-
1
-
-
33644876507
-
The tmRDB and SRPDB resources
-
Andersen ES, Rosenblad MA, Larsen N, Westergaard JC, Burks J, Wower IK, Wower J, Gorodkin J, Samuelsson T, Zwieb C. 2006. The tmRDB and SRPDB resources. Nucleic Acids Res 34: 163-168.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 163-168
-
-
Andersen, E.S.1
Rosenblad, M.A.2
Larsen, N.3
Westergaard, J.C.4
Burks, J.5
Wower, I.K.6
Wower, J.7
Gorodkin, J.8
Samuelsson, T.9
Zwieb, C.10
-
2
-
-
11844296459
-
-
Master's thesis, Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
-
Andronescu MS. 2003. "Algorithms for predicting the secondary structure of pairs and combinatorial sets of nucleic acid strands." Master's thesis, Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
-
(2003)
Algorithms for Predicting the Secondary Structure of Pairs and Combinatorial Sets of Nucleic Acid Strands
-
-
Andronescu, M.S.1
-
3
-
-
77952566596
-
-
PhD thesis, Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
-
Andronescu MS. 2008. "Computational approaches for RNA energy parameter estimation." PhD thesis, Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
-
(2008)
Computational Approaches for RNA Energy Parameter Estimation
-
-
Andronescu, M.S.1
-
4
-
-
11844254846
-
Secondary structure prediction of interacting RNA molecules
-
Andronescu M, Zhang Z, Condon A. 2005. Secondary structure prediction of interacting RNA molecules. J Mol Biol 345: 987-1001.
-
(2005)
J Mol Biol
, vol.345
, pp. 987-1001
-
-
Andronescu, M.1
Zhang, Z.2
Condon, A.3
-
5
-
-
34547840261
-
Efficient parameter estimation for RNA secondary structure prediction
-
Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. 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.H.3
Mathews, D.H.4
Murphy, K.P.5
-
6
-
-
52049083257
-
RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database
-
doi: 10.1186/1471-2105-9-340
-
Andronescu M, Bereg V, Hoos HH, Condon A. 2008. RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database. BMC Bioinformatics 9: 340. doi: 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
-
7
-
-
75649099055
-
Improved energy parameters for RNA pseudoknotted secondary structure prediction
-
Andronescu, M, Pop C, Condon AE. 2010. Improved energy parameters for RNA pseudoknotted secondary structure prediction. RNA 16: 26-42.
-
(2010)
RNA
, vol.16
, pp. 26-42
-
-
Andronescu, M.1
Pop, C.2
Condon, A.E.3
-
8
-
-
0026593806
-
Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops
-
Antao VP, Tinoco I. 1992. Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Res 20: 819-824.
-
(1992)
Nucleic Acids Res
, vol.20
, pp. 819-824
-
-
Antao, V.P.1
Tinoco, I.2
-
9
-
-
0025942059
-
A thermodynamic study of unusually stable RNA and DNA hairpins
-
Antao VP, Lai SY, Tinoco I. 1991. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res 19: 5901-5905.
-
(1991)
Nucleic Acids Res
, vol.19
, pp. 5901-5905
-
-
Antao, V.P.1
Lai, S.Y.2
Tinoco, I.3
-
10
-
-
37249073320
-
Thermodynamic characterization of RNA duplexes containing naturally occurring 1 3 2 nucleotide internal loops
-
Badhwar J, Karri S, Cass CK, Wunderlich EL, Znosko BM. 2007. Thermodynamic characterization of RNA duplexes containing naturally occurring 1 3 2 nucleotide internal loops. Biochemistry 46: 14715-14724.
-
(2007)
Biochemistry
, vol.46
, pp. 14715-14724
-
-
Badhwar, J.1
Karri, S.2
Cass, C.K.3
Wunderlich, E.L.4
Znosko, B.M.5
-
11
-
-
21444457242
-
Programmable ligand-controlled ribo-regulators of eukaryotic gene expression
-
Bayer TS, Smolke CD. 2005. Programmable ligand-controlled ribo-regulators of eukaryotic gene expression. Nat Biotechnol 23: 337-343.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 337-343
-
-
Bayer, T.S.1
Smolke, C.D.2
-
12
-
-
54949106632
-
Model-guided design of ligand-regulated RNAi for programmable control of gene expression
-
doi: 10.1038/msb.2008.62
-
Beisel CL, Bayer TS, Hoff KG, Smolke CD. 2008. Model-guided design of ligand-regulated RNAi for programmable control of gene expression. Mol Syst Biol 4: 224. doi: 10.1038/msb.2008.62.
-
(2008)
Mol Syst Biol
, vol.4
, pp. 224
-
-
Beisel, C.L.1
Bayer, T.S.2
Hoff, K.G.3
Smolke, C.D.4
-
13
-
-
0026742978
-
The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids
-
Berman HM, Olson WK, Beveridge DL, Westbrook J, Gelbin A, Demeny T, Hsieh SH, Srinivasan AR, Schneider B. 1992. The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. Biophys J 63: 751-759.
-
(1992)
Biophys J
, vol.63
, pp. 751-759
-
-
Berman, H.M.1
Olson, W.K.2
Beveridge, D.L.3
Westbrook, J.4
Gelbin, A.5
Demeny, T.6
Hsieh, S.H.7
Srinivasan, A.R.8
Schneider, B.9
-
14
-
-
58249121729
-
RNAalifold: Improved consensus structure prediction for RNA alignments
-
doi: 10.1186/1471-2105-9-474
-
Bernhart SH, Hofacker IL, Will S, Gruber AR, Stadler PF. 2008. RNAalifold: Improved consensus structure prediction for RNA alignments. BMC Bioinformatics 9: 474. doi: 10.1186/1471-2105-9-474.
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 474
-
-
Bernhart, S.H.1
Hofacker, I.L.2
Will, S.3
Gruber, A.R.4
Stadler, P.F.5
-
15
-
-
29244457847
-
Thermodynamics of RNA duplexes with tandem mismatches containing a uracil-uracil pair flanked by C.G/G.C or G.C/A.U closing base pairs
-
Bourdélat-Parks BN, Wartell RM. 2005. Thermodynamics of RNA duplexes with tandem mismatches containing a uracil-uracil pair flanked by C.G/G.C or G.C/A.U closing base pairs. Biochemistry 44: 16710-16717.
-
(2005)
Biochemistry
, vol.44
, pp. 16710-16717
-
-
Bourdélat-Parks, B.N.1
Wartell, R.M.2
-
16
-
-
0344298926
-
The Ribonuclease P Database
-
doi: 10.1093/nar/27.1.314
-
Brown J. 1999. The Ribonuclease P Database. Nucleic Acids Res 27: 314. doi: 10.1093/nar/27.1.314
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 314
-
-
Brown, J.1
-
17
-
-
0035957084
-
Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair
-
Burkard ME, Xia T, Turner DH. 2001. Thermodynamics of RNA internal loops with a guanosine-guanosine pair adjacent to another noncanonical pair. Biochemistry 40: 2478-2483.
-
(2001)
Biochemistry
, vol.40
, pp. 2478-2483
-
-
Burkard, M.E.1
Xia, T.2
Turner, D.H.3
-
18
-
-
2942571539
-
The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs
-
doi: 10.1186/1471-2105-3-2
-
Cannone JJ, Subramanian S, Schnare MN, Collett JR, D'Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Müller KM, et al. 2002. The comparative RNA web (CRW) site: An online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2. doi: 10.1186/1471-2105-3-2.
-
(2002)
BMC Bioinformatics
, vol.3
, pp. 2
-
-
Cannone, J.J.1
Subramanian, S.2
Schnare, M.N.3
Collett, J.R.4
D'Souza, L.M.5
Du, Y.6
Feng, B.7
Lin, N.8
Madabusi, L.V.9
Müller, K.M.10
-
19
-
-
78649405622
-
An interior-point stochastic approximation method and an L1-regularized delta rule
-
MIT Press, Cambridge, MA
-
Carbonetto P, Schmidt M, de Freitas N. 2008. An interior-point stochastic approximation method and an L1-regularized delta rule. In Advances in neural information processing systems 21, pp. 233-240. MIT Press, Cambridge, MA.
-
(2008)
Advances in Neural Information Processing Systems
, vol.21
, pp. 233-240
-
-
Carbonetto, P.1
Schmidt, M.2
De Freitas, N.3
-
20
-
-
33645456129
-
Consecutive GA pairs stabilize mediumsize RNA internal loops
-
Chen G, Turner DH. 2006. Consecutive GA pairs stabilize mediumsize RNA internal loops. Biochemistry 45: 4025-4043.
-
(2006)
Biochemistry
, vol.45
, pp. 4025-4043
-
-
Chen, G.1
Turner, D.H.2
-
21
-
-
4944231969
-
Factors affecting thermodynamic stabilities of RNA 3 X 3 internal loops
-
DOI 10.1021/bi049168d
-
Chen G, Znosko BM, Jiao X, Turner DH. 2004. Factors affecting thermodynamic stabilities of RNA 3 X 3 internal loops. Biochemistry 43: 12865-12876. (Pubitemid 39331806)
-
(2004)
Biochemistry
, vol.43
, Issue.40
, pp. 12865-12876
-
-
Chen, G.1
Znosko, B.M.2
Jiao, X.3
Turner, D.H.4
-
22
-
-
14344256105
-
Solution structure of an RNA internal loop with three consecutive sheared GA pairs
-
DOI 10.1021/bi048079y
-
Chen G, Znosko BM, Kennedy SD, Krugh TR, Turner DH. 2005. Solution structure of an RNA internal loop with three consecutive sheared GA pairs. Biochemistry 44: 2845-2856. (Pubitemid 40293660)
-
(2005)
Biochemistry
, vol.44
, Issue.8
, pp. 2845-2856
-
-
Chen, G.1
Znosko, B.M.2
Kennedy, S.D.3
Krugh, T.R.4
Turner, D.H.5
-
23
-
-
41849129277
-
Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches
-
Christiansen ME, Znosko BM. 2008. Thermodynamic characterization of the complete set of sequence symmetric tandem mismatches in RNA and an improved model for predicting the free energy contribution of sequence asymmetric tandem mismatches. Biochemistry 47: 4329-4336.
-
(2008)
Biochemistry
, vol.47
, pp. 4329-4336
-
-
Christiansen, M.E.1
Znosko, B.M.2
-
24
-
-
0034002687
-
A test of the model to predict unusually stable RNA hairpin loop stability
-
DOI 10.1017/S1355838200992495
-
Dale T, Smith R, Serra MJ. 2000. A test of the model to predict unusually stable RNA hairpin loop stability. RNA 6: 608-615. (Pubitemid 30212238)
-
(2000)
RNA
, vol.6
, Issue.4
, pp. 608-615
-
-
Dale, T.1
Smith, R.2
Serra, M.J.3
-
25
-
-
36248936612
-
Thermodynamic characterization of single mismatches found in naturally occurring RNA
-
Davis AR, Znosko BM. 2007. Thermodynamic characterization of single mismatches found in naturally occurring RNA. Biochemistry 46: 13425-13436.
-
(2007)
Biochemistry
, vol.46
, pp. 13425-13436
-
-
Davis, A.R.1
Znosko, B.M.2
-
26
-
-
0035849554
-
Thermodynamics of three-way multibranch loops in RNA
-
Diamond JM, Turner DH, Mathews DH. 2001. Thermodynamics of three-way multibranch loops in RNA. Biochemistry 40: 6971-6981.
-
(2001)
Biochemistry
, vol.40
, pp. 6971-6981
-
-
Diamond, J.M.1
Turner, D.H.2
Mathews, D.H.3
-
27
-
-
33344474707
-
Statistical and Bayesian approaches to RNA secondary structure prediction
-
DOI 10.1261/rna.2274106
-
Ding Y. 2006. Statistical and Bayesian approaches to RNA secondary structure prediction. RNA 12: 323-331. (Pubitemid 43290860)
-
(2006)
RNA
, vol.12
, Issue.3
, pp. 323-331
-
-
Ding, Y.1
-
28
-
-
0346888665
-
A statistical sampling algorithm for RNA secondary structure prediction
-
DOI 10.1093/nar/gkg938
-
Ding Y, Lawrence CE. 2003. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res 31: 7280-7301. (Pubitemid 38008457)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.24
, pp. 7280-7301
-
-
Ding, Y.1
Lawrence, C.E.2
-
29
-
-
33847609597
-
Thermodynamic analysis of interacting nucleic acid strands
-
Dirks RM, Bois JS, Schaeffer JM, Winfree E, Pierce NA. 2007. Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev 49: 65-88.
-
(2007)
SIAM Rev
, vol.49
, pp. 65-88
-
-
Dirks, R.M.1
Bois, J.S.2
Schaeffer, J.M.3
Winfree, E.4
Pierce, N.A.5
-
30
-
-
33747874580
-
CONTRAfold: RNA secondary structure prediction without physics-based models
-
Do CB, Woods DA, Batzoglou S. 2006. CONTRAfold: RNA secondary structure prediction without physics-based models. Bioinformatics 22: e90-e98.
-
(2006)
Bioinformatics
, vol.22
-
-
Do, C.B.1
Woods, D.A.2
Batzoglou, S.3
-
31
-
-
85161996864
-
Efficient multiple hyperparameter learning for log-linear models
-
MIT Press, Cambridge, MA
-
Do CB, Foo C-S, Ng AY. 2007. Efficient multiple hyperparameter learning for log-linear models. In Advances in neural information processing systems 20, pp. 377-384. MIT Press, Cambridge, MA.
-
(2007)
Advances in Neural Information Processing Systems
, vol.20
, pp. 377-384
-
-
Do, C.B.1
Foo, C.-S.2
Ng, A.Y.3
-
32
-
-
46249114849
-
A max-margin model for efficient simultaneous alignment and folding of RNA sequences
-
Do CB, Foo CS, Batzoglou S. 2008. A max-margin model for efficient simultaneous alignment and folding of RNA sequences. Bioinformatics 24: 68-76.
-
(2008)
Bioinformatics
, vol.24
, pp. 68-76
-
-
Do, C.B.1
Foo, C.S.2
Batzoglou, S.3
-
33
-
-
0034021259
-
RNA folding at elementary step resolution
-
DOI 10.1017/S1355838200992161
-
Flamm C, Fontana W, Hofacker IL, Schuster P. 2000. RNA folding at elementary step resolution. RNA 6: 325-338. (Pubitemid 30161278)
-
(2000)
RNA
, vol.6
, Issue.3
, pp. 325-338
-
-
Flamm, C.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
34
-
-
0023040892
-
Free energy contributions of G.U and other terminal mismatches to helix stability
-
Freier SM, Kierzek R, Caruthers MH, Neilson T, Turner DH. 1986. Free energy contributions of G.U and other terminal mismatches to helix stability. Biochemistry 25: 3209-3213.
-
(1986)
Biochemistry
, vol.25
, pp. 3209-3213
-
-
Freier, S.M.1
Kierzek, R.2
Caruthers, M.H.3
Neilson, T.4
Turner, D.H.5
-
35
-
-
43049086258
-
Folding kinetics of large RNAs
-
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C. 2008. Folding kinetics of large RNAs. J Mol Biol 379: 160-173.
-
(2008)
J Mol Biol
, vol.379
, pp. 160-173
-
-
Geis, M.1
Flamm, C.2
Wolfinger, M.T.3
Tanzer, A.4
Hofacker, I.L.5
Middendorf, M.6
Mandl, C.7
Stadler, P.F.8
Thurner, C.9
-
37
-
-
0032570280
-
Stability of RNA hairpins closed by wobble base pairs
-
DOI 10.1021/bi972050v
-
Giese MR, Betschart K, Dale T, Riley CK, Rowan C, Sprouse KJ, Serra MJ. 1998. Stability of RNA hairpins closed by wobble base pairs. Biochemistry 37: 1094-1100. (Pubitemid 28100612)
-
(1998)
Biochemistry
, vol.37
, Issue.4
, pp. 1094-1100
-
-
Giese, M.R.1
Betschart, K.2
Dale, T.3
Riley, C.K.4
Rowan, C.5
Sprouse, K.J.6
Serra, M.J.7
-
38
-
-
0024295554
-
Characterization of RNA hairpin loop stability
-
Groebe DR, Uhlenbeck OC. 1988. Characterization of RNA hairpin loop stability. Nucleic Acids Res 16: 11725-11735.
-
(1988)
Nucleic Acids Res
, vol.16
, pp. 11725-11735
-
-
Groebe, D.R.1
Uhlenbeck, O.C.2
-
39
-
-
0024579255
-
Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide
-
Groebe DR, Uhlenbeck OC. 1989. Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide. Biochemistry 28: 742-747.
-
(1989)
Biochemistry
, vol.28
, pp. 742-747
-
-
Groebe, D.R.1
Uhlenbeck, O.C.2
-
40
-
-
48449095385
-
The Vienna RNA Websuite
-
Gruber, ARR, Lorenz, R, Bernhart, SHH, Neuböck, R, Hofacker IL. 2008. The Vienna RNA Websuite. Nucleic Acids Res; 36: W70-W74.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Gruber, A.R.R.1
Lorenz, R.2
Bernhart, S.H.H.3
Neuböck, R.4
Hofacker, I.L.5
-
41
-
-
34347256404
-
Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting
-
Hansen TM, Reihani SN, Oddershede LB, Sorensen MA. 2007. Correlation between mechanical strength of messenger RNA pseudoknots and ribosomal frameshifting. Proc Natl Acad Sci 104: 5830-5835.
-
(2007)
Proc Natl Acad Sci
, vol.104
, pp. 5830-5835
-
-
Hansen, T.M.1
Reihani, S.N.2
Oddershede, L.B.3
Sorensen, M.A.4
-
42
-
-
34248632816
-
Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign
-
doi: 10.1186/1471-2105-8-130
-
Harmanci AO, Sharma G, Mathews DH. 2007. Efficient pairwise RNA structure prediction using probabilistic alignment constraints in Dynalign. BMC Bioinformatics 8: 130. doi: 10.1186/1471-2105-8-130.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 130
-
-
Harmanci, A.O.1
Sharma, G.2
Mathews, D.H.3
-
43
-
-
42449109109
-
PARTS: Probabilistic alignment for RNA joinT secondary structure prediction
-
Harmanci AO, Sharma G, Mathews DH. 2008. PARTS: Probabilistic alignment for RNA joinT secondary structure prediction. Nucleic Acids Res 36: 2406-2417.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 2406-2417
-
-
Harmanci, A.O.1
Sharma, G.2
Mathews, D.H.3
-
44
-
-
48749083055
-
NMR-assisted prediction of RNA secondary structure: Identification of a probable pseudoknot in the coding region of an R2 retrotransposon
-
Hart JM, Kennedy SD, Mathews DH, Turner DH. 2008. NMR-assisted prediction of RNA secondary structure: Identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc 130: 10233-10239.
-
(2008)
J Am Chem Soc
, vol.130
, pp. 10233-10239
-
-
Hart, J.M.1
Kennedy, S.D.2
Mathews, D.H.3
Turner, D.H.4
-
45
-
-
35748971022
-
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix
-
DOI 10.1371/journal.pcbi.0030193
-
Havgaard JH, Torarinsson E, 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
-
46
-
-
0026335264
-
Nearest-neighbor parameters for G·U mismatches: 5′GU3′/3′UG5′ is destabilizing in the contexts CGUG/GUGC, UGUA/AUGU, and AGUU/UUGA but stabilizing in GGUC/CUGG
-
He L, Kierzek R, SantaLucia J, Walter AE, Turner DH. 1991. Nearest-neighbor parameters for G·U mismatches: 5′GU3′/ 3′UG5′ is destabilizing in the contexts CGUG/GUGC, UGUA/AUGU, and AGUU/UUGA but stabilizing in GGUC/CUGG. Biochemistry 30: 11124-11132.
-
(1991)
Biochemistry
, vol.30
, pp. 11124-11132
-
-
He, L.1
Kierzek, R.2
SantaLucia, J.3
Walter, A.E.4
Turner, D.H.5
-
47
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures
-
Hofacker IL, Fontana W, Stadler PF, Bonhoeffer LS, Tacker M, 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.L.1
Fontana, W.2
Stadler, P.F.3
Bonhoeffer, L.S.4
Tacker, M.5
Schuster, P.6
-
48
-
-
0035800521
-
A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA
-
Hutvágner G, McLachlan J, Pasquinelli AE, Bálint E, Tuschl T, Zamore PD. 2001. A cellular function for the RNA-interference enzyme dicer in the maturation of the let-7 small temporal RNA. Science 293: 834-838.
-
(2001)
Science
, vol.293
, pp. 834-838
-
-
Hutvágner, G.1
McLachlan, J.2
Pasquinelli, A.E.3
Bálint, E.4
Tuschl, T.5
Zamore, P.D.6
-
49
-
-
3843114319
-
Intramolecular reaction in polycondensations. I. The theory of linear systems
-
Jacobson H, Stockmayer W. 1950. Intramolecular reaction in polycondensations. I. The theory of linear systems. J Chem Phys 18: 1600-1606.
-
(1950)
J Chem Phys
, vol.18
, pp. 1600-1606
-
-
Jacobson, H.1
Stockmayer, W.2
-
50
-
-
0024827733
-
Phylogenetic comparative analysis of RNA secondary structure
-
James BD, Olsen GJ, Pace NR. 1989. Phylogenetic comparative analysis of RNA secondary structure. Methods Enzymol 180: 227-239.
-
(1989)
Methods Enzymol
, vol.180
, pp. 227-239
-
-
James, B.D.1
Olsen, G.J.2
Pace, N.R.3
-
51
-
-
0032844970
-
RNAs that bind and change the permeability of phospholipid membranes
-
Khvorova A, Kwak Y-G, Tamkun M, Majerfeld I, Yarus M. 1999. RNAs that bind and change the permeability of phospholipid membranes. Proc Natl Acad Sci 96: 10649-10654.
-
(1999)
Proc Natl Acad Sci
, vol.96
, pp. 10649-10654
-
-
Khvorova, A.1
Kwak, Y.-G.2
Tamkun, M.3
Majerfeld, I.4
Yarus, M.5
-
52
-
-
0033607261
-
Thermodynamics of single mismatches in RNA duplexes
-
Kierzek R, Burkard ME, Turner DH. 1999. Thermodynamics of single mismatches in RNA duplexes. Biochemistry 38: 14214-14223.
-
(1999)
Biochemistry
, vol.38
, pp. 14214-14223
-
-
Kierzek, R.1
Burkard, M.E.2
Turner, D.H.3
-
53
-
-
0346458628
-
Identification of many microRNAs that copurify with polyribosomes in mammalian neurons
-
DOI 10.1073/pnas.2333854100
-
Kimb J, Krichevskyb A, Grad Y, Hayesb GD. 2004. Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci 101: 360-365. (Pubitemid 38084255)
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, Issue.1
, pp. 360-365
-
-
Kim, J.1
Krichevsky, A.2
Grad, Y.3
Hayes, G.D.4
Kosik, K.S.5
Church, G.M.6
Ruvkun, G.7
-
54
-
-
0035955374
-
Identification of novel genes coding for small expressed RNAs
-
Lagos-Quintana M, Rauhut R, Lendeckel W, Tuschl T. 2001. Identification of novel genes coding for small expressed RNAs. Science 294: 853-858.
-
(2001)
Science
, vol.294
, pp. 853-858
-
-
Lagos-Quintana, M.1
Rauhut, R.2
Lendeckel, W.3
Tuschl, T.4
-
55
-
-
0029861968
-
A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data
-
Laing LG, Hall KB. 1996. A model of the iron responsive element RNA hairpin loop structure determined from NMR and thermodynamic data. Biochemistry 35: 13586-13596.
-
(1996)
Biochemistry
, vol.35
, pp. 13586-13596
-
-
Laing, L.G.1
Hall, K.B.2
-
56
-
-
0025186882
-
Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides
-
Longfellow CE, Kierzek R, Turner DH. 1990. Thermodynamic and spectroscopic study of bulge loops in oligoribonucleotides. Biochemistry 29: 278-285.
-
(1990)
Biochemistry
, vol.29
, pp. 278-285
-
-
Longfellow, C.E.1
Kierzek, R.2
Turner, D.H.3
-
57
-
-
39149106448
-
Efficient siRNA selection using hybridization thermodynamics
-
Lu ZJ, Mathews DH. 2008. Efficient siRNA selection using hybridization thermodynamics. Nucleic Acids Res 36: 640-647.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. 640-647
-
-
Lu, Z.J.1
Mathews, D.H.2
-
58
-
-
33750214512
-
A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation
-
Lu JZ, Turner DH, Mathews DH. 2006. A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation. Nucleic Acids Res 34: 4912-4924.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 4912-4924
-
-
Lu, J.Z.1
Turner, D.H.2
Mathews, D.H.3
-
59
-
-
3342977915
-
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization
-
Mathews D. 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.1
-
60
-
-
0037154101
-
Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops
-
Mathews DH, Turner DH. 2002. Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops. Biochemistry 41: 869-880.
-
(2002)
Biochemistry
, vol.41
, pp. 869-880
-
-
Mathews, D.H.1
Turner, D.H.2
-
61
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews DH, Sabina J, Zuker M, Turner DH. 1999a. 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
-
62
-
-
0032729689
-
Predicting oligonucleotide affinity to nucleic acid targets
-
Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. 1999b. Predicting oligonucleotide affinity to nucleic acid targets. RNA 5: 1458-1469.
-
(1999)
RNA
, vol.5
, pp. 1458-1469
-
-
Mathews, D.H.1
Burkard, M.E.2
Freier, S.M.3
Wyatt, J.R.4
Turner, D.H.5
-
63
-
-
2442626706
-
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure
-
Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. 2004. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci 101: 7287-7292.
-
(2004)
Proc Natl Acad Sci
, vol.101
, pp. 7287-7292
-
-
Mathews, D.H.1
Disney, M.D.2
Childs, J.L.3
Schroeder, S.J.4
Zuker, M.5
Turner, D.H.6
-
64
-
-
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
-
65
-
-
0029805937
-
Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing
-
McDowell JA, Turner DH. 1996. Investigation of the structural basis for thermodynamic stabilities of tandem GU mismatches: Solution structure of (rGAGGUCUC)2 by two-dimensional NMR and simulated annealing. Biochemistry 35: 14077-14089.
-
(1996)
Biochemistry
, vol.35
, pp. 14077-14089
-
-
McDowell, J.A.1
Turner, D.H.2
-
66
-
-
0030739211
-
Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUG UCC)2
-
McDowell JA, He L, Chen X, Turner DH. 1997. Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUG UCC)2. Biochemistry 36: 8030-8038.
-
(1997)
Biochemistry
, vol.36
, pp. 8030-8038
-
-
McDowell, J.A.1
He, L.2
Chen, X.3
Turner, D.H.4
-
67
-
-
0033557138
-
Thermodynamics of RNA hairpins containing single internal mismatches
-
Meroueh M, Chow CS. 1999. Thermodynamics of RNA hairpins containing single internal mismatches. Nucleic Acids Res 27: 1118-1125.
-
(1999)
Nucleic Acids Res
, vol.27
, pp. 1118-1125
-
-
Meroueh, M.1
Chow, C.S.2
-
69
-
-
0028897382
-
Purine-purine mismatches in RNA helices: Evidence for protonated G.A pairs and next-nearest neighbor effects
-
Morse SE, Draper DE. 1995. Purine-purine mismatches in RNA helices: Evidence for protonated G.A pairs and next-nearest neighbor effects. Nucleic Acids Res 23: 302-306.
-
(1995)
Nucleic Acids Res
, vol.23
, pp. 302-306
-
-
Morse, S.E.1
Draper, D.E.2
-
70
-
-
15444376018
-
Stability of 3′ double nucleotide overhangs that model the 3′ ends of siRNA
-
O'Toole AS, Miller S, Serra MJ. 2005. Stability of 3′ double nucleotide overhangs that model the 3′ ends of siRNA. RNA 11: 512-516.
-
(2005)
RNA
, vol.11
, pp. 512-516
-
-
O'Toole, A.S.1
Miller, S.2
Serra, M.J.3
-
71
-
-
33746274670
-
Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson-Crick terminal base pairs
-
O'Toole AS, Miller S, Haines N, Zink MC, Serra MJ. 2006. Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson-Crick terminal base pairs. Nucleic Acids Res 34: 3338-3344.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 3338-3344
-
-
O'Toole, A.S.1
Miller, S.2
Haines, N.3
Zink, M.C.4
Serra, M.J.5
-
72
-
-
27944493648
-
Computational design and experimental validation of oligonucleotide- sensing allosteric ribozymes
-
Penchovsky R, Breaker RR. 2005. Computational design and experimental validation of oligonucleotide-sensing allosteric ribozymes. Nat Biotechnol 23: 1424-1433.
-
(2005)
Nat Biotechnol
, vol.23
, pp. 1424-1433
-
-
Penchovsky, R.1
Breaker, R.R.2
-
73
-
-
0025900996
-
Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops
-
Peritz AE, Kierzek R, Sugimoto N, Turner DH. 1991. Thermodynamic study of internal loops in oligoribonucleotides: Symmetric loops are more stable than asymmetric loops. Biochemistry 30: 6428-6436.
-
(1991)
Biochemistry
, vol.30
, pp. 6428-6436
-
-
Peritz, A.E.1
Kierzek, R.2
Sugimoto, N.3
Turner, D.H.4
-
74
-
-
0037044315
-
Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions
-
Proctor DJ, Schaak JE, Bevilacqua JM, Falzone CJ, Bevilacqua PC. 2002. Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. Biochemistry 41: 12062-12075.
-
(2002)
Biochemistry
, vol.41
, pp. 12062-12075
-
-
Proctor, D.J.1
Schaak, J.E.2
Bevilacqua, J.M.3
Falzone, C.J.4
Bevilacqua, P.C.5
-
75
-
-
4644237189
-
Fast and effective prediction of microRNA/target duplexes
-
Rehmsmeier M, Steffen P, Hochsmann M, Giegerich R. 2004. Fast and effective prediction of microRNA/target duplexes. RNA 10: 1507-1517.
-
(2004)
RNA
, vol.10
, pp. 1507-1517
-
-
Rehmsmeier, M.1
Steffen, P.2
Hochsmann, M.3
Giegerich, R.4
-
76
-
-
34447310821
-
A universal RNAi-based logic evaluator that operates in mammalian cells
-
Rinaudo K, Bleris L, Maddamsetti R, Subramanian S, Weiss R, Benenson Y. 2007. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 25: 795-801.
-
(2007)
Nat Biotechnol
, vol.25
, pp. 795-801
-
-
Rinaudo, K.1
Bleris, L.2
Maddamsetti, R.3
Subramanian, S.4
Weiss, R.5
Benenson, Y.6
-
77
-
-
0031462334
-
Measuring the thermodynamics of RNA secondary structure formation
-
SantaLucia J, Turner DH. 1997. Measuring the thermodynamics of RNA secondary structure formation. Biopolymers 44: 309-319.
-
(1997)
Biopolymers
, vol.44
, pp. 309-319
-
-
SantaLucia, J.1
Turner, D.H.2
-
78
-
-
0025082690
-
Effects of GA mismatches on the structure and thermodynamics of RNA internal loops
-
SantaLucia J, Kierzek R, Turner DH. 1990. Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. Biochemistry 29: 8813-8819.
-
(1990)
Biochemistry
, vol.29
, pp. 8813-8819
-
-
SantaLucia, J.1
Kierzek, R.2
Turner, D.H.3
-
79
-
-
12044257509
-
Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops
-
SantaLucia J, Kierzek R, Turner DH. 1991a. Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops. J Am Chem Soc 113: 4313-4322.
-
(1991)
J Am Chem Soc
, vol.113
, pp. 4313-4322
-
-
SantaLucia, J.1
Kierzek, R.2
Turner, D.H.3
-
80
-
-
0025925206
-
Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs
-
SantaLucia J, Kierzek R, Turner DH. 1991b. Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs. Biochemistry 30: 8242-8251.
-
(1991)
Biochemistry
, vol.30
, pp. 8242-8251
-
-
SantaLucia, J.1
Kierzek, R.2
Turner, D.H.3
-
81
-
-
0034622514
-
Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA
-
Schroeder SJ, Turner DH. 2000. Factors affecting the thermodynamic stability of small asymmetric internal loops in RNA. Biochemistry 39: 9257-9274.
-
(2000)
Biochemistry
, vol.39
, pp. 9257-9274
-
-
Schroeder, S.J.1
Turner, D.H.2
-
82
-
-
0035949443
-
Thermodynamic stabilities of internal loops with GU closing pairs in RNA
-
Schroeder SJ, Turner DH. 2001. Thermodynamic stabilities of internal loops with GU closing pairs in RNA. Biochemistry 40: 11509-11517.
-
(2001)
Biochemistry
, vol.40
, pp. 11509-11517
-
-
Schroeder, S.J.1
Turner, D.H.2
-
83
-
-
0030299990
-
G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides
-
Schroeder S, Kim J, Turner DH. 1996. G.A and U.U mismatches can stabilize RNA internal loops of three nucleotides. Biochemistry 35: 16105-16109.
-
(1996)
Biochemistry
, vol.35
, pp. 16105-16109
-
-
Schroeder, S.1
Kim, J.2
Turner, D.H.3
-
84
-
-
0344198177
-
Thermodynamic stability and structural features of the J4/5 Loop in a Pneumocystis carinii Group I Intron
-
Schroeder SJ, Fountain MA, Kennedy SD, Lukavsky PJ, Puglisi JD, Krugh TR, Turner DH. 2003. Thermodynamic stability and structural features of the J4/5 Loop in a Pneumocystis carinii Group I Intron. Biochemistry 42: 14184-14196.
-
(2003)
Biochemistry
, vol.42
, pp. 14184-14196
-
-
Schroeder, S.J.1
Fountain, M.A.2
Kennedy, S.D.3
Lukavsky, P.J.4
Puglisi, J.D.5
Krugh, T.R.6
Turner, D.H.7
-
85
-
-
0027247971
-
RNA hairpin loop stability depends on closing base pair
-
Serra MJ, Lyttle MH, Axenson TJ, Schadt CA, Turner DH. 1993. RNA hairpin loop stability depends on closing base pair. Nucleic Acids Res 21: 3845-3849.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 3845-3849
-
-
Serra, M.J.1
Lyttle, M.H.2
Axenson, T.J.3
Schadt, C.A.4
Turner, D.H.5
-
86
-
-
0027992843
-
A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides
-
Serra MJ, Axenson TJ, Turner DH. 1994. A model for the stabilities of RNA hairpins based on a study of the sequence dependence of stability for hairpins of six nucleotides. Biochemistry 33: 14289-14296.
-
(1994)
Biochemistry
, vol.33
, pp. 14289-14296
-
-
Serra, M.J.1
Axenson, T.J.2
Turner, D.H.3
-
87
-
-
0030890755
-
Improved parameters for the prediction of RNA hairpin stability
-
Serra MJ, Barnes TW, Betschart K, Gutierrez MJ, Sprouse KJ, Riley CK, Stewart L, Temel RE. 1997. Improved parameters for the prediction of RNA hairpin stability. Biochemistry 36: 4844-4851.
-
(1997)
Biochemistry
, vol.36
, pp. 4844-4851
-
-
Serra, M.J.1
Barnes, T.W.2
Betschart, K.3
Gutierrez, M.J.4
Sprouse, K.J.5
Riley, C.K.6
Stewart, L.7
Temel, R.E.8
-
88
-
-
3042693157
-
Pronounced instability of tandem IU base pairs in RNA
-
Serra MJ, Smolter PE, Westhof E. 2004. Pronounced instability of tandem IU base pairs in RNA. Nucleic Acids Res 32: 1824-1828.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 1824-1828
-
-
Serra, M.J.1
Smolter, P.E.2
Westhof, E.3
-
89
-
-
33748701701
-
Computational models with thermodynamic and composition features improve siRNA design
-
doi: 10.1186/1471-2105-7-65
-
Shabalina S, Spiridonov AN, Ogurtsov AY. 2006. Computational models with thermodynamic and composition features improve siRNA design. BMC Bioinformatics 7: 65. doi: 10.1186/1471-2105-7-65.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 65
-
-
Shabalina, S.1
Spiridonov, A.N.2
Ogurtsov, A.Y.3
-
90
-
-
33749341539
-
The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits
-
Shankar N, Kennedy SD, Chen G, Krugh TR, Turner DH. 2006. The NMR structure of an internal loop from 23S ribosomal RNA differs from its structure in crystals of 50s ribosomal subunits. Biochemistry 45: 11776-11789.
-
(2006)
Biochemistry
, vol.45
, pp. 11776-11789
-
-
Shankar, N.1
Kennedy, S.D.2
Chen, G.3
Krugh, T.R.4
Turner, D.H.5
-
91
-
-
13444288185
-
Compilation of tRNA sequences and sequences of tRNA genes
-
Sprinzl M, Vassilenko KS. 2005. Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Res 33: 139-140.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 139-140
-
-
Sprinzl, M.1
Vassilenko, K.S.2
-
92
-
-
32544440797
-
RNAshapes: An integrated RNA analysis package based on abstract shapes
-
Steffen P, Voss B, Rehmsmeier M, Reeder J, Giegerich R. 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
Voss, B.2
Rehmsmeier, M.3
Reeder, J.4
Giegerich, R.5
-
93
-
-
0023055766
-
Energetics of internal GU mismatches in ribooligonucleotide helixes
-
Sugimoto N, Kierzek R, Freier SM, Turner DH. 1986. Energetics of internal GU mismatches in ribooligonucleotide helixes. Biochemistry 25: 5755-5759.
-
(1986)
Biochemistry
, vol.25
, pp. 5755-5759
-
-
Sugimoto, N.1
Kierzek, R.2
Freier, S.M.3
Turner, D.H.4
-
94
-
-
0023653195
-
Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid
-
Sugimoto N, Kierzek R, Turner DH. 1987. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry 26: 4554-4558.
-
(1987)
Biochemistry
, vol.26
, pp. 4554-4558
-
-
Sugimoto, N.1
Kierzek, R.2
Turner, D.H.3
-
95
-
-
0034705119
-
Structural diversity of self-cleaving ribozymes
-
Tang J, Breaker RR. 2000. Structural diversity of self-cleaving ribozymes. Proc Natl Acad Sci 97: 5784-5789.
-
(2000)
Proc Natl Acad Sci
, vol.97
, pp. 5784-5789
-
-
Tang, J.1
Breaker, R.R.2
-
96
-
-
48449084225
-
Simulating RNA folding kinetics on approximated energy landscapes
-
Tang X, Thomas S, Tapia L, Giedroc DP, Amato NM. 2008. Simulating RNA folding kinetics on approximated energy landscapes. J Mol Biol 381: 1055-1067.
-
(2008)
J Mol Biol
, vol.381
, pp. 1055-1067
-
-
Tang, X.1
Thomas, S.2
Tapia, L.3
Giedroc, D.P.4
Amato, N.M.5
-
98
-
-
31844442382
-
Learning structured prediction models: A large margin approach
-
Bonn, Germany
-
Taskar B, Chatalbashev V, Koller D, Guestrin C. 2005. Learning structured prediction models: A large margin approach. In Proceedings of the 22nd International Conference on Machine Learning. pp. 896-903, Bonn, Germany.
-
(2005)
Proceedings of the 22nd International Conference on Machine Learning
, pp. 896-903
-
-
Taskar, B.1
Chatalbashev, V.2
Koller, D.3
Guestrin, C.4
-
99
-
-
0005822936
-
Improved estimation of secondary structure in ribonucleic acids
-
Tinoco I Jr, Borer PN, Dengler B, Levin MD, Uhlenbeck OC, Crothers DM, Bralla J. 1973. Improved estimation of secondary structure in ribonucleic acids. Nat New Biol 246: 40-41.
-
(1973)
Nat New Biol
, vol.246
, pp. 40-41
-
-
Tinoco Jr., I.1
Borer, P.N.2
Dengler, B.3
Levin, M.D.4
Uhlenbeck, O.C.5
Crothers, D.M.6
Bralla, J.7
-
100
-
-
33846972283
-
NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the structural features that shape the thermodynamic stability of GA pairs
-
Tolbert BS, Kennedy SD, Schroeder SJ, Krugh TR, Turner DH. 2007. NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: Probing the structural features that shape the thermodynamic stability of GA pairs. Biochemistry 46: 1511-1522.
-
(2007)
Biochemistry
, vol.46
, pp. 1511-1522
-
-
Tolbert, B.S.1
Kennedy, S.D.2
Schroeder, S.J.3
Krugh, T.R.4
Turner, D.H.5
-
101
-
-
33745590704
-
Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure
-
Torarinsson E, Sawera M, Havgaard JH, Fredholm M, Gorodkin J. 2006. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Res 16: 885-889.
-
(2006)
Genome Res
, vol.16
, pp. 885-889
-
-
Torarinsson, E.1
Sawera, M.2
Havgaard, J.H.3
Fredholm, M.4
Gorodkin, J.5
-
102
-
-
38349175490
-
-
PhD thesis, Department of Computer Science, University of British Columbia, Vancouver, BC, Canada
-
Tulpan DC. 2006. "Effective heuristic methods for DNA strand design." PhD thesis, Department of Computer Science, University of British Columbia, Vancouver, BC, Canada.
-
(2006)
Effective Heuristic Methods for DNA Strand Design
-
-
Tulpan, D.C.1
-
103
-
-
33744820625
-
Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change
-
Uzilov AV, Keegan JM, Mathews DH. 2006. Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change. BMC Bioinformatics 7: 173.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 173
-
-
Uzilov, A.V.1
Keegan, J.M.2
Mathews, D.H.3
-
104
-
-
4644255364
-
Stability of RNA hairpin loops closed by AU base pairs
-
Vecenie CJ, Serra MJ. 2004. Stability of RNA hairpin loops closed by AU base pairs. Biochemistry 43: 11813-11817.
-
(2004)
Biochemistry
, vol.43
, pp. 11813-11817
-
-
Vecenie, C.J.1
Serra, M.J.2
-
105
-
-
32244434006
-
Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops
-
Vecenie CJ, Morrow CV, Zyra A, Serra MJ. 2006. Sequence dependence of the stability of RNA hairpin molecules with six nucleotide loops. Biochemistry 45: 1400-1407.
-
(2006)
Biochemistry
, vol.45
, pp. 1400-1407
-
-
Vecenie, C.J.1
Morrow, C.V.2
Zyra, A.3
Serra, M.J.4
-
106
-
-
0028085964
-
The stability and structure of tandem GA mismatches in RNA depend on closing base pairs
-
Walter AE, Wu M, Turner DH. 1994. The stability and structure of tandem GA mismatches in RNA depend on closing base pairs. Biochemistry 33: 11349-11354.
-
(1994)
Biochemistry
, vol.33
, pp. 11349-11354
-
-
Walter, A.E.1
Wu, M.2
Turner, D.H.3
-
108
-
-
0037248878
-
The Protein Data Bank and structural genomics
-
DOI 10.1093/nar/gkg068
-
Westbrook J, Feng Z, Chen L, Yang H, Berman HM. 2003. The Protein Data Bank and structural genomics. Nucleic Acids Res 31: 489-491. (Pubitemid 36150437)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 489-491
-
-
Westbrook, J.1
Feng, Z.2
Chen, L.3
Yang, H.4
Berman, H.M.5
-
109
-
-
40849123031
-
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states
-
doi: 10.1371/journal.pbio.0060096
-
Wilkinson KA, Gorelick RJ, Vasa SM, Guex N, Rein A, Mathews DH, Giddings MC, Weeks KM. 2008. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states. PLoS Biol 6: e96. doi: 10.1371/journal.pbio.0060096.
-
(2008)
PLoS Biol
, vol.6
-
-
Wilkinson, K.A.1
Gorelick, R.J.2
Vasa, S.M.3
Guex, N.4
Rein, A.5
Mathews, D.H.6
Giddings, M.C.7
Weeks, K.M.8
-
110
-
-
0028917227
-
A periodic table of symmetric tandem mismatches in RNA
-
Wu M, McDowell JA, Turner DH. 1995. A periodic table of symmetric tandem mismatches in RNA. Biochemistry 34: 3204-3211.
-
(1995)
Biochemistry
, vol.34
, pp. 3204-3211
-
-
Wu, M.1
McDowell, J.A.2
Turner, D.H.3
-
111
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
Wuchty S, Fontana W, Hofacker IL, Schuster P. 1999. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 49: 145-165.
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
112
-
-
0347364655
-
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
-
Xayaphoummine A, Bucher T, Thalmann F, Isambert H. 2003. Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations. Proc Natl Acad Sci 100: 15310-15315.
-
(2003)
Proc Natl Acad Sci
, vol.100
, pp. 15310-15315
-
-
Xayaphoummine, A.1
Bucher, T.2
Thalmann, F.3
Isambert, H.4
-
113
-
-
0030815643
-
Thermodynamics of non-symmetric tandem mismatches adjacent to G.C base pairs in RNA
-
Xia T, McDowell JA, Turner DH. 1997. Thermodynamics of non-symmetric tandem mismatches adjacent to G.C base pairs in RNA. Biochemistry 36: 12486-12497.
-
(1997)
Biochemistry
, vol.36
, pp. 12486-12497
-
-
Xia, T.1
McDowell, J.A.2
Turner, D.H.3
-
114
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
-
Xia T, SantaLucia J, Burkard ME, Kierzek R, Schroeder SJ, Jiao X, Cox C, Turner DH. 1998. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37: 14719-14735.
-
(1998)
Biochemistry
, vol.37
, pp. 14719-14735
-
-
Xia, T.1
SantaLucia, J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.6
Cox, C.7
Turner, D.H.8
-
116
-
-
0043123152
-
Tools for the automatic identification and classification of RNA base pairs
-
Yang H, Jossinet F, Leontis N, Chen L, Westbrook J, Berman H, Westhof E. 2003. Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res 31: 3450-3460.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3450-3460
-
-
Yang, H.1
Jossinet, F.2
Leontis, N.3
Chen, L.4
Westbrook, J.5
Berman, H.6
Westhof, E.7
-
117
-
-
0037143573
-
Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges
-
Znosko BM, Silvestri SB, Volkman H, Boswell B, Serra MJ. 2002. Thermodynamic parameters for an expanded nearest-neighbor model for the formation of RNA duplexes with single nucleotide bulges. Biochemistry 41: 10406-10417.
-
(2002)
Biochemistry
, vol.41
, pp. 10406-10417
-
-
Znosko, B.M.1
Silvestri, S.B.2
Volkman, H.3
Boswell, B.4
Serra, M.J.5
-
118
-
-
10844231043
-
Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns
-
Znosko BM, Kennedy SD, Wille PC, Krugh TR, Turner DH. 2004. Structural features and thermodynamics of the J4/5 loop from the Candida albicans and Candida dubliniensis group I introns. Biochemistry 43: 15822-15837.
-
(2004)
Biochemistry
, vol.43
, pp. 15822-15837
-
-
Znosko, B.M.1
Kennedy, S.D.2
Wille, P.C.3
Krugh, T.R.4
Turner, D.H.5
-
119
-
-
0024477261
-
On finding all suboptimal foldings of an RNA molecule
-
Zuker M. 1989. On finding all suboptimal foldings of an RNA molecule. Science 244: 48-52.
-
(1989)
Science
, vol.244
, pp. 48-52
-
-
Zuker, M.1
-
120
-
-
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
|