-
1
-
-
0003157183
-
Noncoding RNA gene detection using comparative sequence analysis
-
Rivas E, Eddy SR: Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics 2001, 2:.
-
(2001)
BMC Bioinformatics
, vol.2
, pp. 8
-
-
Rivas, E.1
Eddy, S.R.2
-
2
-
-
0035806973
-
Computational identification of noncoding RNAs in E. coli by comparative genomics
-
Rivas E, Klein RJ, Jones TA, Eddy SR: Computational identification of noncoding RNAs in E. coli by comparative genomics. Current Biology 2001, 11:1369-1373.
-
(2001)
Current Biology
, vol.11
, pp. 1369-1373
-
-
Rivas, E.1
Klein, R.J.2
Jones, T.A.3
Eddy, S.R.4
-
4
-
-
2942544566
-
RESEARCH: Finding homologs of single structured RNA sequences
-
Klein RJ, Eddy SR: RESEARCH: Finding homologs of single structured RNA sequences. BMC Bioinformatics 2003, 4:44.
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 44
-
-
Klein, R.J.1
Eddy, S.R.2
-
5
-
-
0000228203
-
A Model of Evolutionary Change in Proteins
-
Issue supplement 3 Edited by: Dayhoff MO. Washington, DC: National Biomedical Research Foundation
-
Dayhoff MO, Schwartz RM, Orcutt BC: A Model of Evolutionary Change in Proteins. In In Atlas of Protein Sequence and Structure Volume 5. Issue supplement 3 Edited by: Dayhoff MO. Washington, DC: National Biomedical Research Foundation; 1978:345-352.
-
(1978)
Atlas of Protein Sequence and Structure Volume 5
, pp. 345-352
-
-
Dayhoff, M.O.1
Schwartz, R.M.2
Orcutt, B.C.3
-
7
-
-
0003991673
-
-
Sinauer Associates, Inc; [ISBN 0878931775]
-
Felsenstein J: Inferring Phylogenies Sinauer Associates, Inc; 2003. [ISBN 0878931775]
-
(2003)
Inferring Phylogenies
-
-
Felsenstein, J.1
-
9
-
-
0141869092
-
Sequence Alignments and Pair Hidden Markov Models Using Evolutionary History
-
Knudsen B, Miyamoto M: Sequence Alignments and Pair Hidden Markov Models Using Evolutionary History. Journal of Molecular Biology 2003, 333(2):453-460.
-
(2003)
Journal of Molecular Biology
, vol.333
, Issue.2
, pp. 453-460
-
-
Knudsen, B.1
Miyamoto, M.2
-
11
-
-
0037311782
-
Gene finding with a hidden Markov model of genome structure and evolution
-
Pedersen JS, Hein J: Gene finding with a hidden Markov model of genome structure and evolution. Bioinformatics 2003, 19(2):219-227.
-
(2003)
Bioinformatics
, vol.19
, Issue.2
, pp. 219-227
-
-
Pedersen, J.S.1
Hein, J.2
-
12
-
-
0032796501
-
RNA secondary structure prediction using stochastic context-free grammars and evolutionary history
-
Knudsen B, Hein J: RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics 1999, 15(6):446-454.
-
(1999)
Bioinformatics
, vol.15
, Issue.6
, pp. 446-454
-
-
Knudsen, B.1
Hein, J.2
-
13
-
-
0034791551
-
Evolutionary HMMs: A Bayesian approach to multiple alignment
-
Holmes I, Bruno WJ: Evolutionary HMMs: a Bayesian approach to multiple alignment. Bioinformatics 2001, 17(9):803-820.
-
(2001)
Bioinformatics
, vol.17
, Issue.9
, pp. 803-820
-
-
Holmes, I.1
Bruno, W.J.2
-
14
-
-
0037252684
-
Rfam: An RNA family database
-
Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR: Rfam: an RNA family database. Nucleic Acids Research 2003, 31:439-441.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 439-441
-
-
Griffiths-Jones, S.1
Bateman, A.2
Marshall, M.3
Khanna, A.4
Eddy, S.R.5
-
18
-
-
13244251724
-
Pairwise RNA structure comparison using stochastic context-free grammars
-
Holmes I, Rubin GM: Pairwise RNA structure comparison using stochastic context-free grammars. Pacific Symposium on Biocomputing 2002.
-
(2002)
Pacific Symposium on Biocomputing
-
-
Holmes, I.1
Rubin, G.M.2
-
19
-
-
0022146059
-
Simultaneous solution of the RNA folding, alignment, and protosequence problems
-
Sankoff D: Simultaneous solution of the RNA folding, alignment, and protosequence problems. SIAM Journal of Applied Mathematics 1985, 45:810-825.
-
(1985)
SIAM Journal of Applied Mathematics
, vol.45
, pp. 810-825
-
-
Sankoff, D.1
-
20
-
-
0030812919
-
Finding the most significant common sequence and structure motifs in a set of RNA sequences
-
Gorodkin J, Heyer LJ, Stormo GD: Finding the most significant common sequence and structure motifs in a set of RNA sequences. Nucleic Acids Research 1997, 25(18):3724-3732.
-
(1997)
Nucleic Acids Research
, vol.25
, Issue.18
, pp. 3724-3732
-
-
Gorodkin, J.1
Heyer, L.J.2
Stormo, G.D.3
-
21
-
-
0036295198
-
Dynalign: An algorithm for finding the secondary structure common to two RNA sequences
-
Mathews DH, Turner DH: Dynalign: an algorithm for finding the secondary structure common to two RNA sequences. Journal of Molecular Biology 2002, 317(2):191-203.
-
(2002)
Journal of Molecular Biology
, vol.317
, Issue.2
, pp. 191-203
-
-
Mathews, D.H.1
Turner, D.H.2
-
22
-
-
0036298990
-
Expectation Maximization algorithm for training hidden substitution models
-
Holmes I, Rubin GM: Expectation Maximization algorithm for training hidden substitution models. J Mol Biol 2002, 317(5): 57-768.
-
(2002)
J. Mol. Biol.
, vol.317
, Issue.5
, pp. 757-768
-
-
Holmes, I.1
Rubin, G.M.2
-
23
-
-
0038210214
-
Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria
-
Mandal M, Boese B, Barrick JE, Winkler WC, Breaker RR: Riboswitches Control Fundamental Biochemical Pathways in Bacillus subtilis and Other Bacteria. Cell 2003, 113:577-586.
-
(2003)
Cell
, vol.113
, pp. 577-586
-
-
Mandal, M.1
Boese, B.2
Barrick, J.E.3
Winkler, W.C.4
Breaker, R.R.5
-
24
-
-
0033695349
-
Overlapping but distinct RNA elements control repression and activation of nanos translation
-
Crucs S, Chatterjee S, Gavis ER: Overlapping but distinct RNA elements control repression and activation of nanos translation. Molecular cell 2000, 5(3):457-467.
-
(2000)
Molecular Cell
, vol.5
, Issue.3
, pp. 457-467
-
-
Crucs, S.1
Chatterjee, S.2
Gavis, E.R.3
-
25
-
-
0035047218
-
Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines
-
Berglund JA, Rosbash M, Schultz SC: Crystal structure of a model branchpoint-U2 snRNA duplex containing bulged adenosines. RNA 2001, 7:682-691.
-
(2001)
RNA
, vol.7
, pp. 682-691
-
-
Berglund, J.A.1
Rosbash, M.2
Schultz, S.C.3
-
26
-
-
0034538974
-
Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA
-
Frank DN, Adamidi C, Ehringer MA, Pitulle C, Pace NR: Phylogenetic-comparative analysis of the eukaryal ribonuclease P RNA. RNA 2000, 6:1895-1904.
-
(2000)
RNA
, vol.6
, pp. 1895-1904
-
-
Frank, D.N.1
Adamidi, C.2
Ehringer, M.A.3
Pitulle, C.4
Pace, N.R.5
-
27
-
-
0035228391
-
An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree
-
Edited by: Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein TE. Singapore: World Scientific
-
Hein J: An Algorithm for Statistical Alignment of Sequences Related by a Binary Tree. In In Pacific Symposium on Biocomputing Edited by: Altman RB, Dunker AK, Hunter L, Lauderdale K, Klein TE. Singapore: World Scientific; 2001:179-190.
-
(2001)
Pacific Symposium on Biocomputing
, pp. 179-190
-
-
Hein, J.1
-
28
-
-
0037252550
-
Finding the common structure shared by two homologous RNAs
-
Perriquet O, Touzet H, Dauchet M: Finding the common structure shared by two homologous RNAs. Bioinformatics 2003, 19:108-116.
-
(2003)
Bioinformatics
, vol.19
, pp. 108-116
-
-
Perriquet, O.1
Touzet, H.2
Dauchet, M.3
-
29
-
-
13244276706
-
A nucleotide substitution model with nearest-neighbour interactions
-
[To appear]
-
Lunter G, Hein J: A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics 2004. [To appear]
-
(2004)
Bioinformatics
-
-
Lunter, G.1
Hein, J.2
-
30
-
-
1542510106
-
Phylogenetic estimation of contextdependent substitution rates by maximum likelihood
-
Siepel A, Haussler D: Phylogenetic estimation of contextdependent substitution rates by maximum likelihood. Molecular Biology and Evolution 2004, 21(3):468-488.
-
(2004)
Molecular Biology and Evolution
, vol.21
, Issue.3
, pp. 468-488
-
-
Siepel, A.1
Haussler, D.2
-
31
-
-
0032927161
-
Topological bias and inconsistency of maximum likelihood using wrong models
-
Bruno WJ, Halpern AL: Topological bias and inconsistency of maximum likelihood using wrong models. Molecular Biology and Evolution 1999, 16:564-566.
-
(1999)
Molecular Biology and Evolution
, vol.16
, pp. 564-566
-
-
Bruno, W.J.1
Halpern, A.L.2
-
32
-
-
0027132974
-
Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites
-
Yang Z: Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites. Molecular Biology and Evolution 1993, 10:1396-1401.
-
(1993)
Molecular Biology and Evolution
, vol.10
, pp. 1396-1401
-
-
Yang, Z.1
-
33
-
-
0036084366
-
SCOR: A structural classification of RNA database
-
Klosterman PS, Tamura M, Holbrook SR, Brenner SE: SCOR: a structural classification of RNA database. Nucleic Acids Research 2002, 30:392-394.
-
(2002)
Nucleic Acids Research
, vol.30
, pp. 392-394
-
-
Klosterman, P.S.1
Tamura, M.2
Holbrook, S.R.3
Brenner, S.E.4
-
34
-
-
2342487400
-
Three-dimensional motifs from the SCOR, structural classification of RNA database: Extruded strands, base triples, tetraloops and U-turns
-
Klosterman PS, Hendrix DK, Tamura M, Holbrook SR, Brenner SE: Three-dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U-turns. Nucleic Acids Research 2004, 32(8):2342-2352.
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.8
, pp. 2342-2352
-
-
Klosterman, P.S.1
Hendrix, D.K.2
Tamura, M.3
Holbrook, S.R.4
Brenner, S.E.5
-
35
-
-
0000810926
-
RNA-protein intermolecular recognition
-
Varani G: RNA-protein intermolecular recognition. Accounts of chemical research 1997, 30(5):190-195.
-
(1997)
Accounts of Chemical Research
, vol.30
, Issue.5
, pp. 190-195
-
-
Varani, G.1
-
36
-
-
3042704491
-
Structural basis for recognition of the AGNN tetraloop RNA fold by the doublestranded RNA-binding domain of Rnt1p RNase III
-
Wu H, Henras A, Chanfreau G, Feigon J: Structural basis for recognition of the AGNN tetraloop RNA fold by the doublestranded RNA-binding domain of Rnt1p RNase III. Proceedings of the National Academy of Sciences of the USA 2004, 101(22):8307-8312.
-
(2004)
Proceedings of the National Academy of Sciences of the USA
, vol.101
, Issue.22
, pp. 8307-8312
-
-
Wu, H.1
Henras, A.2
Chanfreau, G.3
Feigon, J.4
|