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Michael Zuker

TitleProfessor
InstitutionRensselaer Polytechnic Institute
DepartmentMath
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     Bibliographic 
     selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Stephenson W, Keller S, Santiago R, Albrecht JE, Asare-Okai PN, Tenenbaum SA, Zuker M, Li PT. Combining temperature and force to study folding of an RNA hairpin. Phys Chem Chem Phys. 2014 Jan 21; 16(3):906-17.
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    2. Ragan C, Zuker M, Ragan MA. Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. PLoS Comput Biol. 2011 Feb; 7(2):e1001090.
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    3. Agius P, Bennett KP, Zuker M. Comparing RNA secondary structures using a relaxed base-pair score. RNA. 2010 May; 16(5):865-78.
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    4. Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA. Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. PLoS One. 2009; 4(5):e5745.
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    5. Chen YP, Evans JD, Murphy C, Gutell R, Zuker M, Gundensen-Rindal D, Pettis JS. Morphological, molecular, and phylogenetic characterization of Nosema ceranae, a microsporidian parasite isolated from the European honey bee, Apis mellifera. J Eukaryot Microbiol. 2009 Mar-Apr; 56(2):142-7.
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    6. Abdelmaksoud HE, Yau EH, Zuker M, Sullivan JM. Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy. Exp Eye Res. 2009 May; 88(5):859-79.
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    7. Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods Mol Biol. 2008; 453:3-31.
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    8. Mathews DH, Turner DH, Zuker M. RNA secondary structure prediction. Curr Protoc Nucleic Acid Chem. 2007 Mar; Chapter 11:Unit 11.2.
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    9. Markham NR, Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 2005 Jul 1; 33(Web Server issue):W577-81.
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    10. Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, Sharp PA, Tabin CJ, McManus MT. MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression. Nat Genet. 2004 Oct; 36(10):1079-83.
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    11. Steinberger D, Blau N, Goriuonov D, Bitsch J, Zuker M, Hummel S, Müller U. Heterozygous mutation in 5'-untranslated region of sepiapterin reductase gene (SPR) in a patient with dopa-responsive dystonia. Neurogenetics. 2004 Sep; 5(3):187-90.
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    12. Dimitrov RA, Zuker M. Prediction of hybridization and melting for double-stranded nucleic acids. Biophys J. 2004 Jul; 87(1):215-26.
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    13. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A. 2004 May 11; 101(19):7287-92.
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    14. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003 Jul 1; 31(13):3406-15.
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    15. Rouillard JM, Zuker M, Gulari E. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res. 2003 Jun 15; 31(12):3057-62.
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    16. Ben-Dror G, Mizerizky Y, Viar G, Zuker M, Miron D. [The epidemiology and clinical features of Legionella pneumonia (LP) in patients older than 60 years old who were hospitalized with pneumonia in northern Israel]. Harefuah. 2002 Aug; 141(8):680-2, 763.
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    17. Waugh A, Gendron P, Altman R, Brown JW, Case D, Gautheret D, Harvey SC, Leontis N, Westbrook J, Westhof E, Zuker M, Major F. RNAML: a standard syntax for exchanging RNA information. RNA. 2002 Jun; 8(6):707-17.
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    18. Rouillard JM, Herbert CJ, Zuker M. OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics. 2002 Mar; 18(3):486-7.
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    19. Zuker M. Calculating nucleic acid secondary structure. Curr Opin Struct Biol. 2000 Jun; 10(3):303-10.
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    20. Miron D, El AL, Zuker M, Lumelsky D, Murph M, Floyd MM, Brown JM. Mycobacterium fortuitum osteomyelitis of the cuboid after nail puncture wound. Pediatr Infect Dis J. 2000 May; 19(5):483-5.
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    21. Moulton V, Zuker M, Steel M, Pointon R, Penny D. Metrics on RNA secondary structures. J Comput Biol. 2000 Feb-Apr; 7(1-2):277-92.
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    22. Kidd-Ljunggren K, Zuker M, Hofacker IL, Kidd AH. The hepatitis B virus pregenome: prediction of RNA structure and implications for the emergence of deletions. Intervirology. 2000; 43(3):154-64.
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    23. Lyngsø RB, Zuker M, Pedersen CN. Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics. 1999 Jun; 15(6):440-5.
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    24. Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol. 1999 May 21; 288(5):911-40.
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    25. Zuker M, Jacobson AB. Using reliability information to annotate RNA secondary structures. RNA. 1998 Jun; 4(6):669-79.
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    26. Jacobson AB, Arora R, Zuker M, Priano C, Lin CH, Mills DR. Structural plasticity in RNA and its role in the regulation of protein translation in coliphage Q beta. J Mol Biol. 1998 Jan 30; 275(4):589-600.
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    27. Drouin G, Moniz de Sá M, Zuker M. The Giardia lamblia actin gene and the phylogeny of eukaryotes. J Mol Evol. 1995 Dec; 41(6):841-9.
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    28. Zuker M, Jacobson AB. "Well-determined" regions in RNA secondary structure prediction: analysis of small subunit ribosomal RNA. Nucleic Acids Res. 1995 Jul 25; 23(14):2791-8.
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    29. Walter AE, Turner DH, Kim J, Lyttle MH, Müller P, Mathews DH, Zuker M. Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A. 1994 Sep 27; 91(20):9218-22.
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    30. Zhu L, Wigle D, Hinek A, Kobayashi J, Ye C, Zuker M, Dodo H, Keeley FW, Rabinovitch M. The endogenous vascular elastase that governs development and progression of monocrotaline-induced pulmonary hypertension in rats is a novel enzyme related to the serine proteinase adipsin. J Clin Invest. 1994 Sep; 94(3):1163-71.
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    31. Stoltzfus A, Spencer DF, Zuker M, Logsdon JM, Doolittle WF. Testing the exon theory of genes: the evidence from protein structure. Science. 1994 Jul 8; 265(5169):202-7.
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    32. Karlin S, Zuker M, Brocchieri L. Measuring residue associations in protein structures. Possible implications for protein folding. J Mol Biol. 1994 Jun 3; 239(2):227-48.
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    33. Zuker M. Prediction of RNA secondary structure by energy minimization. Methods Mol Biol. 1994; 25:267-94.
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    34. Jacobson AB, Zuker M. Structural analysis by energy dot plot of a large mRNA. J Mol Biol. 1993 Sep 20; 233(2):261-9.
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    35. Zuker M. Suboptimal sequence alignment in molecular biology. Alignment with error analysis. J Mol Biol. 1991 Sep 20; 221(2):403-20.
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    36. Zuker M, Jaeger JA, Turner DH. A comparison of optimal and suboptimal RNA secondary structures predicted by free energy minimization with structures determined by phylogenetic comparison. Nucleic Acids Res. 1991 May 25; 19(10):2707-14.
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    37. Le SY, Zuker M. Predicting common foldings of homologous RNAs. J Biomol Struct Dyn. 1991 Apr; 8(5):1027-44.
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    38. Chan L, Zuker M, Jacobson AB. A computer method for finding common base paired helices in aligned sequences: application to the analysis of random sequences. Nucleic Acids Res. 1991 Jan 25; 19(2):353-8.
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    39. Le SY, Zuker M. Common structures of the 5' non-coding RNA in enteroviruses and rhinoviruses. Thermodynamical stability and statistical significance. J Mol Biol. 1990 Dec 5; 216(3):729-41.
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    40. Jaeger JA, Zuker M, Turner DH. 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. 1990 Nov 6; 29(44):10147-58.
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    41. Willis KJ, Szabo AG, Zuker M, Ridgeway JM, Alpert B. Fluorescence decay kinetics of the tryptophyl residues of myoglobin: effect of heme ligation and evidence for discrete lifetime components. Biochemistry. 1990 Jun 5; 29(22):5270-5.
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    42. Willis KJ, Szabo AG, Drew J, Zuker M, Ridgeway JM. Resolution of heterogeneous fluorescence into component decay-associated excitation spectra. Application to subtilisins. Biophys J. 1990 Feb; 57(2):183-9.
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    43. Jaeger JA, Turner DH, Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods Enzymol. 1990; 183:281-306.
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    44. Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proc Natl Acad Sci U S A. 1989 Oct; 86(20):7706-10.
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    45. Zuker M. On finding all suboptimal foldings of an RNA molecule. Science. 1989 Apr 7; 244(4900):48-52.
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    46. Zuker M. Computer prediction of RNA structure. Methods Enzymol. 1989; 180:262-88.
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    47. Zuker M, Somorjai RL. The alignment of protein structures in three dimensions. Bull Math Biol. 1989; 51(1):55-78.
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    48. Matheson AT, Louie KA, Tak BD, Zuker M. The primary structure of the ribosomal A-protein (L12) from the halophilic eubacterium Haloanaerobium praevalens. Biochimie. 1987 Oct; 69(10):1013-20.
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    49. MacKay RM, Lo A, Willick G, Zuker M, Baird S, Dove M, Moranelli F, Seligy V. Structure of a Bacillus subtilis endo-beta-1,4-glucanase gene. Nucleic Acids Res. 1986 Nov 25; 14(22):9159-70.
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    50. Ingold KU, Burton GW, Foster DO, Zuker M, Hughes L, Lacelle S, Lusztyk E, Slaby M. A new vitamin E analogue more active than alpha-tocopherol in the rat curative myopathy bioassay. FEBS Lett. 1986 Sep 1; 205(1):117-20.
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    51. Hill RJ, Kroft T, Zuker M, Smith IC. Large-scale selection synchrony of Tetrahymena thermophila. J Cell Sci. 1986 Aug; 84:237-51.
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    52. Falkenberg P, Yaguchi M, Roy C, Zuker M, Matheson AT. The primary structure of the ribosomal A-protein (L12) from the moderate halophile NRCC 41227. Biochem Cell Biol. 1986 Jul; 64(7):675-80.
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    53. Jacobson AB, Kumar H, Zuker M. Effect of spermidine on the conformation of bacteriophage MS2 RNA. Electron microscopy and computer modeling. J Mol Biol. 1985 Feb 20; 181(4):517-31.
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    54. Lau PC, Rowsome RW, Zuker M, Visentin LP. Comparative nucleotide sequences encoding the immunity proteins and the carboxyl-terminal peptides of colicins E2 and E3. Nucleic Acids Res. 1984 Nov 26; 12(22):8733-45.
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    55. Jacobson AB, Good L, Simonetti J, Zuker M. Some simple computational methods to improve the folding of large RNAs. Nucleic Acids Res. 1984 Jan 11; 12(1 Pt 1):45-52.
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    56. Cech TR, Tanner NK, Tinoco I, Weir BR, Zuker M, Perlman PS. Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. Proc Natl Acad Sci U S A. 1983 Jul; 80(13):3903-7.
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    57. Fournier NC, Zuker M, Williams RE, Smith IC. Self-association of the cardiac fatty acid binding protein. Influence on membrane-bound, fatty acid dependent enzymes. Biochemistry. 1983 Apr 12; 22(8):1863-72.
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    58. Darlix JL, Zuker M, Spahr PF. Structure-function relationship of Rous sarcoma virus leader RNA. Nucleic Acids Res. 1982 Sep 11; 10(17):5183-96.
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    59. Foster DO, Depocas F, Zuker M. Heterogeneity of the sympathetic innervation of rat interscapular brown adipose tissue via intercostal nerves. Can J Physiol Pharmacol. 1982 Jun; 60(6):747-54.
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    60. Stiegler P, Carbon P, Zuker M, Ebel JP, Ehresmann C. Structural organization of the 16S ribosomal RNA from E. coli. Topography and secondary structure. Nucleic Acids Res. 1981 May 11; 9(9):2153-72.
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    61. Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Res. 1981 Jan 10; 9(1):133-48.
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    62. Stiegler P, Carbon P, Zuker M, Ebel JP, Ehresmann C. [Secondary and topographic structure of ribosomal RNA 16S of Escherichia coli]. C R Seances Acad Sci D. 1980 Dec 8; 291(12):937-40.
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    63. Watson R, Zuker M, Martin SM, Visentin LP. A new site-specific endonuclease from Neisseria cinerea. FEBS Lett. 1980 Aug 25; 118(1):47-54.
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    64. Calleja GB, Zuker M, Johnson BF, Yoo BY. Analyses of fission scars as permanent records of cell division in Schizosaccharomyces pombe. J Theor Biol. 1980 Jun 7; 84(3):523-44.
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    65. Cairnie AB, Prud'homme-Lalonde LF, Harding RK, Zuker M. The measurement of rectal and testis temperature in conscious mice, with observations on the effect of direct heating. Phys Med Biol. 1980 Mar; 25(2):317-22.
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    66. Calleja GB, Zuker M, Johnson BF. Estimation of meiosis and sporulation efficiencies in the fission yeast by ascus analysis. Genet Res. 1979 Apr; 33(2):109-19.
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    67. Willick G, Zuker M. Equivalency of linear least squares curve fitting and reciprocal functions in protein circular dichroic spectra analysis. Biophys Chem. 1977 Nov; 7(3):223-7.
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