To main RNA page.

RNA related publications

  1. P. Stiegler, P. Carbon, M. Zuker, J-P. Ebel & C. Ehresmann
    Structure secondaire et topographie du RNA ribosomique 16S d'Escherichia coli.
    C. R. Acad. Sc. Paris, t. 291, Serie D 937-940 (1980)

  2. M. Zuker & P. Stiegler
    Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information.
    Nucleic Acids Research 9, 133-148 (1981)

  3. P. Stiegler, P. Carbon, M. Zuker, J-P. Ebel & C. Ehresmann
    Structural organization of the 16S ribosomal RNA from E. coli. Topography and secondary structure.
    Nucleic Acids Research 9, 2153-2172 (1981)

  4. J-L. Darlix, M. Zuker & P-F. Spahr
    Structure-function relationship of Rous sarcoma virus leader RNA.
    Nucleic Acids Research 10, 5183-5196 (1982)

  5. T.R. Cech, N.K. Tanner, I. Tinoco Jr., B.R. Weir, M. Zuker & P.S. Perlman
    Secondary structure of the Tetrahymena ribosomal RNA intervening sequence : Structural homology with fungal mitochondrial intervening sequences.
    Proc. Natl. Acad. Sci. USA 80, 3903-3907 (1983)

  6. A.B. Jacobson, L. Good, J. Simonetti & M. Zuker
    Some computational methods to improve the folding of large RNAs.
    Nucleic Acids Research 12, 45-52 (1984)

  7. M. Zuker & D. Sankoff
    RNA Secondary Structures and their Prediction.
    Bull. Mathematical Biology 46, 591-621 (1984)

  8. A.B. Jacobson, H. Kumar & M. Zuker
    Effect of Spermidine on the Conformation of Bacteriophage MS2 RNA: Electron Microscopy and Computer Modeling.
    J. Mol. Biology 181, 517-531 (1985)

  9. M. Zuker
    RNA Folding Prediction: The Continued Need for Interaction Between Biologists and Mathematicians.
    Lectures on Mathematics in the Life Sciences 17, 87-124 (1986)

  10. M. Zuker
    Computer Prediction of RNA Secondary Structures. in Proceedings of the International Symposium on Computer Analysis for Life Science, Hayashibara Forum '85, C. Kawabata and A. R. Bishop eds.
    Ohmsha Ltd., 220-233 (1986)

  11. A.B. Jacobson, M. Zuker & A. Hirashima
    Comparative Studies on the Secondary Structure of the RNAs of Related RNA Coliphages. in Molecular Biology of RNA: New Perspectives, M. Inouye and B. S. Dudock eds.
    Academic Press, Inc., 331-354 (1987)

  12. M. Zuker
    The Use of Dynamic Programming Algorithms in RNA Secondary Structure Prediction. in Mathematical Methods for DNA Sequences, M. S. Waterman ed.
    CRC Press, Inc., 159-184 (1989)

  13. M. Zuker
    Computer Prediction of RNA Structure. in RNA Processing, J. E. Dahlberg and J. N. Abelson eds.
    Methods in Enzymology 180, 262-288 (1989)

  14. M. Zuker
    On Finding All Suboptimal Foldings of an RNA Molecule.
    Science 244, 48-52 (1989)

  15. J.A. Jaeger, D.H. Turner & 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 & M. Zuker
    Predicting Optimal and Suboptimal Secondary Structure for RNA. in Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences, R. F. Doolittle ed.
    Methods in Enzymology 183, 281-306 (1990)

  17. J.A. Jaeger, M. Zuker & D.H. Turner
    Melting and Chemical Modification of a Cyclized Self-Splicing Group I Intron: Similarity of Structures in 1 M Na+, in 10 mM Mg++, and in the Presence of Substrate.
    Biochemistry 29, 10147-10158 (1990)

  18. S-Y. Le & M. Zuker
    Common Structures of the 5' Noncoding RNA in Enteroviruses and Rhinoviruses: Thermodynamical Stability and Statistical Significance.
    J. Mol. Biology 216, 729-741 (1990)

  19. L. Chan, M. Zuker & A.B. Jacobson
    A Computer Method for Finding Common Base Paired Helices in Aligned Sequences: Application to the Analysis of Random Sequences.
    Nucleic Acids Research 19, 353-358 (1991)

  20. S-Y. Le & M. Zuker
    Predicting Common Foldings of Homologous RNAs.
    J. Biomolecular Structure & Dynamics 8, 1027-1044 (1991)

  21. M. Zuker, J.A. Jaeger & 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 Research 19, 2707-2714 (1991)

  22. A.B. Jacobson & M. Zuker
    Structural Analysis by Energy Dot Plot of a Large mRNA.
    J. Mol. Biology 233, 261-269 (1993)

  23. M. Zuker
    Prediction of RNA Secondary Structure by Energy Minimization. in Computer Analysis of Sequence Data A.M. Griffin and H.G. Griffin eds.
    Methods in Molecular Biology, Humana Press Inc., 267-294 (1994)

  24. A.E. Walter, D.H. Turner, J. Kim, M.H. Lyttle, P. Müller, D.H. Mathews & 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)

  25. M. Zuker & A.B. Jacobson
    ``Well-determined'' Regions in RNA Secondary Structure Predictions. Application to small and large subunit rRNA.
    Nucleic Acids Research 23, 2791-2798 (1995)

  26. A.B. Jacobson, R. Arora, M. Zuker, C. Priano, C.H. Lin & D.R. Mills
    Structural Plasticity in RNA and its Role in the Regulation of Protein Translation in Coliphage Qß.
    J. Mol. Biol. 274, 589-600 (1998)

  27. D.H. Mathews, T.C. Andre, J. Kim, D.H. Turner & M. Zuker
    An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Free Energy Parameters.
    American Chemical Society Symposium Series 682, 246-257 (1998), N.B. Leontis and J. SantaLucia Jr., eds.

  28. M. Zuker & A.B. Jacobson
    Using Reliability Information to Annotate RNA Secondary Structures.
    RNA 4, 669-679 (1998)

  29. M. Zuker, D.H. Mathews & D.H. Turner
    Algorithms and Thermodynamics for RNA Secondary Structure Prediction: A Practical Guide
    In RNA Biochemistry and Biotechnology, 11-43, J. Barciszewski & B.F.C. Clark, eds., NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, (1999)

  30. D.H. Mathews, J. Sabina, M. Zuker & D.H. Turner
    Expanded Sequence Dependence of Thermodynamic Parameters Provides Robust Prediction of RNA Secondary Structure
    J. Mol. Biol. 288, 911-940 (1999)

  31. R.B. Lyngsø, M. Zuker & C.N.S. Pedersen
    Internal loops in RNA secondary structure prediction.
    In Proceedings of the 3rd annual international conference on computational molecular biology (RECOMB), 260-267 (1999)

  32. R.B. Lyngsø, M. Zuker & C.N.S. Pedersen
    Fast evaluation of internal loops in RNA secondary structure prediction.
    Bioinformatics 15, 440-445 (1999)

  33. M. Zuker
    Calculating nucleic acid secondary structure.
    Curr Opin Struct Biol. 10, 303-310, (2000)

  34. V. Moulton, M. Zuker, M. Steel, R. Pointon & D. Penny
    Metrics on RNA Secondary Structures.
    J. Computational Biology 7, 277-292, (2000)

  35. K. Kidd-Ljunggren, M. Zuker, I.L. Hofacker & A.H. Kidd
    The Hepatitis B Virus Pregenome: Prediction of RNA Structure and Implications for the Emergence of Deletions.
    Intervirology 43, 154-164, (2000)

  36. D.H. Mathews, D.H. Turner, & M. Zuker RNA Secondary Structure Prediction.
    In Current Protocols in Nucleic Acid Chemistry S. Beaucage, D.E. Bergstrom, G.D. Glick, and R.A. Jones eds., John Wiley & Sons, New York, 11.2.1-11.2.10, (2000)

  37. J.-M. Rouillard, C.J. Herbert & M. Zuker
    OligoArray: Genome-scale oligonucleotide design for microarrays.
    Bioinformatics 18 (3), 486-487, (2002)

  38. R. Altman, J.W. Brown, D. Case, D. Gautheret, S.C. Harvey, N. Leontis, J. Westbrook, E. Westhof, M. Zuker & F. Major
    RNAML: A standard syntax for exchanging RNA information.
    RNA (in press)
Home page

Michael Zuker
Oct 1999.