Lettre à Francis Crick, 1955. ,
Non-Protein Coding RNAs, 2008. ,
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, vol.322, issue.7235, pp.458223-227, 2009. ,
DOI : 10.1038/nature07672
Exceptional structured noncoding RNAs revealed by bacterial metagenome analysis, Nature, vol.17, issue.7273, pp.656-659, 2009. ,
DOI : 10.1038/nature08586
Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001. ,
DOI : 10.1017/S1355838201002515
Extracting Stacking Interaction Parameters for RNA from the Data Set of Native Structures, Journal of Molecular Biology, vol.347, issue.1, pp.53-69, 2005. ,
DOI : 10.1016/j.jmb.2004.12.012
RNA 3D Strutural Motifs : Definition, Identification, Annotation, and Database Searching, Non-Protein Coding RNAs, chapter, pp.8-9, 2009. ,
How RNA Folds, J. Mol. Biol, vol.293, pp.271-281, 1999. ,
The building blocks and motifs of RNA architecture, Current Opinion in Structural Biology, vol.16, issue.3, pp.279-287, 2006. ,
DOI : 10.1016/j.sbi.2006.05.009
URL : https://hal.archives-ouvertes.fr/hal-00094324
Automated motif extraction and classification in RNA tertiary structures, RNA, vol.14, issue.12, pp.1-9, 2008. ,
DOI : 10.1261/rna.1061108
URL : https://hal.archives-ouvertes.fr/hal-00353402
Recurrent structural RNA motifs, Isostericity Matrices and sequence alignments, Nucleic Acids Research, vol.33, issue.8, pp.2396-2409, 2005. ,
DOI : 10.1093/nar/gki535
URL : http://doi.org/10.1093/nar/gki535
Topology of three-way junctions in folded RNAs, RNA, vol.12, issue.1, pp.83-93, 2006. ,
DOI : 10.1261/rna.2208106
URL : https://hal.archives-ouvertes.fr/hal-00094313
Tertiary Motifs Revealed in Analyses of Higher-Order RNA Junctions, Journal of Molecular Biology, vol.393, issue.1, pp.67-82, 2009. ,
DOI : 10.1016/j.jmb.2009.07.089
The influence of the local sequence environment on RNA loop structures, RNA, vol.17, issue.7, pp.1247-1257, 2011. ,
DOI : 10.1261/rna.2550211
Three-Way RNA Junctions with Remote Tertiary Contacts : A Recurrent and Highly Versatile Fold, RNA, vol.15, pp.1949-1964, 2009. ,
Predicting helical coaxial stacking in RNA multibranch loops, RNA, vol.13, issue.7, pp.939-951, 2007. ,
DOI : 10.1261/rna.305307
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures, Journal of Mathematical Biology, vol.31, issue.13, pp.215-252, 2008. ,
DOI : 10.1007/s00285-007-0110-x
RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign, Nucleic Acids Research, vol.36, issue.Database, pp.392-397, 2008. ,
DOI : 10.1093/nar/gkm842
Functional analysis of the pseudoknot structure in human telomerase RNA, Proceedings of the National Academy of Sciences, vol.102, issue.23, pp.8080-8085, 2005. ,
DOI : 10.1073/pnas.0502259102
Theory of RNA Folding: From Hairpins to Ribozymes, Non-Protein Coding RNAs, chapter, 2009. ,
DOI : 10.1007/978-3-540-70840-7_2
Gene regulation by riboswitches, Nature Reviews Molecular Cell Biology, vol.13, issue.6, pp.451-463, 2004. ,
DOI : 10.1002/anie.199410841
Computational approaches to 3D modeling of RNA, Journal of Physics: Condensed Matter, vol.22, issue.28, pp.17-24 ,
DOI : 10.1088/0953-8984/22/28/283101
Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978. ,
DOI : 10.1137/0135006
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research, vol.9, issue.1, pp.133-14848, 1981. ,
DOI : 10.1093/nar/9.1.133
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
A statistical sampling algorithm for RNA secondary structure prediction, Nucleic Acids Research, vol.31, issue.24, pp.7280-7301, 2003. ,
DOI : 10.1093/nar/gkg938
Abstract shapes of RNA, Nucleic Acids Research, vol.32, issue.16, pp.4843-4851, 2004. ,
DOI : 10.1093/nar/gkh779
CONTRAfold: RNA secondary structure prediction without physics-based models, Bioinformatics, vol.22, issue.14, pp.90-98, 2006. ,
DOI : 10.1093/bioinformatics/btl246
RNA Pseudoknot Prediction in Energy-Based Models, Journal of Computational Biology, vol.7, issue.3-4, pp.409-436, 2007. ,
DOI : 10.1089/106652700750050862
A dynamic programming algorithm for RNA structure prediction including pseudoknots11Edited by I. Tinoco, Journal of Molecular Biology, vol.285, issue.5, pp.2053-68, 1999. ,
DOI : 10.1006/jmbi.1998.2436
CyloFold: secondary structure prediction including pseudoknots, Nucleic Acids Research, vol.38, issue.Web Server, pp.368-372, 2010. ,
DOI : 10.1093/nar/gkq432
URL : http://doi.org/10.1093/nar/gkq432
A Combinatorial Framework for the Design of (pseudoknotted ) RNA Algorithms, 2011. ,
Folding Kinetics of Large RNAs, Journal of Molecular Biology, vol.379, issue.1, pp.160-173, 2008. ,
DOI : 10.1016/j.jmb.2008.02.064
Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots, Nucleic Acids Research, vol.33, issue.Web Server, pp.605-615, 2005. ,
DOI : 10.1093/nar/gki447
A Comprehensive Comparison of Comparative RNA Structure Prediction Approaches, BMC Bioinformatics, vol.5, issue.21, pp.20-22, 2004. ,
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Research, vol.22, issue.22, pp.4673-4680, 1994. ,
DOI : 10.1093/nar/22.22.4673
Secondary Structure Prediction for Aligned RNA Sequences, Journal of Molecular Biology, vol.319, issue.5, pp.1059-1066, 2002. ,
DOI : 10.1016/S0022-2836(02)00308-X
Pfold: RNA secondary structure prediction using stochastic context-free grammars, Nucleic Acids Research, vol.31, issue.13, pp.3423-3428, 2003. ,
DOI : 10.1093/nar/gkg614
Simultaneous Solution of the RNA Folding, Alignment and Protosequence Problems, SIAM Journal on Applied Mathematics, vol.45, issue.5, pp.810-825, 1985. ,
DOI : 10.1137/0145048
Pairwise local structural alignment of RNA sequences with sequence similarity less than 40%, Bioinformatics, vol.21, issue.9, pp.1815-1824, 2005. ,
DOI : 10.1093/bioinformatics/bti279
Dynalign: an algorithm for finding the secondary structure common to two RNA sequences, Journal of Molecular Biology, vol.317, issue.2, pp.191-203, 2002. ,
DOI : 10.1006/jmbi.2001.5351
Finding the common structure shared by two homologous RNAs, Bioinformatics, vol.19, issue.1, pp.108-116, 2003. ,
DOI : 10.1093/bioinformatics/19.1.108
Local similarity in RNA secondary structures, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, pp.159-168, 2003. ,
DOI : 10.1109/CSB.2003.1227315
Tree Alignment Model : Algorithms, Implementations and Applications for the Analysis of RNA Secondary Structures, The, 2005. ,
MARNA: multiple alignment and consensus structure prediction of RNAs based on sequence structure comparisons, Bioinformatics, vol.21, issue.16, pp.3352-3359, 2005. ,
DOI : 10.1093/bioinformatics/bti550
RNA2D3D: A program for Generating, Viewing, and Comparing 3-Dimensional Models of RNA, Journal of Biomolecular Structure and Dynamics, vol.407, issue.6, pp.669-83, 2008. ,
DOI : 10.1080/07391102.2008.10531240
Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels, Bioinformatics, vol.26, issue.16, 2010. ,
DOI : 10.1093/bioinformatics/btq321
URL : https://hal.archives-ouvertes.fr/hal-00529831
iFoldRNA: three-dimensional RNA structure prediction and folding, Bioinformatics, vol.24, issue.17, pp.1951-1953, 2008. ,
DOI : 10.1093/bioinformatics/btn328
Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters, RNA, vol.15, issue.2, pp.189-99, 2009. ,
DOI : 10.1261/rna.1270809
Automated de novo prediction of native-like RNA tertiary structures, Proceedings of the National Academy of Sciences, vol.104, issue.37, pp.14664-14673, 2007. ,
DOI : 10.1073/pnas.0703836104
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, Nature, vol.349, issue.7183, pp.51-55, 2008. ,
DOI : 10.1038/nature06684
Automated prediction of three-way junction topological families in RNA secondary structures, Computational Biology and Chemistry, vol.37, pp.2012-2044 ,
DOI : 10.1016/j.compbiolchem.2011.11.001
URL : https://hal.archives-ouvertes.fr/hal-00641738
The Protein Data Bank, Nucleic Acids Research, vol.28, issue.1, pp.235-242, 2000. ,
DOI : 10.1093/nar/28.1.235
Tools for the automatic identification and classification of RNA base pairs, Nucleic Acids Research, vol.31, issue.13, pp.313450-3460, 2003. ,
DOI : 10.1093/nar/gkg529
From knotted to nested RNA structures: A variety of computational methods for pseudoknot removal, RNA, vol.14, issue.3, pp.410-416, 2008. ,
DOI : 10.1261/rna.881308
Analysis of Four-Way Junctions in RNA Structures, Journal of Molecular Biology, vol.390, issue.3, pp.547-559, 2009. ,
DOI : 10.1016/j.jmb.2009.04.084
A standard reference frame for the description of nucleic acid base-pair geometry, Journal of Molecular Biology, vol.313, issue.1, pp.229-237, 2001. ,
DOI : 10.1006/jmbi.2001.4987
A solution for the best rotation to relate two sets of vectors, Acta Crystallographica Section A, vol.32, issue.5, pp.69-132, 1976. ,
DOI : 10.1107/S0567739476001873
An algorithm for drawing general undirected graphs, Information Processing Letters, vol.31, issue.1, pp.7-15, 1989. ,
DOI : 10.1016/0020-0190(89)90102-6
Graph Drawing by Force-Directed Placement. Software ? Practice and Experience, pp.1129-1164, 1991. ,
DOI : 10.1002/spe.4380211102
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.13.8444
Genetic Algorithms, Scientific American, 1992. ,
Genetic Algorithms in Search, Optimization and Machine Learning, 1989. ,
On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. 1859 ,
Theory of Games and Economic Behavior, 1944. ,
Equilibrium Points in N-Person Games, pp.89-90, 1950. ,
Complexity of Finding Nash Equilibria, The. In Algorithmic Game Theory, 2007. ,
On the complexity of the parity argument and other inefficient proofs of existence, Journal of Computer and System Sciences, vol.48, issue.3, 1994. ,
DOI : 10.1016/S0022-0000(05)80063-7
Decentralized learning of Nash equilibria in multi-person stochastic games with incomplete information, IEEE Transactions on Systems, Man, and Cybernetics, vol.24, issue.5, pp.769-777, 1994. ,
DOI : 10.1109/21.293490
A Fictitious Play Approach to Large-Scale Optimization, Operations Research, vol.53, issue.3, pp.477-489, 2005. ,
DOI : 10.1287/opre.1040.0178
Sampled fictitious play for approximate dynamic programming, Computers & Operations Research, vol.38, issue.12, pp.1705-1718, 2011. ,
DOI : 10.1016/j.cor.2011.01.023
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.187.6331
Iterative Solution of Games by Fictitious Play, 1951. ,
An Iterative Method of Solving a Game Comparison of the Predicted and Observed Secondary Structure of T4 Phage Lysozyme, BBA) -Protein Structure, pp.296-301442, 1951. ,
New metrics for comparing and assessing discrepancies between RNA 3D structures and models, RNA, vol.15, issue.10, pp.1875-1885, 2009. ,
DOI : 10.1261/rna.1700409
URL : https://hal.archives-ouvertes.fr/hal-00561427
Graphes Et Hypergraphes, 1969. ,