-
1
-
-
0019876473
-
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information
-
Zuker,M. and Stiegler,P. (1981). Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9, 133-148.
-
(1981)
Nucleic Acids Res.
, vol.9
, pp. 133-148
-
-
Zuker, M.1
Stiegler, P.2
-
2
-
-
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
-
3
-
-
0033080745
-
Complete suboptimal folding of RNA and the stability of secondary structures
-
Wuchty,S., Fontana,W., Hofacker,I.L. and 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
-
4
-
-
0025264854
-
The equilibrium partition function and base pair binding probabilities for RNA secondary structure
-
McCaskill,J.S. (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
-
5
-
-
0346888665
-
A statistical sampling algorithm for RNA secondary structure prediction
-
Ding,Y. and Lawrence,C.E. (2003) A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Res., 31, 7280-7301.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 7280-7301
-
-
Ding, Y.1
Lawrence, C.E.2
-
6
-
-
0011883768
-
Application of computational technologies to ribozyme biotechnology products
-
Christoffersen,R.E., McSwiggen,J.A. and Konings,D. (1994) Application of computational technologies to ribozyme biotechnology products. J. Mol. Structure (Theochem), 311, 273-284.
-
(1994)
J. Mol. Structure (Theochem)
, vol.311
, pp. 273-284
-
-
Christoffersen, R.E.1
McSwiggen, J.A.2
Konings, D.3
-
7
-
-
0032552882
-
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs
-
Xia,T., SantaLucia,J.Jr, Burkard,M.E., Kierzek,R., Schroeder,S.J., Jiao,X., Cox,C. and Turner,D.H. (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 Jr., J.2
Burkard, M.E.3
Kierzek, R.4
Schroeder, S.J.5
Jiao, X.6
Cox, C.7
Turner, D.H.8
-
8
-
-
0033591465
-
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
-
Mathews,D.H., Sabina,J., Zuker,M. and Turner,D.H. (1999) 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
-
9
-
-
0036256430
-
Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells
-
Lee,N.S., Dohjima,T., Bauer,G., Li,H., Li,M.J., Ehsani,A., Salvaterra,P. and Rossi,J. (2002) Expression of small interfering RNAs targeted against HIV-1 rev transcripts in human cells. Nature Biotechnol., 20, 500-505.
-
(2002)
Nature Biotechnol.
, vol.20
, pp. 500-505
-
-
Lee, N.S.1
Dohjima, T.2
Bauer, G.3
Li, H.4
Li, M.J.5
Ehsani, A.6
Salvaterra, P.7
Rossi, J.8
-
10
-
-
0038521255
-
The efficacy of small interfering RNAs targeted to the type 1 Insulin- like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript
-
Bohula,E.A., Salisbury,A.J., Sohail,M., Playford,M.P., Riedemann,J., Southern,E.M. and Macaulay,V.M. (2003) The efficacy of small interfering RNAs targeted to the type 1 Insulin- like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript. J. Biol. Chem., 278, 15991-15997.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 15991-15997
-
-
Bohula, E.A.1
Salisbury, A.J.2
Sohail, M.3
Playford, M.P.4
Riedemann, J.5
Southern, E.M.6
Macaulay, V.M.7
-
11
-
-
0042161890
-
The activity of siRNA in mammalian cells is related to structural target accessibility: A comparison with antisense oligonucleotides
-
Far,R.K. and Sczakiel,G. (2003) The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides. Nucleic Acids Res., 31, 4417-4424
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4417-4424
-
-
Far, R.K.1
Sczakiel, G.2
-
12
-
-
0037470145
-
Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis
-
Vickers,T.A., Koo,S., Bennett,C.F., Crooke,S.T., Dean,N.M. and Baker,B. (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis. J. Biol. Chem., 278, 7108-7118.
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 7108-7118
-
-
Vickers, T.A.1
Koo, S.2
Bennett, C.F.3
Crooke, S.T.4
Dean, N.M.5
Baker, B.6
-
13
-
-
0035283171
-
Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond
-
Ding,Y. and Lawrence,C.E. (2001) Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyond. Nucleic Acids Res., 29, 1034-1046.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 1034-1046
-
-
Ding, Y.1
Lawrence, C.E.2
-
14
-
-
10744225153
-
Asymmetry in the assembly of the RNAi enzyme complex
-
Schwarz,D.S., Hutvagner,G., Du,T., Xu,Z., Aronin,N. and Zamore,P.D. (2003) Asymmetry in the assembly of the RNAi enzyme complex. Cell, 115, 199-208.
-
(2003)
Cell
, vol.115
, pp. 199-208
-
-
Schwarz, D.S.1
Hutvagner, G.2
Du, T.3
Xu, Z.4
Aronin, N.5
Zamore, P.D.6
-
15
-
-
0142165224
-
Functional siRNAs and miRNAs exhibit strand bias
-
Khvorova,A., Reynolds,A. and Jayasena,S.D. (2003) Functional siRNAs and miRNAs exhibit strand bias. Cell, 115, 209-216.
-
(2003)
Cell
, vol.115
, pp. 209-216
-
-
Khvorova, A.1
Reynolds, A.2
Jayasena, S.D.3
-
17
-
-
0026530570
-
Cation-dependent transition between the quadruplex and Watson-Crick hairpin forms of d(CGCG3GCG)
-
Hardin,C.C., Watson,T., Corregan,M. and Bailey,C. (1992) Cation-dependent transition between the quadruplex and Watson-Crick hairpin forms of d(CGCG3GCG). Biochemistry, 31, 833-841.
-
(1992)
Biochemistry
, vol.31
, pp. 833-841
-
-
Hardin, C.C.1
Watson, T.2
Corregan, M.3
Bailey, C.4
-
18
-
-
1542336952
-
Rational siRNA design for RNA interference
-
Reynolds,A., Leake,D., Boese,Q., Scaringe,S., Marshall,W.S. and Khvorova,A. (2004) Rational siRNA design for RNA interference. Nature Biotechnol., 22, 326-330.
-
(2004)
Nature Biotechnol.
, vol.22
, pp. 326-330
-
-
Reynolds, A.1
Leake, D.2
Boese, Q.3
Scaringe, S.4
Marshall, W.S.5
Khvorova, A.6
-
19
-
-
1642346273
-
Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference
-
Ui-Tei,K, Naito,Y., Takahashi,F., Haraguchi,T., Ohki-Hamazaki,H., Juni,A., Ueda,R. and Saigo,K. (2004) Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference. Nucleic Acids Res., 32, 936-948
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 936-948
-
-
Ui-Tei, K.1
Naito, Y.2
Takahashi, F.3
Haraguchi, T.4
Ohki-Hamazaki, H.5
Juni, A.6
Ueda, R.7
Saigo, K.8
-
20
-
-
1642273831
-
An algorithm for selection of functional siRNA sequences
-
Amarzguioui,M. and Prydz,H. (2004) An algorithm for selection of functional siRNA sequences. Biochem. Biophys. Res. Commun. 316, 1050-1058.
-
(2004)
Biochem. Biophys. Res. Commun.
, vol.316
, pp. 1050-1058
-
-
Amarzguioui, M.1
Prydz, H.2
-
21
-
-
0029134549
-
Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes
-
Sugimoto,N., Nakano,S., Katoh,M., Matsumura,A., Nakamuta,H., Ohmichi,T., Yoneyama,M. and Sasaki,M. (1995) Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes. Biochemistry, 34, 11211-11216.
-
(1995)
Biochemistry
, vol.34
, pp. 11211-11216
-
-
Sugimoto, N.1
Nakano, S.2
Katoh, M.3
Matsumura, A.4
Nakamuta, H.5
Ohmichi, T.6
Yoneyama, M.7
Sasaki, M.8
-
22
-
-
0030902471
-
Selecting effective antisense reagents on combinatorial oligonucleotide arrays
-
Milner,N., Mir,K.U. and Southern,E.M. (1997). Selecting effective antisense reagents on combinatorial oligonucleotide arrays. Nature Biotechnol., 15, 537-541.
-
(1997)
Nature Biotechnol.
, vol.15
, pp. 537-541
-
-
Milner, N.1
Mir, K.U.2
Southern, E.M.3
-
23
-
-
0027173194
-
The Leptomonas collosoma spliced leader RNA can switch between two alternate structural forms
-
LeCuyer,K.A. and Crothers,D.M. (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.A.1
Crothers, D.M.2
-
24
-
-
0023984838
-
An improved algorithm for nucleic acid secondary structure display
-
Bruccoleri,R.E. and Heinrich, G. (1988) An improved algorithm for nucleic acid secondary structure display. Comput. Appl. Biosci., 4, 167-173.
-
(1988)
Comput. Appl. Biosci.
, vol.4
, pp. 167-173
-
-
Bruccoleri, R.E.1
Heinrich, G.2
-
25
-
-
0032539693
-
A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
-
SantaLucia,J.Jr (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA., 95, 1460-1465.
-
(1998)
Proc. Natl. Acad. Sci. USA
, vol.95
, pp. 1460-1465
-
-
SantaLucia Jr., J.1
-
26
-
-
0004322434
-
Studies of DNA dumbbells VII: Evaluation of the next-nearest-neighbor sequence-dependent interactions in duplex DNA
-
Owczarzy,R., Vallone,P.M., Goldstein,R.F. and Benight,A.S. (1999) Studies of DNA dumbbells VII: evaluation of the next-nearest-neighbor sequence-dependent interactions in duplex DNA. Biopolymers, 52, 29-56.
-
(1999)
Biopolymers
, vol.52
, pp. 29-56
-
-
Owczarzy, R.1
Vallone, P.M.2
Goldstein, R.F.3
Benight, A.S.4
-
27
-
-
0344012459
-
Thermodynamic criteria for high hit rate antisense oligonucleotide design
-
Matveeva,O.V., Mathews,D.H., Tsodikov,A.D., Shabalina,S.A., Gesteland,R.F., Atkins,J.F. and Freier,S.M. (2003) Thermodynamic criteria for high hit rate antisense oligonucleotide design. Nucleic Acids Res., 31, 4989-4994.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 4989-4994
-
-
Matveeva, O.V.1
Mathews, D.H.2
Tsodikov, A.D.3
Shabalina, S.A.4
Gesteland, R.F.5
Atkins, J.F.6
Freier, S.M.7
-
28
-
-
18444386491
-
RNAML: A standard syntax for exchanging RNA information
-
Waugh,A., Gendron,P., Altman,R., Brown,J.W., Case, D., Gautheret, D., Harvey, S.C., Leontis,N., Westbrook,J., Westhof,E., Zuker,M. and Major,F. (2002) RNAML: a standard syntax for exchanging RNA information. RNA, 8, 707-717.
-
(2002)
RNA
, vol.8
, pp. 707-717
-
-
Waugh, A.1
Gendron, P.2
Altman, R.3
Brown, J.W.4
Case, D.5
Gautheret, D.6
Harvey, S.C.7
Leontis, N.8
Westbrook, J.9
Westhof, E.10
Zuker, M.11
Major, F.12
-
29
-
-
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
|