Michael Zuker - Publications

Rensselaer Polytechnic Institute, Troy, NY, United States 
Computer Science, Molecular Biology

45 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 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. Physical Chemistry Chemical Physics : Pccp. 16: 906-17. PMID 24276015 DOI: 10.1039/c3cp52042k  1
2011 Ragan C, Zuker M, Ragan MA. Quantitative prediction of miRNA-mRNA interaction based on equilibrium concentrations. Plos Computational Biology. 7: e1001090. PMID 21390282 DOI: 10.1371/journal.pcbi.1001090  1
2010 Agius P, Bennett KP, Zuker M. Comparing RNA secondary structures using a relaxed base-pair score. Rna (New York, N.Y.). 16: 865-78. PMID 20360393 DOI: 10.1261/rna.903510  1
2009 Ragan C, Cloonan N, Grimmond SM, Zuker M, Ragan MA. Transcriptome-wide prediction of miRNA targets in human and mouse using FASTH. Plos One. 4: e5745. PMID 19478946 DOI: 10.1371/journal.pone.0005745  1
2009 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. The Journal of Eukaryotic Microbiology. 56: 142-7. PMID 19457054 DOI: 10.1111/j.1550-7408.2008.00374.x  1
2009 Abdelmaksoud HE, Yau EH, Zuker M, Sullivan JM. Development of lead hammerhead ribozyme candidates against human rod opsin mRNA for retinal degeneration therapy. Experimental Eye Research. 88: 859-79. PMID 19094986 DOI: 10.1016/j.exer.2008.11.018  1
2008 Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization. Methods in Molecular Biology (Clifton, N.J.). 453: 3-31. PMID 18712296 DOI: 10.1007/978-1-60327-429-6_1  1
2007 Mathews DH, Turner DH, Zuker M. RNA secondary structure prediction. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 11.2. PMID 18428968 DOI: 10.1002/0471142700.nc1102s28  1
2005 Markham NR, Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Research. 33: W577-81. PMID 15980540 DOI: 10.1093/nar/gki591  1
2004 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. Nature Genetics. 36: 1079-83. PMID 15361871 DOI: 10.1038/ng1421  1
2004 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. 5: 187-190. PMID 15241655 DOI: 10.1007/s10048-004-0182-3  1
2004 Dimitrov RA, Zuker M. Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal. 87: 215-26. PMID 15240459 DOI: 10.1529/biophysj.103.020743  1
2004 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. Proceedings of the National Academy of Sciences of the United States of America. 101: 7287-92. PMID 15123812 DOI: 10.1073/pnas.0401799101  1
2003 Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research. 31: 3406-15. PMID 12824337 DOI: 10.1093/nar/gkg595  1
2003 Rouillard JM, Zuker M, Gulari E. OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Research. 31: 3057-62. PMID 12799432 DOI: 10.1093/nar/gkg426  1
2002 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 (New York, N.Y.). 8: 707-17. PMID 12088144 DOI: 10.1017/S1355838202028017  1
2002 Rouillard JM, Herbert CJ, Zuker M. OligoArray: genome-scale oligonucleotide design for microarrays. Bioinformatics (Oxford, England). 18: 486-7. PMID 11934750 DOI: 10.1093/bioinformatics/18.3.486  1
2000 Moulton V, Zuker M, Steel M, Pointon R, Penny D. Metrics on RNA secondary structures. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 7: 277-92. PMID 10890402 DOI: 10.1089/10665270050081522  1
1999 Lyngsø RB, Zuker M, Pedersen CN. Fast evaluation of internal loops in RNA secondary structure prediction. Bioinformatics (Oxford, England). 15: 440-5. PMID 10383469 DOI: 10.1093/bioinformatics/15.6.440  1
1999 Mathews DH, Sabina J, Zuker M, Turner DH. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. Journal of Molecular Biology. 288: 911-40. PMID 10329189 DOI: 10.1006/jmbi.1999.2700  1
1998 Mathews DH, Andre TC, Kim J, Turner DH, Zuker M. An Updated Recursive Algorithm for RNA Secondary Structure Prediction with Improved Thermodynamic Parameters Acs Symposium Series. 682: 246-257.  1
1994 Stoltzfus A, Spencer DF, Zuker M, Logsdon JM, Doolittle WF. Testing the exon theory of genes: the evidence from protein structure. Science (New York, N.Y.). 265: 202-7. PMID 8023140 DOI: 10.1126/science.8023140  1
1994 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. Proceedings of the National Academy of Sciences of the United States of America. 91: 9218-22. PMID 7524072 DOI: 10.1073/pnas.91.20.9218  1
1994 Zuker M. Prediction of RNA secondary structure by energy minimization. Methods in Molecular Biology (Clifton, N.J.). 25: 267-94. PMID 7516239 DOI: 10.1385/0-89603-276-0:267  1
1991 Zuker M. Suboptimal sequence alignment in molecular biology. Alignment with error analysis. Journal of Molecular Biology. 221: 403-20. PMID 1920426 DOI: 10.1016/0022-2836(91)80062-Y  1
1991 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 Research. 19: 2707-14. PMID 1710343 DOI: 10.1093/nar/19.10.2707  1
1990 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. 29: 5270-5275. PMID 2383545 DOI: 10.1021/bi00474a008  1
1990 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. 29: 10147-58. PMID 2271644 DOI: 10.1021/bi00496a002  1
1990 Willis KJ, Szabo AG, Drew J, Zuker M, Ridgeway JM. Resolution of heterogeneous fluorescence into component decay-associated excitation spectra. Application to subtilisins Biophysical Journal. 57: 183-189. PMID 2180489 DOI: 10.1016/S0006-3495(90)82521-2  1
1990 Jaeger JA, Turner DH, Zuker M. Predicting optimal and suboptimal secondary structure for RNA. Methods in Enzymology. 183: 281-306. PMID 1690335 DOI: 10.1016/0076-6879(90)83019-6  1
1989 Zuker M, Somorjai RL. The alignment of protein structures in three dimensions. Bulletin of Mathematical Biology. 51: 55-78. PMID 2706402 DOI: 10.1007/BF02458836  1
1989 Zuker M. Computer prediction of RNA structure. Methods in Enzymology. 180: 262-88. PMID 2482418 DOI: 10.1016/0076-6879(89)80106-5  1
1989 Jaeger JA, Turner DH, Zuker M. Improved predictions of secondary structures for RNA. Proceedings of the National Academy of Sciences of the United States of America. 86: 7706-10. PMID 2479010 DOI: 10.1073/pnas.86.20.7706  1
1989 Zuker M. On finding all suboptimal foldings of an RNA molecule. Science (New York, N.Y.). 244: 48-52. PMID 2468181 DOI: 10.1126/science.2468181  1
1987 Tanny SM, Zuker M. The sensitivity of eigenvalues under elementary matrix perturbations Linear Algebra and Its Applications. 86: 123-143. DOI: 10.1016/0024-3795(87)90290-4  1
1986 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 Letters. 205: 117-20. PMID 3743765 DOI: 10.1016/0014-5793(86)80877-8  1
1985 Zuker M, Szabo AG, Bramall L, Krajcarski DT, Selinger B. Delta function convolution method (DFCM) for fluorescence decay experiments Review of Scientific Instruments. 56: 14-22. DOI: 10.1063/1.1138457  1
1984 Jacobson AB, Good L, Simonetti J, Zuker M. Some simple computational methods to improve the folding of large RNAs Nucleic Acids Research. 12: 45-52. PMID 6198623 DOI: 10.1093/nar/12.1Part1.45  1
1984 Szabo AG, Kpajcarski D, Zuker M, Alpert B. Conformational heterogeneity in hemoglobin as determined by picosecond fluorescence decay measurements of the tryptopran residues1 1 Issued as NRCC No. 23193 Chemical Physics Letters. 108: 145-149. DOI: 10.1016/0009-2614(84)85709-7  1
1984 Zuker M, Sankoff D. RNA secondary structures and their prediction Bulletin of Mathematical Biology. 46: 591-621. DOI: 10.1007/BF02459506  1
1983 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. Proceedings of the National Academy of Sciences of the United States of America. 80: 3903-7. PMID 6306649 DOI: 10.1073/pnas.80.13.3903  1
1983 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. 22: 1863-72. PMID 6303395 DOI: 10.1021/bi00277a019  1
1980 Zuker M, Mihailov G, Romanowski M. Systematic search for orthogonal systems in the calibrations of submultiples and multiples of the unit of mass Metrologia. 16: 51-54. DOI: 10.1088/0026-1394/16/1/007  1
1978 Tanny SM, Zuker M. Analytic methods applied to a sequence of binomial coefficients Discrete Mathematics. 24: 299-310. DOI: 10.1016/0012-365X(78)90101-2  1
1974 Tanny SM, Zuker M. On a unimodal sequence of binomial coefficients Discrete Mathematics. 9: 78-89. DOI: 10.1016/0012-365X(74)90073-9  1
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