next up previous   Next: About this document Up: Prediction of RNA Previous: Acknowledgements


  1. F. Major, M. Turcotte, D. Gautheret, G. Lapalme, E. Fillion, and R.J. Cedergren. The combination of symbolic and numerical computation for three- dimensional modeling of rna. Science, 253:1255-1260, 1991.
  2. M.H. de Smit and J. van Duin. Control of prokaryotic translation initiation by mrna secondary structure. Progress in Nucleic Acid Research in Molecular Biology, 38:1-35, 1990.
  3. D.R. Mills, C. Priano, P.A. Merz, and B.D. Binderow. Qβ rna bacteriophage: mapping cis-acting elements within an rna genome. J. Virol., 64:3872-3881, 1990.
  4. F. Michel and E. Westhof. Modelling of the three-dimensional architecture of group i catalytic introns based on comparative sequence analysis. J. Mol. Biol., 216:585-610, 1990.
  5. C.R. Woese, R.R. Gutell, R. Gupta, and H.F. Noller. Detailed analysis of the higher order structure of 16s-like ribosomal ribonucleic acids. Microbiological Reviews, 47:621-669, 1983.
  6. S. Winker, R. Overbeek, C.R. Woese, G.J. Olsen, and N. Pfluger. Structure detection through automated covariance search. Comput. Appl. Biosci., 6:365-371, 1990.
  7. D. Sankoff. Evolution of secondary structure of 5s ribosomal rna. Paper presented at Tenth Numerical Taxonomy Conference, Lawrence, Kansas., 1976.
  8. M.S. Waterman and T.F. Smith. Rna secondary structure: a complete mathematical analysis. Math. Biosci., 42:257-266, 1978.
  9. R. Nussinov, G. Pieczenik, J.R. Griggs, and D.J. Kleitman. Algorithm for loop matchings. SIAM J. Appl. Math., 35:68-82, 1978.
  10. R. Nussinov and A.B. Jacobson. Fast algorithm for predicting the secondary structure of single- stranded rna. Proc. Natl. Acad. Sci. USA., 77:6309-6313, 1980.
  11. M. Zuker and P. Stiegler. Optimal computer folding of large rna sequences using thermodynamics and auxiliary information. Nucleic Acids Res., 9:133-148, 1981.
  12. D. Sankoff, J.B. Kruskal, S. Mainville, and R.J. Cedergren. Fast algorithms to determine RNA secondary structures containing multiple loops., chapter 3, pages 93-120. Time warps, string edits, and macromolecules: the theory and practice of sequence comparison, Sankoff D., Kruskal J.B., Eds. Addison-Wesley, Reading, MA, 1983.
  13. M. Zuker and D. Sankoff. Rna secondary structures and their prediction. Bull. Math. Biol., 46:591-621, 1984.
  14. M. Zuker. On finding all suboptimal foldings of an rna molecule. Science, 244:48-52, 1989.
  15. J.A. Jaeger, D.H. Turner, and M. Zuker. Improved predictions of secondary structures for rna. Proc. Natl. Acad. Sci. USA., 86:7706-7710, 1989.
  16. J.A. Jaeger, D.H. Turner, and M. Zuker. Predicting optimal and suboptimal secondary structure for rna. Meth. Enzymol., 183:281-306, 1990.
  17. S.M. Freier, R. Kierzek, J.A. Jaeger, N. Sugimoto, M.H. Caruthers, T. Neilson, and D.H. Turner. Improved free-energy parameters for predictions of rna duplex stability. Proc. Natl. Acad. Sci. USA, 83:9373-9377, 1986.
  18. D.H. Turner, N. Sugimoto, J.A. Jaeger, C.E. Longfellow, S.M. Freier, and R. Kierzek. Improved parameters for prediction of rna structure. Cold Spring Harb. Symp. Quant. Biol., 52:123-133, 1987.
  19. D.H. Turner and N. Sugimoto. Rna structure prediction. Annu. Rev. Biophys. Biophys. Chem., 17:167-192, 1988.
  20. C.W. Pleij and L. Bosch. Rna pseudoknots: structure, detection, and prediction. Meth. Enzymol., 180:289-303, 1989.
  21. M. Zuker. Computer prediction of rna structure. Meth. Enzymol., 180:262-288, 1989.
  22. J. Devereux, P. Haeberli, and O. Smithies. A comprehensive set of sequence analysis programs for the vax. Nucleic Acids Res., 12:387-395, 1984.
  23. M. Zuker, J.A. Jaeger, and D.H. Turner. A comparison of optimal and suboptimal rna secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res., 19:2707-2714, 1991.
  24. H.S. Bilofsky and C. Burks. The genbank genetic sequence data bank. Nucleic Acids Res., 16:1861-1863, 1988.
  25. G.N. Cameron. The embl data library. Nucleic Acids Res., 16:1865-1867, 1988.
  26. K.E. Sidman, D.G. George, W.C. Barker, and L.T. Hunt. The protein identification resource. Nucleic Acids Res., 16:1869-1871, 1988.
  27. D. Roode, R. Liebschutz, S. Maulik, T. Friedmann, D. Benton, and D. Kristofferson. New developments at bionet. Nucleic Acids Res., pages 1857-1859., 1988.
  28. C.R. Woese, S. Winker, and R.R. Gutell. Architecture of ribosomal rna: constraints on the sequence of ``tetra-loops''. Proc Natl Acad Sci USA, 87:8467-71, 1990.
  29. D. Labuda and G. Striker. Sequence conservation in alu evolution. Nucleic Acids Res., 17:2477-2491, 1989.
  30. M. Zuker. The use of dynamic programming algorithms in RNA secondary structure prediction., chapter 7, pages 159-184. Mathematical methods for DNA sequences, Waterman M.S., Ed. CRC Press, Inc., Boca Raton, Florida, 1989.
  31. B.A. Shapiro, J.V.Jr. Maizel, L.E. Lipkin, K.M. Currey, and C. Whitney. Generating non-overlapping displays of nucleic acid secondary structure. Nucleic Acids Res., 12:75-88, 1984.
  32. R.E. Bruccoleri and G. Heinrich. An improved algorithm for nucleic acid secondary structure display. Comput. Appl. Biosci., 4:167-173, 1988.
  33. R.C. Beach. The Unified Graphics System for Fortran 77 Programming Manual. Stanford Linear Accelerator Center Computational Research Group, Stanford, CA, 1981. Technical Memo 203.
  34. M. Zuker. Prediction of RNA Secondary Strcture by Energy Minimization., volume 25 of Computer Analysis of Sequence Data, Part II, A.M. Griffin & H.G Griffin, Eds., chapter 23, pages 267-294. CRC Press, Inc., Totowa, NJ, 1994.

Michael Zuker
Thu Nov 2 14:28:14 CST 1995