-
1
-
-
33344469705
-
RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers
-
Bindewald,E. and Shapiro,B.A. (2006) RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers. RNA, 12, 342-352.
-
(2006)
RNA
, vol.12
, pp. 342-352
-
-
Bindewald, E.1
Shapiro, B.A.2
-
2
-
-
58249121729
-
RNAalifold: improved consensus structure prediction for RNA alignments
-
Bernhart,S.H. et al. (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics, 9, 474-487.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474-487
-
-
Bernhart, S.H.1
-
3
-
-
42149083815
-
Centroid estimation in discrete high-dimensional spaces with applications in biology
-
Carvalho,L. and Lawrence,C. (2008) Centroid estimation in discrete high-dimensional spaces with applications in biology. Proc. Natl Acad. Sci. USA, 105, 3209-3214.
-
(2008)
Proc. Natl Acad. Sci. USA
, vol.105
, pp. 3209-3214
-
-
Carvalho, L.1
Lawrence, C.2
-
5
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
Chenna,R. et al. (2003) Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res., 31, 3497-3500.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3497-3500
-
-
Chenna, R.1
-
6
-
-
23644448438
-
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
-
Ding,Y. et al. (2005) RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA, 11, 1157-1166.
-
(2005)
RNA
, vol.11
, pp. 1157-1166
-
-
Ding, Y.1
-
7
-
-
33646784027
-
Clustering of RNA secondary structures with application to messenger RNAs
-
Ding,Y. et al. (2006) Clustering of RNA secondary structures with application to messenger RNAs. J. Mol. Biol., 359, 554-571.
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 554-571
-
-
Ding, Y.1
-
8
-
-
14644430471
-
ProbCons: probabilistic consistency-based multiple sequence alignment
-
Do,C.B. et al. (2005) ProbCons: probabilistic consistency-based multiple sequence alignment. Genome Res., 15, 330-340.
-
(2005)
Genome Res.
, vol.15
, pp. 330-340
-
-
Do, C.B.1
-
9
-
-
33747874580
-
CONTRAfold: RNA secondary structure prediction without physics-based models
-
Do,C.B. et al. (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics, 22, e90-e98.
-
(2006)
Bioinformatics
, vol.22
-
-
Do, C.B.1
-
10
-
-
46249114849
-
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
-
Do,C.B. et al. (2008) A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics, 24, i68-i76.
-
(2008)
Bioinformatics
, vol.24
-
-
Do, C.B.1
-
11
-
-
0028272315
-
RNA sequence analysis using covariance models
-
Eddy,S.R. and Durbin,R. (1994) RNA sequence analysis using covariance models. Nucleic Acids Res., 22, 2079-2088.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 2079-2088
-
-
Eddy, S.R.1
Durbin, R.2
-
12
-
-
17844386108
-
A benchmark of multiple sequence alignment programs upon structural RNAs
-
Gardner,P.P. et al. (2005) A benchmark of multiple sequence alignment programs upon structural RNAs. Nucleic Acids Res., 33, 2433-2439.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 2433-2439
-
-
Gardner, P.P.1
-
13
-
-
0021518209
-
Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images
-
Geman,S. and Geman,D. (1984) Stochastic relaxation, Gibbs distributions, and the Bayesian restoration of images. IEEE PAMI, 6, 721-741.
-
(1984)
IEEE PAMI
, vol.6
, pp. 721-741
-
-
Geman, S.1
Geman, D.2
-
14
-
-
4544339512
-
Abstract shapes of RNA
-
Giegerich,R. et al. (2004) Abstract shapes of RNA. Nucleic Acids Res., 32, 4843-4851.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 4843-4851
-
-
Giegerich, R.1
-
15
-
-
13444252847
-
Rfam: annotating non-coding RNAs in complete genomes
-
Griffiths-Jones,S. et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res., 33, D121-D124.
-
(2005)
Nucleic Acids Res.
, vol.33
-
-
Griffiths-Jones, S.1
-
16
-
-
0026466830
-
Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods
-
Gutell,R.R. et al. (1992) Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods. Nucleic Acids Res., 20, 5785-5795.
-
(1992)
Nucleic Acids Res.
, vol.20
, pp. 5785-5795
-
-
Gutell, R.R.1
-
17
-
-
60149094002
-
Prediction of RNA secondary structure using generalized centroid estimators
-
Hamada,M. et al. (2009) Prediction of RNA secondary structure using generalized centroid estimators. Bioinformatics, 25, 465-473.
-
(2009)
Bioinformatics
, vol.25
, pp. 465-473
-
-
Hamada, M.1
-
18
-
-
79551480068
-
Improving the accuracy of predicting secondary structure for aligned RNA sequences
-
Hamada,M. et al. (2011) Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res., 39, 393-402.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 393-402
-
-
Hamada, M.1
-
19
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker,I.L. et al. (1994) Fast folding and comparison of RNA secondary structures. Monatshefte f. Chemie, 125, 167-188.
-
(1994)
Monatshefte f. Chemie
, vol.125
, pp. 167-188
-
-
Hofacker, I.L.1
-
20
-
-
0036301332
-
Secondary structure prediction for aligned RNA sequences
-
Hofacker,I.L. et al. (2002) Secondary structure prediction for aligned RNA sequences. J. Mol. Biol., 319, 1059-1066.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1059-1066
-
-
Hofacker, I.L.1
-
21
-
-
3543051100
-
A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences
-
Ji,Y. et al. (2004) A graph theoretical approach for predicting common RNA secondary structure motifs including pseudoknots in unaligned sequences. Bioinformatics, 20, 1591-1602.
-
(2004)
Bioinformatics
, vol.20
, pp. 1591-1602
-
-
Ji, Y.1
-
22
-
-
34547844102
-
Murlet: a practical multiple alignment tool for structural RNA sequences
-
Kiryu,H. et al. (2007a) Murlet: a practical multiple alignment tool for structural RNA sequences. Bioinformatics, 23, 1588-1598.
-
(2007)
Bioinformatics
, vol.23
, pp. 1588-1598
-
-
Kiryu, H.1
-
23
-
-
33847262911
-
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
-
Kiryu,H. et al. (2007b) Robust prediction of consensus secondary structures using averaged base pairing probability matrices. Bioinformatics, 23, 434-441.
-
(2007)
Bioinformatics
, vol.23
, pp. 434-441
-
-
Kiryu, H.1
-
24
-
-
0032796501
-
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
-
Knudsen,B. and Hein,J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15, 446-454.
-
(1999)
Bioinformatics
, vol.15
, pp. 446-454
-
-
Knudsen, B.1
Hein, J.2
-
25
-
-
36949011603
-
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing
-
Lindgreen,S. et al. (2007) MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics, 23, 3304-3311.
-
(2007)
Bioinformatics
, vol.23
, pp. 3304-3311
-
-
Lindgreen, S.1
-
26
-
-
79951870792
-
The collapsed Gibbs Sampler in Bayesian computations with applications to a gene regulation problem
-
Liu,J.S. (1994) The collapsed Gibbs Sampler in Bayesian computations with applications to a gene regulation problem. J. Am. Stat. Assoc., 89, 958-966.
-
(1994)
J. Am. Stat. Assoc.
, vol.89
, pp. 958-966
-
-
Liu, J.S.1
-
27
-
-
3342977915
-
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
-
Mathews,D.H. (2004) Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA, 10, 1178-1190.
-
(2004)
RNA
, vol.10
, pp. 1178-1190
-
-
Mathews, D.H.1
-
28
-
-
33746320475
-
Revolutions in RNAsecondary structure prediction
-
Mathews,D.H. (2006) Revolutions in RNAsecondary structure prediction. J. Mol. Biol., 359, 526-532.
-
(2006)
J. Mol. Biol.
, vol.359
, pp. 526-532
-
-
Mathews, D.H.1
-
29
-
-
34548443728
-
SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework
-
Meyer,I.M. and Miklos,I. (2007) SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework. PLoS Comput. Biol., 3, e149.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Meyer, I.M.1
Miklos, I.2
-
30
-
-
34047240607
-
Query-dependent banding (QDB) for faster RNA similarity searches
-
Nawrocki,E.P. and Eddy,S.R. (2007) Query-dependent banding (QDB) for faster RNA similarity searches. PLoS Comput. Biol., 3, e56.
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Nawrocki, E.P.1
Eddy, S.R.2
-
31
-
-
65549111754
-
Infernal 1.0: inference of RNA alignments
-
Nawrocki,E.P. et al. (2009) Infernal 1.0: inference of RNA alignments. Bioinformatics, 25, 1335-1337.
-
(2009)
Bioinformatics
, vol.25
, pp. 1335-1337
-
-
Nawrocki, E.P.1
-
32
-
-
58149236993
-
Exact calculation of distributions on integers, with application to sequence alignment
-
Newberg,L.A. and Lawrence,C.E. (2009) Exact calculation of distributions on integers, with application to sequence alignment. J. Comput. Biol., 16, 1-18.
-
(2009)
J. Comput. Biol.
, vol.16
, pp. 1-18
-
-
Newberg, L.A.1
Lawrence, C.E.2
-
33
-
-
0028593508
-
Stochastic context-free grammers for tRNA modeling
-
Sakakibara,Y. et al. (1994) Stochastic context-free grammers for tRNA modeling. Nucleic Acids Res., 22, 5112-5120.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 5112-5120
-
-
Sakakibara, Y.1
-
34
-
-
0022146059
-
Simultaneous solution of the RNA folding, alignment and protosequence problems
-
Sankoff,D. (1985) Simultaneous solution of the RNA folding, alignment and protosequence problems. SIAM J. Appl. Math., 45, 810-825.
-
(1985)
SIAM J. Appl. Math.
, vol.45
, pp. 810-825
-
-
Sankoff, D.1
-
35
-
-
56649099274
-
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
-
Seemann,S.E. et al. (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
-
36
-
-
24044519380
-
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
-
Siebert,S. and Backofen,R. (2005) MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons. Bioinformatics, 21, 3352-3359.
-
(2005)
Bioinformatics
, vol.21
, pp. 3352-3359
-
-
Siebert, S.1
Backofen, R.2
-
37
-
-
32544440797
-
RNAshapes: an integrated RNA analysis package based on abstract shapes
-
Steffen,P. et al. (2006) RNAshapes: an integrated RNA analysis package based on abstract shapes. Bioinformatics, 22, 500-503.
-
(2006)
Bioinformatics
, vol.22
, pp. 500-503
-
-
Steffen, P.1
-
38
-
-
0031730497
-
An RNA folding method capable of identifying pseudoknots and base triples
-
Tabaska,J.E. et al. (1998) An RNA folding method capable of identifying pseudoknots and base triples. Bioinformatics, 14, 691-699.
-
(1998)
Bioinformatics
, vol.14
, pp. 691-699
-
-
Tabaska, J.E.1
-
39
-
-
34249699636
-
Multiple structural alignment and clustering of RNA sequences
-
Torarinsson,E. et al. (2007) Multiple structural alignment and clustering of RNA sequences. Bioinformatics, 23, 926-932.
-
(2007)
Bioinformatics
, vol.23
, pp. 926-932
-
-
Torarinsson, E.1
-
40
-
-
0036493242
-
BALSA: Bayesian algorithm for local sequence alignment
-
Webb,B.M. et al. (2002) BALSA: Bayesian algorithm for local sequence alignment. Nucleic Acids Res., 30, 1268-1277.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 1268-1277
-
-
Webb, B.M.1
-
41
-
-
44949258055
-
Measuring global credibility with application to local sequence alignment
-
Webb-Robertson,B.M. et al. (2008) Measuring global credibility with application to local sequence alignment. PLoS Comput. Biol., 4, e1000077
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Webb-Robertson, B.M.1
-
42
-
-
34247598415
-
Inferring noncoding RNAfamilies and classes by means of genomescale structure-based clustering
-
Will,S. et al. (2007) Inferring noncoding RNAfamilies and classes by means of genomescale structure-based clustering. PLoS Comput. Biol., 3, e65
-
(2007)
PLoS Comput. Biol.
, vol.3
-
-
Will, S.1
-
43
-
-
34548131258
-
RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment
-
Xing,X. et al. (2007) RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment. Bioinformatics, 23, 1883-1891.
-
(2007)
Bioinformatics
, vol.23
, pp. 1883-1891
-
-
Xing, X.1
-
44
-
-
32544452741
-
CMfinder - a covariance model based RNAmotif finding algorithm
-
Yao,Z. et al. (2006) CMfinder - a covariance model based RNAmotif finding algorithm. Bioinformatics, 22, 445-452.
-
(2006)
Bioinformatics
, vol.22
, pp. 445-452
-
-
Yao, Z.1
-
45
-
-
0019876473
-
Optimal computer folding of largeRNAsequences using thermodynamics and auxiliary information
-
Zuker,M. and Stiegler,P. (1981) Optimal computer folding of largeRNAsequences using thermodynamics and auxiliary information. Nucleic Acids Res., 109, 133-148.
-
(1981)
Nucleic Acids Res.
, vol.109
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
|