F. J. Isaacs, D. J. Dwyer, C. , and J. J. , RNA synthetic biology, Nature Biotechnology, vol.96, issue.5, pp.545-554, 2006.
DOI : 10.1038/nbt1208

C. Hammann and E. Westhof, Searching genomes for ribozymes and riboswitches, Genome Biology, vol.8, issue.4, p.210, 2007.
DOI : 10.1186/gb-2007-8-4-210
URL : https://hal.archives-ouvertes.fr/hal-00167549

R. J. Taft, K. C. Pang, T. R. Mercer, M. Dinger, and J. S. Mattick, Non-coding RNAs: regulators of disease, The Journal of Pathology, vol.444, issue.2, pp.126-139, 2010.
DOI : 10.1002/path.2638

S. A. Strobel and J. C. Cochrane, RNA catalysis: ribozymes, ribosomes, and riboswitches, Current Opinion in Chemical Biology, vol.11, issue.6, pp.636-643, 2007.
DOI : 10.1016/j.cbpa.2007.09.010

R. R. Breaker, Prospects for Riboswitch Discovery and Analysis, Molecular Cell, vol.43, issue.6, pp.867-879, 2011.
DOI : 10.1016/j.molcel.2011.08.024

A. Serganov and E. Nudler, A Decade of Riboswitches, Cell, vol.152, issue.1-2, pp.17-24, 2013.
DOI : 10.1016/j.cell.2012.12.024

S. Findeiss, M. Wachsmuth, M. Mörl, and P. F. Stadler, Design of Transcription Regulating Riboswitches, Methods Enzymol, vol.550, pp.1-22, 2015.
DOI : 10.1016/bs.mie.2014.10.029

M. Wachsmuth, G. Domin, R. Lorenz, R. Serfling, S. Findeiß et al., Design criteria for synthetic riboswitches acting on transcription, RNA Biology, vol.12, issue.2, pp.221-231, 2015.
DOI : 10.1016/j.jbiotec.2012.01.007

G. A. Soukup and R. R. Breaker, Nucleic acid molecular switches, Trends in Biotechnology, vol.17, issue.12, pp.469-476, 1999.
DOI : 10.1016/S0167-7799(99)01383-9

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, 2012.
DOI : 10.1016/j.copbio.2012.01.005

C. Berens and B. Suess, Riboswitch engineering ??? making the all-important second and third steps, Current Opinion in Biotechnology, vol.31, pp.10-15, 2015.
DOI : 10.1016/j.copbio.2014.07.014

I. L. Hofacker, W. Fontana, P. F. Stadler, L. S. Bonhoeffer, M. Tacker et al., Schnelle Faltung und Vergleich von Sekund???rstrukturen von RNA, Monatshefte f???r Chemie Chemical Monthly, vol.157, issue.2, pp.167-188, 1994.
DOI : 10.1007/BF00818163

D. Retwitzer, M. Kifer, I. Sengupta, S. Yakhini, Z. Barash et al., An Efficient Minimum Free Energy Structure-Based Search Method for Riboswitch Identification Based on Inverse RNA Folding, PLOS ONE, vol.19, issue.12, p.134262, 2015.
DOI : 10.1371/journal.pone.0134262.t001

I. Dotu, G. Lozano, P. Clote, and E. Martinez-salas, Using RNA inverse folding to identify IRES-like structural subdomains, RNA Biology, vol.67, issue.12, pp.1842-1852, 2013.
DOI : 10.1016/S0076-6879(09)68004-6

W. L. Ruzzo and J. Gorodkin, De Novo Discovery of Structured ncRNA Motifs in Genomic Sequences, Methods Mol Biol, vol.1097, pp.303-318, 2014.
DOI : 10.1007/978-1-62703-709-9_15

I. L. Hofacker, Vienna RNA secondary structure server, Nucleic Acids Research, vol.31, issue.13, pp.31-3429, 2003.
DOI : 10.1093/nar/gkg599

M. Zuker, D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder et al., Mfold web server for nucleic acid folding and hybridization prediction) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, PubMed:12824337] [PubMed Central:PMC169194]. [18], pp.31-3406, 2003.

A. Busch and R. Backofen, INFO-RNA--a fast approach to inverse RNA folding, Bioinformatics, vol.22, issue.15, pp.1823-1831, 2006.
DOI : 10.1093/bioinformatics/btl194

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, pp.341471-2105, 2007.

J. N. Zadeh, B. R. Wolfe, P. , and N. A. , Nucleic acid sequence design via efficient ensemble defect optimization, Journal of Computational Chemistry, vol.451, issue.3
DOI : 10.1002/jcc.21633

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

B. Cohen and S. Skiena, Natural Selection and Algorithmic Design of mRNA, Journal of Computational Biology, vol.10, issue.3-4, pp.419-432, 2003.
DOI : 10.1089/10665270360688101

A. Taneda, Multi-Objective Genetic Algorithm for Pseudoknotted RNA Sequence Design. Front, Gene, vol.3, p.36, 2012.

A. Esmaili-taheri and M. Ganjtabesh, ERD: a fast and reliable tool for RNA design including constraints, BMC Bioinformatics, vol.25, issue.2, p.20, 2015.
DOI : 10.1137/1025045

R. Kleinkauf, M. Mann, and R. Backofen, antaRNA: ant colony-based RNA sequence design, Bioinformatics, vol.31, issue.19, pp.31-3114, 2015.
DOI : 10.1093/bioinformatics/btv319

J. A. Garcia-martin, I. Dotu, C. , and P. , RNAiFold 2.0: a web server and software to design custom and Rfam-based RNA molecules, Nucleic Acids Research, vol.43, issue.W1, pp.43-513, 2015.
DOI : 10.1093/nar/gkv460

E. Bindewald, K. Afonin, L. Jaeger, and B. A. Shapiro, Multistrand RNA Secondary Structure Prediction and Nanostructure Design Including Pseudoknots, ACS Nano, vol.5, issue.12, pp.9542-9551, 2011.
DOI : 10.1021/nn202666w

J. D. Yesselman and R. Das, RNA-Redesign: a web server for fixed-backbone 3D design of RNA: Figure 1., Nucleic Acids Research, vol.43, issue.W1, p.43, 2015.
DOI : 10.1093/nar/gkv465

N. Dromi, A. Avihoo, and D. Barash, ) Reconstruction of natural RNA sequences from RNA shape, thermodynamic stability, Nucleic Acids Research, issue.9, 2008.

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, pp.3191471-2105, 2011.
DOI : 10.1016/0303-2647(95)01568-X

L. Weinbrand, A. Avihoo, and D. Barash, RNAfbinv: an interactive Java application for fragment-based design of RNA sequences, Bioinformatics, vol.29, issue.22, pp.2938-2940, 2013.
DOI : 10.1093/bioinformatics/btt494

B. A. Shapiro, An algorithm for comparing multiple RNA secondary structures, Bioinformatics, vol.4, issue.3, pp.387-393, 1988.
DOI : 10.1093/bioinformatics/4.3.387

V. Reinharz, Y. Ponty, and J. Waldispühl, A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution, Bioinformatics, vol.29, issue.13, pp.308-315, 2013.
DOI : 10.1093/bioinformatics/btt217
URL : https://hal.archives-ouvertes.fr/hal-00840260

K. Darty, A. Denise, and Y. Ponty, VARNA: Interactive drawing and editing of the RNA secondary structure, Bioinformatics, vol.25, issue.15, pp.25-1974, 2009.
DOI : 10.1093/bioinformatics/btp250
URL : https://hal.archives-ouvertes.fr/hal-00432548