R. Aguirre-hernández, H. H. Hoos, and A. Condon, Computational RNA secondary structure design: empirical complexity and improved methods, BMC Bioinformatics, vol.8, issue.1, p.34, 2007.
DOI : 10.1186/1471-2105-8-34

M. Andronescu, V. Bereg, H. Hoos, and A. Condon, RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database, BMC Bioinformatics, vol.9, issue.1, p.340, 2008.
DOI : 10.1186/1471-2105-9-340

A. Avihoo, A. Churkin, and D. Barash, RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences, BMC Bioinformatics, vol.12, issue.1, p.319, 2011.
DOI : 10.1016/0303-2647(95)01568-X

O. Bodini and Y. Ponty, Multi-dimensional Boltzmann Sampling of Languages, DMTCS Proceedings, number 01 in AM, pp.49-64, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00450763

A. Busch and R. Backofen, INFO-RNA--a fast approach to inverse RNA folding, Bioinformatics, vol.22, issue.15, pp.22-1823, 2006.
DOI : 10.1093/bioinformatics/btl194

A. L. Chang, J. J. Wolf, and C. D. Smolke, Synthetic RNA switches as a tool for temporal and spatial control over gene expression, Current Opinion in Biotechnology, vol.23, issue.5, pp.679-88, 2012.
DOI : 10.1016/j.copbio.2012.01.005

Y. Ding and E. Lawrence, A statistical sampling algorithm for RNA secondary structure prediction, Nucleic Acids Research, vol.31, issue.24, pp.31-7280, 2003.
DOI : 10.1093/nar/gkg938

J. A. Garcia-martin, P. Clote, and I. Dotu, RNAiFOLD: A CONSTRAINT PROGRAMMING ALGORITHM FOR RNA INVERSE FOLDING AND MOLECULAR DESIGN, Journal of Bioinformatics and Computational Biology, vol.11, issue.02, 2013.
DOI : 10.1142/S0219720013500017

I. L. Hofacker, W. Fontana, P. F. Stadler, S. Bonhoeffer, M. Tacker et al., Schnelle Faltung und Vergleich von Sekund???rstrukturen von RNA, Monatshefte für Chemie, pp.167-188, 1994.
DOI : 10.1007/BF00818163

A. Levin, M. Lis, Y. Ponty, C. W. O-'donnell, S. Devadas et al., A global sampling approach to designing and reengineering RNA secondary structures, Nucleic Acids Research, vol.40, issue.20, pp.40-10041, 2012.
DOI : 10.1093/nar/gks768

URL : https://hal.archives-ouvertes.fr/hal-00733924

R. B. Lyngsø, J. W. Anderson, E. Sizikova, A. Badugu, T. Hyland et al., Frnakenstein: multiple target inverse RNA folding, BMC Bioinformatics, vol.13, issue.1, p.260, 2012.
DOI : 10.1093/nar/gkg068

Y. Ponty and C. Saule, A Combinatorial Framework for Designing (Pseudoknotted) RNA Algorithms, WABI -11th Workshop on Algorithms in Bioinformatics -2011, 2011.
DOI : 10.1093/nar/9.1.133

URL : https://hal.archives-ouvertes.fr/inria-00601060

V. Reinharz, Y. Ponty, and J. Waldispühl, A linear inside-outside algorithm for correcting sequencing errors in structured rna sequences, Proceeding of the 17th Annual International Conference on Research in Computational Molecular Biology, 2013.
URL : https://hal.archives-ouvertes.fr/hal-00766781

G. Rodrigo, T. E. Landrain, and A. Jaramillo, De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells, Proceedings of the National Academy of Sciences, vol.109, issue.38, pp.15271-15277, 2012.
DOI : 10.1073/pnas.1203831109

E. Senter, S. Sheikh, I. Dotu, Y. Ponty, C. et al., Using the Fast Fourier Transform to Accelerate the Computational Search for RNA Conformational Switches, PLoS ONE, vol.93, issue.(5), p.50506, 2012.
DOI : 10.1371/journal.pone.0050506.s001

URL : https://hal.archives-ouvertes.fr/hal-00769740

D. H. Turner and D. H. Mathews, NNDB: the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic Acids Research, vol.38, issue.Database, pp.280-282, 2010.
DOI : 10.1093/nar/gkp892

J. Waldispühl and Y. Ponty, An Unbiased Adaptive Sampling Algorithm for the Exploration of RNA Mutational Landscapes Under Evolutionary Pressure, Journal of Computational Biology, vol.18, issue.11, pp.1465-79, 2011.
DOI : 10.1089/cmb.2011.0181

J. Waldispühl, S. Devadas, B. Berger, C. , and P. , Efficient Algorithms for Probing the RNA Mutation Landscape, PLoS Computational Biology, vol.67, issue.245, p.1000124, 2008.
DOI : 10.1371/journal.pcbi.1000124.s001

H. S. Wilf, A unified setting for sequencing, ranking, and selection algorithms for combinatorial objects, Advances in Mathematics, vol.24, issue.2, pp.281-291, 1977.
DOI : 10.1016/S0001-8708(77)80046-7