-
1
-
-
0001084566
-
Secondary structure in ribonucleic acids
-
Doty, P., Boedtker, H., Fresco, J.R., Haselkorn, R. and Litt, M. (1959) Secondary structure in ribonucleic acids. Proc. Natl Acad. Sci. USA, 45, 482-499.
-
(1959)
Proc. Natl Acad. Sci. USA
, vol.45
, pp. 482-499
-
-
Doty, P.1
Boedtker, H.2
Fresco, J.R.3
Haselkorn, R.4
Litt, M.5
-
2
-
-
0002556146
-
Some molecular details of the secondary structure of ribonucleic acid
-
Fresco, J.R., Alberts, B.M. and Doty, P. (1960) Some molecular details of the secondary structure of ribonucleic acid. Nature, 188, 98-101.
-
(1960)
Nature
, vol.188
, pp. 98-101
-
-
Fresco, J.R.1
Alberts, B.M.2
Doty, P.3
-
3
-
-
0016189342
-
Stability of ribonucleic acid double-stranded helices
-
Borer, P.N., Dengler, B., Tinoco, I., Jr and Uhlenbeck, O.C. (1974) Stability of ribonucleic acid double-stranded helices. J. Mol. Biol., 86, 843-853.
-
(1974)
J. Mol. Biol.
, vol.86
, pp. 843-853
-
-
Borer, P.N.1
Dengler, B.2
Tinoco Jr., I.3
Uhlenbeck, O.C.4
-
4
-
-
0015216137
-
Estimation of secondary structure in ribonucleic acids
-
Tinoco, I. Jr and Uhlenbeck, O.C. (1971) Estimation of secondary structure in ribonucleic acids. Nature, 230, 362-367.
-
(1971)
Nature
, vol.230
, pp. 362-367
-
-
Tinoco Jr., I.1
Uhlenbeck, O.C.2
-
5
-
-
0005822936
-
Improved estimation of secondary structure in ribonucleic acids
-
Tinoco, I., Jr, Borer, P.N., Dengler, B., Levine, M.D., Uhlenbeck, O.C., Crothers,D.M. and Gralla,J. (1973) Improved estimation of secondary structure in ribonucleic acids. Nature New Biol., 246, 40-41.
-
(1973)
Nature New Biol.
, vol.246
, pp. 40-41
-
-
Tinoco Jr., I.1
Borer, P.N.2
Dengler, B.3
Levine, M.D.4
Uhlenbeck, O.C.5
Crothers, D.M.6
Gralla, J.7
-
8
-
-
0018254569
-
RNA secondary structure: A complete mathematical analysis
-
Waterman, M.S. and Smith, T.M. (1978) RNA secondary structure: a complete mathematical analysis. Math. Biosci., 42, 257-266.
-
(1978)
Math. Biosci.
, vol.42
, pp. 257-266
-
-
Waterman, M.S.1
Smith, T.M.2
-
9
-
-
0001509501
-
Secondary structure of single-stranded nucleic acids
-
Rota, G.-C. (ed.), Academic Press, NY
-
Waterman, M.S. (1978) Secondary structure of single-stranded nucleic acids. In Rota, G.-C. (ed.), Studies in Foundations and Combinatorics number 1 in Advances in Mathematics, Supplementary Studies. Academic Press, NY, pp. 167-212.
-
(1978)
Studies in Foundations and Combinatorics Number 1 in Advances in Mathematics, Supplementary Studies
, pp. 167-212
-
-
Waterman, M.S.1
-
10
-
-
0002213113
-
Algorithm for loop matchings
-
Nussinov, R., Pieczenik, G., Griggs, J.R. and Kleitman, D.J. (1978) Algorithm for loop matchings. SIAM J. Appl. Math., 35, 68-82.
-
(1978)
SIAM J. Appl. Math.
, vol.35
, pp. 68-82
-
-
Nussinov, R.1
Pieczenik, G.2
Griggs, J.R.3
Kleitman, D.J.4
-
11
-
-
0019082587
-
Fast algorithm for predicting the secondary structure of single-stranded RNA
-
Nussinov, R. and Jacobson, A.B. (1980) Fast algorithm for predicting the secondary structure of single-stranded RNA. Proc. Natl Acad. Sci. USA, 77, 6309-6313.
-
(1980)
Proc. Natl Acad. Sci. USA
, vol.77
, pp. 6309-6313
-
-
Nussinov, R.1
Jacobson, A.B.2
-
12
-
-
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
-
13
-
-
0342699024
-
Fast algorithms to determine RNA secondary structures containing multiple loops
-
Chapter 3 Sankoff,D. and Kruskal,J.B. (eds), Addison-Wesley Reading, MA
-
Sankoff, D., Kruskal, J.B., Mainville, S. and Cedergren, R.J. (1983) Fast algorithms to determine RNA secondary structures containing multiple loops. chapter 3. In Sankoff,D. and Kruskal,J.B. (eds), Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, Addison-Wesley Reading, MA, pp. 93-120.
-
(1983)
Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison
, pp. 93-120
-
-
Sankoff, D.1
Kruskal, J.B.2
Mainville, S.3
Cedergren, R.J.4
-
14
-
-
0024806949
-
Computer prediction of RNA structure
-
Zuker M. (1989) Computer prediction of RNA structure. Methods Enzymol., 180, 262-288.
-
(1989)
Methods Enzymol.
, vol.180
, pp. 262-288
-
-
Zuker, M.1
-
15
-
-
0021760092
-
A comprehensive set of sequence analysis programs for the VAX
-
Devereux, J., Haeberli, P. and Smithies, O. (1984) A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res., 12, 387-395.
-
(1984)
Nucleic Acids Res.
, vol.12
, pp. 387-395
-
-
Devereux, J.1
Haeberli, P.2
Smithies, O.3
-
16
-
-
0017719636
-
Globin mRNA sequences: Analysis of base pairing and evolutionary implications
-
Salser, W. (1977) Globin mRNA sequences: analysis of base pairing and evolutionary implications. Cold Spring Harbor Symp. Quant. Biol., 42, 985-1002.
-
(1977)
Cold Spring Harbor Symp. Quant. Biol.
, vol.42
, pp. 985-1002
-
-
Salser, W.1
-
17
-
-
0000075467
-
Improved free-energy parameters for predictions of RNA duplex stability
-
Freier, S.M., Kierzek, R., Jaeger, J.A., Sugimoto, N., Caruthers, M.M., Neilson, T. and Turner, D.H. (1986) Improved free-energy parameters for predictions of RNA duplex stability. Proc. Natl Acad. Sci. USA, 83, 9373-9377.
-
(1986)
Proc. Natl Acad. Sci. USA
, vol.83
, pp. 9373-9377
-
-
Freier, S.M.1
Kierzek, R.2
Jaeger, J.A.3
Sugimoto, N.4
Caruthers, M.M.5
Neilson, T.6
Turner, D.H.7
-
18
-
-
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
-
19
-
-
0345005029
-
Improved predictions of secondary structures for RNA
-
Jaeger, J.A., Turner, D.H. and Zuker, M. (1989) Improved predictions of secondary structures for RNA. Proc. Natl Acad. Sci. USA, 86, 7706-7710.
-
(1989)
Proc. Natl Acad. Sci. USA
, vol.86
, pp. 7706-7710
-
-
Jaeger, J.A.1
Turner, D.H.2
Zuker, M.3
-
20
-
-
0025361553
-
Predicting optimal and suboptimal secondary structure for RNA
-
Jaeger, J.A., Turner, D.H. and Zuker, M. (1990) Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol., 183, 281-306.
-
(1990)
Methods Enzymol.
, vol.183
, pp. 281-306
-
-
Jaeger, J.A.1
Turner, D.H.2
Zuker, M.3
-
21
-
-
0028249154
-
Prediction of RNA secondary structure by energy minimization
-
Chapter 23 Griffin,A.M. and Griffin,H.G. (eds), Humana Press, Inc., Totowa, NJ
-
Zuker, M. (1994) Prediction of RNA secondary structure by energy minimization. chapter 23. In Griffin,A.M. and Griffin,H.G. (eds), Computer Analysis of Sequence Data, Vol. 25, Part II, Humana Press, Inc., Totowa, NJ, pp. 267-294.
-
(1994)
Computer Analysis of Sequence Data
, vol.25
, Issue.PART II
, pp. 267-294
-
-
Zuker, M.1
-
22
-
-
0002287019
-
Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
-
Barciszewski,J. and Clark,B.F.C. (ed.), chapter 2, Kluwer Academic Publishers Dordrecht, The Netherlands
-
Zuker, M., Mathews, D.H. and Turner, D.H. (1999) Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide. In Barciszewski,J. and Clark,B.F.C. (ed.), RNA Biochemistry and Biotechnology, number 70 in NATO Science Partnership Sub-Series: 3: High Technology. chapter 2, Kluwer Academic Publishers Dordrecht, The Netherlands, pp. 11-43.
-
(1999)
RNA Biochemistry and Biotechnology, Number 70 in NATO Science Partnership Sub-Series: 3: High Technology
, pp. 11-43
-
-
Zuker, M.1
Mathews, D.H.2
Turner, D.H.3
-
23
-
-
0004286966
-
An updated recursive algorithm for RNA secondary structure prediction with improved free energy parameters
-
Chapter 15 Leontis,N.B. and SantaLucia,J.,Jr (eds), American Chemical Society Washington, DC
-
Mathews, D.H., Andre, T.C., Kim, J., Turner, D.H. and Zuker, M. (1998) An updated recursive algorithm for RNA secondary structure prediction with improved free energy parameters. chapter 15. In Leontis,N.B. and SantaLucia,J.,Jr (eds), American Chemical Society Symposium Series 682, American Chemical Society Washington, DC, pp. 246-257.
-
(1998)
American Chemical Society Symposium Series 682
, pp. 246-257
-
-
Mathews, D.H.1
Andre, T.C.2
Kim, J.3
Turner, D.H.4
Zuker, M.5
-
24
-
-
0003251874
-
RNA secondary structure prediction
-
Chapter 11.2 Beaucage,S., Bergstrom,D.E., Glick,G.D. and Jones,R.A. (eds), John Wiley & Sons New York, NY
-
Mathews, D.H., Turner, D.H. and Zuker, M. (2000) RNA secondary structure prediction. chapter 11.2. In Beaucage,S., Bergstrom,D.E., Glick,G.D. and Jones,R.A. (eds), Current Protocols in Nucleic Acid Chemistry, John Wiley & Sons New York, NY, pp. 1-10.
-
(2000)
Current Protocols in Nucleic Acid Chemistry
, pp. 1-10
-
-
Mathews, D.H.1
Turner, D.H.2
Zuker, M.3
-
25
-
-
0028000994
-
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding
-
Walter, A.E., Turner, D.H., Kim, J., Lyttle, M.H., Müller, P., Mathews, D.H. 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.E.1
Turner, D.H.2
Kim, J.3
Lyttle, M.H.4
Müller, P.5
Mathews, D.H.6
Zuker, M.7
-
26
-
-
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
-
27
-
-
0032539693
-
A unified view of polymer, dumbell, and oligonucleotide DNA nearest-neighbor thermodynamics
-
SantaLucia, J. Jr (1998) A unified view of polymer, dumbell, 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
-
28
-
-
0030875847
-
Thermodynamics and NMR of internal G·T mismatches in DNA
-
Allawi, H.T. and SantaLucia, J., Jr (1997) Thermodynamics and NMR of internal G·T mismatches in DNA. Biochemistry, 36, 10581-10594.
-
(1997)
Biochemistry
, vol.36
, pp. 10581-10594
-
-
Allawi, H.T.1
SantaLucia Jr., J.2
-
29
-
-
0032562140
-
Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA
-
Allawi, H.T. and SantaLucia, J., Jr (1998) Nearest neighbor thermodynamic parameters for internal G·A mismatches in DNA. Biochemistry, 37, 2170-2179.
-
(1998)
Biochemistry
, vol.37
, pp. 2170-2179
-
-
Allawi, H.T.1
SantaLucia Jr., J.2
-
30
-
-
0032102940
-
Thermodynamics of internal C·T mismatches in DNA
-
Allawi, H.T. and SantaLucia, J., Jr (1998) Thermodynamics of internal C·T mismatches in DNA. Nucleic Acids Res., 26, 2694-2701.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 2694-2701
-
-
Allawi, H.T.1
SantaLucia Jr., J.2
-
31
-
-
0032581024
-
Nearest-neighbor thermodynamics of internal A·C mismatches in DNA: Sequence dependence and pH effects
-
Allawi, H.T. and SantaLucia, J., Jr (1998) Nearest-neighbor thermodynamics of internal A·C mismatches in DNA: Sequence dependence and pH effects. Biochemistry, 37, 9435-9444.
-
(1998)
Biochemistry
, vol.37
, pp. 9435-9444
-
-
Allawi, H.T.1
SantaLucia Jr., J.2
-
32
-
-
0033596964
-
Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G, and T·T mismatches
-
Peyret, N., Senevirtne, P.A., Allawi, H.T. and SantaLucia, J., Jr (1999) Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A·A, C·C, G·G, and T·T mismatches. Biochemistry, 38, 3468-3477.
-
(1999)
Biochemistry
, vol.38
, pp. 3468-3477
-
-
Peyret, N.1
Senevirtne, P.A.2
Allawi, H.T.3
SantaLucia Jr., J.4
-
33
-
-
0034194135
-
Thermodynamic parameters for DNA sequences with dangling ends
-
Bommarito, S., Peyret, N. and SantaLucia, J., Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res., 28, 1929-1934.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 1929-1934
-
-
Bommarito, S.1
Peyret, N.2
SantaLucia Jr., J.3
-
35
-
-
0022422660
-
Nomenclature for incompletely specified bases in nucleic acid sequences: Recommendations 1984
-
Cornish-Bowden, A. (1985) Nomenclature for incompletely specified bases in nucleic acid sequences: recommendations 1984. Nucleic Acids Res., 13, 3021-3030.
-
(1985)
Nucleic Acids Res.
, vol.13
, pp. 3021-3030
-
-
Cornish-Bowden, A.1
-
36
-
-
0031745782
-
Using reliability information to annotate RNA secondary structures
-
Zuker,M. and Jacobson,A. (1998) Using reliability information to annotate RNA secondary structures. RNA, 4, 669-679.
-
(1998)
RNA
, vol.4
, pp. 669-679
-
-
Zuker, M.1
Jacobson, A.2
-
37
-
-
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. et al. (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
-
38
-
-
0029131459
-
'Well-determined' regions in RNA secondary structure prediction. application to small and large subunit rRNA
-
Zuker,M. and Jacobson,A.G. (1995) 'Well-determined' regions in RNA secondary structure prediction. application to small and large subunit rRNA. Nucleic Acids Res., 23, 2791-2798.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2791-2798
-
-
Zuker, M.1
Jacobson, A.G.2
-
39
-
-
0023984838
-
An improved algorithm for nucleic acid secondary structure display
-
Bruccoleri,R. 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.1
Heinrich, G.2
-
40
-
-
0036208669
-
OligoArray: Genome-scale oligonucleotide design for microarrays
-
Rouillard,J.-M., Herbert,C.J. and Zuker,M. (2002) OligoArray: Genome-scale oligonucleotide design for microarrays. Bioinformatics, 18, 486-487.
-
(2002)
Bioinformatics
, vol.18
, pp. 486-487
-
-
Rouillard, J.-M.1
Herbert, C.J.2
Zuker, M.3
-
41
-
-
0344843280
-
Prediction of hybridization and melting for double stranded nucleic acids
-
In press
-
Dimitrov,R.A. and Zuker,M. (2003) Prediction of hybridization and melting for double stranded nucleic acids. Biophys. J., in press.
-
(2003)
Biophys. J.
-
-
Dimitrov, R.A.1
Zuker, M.2
-
42
-
-
0032520637
-
Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips
-
Fotin,A.V., Drobyshev,A.L., Proudnikov,D.Y., Perov,A.N. and Mirzabekov, A.D. (1998) Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips. Nucleic Acids Res., 26, 1515-1521.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 1515-1521
-
-
Fotin, A.V.1
Drobyshev, A.L.2
Proudnikov, D.Y.3
Perov, A.N.4
Mirzabekov, A.D.5
|