TY - JOUR AU - Waterman, M. S. AU - Smith, T. F. PY - 1978 DA - 1978// TI - RNA secondary structure: a complete mathematical analysis JO - Mathematical Biosciences VL - 42 UR - https://doi.org/10.1016/0025-5564(78)90099-8 DO - 10.1016/0025-5564(78)90099-8 ID - Waterman1978 ER - TY - JOUR AU - Zuker, M. PY - 2000 DA - 2000// TI - Calculating nucleic acid secondary structure JO - Current Opinion in Structural Biology VL - 10 UR - https://doi.org/10.1016/S0959-440X(00)00088-9 DO - 10.1016/S0959-440X(00)00088-9 ID - Zuker2000 ER - TY - JOUR AU - Nussinov, R. AU - Jacobson, A. B. PY - 1980 DA - 1980// TI - Fast algorithm for predicting the secondary structure of single-stranded RNA JO - Proceedings of the National Academy of Sciences VL - 77 UR - https://doi.org/10.1073/pnas.77.11.6309 DO - 10.1073/pnas.77.11.6309 ID - Nussinov1980 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. AU - Sankoff, D. PY - 1984 DA - 1984// TI - RNA secondary structures and their prediction JO - Bulletin of Mathematical Biology VL - 46 UR - https://doi.org/10.1007/BF02459506 DO - 10.1007/BF02459506 ID - Zuker1984 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 - Hofacker, I. L. PY - 2003 DA - 2003// TI - Vienna RNA secondary structure server JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg599 DO - 10.1093/nar/gkg599 ID - Hofacker2003 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 parameters improves prediction of RNA secondary structure JO - Journal of Molecular Biology VL - 288 UR - https://doi.org/10.1006/jmbi.1999.2700 DO - 10.1006/jmbi.1999.2700 ID - Mathews1999 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 - Current Opinion in Structural Biology 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 - Zimmerman, J. M. AU - Maher, L. J. PY - 2002 DA - 2002// TI - In vivo selection of spectinomycin-binding RNAs JO - Nucleic Acids Research VL - 30 UR - https://doi.org/10.1093/nar/gkf687 DO - 10.1093/nar/gkf687 ID - Zimmerman2002 ER - TY - JOUR AU - Barash, D. AU - Comaniciu, D. PY - 2003 DA - 2003// TI - A common viewpoint on broad kernel filtering and nonlinear diffusion JO - Proceedings of the 4th International Conference on Scale-Space Theories in Computer Vision (Scale-Space '03) VL - 2695 ID - Barash2003 ER - TY - JOUR AU - Shokoufandeh, A. AU - Macrini, D. AU - Dickinson, S. AU - Siddiqi, K. AU - Zucker, S. W. PY - 2005 DA - 2005// TI - Indexing hierarchical structures using graph spectra JO - IEEE Transactions on Pattern Analysis and Machine Intelligence VL - 27 UR - https://doi.org/10.1109/TPAMI.2005.142 DO - 10.1109/TPAMI.2005.142 ID - Shokoufandeh2005 ER - TY - JOUR AU - Barash, D. PY - 2004 DA - 2004// TI - Second eigenvalue of the Laplacian matrix for predicting RNA conformational switch by mutation JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth157 DO - 10.1093/bioinformatics/bth157 ID - Barash2004 ER - TY - JOUR AU - Hofacker, I. L. AU - Fontana, W. AU - Stadler, P. F. AU - Bonhoeffer, L. S. AU - Tacker, M. AU - Schuster, P. PY - 1994 DA - 1994// TI - Fast folding and comparison of RNA secondary structures JO - Monatshefte für Chemie VL - 125 UR - https://doi.org/10.1007/BF00818163 DO - 10.1007/BF00818163 ID - Hofacker1994 ER - TY - JOUR AU - Le, S. -. Y. AU - Nussinov, R. AU - Maizel, J. V. PY - 1989 DA - 1989// TI - Tree graphs of RNA secondary structures and their comparisons JO - Computers and Biomedical Research VL - 22 UR - https://doi.org/10.1016/0010-4809(89)90039-6 DO - 10.1016/0010-4809(89)90039-6 ID - Le1989 ER - TY - JOUR AU - Shapiro, B. A. PY - 1988 DA - 1988// TI - An algorithm for comparing multiple RNA secondary structures JO - Computer Applications in the Biosciences VL - 4 ID - Shapiro1988 ER - TY - JOUR AU - Margalit, H. AU - Shapiro, B. A. AU - Oppenheim, A. B. AU - Maizel, J. V. PY - 1989 DA - 1989// TI - Detection of common motifs in RNA secondary structures JO - Nucleic Acids Research VL - 17 UR - https://doi.org/10.1093/nar/17.12.4829 DO - 10.1093/nar/17.12.4829 ID - Margalit1989 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 - Journal of Computational Biology VL - 9 UR - https://doi.org/10.1089/10665270252935511 DO - 10.1089/10665270252935511 ID - Jiang2002 ER - TY - JOUR AU - Kitagawa, J. AU - Futamura, Y. AU - Yamamoto, K. PY - 2003 DA - 2003// TI - Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures JO - Nucleic Acids Research VL - 31 UR - https://doi.org/10.1093/nar/gkg288 DO - 10.1093/nar/gkg288 ID - Kitagawa2003 ER - TY - JOUR AU - Shapiro, B. A. AU - Zhang, K. PY - 1990 DA - 1990// TI - Comparing multiple RNA secondary structures using tree comparisons JO - Computer Applications in the Biosciences VL - 6 ID - Shapiro1990 ER - TY - JOUR AU - Fiedler, M. PY - 1973 DA - 1973// TI - Algebraic connectivity of graphs JO - Czechoslovak Mathematical Journal VL - 23 ID - Fiedler1973 ER - TY - JOUR AU - Grone, R. AU - Merris, R. AU - Sunder, V. S. PY - 1990 DA - 1990// TI - The Laplacian spectrum of a graph JO - SIAM Journal on Matrix Analysis and Applications VL - 11 UR - https://doi.org/10.1137/0611016 DO - 10.1137/0611016 ID - Grone1990 ER - TY - JOUR AU - Grone, R. AU - Merris, R. PY - 1987 DA - 1987// TI - Algebraic connectivity of trees JO - Czechoslovak Mathematical Journal VL - 37 ID - Grone1987 ER - TY - JOUR AU - Merris, R. PY - 1987 DA - 1987// TI - Characteristic vertices of trees JO - Linear and Multilinear Algebra VL - 22 UR - https://doi.org/10.1080/03081088708817827 DO - 10.1080/03081088708817827 ID - Merris1987 ER - TY - JOUR AU - Smith, D. B. AU - Simmonds, P. PY - 1997 DA - 1997// TI - Characteristics of nucleotide substitution in the hepatitis C virus genome: constraints on sequence change in coding regions at both ends of the genome JO - Journal of Molecular Evolution VL - 45 UR - https://doi.org/10.1007/PL00006226 DO - 10.1007/PL00006226 ID - Smith1997 ER - TY - JOUR AU - You, S. AU - Stump, D. D. AU - Branch, A. D. AU - Rice, C. M. PY - 2004 DA - 2004// TI - A cis-acting replication element in the sequence encoding the NS5B RNA-dependent RNA polymerase is required for Hepatitis C virus RNA replication JO - Journal of Virology VL - 78 UR - https://doi.org/10.1128/JVI.78.3.1352-1366.2004 DO - 10.1128/JVI.78.3.1352-1366.2004 ID - You2004 ER -