, Gnu linear programming kit
Local Search Algorithms, The Atrium, 1997. ,
Comparing RNA secondary structures using a relaxed base-pair score, RNA, vol.16, issue.5, pp.865-878, 2010. ,
taveRNA : a web suite for RNA algorithms and applications, Nucleic Acids Research, vol.35, issue.suppl_2, pp.325-329, 2007. ,
Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots, Discrete Applied Mathematics, vol.104, issue.1, pp.45-62, 2000. ,
RNA-RNA interaction prediction and antisense RNA target search, Journal of Computational Biology, vol.13, issue.2, pp.267-282, 2006. ,
A multiple layer model to compare RNA secondary structures. Software : Practice and Experience, vol.38, pp.775-792, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00306662
Anti-human immunodeficiency virus hematopoietic progenitor cell-delivered ribozyme in a phase i study : Myeloid and lymphoid reconstitution in human immunodeficiency virus type-1-infected patients, Human gene therapy, vol.15, issue.3, pp.251-262, 2004. ,
The trouble with long-range base pairs in RNA folding, Brazilian Symposium on Bioinformatics, pp.1-11, 2013. ,
Secondary structure prediction of interacting RNA molecules, Journal of Molecular Biology, vol.345, issue.5, pp.987-1001, 2005. ,
RNA STRAND : the RNA secondary structure and statistical analysis database, BMC Bioinformatics, vol.9, issue.1, p.340, 2008. ,
Improved free energy parameters for RNA pseudoknotted secondary structure prediction, RNA, vol.16, issue.1, pp.26-42, 2010. ,
Therapeutic targeting of long noncoding RNAs in cancer, Trends in molecular medicine, vol.24, issue.3, pp.257-277, 2018. ,
Canonical cuts on the unit hypercube, SIAM Journal on Applied Mathematics, vol.23, issue.1, pp.61-69, 1972. ,
Lagrangian relaxation, Modern heuristic techniques for combinatorial problems, pp.243-303, 1993. ,
ProbKnot : fast prediction of RNA secondary structure including pseudoknots, RNA, vol.16, issue.10, pp.1870-1880, 2010. ,
Breakout local search for maximum clique problems, Computers & Operations Research, vol.40, issue.1, pp.192-206, 2013. ,
The nucleic acid database. a comprehensive relational database of three-dimensional structures of nucleic acids, Biophysical journal, vol.63, issue.3, p.751, 1992. ,
The protein data bank, Protein Structure, pp.394-410, 2003. ,
Cryo-EM structure of a pre-catalytic human spliceosome primed for activation, Cell, vol.170, issue.4, pp.701-713, 2017. ,
An exact -constraint method for bi-objective combinatorial optimization problems : Application to the Traveling Salesman Problem with Profits, European Journal of Operational Research, vol.194, issue.1, pp.39-50, 2009. ,
Cylofold : secondary structure prediction including pseudoknots, Nucleic Acids Research, vol.38, issue.2, pp.368-372, 2010. ,
Multistrand RNA secondary structure prediction and nanostructure design including pseudoknots, ACS nano, vol.5, issue.12, pp.9542-9551, 2011. ,
Correlating SHAPE signatures with threedimensional RNA structures, RNA, 2011. ,
Multistrand structure prediction of nucleic acid assemblies and design of RNA switches, Nano Letters, vol.16, issue.3, pp.1726-1735, 2016. ,
PR2S2Clust : patched RNA-seq read segments' structureoriented clustering, Journal of bioinformatics and computational biology, vol.14, issue.05, p.1650027, 2016. ,
Alignments of RNA structures, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.2, pp.309-322, 2008. ,
URL : https://hal.archives-ouvertes.fr/hal-00506348
The maximum clique problem, Handbook of combinatorial optimization, pp.1-74, 1999. ,
TT2NE : a novel algorithm to predict RNA secondary structures with pseudoknots, Nucleic Acids Research, vol.39, issue.14, pp.93-93, 2011. ,
URL : https://hal.archives-ouvertes.fr/cea-00666032
McGenus : a Monte Carlo algorithm to predict RNA secondary structures with pseudoknots, Nucleic Acids Research, vol.41, issue.3, pp.1895-1900, 2012. ,
IntaRNA : efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions, Bioinformatics, vol.24, issue.24, pp.2849-2856, 2008. ,
Stochastic modeling of RNA pseudoknotted structures : a grammatical approach, Bioinformatics, vol.19, issue.suppl_1, pp.66-73, 2003. ,
Predicting RNA pseudoknot folding thermodynamics, Nucleic Acids Research, vol.34, issue.9, pp.2634-2652, 2006. ,
Predicting structures and stabilities for H-type pseudoknots with interhelix loops, RNA, vol.15, issue.4, pp.696-706, 2009. ,
On the k-coloring of intervals, Discrete Applied Mathematics, vol.59, issue.3, pp.225-235, 1995. ,
A secondary and tertiary structure editor for nucleic acids, Bioinformatics, vol.4, issue.1, pp.143-146, 1988. ,
A branch-and-bound method for the bi-objective simple line assembly balancing problem, International Journal of Production Research, pp.1-20, 2018. ,
URL : https://hal.archives-ouvertes.fr/emse-01961748
An O (n 5 ) algorithm for MFE prediction of kissing hairpins and 4-chains in nucleic acids, Journal of Computational Biology, vol.16, issue.6, pp.803-815, 2009. ,
FlexStem : improving predictions of RNA secondary structures with pseudoknots by reducing the search space, Bioinformatics, vol.24, issue.18, 1994. ,
On the performance metrics of multiobjective optimization, Advances in Swarm Intelligence, pp.504-512, 2012. ,
A map of cytoplasmic RNA transcripts from lytic adenovirus type 2, determined by electron microscopy of RNA : DNA hybrids, Cell, vol.11, issue.4, pp.819-836, 1977. ,
On the page number of RNA secondary structures with pseudoknots, Journal of Mathematical Biology, vol.65, issue.6-7, pp.1337-1357, 2012. ,
Quantitative dimethyl sulfate mapping for automated RNA secondary structure inference, Biochemistry, vol.51, issue.36, pp.7037-7039, 2012. ,
Fast neighborhood subgraph pairwise distance kernel, Proceedings of the 26th International Conference on Machine Learning, pp.255-262, 2010. ,
Probing RNA folding by hydroxyl radical footprinting, RNA Folding, pp.119-142, 2014. ,
Exploring alternative RNA structure sets using MC-flashfold and db2cm, RNA Structure Determination, pp.237-251, 2016. ,
A history of scientific computing. Reading, Ma, USA, chapter Origins of the simplex method, pp.141-151, 1990. ,
VARNA : Interactive drawing and editing of the RNA secondary structure, Bioinformatics, vol.25, issue.15, 1974. ,
URL : https://hal.archives-ouvertes.fr/hal-00432548
A new entropy model for RNA : part IV, The Minimum Free Energy (MFE) and the thermodynamically most-probable folding pathway (TMPFP), Journal of Nucleic Acids Investigation, vol.5, issue.1, 2014. ,
A method for finding optimal RNA secondary structures using a new entropy model (VSfold) ,
, Nucleosides, Nucleotides, and Nucleic Acids, vol.25, issue.2, pp.171-189, 2006.
A new entropy model for RNA : part II. Persistence-related entropic contributions to RNA secondary structure free energy calculations, Journal of Nucleic Acids Investigation, vol.4, issue.1, pp.2-2, 2013. ,
A new entropy model for RNA : part III. Is the folding free energy landscape of RNA funnel shaped, Journal of Nucleic Acids Investigation, vol.5, issue.1, 2014. ,
Structural basis for the inhibition of the eukaryotic ribosome, Nature, vol.513, issue.7519, p.517, 2014. ,
Accurate SHAPEdirected RNA structure prediction, vol.23, 2009. ,
Prediction of RNA secondary structure, Proceedings of the National Academy of Sciences, vol.68, pp.2682-2685, 1971. ,
A new exact method to solve multi-objective combinatorial optimization problems, European Journal of Operational Research, vol.200, issue.1, pp.45-53, 2010. ,
URL : https://hal.archives-ouvertes.fr/inria-00522771
Self-assembling RNA square, Proceedings of the National Academy of Sciences, vol.108, issue.16, pp.6405-6408, 2011. ,
A statistical sampling algorithm for RNA secondary structure prediction, Nucleic Acids Research, vol.31, issue.24, pp.7280-7301, 2003. ,
Sfold web server for statistical folding and rational design of nucleic acids, Nucleic Acids Research, vol.32, issue.suppl_2, pp.135-141, 2004. ,
RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble, RNA, vol.11, issue.8, pp.1157-1166, 2005. ,
In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features, Nature, vol.505, issue.7485, p.696, 2014. ,
A partition function algorithm for nucleic acid secondary structure including pseudoknots, Journal of computational chemistry, vol.24, issue.13, pp.1664-1677, 2003. ,
Thermodynamic analysis of interacting nucleic acid strands, SIAM review, vol.49, issue.1, pp.65-88, 2007. ,
Algorithmes de graphes pour la recherche de motifs récurrents dans les structures tertiaires d'ARN, 2009. ,
CONTRAfold : RNA secondary structure prediction without physics-based models, Bioinformatics, vol.22, issue.14, pp.90-98, 2006. ,
Secondary structure in ribonucleic acids, Proceedings of the National Academy of Sciences of the United States of America, vol.45, p.482, 1959. ,
A review of fuzzy sets in decision sciences : Achievements, limitations and perspectives, Multiple Criteria Decision Analysis, pp.637-691, 2016. ,
URL : https://hal.archives-ouvertes.fr/hal-01345443
RNA sequence analysis using covariance models, Nucleic Acids Research, vol.22, issue.11, pp.2079-2088, 1994. ,
Probing the structure of RNAs in solution, Nucleic Acids Research, vol.15, issue.22, pp.9109-9128, 1987. ,
Multicriteria optimization, vol.491, 2005. ,
A level set method for multiobjective combinatorial optimization : Application to the quadratic assignment problem, vol.84, 2002. ,
Tfold : efficient in silico prediction of non-coding RNA secondary structures, Nucleic Acids Research, vol.38, issue.7, pp.2453-2466, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00647876
Some molecular details of the secondary structure of ribonucleic acid, Nature, vol.188, pp.98-101, 1960. ,
Boltzmann probability of RNA structural neighbors and riboswitch detection, Bioinformatics, vol.23, issue.16, pp.2054-2062, 2007. ,
RNAbor : a web server for RNA structural neighbors, Nucleic Acids Research, vol.35, issue.suppl_2, pp.305-309, 2007. ,
RIblast : An ultrafast RNA-RNA interaction prediction system for comprehensive lncRNA interaction analysis, BioRxiv, p.77271, 2016. ,
Developments in x-ray crystallographic structure determination of biological macromolecules, Science, vol.343, issue.6175, pp.1102-1108, 2014. ,
An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints, Journal of molecular biology, vol.254, issue.2, pp.163-174, 1995. ,
URL : https://hal.archives-ouvertes.fr/hal-02705265
Structure, stability and function of RNA pseudoknots involved in stimulating ribosomal frameshifting, Journal of molecular biology, vol.298, issue.2, pp.167-185, 2000. ,
Abstract shapes of RNA, Nucleic Acids Research, vol.32, issue.16, pp.4843-4851, 2004. ,
Algorithms and analyses for maximal vector computation. The VLDB Journal-The International Journal on Very Large Data Bases, vol.16, pp.5-28, 2007. ,
Rfam : annotating non-coding RNAs in complete genomes, Nucleic Acids Research, vol.33, issue.suppl_1, pp.121-124, 2005. ,
HIV-1 replication and the cellular eukaryotic translation apparatus, Viruses, vol.7, issue.1, pp.199-218, 2015. ,
RNA StrAT : RNA Structure Analysis Toolkit, 16th Annual International Conference on Intelligent Systems for Molecular Biology, p.31, 2008. ,
Optimization. Gurobi optimizer reference manual, 2015. ,
Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots, Proceedings of the National Academy of Sciences, vol.110, issue.14, pp.5498-5503, 2013. ,
K best solutions to combinatorial optimization problems, Annals of Operations Research, vol.4, issue.1, pp.123-143, 1985. ,
Prediction of RNA secondary structure using generalized centroid estimators, Bioinformatics, vol.25, issue.4, pp.465-473, 2008. ,
Clique is hard to approximate within n 1?, Proceedings of 37th Conference on Foundations of Computer Science, pp.627-636, 1996. ,
Etude algorithmique et statistique de la comparaison des structures secondaires d'ARN, vol.1, 2007. ,
GraphClust : alignment-free structural clustering of local RNA secondary structures, Bioinformatics, vol.28, issue.12, pp.224-232, 2012. ,
Local similarity in RNA secondary structures, Computational Systems Bioinformatics. CSB2003. Proceedings of the 2003 IEEE Bioinformatics Conference. CSB2003, pp.159-168, 2003. ,
Vienna RNA secondary structure server, Nucleic Acids Research, vol.31, issue.13, pp.3429-3431, 2003. ,
Abstract folding space analysis based on helices, RNA, vol.18, issue.12, pp.2135-2147, 2012. ,
High sensitivity RNA pseudoknot prediction, Nucleic Acids Research, vol.35, issue.2, pp.656-663, 2006. ,
, , pp.2018-2021
RNA tectonics (tectoRNA) for RNA nanostructure design and its application in synthetic biology, Wiley Interdisciplinary Reviews : RNA, vol.4, issue.6, pp.651-664, 2013. ,
Knotty : efficient and accurate prediction of complex RNA pseudoknot structures, Bioinformatics, vol.34, issue.22, pp.3849-3856, 2018. ,
Characterization of ribosomal frameshifting in HIV-1 gag-pol expression, Nature, vol.331, issue.6153, p.280, 1988. ,
Improved predictions of secondary structures for RNA, Proceedings of the National Academy of Sciences, vol.86, pp.7706-7710, 1989. ,
The RNA shapes studio, Bioinformatics, vol.31, issue.3, pp.423-425, 2014. ,
Graph coloring problems, vol.39, 2011. ,
Accurate prediction of secondary structure of tRNAs, Biochemical and biophysical research communications, vol.509, issue.1, pp.64-68, 2019. ,
Alignment of trees-an alternative to tree edit, Theoretical Computer Science, vol.143, issue.1, pp.137-148, 1995. ,
A general edit distance between RNA structures, Journal of computational biology, vol.9, issue.2, pp.371-388, 2002. ,
Multi-objective meta-heuristics : An overview of the current state-of-the-art, European journal of operational research, vol.137, issue.1, pp.1-9, 2002. ,
Reducibility among combinatorial problems, In Complexity of computer computations, pp.85-103, 1972. ,
An accessibility-incorporated method for accurate prediction of RNA-RNA interactions from sequence data, Bioinformatics, vol.33, issue.2, pp.202-209, 2017. ,
Forna (force-directed RNA) : simple and effective online RNA secondary structure diagrams, Bioinformatics, vol.31, issue.20, pp.3377-3379, 2015. ,
Genome-wide measurement of RNA secondary structure in yeast, Nature, vol.467, issue.7311, p.103, 2010. ,
A new algorithm for generating all nondominated solutions of multiobjective discrete optimization problems, European Journal of Operational Research, vol.232, issue.3, pp.479-488, 2014. ,
Rfold : an exact algorithm for computing local base pairing probabilities, Bioinformatics, vol.24, issue.3, pp.367-373, 2007. ,
A detailed investigation of accessibilities around target sites of siRNAs and miRNAs, Bioinformatics, vol.27, issue.13, pp.1788-1797, 2011. ,
An algorithm for the multiple objective integer linear programming problem, European Journal of Operational Research, vol.9, issue.4, pp.378-385, 1982. ,
Enzymatic approaches to probing of RNA secondary and tertiary structure, In Methods in enzymology, vol.180, pp.192-212, 1989. ,
Multi-objective optimization using genetic algorithms : A tutorial, Reliability Engineering & System Safety, vol.91, issue.9, pp.992-1007, 2006. ,
RNAhybrid : microRNA target prediction easy, fast and flexible, Nucleic Acids Research, vol.34, issue.suppl_2, pp.451-454, 2006. ,
Problems of optimization : an exact algorithm for finding a maximum clique optimized for dense graphs, Proceedings-Estonian Academy of Sciences Physics Mathematics, vol.54, p.79, 2005. ,
On finding the maxima of a set of vectors, Journal of the ACM (JACM), vol.22, issue.4, pp.469-476, 1975. ,
A comprehensive comparison of general RNA-RNA interaction prediction methods, Nucleic Acids Research, vol.44, issue.7, pp.61-61, 2015. ,
A procedure for computing the k best solutions to discrete optimization problems and its application to the shortest path problem. Management science, vol.18, pp.401-405, 1972. ,
Bi-objective integer programming for RNA secondary structure prediction with pseudoknots, BMC bioinformatics, vol.19, issue.1, p.13, 2018. ,
URL : https://hal.archives-ouvertes.fr/hal-01696144
RCPred : RNA complex prediction as a constrained maximum weight clique problem, BMC bioinformatics, vol.20, issue.3, p.128, 2019. ,
URL : https://hal.archives-ouvertes.fr/hal-02105691
Parallel partitioning method (PPM) : A new exact method to solve bi-objective problems, Computers & operations research, vol.34, issue.8, pp.2450-2462, 2007. ,
URL : https://hal.archives-ouvertes.fr/inria-00269956
Geometric nomenclature and classification of RNA base pairs, RNA, vol.7, issue.4, pp.499-512, 2001. ,
Characterization and visualization of RNA secondary structure Boltzmann ensemble via information theory, BMC bioinformatics, vol.19, issue.1, p.82, 2018. ,
RNACluster : An integrated tool for RNA secondary structure comparison and clustering, Journal of computational chemistry, vol.29, issue.9, pp.1517-1526, 2008. ,
Fuzzy kernel clustering of RNA secondary structure ensemble using a novel similarity metric, Journal of Biomolecular Structure and Dynamics, vol.25, issue.6, pp.685-696, 2008. ,
Finding all nondominated points of multi-objective integer programs, Journal of Global Optimization, vol.57, issue.2, pp.347-365, 2013. ,
ViennaRNA package 2.0, Algorithms for Molecular Biology, vol.6, issue.1, p.26, 2011. ,
SHAPE-Seq 2.0 : systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing, Nucleic Acids Research, vol.42, issue.21, pp.165-165, 2014. ,
SHAPE-directed RNA secondary structure prediction, Methods, vol.52, issue.2, pp.150-158, 2010. ,
RiboSketch : versatile visualization of multi-stranded RNA and DNA secondary structure, Bioinformatics, vol.34, issue.24, pp.4297-4299, 2018. ,
Improved RNA secondary structure prediction by maximizing expected pair accuracy, RNA, vol.15, pp.1805-1813, 2009. ,
RNA pseudoknot prediction in energy-based models, Journal of computational biology, vol.7, issue.3-4, pp.409-427, 2000. ,
, UNAFold. In Bioinformatics, pp.3-31, 2008.
A complementary pivoting approach to the maximum weight clique problem, SIAM Journal on Optimization, vol.12, issue.4, pp.928-948, 2002. ,
Predicting oligonucleotide affinity to nucleic acid targets, RNA, vol.5, issue.11, pp.1458-1469, 1999. ,
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of molecular biology, vol.288, issue.5, pp.911-940, 1999. ,
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure, Proceedings of the National Academy of Sciences, vol.101, issue.19, pp.7287-7292, 2004. ,
Functionally conserved architecture of hepatitis C virus RNA genomes, Proceedings of the National Academy of Sciences, vol.112, issue.12, pp.3692-3697, 2015. ,
Effective implementation of the ?-constraint method in multi-objective mathematical programming problems, Applied mathematics and computation, vol.213, issue.2, pp.455-465, 2009. ,
An improved version of the augmented ?-constraint method (AUGMECON2) for finding the exact pareto set in multi-objective integer programming problems, Applied Mathematics and Computation, vol.219, issue.18, pp.9652-9669, 2013. ,
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. ,
On the implementation of a primal-dual interior point method, SIAM Journal on optimization, vol.2, issue.4, pp.575-601, 1992. ,
Predicting RNA secondary structures with pseudoknots by MCMC sampling, Journal of mathematical biology, vol.56, issue.1-2, pp.161-181, 2008. ,
RNAscClust : clustering RNA sequences using structure conservation and graph based motifs, Bioinformatics, vol.33, issue.14, pp.2089-2096, 2017. ,
Integration of accessibility data from structure probing into RNA-RNA interaction prediction. bioRxiv, p.359323, 2018. ,
Novel HIV-1 fusion inhibition peptides : designing the next generation of drugs, Antiviral Chemistry and Chemotherapy, vol.22, issue.4, pp.151-158, 2012. ,
Gibbs/MCMC sampling for multiple RNA interaction with sub-optimal solutions, International Conference on Algorithms for Computational Biology, pp.78-90, 2016. ,
RNA-RNA interaction prediction using genetic algorithm, Algorithms for Molecular Biology, vol.9, issue.1, p.17, 2014. ,
Barrier heights between ground states in a model of RNA secondary structure, Journal of Physics A : Mathematical and General, vol.31, issue.14, p.3153, 1998. ,
Algebraic and combinatorial properties of common RNA pseudoknot classes with applications, Journal of Computational Biology, vol.19, issue.10, pp.1134-1150, 2012. ,
On spectral clustering : Analysis and an algorithm, Advances in neural information processing systems, pp.849-856, 2002. ,
Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease, Nature reviews drug discovery, vol.5, issue.2, 2006. ,
Fast algorithm for predicting the secondary structure of single-stranded RNA, Proceedings of the National Academy of Sciences, vol.77, issue.11, pp.6309-6313, 1980. ,
Algorithms for loop matchings, SIAM Journal on Applied mathematics, vol.35, issue.1, pp.68-82, 1978. ,
A new algorithm for the maximum-weight clique problem, Electronic Notes in Discrete Mathematics, vol.3, pp.153-156, 1999. ,
Local similarity between quotiented ordered trees, Journal of Discrete Algorithms, vol.5, issue.1, pp.23-35, 2007. ,
URL : https://hal.archives-ouvertes.fr/hal-00307119
SeqFold : genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data, Genome Research, vol.23, issue.2, pp.377-387, 2013. ,
Multi-objective integer programming : a general approach for generating all non-dominated solutions, European Journal of Operational Research, vol.199, issue.1, pp.25-35, 2009. ,
Multi-objective integer programming : An improved recursive algorithm, Journal of Optimization Theory and Applications, vol.160, issue.2, pp.470-482, 2014. ,
On the approximability of trade-offs and optimal access of web sources, Proceedings 41st Annual Symposium on Foundations of Computer Science, pp.86-92, 2000. ,
The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data, Nature, vol.452, issue.7183, p.51, 2008. ,
Automated classification of RNA 3D motifs and the RNA 3D motif atlas, Rna, vol.19, issue.10, pp.1327-1340, 2013. ,
Prespliceosome structure provides insights into spliceosome assembly and regulation, Nature, vol.559, issue.7714, p.419, 2018. ,
Prediction of RNA secondary structure with pseudoknots using integer programming, BMC bioinformatics, vol.10, issue.1, p.38, 2009. ,
Dynamic programming algorithms for RNA structure prediction with binding sites, Biocomputing 2010, pp.98-107, 2010. ,
CoFold : an RNA structure prediction method that takes co-transcriptional folding into account, 2012. ,
A two phase method for multi-objective integer programming and its application to the assignment problem with three objectives, Discrete Optimization, vol.7, issue.3, pp.149-165, 2010. ,
URL : https://hal.archives-ouvertes.fr/hal-00485936
Conformation of the TAR RNA-arginine complex by NMR spectroscopy, Science, vol.257, issue.5066, pp.76-80, 1992. ,
Approximating the maximum vertex/edge weighted clique using local search, Journal of Heuristics, vol.14, issue.2, pp.117-134, 2008. ,
Evaluation of the information content of RNA structure mapping data for secondary structure prediction, RNA, 2010. ,
The impact of quality indicators on the rating of multi-objective evolutionary algorithms, Applied Soft Computing, vol.55, pp.265-275, 2017. ,
Locomotif : from graphical motif description to RNA motif search, Bioinformatics, vol.23, issue.13, pp.392-400, 2007. ,
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics, BMC bioinformatics, vol.5, issue.1, p.104, 2004. ,
RNA secondary structure analysis using the RNAshapes package, Current protocols in bioinformatics, vol.26, issue.1, pp.12-20, 2009. ,
In-line probing analysis of riboswitches, post-transcriptional gene regulation, pp.53-67, 2008. ,
Topology and prediction of RNA pseudoknots, Bioinformatics, vol.27, issue.8, pp.1076-1085, 2011. ,
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.207-214, 2012. ,
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
HotKnots : heuristic prediction of RNA secondary structures including pseudoknots, RNA, vol.11, issue.10, pp.1494-1504, 2005. ,
RNAstructure : software for RNA secondary structure prediction and analysis, BMC bioinformatics, vol.11, issue.1, p.129, 2010. ,
A dynamic programming algorithm for RNA structure prediction including pseudoknots, Journal of Molecular Biology, vol.285, issue.5, pp.2053-2068, 1999. ,
Profiling small RNA reveals multimodal substructural signals in a boltzmann ensemble, Nucleic Acids Research, vol.42, issue.22, pp.171-171, 2014. ,
An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots, Bioinformatics, vol.20, issue.1, pp.58-66, 2004. ,
MicroRNA therapeutics : towards a new era for the management of cancer and other diseases, Nature reviews Drug discovery, vol.16, issue.3, p.203, 2017. ,
Pareto front approximation with adaptive weighted sum method in multiobjective simulation optimization, Winter Simulation Conference, pp.623-633, 2009. ,
An integrative approach for predicting the RNA secondary structure for the HIV-1 Gag UTR using probing data, JOBIM -Journées Ouvertes en Biologie, Informatique et Mathématiques -2017, vol.102, 2017. ,
URL : https://hal.archives-ouvertes.fr/hal-01534587
Stochastic context-free grammars for tRNA modeling, Nucleic Acids Research, vol.22, issue.23, pp.5112-5120, 1994. ,
Fast prediction of RNA-RNA interaction, Algorithms for Molecular Biology, vol.5, issue.1, 2010. ,
Globin mRNA sequences : analysis of base pairing and evolutionary implications, Cold Spring Harbor symposia on quantitative biology, vol.42, pp.985-1002, 1978. ,
Determining the total colouring number is NP-hard, Discrete Mathematics, vol.78, issue.3, pp.315-319, 1989. ,
IPknot : fast and accurate prediction of RNA secondary structures with pseudoknots using integer programming, Bioinformatics, vol.27, issue.13, pp.85-93, 2011. ,
Pareto optimization in algebraic dynamic programming, Algorithms for Molecular Biology, vol.10, issue.1, p.22, 2015. ,
Massively parallel RNA chemical mapping with a reduced bias MAP-seq protocol, RNA Folding, pp.95-117 ,
, , 2014.
Nano RNA aptamer wire for analysis of vitamin B12, Analytical biochemistry, vol.427, issue.2, pp.151-157, 2012. ,
Predicting thermodynamic properties of RNA, Methods in enzymology, vol.259, pp.242-261, 1995. ,
Comparing multiple RNA secondary structures using tree comparisons, Bioinformatics, vol.6, issue.4, pp.309-318, 1990. ,
Impact of the energy model on the complexity of RNA folding with pseudoknots, Annual Symposium on Combinatorial Pattern Matching, pp.321-333, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-00670232
Local search based evolutionary multi-objective optimization algorithm for constrained and unconstrained problems, IEEE Congress on Evolutionary Computation, pp.2919-2926, 2009. ,
A hybrid heuristic for the maximum clique problem, Journal of Heuristics, vol.12, issue.1-2, pp.5-22, 2006. ,
Improving RNA secondary structure prediction with structure mapping data, Methods in enzymology, vol.553, pp.91-114, 2015. ,
Modeling RNA secondary structure folding ensembles using SHAPE mapping data, Nucleic Acids Research, vol.46, issue.1, pp.314-323, 2017. ,
Tandem riboswitch architectures exhibit complex gene control functions, Science, vol.314, issue.5797, pp.300-304, 2006. ,
Cryo-EM structure of the Ebola virus nucleoprotein-RNA complex at 3.6 å resolution, Nature, vol.563, issue.7729, p.137, 2018. ,
A method for finding the set of non-dominated vectors for multiple objective integer linear programs, European Journal of Operational Research, vol.158, issue.1, pp.46-55, 2004. ,
A method for finding well-dispersed subsets of nondominated vectors for multiple objective mixed integer linear programs, European Journal of Operational Research, vol.180, issue.3, pp.1011-1027, 2007. ,
RNAplex : a fast tool for RNA-RNA interaction search, Bioinformatics, vol.24, issue.22, pp.2657-2663, 2008. ,
Fast accessibility-based prediction of RNA-RNA interactions, Bioinformatics, vol.27, issue.14, pp.1934-1940, 2011. ,
StructureFold : genome-wide RNA secondary structure mapping and reconstruction in vivo, Bioinformatics, vol.31, issue.16, pp.2668-2675, 2015. ,
Pseudobase++ : an extension of pseudobase for easy searching, formatting and visualization of pseudoknots, Nucleic Acids Research, vol.37, issue.1, pp.127-135, 2009. ,
Estimation of secondary structure in ribonucleic acids, Nature, vol.230, issue.5293, p.362, 1971. ,
Improved estimation of secondary structure in ribonucleic acids, Nature New Biology, vol.246, issue.150, p.40, 1973. ,
TargetRNA : a tool for predicting targets of small RNA action in bacteria, Nucleic Acids Research, vol.36, issue.suppl_2, pp.109-113, 2008. ,
Approximating the maximum multiple RNA interaction problem, Theoretical Computer Science, vol.556, pp.63-70, 2014. ,
Finding multiple solutions to general integer linear programs, European Journal of Operational Research, vol.184, issue.2, pp.802-809, 2008. ,
NNDB : the nearest neighbor parameter database for predicting stability of nucleic acid secondary structure, Nucleic Acids Research, vol.38, issue.suppl_1, pp.280-282, 2009. ,
, RNA structure prediction. Annual review of biophysics and biophysical chemistry, vol.17, issue.1, pp.167-192, 1988.
Tree adjoining grammars for RNA structure prediction, Theoretical computer science, vol.210, issue.2, pp.277-303, 1999. ,
The two phases method : An efficient procedure to solve bi-objective combinatorial optimization problems, Foundations of Computing and Decision Sciences, vol.20, issue.2, pp.149-165, 1995. ,
FragSeq : transcriptomewide RNA structure probing using high-throughput sequencing, Nature methods, vol.7, issue.12, p.995, 2010. ,
Gradientbased pareto front approximation applied to turbomachinery shape optimization. Engineering with Computers, pp.1-11, 2019. ,
A tutorial on spectral clustering, Statistics and computing, vol.17, issue.4, pp.395-416, 2007. ,
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding, Proceedings of the National Academy of Sciences, vol.91, issue.20, pp.9218-9222, 1994. ,
Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing, Nature protocols, vol.8, issue.5, p.849, 2013. ,
Landscape and variation of RNA secondary structure across the human transcriptome, Nature, vol.505, issue.7485, p.706, 2014. ,
DMfold : A novel method to predict RNA secondary structure with pseudoknots based on deep learning and improved base pair maximization principle, Frontiers in genetics, vol.10, p.143, 2019. ,
Combinatorial branch-and-bound for the maximum weight independent set problem. Relatório técnico, 2006. ,
RNA folding with soft constraints : reconciliation of probing data and thermodynamic secondary structure prediction, Nucleic Acids Research, vol.40, issue.10, pp.4261-4272, 2012. ,
Secondary structure of single-stranded nucleic acids, Adv. math. suppl. studies, vol.1, pp.167-212, 1978. ,
Architecture and secondary structure of an entire HIV-1 RNA genome, Nature, vol.460, issue.7256, p.711, 2009. ,
High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states, PLoS biology, vol.6, issue.4, p.96, 2008. ,
Spliceosome structure and function. Cold Spring Harbor perspectives in biology, vol.3, p.3707, 2011. ,
Model building in mathematical programming, The Atrium, 1999. ,
Phylogenetic analysis of tmRNA secondary structure, Rna, vol.2, issue.12, pp.1306-1310, 1996. ,
A dynamic programming algorithm for finding alternative RNA secondary structure, Nucleic Acids Research, vol.14, issue.1, pp.299-315, 1986. ,
Ribosome biogenesis in the yeast saccharomyces cerevisiae, Genetics, vol.195, issue.3, pp.643-681, 2013. ,
Multi-neighborhood tabu search for the maximum weight clique problem, Annals of Operations Research, vol.196, issue.1, pp.611-634, 2012. ,
URL : https://hal.archives-ouvertes.fr/hal-01389283
Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data, Nucleic Acids Research, vol.43, issue.15, pp.7247-7259, 2015. ,
RNAex : an RNA secondary structure prediction server enhanced by high-throughput structure-probing data, Nucleic Acids Research, vol.44, issue.W1, pp.294-301, 2016. ,
Complete suboptimal folding of RNA and the stability of secondary structures, Biopolymers : Original Research on Biomolecules, vol.49, issue.2, pp.145-165, 1999. ,
Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs, Biochemistry, vol.37, issue.42, pp.14719-14735, 1998. ,
A comprehensive survey of clustering algorithms, Annals of Data Science, vol.2, issue.2, pp.165-193, 2015. ,
VfoldCPX server : Predicting RNA-RNA complex structure and stability, PloS One, vol.11, issue.9, p.163454, 2016. ,
An improved algorithm for the prediction of optimum and suboptimum folding structures of long single-stranded RNA, Bioinformatics, vol.3, issue.1, pp.31-35, 1987. ,
Tools for the automatic identification and classification of RNA base pairs, Nucleic Acids Research, vol.31, issue.13, pp.3450-3460, 2003. ,
NUPACK : analysis and design of nucleic acid systems, Journal of computational chemistry, vol.32, issue.1, pp.170-173, 2011. ,
Integrating chemical footprinting data into RNA secondary structure prediction, PLoS One, vol.7, issue.10, p.45160, 2012. ,
Function of hexameric RNA in packaging of bacteriophage ?29 DNA in vitro, Molecular cell, vol.2, issue.1, pp.141-147, 1998. ,
Simple fast algorithms for the editing distance between trees and related problems, SIAM journal on computing, vol.18, issue.6, pp.1245-1262, 1989. ,
A simple augmented -constraint method for multiobjective mathematical integer programming problems, European Journal of Operational Research, vol.234, issue.1, pp.15-24, 2014. ,
An atomic structure of the human spliceosome, Cell, vol.169, issue.5, pp.918-929, 2017. ,
NONCODE 2016 : an informative and valuable data source of long non-coding RNAs, Nucleic Acids Research, vol.44, issue.D1, pp.203-208, 2015. ,
Computer prediction of RNA structure, In Methods in enzymology, vol.180, pp.262-288, 1989. ,
On finding all suboptimal foldings of an RNA molecule, Science, vol.244, issue.4900, pp.48-52, 1989. ,
Mfold web server for nucleic acid folding and hybridization prediction, Nucleic Acids Research, vol.31, issue.13, pp.3406-3415, 2003. ,
RNA secondary structures and their prediction, Bulletin of mathematical biology, vol.46, issue.4, pp.591-621, 1984. ,
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information, Nucleic Acids Research, vol.9, issue.1, pp.133-148, 1981. ,