Bibliography

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Bibliography

  1. P.M. MacDonald.
    Bicoid mRNA localization signal: phylogenetic conservation of function and RNA secondary structure.
    Development, 110:161-171, 1990.
  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. C.I. Brannan, E.C. Dees, R.S. Ingram, and S.M. Tilghman.
    The product of the h19 gene may function as an RNA.
    Mol. Cell. Biol., 10:28-36, 1990.
  5. C.J. Brown, A. Ballabio, J.L. Rupert, R.G. Lafreniere, M. Grompe, R. Tonlorenzi, and H.F. Willard.
    A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome.
    Nature, 349:38-44, 1991.
  6. T.R. Cech and B.L. Bass.
    Biological catalysis by RNA.
    Ann. Rev. Biochem., 55:599-629, 1986.
  7. T.R. Cech.
    Self-splicing of group I introns.
    Ann. Rev. Biochem., 59:543-568, 1990.
  8. S.C. Darr, J.W. Brown, and N.R. Pace.
    The varieties of Ribonuclease P.
    Trends Biochem. Sci., 17:178-182, 1992.
  9. S.H. Kim, F.L. Suddath, G.J. Quigley, A. McPherson, and J.L. Sussman.
    Three dimensional tertiary structure of yeast phenylalanine transfer RNA.
    Science, 185:435-440, 1974.
  10. J.D. Robertus, J.E. Ladner, J.T. Finch, D. Rhodes, and R.S. Brown.
    Structure of yeast phenylalanine tRNA at 3 Å resolution.
    Nature, 250:546-551, 1974.
  11. H.W. Pley, K.M Flaherty, and D.B. McKay.
    Three-dimensional structure of a hammerhead ribozyme.
    Nature, 372:68-74, 1994.
  12. R.R. Gutell, 1995.
    personal communication.
  13. 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.
  14. 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.
  15. F. Major, D. Gautheret, and R. Cedergren.
    Reproducing the three-dimensional structure of a tRNA molecule from structural constraints.
    Proc. Natl. Acad. Sci. USA, 90:9408-9412, 1993.
  16. M. Zuker.
    On finding all suboptimal foldings of an RNA molecule.
    Science, 244:48-52, 1989.
  17. 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.
  18. J.A. Jaeger, D.H. Turner, and M. Zuker.
    Predicting optimal and suboptimal secondary structure for RNA.
    Meth. Enzymol., 183:281-306, 1990.
  19. 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.
  20. D.H. Mathews, T.C. Andre, J. Kim, D.H. Turner, and M. Zuker.
    An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Free Energy Parameters., chapter 15, pages 246-257.
    American Chemical Society Symposium Series 682. American Chemical Society, Washington, DC, 1998.
  21. 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.
  22. M. Zuker and D. Sankoff.
    RNA secondary structures and their prediction.
    Bull. Math. Biol., 46:591-621, 1984.
  23. M. Zuker.
    RNA folding prediction: The continued need for interaction between biologists and mathematicians.
    Lectures on Mathematics in the Life Sciences, 17:86-123, 1986.
  24. C.W. Pleij and L. Bosch.
    RNA pseudoknots: structure, detection, and prediction.
    Meth. Enzymol., 180:289-303, 1989.
  25. J.P.Abrahams, M. van den Berg, E. van Batenburg, and C.W. Pleij.
    Prediction of RNA secondary structure, including pseudoknotting, by computer simulation.
    Nucleic Acids Res., 18:3035-3044, 1990.
  26. R.R. Gutell and C.R. Woese.
    Higher order structural elements in ribosomal RNAs: Pseudo-knots and the use of noncanonical pairs.
    Proc. Natl. Acad. Sci. USA, 87:663-667, 1990.
  27. E. Dam, K. Pleij, and D. Draper.
    Structural and functional aspects of RNA pseudoknots.
    Biochemistry, 31:11665-11676, 1992.
  28. C.W. Pleij.
    RNA pseudoknots.
    Curr. Opin. Struct. Biol., 4:337-344, 1994.
  29. Z. Du, D.P. Giedroc, and D.W. Hoffman.
    Structure of the autoregulatory pseudoknot within the gene 32 messenger RNA of bacteriophages T2 and T6: A model for a possible family of structurally related RNA pseudoknots.
    Biochemistry, 35(13):4187-4198, 1996.
  30. H. Jacobson and W.H. Stockmayer.
    Intramolecular reaction in polycondensations. I. The theory of linear systems.
    J. Chem. Phys., 18:1600-1606, 1950.
  31. 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.
  32. 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.
  33. D.H. Turner, N. Sugimoto, and S.M. Freier.
    RNA structure prediction.
    Annu. Rev. Biophys. Biophys. Chem., 17:167-192, 1988.
  34. M. Wu, J.A. McDowell, and D.H. Turner.
    A periodic table of symmetric tandem mismatches in RNA.
    Biochemistry, 34:3204-3211, 1995.
  35. A.E. Walter, D.H. Turner, J. Kim, M.H. Lyttle, P. Muller, D.H. Mathews, and M. Zuker.
    Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding.
    Proc Natl Acad Sci USA, 91:9218-9222, 1994.
  36. J.Jr. SantaLucia.
    A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics.
    Proc. Natl. Acad. Sci. USA, 95:1460-1465, 1998.
  37. N. Sugimoto, S. Nakano, M. Katoh, A. Matsumura, H. Nakamuta, T. Ohmichi, M. Yoneyama, and M. Sasaki.
    Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes.
    Biochemistry, 34:11211-11216, 1995.
  38. M. Zuker and A.B. Jacobson.
    Using Reliability Information to Annotate RNA Secondary Structures.
    RNA, 4:669-679, 1998.
  39. 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.
  40. 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.
  41. R.E. Bruccoleri and G. Heinrich.
    An improved algorithm for nucleic acid secondary structure display.
    Comput. Appl. Biosci., 4:167-173, 1988.



Michael Zuker
Center for Computational Biology
Washington University in St. Louis
1998-12-05