TY - JOUR AU - Washietl, S. AU - Hofacker, I. L. AU - Lukasser, M. AU - Hüttenhofer, A. AU - Stadler, P. F. PY - 2005 DA - 2005// TI - Genome-wide mapping of conserved RNA secondary structure structures predicts thousands of functional non-coding RNAs in human JO - Nature Biotechnology VL - 23 UR - https://doi.org/10.1038/nbt1144 DO - 10.1038/nbt1144 ID - Washietl2005 ER - TY - JOUR AU - Pedersen, J. S. AU - Bejerano, G. AU - Siepel, A. AU - Rosenbloom, K. AU - Lindblad-Toh, K. AU - Lander, E. S. AU - Kent, J. AU - Miller, W. AU - Haussler, D. PY - 2006 DA - 2006// TI - Identification and classification of conserved RNA secondary structures in the human genome JO - PLoS Comput Biol VL - 2 UR - https://doi.org/10.1371/journal.pcbi.0020033 DO - 10.1371/journal.pcbi.0020033 ID - Pedersen2006 ER - TY - JOUR AU - Torarinsson, E. AU - Sawera, M. AU - Havgaard, J. H. AU - Fredholm, M. AU - Gorodkin, J. PY - 2006 DA - 2006// TI - Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure JO - Genome Research VL - 16 UR - https://doi.org/10.1101/gr.5226606 DO - 10.1101/gr.5226606 ID - Torarinsson2006 ER - TY - JOUR AU - Uzilov, A. V. AU - Keegan, J. M. AU - Mathews, D. H. PY - 2006 DA - 2006// TI - Detection of non-coding RNAs on the basis of predicted secondary structure formation free energy change JO - BMC Bioinformatics VL - 7 UR - https://doi.org/10.1186/1471-2105-7-173 DO - 10.1186/1471-2105-7-173 ID - Uzilov2006 ER - TY - JOUR AU - Washietl, S. AU - Pedersen, J. S. AU - Korbel, J. O. AU - Stocsits, C. AU - Gruber, A. R. AU - Hackermüller, J. AU - Hertel, J. AU - Lindemeyer, M. AU - Reiche, K. AU - Tanzer, A. AU - Ucla, C. AU - Wyss, C. AU - Antonarakis, S. E. AU - Denoeud, F. AU - Lagarde, J. AU - Drenkow, J. AU - Kapranov, P. AU - Gingeras, T. R. AU - Guigó, R. AU - Snyder, M. AU - Gerstein, M. B. AU - Reymond, A. AU - Hofacker, I. L. AU - Stadler, P. F. PY - 2007 DA - 2007// TI - Structured RNAs in the ENCODE selected regions of the human genome JO - Genome Research VL - 17 UR - https://doi.org/10.1101/gr.5650707 DO - 10.1101/gr.5650707 ID - Washietl2007 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 Computational Biology VL - 3 UR - https://doi.org/10.1371/journal.pcbi.0030065 DO - 10.1371/journal.pcbi.0030065 ID - Will2007 ER - TY - JOUR AU - Torarinsson, E. AU - Yao, Z. AU - Wiklund, E. D. AU - Bramsen, J. B. AU - Hansen, C. AU - Kjems, J. AU - Tommerup, N. AU - Ruzzo, W. L. AU - Gorodkin, J. PY - 2008 DA - 2008// TI - Comparative genomics beyond sequence based alignments: RNA structures in the ENCODE regions JO - Genome Research VL - 18 UR - https://doi.org/10.1101/gr.6887408 DO - 10.1101/gr.6887408 ID - Torarinsson2008 ER - TY - CHAP AU - Backofen, R. AU - Hess, W. R. PY - 2010 DA - 2010// TI - Computational prediction of sRNAs and their targets in bacteria BT - RNA Biol ID - Backofen2010 ER - TY - JOUR AU - Mückstein, U. AU - Tafer, H. AU - Hackermüller, J. AU - Bernhart, S. H. AU - Stadler, P. F. AU - Hofacker, I. L. PY - 2006 DA - 2006// TI - Thermodynamics of RNA-RNA binding JO - Bioinformatics VL - 22 UR - https://doi.org/10.1093/bioinformatics/btl024 DO - 10.1093/bioinformatics/btl024 ID - Mückstein2006 ER - TY - JOUR AU - Busch, A. AU - Richter, A. S. AU - Backofen, R. PY - 2008 DA - 2008// TI - IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions JO - Bioinformatics VL - 24 UR - https://doi.org/10.1093/bioinformatics/btn544 DO - 10.1093/bioinformatics/btn544 ID - Busch2008 ER - TY - JOUR AU - Argaman, L. AU - Altuvia, S. PY - 2000 DA - 2000// TI - fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex JO - Journal of Molecular Biology VL - 300 UR - https://doi.org/10.1006/jmbi.2000.3942 DO - 10.1006/jmbi.2000.3942 ID - Argaman2000 ER - TY - JOUR AU - Andronescu, M. AU - Zhang, Z. C. AU - Condon, A. PY - 2005 DA - 2005// TI - Secondary structure prediction of interacting RNA molecules JO - Journal of Molecular Biology VL - 345 UR - https://doi.org/10.1016/j.jmb.2004.10.082 DO - 10.1016/j.jmb.2004.10.082 ID - Andronescu2005 ER - TY - JOUR AU - Bernhart, S. H. AU - Tafer, H. AU - Mückstein, U. AU - Flamm, C. AU - Stadler, P. F. AU - Hofacker, I. L. PY - 2006 DA - 2006// TI - Partition function and base pairing probabilities of RNA heterodimers JO - Algorithms Mol Biol VL - 1 UR - https://doi.org/10.1186/1748-7188-1-3 DO - 10.1186/1748-7188-1-3 ID - Bernhart2006 ER - TY - JOUR AU - Dirks, R. M. AU - Bois, J. S. AU - Schaeffer, J. M. AU - Winfree, E. AU - Pierce, N. A. PY - 2007 DA - 2007// TI - Thermodynamic Analysis of Interacting Nucleic Acid Strands JO - SIAM Review VL - 49 UR - https://doi.org/10.1137/060651100 DO - 10.1137/060651100 ID - Dirks2007 ER - TY - JOUR AU - Zuker, M. PY - 1994 DA - 1994// TI - Prediction of RNA secondary structure by energy minimization JO - Methods in Molecular Biology VL - 25 ID - Zuker1994 ER - TY - JOUR AU - Hofacker, I. L. AU - Fontana, W. AU - Stadler, P. F. AU - Bonhoeffer, S. AU - Tacker, M. AU - Schuster, P. PY - 1994 DA - 1994// TI - Fast Folding and Comparison of RNA Secondary Structures JO - Monatshefte Chemie VL - 125 UR - https://doi.org/10.1007/BF00818163 DO - 10.1007/BF00818163 ID - Hofacker1994 ER - TY - JOUR AU - Pervouchine, D. D. PY - 2004 DA - 2004// TI - IRIS: intermolecular RNA interaction search JO - Genome Inform VL - 15 ID - Pervouchine2004 ER - TY - JOUR AU - Alkan, C. AU - Karakoc, E. AU - Nadeau, J. H. AU - Sahinalp, S. C. AU - Zhang, K. PY - 2006 DA - 2006// TI - RNA-RNA interaction prediction and antisense RNA target search JO - Journal of Computational Biology VL - 13 UR - https://doi.org/10.1089/cmb.2006.13.267 DO - 10.1089/cmb.2006.13.267 ID - Alkan2006 ER - TY - JOUR AU - Chitsaz, H. AU - Salari, R. AU - Sahinalp, S. C. AU - Backofen, R. PY - 2009 DA - 2009// TI - A partition function algorithm for interacting nucleic acid strands JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp212 DO - 10.1093/bioinformatics/btp212 ID - Chitsaz2009 ER - TY - JOUR AU - Huang, F. W. D. AU - Qin, J. AU - Reidys, C. M. AU - Stadler, P. F. PY - 2009 DA - 2009// TI - Partition function and base pairing probabilities for RNA-RNA interaction prediction JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp481 DO - 10.1093/bioinformatics/btp481 ID - Huang2009 ER - TY - JOUR AU - Huang, F. W. D. AU - Qin, J. AU - Reidys, C. M. AU - Stadler, P. F. PY - 2010 DA - 2010// TI - Target prediction and a statistical sampling algorithm for RNA-RNA interaction JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btp635 DO - 10.1093/bioinformatics/btp635 ID - Huang2010 ER - TY - CHAP AU - Chitsaz, H. AU - Backofen, R. AU - Sahinalp, S. C. ED - Salzberg, S. ED - Warnow, T. PY - 2009 DA - 2009// TI - biRNA: Fast RNA-RNA Binding Sites Prediction BT - Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), Volume 5724 of Lecture Notes in Computer Science ID - Chitsaz2009 ER - TY - CHAP AU - Salari, R. AU - Backofen, R. AU - Sahinalp, S. C. ED - Salzberg, S. ED - Warnow, T. PY - 2009 DA - 2009// TI - Fast prediction of RNA-RNA Interaction BT - Proc. of the 9th Workshop on Algorithms in Bioinformatics (WABI), Volume 5724 of Lecture Notes in Computer Science ID - Salari2009 ER - TY - CHAP AU - Salari, R. AU - Möhl, M. AU - Will, S. AU - Sahinalp, S. C. AU - Backofen, R. PY - 2010 DA - 2010// TI - Time and space efficient RNA-RNA interaction prediction via sparse folding BT - Proc of RECOMB 2010 ID - Salari2010 ER - TY - JOUR AU - Seemann, S. E. AU - Gorodkin, J. AU - Backofen, R. PY - 2008 DA - 2008// TI - Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments JO - Nucleic Acids Research VL - 36 UR - https://doi.org/10.1093/nar/gkn544 DO - 10.1093/nar/gkn544 ID - Seemann2008 ER - TY - JOUR AU - Gaspin, C. AU - Westhof, E. PY - 1995 DA - 1995// TI - An interactive framework for RNA secondary structure prediction with a dynamical treatment of constraints JO - J Mol Biol VL - 254 UR - https://doi.org/10.1006/jmbi.1995.0608 DO - 10.1006/jmbi.1995.0608 ID - Gaspin1995 ER - TY - CHAP AU - Jabbari, H. AU - Condon, A. AU - Pop, A. AU - Pop, C. AU - Zhao, Y. ED - Giancarlo, R. ED - Hannenhalli, S. PY - 2007 DA - 2007// TI - HFold: RNA Pseudoknotted Secondary Structure Prediction Using Hierarchical Folding BT - In Algorithms in Bioinformatics, 7th International Workshop, WABI Philadelphia, PA, USA, September 8-9, 2007, Proceedings ID - Jabbari2007 ER - TY - JOUR AU - Knudsen, B. AU - Hein, J. J. PY - 1999 DA - 1999// TI - RNA secondary structure prediction using stochastic context-free grammars and evolutionary history JO - Bioinformatics VL - 15 UR - https://doi.org/10.1093/bioinformatics/15.6.446 DO - 10.1093/bioinformatics/15.6.446 ID - Knudsen1999 ER - TY - JOUR AU - McCaskill, J. S. PY - 1990 DA - 1990// TI - The equilibrium partition function and base pair binding probabilities for RNA secondary structure JO - Biopolymers VL - 29 UR - https://doi.org/10.1002/bip.360290621 DO - 10.1002/bip.360290621 ID - McCaskill1990 ER - TY - JOUR AU - Nussinov, R. AU - Pieczenik, G. AU - Griggs, J. R. AU - Kleitman, D. J. PY - 1978 DA - 1978// TI - Algorithms for Loop Matchings JO - SIAM Journal on Applied Mathematics VL - 35 UR - https://doi.org/10.1137/0135006 DO - 10.1137/0135006 ID - Nussinov1978 ER - TY - JOUR AU - Ding, Y. AU - Chan, C. Y. AU - Lawrence, C. E. PY - 2005 DA - 2005// TI - RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble JO - RNA VL - 11 UR - https://doi.org/10.1261/rna.2500605 DO - 10.1261/rna.2500605 ID - Ding2005 ER - TY - JOUR AU - Knudsen, B. AU - Andersen, E. S. AU - Damgaard, C. AU - Kjems, J. AU - Gorodkin, J. PY - 2004 DA - 2004// TI - Evolutionary rate variation and RNA secondary structure prediction JO - Comput Biol Chem VL - 28 UR - https://doi.org/10.1016/j.compbiolchem.2004.04.001 DO - 10.1016/j.compbiolchem.2004.04.001 ID - Knudsen2004 ER - TY - JOUR AU - Waterhouse, A. M. AU - Procter, J. B. AU - Martin, D. M. A. AU - Clamp, M. AU - Barton, G. J. PY - 2009 DA - 2009// TI - Jalview Version 2-a multiple sequence alignment editor and analysis workbench JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp033 DO - 10.1093/bioinformatics/btp033 ID - Waterhouse2009 ER -