Bagheri,S. and Kashani-Sabet,M. (2004). Ribozymes in the age of molecular therapeutics. Curr. Mol. Med. 4, 489-506.

Breaker,R.R. (2004). Natural and engineered nucleic acids as tools to explore biology. Nature 432, 838-845.

Chworos,A., Severcan,I., Koyfman,A.Y., Weinkam,P., Oroudjev,E., Hansma,H.G., and Jaeger,L. (2004). Building programmable jigsaw puzzles with RNA. Science 306, 2068-2072.

Doudna,J.A. and Cech,T.R. (2002). The chemical repertoire of natural ribozymes. Nature 418, 222-228.

Ellington,A.D. and Szostak,J.W. (1990). Invitro Selection of Rna Molecules That Bind Specific Ligands. Nature 346, 818-822.

Famulok,M. and Verma,S. (2002). In vivo-applied functional RNAs as tools in proteomics and genomics research. Trends Biotechnol. 20, 462-466.

Fera,D., Kim,N., Shiffeldrim,N., Zorn,J., Laserson,U., Gan,H.H., and Schlick,T. (2004). RAG: RNA-As-Graphs web resource. Bmc Bioinformatics 5.

Gan,H.H., Fera,D., Zorn,J., Shiffeldrim,N., Tang,M., Laserson,U., Kim,N., and Schlick,T. (2004). RAG: RNA-As-Graphs Database - Concepts, Analysis, and Features. Bioinformatics 20, 1285-1291.

Gan,H.H., Pasquali,S., and Schlick,T. (2003). Exploring the repertoire of RNA secondary motifs using graph theory; implications for RNA design. Nucleic Acids Res. 31, 2926-2943.

Gevertz,J., Gan,H.H., and Schlick,T. (2005). In vitro RNA random pools are not structurally diverse: A computational analysis. RNA 11, 853-863.

Hayashizaki,Y. and Carninci,P. (2006). Genome Network and FANTOM3: assessing the complexity of the transcriptome. PLoS. Genet. 2, e63.

Hermann,T. and Patel,D.J. (2000). Biochemistry - Adaptive recognition by nucleic acid aptamers. Science 287, 820-825.

Jaeger,L., Westhof,E., and Leontis,N.B. (2001). TectoRNA: modular assembly units for the construction of RNA nano-objects. Nucleic Acids Research 29, 455-463.

Jaschke,A. (2001). Artificial ribozymes and deoxyribozymes. Curr. Opin. Struct. Biol. 11, 321-326.

Joyce,G.F. (2004). Directed evolution of nucleic acid enzymes. Annu. Rev. Biochem. 73, 791-836.

Kim,N., Gan,H.H., and Schlick,T. (2007a). A computational proposal for designing structured RNA pools for in vitro selection of RNAs. RNA. 13, 478-492.

Kim,N., Shiffeldrim,N., Gan,H.H., and Schlick,T. (2004). Candidates for novel RNA topologies. J. Mol. Biol. 341, 1129-1144.

Kim,N., Shin,J.S., Elmetwaly,S., Gan,H.H., and Schlick,T. (2007c). RagPools: RNA-As-Graph-Pools--a web server for assisting the design of structured RNA pools for in vitro selection. Bioinformatics. 23, 2959-2960.

Laing,C., Jung,S., Iqbal,A., and Schlick,T. (2009). Tertiary motifs revealed in analyses of higher-order RNA junctions. J. Mol. Biol. 393, 67-82.

Laing,C. and Schlick,T. (2009). Analysis of four-way junctions in RNA structures. J. Mol. Biol. 390, 547-559.

Mattick,J.S. and Makunin,I.V. (2005). Small regulatory RNAs in mammals. Hum. Mol. Genet. 14 Spec No 1, R121-R132.

Pasquali,S., Gan,H.H., and Schlick,T. (2005). Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nucleic Acids Res. 33, 1384-1398.

Peracchi,A. (2004). Prospects for antiviral ribozymes and deoxyribozymes. Rev. Med. Virol. 14, 47-64.

Soukup,G.A. and Breaker,R.R. (1999a). Engineering precision RNA molecular switches. Proc. Natl. Acad. Sci. U. S. A 96, 3584-3589.

Soukup,G.A. and Breaker,R.R. (1999b). Nucleic acid molecular switches. Trends Biotechnol. 17, 469-476.

Soukup,G.A. and Breaker,R.R. (2000). Allosteric nucleic acid catalysts. Curr. Opin. Struct. Biol. 10, 318-325.

Storz,G. (2002). An expanding universe of noncoding RNAs. Science 296, 1260-1263.

Toulme,J.J., Di Primo,C., and Boucard,D. (2004). Regulating eukaryotic gene expression with aptamers. FEBS Lett. 567, 55-62.

Tuerk,C. and Gold,L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase. Science 249, 505-510.

Wilson,D.S. and Szostak,J.W. (1999). In vitro selection of functional nucleic acids. Annu. Rev. Biochem. 68, 611-647.

Xin,Y., Quarta,G., Gan,H.H., and Schlick,T. (2008). Estimating the fraction of noncoding RNAs in mammalian transcriptomes. Bioinformatics and Biology Insights 2, 77-95.