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A Permutation Based Simulated Annealing Algorithm to Predict Pseudoknotted RNA Secondary Structures

, and . Int. J. Bioinformatics Res. Appl., 11 (5): 375--396 (September 2015)
DOI: 10.1504/IJBRA.2015.071938

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EvoDNN - An Evolutionary Deep Neural Network with Heterogeneous Activation Functions., , and . CEC, page 2362-2369. IEEE, (2019)Improved Covariance Model Parameter Estimation Using RNA Thermodynamic Properties., and . BIONETICS, page 185-191. ICST / IEEE, (2007)Analysis of Thermodynamic Models and Performance in RnaPredict - An Evolutionary Algorithm for RNA Folding., , and . CIBCB, page 1-9. IEEE, (2006)A hybrid clustering/evolutionary algorithm for RNA folding., and . CIBCB, page 15-21. IEEE, (2008)SARNA-Predict-pk: Predicting RNA Secondary Structures Including Pseudoknots, and . Proceedings of the IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, page 1--8. (2008)Ebbie: automated analysis and storage of small RNA cloning data using a dynamic web server., , and . BMC Bioinform., (2006)Numerical integration methods and layout improvements in the context of dynamic RNA visualization., and . BMC Bioinform., 18 (1): 282:1-282:18 (2017)A parallel evolutionary algorithm for RNA secondary structure prediction using stacking-energies (INN and INN-HB)., , and . CIBCB, page 223-230. IEEE, (2004)Convergence Characteristics of Keep-Best Reproduction., and . SAC, page 312-318. ACM, (1999)Permutation-based RNA secondary structure prediction via a genetic algorithm., , and . IEEE Congress on Evolutionary Computation, page 335-342. IEEE, (2003)