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Markus E. Nebel, Anika Scheid, "Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 8, no. 6, pp. 14681482, November/December, 2011.  
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@article{ 10.1109/TCBB.2010.126, author = {Markus E. Nebel and Anika Scheid}, title = {Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {8}, number = {6}, issn = {15455963}, year = {2011}, pages = {14681482}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2010.126}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Analysis of the Free Energy in a Stochastic RNA Secondary Structure Model IS  6 SN  15455963 SP1468 EP1482 EPD  14681482 A1  Markus E. Nebel, A1  Anika Scheid, PY  2011 KW  RNA folding KW  RNA secondary structure KW  RNA structure prediction KW  free energy KW  generating functions. VL  8 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] M.S. Waterman, “Secondary Structure of SingleStranded Nucleic Acids,” Advances in Math. Supplementary Studies, vol. 1, pp. 167212, 1978.
[2] P.R. Stein and M.S. Waterman, “On Some New Sequences Generalizing the Catalan and Motzkin Numbers,” Discrete Math., vol. 26, pp. 216272, 1978.
[3] G. Viennot and M. Vauchaussade de Chaumont, “Enumeration of RNA Secondary Structures by Complexity,” Mathematics in Medicine and Biology, vol. 57, pp. 360365, 1985.
[4] M.E. Nebel, “Combinatorial Properties of RNA Secondary Structures,” J. Computational Biology, vol. 9, no. 3, pp. 541574, 2002.
[5] I.L. Hofacker, P. Schuster, and P.F. Stadler, “Combinatorics of RNA Secondary Structures,” Discrete Applied Math., vol. 88, pp. 207237, 1998.
[6] M.E. Nebel, “Investigation of the BernoulliModel of RNA Secondary Structures,” Bull. Math. Biology, vol. 66, pp. 925964, 2004.
[7] M. Zuker and D. Sankoff, “RNA Secondary Structures and Their Prediction,” Bull. Math. Biology, vol. 46, pp. 591621, 1984.
[8] M.E. Nebel, “On a Statistical Filter for RNA Secondary Structures,” technical report, Frankfurter InformatikBerichte, 2002.
[9] M.E. Nebel, “Identifying Good Predictions of RNA Secondary Structure,” Proc. Pacific Symp. Biocomputing, pp. 423434, 2004.
[10] M. Zuker, D.H. Mathews, and D.H. Turner, “Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide,” RNA Biochemistry and Biotechnology, J. Barciszewski and B.F.C. Clark, eds., pp. 1143, Kluwer Academic Publishers, 1999.
[11] M. Zuker, “RNA Folding Prediction: The Continued Need for Interaction between Biologists and Mathematicians,” Lectures on Mathematics in the Life Sciences, vol. 17, pp. 87124, 1986.
[12] D. Sankoff, J.B. Kruskal, S. Mainville, and R.J. Cedergren, “Fast Algorithms to Determine RNA Secondary Structures Containing Multiple Loops,” Time Warps, String Edits, and Macromolecules: The Theory and Practice of Sequence Comparison, ch. 3, pp. 93120, AddisonWesley, 1983.
[13] B. Knudsen and J. Hein, “RNA Secondary Structure Prediction Using Stochastic ContextFree Grammars and Evolutionary History,” Bioinformatics, vol. 15, no. 6, pp. 446454, 1999.
[14] B. Knudsen and J. Hein, “Pfold: RNA Secondary Structure Prediction Using Stochastic ContextFree Grammars,” Nucleic Acids Research, vol. 31, no. 13, pp. 34233428, 2003.
[15] R. Nussinov, G. Pieczenik, J.R. Griggs, and D.J. Kleitman, “Algorithms for Loop Matchings,” SIAM J. Applied Math., vol. 35, pp. 6882, 1978.
[16] M. Zuker and P. Stiegler, “Optimal Computer Folding of Large RNA Sequences Using Thermodynamics and Auxiliary Information,” Nucleic Acids Research, vol. 9, pp. 133148, 1981.
[17] M. Zuker, “Computer Prediction of RNA Structure,” RNA Processing, J.E. Dahlberg and J.N. Abelson, eds., vol. 180, pp. 262288, Academic Press, 1989.
[18] S. Wuchty, W. Fontana, I. Hofacker, and P. Schuster, “Complete Suboptimal Folding of RNA and the Stability of Secondary Structures,” Biopolymers, vol. 49, pp. 145165, 1999.
[19] M. Zuker, “On Finding All Suboptimal Foldings of an RNA Molecule,” Science, vol. 244, pp. 4852, 1989.
[20] M. Zuker, “Mfold Web Server for Nucleic Acid Folding and Hybridization Prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 34063415, 2003.
[21] I.L. Hofacker, “The Vienna RNA Secondary Structure Server,” Nucleic Acids Research, vol. 31, no. 13, pp. 34293431, 2003.
[22] J. Gralla and D.M. Crothers, “Free Energy of Imperfect Nucleic Acid Helices: II. Small Hairpin Loops,” J. Molecular Biology, vol. 73, pp. 497511, 1973.
[23] P.N. Borer, B. Dengler, I. Tinoco,Jr., and O.C. Uhlenbeck, “Stability of Ribonucleic Acid DoubleStranded Helices,” J. Molecular Biology, vol. 86, pp. 843853, 1974.
[24] T. Xia, J. SantaLucia,Jr., M.E. Burkard, R. Kierzek, S.J. Schroeder, X. Jiao, C. Cox, and D.H. Turner, “Thermodynamic Parameters for an Expanded NearestNeighbor Model for Formation of RNA Duplexes with WatsonCrick Base Pairs,” Biochemistry, vol. 37, pp. 1471914735, 1998.
[25] D.H. Mathews, J. Sabina, M. Zuker, and D.H. Turner, “Expanded Sequence Dependence of Thermodynamic Parameters Improves Prediction of RNA Secondary Structure,” J. Molecular Biology, vol. 288, pp. 911940, 1999.
[26] M.J. Serra and D.H. Turner, “Predicting Thermodynamic Properties of RNA,” Methods in Enzymology, vol. 259, pp. 242261, 1995.
[27] Y. Sakakibara, M. Brown, R. Hughey, I.S. Mian, K. Sjölander, R.C. Underwood, and D. Haussler, “Stochastic ContextFree Grammars for tRNA modeling,” Nucleic Acids Research, vol. 22, pp. 51125120, 1994.
[28] T. Huang and K.S. Fu, “On Stochastic ContextFree Languages,” Information Sciences, vol. 3, pp. 201224, 1971.
[29] T. Chi and S. Geman, “Estimation of Probabilistic ContextFree Grammars,” Computational Linguistics, vol. 24, no. 2, pp. 299305, 1998.
[30] N. Chomsky and M.P. Schützenberger, “The Algebraic Theory of ContextFree Languages,” Computer Programming and Formal Systems, P. Braffort and D. Hirschberg, eds., pp. 118161, Amsterdam NorthHolland, 1963.
[31] R. Sedgewick and P. Flajolet, An Introduction to the Analysis of Algorithms, second ed. AddisonWesley Publishing Company, Inc., Sept. 2001.
[32] P. Flajolet and R. Sedgewick, Analytic Combinatorics, Cambridge Univ. Press, Jan. 2009.
[33] M. Sprinzl, C. Horn, M. Brown, A. Ioudovitch, and S. Steinberg, “Compilation of tRNA Sequences and Sequences of tRNA Genes,” Nucleic Acids Research, vol. 26, pp. 148153, 1998.
[34] M. Szymanski, M.Z. Barciszewska, V.A. Erdmann, and J. Barciszewski, “5S Ribosomal RNA Database,” Nucleic Acids Research, vol. 30, pp. 176178, 2002.
[35] J. Wuyts, Y.V. de Peer, T. Winkelmans, and R.D. Wachter, “The European Database on Small Subunit Ribosomal RNA,” Nucleic Acids Research, vol. 30, no. 1, pp. 183185, 2002.
[36] J. Wuyts, P.D. Rijk, Y.V. de Peer, T. Winkelmans, and R.D. Wachter, “The European Large Subunit Ribosomal RNA Database,” Nucleic Acids Research, vol. 29, no. 1, pp. 175177, 2001.
[37] F. Weinberg and M.E. Nebel, “Non Uniform Generation of Combinatorial Objects,” technical report, University of Kaiserslautern, 2010.
[38] M.E. Nebel and A. Scheid, “Random Generation of RNA Secondary Structures According to Native Distributions,” submitted for publication.
[39] M. Hofri, Analysis of Algorithms: Computational Methods and Mathematical Tools, Oxford Univ. Press, 1995.
[40] D.E. Knuth and H.S. Wilf, “A Short Proof of Darboux's Lemma,” Applied Math. Letters, vol. 2, pp. 139140, 1989.