-
1
-
-
0842268067
-
A new algorithm for RNA secondary structure design
-
Andronescu, M., Fejes, A. P., Hutter, F., Hoos, H. H., and Condon, A. (2004). A new algorithm for RNA secondary structure design. J. Mol. Biol. 336, 607-624.
-
(2004)
J. Mol. Biol.
, vol.336
, pp. 607-624
-
-
Andronescu, M.1
Fejes, A.P.2
Hutter, F.3
Hoos, H.H.4
Condon, A.5
-
2
-
-
0033954144
-
PseudoBase: a database with RNA pseudoknots
-
Batenburg, F. H. V., Gultyaev, A. P., Pleij, C. W., Ng, J., and Oliehoek, J. (2000). PseudoBase: a database with RNA pseudoknots. Nucleic Acids Res. 28, 201-204.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 201-204
-
-
Batenburg, F.H.V.1
Gultyaev, A.P.2
Pleij, C.W.3
Ng, J.4
Oliehoek, J.5
-
3
-
-
11144330098
-
Natural and engineered nucleic acids as tools to explore biology
-
Breaker, R. R. (2004). Natural and engineered nucleic acids as tools to explore biology. Nature 432, 838-845.
-
(2004)
Nature
, vol.432
, pp. 838-845
-
-
Breaker, R.R.1
-
4
-
-
33747840719
-
INFO-RNA-a fast approach to inverse RNA folding
-
Busch, A., and Backofen, R. (2006). INFO-RNA-a fast approach to inverse RNA folding. Bioinformatics 22, 1823-1831.
-
(2006)
Bioinformatics
, vol.22
, pp. 1823-1831
-
-
Busch, A.1
Backofen, R.2
-
5
-
-
2442466703
-
Classifying RNA pseudoknotted structures
-
Condon, A., Davy, B., Rastegari, B., Zhao, S., and Tarrant, F. (2004). Classifying RNA pseudoknotted structures. Theor. Comp. Sci. 320, 35-50.
-
(2004)
Theor. Comp. Sci.
, vol.320
, pp. 35-50
-
-
Condon, A.1
Davy, B.2
Rastegari, B.3
Zhao, S.4
Tarrant, F.5
-
6
-
-
2142738304
-
WebLogo: a sequence logo generator
-
Crooks, G. E., Hon, G., Chandonia, J. M., and Brenner, S. E. (2004). WebLogo: a sequence logo generator. Genome Res. 14, 1188-1190.
-
(2004)
Genome Res
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
7
-
-
35548950310
-
Automated de novo prediction of native-like RNA tertiary structures
-
Das, R., and Baker, D. (2007). Automated de novo prediction of native-like RNA tertiary structures. Proc. Natl. Acad. Sci. U.S.A. 104, 14664-14669.
-
(2007)
Proc. Natl. Acad. Sci. U. S. A.
, vol.104
, pp. 14664-14669
-
-
Das, R.1
Baker, D.2
-
9
-
-
77953712538
-
Inverse folding of RNA pseudoknot structures
-
Gao, J. Z., Li, L. Y., and Reidys, C. M. (2010). Inverse folding of RNA pseudoknot structures. Algorithms Mol. Biol. 5, 27.
-
(2010)
Algorithms Mol. Biol.
, vol.5
, pp. 27
-
-
Gao, J.Z.1
Li, L.Y.2
Reidys, C.M.3
-
11
-
-
60149094002
-
Prediction of RNA secondary structure using generalized centroid estimators
-
Hamada, M., Kiryu, H., Sato, K., Mituyama, T., and Asai, K. (2009). Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics 25, 465-473.
-
(2009)
Bioinformatics
, vol.25
, pp. 465-473
-
-
Hamada, M.1
Kiryu, H.2
Sato, K.3
Mituyama, T.4
Asai, K.5
-
12
-
-
0043123153
-
Vienna RNA secondary structure server
-
Hofacker, I. (2003). Vienna RNA secondary structure server. Nucleic Acids Res. 31, 3429-3431.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.1
-
13
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker, I., Fontana, W., Stadler, P., Bonhoeffer, L., Tacker, M., and Schuster, P. (1994). Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125, 167-188.
-
(1994)
Monatsh. Chem.
, vol.125
, pp. 167-188
-
-
Hofacker, I.1
Fontana, W.2
Stadler, P.3
Bonhoeffer, L.4
Tacker, M.5
Schuster, P.6
-
15
-
-
0035863772
-
TectoRNA: modular assembly units for the construction of RNA nano-objects
-
Jaeger, L., Westhof, E., and Leontis, N. B. (2001). TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res. 29, 455-463.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 455-463
-
-
Jaeger, L.1
Westhof, E.2
Leontis, N.B.3
-
16
-
-
84934438960
-
UNAFold: software for nucleic acid folding and hybridization
-
Markham, N. R., and Zuker, M. (2008). UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol. 453, 3-31.
-
(2008)
Methods Mol. Biol.
, vol.453
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
17
-
-
40449139010
-
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data
-
Parisien, M., and Major, F. (2008). The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature 452, 51-55.
-
(2008)
Nature
, vol.452
, pp. 51-55
-
-
Parisien, M.1
Major, F.2
-
18
-
-
25844447772
-
HotKnots: heuristic prediction of RNA secondary structures including pseudoknots.
-
Ren, J., Rastegari, B., Condon, A., and Hoos, H. H. (2005). HotKnots: heuristic prediction of RNA secondary structures including pseudoknots. RNA 11, 1494-1504.
-
(2005)
RNA
, vol.11
, pp. 1494-1504
-
-
Ren, J.1
Rastegari, B.2
Condon, A.3
Hoos, H.H.4
-
19
-
-
79959465715
-
IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming
-
Sato, K., Kato, Y., Hamada, M., Akutsu, T., and Asai, K. (2011). IPknot: fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming. Bioinformatics 27, 85-93.
-
(2011)
Bioinformatics
, vol.27
, pp. 85-93
-
-
Sato, K.1
Kato, Y.2
Hamada, M.3
Akutsu, T.4
Asai, K.5
-
20
-
-
0034698298
-
One sequence, two ribozymes: implications for the emergence of new ribozyme folds
-
Schultes, E. A., and Bartel, D. P. (2000). One sequence, two ribozymes: implications for the emergence of new ribozyme folds. Science 289, 448-452.
-
(2000)
Science
, vol.289
, pp. 448-452
-
-
Schultes, E.A.1
Bartel, D.P.2
-
21
-
-
33745393624
-
Highly specific gene silencing by artificial microRNAs in Arabidopsis
-
Schwab, R., Ossowski, S., Riester, M., Warthmann, N., and Weigel, D. (2006). Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18, 1121-1133.
-
(2006)
Plant Cell
, vol.18
, pp. 1121-1133
-
-
Schwab, R.1
Ossowski, S.2
Riester, M.3
Warthmann, N.4
Weigel, D.5
-
22
-
-
22744455135
-
Pseudoknots: RNA structures with diverse functions
-
doi:10.1371/journal.pbio.0030213
-
Staple, D. W., and Butcher, S. E. (2005). Pseudoknots: RNA structures with diverse functions. PLoS Biol. 3, e213. doi:10.1371/journal.pbio.0030213
-
(2005)
PLoS Biol
, vol.3
-
-
Staple, D.W.1
Butcher, S.E.2
-
23
-
-
79961002039
-
MODENA: a multi-objective RNA inverse folding
-
Taneda, A. (2011). MODENA: a multi-objective RNA inverse folding. Adv. Appl. Bioinform. Chem. 4, 1-12.
-
(2011)
Adv. Appl. Bioinform. Chem.
, vol.4
, pp. 1-12
-
-
Taneda, A.1
-
24
-
-
78149355812
-
NUPACK: analysis and design of nucleic acid systems
-
Zadeh, J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., and Pierce, N. A. (2011). NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170-173.
-
(2011)
J. Comput. Chem.
, vol.32
, pp. 170-173
-
-
Zadeh, J.N.1
Steenberg, C.D.2
Bois, J.S.3
Wolfe, B.R.4
Pierce, M.B.5
Khan, A.R.6
Dirks, R.M.7
Pierce, N.A.8
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