-
1
-
-
42149083815
-
Centroid estimation in discrete high-dimensional spaces with applications in biology
-
Carvalho L, 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
-
2
-
-
67049158348
-
Fast statistical alignment
-
Bradley RK, Roberts A, Smoot M, Juvekar S, Do J, et al. (2009) Fast statistical alignment. PLoS Comput Biol 5: e1000392.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Bradley, R.K.1
Roberts, A.2
Smoot, M.3
Juvekar, S.4
Do, J.5
-
3
-
-
56649119162
-
Specific alignment of structured RNA: stochastic grammars and sequence annealing
-
Bradley RK, Pachter L, Holmes I, (2008) Specific alignment of structured RNA: stochastic grammars and sequence annealing. Bioinformatics 24: 2677-2683.
-
(2008)
Bioinformatics
, vol.24
, pp. 2677-2683
-
-
Bradley, R.K.1
Pachter, L.2
Holmes, I.3
-
5
-
-
33747874580
-
CONTRAfold: RNA secondary structure prediction without physics-based models
-
Do C, Woods D, Batzoglou S, (2006) CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22: e90-98.
-
(2006)
Bioinformatics
, vol.22
-
-
Do, C.1
Woods, D.2
Batzoglou, S.3
-
6
-
-
70349131635
-
Improved RNA secondary structure prediction by maximizing expected pair accuracy
-
Lu ZJ, Gloor JW, Mathews DH, (2009) Improved RNA secondary structure prediction by maximizing expected pair accuracy. RNA 15: 1805-1813.
-
(2009)
RNA
, vol.15
, pp. 1805-1813
-
-
Lu, Z.J.1
Gloor, J.W.2
Mathews, D.H.3
-
7
-
-
33847262911
-
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
-
Kiryu H, Kin T, Asai K, (2007) 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
Kin, T.2
Asai, K.3
-
8
-
-
56649099274
-
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
-
Seemann S, Gorodkin J, 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.1
Gorodkin, J.2
Backofen, R.3
-
9
-
-
29144483361
-
An HMM posterior decoder for sequence feature prediction that includes homology information
-
Kall L, Krogh A, Sonnhammer EL, (2005) An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics 21 (Suppl 1): i251-257.
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Kall, L.1
Krogh, A.2
Sonnhammer, E.L.3
-
10
-
-
77956503102
-
RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
-
Kato Y, Sato K, Hamada M, Watanabe Y, Asai K, et al. (2010) RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming. Bioinformatics 26: i460-466.
-
(2010)
Bioinformatics
, vol.26
-
-
Kato, Y.1
Sato, K.2
Hamada, M.3
Watanabe, Y.4
Asai, K.5
-
11
-
-
40449115745
-
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction
-
Gross S, Do C, Sirota M, Batzoglou S, (2007) CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol 8: R269.
-
(2007)
Genome Biol
, vol.8
-
-
Gross, S.1
Do, C.2
Sirota, M.3
Batzoglou, S.4
-
12
-
-
60149094002
-
Prediction of RNA secondary structure using generalized centroid estimators
-
Hamada M, Kiryu H, Sato K, Mituyama T, 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
-
13
-
-
0029595355
-
A reliable sequence alignment method based on probabilities of residue correspondences
-
Miyazawa S, (1995) A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng 8: 999-1009.
-
(1995)
Protein Eng
, vol.8
, pp. 999-1009
-
-
Miyazawa, S.1
-
14
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill JS, (1990) The equilibrium partition function and base pair binding probabilities for RNA secondary structure. Biopolymers 29: 1105-1119.
-
(1990)
Biopolymers
, vol.29
, pp. 1105-1119
-
-
McCaskill, J.S.1
-
15
-
-
67849086863
-
CENTROIDFOLD: a web server for RNA secondary structure prediction
-
Sato K, Hamada M, Asai K, Mituyama T, (2009) CENTROIDFOLD: a web server for RNA secondary structure prediction. Nucleic Acids Res 37: W277-280.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Sato, K.1
Hamada, M.2
Asai, K.3
Mituyama, T.4
-
16
-
-
5744249209
-
Equations of state calculations by fast computing machine
-
Metropolis N, Rosenbluth A, Teller M, Teller E, (1953) Equations of state calculations by fast computing machine. J Chem Phys 21: 1087-1091.
-
(1953)
J Chem Phys
, vol.21
, pp. 1087-1091
-
-
Metropolis, N.1
Rosenbluth, A.2
Teller, M.3
Teller, E.4
-
18
-
-
77958057991
-
An intuitive, informative, and most balanced representation of phylogenetic topologies
-
Iwasaki W, Takagi T, (2010) An intuitive, informative, and most balanced representation of phylogenetic topologies. Syst Biol 59: 584-593.
-
(2010)
Syst Biol
, vol.59
, pp. 584-593
-
-
Iwasaki, W.1
Takagi, T.2
-
19
-
-
14644430471
-
ProbCons: Probabilistic consistency-based multiple sequence alignment
-
Do C, Mahabhashyam M, Brudno M, Batzoglou S, (2005) ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome Res 15: 330-340.
-
(2005)
Genome Res
, vol.15
, pp. 330-340
-
-
Do, C.1
Mahabhashyam, M.2
Brudno, M.3
Batzoglou, S.4
-
20
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: an overview
-
Baldi P, Brunak S, Chauvin Y, Andersen CA, Nielsen H, (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 16: 412-424.
-
(2000)
Bioinformatics
, vol.16
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.4
Nielsen, H.5
-
22
-
-
78649469968
-
Prediction of RNA secondary structure by maximizing pseudo-expected accuracy
-
Hamada M, Sato K, Asai K, (2010) Prediction of RNA secondary structure by maximizing pseudo-expected accuracy. BMC Bioinformatics 11: 586.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 586
-
-
Hamada, M.1
Sato, K.2
Asai, K.3
-
23
-
-
66349124254
-
Predictions of RNA secondary structure by combining homologous sequence information
-
Hamada M, Sato K, Kiryu H, Mituyama T, Asai K, (2009) Predictions of RNA secondary structure by combining homologous sequence information. Bioinformatics 25: i330-338.
-
(2009)
Bioinformatics
, vol.25
-
-
Hamada, M.1
Sato, K.2
Kiryu, H.3
Mituyama, T.4
Asai, K.5
-
24
-
-
23644448438
-
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble
-
Ding Y, Chan C, Lawrence C, (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
Chan, C.2
Lawrence, C.3
-
25
-
-
33751004142
-
Probalign: multiple sequence alignment using partition function posterior probabilities
-
Roshan U, Livesay D, (2006) Probalign: multiple sequence alignment using partition function posterior probabilities. Bioinformatics 22: 2715-2721.
-
(2006)
Bioinformatics
, vol.22
, pp. 2715-2721
-
-
Roshan, U.1
Livesay, D.2
-
26
-
-
33745783706
-
-
In: Apostolico A, Guerra C, Istrail S, Pevzner PA, Waterman MS, editors, RECOMB. Springer, volume 3909 of Lecture Notes in Computer Science
-
Do CB, Gross SS, Batzoglou S, (2006) Contralign: Discriminative training for protein sequence alignment. In: Apostolico A, Guerra C, Istrail S, Pevzner PA, Waterman MS, editors. pp. 160-174 RECOMB. Springer, volume 3909 of Lecture Notes in Computer Science.
-
(2006)
Contralign: Discriminative training for protein sequence alignment
, pp. 160-174
-
-
Do, C.B.1
Gross, S.S.2
Batzoglou, S.3
-
27
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews DH, Sabina J, Zuker M, Turner DH, (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288: 911-940.
-
(1999)
J Mol Biol
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
28
-
-
13244260785
-
Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction
-
Dowell R, Eddy S, (2004) Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction. BMC Bioinformatics 5: 71.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 71
-
-
Dowell, R.1
Eddy, S.2
-
29
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist F, Huelsenbeck JP, (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.P.2
-
30
-
-
0034849408
-
MRBAYES: Bayesian inference of phylogenetic trees
-
Huelsenbeck JP, Ronquist F, (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
-
(2001)
Bioinformatics
, vol.17
, pp. 754-755
-
-
Huelsenbeck, J.P.1
Ronquist, F.2
-
31
-
-
0003516147
-
-
Cambridge, UK, Cambridge University press
-
Durbin R, Eddy S, Krogh A, Mitchison G, (1998) Biological sequence analysis. Cambridge, UK Cambridge University press.
-
(1998)
Biological sequence analysis
-
-
Durbin, R.1
Eddy, S.2
Krogh, A.3
Mitchison, G.4
-
32
-
-
0014757386
-
A general method applicable to the search for similarities in the amino acid sequence of two proteins
-
Needleman S, Wunsch C, (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. J Mol Biol 48: 443-453.
-
(1970)
J Mol Biol
, vol.48
, pp. 443-453
-
-
Needleman, S.1
Wunsch, C.2
-
33
-
-
77954139210
-
Incorporating sequence quality data into alignment improves DNA read mapping
-
Frith MC, Wan R, Horton P, (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucleic Acids Res 38: e100.
-
(2010)
Nucleic Acids Res
, vol.38
-
-
Frith, M.C.1
Wan, R.2
Horton, P.3
-
34
-
-
0031721576
-
Dynamic programming alignment accuracy
-
Holmes I, Durbin R, (1998) Dynamic programming alignment accuracy. J Comput Biol 5: 493-504.
-
(1998)
J Comput Biol
, vol.5
, pp. 493-504
-
-
Holmes, I.1
Durbin, R.2
-
35
-
-
13444252847
-
Rfam: annotating non-coding RNAs in complete genomes
-
Griffiths-Jones S, Moxon S, Marshall M, Khanna A, Eddy SR, et al. (2005) Rfam: annotating non-coding RNAs in complete genomes. Nucleic Acids Res 33: 121-124.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 121-124
-
-
Griffiths-Jones, S.1
Moxon, S.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
36
-
-
34547840261
-
Efficient parameter estimation for RNA secondary structure prediction
-
Andronescu M, Condon A, Hoos H, Mathews D, Murphy K, (2007) Efficient parameter estimation for RNA secondary structure prediction. Bioinformatics 23: 19-28.
-
(2007)
Bioinformatics
, vol.23
, pp. 19-28
-
-
Andronescu, M.1
Condon, A.2
Hoos, H.3
Mathews, D.4
Murphy, K.5
-
37
-
-
0002213113
-
Algorithms for loop matchings
-
Nussinov R, Pieczenk G, Griggs J, Kleitman D, (1978) Algorithms for loop matchings. SIAM Journal of Applied Mathematics 35: 68-82.
-
(1978)
SIAM Journal of Applied Mathematics
, vol.35
, pp. 68-82
-
-
Nussinov, R.1
Pieczenk, G.2
Griggs, J.3
Kleitman, D.4
-
38
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
Zuker M, (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
-
39
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker I, Fontana W, Stadler P, Bonhoeffer S, Tacker M, et al. (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, S.4
Tacker, M.5
-
40
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
Mathews D, Disney M, Childs J, Schroeder S, Zuker M, et al. (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci USA 101: 7287-7292.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 7287-7292
-
-
Mathews, D.1
Disney, M.2
Childs, J.3
Schroeder, S.4
Zuker, M.5
-
41
-
-
27544437866
-
Structure clustering features on the Sfold Web server
-
Chan CY, Lawrence CE, Ding Y, (2005) Structure clustering features on the Sfold Web server. Bioinformatics 21: 3926-3928.
-
(2005)
Bioinformatics
, vol.21
, pp. 3926-3928
-
-
Chan, C.Y.1
Lawrence, C.E.2
Ding, Y.3
-
42
-
-
3242877996
-
Sfold web server for statistical folding and rational design of nucleic acids
-
Ding Y, Chan CY, Lawrence CE, (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32: 135-141.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 135-141
-
-
Ding, Y.1
Chan, C.Y.2
Lawrence, C.E.3
-
44
-
-
67449104206
-
Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships
-
Schroeder SJ, (2009) Advances in RNA structure prediction from sequence: new tools for generating hypotheses about viral RNA structure-function relationships. J Virol 83: 6326-6334.
-
(2009)
J Virol
, vol.83
, pp. 6326-6334
-
-
Schroeder, S.J.1
-
45
-
-
70350653828
-
Accurate and efficient reconstruction of deep phylogenies from structured RNAs
-
Stocsits RR, Letsch H, Hertel J, Misof B, Stadler PF, (2009) Accurate and efficient reconstruction of deep phylogenies from structured RNAs. Nucleic Acids Res 37: 6184-6193.
-
(2009)
Nucleic Acids Res
, vol.37
, pp. 6184-6193
-
-
Stocsits, R.R.1
Letsch, H.2
Hertel, J.3
Misof, B.4
Stadler, P.F.5
-
47
-
-
27944464131
-
Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome
-
Washietl S, Hofacker IL, Lukasser M, Huttenhofer A, Stadler PF, (2005) Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome. Nat Biotechnol 23: 1383-1390.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1383-1390
-
-
Washietl, S.1
Hofacker, I.L.2
Lukasser, M.3
Huttenhofer, A.4
Stadler, P.F.5
-
48
-
-
79551474846
-
Improvement of structure conservation index with centroid estimators
-
Okada Y, Sato K, Sakakibara Y, (2010) Improvement of structure conservation index with centroid estimators. Pac Symp Biocomput pp. 88-97.
-
(2010)
Pac Symp Biocomput
, pp. 88-97
-
-
Okada, Y.1
Sato, K.2
Sakakibara, Y.3
-
49
-
-
79551480068
-
Improving the accuracy of predicting secondary structure for aligned RNA sequences
-
doi: 10.1093/nar/gkq792
-
Hamada M, Sato K, Asai K, (2010) Improving the accuracy of predicting secondary structure for aligned RNA sequences. Nucleic Acids Res doi:10.1093/nar/gkq792.
-
(2010)
Nucleic Acids Res
-
-
Hamada, M.1
Sato, K.2
Asai, K.3
-
50
-
-
58249121729
-
RNAalifold: improved consensus structure prediction for RNA alignments
-
Bernhart S, Hofacker I, Will S, Gruber A, Stadler P, (2008) RNAalifold: improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9: 474.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474
-
-
Bernhart, S.1
Hofacker, I.2
Will, S.3
Gruber, A.4
Stadler, P.5
-
51
-
-
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 pp. 810-825.
-
(1985)
SIAM J Appl Math
, pp. 810-825
-
-
Sankoff, D.1
-
52
-
-
75849160582
-
CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score
-
Hamada M, Sato K, Kiryu H, Mituyama T, Asai K, (2009) CentroidAlign: fast and accurate aligner for structured RNAs by maximizing expected sum-of-pairs score. Bioinformatics 25: 3236-3243.
-
(2009)
Bioinformatics
, vol.25
, pp. 3236-3243
-
-
Hamada, M.1
Sato, K.2
Kiryu, H.3
Mituyama, T.4
Asai, K.5
|