O. M. Becker and M. Karplus, The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics, The Journal of chemical physics, vol.106, issue.4, pp.1495-1517, 1997.

C. K. Biebricher and R. Luce, In vitro recombination and terminal elongation of RNA by Q beta replicase, The EMBO journal, vol.11, issue.13, pp.5129-5135, 1992.

J. Cupal, C. Flamm, A. Renner, and P. F. Stadler, Density of states, metastable states, and saddle points: Exploring the energy landscape of an RNA molecule, ISMB, pp.88-91, 1997.

Y. Ding and C. E. Lawrence, A statistical sampling algorithm for RNA secondary structure prediction, Nucleic acids research, vol.31, issue.24, pp.7280-7301, 2003.

Y. Ding, C. Y. Chan, and C. E. Lawrence, RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, Rna, vol.11, issue.8, pp.1157-1166, 2005.

S. R. Eddy, Noncoding RNA genes, Current Opinion in Genetics & Development, vol.9, issue.6, pp.695-699, 1999.

G. Entzian and M. Raden, pourRNA-a time-and memory-efficient approach for the guided exploration of RNA energy landscapes, Bioinformatics, vol.36, issue.2, pp.462-469, 2019.

C. Flamm, W. Fontana, I. L. Hofacker, and P. Schuster, RNA folding at elementary step resolution, RNA, vol.6, issue.3, pp.325-338, 2000.

C. Flamm, I. L. Hofacker, P. F. Stadler, and M. T. Wolfinger, Barrier trees of degenerate landscapes. Zeitschrift für physikalische chemie, vol.216, p.155, 2002.

E. Freyhult, V. Moulton, C. , and P. , Boltzmann probability of RNA structural neighbors and riboswitch detection, Bioinformatics, vol.23, issue.16, pp.2054-2062, 2007.

R. Giegerich, B. Voß, and M. Rehmsmeier, Abstract shapes of RNA, Nucleic Acids Research, vol.32, issue.16, pp.4843-4851, 2004.

I. L. Hofacker, P. Schuster, and P. F. Stadler, Combinatorics of rna secondary structures, Discrete Applied Mathematics, vol.88, issue.1-3, pp.207-237, 1998.

T. Huber, A. E. Torda, and W. F. Van-gunsteren, Local elevation: a method for improving the searching properties of molecular dynamics simulation, Journal of computer-aided molecular design, vol.8, issue.6, pp.695-708, 1994.

M. Kucharík, I. L. Hofacker, P. F. Stadler, and J. Qin, Basin Hopping Graph: a computational framework to characterize RNA folding landscapes, Bioinformatics, vol.30, issue.14, pp.2009-2017, 2014.

A. Laio and M. Parrinello, Escaping free-energy minima, Proceedings of the National Academy of Sciences, vol.99, issue.20, pp.12562-12566, 2002.

Y. Li and S. Zhang, Finding stable local optimal RNA secondary structures, Bioinformatics, vol.27, issue.21, pp.2994-3001, 2011.

R. Lorenz, C. Flamm, and I. L. Hofacker, 2D projections of RNA folding landscapes, German conference on bioinformatics, 2009.

R. Lorenz, S. H. Bernhart, C. H. Zu-siederdissen, H. Tafer, C. Flamm et al., ViennaRNA Package 2.0, Algorithms for Molecular Biology, vol.6, issue.1, p.26, 2011.

R. Lorenz, I. L. Hofacker, and P. F. Stadler, RNA folding with hard and soft constraints, Algorithms Mol. Biol, vol.11, issue.1, 2016.

W. A. Lorenz and P. Clote, Computing the partition function for kinetically trapped RNA secondary structures, PLoS One, vol.6, issue.1, p.16178, 2011.

J. Ma?uch, C. Thachuk, L. Stacho, and A. Condon, Np-completeness of the direct energy barrier problem without pseudoknots, International Workshop on DNA-Based Computers, pp.106-115, 2009.

N. R. Markham and M. Zuker, , pp.3-31, 2008.

J. S. Mccaskill, The equilibrium partition function and base pair binding probabilities for RNA secondary structure, Biopolymers: Original Research on Biomolecules, vol.29, issue.6-7, pp.1105-1119, 1990.

J. Michálik, H. Touzet, and Y. Ponty, Efficient approximations of RNA kinetics landscape using non-redundant sampling, Bioinformatics, vol.33, issue.14, pp.283-292, 2017.

Y. Ponty, Efficient sampling of RNA secondary structures from the boltzmann ensemble of low-energy, Journal of mathematical biology, vol.56, issue.1-2, pp.107-127, 2008.
URL : https://hal.archives-ouvertes.fr/inria-00548863

J. S. Reuter and D. H. Mathews, RNAstructure: software for RNA secondary structure prediction and analysis, BMC bioinformatics, vol.11, issue.1, p.129, 2010.

S. Sahoo and A. A. Albrecht, Approximating the set of local minima in partial RNA folding landscapes, Bioinformatics, vol.28, issue.4, pp.523-530, 2012.

S. Saito, H. Kakeshita, and K. Nakamura, Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis, Gene, vol.428, issue.1, pp.2-8, 2009.

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, pp.280-282, 2009.

M. T. Wolfinger, W. A. Svrcek-seiler, C. Flamm, I. L. Hofacker, and P. F. Stadler, Efficient computation of RNA folding dynamics, Journal of Physics A: Mathematical and General, vol.37, issue.17, p.4731, 2004.

S. Wuchty, W. Fontana, I. L. Hofacker, and P. Schuster, Complete suboptimal folding of RNA and the stability of secondary structures, Biopolymers: Original Research on Biomolecules, vol.49, issue.2, pp.145-165, 1999.

A. Xayaphoummine, T. Bucher, F. Thalmann, and H. Isambert, Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations, Proc. Natl. Acad. Sci. U.S.A, vol.100, issue.26, pp.15310-15315, 2003.
URL : https://hal.archives-ouvertes.fr/hal-00000641

M. Zuker and P. Stiegler, Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Res, vol.9, issue.1, pp.133-148, 1981.