Publications

1. S. M. Tanny & M. Zuker. On a Unimodal Sequence of Binomial Coefficients. Discrete Mathematics 9, 79-89 (1974)

2. S. M. Tanny & M. Zuker. On a Unimodal Sequence of Binomial Coefficients II. J. Combinat. Info. & Sys. Sci. 1, 81-91 (1976)

3. G. E. Willick & M. Zuker. Equivalency of Linear Least Squares Curve Fitting and Reciprocal Functions in Protein Circular Dichroic Spectra Analysis. Biophys. Chem. 7, 223-227 (1977)

4. N. T Gridgeman & M. Zuker. Mercator, the Antigudermannian, and a Fluke. The Canadian Cartographer 15, 50-57 (1978)

5. S. M. Tanny & M. Zuker. Analytic Methods Applied to a Sequence of Binomial Coefficients. Discrete Mathematics 24, 299-310 (1978)

6. G. B. Calleja, B. F. Johnson, M. Zuker & A. P. James. The Mating System of a Homothallic Fission Yeast. Molec. Gen. Genet. 172, 1-6 (1979)

7. G. B. Calleja, M. Zuker & B. F. Johnson. Estimation of meiosis and sporulation efficiencies in the fission yeast by ascus analysis. Genet. Res. Camb. 33, 109-119 (1979)

8. M. Zuker, J. M. Ridgeway & D. R. Miller. A Study of Atmospheric Radionuclide Transport and Exposure Using Trajectory Analysis. (IAEA-SM-237/26) Biological Implications of Radionuclides Released from Nuclear Industries. Vienna, Vol. II, 381-398 (1979)

9. M. Yaguchi, A. T. Matheson, L. P. Visentin & M. Zuker. Molecular Evolution of the Alanine-Rich Acidic Ribosomal A Protein. In Genetics and Evolution of RNA Polymerase, tRNA and Ribosomes, S. Osawa, H. Ozeki, H. Uchida and T. Yura eds. University of Tokyo Press, 585-599 (1980)

10. A. B. Cairnie, L. F. Prud'homme-Lalonde, R. K. Harding & M. Zuker. The measurement of rectal and testis temperature in conscious mice, with observations on the effect of direct heating. Physics in Medicine and Biology 25, 317-322 (1980)

11. M. Zuker, G. Mihailov & M. Romanowski. Systematic Search for Orthogonal Systems in the Calibrations of Submultiples and Multiples of the Unit of Mass. Metrologia 16, 51-54 (1980)

12. D. Rose, C. M. Pearson, M. Zuker & J. R. Roberts. Ethylenethiorea: Criteria for the Assessment of its Effects on Man. Associate Committee on Scientific Criteria for Environmental Quality ISSN 0316-0114 NRCC No. 18469 (1980)

13. G. B. Calleja, M. Zuker, B. F. Johnson & B. Y. Yoo. Analysis of Fission Scars as Permanent Records of Cell Division in Schizosaccharomyces pombe. J. Theoretical Biology 84, 523-544 (1980)

14. R. Watson, M. Zuker, S. M. Martin & L. P. Visentin. A New Site-specific Endonuclease from Neisseria cinerea. FEBS Letters 118, 47-50 (1980)

15. 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)

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

17. 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 Res. 9, 2153-2172 (1981)

18. G. B. Calleja, M. Zuker & B. F. Johnson. Temporal Asymmetry of Sex Interconversion in a Strain of the Homothallic Fission Yeast Schizosaccharomyces pombe. Current Microbiology 6, 225-227 (1981)

19. M. Yaguchi, L. P. Visentin, M. Zuker, A. T. Matheson, C. Roy & A. R. Strom. Amino-Terminal Sequences of Ribosomal Proteins from the 30S Subunit of Archaebacterium Halobacterium cutirubrum. Zentralblatt für Bakteriologie, I. Abt. Orig. C3, 200-208 (1982)

20. B. F. Johnson, G. B. Calleja, B. Y. Yoo, M. Zuker & I. J. McDonald. Cell Division: Key to Cellular Morphogenesis in the Fission Yeast, Schizosaccharomyces. In International Review of Cytology, G. H. Bourne and J. F. Danielli eds. , Volume 75, Academic Press (1982)

21. D. O. Foster, F. Depocas & M. Zuker. Heterogeneity of the sympathetic innervation of rat interscapular brown adipose tissue via intercostal nerves. Can. J. Physiology and Pharmacology 60, 747-754 (1982)

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

23. N. C. Fournier, M. Zuker, R. E. Williams & I. C. P. Smith. Self-Association of the Cardiac Fatty Acid Binding Protein. Influence on Membrane-Bound, Fatty Acid Dependent Enzymes. Biochemistry 22, 1863-1872 (1983)

24. 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)

25. S. M. Tanny & M. Zuker. Signs of Terms in a Combinatorial Recursion. Siam J. Alg. Disc. Meth. 4, 437-441 (1983)

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

27. B. F. Johnson, G. B. Calleja & M. Zuker. Mating-Type Gene Switching in a Homothallic Fission Yeast. J. Theoretical Biology 110, 299-312 (1984)

28. A. G. Szabo, D. Krajcarski, M. Zuker & B. Alpert. Conformational Heterogeneity in Hemoglobin as Determined by Picosecond Fluorescence Decay Measurements of the Tryptophan Residues. Chemical Physics Letters 108, 145-149 (1984)

29. P. C. K Lau, R. W. Rowsome, M. Zuker & L. P. Visentin. Comparative nucleotide sequences encoding the immunity proteins and the carboxyl-terminal peptides of colicins E2 and E3. Nucleic Acids Res. 12, 8733-8745 (1984)

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

31. M. Zuker, A. G. Szabo, L. Bramall, D. T. Krajcarski & B. Selinger. Delta function convolution method (DFCM) for fluorescence decay experiments. The Review of Scientific Instruments 56, 14-22 (1985)

32. 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)

33. 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)

34. R. J. Hill, T. Kroft, M. Zuker & I. C. P. Smith. Large-scale selection synchrony of Tetrahymena thermophila. J. Cell Science 84, 237-251 (1986)

35. P. Falkenberg, M. Yaguchi, C. Roy, M. Zuker & A. T. Matheson. The primary structure of the ribosomal A-protein (L12) from the moderate halophile NRCC 41227. Biochemistry and Cell Biology 64, 675-680 (1986)

36. K. U. Ingold, G. W. Burton, D. O. Foster, M. Zuker, L. Hughes, S. Lacelle, E. Lusztyk & M. Slaby. A new vitamin E analogue more active than $\alpha$-tocopherol in the rat curative myopathy bioassay. FEBS Letters 205, 117-120 (1986)

37. R. M. MacKay, A. Lo, G. Willick, M. Zuker, S. Baird, M. Dove, F. Moranelli & V. Seligy. Structure of a Bacillus subtilis endo-$\beta$-1,4-glucanase gene. Nucleic Acids Res. 14, 9159-9170 (1986)

38. 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)

39. S. M. Tanny & M. Zuker. The Sensitivity of Eigenvalues under Elementary Matrix Perturbations. Linear Algebra and its Applications 86, 123-143 (1987)

40. 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)

41. A. T. Matheson, K. A. Louie, B. D. Tak & M. Zuker. The primary structure of the ribosomal A-protein (L12) from the halophilic eubacterium Haloanaerobium praevalens. Biochemie 69, 1013-1020 (1987)

42. 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)

43. M. Zuker & R. L. Somorjai. The Alignment of Protein Structures in Three Dimensions. Bull. Mathematical Biology 51, 55-78 (1989)

44. 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)

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

46. J. A. Jaeger, D. H. Turner & M. Zuker. Improved Predictions of Secondary Structures for RNA. Proc. Natl. Acad. Sci. USA 86, 7706-7710 (1989)

47. K. J. Willis, A. G. Szabo, J. Drew, M. Zuker & J. M. Ridgeway . Resolution of heterogeneous fluorescence into component decay-associated excitation spectra. Application to subtilisins. Biophysical Journal 57, 183-190 (1990)

48. 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)

49. K. J. Willis, A. G. Szabo, M. Zuker, J. M. Ridgeway & B. Alpert. Fluorescence Decay Kinetics of the Tryptophyl Residues of Myoglobin: Effect of Heme Ligation and Evidence for Discrete Lifetime Components. Biochemistry 29, 5270-5275 (1990)

50. 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 Mg²⁺, and in the Presence of Substrate. Biochemistry 29, 10147-10158 (1990)

51. S-Y. Le & M. Zuker. Common Structures of the $5^{\prime}$ Noncoding RNA in Enteroviruses and Rhinoviruses: Thermodynamical Stability and Statistical Significance. J. Mol. Biology 216, 729-741 (1990)

52. 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 Res. 19, 353-358 (1991)

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

54. 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 Res. 19, 2707-2714 (1991)

55. M. Zuker. Suboptimal Sequence Alignment in Molecular Biology: Alignment with Error Analysis J. Mol. Biology 221, 403-420 (1991)

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

57. 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)

58. S. Karlin, M. Zuker & L. Brocchieri. Measuring Residue Associations in Protein Structures: Possible Implications for Protein Folding J. Mol. Biology 239, 227-248 (1994)

59. A. Stoltzfus, D. Spencer, M. Zuker, J. Logsdon, W. F. Doolittle. Testing the Exon Theory of Genes: The Evidence from Protein Structure Science 265, 202-207 (1994)

60. 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)

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

62. G. Drouin, M. Moniz de Sá & M. Zuker. The Giardia lamblia actin gene and the phylogeny of eukaryotes. J. Mol. Evol. 41, 841-849 (1996)

63. 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 Q$\beta$. J. Mol. Biol. 275 (4), 589-600, (1998)

64. 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. In American Chemical Society Symposium Series, 682, N. B. Leontis and J. SantaLucia Jr. , eds. , 246-257 (1998)

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

66. 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 and B. F. C. Clark, eds. , NATO ASI Series, Kluwer Academic Publishers, Dordrecht, NL, (1999)

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

68. 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).

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

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

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

72. 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)

73. 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)

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

75. A. Waugh, P. Gendron, 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 8 (6), 707-717, (2002)

76. M. Zuker. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 31 (13), 3406-3415, (2003)

77. J. -M. Rouillard, M. Zuker & E. Gulari. OligoArray 2. 0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 31 (12), 3057-3062, (2003)

78. R. A. Dimitrov & M. Zuker. Prediction of Hybridization and Melting for Double-Stranded Nucleic Acids. Biophysical J. 87, 215-226, (2004)

79. D. H. Mathews, M. D. Disney, J. L. Childs, S. J. Schroeder, M. Zuker & D. H. Turner. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc. Natl. Acad. Sci. USA 101 (19), 7287-7292, (2004)

80. D. Steinberger, N. Blau, D. Goriuonov, J. Bitsch, M. Zuker, S. Hummel & U. Müller. Heterozygous mutation in $5^{\prime}$-untranslated region of sepiapterin reductase gene (SPR) in a patient with dopa-responsive dystonia. Neurogenetics 5 (3), 187-90, (2004)

81. J. H. Mansfield, B. D. Harfe, R. Nissen, J. Obenauer, J. Srineel, A. Chaudhuri, R. Farzan-Kashani, M. Zuker, A. E. Pasquinelli, G. Ruvkun, P. A. Sharp, C. J. Tabin, M. T. McManus. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet. 36 (10) 1079-83, (2004)

82. D. H. Mathews & M. Zuker. RNA secondary structure prediction. In Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics P. Clote ed. , John Wiley & Sons, New York, ``Programming Paradigms'', Vol. 1, (2005)

83. D. H. Mathews & M. Zuker. Predictive Methods Using RNA Sequences. In Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins A. Baxevanis and F. Ouellette eds. , 3rd edition, John Wiley & Sons, New York, Chapter 7, (2005)

84. N. R. Markham & M. Zuker. DINAMelt Web Server for Nucleic Acid Melting Prediction. Nucleic Acids Res. 33, Wxx-Wyy, (2005)