A. Ankan and A. Panda, pgmpy: Probabilistic graphical models using python, Proceedings of the 14th Python in Science Conference (SCIPY 2015), 2015.

L. Argaman and S. Altuvia, fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex, J. Mol. Biol, vol.300, issue.5, pp.1101-1112, 2000.

F. R. Bach and M. I. Jordan, Thin junction trees, Advances in Neural Information Processing Systems, pp.569-576, 2002.

R. H. Beelen, D. M. Fluitsma, J. W. Van-der-meer, and E. C. Hoefsmit, Development of different peroxidatic activity patterns in pertoneal macrophages in vivo and in vitro, J Reticuloendothel Soc, vol.25, issue.5, pp.513-523, 1979.

H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat et al., The protein data bank, Nucleic acids research, vol.28, pp.235-242, 2000.

H. L. Bodlaender, Dynamic programming on graphs with bounded treewidth, International Colloquium on Automata, Languages, and Programming, pp.105-118, 1988.

G. Chojnowski, T. Walen, and J. M. Bujnicki, Rna bricks-a database of rna 3d motifs and their interactions, Nucleic Acids Res, vol.42, pp.123-154, 2014.

J. A. Cruz and E. Westhof, Sequence-based identification of 3D structural modules in RNA with RMDetect, Nat Methods, vol.8, issue.6, pp.513-534, 2011.

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

M. Djelloul and A. Denise, Automated motif extraction and classification in rna tertiary structures, RNA, vol.14, issue.12, pp.2489-97, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00353402

Z. Du, K. E. Lind, and T. L. James, Structure of TAR RNA complexed with a Tat-TAR interaction nanomolar inhibitor that was identified by computational screening, Chem. Biol, vol.9, issue.6, pp.707-712, 2002.

P. Ge, S. Islam, C. Zhong, and S. Zhang, De novo discovery of structural motifs in RNA 3D structures through clustering, Nucleic Acids Research, vol.46, issue.9, pp.4783-4793, 2018.

L. Huck, A. Scherrer, L. Terzi, A. E. Johnson, H. D. Bernstein et al., Conserved tertiary base pairing ensures proper RNA folding and efficient assembly of the signal recognition particle Alu domain, Nucleic Acids Res, vol.32, issue.16, pp.4915-4924, 2004.

I. Kalvari, J. Argasinska, N. Quinones-olvera, E. P. Nawrocki, E. Rivas et al., Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families, Nucleic Acids Research, vol.46, issue.D1, pp.335-342, 2017.

L. Lancaster, N. J. Lambert, E. J. Maklan, L. H. Horan, and H. F. Noller, The sarcin-ricin loop of 23S rRNA is essential for assembly of the functional core of the 50S ribosomal subunit, RNA, vol.14, issue.10, pp.1999-2012, 2008.

N. B. Leontis and E. Westhof, Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001.

N. B. Leontis and E. Westhof, Geometric nomenclature and classification of rna base pairs, RNA, vol.7, pp.499-512, 2001.

N. B. Leontis and C. L. Zirbel, Nonredundant 3d structure datasets for rna knowledge extraction and benchmarking, RNA 3D structure analysis and prediction, pp.281-298, 2012.

A. Lescoute, N. B. Leontis, C. Massire, and E. Westhof, Recurrent structural rna motifs, isostericity matrices and sequence alignments, Nucleic acids research, vol.33, pp.2395-2409, 2005.

R. Lorenz, S. H. Bernhart, C. Höner-zu-siederdissen, H. Tafer, C. Flamm et al., mabseher: A small but efficient c++ library for computing (customized) tree and hypertree decompositions, Algorithms Mol Biol, vol.6, 2011.

D. H. Mathews, RNA secondary structure analysis using RNAstructure, Curr Protoc Bioinformatics Chapter, vol.12, issue.6, 2006.

J. S. Mccaskill, The equilibrium partition function and base pair binding probabilities for rna secondary structure, Biopolymers, vol.29, pp.1105-1119, 1990.

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

A. M. Mustoe, C. L. Brooks, and H. M. Al-hashimi, Hierarchy of RNA functional dynamics, Annu. Rev. Biochem, vol.83, pp.441-466, 2014.

A. Peselis and A. Serganov, Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch, Nature structural & molecular biology, vol.19, issue.11, p.1182, 2012.

A. I. Petrov, C. L. Zirbel, and N. B. Leontis, Automated classification of rna 3d motifs and the rna 3d motif atlas, RNA, vol.19, issue.10, pp.1327-1367, 2013.

M. Popenda, M. Szachniuk, M. Blazewicz, S. Wasik, E. K. Burke et al., RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, BMC Bioinformatics, vol.11, 2010.

V. Reinharz, F. Major, and J. Waldispühl, Towards 3D structure prediction of large rna molecules: an integer programming framework to insert local 3D motifs in RNA secondary structure, Bioinformatics, vol.28, issue.12, pp.207-221, 2012.

V. Reinharz, A. Soulé, E. Westhof, J. Waldispühl, and A. Denise, Mining for recurrent long-range interactions in rna structures reveals embedded hierarchies in network families, Nucleic Acids Research, vol.46, issue.8, pp.3841-3851, 2018.
URL : https://hal.archives-ouvertes.fr/hal-01745345

C. Rovetta, J. Michálik, R. Lorenz, A. Tanzer, and Y. Ponty, Non-redundant sampling and statistical estimators for RNA structural properties at the thermodynamic equilibrium (2019), under review

R. Sarrazin-gendron, V. Reinharz, C. G. Oliver, N. Moitessier, and J. Waldispühl, Automated, customizable and efficient identification of 3d base pair modules with bayespairing, Nucleic acids research, 2019.

A. Serganov and E. Nudler, A decade of riboswitches, Cell, vol.152, issue.1-2, pp.17-24, 2013.

C. Theis, C. L. Zirbel, C. H. Zu-siederdissen, C. Anthon, I. L. Hofacker et al., RNA 3D modules in genome-wide predictions of RNA 2D structure, PLoS One, vol.10, issue.10, p.139900, 2015.

B. C. Thiel, R. Ochsenreiter, V. P. Gadekar, A. Tanzer, and I. L. Hofacker, RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates, vol.9, 2018.

I. Tinoco and C. Bustamante, How RNA folds, J Mol Biol, vol.293, issue.2, pp.271-81, 1999.

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, 2010.

D. E. Wood and S. L. Salzberg, Kraken: ultrafast metagenomic sequence classification using exact alignments, Genome biology, vol.15, issue.3, p.46, 2014.

C. Xue, F. Li, T. He, G. P. Liu, Y. Li et al., Classification of real and pseudo microrna precursors using local structure-sequence features and support vector machine, BMC bioinformatics, vol.6, issue.1, p.310, 2005.

C. L. Zirbel, J. Roll, B. A. Sweeney, A. I. Petrov, M. Pirrung et al., Identifying novel sequence variants of RNA 3D motifs, Nucleic Acids Res, vol.43, issue.15, pp.7504-7524, 2015.