-
1
-
-
0031828145
-
Destabilizing effect of an rRNA stem-loop on an attenuator hairpin in the 5′ exon of the Tetrahymena pre-rRNA
-
Cao,Y. and Woodson,S. (1998) Destabilizing effect of an rRNA stem-loop on an attenuator hairpin in the 5′ exon of the Tetrahymena pre-rRNA. RNA, 4, 901-914.
-
(1998)
RNA
, vol.4
, pp. 901-914
-
-
Cao, Y.1
Woodson, S.2
-
2
-
-
0037096843
-
Regulated HIV-2 RNA dimerization by means of alternative RNA conformations
-
Dirac,A., Huthoff,H., Kjems,J. and Berkhout,B. (2002) Regulated HIV-2 RNA dimerization by means of alternative RNA conformations. Nucleic Acids Res., 30, 2647-2655.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 2647-2655
-
-
Dirac, A.1
Huthoff, H.2
Kjems, J.3
Berkhout, B.4
-
3
-
-
0038476616
-
The riboswitch-mediated control of sulfur metabolism in bacteria
-
Epshtein,V., Mironov,A. and Nudler,E. (2003) The riboswitch-mediated control of sulfur metabolism in bacteria. Proc. Natl Acad. Sci., USA, 100, 5052-5056.
-
(2003)
Proc. Natl. Acad. Sci. USA
, vol.100
, pp. 5052-5056
-
-
Epshtein, V.1
Mironov, A.2
Nudler, E.3
-
4
-
-
0021064616
-
Escherichia coli phenylalanyl-tRNA synthetase operon region
-
Fayat,G., Mayaux,J., Sacerdot,C., Formant,M., Springer,M., Grunberg-Manago,M. and Blanquet,S. (1983) Escherichia coli phenylalanyl-tRNA synthetase operon region. J. Mol. Biol., 171, 239-261.
-
(1983)
J. Mol. Biol.
, vol.171
, pp. 239-261
-
-
Fayat, G.1
Mayaux, J.2
Sacerdot, C.3
Formant, M.4
Springer, M.5
Grunberg-Manago, M.6
Blanquet, S.7
-
5
-
-
0035257394
-
Design of multistable RNA molecules
-
Flamm,C., Hofacker,I., Maurer-Stroh,S., Stadler,P. and Zehl,M. (2001) Design of multistable RNA molecules. RNA, 7, 254-265.
-
(2001)
RNA
, vol.7
, pp. 254-265
-
-
Flamm, C.1
Hofacker, I.2
Maurer-Stroh, S.3
Stadler, P.4
Zehl, M.5
-
6
-
-
0036340121
-
Barrier trees of degenerate landscapes
-
Flamm,C., Hofacker,I., Stadler,P. and Wolfinger,M. (2002) Barrier trees of degenerate landscapes. Z. Phys. Chem., 216, 155-173.
-
(2002)
Z. Phys. Chem.
, vol.216
, pp. 155-173
-
-
Flamm, C.1
Hofacker, I.2
Stadler, P.3
Wolfinger, M.4
-
7
-
-
0031576356
-
Programmed cell death by hok/sok of plasmid R1: Processing at the hok mRNA 3′-end triggers structural rearrangements that allow translation and antisense RNA binding
-
Franch,T., Gultyaev,A., Öistämö,K., Gerdes,K. and Pleij,C. (1997) Programmed cell death by hok/sok of plasmid R1: processing at the hok mRNA 3′-end triggers structural rearrangements that allow translation and antisense RNA binding. J. Mol. Biol., 273, 38-51.
-
(1997)
J. Mol. Biol.
, vol.273
, pp. 38-51
-
-
Franch, T.1
Gultyaev, A.2
Öistämö, K.3
Gerdes, K.4
Pleij, C.5
-
9
-
-
3543066685
-
From RNA folding to thermodynamic matching, including pseudoknots
-
Technical Report Nr 2003-03 Technische Fakultät, Universität Bielefeld
-
Giegerich,R. and Reeder,J. (2003) From RNA folding to thermodynamic matching, including pseudoknots. Technical Report Nr 2003-03, Technische Fakultät, Universität Bielefeld.
-
(2003)
-
-
Giegerich, R.1
Reeder, J.2
-
10
-
-
0029258675
-
Translational control of maturation-protein synthesis in phage MS2: A role for the kinetics of RNA folding?
-
Groeneveld,H., Thimon,K. and van Duin,J. (1995) Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? RNA, 1, 79-88.
-
(1995)
RNA
, vol.1
, pp. 79-88
-
-
Groeneveld, H.1
Thimon, K.2
van Duin, J.3
-
11
-
-
84960387766
-
Local similarity in RNA secondary structures
-
Höchsmann,M., Töller,T., Giegerich,R. and Kurtz,S. (2003) Local similarity in RNA secondary structures. Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB), pp. 159-168.
-
(2003)
Proceedings of the IEEE Computer Society Bioinformatics Conference (CSB)
, pp. 159-168
-
-
Höchsmann, M.1
Töller, T.2
Giegerich, R.3
Kurtz, S.4
-
12
-
-
34249772381
-
Fast folding and comparison of RNA secondary structures (the Vienna RNA package)
-
Hofacker,I., Fontana,W., Stadler,P., Bonhoeffer,L., Tacker,M. and Schuster,P. (1994) Fast folding and comparison of RNA secondary structures (the Vienna RNA package). Chem. Monthly, 125, 167-188.
-
(1994)
Chem. Monthly
, vol.125
, pp. 167-188
-
-
Hofacker, I.1
Fontana, W.2
Stadler, P.3
Bonhoeffer, L.4
Tacker, M.5
Schuster, P.6
-
13
-
-
0035038089
-
Two alternating structures of the HIV-1 leader RNA
-
Huthoff,H. and Berkhout,B. (2001) Two alternating structures of the HIV-1 leader RNA. RNA, 7, 143-157.
-
(2001)
RNA
, vol.7
, pp. 143-157
-
-
Huthoff, H.1
Berkhout, B.2
-
14
-
-
0037388109
-
Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures
-
Kitagawa,J., Futamura,Y. and Yamamoto,K. (2003) Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures. Nucleic Acids Res., 31, 2006-2013.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 2006-2013
-
-
Kitagawa, J.1
Futamura, Y.2
Yamamoto, K.3
-
15
-
-
0029295386
-
Regulation of the hepatitis delta virus ribozymes: To cleave or not to cleave?
-
Lazinski,D. and Taylor,J. (1995) Regulation of the hepatitis delta virus ribozymes: to cleave or not to cleave? RNA, 1, 225-233.
-
(1995)
RNA
, vol.1
, pp. 225-233
-
-
Lazinski, D.1
Taylor, J.2
-
16
-
-
0034730125
-
A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures
-
Lease,R. and Belfort,M. (2000) A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structures. Proc. Natl Acad. Sci., USA, 97, 9919-9924.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 9919-9924
-
-
Lease, R.1
Belfort, M.2
-
17
-
-
0027173194
-
The Leptomonas collosoma Spliced Leader RNA can switch between two alternate structural forms
-
LeCuyer,K. and Crothers,D. (1993) The Leptomonas collosoma Spliced Leader RNA can switch between two alternate structural forms. Biochemistry, 32, 5301-5311.
-
(1993)
Biochemistry
, vol.32
, pp. 5301-5311
-
-
LeCuyer, K.1
Crothers, D.2
-
18
-
-
0026486883
-
A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome
-
Madhani,H. and Guthrie,C. (1992) A novel base-pairing interaction between U2 and U6 snRNAs suggests a mechanism for the catalytic activation of the spliceosome. Cell, 71, 803-817.
-
(1992)
Cell
, vol.71
, pp. 803-817
-
-
Madhani, H.1
Guthrie, C.2
-
19
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure
-
Mathews,D., Sabina,J., Zucker,M. and Turner,H. (1999) Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol., 288, 911-940.
-
(1999)
J. Mol. Biol.
, vol.288
, pp. 911-940
-
-
Mathews, D.1
Sabina, J.2
Zucker, M.3
Turner, H.4
-
20
-
-
0036753365
-
Genetic control by a metabolite binding mRNA
-
Nahvi,A., Sudarsan,N., Ebert,M., Zou,X., Brown,K. and Breaker,R. (2002) Genetic control by a metabolite binding mRNA. Chem. Biol., 9, 1043-1049.
-
(2002)
Chem. Biol.
, vol.9
, pp. 1043-1049
-
-
Nahvi, A.1
Sudarsan, N.2
Ebert, M.3
Zou, X.4
Brown, K.5
Breaker, R.6
-
21
-
-
0033198767
-
A conformational switch at the 3′ end of a plant virus RNA regulates viral replication
-
Olsthoorn,R., Mertens,S., Brederode,F. and Bol,J. (1999) A conformational switch at the 3′ end of a plant virus RNA regulates viral replication. EMBO J., 18, 4856-4864.
-
(1999)
EMBO J.
, vol.18
, pp. 4856-4864
-
-
Olsthoorn, R.1
Mertens, S.2
Brederode, F.3
Bol, J.4
-
22
-
-
0036087522
-
UTRdb and UTRsite: Specialized database of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002
-
Pesole,G., Luini,S., Grillo,G., Licciulli,F., Mignone,F., Gissi,C. and Saccone,C. (2002) UTRdb and UTRsite: specialized database of sequences and functional elements of 5′ and 3′ untranslated regions of eukaryotic mRNAs. Update 2002. Nucleic Acids Res., 30, 335-340.
-
(2002)
Nucleic Acids Res.
, vol.30
, pp. 335-340
-
-
Pesole, G.1
Luini, S.2
Grillo, G.3
Licciulli, F.4
Mignone, F.5
Gissi, C.6
Saccone, C.7
-
23
-
-
0028838032
-
Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15
-
Philippe,C., Benard,L., Portier,C., Westhof,E., Ehresmann,B. and Ehresmann,C. (1995) Molecular dissection of the pseudoknot governing the translational regulation of Escherichia coli ribosomal protein S15. Nucleic Acids Res., 23, 18-28.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 18-28
-
-
Philippe, C.1
Benard, L.2
Portier, C.3
Westhof, E.4
Ehresmann, B.5
Ehresmann, C.6
-
24
-
-
0033524952
-
A dynamic programming algorithm for RNA structure prediction including pseudoknots
-
Rivas,E. and Eddy,S. (1999) A dynamic programming algorithm for RNA structure prediction including pseudoknots. J. Mol. Biol., 285, 2053-2068.
-
(1999)
J. Mol. Biol.
, vol.285
, pp. 2053-2068
-
-
Rivas, E.1
Eddy, S.2
-
25
-
-
0035914362
-
Translational repression of the Escherichia coli α operon mRNA
-
Schlax,P., Xavier,K.A., Gluick,T. and Draper,D. (2001) Translational repression of the Escherichia coli α operon mRNA. J. Biol. Chem., 276, 38494-38501.
-
(2001)
J. Biol. Chem.
, vol.276
, pp. 38494-38501
-
-
Schlax, P.1
Xavier, K.A.2
Gluick, T.3
Draper, D.4
-
26
-
-
0028196714
-
From sequences to shapes and back: A case study in RNA secondary structures
-
Schuster,P., Fontana,W., Stadler,P. and Hofacker,I. (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc. R. Soc. Lond. B, 255, 279-284.
-
(1994)
Proc. R. Soc. Lond. B
, vol.255
, pp. 279-284
-
-
Schuster, P.1
Fontana, W.2
Stadler, P.3
Hofacker, I.4
-
27
-
-
0032079494
-
A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo
-
Semrad,K. and Schroeder,R. (1998) A ribosomal function is necessary for efficient splicing of the T4 phage thymidylate synthase intron in vivo. Genes Dev., 12, 1327-1337.
-
(1998)
Genes Dev.
, vol.12
, pp. 1327-1337
-
-
Semrad, K.1
Schroeder, R.2
-
28
-
-
0025187499
-
Comparing multiple RNA secondary structures using tree comparisons
-
Shapiro,B. and Zhang,K. (1990) Comparing multiple RNA secondary structures using tree comparisons. CABIOS, 6, 309-318.
-
(1990)
CABIOS
, vol.6
, pp. 309-318
-
-
Shapiro, B.1
Zhang, K.2
-
29
-
-
0028000994
-
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
-
Walter,A., Turner,D., Kim,J., Lyttle,M., Müller,P., Mathews,D. and Zuker,M. (1994) Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc. Natl Acad. Sci., USA, 91, 9218-9222.
-
(1994)
Proc. Natl. Acad. Sci. USA
, vol.91
, pp. 9218-9222
-
-
Walter, A.1
Turner, D.2
Kim, J.3
Lyttle, M.4
Müller, P.5
Mathews, D.6
Zuker, M.7
-
30
-
-
84944178665
-
Hierarchical grouping to optimize an objective function
-
Ward,J. (1963) Hierarchical grouping to optimize an objective function. JASA, 58, 236-244.
-
(1963)
JASA
, vol.58
, pp. 236-244
-
-
Ward, J.1
-
32
-
-
0037058920
-
An mRNA structure that controls gene expression by binding FMN
-
Winkler,W., Cohen-Chalamish,S. and Breaker,R. (2002a) An mRNA structure that controls gene expression by binding FMN. Proc. Natl Acad. Sci., USA, 99, 15908-15913.
-
(2002)
Proc. Natl. Acad. Sci. USA
, vol.99
, pp. 15908-15913
-
-
Winkler, W.1
Cohen-Chalamish, S.2
Breaker, R.3
-
33
-
-
0037206833
-
Thiamine derivatives bind messenger RNAs directly to regulate gene expression
-
Winkler,W., Nahvi,A. and Breaker,R. (2002b) Thiamine derivatives bind messenger RNAs directly to regulate gene expression. Nature, 419, 952-956.
-
(2002)
Nature
, vol.419
, pp. 952-956
-
-
Winkler, W.1
Nahvi, A.2
Breaker, R.3
-
34
-
-
0026690643
-
Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation
-
Wool,I., Glück,A. and Endo,Y. (1992) Ribotoxin recognition of ribosomal RNA and a proposal for the mechanism of translocation. Trends Biochem. Sci., 17, 266-269.
-
(1992)
Trends Biochem. Sci.
, vol.17
, pp. 266-269
-
-
Wool, I.1
Glück, A.2
Endo, Y.3
-
35
-
-
0033572893
-
No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution
-
Workman,C. and Krogh,A. (1999) No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution. Nucleic Acids Res., 27, 4816-4822.
-
(1999)
Nucleic Acids Res.
, vol.27
, pp. 4816-4822
-
-
Workman, C.1
Krogh, A.2
-
36
-
-
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
-
37
-
-
0002287019
-
Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
-
Barciszewski,J. and Clark,B. (eds), NATO ASI Series, Kluwer Academic Publishers
-
Zuker,M., Mathews,D. and Turner,D. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide. In Barciszewski,J. and Clark,B. (eds), RNA Biochemistry and Biotechnology. NATO ASI Series, Kluwer Academic Publishers.
-
(1999)
RNA Biochemistry and Biotechnology
-
-
Zuker, M.1
Mathews, D.2
Turner, D.3
|