
-
doi:10.1111/j.1364-3703.2011.00776.x
-
Xu, W., Bolduc, F., Hong, N., & Perreault, J.P. The use of a combination of computer-assisted structure prediction and SHAPE probing to elucidate the secondary structures of five viroids. Mol. Plant Pathol. doi:10.1111/j.1364-3703.2011.00776.x (2012).
-
(2012)
Mol. Plant Pathol
-
-
Xu, W.1
Bolduc, F.2
Hong, N.3
Perreault, J.P.4
-
7
-
-
84862195751
-
Structural architecture of the human long non-coding RNA, steroid receptor RNA activator
-
doi:10.1093/nar/gks071
-
Novikova, I.V., Hennelly, S.P., & Sanbonmatsu, K.Y. Structural architecture of the human long non-coding RNA, steroid receptor RNA activator. Nucleic Acids Res. 40, 5034-5051, doi:10.1093/nar/gks071 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
, pp. 5034-5051
-
-
Novikova, I.V.1
Hennelly, S.P.2
Sanbonmatsu, K.Y.3
-
8
-
-
79956159490
-
High-throughput structural analysis of yeast ribosomes using hSHAPE
-
Leshin, J.A., Heselpoth, R., Belew, A.T., & Dinman, J. High-throughput structural analysis of yeast ribosomes using hSHAPE. RNA Biol. 8, 478-487 (2011).
-
(2011)
RNA Biol
, vol.8
, pp. 478-487
-
-
Leshin, J.A.1
Heselpoth, R.2
Belew, A.T.3
Dinman, J.4
-
9
-
-
80053542128
-
A powerful approach for the selection of 2-aminopurine substitution sites to investigate RNA folding
-
doi:10.1021/ja2063583
-
Souliere, M.F., Haller, A., Rieder, R., & Micura, R. A powerful approach for the selection of 2-aminopurine substitution sites to investigate RNA folding. J. Am. Chem. Soc. 133, 16161-16167, doi:10.1021/ja2063583 (2011).
-
(2011)
J. Am. Chem. Soc
, vol.133
, pp. 16161-16167
-
-
Souliere, M.F.1
Haller, A.2
Rieder, R.3
Micura, R.4
-
10
-
-
33947720028
-
Selective 2 '-hydroxyl acylation analyzed by primer extension (SHAPE): Quantitative RNA structure analysis at single nucleotide resolution
-
doi:10.1038/nprot.2006.249
-
Wilkinson, K.A., Merino, E.J., & Weeks, K.M. Selective 2 '-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolution. Nat. Protoc. 1, 1610-1616, doi:10.1038/nprot.2006.249 (2006).
-
(2006)
Nat. Protoc
, vol.1
, pp. 1610-1616
-
-
Wilkinson, K.A.1
Merino, E.J.2
Weeks, K.M.3
-
11
-
-
77954183805
-
High-Throughput Shape and Hydroxyl Radical Analysis of Rna Structure and Ribonucleoprotein Assembly
-
doi:10.1016/S0076-6879(09)68004-6
-
McGinnis, J.L., Duncan, C.D.S. & Weeks, K.M. High-Throughput Shape and Hydroxyl Radical Analysis of Rna Structure and Ribonucleoprotein Assembly. Method Enzymol. 468, 67-89, doi:10.1016/S0076-6879(09)68004-6 (2009).
-
(2009)
Method Enzymol
, vol.468
, pp. 67-89
-
-
McGinnis, J.L.1
Duncan, C.D.S.2
Weeks, K.M.3
-
12
-
-
77957139491
-
SHAPE-directed RNA secondary structure prediction
-
doi:10.1016/j.ymeth.2010.06.007
-
Low, J.T. & Weeks, K.M. SHAPE-directed RNA secondary structure prediction. Methods. 52, 150-158, doi:10.1016/j.ymeth.2010.06.007 (2010).
-
(2010)
Methods
, vol.52
, pp. 150-158
-
-
Low, J.T.1
Weeks, K.M.2
-
13
-
-
13944278373
-
SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments
-
doi:10.1261/Rna.7214405
-
Das, R., Laederach, A., Pearlman, S.M., Herschlag, D., & Altman, R.B. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid footprinting experiments. Rna-a Publication of the Rna Society. 11, 344-354, doi:10.1261/Rna.7214405 (2005).
-
(2005)
Rna-a Publication of the Rna Society
, vol.11
, pp. 344-354
-
-
Das, R.1
Laederach, A.2
Pearlman, S.M.3
Herschlag, D.4
Altman, R.B.5
-
14
-
-
77956306662
-
Genome-wide measurement of RNA secondary structure in yeast
-
doi:10.1038/nature09322
-
Kertesz, M., et al. Genome-wide measurement of RNA secondary structure in yeast. Nature. 467, 103-107, doi:10.1038/nature09322 (2010).
-
(2010)
Nature
, vol.467
, pp. 103-107
-
-
Kertesz, M.1
-
15
-
-
78649690492
-
FragSeq: Transcriptome-wide RNA structure probing using high-throughput sequencing
-
doi:10.1038/nmeth.1529
-
Underwood, J.G., et al. FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing. Nat. Methods. 7, 995-1001, doi:10.1038/nmeth.1529 (2010).
-
(2010)
Nat. Methods
, vol.7
, pp. 995-1001
-
-
Underwood, J.G.1
-
16
-
-
78149354414
-
Toward global RNA structure analysis
-
doi:10.1038/nbt1110-1178
-
Mauger, D.M. & Weeks, K.M. Toward global RNA structure analysis. Nat. Biotechnol. 28, 1178-1179, doi:10.1038/nbt1110-1178 (2010).
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 1178-1179
-
-
Mauger, D.M.1
Weeks, K.M.2
-
17
-
-
79960571755
-
Multiplexed RNA Structure Characterization With Selective 2'-hydroxyl Acylation Analyzed By Primer Extension Sequencing (SHAPE-Seq)
-
doi:10.1073/pnas.1106501108
-
Lucks, J.B., et al. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proc. Natl. Acad. Sci. USA. 108, 11063-11068, doi:10.1073/pnas.1106501108 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 11063-11068
-
-
Lucks, J.B.1
-
18
-
-
52949152433
-
ShapeFinder: A software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis
-
doi:10.1261/rna.1166808
-
Vasa, S.M., Guex, N., Wilkinson, K.A., Weeks, K.M., & Giddings, M.C. ShapeFinder: a software system for high-throughput quantitative analysis of nucleic acid reactivity information resolved by capillary electrophoresis. RNA. 14, 1979-1990, doi:10.1261/rna.1166808 (2008).
-
(2008)
RNA
, vol.14
, pp. 1979-1990
-
-
Vasa, S.M.1
Guex, N.2
Wilkinson, K.A.3
Weeks, K.M.4
Giddings, M.C.5
-
19
-
-
77949447172
-
RNAstructure: Software for RNA secondary structure prediction and analysis
-
doi:10.1186/1471-2105-11-129
-
Reuter, J.S. & Mathews, D.H. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics. 11, 129, doi:10.1186/1471-2105-11-129 (2010).
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 129
-
-
Reuter, J.S.1
Mathews, D.H.2
-
20
-
-
83755205383
-
Simplified RNA secondary structure mapping by automation of SHAPE data analysis
-
doi:10.1093/nar/gkr773
-
Pang, P.S., Elazar, M., Pham, E.A., & Glenn, J.S. Simplified RNA secondary structure mapping by automation of SHAPE data analysis. Nucleic Acids Res. 39, e151, doi:10.1093/nar/gkr773 (2011).
-
(2011)
Nucleic Acids Res
, vol.39
-
-
Pang, P.S.1
Elazar, M.2
Pham, E.A.3
Glenn, J.S.4
-
21
-
-
58549109608
-
Accurate SHAPE-directed RNA structure determination
-
doi:DOI 10.1073/pnas.0806929106
-
Deigan, K.E., Li, T.W., Mathews, D.H., & Weeks, K.M. Accurate SHAPE-directed RNA structure determination. Proc. Natl. Acad. Sci. USA. 106, 97-102, doi:DOI 10.1073/pnas.0806929106 (2009).
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 97-102
-
-
Deigan, K.E.1
Li, T.W.2
Mathews, D.H.3
Weeks, K.M.4
-
22
-
-
67650727366
-
VARNA: Interactive drawing and editing of the RNA secondary structure
-
doi:10.1093/bioinformatics/btp250
-
Darty, K., Denise, A., & Ponty, Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics. 25, 1974-1975, doi:10.1093/bioinformatics/btp250 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 1974-1975
-
-
Darty, K.1
Denise, A.2
Ponty, Y.3
-
23
-
-
33747830257
-
PseudoViewer: Web application and web service for visualizing RNA pseudoknots and secondary structures
-
doi:10.1093/nar/gkl210
-
Byun, Y. & Han, K. PseudoViewer: web application and web service for visualizing RNA pseudoknots and secondary structures. Nucleic Acids Res. 34, W416-422, doi:10.1093/nar/gkl210 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Byun, Y.1
Han, K.2
-
24
-
-
84878654910
-
-
ed F. Eckstein, IRL Press
-
Brown, T. & Brown, D.J.S. (ed F. Eckstein) 20 (IRL Press, 1990).
-
(1990)
, pp. 20
-
-
Brown, T.1
Brown, D.J.S.2
-
25
-
-
78650668061
-
The RNA Transport Element of the Murine musD Retrotransposon Requires Long-range Intramolecular Interactions for Function
-
doi:DOI 10.1074/jbc.M110.182840
-
Legiewicz, M., et al. The RNA Transport Element of the Murine musD Retrotransposon Requires Long-range Intramolecular Interactions for Function. J. Biol. Chem. 285, 42097-42104, doi:DOI 10.1074/jbc.M110.182840 (2010).
-
(2010)
J. Biol. Chem
, vol.285
, pp. 42097-42104
-
-
Legiewicz, M.1
-
27
-
-
34247162792
-
A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry
-
doi:10.1021/ja0704028
-
Mortimer, S.A. & Weeks, K.M. A fast-acting reagent for accurate analysis of RNA secondary and tertiary structure by SHAPE chemistry. J. Am. Chem. Soc. 129, 4144-4145, doi:10.1021/ja0704028 (2007).
-
(2007)
J. Am. Chem. Soc
, vol.129
, pp. 4144-4145
-
-
Mortimer, S.A.1
Weeks, K.M.2
-
28
-
-
46349099944
-
High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis
-
doi:10.1093/nar/gkn267
-
Mitra, S., Shcherbakova, I.V., Altman, R.B., Brenowitz, M., & Laederach, A. High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res. 36, e63, doi:10.1093/nar/gkn267 (2008).
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Mitra, S.1
Shcherbakova, I.V.2
Altman, R.B.3
Brenowitz, M.4
Laederach, A.5
-
29
-
-
0031829501
-
A software system for data analysis in automated DNA sequencing
-
Giddings, M.C., Severin, J., Westphall, M., Wu, J., & Smith, L.M. A software system for data analysis in automated DNA sequencing. Genome Res. 8, 644-665 (1998).
-
(1998)
Genome Res
, vol.8
, pp. 644-665
-
-
Giddings, M.C.1
Severin, J.2
Westphall, M.3
Wu, J.4
Smith, L.M.5
-
30
-
-
79960581588
-
Modeling and automation of sequencing-based characterization of RNA structure
-
doi:10.1073/pnas.1106541108
-
Aviran, S., et al. Modeling and automation of sequencing-based characterization of RNA structure. Proc. Natl. Acad. Sci. USA. 108, 11069-11074, doi:10.1073/pnas.1106541108 (2011).
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 11069-11074
-
-
Aviran, S.1
|