TY - BOOK AU - Durbin, R. AU - Eddy, S. R. AU - Krogh, A. AU - Mitchison, G. PY - 1999 DA - 1999// TI - Biological Sequence Analysis : Probabilistic Models of Proteins and Nucleic Acids PB - Cambridge University Press CY - Cambridge, UK ID - Durbin1999 ER - TY - JOUR AU - Eddy, S. R. PY - 2001 DA - 2001// TI - Non-coding RNA Genes and the modern RNA World JO - Nat Rev VL - 2 UR - https://doi.org/10.1038/35103511 DO - 10.1038/35103511 ID - Eddy2001 ER - TY - CHAP AU - Pace, N. R. AU - Thomas, B. C. AU - Woese, C. R. PY - 1999 DA - 1999// TI - Probing RNA structure, function and history by comparative analysis BT - The RNA World ID - Pace1999 ER - TY - JOUR AU - Sankoff, D. PY - 1985 DA - 1985// TI - Simultaneous Solution of RNA Folding, Alignment and Protosequence Problems JO - SIAM J App Math 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 - 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 - Mathews, D. H. PY - 2005 DA - 2005// TI - Predicting a set of minimal free energy RNA secondary structures common to two sequences JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti349 DO - 10.1093/bioinformatics/bti349 ID - Mathews2005 ER - TY - JOUR AU - Bahl, L. R. AU - Cocke, J. AU - Jelinek, F. AU - Raviv, J. PY - 1974 DA - 1974// TI - Optimal Decoding of Linear Codes for Minimizing Symbol Error Rate JO - IEEE Trans Info Theory VL - 20 UR - https://doi.org/10.1109/TIT.1974.1055186 DO - 10.1109/TIT.1974.1055186 ID - Bahl1974 ER - TY - CHAP AU - Berrou, C. AU - Glavieux, A. AU - Thitimajshima, P. PY - 1993 DA - 1993// TI - Near Shannon limit error-correcting coding and decoding: Turbo-codes BT - Proc IEEE Intl Conf Communications PB - Geneva CY - Switzerland UR - https://doi.org/10.1109/ICC.1993.397441 DO - 10.1109/ICC.1993.397441 ID - Berrou1993 ER - TY - JOUR AU - MacKay, D. J. C. PY - 1999 DA - 1999// TI - Good Error Correcting Codes based on Very Sparse Matrices JO - IEEE Trans Info Theory VL - 45 UR - https://doi.org/10.1109/18.748992 DO - 10.1109/18.748992 ID - MacKay1999 ER - TY - JOUR AU - Rabiner, L. R. AU - Juang, B. H. PY - 1986 DA - 1986// TI - An Introduction to Hidden Markov Models JO - "IEEE ASSP Mag" VL - 3 UR - https://doi.org/10.1109/MASSP.1986.1165342 DO - 10.1109/MASSP.1986.1165342 ID - Rabiner1986 ER - TY - JOUR AU - Holmes, I. PY - 2005 DA - 2005// TI - Accelerated probabilistic inference of RNA structure evolution JO - BMC Bioinformatics VL - 6 UR - https://doi.org/10.1186/1471-2105-6-73 DO - 10.1186/1471-2105-6-73 ID - Holmes2005 ER - TY - CHAP AU - Holmes, I. AU - Rubin, G. M. PY - 2002 DA - 2002// TI - Pairwise RNA structure comparison using stochastic context-free grammars BT - Pacific Symposium on Biocomputing ID - Holmes2002 ER - TY - JOUR AU - Tinoco, I. AU - Bustamante, C. PY - 1999 DA - 1999// TI - How RNA folds JO - J Mol Biol VL - 293 UR - https://doi.org/10.1006/jmbi.1999.3001 DO - 10.1006/jmbi.1999.3001 ID - Tinoco1999 ER - TY - JOUR AU - Crothers, D. M. AU - Cole, P. E. AU - Hilbers, C. W. AU - Schulman, R. G. PY - 1974 DA - 1974// TI - The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA JO - J Mol Biol VL - 87 UR - https://doi.org/10.1016/0022-2836(74)90560-9 DO - 10.1016/0022-2836(74)90560-9 ID - Crothers1974 ER - TY - JOUR AU - Banerjee, A. R. AU - Jaeger, J. A. AU - Turner, D. H. PY - 1993 DA - 1993// TI - Thermal unfolding of a group I ribozyme: The low temperature transition is primarily a disruption of tertiary structure JO - Biochemistry VL - 32 UR - https://doi.org/10.1021/bi00052a021 DO - 10.1021/bi00052a021 ID - Banerjee1993 ER - TY - JOUR AU - Mathews, D. H. AU - Banerjee, A. R. AU - Luan, D. D. AU - Eickbush, T. H. AU - Turner, D. H. PY - 1997 DA - 1997// TI - Secondary structure model of the RNA recognized by the reverse transcriptase from the R2 retrotransposable element JO - RNA VL - 3 ID - Mathews1997 ER - TY - JOUR AU - Woodson, S. A. PY - 2000 DA - 2000// TI - Recent insights on RNA folding mechanisms from catalytic RNA JO - Cell Mol Life Sci VL - 57 UR - https://doi.org/10.1007/s000180050042 DO - 10.1007/s000180050042 ID - Woodson2000 ER - TY - JOUR AU - Gutell, R. R. AU - Lee, J. C. AU - Cannone, J. J. PY - 2002 DA - 2002// TI - The accuracy of ribosomal RNA comparative structure models JO - Curr Opin Struct Biol VL - 12 UR - https://doi.org/10.1016/S0959-440X(02)00339-1 DO - 10.1016/S0959-440X(02)00339-1 ID - Gutell2002 ER - TY - JOUR AU - Mathews, D. H. AU - Disney, M. D. AU - Childs, J. L. AU - Schroeder, S. J. AU - Zuker, M. AU - Turner, D. H. PY - 2004 DA - 2004// TI - Incorporating chemical mod ification constraints into a dynamic programming algorithm for prediction of RNA secondary structure JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0401799101 DO - 10.1073/pnas.0401799101 ID - Mathews2004 ER - TY - JOUR AU - Ding, Y. AU - Lawrence, C. E. PY - 2003 DA - 2003// TI - A statistical sampling algorithm for RNA secondary structure prediction JO - Nucleic Acids Res VL - 31 UR - https://doi.org/10.1093/nar/gkg938 DO - 10.1093/nar/gkg938 ID - Ding2003 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 - TY - JOUR AU - Mathews, D. H. PY - 2004 DA - 2004// TI - Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization JO - RNA VL - 10 UR - https://doi.org/10.1261/rna.7650904 DO - 10.1261/rna.7650904 ID - Mathews2004 ER - TY - JOUR AU - Wuchty, S. AU - Fontana, W. AU - Hofacker, I. L. AU - Schuster, P. PY - 1999 DA - 1999// TI - Complete suboptimal folding of RNA and the stability of secondary structures JO - Biopolymers VL - 49 UR - https://doi.org/3.0.CO;2-G DO - 3.0.CO;2-G ID - Wuchty1999 ER - TY - JOUR AU - Mathews, D. H. AU - Sabina, J. AU - Zuker, M. AU - Turner, D. H. PY - 1999 DA - 1999// TI - Expanded sequence dependence of thermodynamic pa rameters provides improved prediction of RNA secondary structure JO - J Mol Biol VL - 288 UR - https://doi.org/10.1006/jmbi.1999.2700 DO - 10.1006/jmbi.1999.2700 ID - Mathews1999 ER - TY - JOUR AU - Xia, T. AU - SantaLucia, J. J. AU - Kierzek, R. AU - Schroeder, S. J. AU - Jiao, X. AU - Cox, C. AU - Turner, D. H. PY - 1998 DA - 1998// TI - Thermodynamic Parameters for an Expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick pairs JO - Biochemistry VL - 37 UR - https://doi.org/10.1021/bi9809425 DO - 10.1021/bi9809425 ID - Xia1998 ER - TY - JOUR AU - Dowell, R. D. AU - Eddy, S. R. PY - 2004 DA - 2004// TI - Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-71 DO - 10.1186/1471-2105-5-71 ID - Dowell2004 ER - TY - JOUR AU - Doshi, K. J. AU - Cannone, J. J. AU - Cobaugh, C. W. AU - Gutell, R. R. PY - 2004 DA - 2004// TI - Evaluation of the suitability of free-energy minimization using nearest-neighbor energy parameters for RNA secondary structure prediction JO - BMC Bioinformatics VL - 5 UR - https://doi.org/10.1186/1471-2105-5-105 DO - 10.1186/1471-2105-5-105 ID - Doshi2004 ER - TY - JOUR AU - Mathews, D. H. PY - 2006 DA - 2006// TI - Revolutions in RNA secondary structure prediction JO - J Mol Biol VL - 359 UR - https://doi.org/10.1016/j.jmb.2006.01.067 DO - 10.1016/j.jmb.2006.01.067 ID - Mathews2006 ER - TY - CHAP AU - Mathews, D. H. AU - Schroeder, S. J. AU - Turner, D. H. AU - Zuker, M. PY - 2005 DA - 2005// TI - Predicting RNA secondary structure BT - The RNA World ID - Mathews2005 ER - TY - JOUR AU - Mathews, D. H. AU - Turner, D. H. PY - 2006 DA - 2006// TI - Prediction of RNA secondary structure by free energy minimization JO - Curr Opin Struct Biol VL - 16 UR - https://doi.org/10.1016/j.sbi.2006.05.010 DO - 10.1016/j.sbi.2006.05.010 ID - Mathews2006 ER - TY - JOUR AU - Chen, J. AU - Le, S. AU - Maizel, J. V. PY - 2000 DA - 2000// TI - Prediction of common secondary structures of RNAs: A genetic algorithm approach JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.4.991 DO - 10.1093/nar/28.4.991 ID - Chen2000 ER - TY - JOUR AU - Gorodkin, J. AU - Heyer, L. J. AU - Stormo, G. D. PY - 1997 DA - 1997// TI - Finding the most significant common sequence and structure in a set of RNA sequences JO - Nucleic Acids Res VL - 25 UR - https://doi.org/10.1093/nar/25.18.3724 DO - 10.1093/nar/25.18.3724 ID - Gorodkin1997 ER - TY - JOUR AU - Havgaard, J. H. AU - Lyngso, R. B. AU - Stormo, G. D. AU - Gorodkin, J. PY - 2005 DA - 2005// TI - Pairwise local structural alignment of RNA sequences with sequence similarity lessthan 40% JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti279 DO - 10.1093/bioinformatics/bti279 ID - Havgaard2005 ER - TY - STD TI - Dowell RD, Eddy SR: Efficient Pairwise RNA Structure Prediction and Alignment Using Sequence Alignment Constraints. BMC Bioinformatics. 2006, 7 (400): ID - ref34 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 - Notredame, C. AU - Higgins, D. G. AU - Heringa, J. PY - 2000 DA - 2000// TI - T-Coffee: A Novel Method for Fast and Accurate Multiple Sequence Alignment JO - J Mol Biol VL - 302 UR - https://doi.org/10.1006/jmbi.2000.4042 DO - 10.1006/jmbi.2000.4042 ID - Notredame2000 ER - TY - JOUR AU - Griffiths-Jones, S. AU - Bateman, A. AU - Marshall, M. AU - Khanna, A. AU - Eddy, S. R. PY - 2002 DA - 2002// 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-Jones2002 ER - TY - JOUR AU - Szymanski, M. AU - Barciszewska, M. Z. AU - Barciszewski, J. AU - Erdmann, V. A. PY - 2000 DA - 2000// TI - 5S ribosomal RNA database Y2K JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.166 DO - 10.1093/nar/28.1.166 ID - Szymanski2000 ER - TY - JOUR AU - Sprinzl, M. AU - Horn, C. AU - Brown, M. AU - Ioudovitch, A. AU - Steinberg, S. PY - 1998 DA - 1998// TI - Compilation of tRNA sequences and sequences of tRNA genes JO - Nucleic Acids Res VL - 26 UR - https://doi.org/10.1093/nar/26.1.148 DO - 10.1093/nar/26.1.148 ID - Sprinzl1998 ER - TY - JOUR AU - Hofacker, I. L. AU - Bernhart, S. H. AU - Stadler, P. F. PY - 2004 DA - 2004// TI - Alignment of RNA base pairing probability matrices JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth229 DO - 10.1093/bioinformatics/bth229 ID - Hofacker2004 ER - TY - JOUR AU - Masoumi, B. AU - Turcotte, M. PY - 2005 DA - 2005// TI - Simultaneous alignment and structure prediction of three RNA sequences JO - Int J Bioinformatics Research and Applications VL - 1 UR - https://doi.org/10.1504/IJBRA.2005.007581 DO - 10.1504/IJBRA.2005.007581 ID - Masoumi2005 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 Res VL - 16 UR - https://doi.org/10.1101/gr.5226606 DO - 10.1101/gr.5226606 ID - Torarinsson2006 ER - TY - JOUR AU - Rivas, E. AU - Eddy, S. R. PY - 2001 DA - 2001// TI - Noncoding RNA gene detection using comparative sequence analysis JO - BMC Bioinformatics VL - 2 UR - https://doi.org/10.1186/1471-2105-2-8 DO - 10.1186/1471-2105-2-8 ID - Rivas2001 ER - TY - JOUR AU - Washietl, S. AU - Hofacker, I. L. AU - Stadler, P. F. PY - 2005 DA - 2005// TI - Fast and Reliable Prediction of noncoding RNAs JO - Proc Nat Acad Sci VL - 102 UR - https://doi.org/10.1073/pnas.0409169102 DO - 10.1073/pnas.0409169102 ID - Washietl2005 ER - TY - CHAP AU - Harmanci, A. O. AU - Sharma, G. AU - Mathews, D. H. PY - 2007 DA - 2007// TI - Toward Turbo Decoding of RNA Secondary Structure BT - Proc IEEE Intl Conf Acoustics Speech and Sig Proc ID - Harmanci2007 ER - TY - STD TI - RNA Structure and Dynalign. 2007, [http://rna.urmc.rochester.edu] UR - http://rna.urmc.rochester.edu ID - ref46 ER - TY - JOUR AU - Rabiner, L. R. PY - 1989 DA - 1989// TI - A tutorial on hidden Markov models and selected applications in speech recognition JO - Proc IEEE VL - 77 UR - https://doi.org/10.1109/5.18626 DO - 10.1109/5.18626 ID - Rabiner1989 ER - TY - JOUR AU - Lu, Z. J. AU - Turner, D. H. AU - Mathews, D. H. PY - 2006 DA - 2006// TI - A set of neighbor parameters for predicting the enthalpy change of RNA secondary structure formation JO - Nucleic Acids Res VL - 34 UR - https://doi.org/10.1093/nar/gkl472 DO - 10.1093/nar/gkl472 ID - Lu2006 ER - TY - JOUR AU - Zuker, M. PY - 1989 DA - 1989// TI - Computer prediction of RNA structure JO - Methods in Enzymology VL - 180 UR - https://doi.org/10.1016/0076-6879(89)80106-5 DO - 10.1016/0076-6879(89)80106-5 ID - Zuker1989 ER - TY - JOUR AU - MacKay, D. J. C. PY - 2001 DA - 2001// TI - Errata for "Good Error Correcting Codes based on Very Sparse Matrices" JO - IEEE Trans Info Theory VL - 47 UR - https://doi.org/10.1109/TIT.2001.930952 DO - 10.1109/TIT.2001.930952 ID - MacKay2001 ER -