-
1
-
-
34250305146
-
Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
-
The ENCODE 2212820 17571346 10.1038/nature05874
-
The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 2007, 447:799-816. 2212820 17571346 10.1038/nature05874
-
(2007)
Nature
, vol.447
, pp. 799-816
-
-
-
2
-
-
24644519490
-
The Transcriptional Landscape of the Mammalian Genome
-
The FANTOM Consortium 10.1126/science.1112014
-
The FANTOM Consortium The Transcriptional Landscape of the Mammalian Genome Science 2005, 309:1159-1563. 10.1126/science.1112014
-
(2005)
Science
, vol.309
, pp. 1159-1563
-
-
-
3
-
-
33847183553
-
RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
-
The Athanasius F Bompfünewerer RNA Consortium 10.1002/jez.b.21130
-
The Athanasius F Bompfünewerer RNA Consortium RNAs Everywhere: Genome-Wide Annotation of Structured RNAs J Exp Zool B Mol Dev Evol 2007, 308B:1-25. 10.1002/jez.b.21130
-
(2007)
J Exp Zool B Mol Dev Evol
, vol.308 B
, pp. 1-25
-
-
-
4
-
-
0036301332
-
Secondary Structure Prediction for Aligned RNA Sequences
-
10.1016/S0022-2836(02)00308-X 12079347
-
Hofacker IL Fekete M Stadler PF Secondary Structure Prediction for Aligned RNA Sequences J Mol Biol 2002, 319:1059-1066. 10.1016/ S0022-2836(02)00308-X 12079347
-
(2002)
J Mol Biol
, vol.319
, pp. 1059-1066
-
-
Hofacker, I.L.1
Fekete, M.2
Stadler, P.F.3
-
5
-
-
0022146059
-
Simultaneous solution of the RNA folding, alignment, and proto-sequence problems
-
10.1137/0145048
-
Sankoff D Simultaneous solution of the RNA folding, alignment, and proto-sequence problems SIAM J Appl Math 1985, 45:810-825. 10.1137/ 0145048
-
(1985)
SIAM J Appl Math
, vol.45
, pp. 810-825
-
-
Sankoff, D.1
-
6
-
-
34248632816
-
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
-
1868766 17445273 10.1186/1471-2105-8-130
-
Harmanci AO Sharma G Mathews DH Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign BMC Bioinformatics 2007, 8:130. 1868766 17445273 10.1186/1471-2105-8-130
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 130
-
-
Harmanci, A.O.1
Sharma, G.2
Mathews, D.H.3
-
7
-
-
25444433586
-
Accelerated probabilistic inference of RNA structure evolution
-
1090553 15790387 10.1186/1471-2105-6-73
-
Holmes I Accelerated probabilistic inference of RNA structure evolution BMC Bioinformatics 2005, 6:73. 1090553 15790387 10.1186/1471-2105-6-73
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 73
-
-
Holmes, I.1
-
8
-
-
35748971022
-
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
-
2014794 17937495 10.1371/journal.pcbi.0030193
-
Havgaard JH Torarinsson E Gorodkin J Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix PLoS Comput Biol 2007, 3:1896-1908. 2014794 17937495 10.1371/journal.pcbi.0030193
-
(2007)
PLoS Comput Biol
, vol.3
, pp. 1896-1908
-
-
Havgaard, J.H.1
Torarinsson, E.2
Gorodkin, J.3
-
9
-
-
34247598415
-
Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering
-
10.1371/journal.pcbi.0030065
-
Will S Reiche K Hofacker IL Stadler PF Backofen R Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering PLoS Comput Biol 2007, 3(4):400. 10.1371/journal.pcbi.0030065
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.4
, pp. 400
-
-
Will, S.1
Reiche, K.2
Hofacker, I.L.3
Stadler, P.F.4
Backofen, R.5
-
10
-
-
33749412683
-
Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints
-
1579236 16952317 10.1186/1471-2105-7-400
-
Dowell RD Eddy SR Efficient pairwise RNA structure prediction and alignment using sequence alignment constraints BMC Bioinformatics 2006, 7:400. 1579236 16952317 10.1186/1471-2105-7-400
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 400
-
-
Dowell, R.D.1
Eddy, S.R.2
-
11
-
-
33745612985
-
STRAL: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time
-
10.1093/bioinformatics/btl142 16613908
-
Dalli D Wilm A Mainz I G S STRAL: Progressive alignment of non-coding RNA using base pairing probability vectors in quadratic time Bioinformatics 2006, 22:1593-1599. 10.1093/bioinformatics/btl142 16613908
-
(2006)
Bioinformatics
, vol.22
, pp. 1593-1599
-
-
Dalli, D.1
Wilm, A.2
Mainz, I.G.S.3
-
13
-
-
24044519380
-
MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons
-
10.1093/bioinformatics/bti550 15972285
-
Siebert S Backofen R MARNA: Multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons Bioinformatics 2005, 21:3352-3359. 10.1093/bioinformatics/bti550 15972285
-
(2005)
Bioinformatics
, vol.21
, pp. 3352-3359
-
-
Siebert, S.1
Backofen, R.2
-
14
-
-
34247598415
-
Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
-
10.1371/journal.pcbi.0030065
-
Will S Missal K Hofacker IL Stadler PF Backofen R Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering PLoS Comp Biol 2007, 3:e65. 10.1371/journal.pcbi.0030065
-
(2007)
PLoS Comp Biol
, vol.3
-
-
Will, S.1
Missal, K.2
Hofacker, I.L.3
Stadler, P.F.4
Backofen, R.5
-
15
-
-
37249037158
-
RNAspa a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules
-
2147038 17908318 10.1186/1471-2105-8-366
-
Horesh Y Doniger T Michaeli S Unger R RNAspa a shortest path approach for comparative prediction of the secondary structure of ncRNA molecules BMC Bioinformatics 2007, 8:366. 2147038 17908318 10.1186/1471-2105-8-366
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 366
-
-
Horesh, Y.1
Doniger, T.2
Michaeli, S.3
Unger, R.4
-
16
-
-
24144497144
-
Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction
-
10.1093/bioinformatics/bti577 16020472
-
Reeder J Giegerich R Consensus shapes: An alternative to the Sankoff algorithm for RNA consensus structure prediction Bioinformatics 2005, 21:3516-3523. 10.1093/bioinformatics/bti577 16020472
-
(2005)
Bioinformatics
, vol.21
, pp. 3516-3523
-
-
Reeder, J.1
Giegerich, R.2
-
17
-
-
33847262911
-
Robust prediction of consensus secondary structures using averaged base pairing probability matrices
-
10.1093/bioinformatics/btl636 17182698
-
Kiryu H Kin T Asai K Robust prediction of consensus secondary structures using averaged base pairing probability matrices Bioinformatics 2007, 23:434-441. 10.1093/bioinformatics/btl636 17182698
-
(2007)
Bioinformatics
, vol.23
, pp. 434-441
-
-
Kiryu, H.1
Kin, T.2
Asai, K.3
-
18
-
-
44649166879
-
ConStruct: Improved construction of RNA consensus structures
-
2408607 18442401 10.1186/1471-2105-9-219
-
Wilm A Linnenbrink K Steger G ConStruct: Improved construction of RNA consensus structures BMC Bioinformatics 2008, 9:219. 2408607 18442401 10.1186/1471-2105-9-219
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 219
-
-
Wilm, A.1
Linnenbrink, K.2
Steger, G.3
-
19
-
-
0033563463
-
Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes
-
10.1016/S0097-8485(99)00013-3
-
Hofacker IL Stadler PF Automatic Detection of Conserved Base Pairing Patterns in RNA Virus Genomes Comp & Chem 1999, 23:401-414. 10.1016/ S0097-8485(99)00013-3
-
(1999)
Comp & Chem
, vol.23
, pp. 401-414
-
-
Hofacker, I.L.1
Stadler, P.F.2
-
20
-
-
33744790273
-
Prediction of RNA secondary structure by free energy minimization
-
10.1016/j.sbi.2006.05.010 16713706
-
Mathews DH Turner DH Prediction of RNA secondary structure by free energy minimization Curr Opin Struct Biol 2006, 16:270-278. 10.1016/ j.sbi.2006.05.010 16713706
-
(2006)
Curr Opin Struct Biol
, vol.16
, pp. 270-278
-
-
Mathews, D.H.1
Turner, D.H.2
-
21
-
-
44649166879
-
ConStruct: Improved construction of RNA consensus structures
-
2408607 18442401 10.1186/1471-2105-9-219
-
Wilm A Linnenbrink K Steger G ConStruct: Improved construction of RNA consensus structures BMC Bioinformatics 2008, 9:219. 2408607 18442401 10.1186/1471-2105-9-219
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 219
-
-
Wilm, A.1
Linnenbrink, K.2
Steger, G.3
-
22
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
326673 6163133 10.1093/nar/9.1.133
-
Zuker M Stiegler P Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucleic Acids Res 1981, 9:133-148. 326673 6163133 10.1093/nar/9.1.133
-
(1981)
Nucleic Acids Res
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
23
-
-
33646867882
-
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures
-
10.1093/bioinformatics/btl023 16452114
-
Hofacker IL Stadler PF Memory Efficient Folding Algorithms for Circular RNA Secondary Structures Bioinformatics 2006, 22:1172-1176. 10.1093/ bioinformatics/btl023 16452114
-
(2006)
Bioinformatics
, vol.22
, pp. 1172-1176
-
-
Hofacker, I.L.1
Stadler, P.F.2
-
25
-
-
34547840261
-
Efficient parameter estimation for RNA secondary structure prediction
-
10.1093/bioinformatics/btm223 17646296
-
Andronescu M Condon A Hoos HH Mathews DH Murphy KP Efficient parameter estimation for RNA secondary structure prediction Bioinformatics 2007, 23:i19-i28. 10.1093/bioinformatics/btm223 17646296
-
(2007)
Bioinformatics
, vol.23
-
-
Andronescu, M.1
Condon, A.2
Hoos, H.H.3
Mathews, D.H.4
Murphy, K.P.5
-
26
-
-
0027496980
-
Weighting in sequence space: A comparison of methods in terms of generalized sequences
-
47443 8415606 10.1073/pnas.90.19.8777
-
Vingron M Sibbald PR Weighting in sequence space: A comparison of methods in terms of generalized sequences Proc Natl Acad Sci USA 1993, 90:8777-8781. 47443 8415606 10.1073/pnas.90.19.8777
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 8777-8781
-
-
Vingron, M.1
Sibbald, P.R.2
-
27
-
-
2942544566
-
RSEARCH: Finding homologs of single structured RNA sequences
-
239859 14499004 10.1186/1471-2105-4-44
-
Klein RJ Eddy SR RSEARCH: Finding homologs of single structured RNA sequences BMC Bioinformatics 2003, 4:44. 239859 14499004 10.1186/ 1471-2105-4-44
-
(2003)
BMC Bioinformatics
, vol.4
, pp. 44
-
-
Klein, R.J.1
Eddy, S.R.2
-
28
-
-
0346494979
-
The European ribosomal RNA database
-
308799 14681368 10.1093/nar/gkh065
-
Wuyts J Perrière G Peer Van De Y The European ribosomal RNA database Nucleic Acids Res 2004 32: D101-D103. 308799 14681368 10.1093/ nar/gkh065
-
(2004)
Nucleic Acids Res
, vol.32
-
-
Wuyts, J.1
Perrière, G.2
Peer, Y.3
-
29
-
-
0043123155
-
Pfold: RNA secondary structure prediction using stochastic context-free grammars
-
169020 12824339 10.1093/nar/gkg614
-
Knudsen B Hein J Pfold: RNA secondary structure prediction using stochastic context-free grammars Nucleic Acids Res 2003, 31:3423-3428. 169020 12824339 10.1093/nar/gkg614
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3423-3428
-
-
Knudsen, B.1
Hein, J.2
-
30
-
-
42149083815
-
Centroid estimation in discrete high-dimensional spaces with applications in biology
-
2265131 18305160 10.1073/pnas.0712329105
-
Carvalho LE Lawrence CE Centroid estimation in discrete high-dimensional spaces with applications in biology Proc Natl Acad Sci USA 2008, 105(9):3209-3214. 2265131 18305160 10.1073/pnas.0712329105
-
(2008)
Proc Natl Acad Sci USA
, vol.105
, Issue.9
, pp. 3209-3214
-
-
Carvalho, L.E.1
Lawrence, C.E.2
-
32
-
-
0033563515
-
A bayesian statistical algorithm for RNA secondary structure prediction
-
10.1016/S0097-8485(99)00010-8 10404626
-
Ding Y Lawrence CE A bayesian statistical algorithm for RNA secondary structure prediction Comput Chem 1999, 23(3-4):387-400. 10.1016/ S0097-8485(99)00010-8 10404626
-
(1999)
Comput Chem
, vol.23
, Issue.3-4
, pp. 387-400
-
-
Ding, Y.1
Lawrence, C.E.2
-
34
-
-
52049083257
-
RNA STRAND: The RNA secondary structure and statistical analysis database
-
2536673 18700982 10.1186/1471-2105-9-340
-
Andronescu M Bereg V Hoos HH Condon A RNA STRAND: The RNA secondary structure and statistical analysis database BMC Bioinformatics 2008, 9:340. 2536673 18700982 10.1186/1471-2105-9-340
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 340
-
-
Andronescu, M.1
Bereg, V.2
Hoos, H.H.3
Condon, A.4
-
35
-
-
35549004515
-
Semiautomated improvement of RNA alignments
-
2040093 17804647 10.1261/rna.215407
-
Andersen ES Lind-Thomsen A Knudsen B Kristensen SE Havgaard JH Torarinsson E Larsen N Zwieb C Ses-toft P Kjems J Gorodkin J Semiautomated improvement of RNA alignments RNA 2007, 13(11):1850-1859. 2040093 17804647 10.1261/rna.215407
-
(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
Ses-Toft, P.9
Kjems, J.10
Gorodkin, J.11
-
36
-
-
32544452741
-
CMfinder-a covariance model based RNA motif finding algorithm
-
10.1093/bioinformatics/btk008 16357030
-
Yao Z Weinberg Z Ruzzo WL CMfinder-a covariance model based RNA motif finding algorithm Bioinformatics 2006, 22(4):445-452. 10.1093/ bioinformatics/btk008 16357030
-
(2006)
Bioinformatics
, vol.22
, Issue.4
, pp. 445-452
-
-
Yao, Z.1
Weinberg, Z.2
Ruzzo, W.L.3
-
37
-
-
56649099274
-
Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments
-
2582601 18836192
-
Seemann SE Gorodkin J Backofen R Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments NAR 2008. 2582601 18836192
-
(2008)
NAR
-
-
Seemann, S.E.1
Gorodkin, J.2
Backofen, R.3
-
38
-
-
33344469705
-
RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers
-
1383574 16495232 10.1261/rna.2164906
-
Bindewald E Shapiro BA RNA secondary structure prediction from sequence alignments using a network of k-nearest neighbor classifiers RNA 2006, 12:342-352. 1383574 16495232 10.1261/rna.2164906
-
(2006)
RNA
, vol.12
, pp. 342-352
-
-
Bindewald, E.1
Shapiro, B.A.2
-
39
-
-
13344262673
-
A comprehensive comparison of comparative RNA structure prediction approaches
-
526219 15458580 10.1186/1471-2105-5-140
-
Gardner PP Giegerich R A comprehensive comparison of comparative RNA structure prediction approaches BMC Bioinformatics 2004, 5:140. 526219 15458580 10.1186/1471-2105-5-140
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 140
-
-
Gardner, P.P.1
Giegerich, R.2
-
40
-
-
0042121237
-
Multiple sequence alignment with the Clustal series of programs
-
168907 12824352 10.1093/nar/gkg500
-
Chenna R Sugawara H Koike T Lopez R Gibson TJ Higgins DG Thompson JD Multiple sequence alignment with the Clustal series of programs Nucleic Acids Research 2003, 31(13):3497-500. 168907 12824352 10.1093/nar/gkg500
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.13
, pp. 3497-3500
-
-
Chenna, R.1
Sugawara, H.2
Koike, T.3
Lopez, R.4
Gibson, T.J.5
Higgins, D.G.6
Thompson, J.D.7
-
41
-
-
4143149651
-
Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics
-
10.1016/j.jmb.2004.07.018 15313604
-
Washietl S Hofacker IL Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics J Mol Biol 2004, 342:19-39. 10.1016/j.jmb.2004.07.018 15313604
-
(2004)
J Mol Biol
, vol.342
, pp. 19-39
-
-
Washietl, S.1
Hofacker, I.L.2
-
42
-
-
14044272835
-
Fast and reliable prediction of noncoding RNAs
-
548974 15665081 10.1073/pnas.0409169102
-
Washietl S Hofacker IL Stadler PF Fast and reliable prediction of noncoding RNAs Proc Natl Acad Sci USA 2005, 102:2454-2459. 548974 15665081 10.1073/pnas.0409169102
-
(2005)
Proc Natl Acad Sci USA
, vol.102
, pp. 2454-2459
-
-
Washietl, S.1
Hofacker, I.L.2
Stadler, P.F.3
-
43
-
-
47249140906
-
Dinucleotide controlled null models for comparative RNA gene prediction
-
2453142 18505553 10.1186/1471-2105-9-248
-
Gesell T Washietl S Dinucleotide controlled null models for comparative RNA gene prediction BMC Bioinformatics 2008, 9:248-248. 2453142 18505553 10.1186/1471-2105-9-248
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 248
-
-
Gesell, T.1
Washietl, S.2
-
44
-
-
42949090850
-
Strategies for measuring evolutionary conservation of RNA secondary structures
-
2335298 18302738 10.1186/1471-2105-9-122
-
Gruber AR Bernhart SH Hofacker IL Washietl S Strategies for measuring evolutionary conservation of RNA secondary structures BMC Bioinformatics 2008, 9:122. 2335298 18302738 10.1186/1471-2105-9-122
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 122
-
-
Gruber, A.R.1
Bernhart, S.H.2
Hofacker, I.L.3
Washietl, S.4
|