-
2
-
-
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
-
3
-
-
0028249154
-
Prediction of RNA secondary structure by energy minimization
-
Zuker, M. (1994) Prediction of RNA secondary structure by energy minimization. Methods Mol. Biol., 25, 267-294.
-
(1994)
Methods Mol. Biol.
, vol.25
, pp. 267-294
-
-
Zuker, M.1
-
4
-
-
0043123155
-
Pfold: RNA secondary structure prediction using stochastic context-free grammars
-
DOI 10.1093/nar/gkg614
-
Knudsen, B. and Hein, J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31, 3423-3428. (Pubitemid 37442171)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3423-3428
-
-
Knudsen, B.1
Hein, J.2
-
5
-
-
56649099274
-
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
-
Seemann, S.E., Gorodkin, J. and Backofen, R. (2008) Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments. Nucleic Acids Res., 36, 6355-6362.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 6355-6362
-
-
Seemann, S.E.1
Gorodkin, J.2
Backofen, R.3
-
6
-
-
77952448550
-
Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions
-
Seemann, S.E., Richter, A.S., Gorodkin, J. and Backofen, R. (2010) Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions. Algorithms Mol. Biol., 5, 22.
-
(2010)
Algorithms Mol. Biol.
, vol.5
, pp. 22
-
-
Seemann, S.E.1
Richter, A.S.2
Gorodkin, J.3
Backofen, R.4
-
7
-
-
78651415661
-
PETcofold: Predicting conserved interactions and structures of two multiple alignments of RNA sequences
-
Seemann, S.E., Richter, A.S., Gesell, T., Backofen, R. and Gorodkin, J. (2011) PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences. Bioinformatics, 27, 211-219.
-
(2011)
Bioinformatics
, vol.27
, pp. 211-219
-
-
Seemann, S.E.1
Richter, A.S.2
Gesell, T.3
Backofen, R.4
Gorodkin, J.5
-
8
-
-
48449095385
-
The Vienna RNA websuite
-
Gruber, A.R., Lorenz, R., Bernhart, S.H., Neubck, R. and Hofacker, I.L. (2008) The Vienna RNA websuite. Nucleic Acids Res, 36, W70-W74.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Gruber, A.R.1
Lorenz, R.2
Bernhart, S.H.3
Neubck, R.4
Hofacker, I.L.5
-
9
-
-
77954269050
-
Freiburg RNA Tools: A web server integrating INTARNA, EXPARNA and LOCARNA
-
Smith, C., Heyne, S., Richter, A.S., Will, S. and Backofen, R. (2010) Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA. Nucleic Acids Res, 38, W373-W377.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Smith, C.1
Heyne, S.2
Richter, A.S.3
Will, S.4
Backofen, R.5
-
10
-
-
58149191274
-
Rfam: Updates to the RNA families database
-
Gardner, P.P., Daub, J., Tate, J.G., Nawrocki, E.P., Kolbe, D.L., Lindgreen, S., Wilkinson, A.C., Finn, R.D., Griffiths-Jones, S., Eddy, S.R. et al. (2009) Rfam: updates to the RNA families database. Nucleic Acids Res., 37, D136-D140.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Gardner, P.P.1
Daub, J.2
Tate, J.G.3
Nawrocki, E.P.4
Kolbe, D.L.5
Lindgreen, S.6
Wilkinson, A.C.7
Finn, R.D.8
Griffiths-Jones, S.9
Eddy, S.R.10
-
11
-
-
0025008168
-
Sequence logos: A new way to display consensus sequences
-
Schneider, T.D. and Stephens, R. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
-
(1990)
Nucleic Acids Res.
, vol.18
, pp. 6097-6100
-
-
Schneider, T.D.1
Stephens, R.2
-
12
-
-
0035420790
-
Bulged residues promote the progression of a loop-loop interaction to a stable and inhibitory antisense-target RNA complex
-
Kolb, F.A., Westhof, E., Ehresmann, C., Ehresmann, B., Wagner, E.G. and Romby, P. (2001) Bulged residues promote the progression of a loop-loop interaction to a stable and inhibitory antisense-target RNA complex. Nucleic Acids Res., 29, 3145-3153. (Pubitemid 32750560)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.15
, pp. 3145-3153
-
-
Kolb, F.A.1
Westhof, E.2
Ehresmann, C.3
Ehresmann, B.4
Wagner, E.G.H.5
Romby, P.6
-
13
-
-
0347504844
-
FinO is an RNA chaperone that facilitates sense-antisense RNA interactions
-
DOI 10.1093/emboj/cdg607
-
Arthur, D.C., Ghetu, A.F., Gubbins, M.J., Edwards, R.A., Frost, L.S. and Glover, J.N.M. (2003) FinO is an RNA chaperone that facilitates sense-antisense RNA interactions. EMBO J., 22, 6346-6355, Dec. (Pubitemid 37522591)
-
(2003)
EMBO Journal
, vol.22
, Issue.23
, pp. 6346-6355
-
-
Arthur, D.C.1
Ghetu, A.F.2
Gubbins, M.J.3
Edwards, R.A.4
Frost, L.S.5
Glover, J.N.M.6
-
14
-
-
35748971022
-
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
-
DOI 10.1371/journal.pcbi.0030193
-
Havgaard, J.H., Torarinsson, E. and Gorodkin, J. (2007) Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput. Biol., 3, 1896-1908. (Pubitemid 350043406)
-
(2007)
PLoS Computational Biology
, vol.3
, Issue.10
, pp. 1896-1908
-
-
Havgaard, J.H.1
Torarinsson, E.2
Gorodkin, J.3
-
15
-
-
23144449520
-
The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search
-
DOI 10.1093/nar/gki473
-
Havgaard, J.H., Lyngsø, R.B. and Gorodkin, J. (2005) The FOLDALIGN web server for pairwise structural RNA alignment and mutual motif search. Nucleic Acids Res., 33, W650-W653. (Pubitemid 44530002)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.WEB. SERV. ISSUE
-
-
Havgaard, J.H.1
Lyngsoo, R.B.2
Gorodkin, J.3
-
16
-
-
34247598415
-
Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering
-
Will, S., Reiche, K., Hofacker, I.L., Stadler, P.F. and Backofen, R. (2007) Inferring non-coding RNA families and classes by means of genome-scale structure-based clustering. PLOS Comput. Biol., 3, e65.
-
(2007)
PLOS Comput. Biol.
, vol.3
-
-
Will, S.1
Reiche, K.2
Hofacker, I.L.3
Stadler, P.F.4
Backofen, R.5
-
17
-
-
35549004515
-
Semiautomated improvement of RNA alignments
-
DOI 10.1261/rna.215407
-
Andersen, E.S., Lind-Thomsen, A., Knudsen, B., Kristensen, S.E., Havgaard, J.H., Torarinsson, E., Larsen, N., Zwieb, C., Sestoft, P., Kjems, J. et al. (2007) Semiautomated improvement of RNA alignments. RNA, 13, 1850-1859. (Pubitemid 350005210)
-
(2007)
RNA
, vol.13
, Issue.11
, pp. 1850-1859
-
-
Andersen, E.S.1
Lind-Thomsen, A.2
Knudsen, B.3
Kristensen, S.E.4
Havgaard, J.H.5
Torarinsson, E.6
Larsen, N.7
Zwieb, C.8
Sestoft, P.9
Kjems, J.10
Gorodkin, J.11
-
18
-
-
0031473030
-
Displaying the information contents of structural RNA alignments: The structure logos
-
Gorodkin, J., Heyer, L.J., Brunak, S. and Stormo, G.D. (1997) Displaying the information contents of structural RNA alignments: the structure logos. Comput. Appl. Biosci., 13, 583-586. (Pubitemid 28039651)
-
(1997)
Computer Applications in the Biosciences
, vol.13
, Issue.6
, pp. 583-586
-
-
Gorodkin, J.1
Heyer, L.J.2
Brunak, S.3
Stormo, G.D.4
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