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REFERENCES
Note: OCR errors may be found in this Reference List extracted from the full text article. ACM has opted to expose the complete List rather than only correct and linked references.
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1
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D. H. Burke, D. Hoffman, A. Brown, M. Hansen, A. Pardi, and L. Gold. RNA aptamers to the peptidyl transferase inhibitor chloramphenicol.Chem. Biol., 4:833--843, 1997.
|
| |
2
|
J. A. Doudna and T. R. Cech. The chemical repertoire of natural ribozymes. Nature 418:222--228, 2002.
|
| |
3
|
R. Durbin, S. Eddy, A. Krogh, and G. Mitchison. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids Cambridge University Press, 1998.
|
| |
4
|
Hin Hark Gan , Daniela Fera , Julie Zorn , Nahum Shiffeldrim , Michael Tang , Uri Laserson , Namhee Kim , Tamar Schlick, RAG: RNA-As-Graphs database---concepts, analysis, and features, Bioinformatics, v.20 n.8, p.1285-1291, May 2004
[doi> 10.1093/bioinformatics/bth084]
|
| |
5
|
H. H. Gan, S. Pasquali, and T. Schlick. Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucl. Acids Res., 31:2926--2943, 2003.
|
| |
6
|
F. Harary. The number of homeomorphically irreducible trees and other species. Acta Math., 101:141--162, 1959.
|
| |
7
|
F. Harary. Graph Theory Addison-Wesley, 1969.
|
| |
8
|
I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker, and P.Schuster. Fast folding and comparison of RNA secondary structures. Monatsh. Chem., 125:167--188, 1994.
|
| |
9
|
L. Jiang, A. Majumdar, W. Hu, T. J. Jaishree, W. Xu, and D. J. Patel. Saccharide-RNA recognition in a complex formed between neomycin B and an RNA aptamer. Structure Fold Des., 7:817--827, 1999.
|
| |
10
|
T. J. Macke, D. J. Ecker, R. R. Gutell, D. Gautheret, D. A. Case, and R. Sampath. RNAMotif, an RNA secondary structure definition and search algorithm. Nucl. Acids Res., 29:4724--4735, 2001.
|
 |
11
|
|
| |
12
|
A. Nahvi, N. Sudarsan, M. S. Ebert, X. Zou, K. L. Brown, and R. R. Breaker. Genetic control by a metabolite binding mRNA. Chem. Biol., 9:1043--1049, 2002.
|
| |
13
|
G. Reinert, S. Schbath, and M. S. Waterman. Probabilistic and statistical properties of words: an overview. J. Comput. Biol., 7:1--46, 2000.
|
| |
14
|
|
| |
15
|
G. Storz. An expanding universe of noncoding RNAs. Science 296:1260--1263, 2002.
|
| |
16
|
V. Tereshko, E. Skripkin, and D. J. Patel. Encapsulating streptomycin within a small 40-mer RNA. Chem. Biol., 10:175--187, 2003.
|
| |
17
|
I. Tinoco, Jr. and C. Bustamante. How RNA folds. J. Mol. Biol., 293:271--281, 1999.
|
| |
18
|
S. T. Wallace and R. Schroeder. In vitro selection and characterization of streptomycin-binding RNAs: Recognition discrimination between antibiotics. RNA 4:112--123, 1998.
|
| |
19
|
D. S. Wilson and J. W. Szostak. In vitro selection of functional nucleic acids. Ann. Rev. Biochem., 68:611--647, 1999.
|
| |
20
|
W. Winkler, A. Nahvi, and R. R. Breaker. Thiamine derivatives bind messenger RNAs directly to regulate bacterial expression. Nature 419:952--956, 2002.
|
| |
21
|
W. C. Winkler, S. Cohen-Chalamish, and R. R. Breaker. An mRNA structure that controls gene expression by binding FMN. Proc. Natl. Acad. Sci. USA 99:15908--15913, 2002.
|
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