TY - JOUR AU - Shabalina, S. A. AU - Spiridonov, N. A. PY - 2004 DA - 2004// TI - The mammalian transcriptome and the function of non-coding DNA sequences JO - Genome Biology VL - 5 UR - https://doi.org/10.1186/gb-2004-5-4-105 DO - 10.1186/gb-2004-5-4-105 ID - Shabalina2004 ER - TY - JOUR AU - Batenburg, F. H. D. v. a. n. AU - Gultyaev, A. P. AU - Pleij, C. W. A. AU - Ng, J. AU - Oliehoek, J. PY - 2000 DA - 2000// TI - PseudoBase: a database with RNA pseudoknots JO - Nucleic Acids Research VL - 28 UR - https://doi.org/10.1093/nar/28.1.201 DO - 10.1093/nar/28.1.201 ID - Batenburg2000 ER - TY - JOUR AU - Zuker, M. AU - Stiegler, P. PY - 1981 DA - 1981// TI - Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information JO - Nucleic Acids Research VL - 9 UR - https://doi.org/10.1093/nar/9.1.133 DO - 10.1093/nar/9.1.133 ID - Zuker1981 ER - TY - JOUR AU - Zuker, M. PY - 2003 DA - 2003// TI - Mfold web server for nucleic acid folding and hybridization prediction JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg595 DO - 10.1093/nar/gkg595 ID - Zuker2003 ER - TY - JOUR AU - Rivas, E. AU - Eddy, S. R. PY - 1999 DA - 1999// TI - A dynamic programming algorithm for RNA structure prediction including pseudoknots JO - Journal of Molecular Biology VL - 285 UR - https://doi.org/10.1006/jmbi.1998.2436 DO - 10.1006/jmbi.1998.2436 ID - Rivas1999 ER - TY - CHAP AU - Reeder, J. AU - Giegerich, R. PY - 2004 DA - 2004// TI - Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics BT - BMC Bioinformatics ID - Reeder2004 ER - TY - JOUR AU - Ruan, J. AU - Stormo, G. D. AU - Zhang, W. PY - 2004 DA - 2004// TI - An iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/btg373 DO - 10.1093/bioinformatics/btg373 ID - Ruan2004 ER - TY - JOUR AU - Akutsu, T. PY - 2000 DA - 2000// TI - Dynamic programming algorithms for RNA secondary structure prediction with pseudoknots JO - Discrete Applied Mathematics VL - 104 UR - https://doi.org/10.1016/S0166-218X(00)00186-4 DO - 10.1016/S0166-218X(00)00186-4 ID - Akutsu2000 ER - TY - JOUR AU - Lyngsø, R. B. AU - Pedersen, C. N. S. PY - 2000 DA - 2000// TI - RNA pseudoknot prediction in energy-based models JO - Journal of Computational Biology VL - 7 UR - https://doi.org/10.1089/106652700750050862 DO - 10.1089/106652700750050862 ID - Lyngsø2000 ER - TY - JOUR AU - Uemura, Y. AU - Hasegawa, A. AU - Kobayashi, S. AU - Yokomori, T. PY - 1999 DA - 1999// TI - Tree adjoining grammars for RNA structure prediction JO - Theoretical Computer Science VL - 210 UR - https://doi.org/10.1016/S0304-3975(98)00090-5 DO - 10.1016/S0304-3975(98)00090-5 ID - Uemura1999 ER - TY - JOUR AU - Matsui, H. AU - Sato, K. AU - Sakakibara, Y. PY - 2005 DA - 2005// TI - Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti385 DO - 10.1093/bioinformatics/bti385 ID - Matsui2005 ER - TY - JOUR AU - Rivas, E. AU - Eddy, S. R. PY - 2000 DA - 2000// TI - The language of RNA: a formal grammar that includes pseudoknots JO - Bioinformatics VL - 16 UR - https://doi.org/10.1093/bioinformatics/16.4.334 DO - 10.1093/bioinformatics/16.4.334 ID - Rivas2000 ER - TY - JOUR AU - Cai, L. AU - Malmberg, R. L. AU - Wu, Y. PY - 2003 DA - 2003// TI - Stochastic modeling of RNA pseudoknotted structures: a grammatical approach JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg1007 DO - 10.1093/bioinformatics/btg1007 ID - Cai2003 ER - TY - JOUR AU - Kato, Y. AU - Seki, H. AU - Kasami, T. PY - 2006 DA - 2006// TI - RNA pseudoknotted structure prediction using stochastic multiple context-free grammar JO - IPSJ Transactions on Bioinformatics VL - 47 ID - Kato2006 ER - TY - JOUR AU - Sankoff, D. PY - 1985 DA - 1985// TI - Simultaneous solution of the RNA folding, alignment and protosequence problems JO - SIAM Journal on Applied Mathematics VL - 45 UR - https://doi.org/10.1137/0145048 DO - 10.1137/0145048 ID - Sankoff1985 ER - TY - JOUR AU - Mathews, D. H. AU - Turner, D. H. PY - 2002 DA - 2002// TI - Dynalign: an algorithm for finding the secondary structure common to two RNA sequences JO - Journal of Molecular Biology VL - 317 UR - https://doi.org/10.1006/jmbi.2001.5351 DO - 10.1006/jmbi.2001.5351 ID - Mathews2002 ER - TY - JOUR AU - Parisien, M. AU - Major, F. PY - 2008 DA - 2008// TI - The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data JO - Nature VL - 452 UR - https://doi.org/10.1038/nature06684 DO - 10.1038/nature06684 ID - Parisien2008 ER - TY - JOUR AU - Xu, J. AU - Li, M. AU - Kim, D. AU - Xu, Y. PY - 2003 DA - 2003// TI - RAPTOR: optimal protein threading by linear programming JO - J Bioinform Comput Biol VL - 1 UR - https://doi.org/10.1142/S0219720003000186 DO - 10.1142/S0219720003000186 ID - Xu2003 ER - TY - STD TI - ILOG CPLEX. [http://www.ilog.com/products/cplex/] UR - http://www.ilog.com/products/cplex/ ID - ref19 ER - TY - JOUR AU - Griffiths-Jones, S. AU - Moxon, S. AU - Marshall, M. AU - Khanna, A. AU - Eddy, S. R. AU - Bateman, A. PY - 2005 DA - 2005// TI - Rfam: annotating non-coding RNAs in complete genomes JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki081 DO - 10.1093/nar/gki081 ID - Griffiths-Jones2005 ER - TY - JOUR AU - Zuker, M. PY - 1989 DA - 1989// TI - On finding all suboptimal foldings of an RNA molecule JO - Science VL - 244 UR - https://doi.org/10.1126/science.2468181 DO - 10.1126/science.2468181 ID - Zuker1989 ER -