-
1
-
-
0020475229
-
Structural analysis of self-replicating RNA synthesized by Qbeta replicase
-
10.1016/S0022-2836(82)80019-3, 7086897
-
Biebricher CK, Diekmann S, Luce R. Structural analysis of self-replicating RNA synthesized by Qbeta replicase. J Mol Biol 1982, 154:629-648. 10.1016/S0022-2836(82)80019-3, 7086897.
-
(1982)
J Mol Biol
, vol.154
, pp. 629-648
-
-
Biebricher, C.K.1
Diekmann, S.2
Luce, R.3
-
2
-
-
0027050568
-
In vitro recombination and terminal elongation of RNA by Q beta replicase
-
556991, 1281452
-
Biebricher CK, Luce R. In vitro recombination and terminal elongation of RNA by Q beta replicase. EMBO J 1992, 11:5129-5135. 556991, 1281452.
-
(1992)
EMBO J
, vol.11
, pp. 5129-5135
-
-
Biebricher, C.K.1
Luce, R.2
-
3
-
-
0027319272
-
Regulation of the Escherichia coli heat-shock response
-
10.1111/j.1365-2958.1993.tb01727.x, 7901731
-
Bukau B. Regulation of the Escherichia coli heat-shock response. Mol Microbiol 1993, 9:671-680. 10.1111/j.1365-2958.1993.tb01727.x, 7901731.
-
(1993)
Mol Microbiol
, vol.9
, pp. 671-680
-
-
Bukau, B.1
-
4
-
-
0035957720
-
Reversible unfolding of single RNA molecules by mechanical force
-
10.1126/science.1058498, 11326101
-
Liphardt J, Onoa B, Smith SB, Tinoco I, Bustamante C. Reversible unfolding of single RNA molecules by mechanical force. Science 2001, 292:733-737. 10.1126/science.1058498, 11326101.
-
(2001)
Science
, vol.292
, pp. 733-737
-
-
Liphardt, J.1
Onoa, B.2
Smith, S.B.3
Tinoco, I.4
Bustamante, C.5
-
5
-
-
0036428766
-
MRNA-mediated detection of environmental conditions
-
10.1007/s00203-002-0481-8, 12420159
-
Narberhaus F. mRNA-mediated detection of environmental conditions. Arch Microbiol 2002, 178:404-410. 10.1007/s00203-002-0481-8, 12420159.
-
(2002)
Arch Microbiol
, vol.178
, pp. 404-410
-
-
Narberhaus, F.1
-
6
-
-
33644884747
-
RNA thermometers
-
10.1111/j.1574-6976.2005.004.x, 16438677
-
Narberhaus F, Waldminghaus T, Chowdhury S. RNA thermometers. FEMS Microbiol Rev 2006, 30:3-16. 10.1111/j.1574-6976.2005.004.x, 16438677.
-
(2006)
FEMS Microbiol Rev
, vol.30
, pp. 3-16
-
-
Narberhaus, F.1
Waldminghaus, T.2
Chowdhury, S.3
-
7
-
-
48249104039
-
Riboswitches: emerging themes in RNA structure and function
-
10.1146/annurev.biophys.37.032807.130000, 18573075
-
Montange RK, Batey RT. Riboswitches: emerging themes in RNA structure and function. Annu Rev Biophys 2008, 37:117-133. 10.1146/annurev.biophys.37.032807.130000, 18573075.
-
(2008)
Annu Rev Biophys
, vol.37
, pp. 117-133
-
-
Montange, R.K.1
Batey, R.T.2
-
8
-
-
67650713931
-
The structural and functional diversity of metabolite-binding riboswitches
-
10.1146/annurev.biochem.78.070507.135656, 19298181
-
Roth A, Breaker RR. The structural and functional diversity of metabolite-binding riboswitches. Annu Rev Biochem 2009, 78:305-334. 10.1146/annurev.biochem.78.070507.135656, 19298181.
-
(2009)
Annu Rev Biochem
, vol.78
, pp. 305-334
-
-
Roth, A.1
Breaker, R.R.2
-
9
-
-
34548454557
-
Structural features of metabolite-sensing riboswitches
-
10.1016/j.tibs.2007.08.005, 2933830, 17764952
-
Wakeman CA, Winkler WC, Dann CE. Structural features of metabolite-sensing riboswitches. Trends Biochem Sci 2007, 32:415-424. 10.1016/j.tibs.2007.08.005, 2933830, 17764952.
-
(2007)
Trends Biochem Sci
, vol.32
, pp. 415-424
-
-
Wakeman, C.A.1
Winkler, W.C.2
Dann, C.E.3
-
10
-
-
44949246374
-
Nought may endure but mutability: spliceosome dynamics and the regulation of splicing
-
10.1016/j.molcel.2008.04.013, 2610350, 18570869
-
Smith DJ, Query CC, Konarska MM. Nought may endure but mutability: spliceosome dynamics and the regulation of splicing. Mol Cell 2008, 30:657-666. 10.1016/j.molcel.2008.04.013, 2610350, 18570869.
-
(2008)
Mol Cell
, vol.30
, pp. 657-666
-
-
Smith, D.J.1
Query, C.C.2
Konarska, M.M.3
-
11
-
-
71849084955
-
RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs
-
2784224, 19501200
-
Simon AE, Gehrke L. RNA conformational changes in the life cycles of RNA viruses, viroids, and virus-associated RNAs. Biochim Biophys Acta 2009, 1789:571-583. 2784224, 19501200.
-
(2009)
Biochim Biophys Acta
, vol.1789
, pp. 571-583
-
-
Simon, A.E.1
Gehrke, L.2
-
12
-
-
77649169870
-
MRNA secondary structures fold sequentially but exchange rapidly in vivo
-
10.1371/journal.pbio.1000307, 2817708, 20161716
-
Mahen EM, Watson PY, Cottrell JW, Fedor MJ. mRNA secondary structures fold sequentially but exchange rapidly in vivo. PLoS Biol 2010, 8:e1000307. 10.1371/journal.pbio.1000307, 2817708, 20161716.
-
(2010)
PLoS Biol
, vol.8
-
-
Mahen, E.M.1
Watson, P.Y.2
Cottrell, J.W.3
Fedor, M.J.4
-
13
-
-
0031455172
-
Antisense RNA-regulated programmed cell death
-
10.1146/annurev.genet.31.1.1, 9442888
-
Gerdes K, Gultyaev AP, Franch T, Pedersen K, Mikkelsen ND. Antisense RNA-regulated programmed cell death. Annu Rev Genet 1997, 31:1-31. 10.1146/annurev.genet.31.1.1, 9442888.
-
(1997)
Annu Rev Genet
, vol.31
, pp. 1-31
-
-
Gerdes, K.1
Gultyaev, A.P.2
Franch, T.3
Pedersen, K.4
Mikkelsen, N.D.5
-
14
-
-
0019082587
-
Fast algorithm for predicting the secondary structure of single-stranded RNA
-
10.1073/pnas.77.11.6309, 350273, 6161375
-
Nussinov R, Jacobson AB. Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc Natl Acad Sci USA 1980, 77:6309-6313. 10.1073/pnas.77.11.6309, 350273, 6161375.
-
(1980)
Proc Natl Acad Sci USA
, vol.77
, pp. 6309-6313
-
-
Nussinov, R.1
Jacobson, A.B.2
-
15
-
-
0002213113
-
Algorithms for loop matchings
-
Nussinov R, Pieczenik G, Griggs JR, Kleitman DJ. Algorithms for loop matchings. SIAM Journal on Applied Mathematics 1978, 35:68-82.
-
(1978)
SIAM Journal on Applied Mathematics
, vol.35
, pp. 68-82
-
-
Nussinov, R.1
Pieczenik, G.2
Griggs, J.R.3
Kleitman, D.J.4
-
16
-
-
0032502487
-
Barrier heights between ground states in a model of RNA secondary structure
-
Morgan S, Higgs P. Barrier heights between ground states in a model of RNA secondary structure. J Phys A 1998, 31(14):3153.
-
(1998)
J Phys A
, vol.31
, Issue.14
, pp. 3153
-
-
Morgan, S.1
Higgs, P.2
-
17
-
-
84873050372
-
An algorithm for the energy barrier problem without pseudoknots and temporary arcs
-
Thachuk C, Manuch J, Rafiey A, Mathieson LA, Stacho L, Condon A. An algorithm for the energy barrier problem without pseudoknots and temporary arcs. Pac Symp Biocomput 2010, 108-119.
-
(2010)
Pac Symp Biocomput
, pp. 108-119
-
-
Thachuk, C.1
Manuch, J.2
Rafiey, A.3
Mathieson, L.A.4
Stacho, L.5
Condon, A.6
-
18
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
10.1006/jmbi.1999.2700, 10329189
-
Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 1999, 288:911-940. 10.1006/jmbi.1999.2700, 10329189.
-
(1999)
J Mol Biol
, vol.288
, pp. 911-940
-
-
Mathews, D.H.1
Sabina, J.2
Zuker, M.3
Turner, D.H.4
-
19
-
-
0023785594
-
RNA structure prediction
-
10.1146/annurev.bb.17.060188.001123, 2456074
-
Turner DH, Sugimoto N, Freier SM. RNA structure prediction. Annu Rev Biophys Biophys Chem 1988, 17:167-192. 10.1146/annurev.bb.17.060188.001123, 2456074.
-
(1988)
Annu Rev Biophys Biophys Chem
, vol.17
, pp. 167-192
-
-
Turner, D.H.1
Sugimoto, N.2
Freier, S.M.3
-
20
-
-
0034021259
-
RNA folding at elementary step resolution
-
10.1017/S1355838200992161, 1369916, 10744018
-
Flamm C, Fontana W, Hofacker IL, Schuster P. RNA folding at elementary step resolution. RNA 2000, 6:325-338. 10.1017/S1355838200992161, 1369916, 10744018.
-
(2000)
RNA
, vol.6
, pp. 325-338
-
-
Flamm, C.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
21
-
-
0036340121
-
Barrier trees of degenerate landscapes
-
Flamm C, Hofacker IL, Stadler P, Wolfinger M. Barrier trees of degenerate landscapes. Z Phys Chem 2002, 216:155-173.
-
(2002)
Z Phys Chem
, vol.216
, pp. 155-173
-
-
Flamm, C.1
Hofacker, I.L.2
Stadler, P.3
Wolfinger, M.4
-
22
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
Wuchty S, Fontana W, Hofacker IL, Schuster P. Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers 1999, 49:145-165.
-
(1999)
Biopolymers
, vol.49
, pp. 145-165
-
-
Wuchty, S.1
Fontana, W.2
Hofacker, I.L.3
Schuster, P.4
-
23
-
-
71549170506
-
NP completeness of the direct energy barrier problem without pseudoknots
-
Berlin, Heidelberg: Springer-Verlag, Deaton R, Suyama A
-
Manuch J, Thachuk C, Stacho L, Condon A. NP completeness of the direct energy barrier problem without pseudoknots. 15th International Conference DNA Computing and Molecular Programming 2009, 106-115. Berlin, Heidelberg: Springer-Verlag, Deaton R, Suyama A., http://dx.doi.org/10.1007/978-3-642-10604-0_11
-
(2009)
15th International Conference DNA Computing and Molecular Programming
, pp. 106-115
-
-
Manuch, J.1
Thachuk, C.2
Stacho, L.3
Condon, A.4
-
24
-
-
0035257394
-
Design of multistable RNA molecules
-
10.1017/S1355838201000863, 1370083, 11233982
-
Flamm C, Hofacker IL, Maurer-Stroh S, Stadler PF, Zehl M. Design of multistable RNA molecules. RNA 2001, 7:254-265. 10.1017/S1355838201000863, 1370083, 11233982.
-
(2001)
RNA
, vol.7
, pp. 254-265
-
-
Flamm, C.1
Hofacker, I.L.2
Maurer-Stroh, S.3
Stadler, P.F.4
Zehl, M.5
-
25
-
-
0043123153
-
Vienna RNA secondary structure server
-
10.1093/nar/gkg599, 169005, 12824340
-
Hofacker IL. Vienna RNA secondary structure server. Nucleic Acids Res 2003, 31:3429-3431. 10.1093/nar/gkg599, 169005, 12824340.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
26
-
-
3543128223
-
Evaluating the predictability of conformational switching in RNA
-
10.1093/bioinformatics/bth129, 14962925
-
Voss B, Meyer C, Giegerich R. Evaluating the predictability of conformational switching in RNA. Bioinformatics 2004, 20:1573-1582. 10.1093/bioinformatics/bth129, 14962925.
-
(2004)
Bioinformatics
, vol.20
, pp. 1573-1582
-
-
Voss, B.1
Meyer, C.2
Giegerich, R.3
-
27
-
-
43049086258
-
Folding kinetics of large RNAs
-
10.1016/j.jmb.2008.02.064, 18440024
-
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C. Folding kinetics of large RNAs. J Mol Biol 2008, 379:160-173. 10.1016/j.jmb.2008.02.064, 18440024.
-
(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
-
28
-
-
77950494855
-
Computing folding pathways between RNA secondary structures
-
10.1093/nar/gkp1054, 2836545, 20044352
-
Dotu I, Lorenz WA, Van Hentenryck P, Clote P. Computing folding pathways between RNA secondary structures. Nucleic Acids Res 2010, 38:1711-1722. 10.1093/nar/gkp1054, 2836545, 20044352.
-
(2010)
Nucleic Acids Res
, vol.38
, pp. 1711-1722
-
-
Dotu, I.1
Lorenz, W.A.2
Van Hentenryck, P.3
Clote, P.4
-
29
-
-
84871238810
-
Shape-based barrier estimation for RNAs
-
Bogomolov S, Mann M, Voß B, Podelski A, Backofen R. Shape-based barrier estimation for RNAs. German Conference on Bioinformatics 2010, 41-50.
-
(2010)
German Conference on Bioinformatics
, pp. 41-50
-
-
Bogomolov, S.1
Mann, M.2
Voß, B.3
Podelski, A.4
Backofen, R.5
-
31
-
-
43749099405
-
Beyond energy minimization: Approaches to the kinetic folding of RNA
-
Flamm C, Hofacker IL. Beyond energy minimization: Approaches to the kinetic folding of RNA. Monatsh Chem 2008, 139:447-457.
-
(2008)
Monatsh Chem
, vol.139
, pp. 447-457
-
-
Flamm, C.1
Hofacker, I.L.2
-
32
-
-
57549096731
-
Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs
-
10.1016/j.cbpa.2008.09.017, 2739931, 18926923
-
Shcherbakova I, Mitra S, Laederach A, Brenowitz M. Energy barriers, pathways, and dynamics during folding of large, multidomain RNAs. Curr Opin Chem Biol 2008, 12:655-666. 10.1016/j.cbpa.2008.09.017, 2739931, 18926923.
-
(2008)
Curr Opin Chem Biol
, vol.12
, pp. 655-666
-
-
Shcherbakova, I.1
Mitra, S.2
Laederach, A.3
Brenowitz, M.4
-
33
-
-
27844604240
-
A complex adaptive systems approach to the kinetic folding of RNA
-
10.1016/j.biosystems.2005.08.004, 16171941
-
Ndifon W. A complex adaptive systems approach to the kinetic folding of RNA. Biosystems 2005, 82:257-265. 10.1016/j.biosystems.2005.08.004, 16171941.
-
(2005)
Biosystems
, vol.82
, pp. 257-265
-
-
Ndifon, W.1
-
34
-
-
33748621478
-
Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterizaion of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs
-
Sponer J, Leszczynski J, Hobza P. Nature of nucleic acid-base stacking: nonempirical ab initio and empirical potential characterizaion of 10 stacked base dimers. Comparison of stacked and H-bonded base pairs. J Phys Chem 1996, 100(13):5590-5596.
-
(1996)
J Phys Chem
, vol.100
, Issue.13
, pp. 5590-5596
-
-
Sponer, J.1
Leszczynski, J.2
Hobza, P.3
-
35
-
-
32644434270
-
Base-stacking and base-pairing contributions into thermal stability of the DNA double helix
-
10.1093/nar/gkj454, 1360284, 16449200
-
Yakovchuk P, Protozanova E, Frank-Kamenetskii MD. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 2006, 34:564-574. 10.1093/nar/gkj454, 1360284, 16449200.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 564-574
-
-
Yakovchuk, P.1
Protozanova, E.2
Frank-Kamenetskii, M.D.3
-
36
-
-
77951637361
-
Predicting secondary structural folding kinetics for nucleic acids
-
10.1016/j.bpj.2009.12.4319, 2856163, 20409482
-
Zhao P, Zhang WB, Chen SJ. Predicting secondary structural folding kinetics for nucleic acids. Biophys J 2010, 98:1617-1625. 10.1016/j.bpj.2009.12.4319, 2856163, 20409482.
-
(2010)
Biophys J
, vol.98
, pp. 1617-1625
-
-
Zhao, P.1
Zhang, W.B.2
Chen, S.J.3
-
37
-
-
27844448362
-
Evolutionary computing: the most powerful problem solver in the universe?
-
Eiben A. Evolutionary computing: the most powerful problem solver in the universe?. Dutch Mathematical Archive 2002, 5:126-131.
-
(2002)
Dutch Mathematical Archive
, vol.5
, pp. 126-131
-
-
Eiben, A.1
-
38
-
-
33645984848
-
Consensus folding of unaligned RNA sequences revisited
-
10.1089/cmb.2006.13.283, 16597240
-
Bafna V, Tang H, Zhang S. Consensus folding of unaligned RNA sequences revisited. J Comput Biol 2006, 13:283-295. 10.1089/cmb.2006.13.283, 16597240.
-
(2006)
J Comput Biol
, vol.13
, pp. 283-295
-
-
Bafna, V.1
Tang, H.2
Zhang, S.3
-
39
-
-
0038210214
-
Riboswitches control fundamental biochemical pathways in Bacillus subtilis and other bacteria
-
10.1016/S0092-8674(03)00391-X, 12787499
-
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. 10.1016/S0092-8674(03)00391-X, 12787499.
-
(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
-
40
-
-
84874518862
-
PaRNAss
-
paRNAss. , http://bibiserv.techfak.uni-bielefeld.de/parnass/examples.html
-
-
-
-
41
-
-
34548604264
-
Boltzmann probability of RNA structural neighbors and riboswitch detection
-
10.1093/bioinformatics/btm314, 17573364
-
Freyhult E, Moulton V, Clote P. Boltzmann probability of RNA structural neighbors and riboswitch detection. Bioinformatics 2007, 23:2054-2062. 10.1093/bioinformatics/btm314, 17573364.
-
(2007)
Bioinformatics
, vol.23
, pp. 2054-2062
-
-
Freyhult, E.1
Moulton, V.2
Clote, P.3
|