TY - JOUR AU - Pleij, C. W. A. AU - Rietveld, K. AU - Bosch, L. PY - 1985 DA - 1985// TI - A new principle of RNA folding based on pseudoknotting JO - Nucleic Acids Res VL - 13 UR - https://doi.org/10.1093/nar/13.5.1717 DO - 10.1093/nar/13.5.1717 ID - Pleij1985 ER - TY - JOUR AU - Xin, Y. AU - Laing, C. AU - Leontis, N. B. AU - Schlick, T. PY - 2008 DA - 2008// TI - Annotation of tertiary interactions in RNA structures reveals variations and correlations JO - RNA VL - 14 UR - https://doi.org/10.1261/rna.1249208 DO - 10.1261/rna.1249208 ID - Xin2008 ER - TY - JOUR AU - Laing, C. AU - Wen, D. AU - Wang, J. T. L. AU - Schlick, T. PY - 2012 DA - 2012// TI - Predicting coaxial helical stacking in RNA junctions JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gkr629 DO - 10.1093/nar/gkr629 ID - Laing2012 ER - TY - JOUR AU - Huang, Z. AU - Wu, Y. AU - Robertson, J. AU - Feng, L. AU - Malmberg, R. AU - Cai, L. PY - 2008 DA - 2008// TI - Fast and accurate search for non-coding RNA pseudoknot structures in genomes JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn393 DO - 10.1093/bioinformatics/btn393 ID - Huang2008 ER - TY - JOUR AU - Griffiths-Jones, S. AU - Bateman, A. AU - Marshall, M. AU - Khanna, A. AU - Eddy, S. R. PY - 2003 DA - 2003// TI - Rfam: an RNA family database JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg006 DO - 10.1093/nar/gkg006 ID - Griffiths-Jones2003 ER - TY - JOUR AU - Adams, P. L. AU - Stahley, M. R. AU - Kosek, A. B. AU - Wang, J. AU - Strobel, S. A. PY - 2004 DA - 2004// TI - Crystal structure of a self-splicing group I intron with both exons JO - Nature VL - 430 UR - https://doi.org/10.1038/nature02642 DO - 10.1038/nature02642 ID - Adams2004 ER - TY - JOUR AU - Theimer, C. A. AU - Blois, C. A. AU - Feigon, J. PY - 2005 DA - 2005// TI - Structure of the human telomerase RNA pseudoknot reveals conserved tertiary interactions essential for function JO - Mol Cell VL - 17 UR - https://doi.org/10.1016/j.molcel.2005.01.017 DO - 10.1016/j.molcel.2005.01.017 ID - Theimer2005 ER - TY - JOUR AU - Staple, D. W. AU - Butcher, S. E. PY - 2005 DA - 2005// TI - Pseudoknots: RNA structures with diverse functions JO - PLoS Biol VL - 3 UR - https://doi.org/10.1371/journal.pbio.0030213 DO - 10.1371/journal.pbio.0030213 ID - Staple2005 ER - TY - JOUR AU - Reidys, C. M. AU - Huang, F. W. D. AU - Andersen, J. E. AU - Penner, R. C. AU - Stadler, P. F. AU - Nebel, M. E. PY - 2011 DA - 2011// TI - Topology and prediction of RNA pseudoknots JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr090 DO - 10.1093/bioinformatics/btr090 ID - Reidys2011 ER - TY - JOUR AU - Nixon, P. L. AU - Rangan, A. AU - Kim, Y. G. AU - Rich, A. AU - Hoffman, D. W. AU - Hennig, M. PY - 2002 DA - 2002// TI - Solution structure of a luteoviral P1-P2 frameshifting mRNA pseudoknot JO - J Mol Biol VL - 322 UR - https://doi.org/10.1016/S0022-2836(02)00779-9 DO - 10.1016/S0022-2836(02)00779-9 ID - Nixon2002 ER - TY - JOUR AU - Xu, X. AU - Ji, Y. AU - Stormo, G. D. PY - 2007 DA - 2007// TI - RNA Sampler: a new sampling based algorithm for common RNA secondary structure prediction and structural alignment JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm272 DO - 10.1093/bioinformatics/btm272 ID - Xu2007 ER - TY - JOUR AU - Sato, K. AU - Kato, Y. AU - Akutsu, T. AU - Asai, K. AU - Sakakibara, Y. PY - 2012 DA - 2012// TI - DAFS: simultaneous aligning and folding of RNA sequences via dual decomposition JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts612 DO - 10.1093/bioinformatics/bts612 ID - Sato2012 ER - TY - JOUR AU - Meyer, I. M. AU - Miklos, I. PY - 2007 DA - 2007// TI - SimulFold: simultaneously inferring RNA structures including pseudoknots, alignments, and trees using a Bayesian MCMC framework JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030149 DO - 10.1371/journal.pcbi.0030149 ID - Meyer2007 ER - TY - JOUR AU - Sorescu, D. A. AU - Mohl, M. AU - Mann, M. AU - Backofen, R. AU - Will, S. PY - 2012 DA - 2012// TI - CARNA-alignment of RNA structure ensembles JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks491 DO - 10.1093/nar/gks491 ID - Sorescu2012 ER - TY - JOUR AU - Andronescu, M. AU - Bereg, V. AU - Hoos, H. H. AU - Condon, A. PY - 2008 DA - 2008// TI - RNA STRAND: the RNA secondary structure and statistical analysis database JO - BMC Bioinformatics. VL - 9 UR - https://doi.org/10.1186/1471-2105-9-340 DO - 10.1186/1471-2105-9-340 ID - Andronescu2008 ER - TY - JOUR AU - Berman, H. M. AU - Westbrook, J. AU - Feng, Z. AU - Gilliland, G. AU - Bhat, T. N. AU - Weissig, H. PY - 2000 DA - 2000// TI - The protein data bank JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.235 DO - 10.1093/nar/28.1.235 ID - Berman2000 ER - TY - JOUR AU - Batenburg, F. H. D. 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 Res 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 - Taufer, M. AU - Licon, A. AU - Araiza, R. AU - Mireles, D. AU - Batenburg, F. H. AU - Gultyaev, A. P. PY - 2009 DA - 2009// TI - PseudoBase++: an extension of PseudoBase for easy searching, formatting and visualization of pseudoknots JO - Nucleic Acids Res VL - 37 UR - https://doi.org/10.1093/nar/gkn806 DO - 10.1093/nar/gkn806 ID - Taufer2009 ER - TY - JOUR AU - Miyazawa, S. PY - 1995 DA - 1995// TI - A reliable sequence alignment method based on probabilities of residue correspondences JO - Protein Eng VL - 8 UR - https://doi.org/10.1093/protein/8.10.999 DO - 10.1093/protein/8.10.999 ID - Miyazawa1995 ER - TY - JOUR AU - Roshan, U. AU - Livesay, D. R. PY - 2006 DA - 2006// TI - Probalign: multiple sequence alignment using partition function posterior probabilities JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl472 DO - 10.1093/bioinformatics/btl472 ID - Roshan2006 ER - TY - JOUR AU - Do, C. B. AU - Mahabhashyam, M. S. AU - Brudno, M. AU - Batzoglou, S. PY - 2005 DA - 2005// TI - ProbCons: probabilistic consistency-based multiple sequence alignment JO - Genome Res VL - 15 UR - https://doi.org/10.1101/gr.2821705 DO - 10.1101/gr.2821705 ID - Do2005 ER - TY - JOUR AU - Will, S. AU - Joshi, T. AU - Hofacker, I. L. AU - Stadler, P. F. AU - Backofen, R. PY - 2012 DA - 2012// TI - LocARNA-P: accurate boundary prediction and improved detection of structural RNAs JO - RNA VL - 18 UR - https://doi.org/10.1261/rna.029041.111 DO - 10.1261/rna.029041.111 ID - Will2012 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 - J Mol Biol VL - 317 UR - https://doi.org/10.1006/jmbi.2001.5351 DO - 10.1006/jmbi.2001.5351 ID - Mathews2002 ER - TY - JOUR AU - Torarinsson, E. AU - Havgaard, J. H. AU - Gorodkin, J. PY - 2007 DA - 2007// TI - Multiple structural alignment and clustering of RNA sequences JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm049 DO - 10.1093/bioinformatics/btm049 ID - Torarinsson2007 ER - TY - JOUR AU - Will, S. AU - Reiche, K. AU - Hofacker, I. L. AU - Stadler, P. F. AU - Backofen, R. PY - 2007 DA - 2007// TI - Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering JO - PLoS Comput Biol VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030065 DO - 10.1371/journal.pcbi.0030065 ID - Will2007 ER - TY - JOUR AU - Mohl, M. AU - Will, S. AU - Backofen, R. PY - 2010 DA - 2010// TI - Lifting prediction to alignment of RNA pseudoknots JO - J Comput Biol VL - 17 UR - https://doi.org/10.1089/cmb.2009.0168 DO - 10.1089/cmb.2009.0168 ID - Mohl2010 ER - TY - JOUR AU - Han, B. AU - Dost, B. AU - Bafna, V. AU - Zhang, S. PY - 2008 DA - 2008// TI - Structural alignment of pseudoknotted RNA JO - J Comput Biol VL - 15 UR - https://doi.org/10.1089/cmb.2007.0214 DO - 10.1089/cmb.2007.0214 ID - Han2008 ER - TY - JOUR AU - Yoon, B. J. PY - 2009 DA - 2009// TI - Efficient alignment of RNAs with pseudoknots using sequence alignment constrains JO - EURASIP J Bioinform Syst Biol. VL - 2009 UR - https://doi.org/10.1155/2009/491074 DO - 10.1155/2009/491074 ID - Yoon2009 ER - TY - JOUR AU - Wong, T. K. F. AU - Wan, K. L. AU - Hsu, B. Y. AU - Cheung, B. W. AU - Hon, W. K. AU - Lam, T. W. PY - 2011 DA - 2011// TI - RNASAlign: RNA structural alignment system JO - Bioinformatics VL - 27 UR - https://doi.org/10.1093/bioinformatics/btr338 DO - 10.1093/bioinformatics/btr338 ID - Wong2011 ER - TY - JOUR AU - Puton, T. AU - Kozlowski, L. P. AU - Rother, K. M. AU - Bujnicki, J. M. PY - 2013 DA - 2013// TI - CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt101 DO - 10.1093/nar/gkt101 ID - Puton2013 ER - TY - JOUR AU - Ferre, F. AU - Ponty, Y. AU - Lorenz, W. A. AU - Clote, P. PY - 2007 DA - 2007// TI - DIAL: a web server for the pairwise alignment of two RNA three-dimensional structures using nucleotide, dihedral angle and base-pairing similarities JO - Nucleic Acids Res. VL - 35 UR - https://doi.org/10.1093/nar/gkm334 DO - 10.1093/nar/gkm334 ID - Ferre2007 ER - TY - JOUR AU - Capriotti, E. AU - Marti-Renom, M. A. PY - 2009 DA - 2009// TI - SARA: a server for function annotation of RNA structures JO - Nucleic Acids Res. VL - 37 UR - https://doi.org/10.1093/nar/gkp433 DO - 10.1093/nar/gkp433 ID - Capriotti2009 ER - TY - JOUR AU - Chang, Y. F. AU - Huang, Y. L. AU - Lu, C. L. PY - 2008 DA - 2008// TI - SARSA: a web tool for structural alignment of RNA using a structural alphabet JO - Nucleic Acids Res. VL - 36 UR - https://doi.org/10.1093/nar/gkn327 DO - 10.1093/nar/gkn327 ID - Chang2008 ER - TY - JOUR AU - Wang, C. W. AU - Chen, K. T. AU - Lu, C. L. PY - 2010 DA - 2010// TI - iPARTS: an improved tool of pairwise alignment of RNA tertiary structures JO - Nucleic Acids Res. VL - 38 UR - https://doi.org/10.1093/nar/gkq483 DO - 10.1093/nar/gkq483 ID - Wang2010 ER - TY - JOUR AU - Hoksza, D. AU - Svozil, D. PY - 2012 DA - 2012// TI - Efficient RNA pairwise structure comparison by SETTER method JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts301 DO - 10.1093/bioinformatics/bts301 ID - Hoksza2012 ER - TY - JOUR AU - Rahrig, R. R. AU - Leontis, N. B. AU - Zirbel, C. L. PY - 2010 DA - 2010// TI - R3D Align: global pairwise alignment of RNA 3D structures using local superpositions JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq506 DO - 10.1093/bioinformatics/btq506 ID - Rahrig2010 ER - TY - JOUR AU - He, G. AU - Steppi, A. AU - Laborde, J. AU - Srivastava, A. AU - Zhao, P. AU - Zhang, J. PY - 2014 DA - 2014// TI - RASS: a web server for RNA alignment in the joint sequence-structure space JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku429 DO - 10.1093/nar/gku429 ID - He2014 ER - TY - JOUR AU - Zhong, C. AU - Zhang, S. PY - 2013 DA - 2013// TI - Efficient alignment of RNA secondary structures using sparse dynamic programming JO - BMC Bioinformatics. VL - 14 UR - https://doi.org/10.1186/1471-2105-14-269 DO - 10.1186/1471-2105-14-269 ID - Zhong2013 ER - TY - JOUR AU - Shapiro, B. A. AU - Zhang, K. PY - 1990 DA - 1990// TI - Comparing multiple RNA secondary structures using tree comparisons JO - Comput Appl Biosci VL - 6 ID - Shapiro1990 ER - TY - JOUR AU - Liu, J. AU - Wang, J. T. L. AU - Hu, J. AU - Tian, B. PY - 2005 DA - 2005// TI - A method for aligning RNA secondary structures and its application to RNA motif detection JO - BMC Bioinformatics. VL - 6 UR - https://doi.org/10.1186/1471-2105-6-89 DO - 10.1186/1471-2105-6-89 ID - Liu2005 ER - TY - JOUR AU - Höchsmann, M. AU - Voss, B. AU - Giegerich, R. PY - 2004 DA - 2004// TI - Pure multiple RNA secondary structure alignments: a progressive profile approach JO - IEEE/ACM Trans Comput Biol Bioinform VL - 1 UR - https://doi.org/10.1109/TCBB.2004.11 DO - 10.1109/TCBB.2004.11 ID - Höchsmann2004 ER - TY - JOUR AU - Jiang, T. AU - Lin, G. AU - Ma, B. AU - Zhang, K. PY - 2002 DA - 2002// TI - A general edit distance between RNA structures JO - J Comput Biol VL - 9 UR - https://doi.org/10.1089/10665270252935511 DO - 10.1089/10665270252935511 ID - Jiang2002 ER - TY - JOUR AU - Klein, R. J. AU - Eddy, S. R. PY - 2003 DA - 2003// TI - RSEARCH: finding homologs of single structured RNA sequences JO - BMC Bioinformatics. VL - 4 UR - https://doi.org/10.1186/1471-2105-4-44 DO - 10.1186/1471-2105-4-44 ID - Klein2003 ER - TY - JOUR AU - Gardner, P. P. AU - Wilm, A. AU - Washietl, S. PY - 2005 DA - 2005// TI - A benchmark of multiple sequence alignment programs upon structural RNAs JO - Nucleic Acids Res VL - 33 UR - https://doi.org/10.1093/nar/gki541 DO - 10.1093/nar/gki541 ID - Gardner2005 ER - TY - JOUR AU - Brown, J. W. PY - 1999 DA - 1999// TI - The Ribonuclease P Database JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.1.314 DO - 10.1093/nar/27.1.314 ID - Brown1999 ER - TY - JOUR AU - Burge, S. W. AU - Daub, J. AU - Eberhardt, R. AU - Tate, J. AU - Barquist, L. AU - Nawrocki, E. P. PY - 2013 DA - 2013// TI - Rfam 11.0: 10 years of RNA families JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1005 DO - 10.1093/nar/gks1005 ID - Burge2013 ER - TY - JOUR AU - Yang, H. AU - Jossinet, F. AU - Leontis, N. AU - Chen, L. AU - Westbrook, J. AU - Berman, H. PY - 2003 DA - 2003// TI - Tools for the automatic identification and classification of RNA base pairs JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg529 DO - 10.1093/nar/gkg529 ID - Yang2003 ER - TY - JOUR AU - Wilcoxon, F. PY - 1947 DA - 1947// TI - Probability table for individual comparisons by ranking methods JO - Biometrics VL - 3 UR - https://doi.org/10.2307/3001946 DO - 10.2307/3001946 ID - Wilcoxon1947 ER - TY - JOUR AU - Wilm, A. AU - Mainz, I. AU - Steger, G. PY - 2006 DA - 2006// TI - An enhanced RNA alignment benchmark for sequence alignment programs JO - Algorithms Mol Biol. VL - 1 UR - https://doi.org/10.1186/1748-7188-1-19 DO - 10.1186/1748-7188-1-19 ID - Wilm2006 ER - TY - JOUR AU - Nuin, P. A. AU - Wang, Z. AU - Tillier, E. R. PY - 2006 DA - 2006// TI - The accuracy of several multiple sequence alignment programs for proteins JO - BMC Bioinformatics. VL - 7 UR - https://doi.org/10.1186/1471-2105-7-471 DO - 10.1186/1471-2105-7-471 ID - Nuin2006 ER - TY - JOUR AU - Thompson, J. D. AU - Plewniak, F. AU - Poch, O. PY - 1999 DA - 1999// TI - A comprehensive comparison of multiple sequence alignment programs JO - Nucleic Acids Res VL - 27 UR - https://doi.org/10.1093/nar/27.13.2682 DO - 10.1093/nar/27.13.2682 ID - Thompson1999 ER - TY - JOUR AU - Bremges, A. AU - Schirmer, S. AU - Giegerich, R. PY - 2010 DA - 2010// TI - Fine-tuning structural RNA alignments in the twilight zone JO - BMC Bioinformatics. VL - 11 UR - https://doi.org/10.1186/1471-2105-11-222 DO - 10.1186/1471-2105-11-222 ID - Bremges2010 ER - TY - JOUR AU - Rahrig, R. R. AU - Petrov, A. I. AU - Leontis, N. B. AU - Zirbel, C. L. PY - 2013 DA - 2013// TI - R3D Align web server for global nucleotide to nucleotide alignments of RNA 3D structures JO - Nucleic Acids Res. VL - 41 UR - https://doi.org/10.1093/nar/gkt417 DO - 10.1093/nar/gkt417 ID - Rahrig2013 ER - TY - JOUR AU - Song, Y. AU - Liu, C. AU - Malmberg, R. AU - Pan, F. AU - Cai, L. PY - 2005 DA - 2005// TI - Tree decomposition based fast search of RNA structures including pseudoknots in genomes JO - Proc IEEE Comput Syst Bioinform Conf VL - 1 ID - Song2005 ER - TY - JOUR AU - Belew, A. T. AU - Meskauskas, A. AU - Musalgaonkar, S. AU - Advani, V. M. AU - Sulima, S. O. AU - Kasprzak, W. K. PY - 2014 DA - 2014// TI - Ribosomal frameshifting in the CCR5 mRNA is regulated by miRNAs and the NMD pathway JO - Nature VL - 512 UR - https://doi.org/10.1038/nature13429 DO - 10.1038/nature13429 ID - Belew2014 ER - TY - JOUR AU - Gao, F. AU - Kasprzak, W. K. AU - Szarko, C. AU - Shapiro, B. A. AU - Simon, A. E. PY - 2014 DA - 2014// TI - The 3' untranslated region of Pea Enation Mosaic Virus contains two T-shaped, ribosome-binding, cap-independent translation enhancers JO - J Virol VL - 88 UR - https://doi.org/10.1128/JVI.01433-14 DO - 10.1128/JVI.01433-14 ID - Gao2014 ER - TY - JOUR AU - Gao, F. AU - Kasprzak, W. AU - Stupina, V. A. AU - Shapiro, B. A. AU - Simon, A. E. PY - 2012 DA - 2012// TI - A ribosome-binding, 3' translational enhancer has a T-shaped structure and engages in a long-distance RNA-RNA interaction JO - J Virol VL - 86 UR - https://doi.org/10.1128/JVI.00677-12 DO - 10.1128/JVI.00677-12 ID - Gao2012 ER - TY - JOUR AU - Stupina, V. A. AU - Meskauskas, A. AU - McCormack, J. C. AU - Yingling, Y. G. AU - Shapiro, B. A. AU - Dinman, J. D. PY - 2008 DA - 2008// TI - The 3' proximal translational enhancer of Turnip crinkle virus binds to 60S ribosomal subunits JO - RNA VL - 14 UR - https://doi.org/10.1261/rna.1227808 DO - 10.1261/rna.1227808 ID - Stupina2008 ER - TY - JOUR AU - McCormack, J. C. AU - Yuan, X. AU - Yingling, Y. G. AU - Kasprzak, W. AU - Zamora, R. E. AU - Shapiro, B. A. PY - 2008 DA - 2008// TI - Structural domains within the 3' untranslated region of Turnip crinkle virus JO - J Virol VL - 82 UR - https://doi.org/10.1128/JVI.00416-08 DO - 10.1128/JVI.00416-08 ID - McCormack2008 ER - TY - BOOK AU - Han, J. AU - Kamber, M. AU - Pei, J. PY - 2011 DA - 2011// TI - Data Mining: Concepts and Techniques PB - Morgan Kaufmann Publishers CY - Waltham, Massachusetts ID - Han2011 ER - TY - JOUR AU - Hofacker, I. L. PY - 2003 DA - 2003// TI - Vienna RNA, secondary structure server JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg599 DO - 10.1093/nar/gkg599 ID - Hofacker2003 ER -