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Michael Zuker - Publications

Affiliations: 
Rensselaer Polytechnic Institute, Troy, NY, United States 
Area:
Computer Science, Molecular Biology
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54 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  0.437
2014 Stephenson WT, Keller S, Tenenbaum SA, Zuker M, Li PT. Structural Polymorphism of (Cag)N Repeat RNA Elucidated using Single Molecule Nanomanipulation Biophysical Journal. 106: 282a. DOI: 10.1016/J.Bpj.2013.11.1653  0.425
2013 Stephenson W, Santiago R, Keller S, Tenenbaum S, Zuker M, Li PT. 40 Probing single molecule RNA folding using temperature and force Journal of Biomolecular Structure and Dynamics. 31: 24-25. DOI: 10.1080/07391102.2013.786473  0.406
2013 Stephenson WT, Santiago R, Keller S, Tenenbaum S, Zuker M, Li PT. Combining Temperature and Force to Study Folding of Single RNA Molecules Biophysical Journal. 104: 412a. DOI: 10.1016/J.Bpj.2012.11.2296  0.418
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  0.348
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  0.386
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  0.359
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  0.67
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  0.469
2006 Mathews DH, Schroeder SJ, Turner DH, Zuker M. 22 Predicting RNA Secondary Structure Cold Spring Harbor Monograph Archive. 43: 631-657. DOI: 10.1101/087969739.43.631  0.409
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  0.663
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  0.501
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  0.451
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  0.469
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  0.382
2003 Zuker M. Predicting Nucleic Acid Hybridization and Melting Profiles Genome Informatics. 14: 266-268. DOI: 10.11234/Gi1990.14.266  0.394
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  0.456
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  0.3
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  0.331
2000 Zuker M. Calculating nucleic acid secondary structure. Current Opinion in Structural Biology. 10: 303-10. PMID 10851192 DOI: 10.1016/S0959-440X(00)00088-9  0.45
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  0.476
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  0.434
1999 Lyngsø RB, Zuker M, Pedersen CNS. An Improved Algorithm for RNA Secondary Structure Prediction Brics Report Series. 6. DOI: 10.7146/Brics.V6I15.20072  0.41
1998 Zuker M, Jacobson AB. Using reliability information to annotate RNA secondary structures Rna. 4: 669-679. PMID 9622126 DOI: 10.1017/S1355838298980116  0.471
1998 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 Qβ Journal of Molecular Biology. 275: 589-600. PMID 9466933 DOI: 10.1006/Jmbi.1997.1472  0.407
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.  0.361
1995 Drouin G, Moniz de Sá M, Zuker M. The Giardia lamblia actin gene and the phylogeny of eukaryotes. Journal of Molecular Evolution. 41: 841-9. PMID 8587128 DOI: 10.1007/Bf00173163  0.338
1995 Zuker M, Jacobson AB. 'well-determined' regions in RNA secondary structure prediction: Analysis of small subunit ribosomal RNA Nucleic Acids Research. 23: 2791-2798. PMID 7544463 DOI: 10.1093/Nar/23.14.2791  0.459
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  0.417
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  0.429
1993 Jacobson AB, Zuker M. Structural analysis by energy dot plot of a large mRNA Journal of Molecular Biology. 233: 261-269. PMID 8377202 DOI: 10.1006/Jmbi.1993.1504  0.47
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  0.328
1991 Le SY, Zuker M. Predicting common foldings of homologous RNAs. Journal of Biomolecular Structure & Dynamics. 8: 1027-44. PMID 1715169 DOI: 10.1080/07391102.1991.10507863  0.45
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  0.442
1991 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 Research. 19: 353-358. PMID 1707523 DOI: 10.1093/Nar/19.2.353  0.377
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  0.346
1990 Le SY, Zuker M. Common structures of the 5' non-coding RNA in enteroviruses and rhinoviruses. Thermodynamical stability and statistical significance. Journal of Molecular Biology. 216: 729-41. PMID 2175364 DOI: 10.1016/0022-2836(90)90395-3  0.412
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  0.474
1989 Zuker M, Somorjai RL. The alignment of protein structures in three dimensions. Bulletin of Mathematical Biology. 51: 55-78. PMID 2706402 DOI: 10.1016/S0092-8240(89)80048-5  0.317
1989 Zuker M. Computer prediction of RNA structure. Methods in Enzymology. 180: 262-88. PMID 2482418 DOI: 10.1016/0076-6879(89)80106-5  0.463
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  0.448
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  0.478
1987 Matheson AT, Louie KA, Tak BD, Zuker M. The primary structure of the ribosomal A-protein (L12) from the halophilic eubacterium Haloanaerobium praevalens. Biochimie. 69: 1013-20. PMID 3126821 DOI: 10.1016/0300-9084(87)90001-0  0.306
1986 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. Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire. 64: 675-80. PMID 3756001 DOI: 10.1139/O86-093  0.331
1986 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 Research. 14: 9159-70. PMID 3024130 DOI: 10.1093/Nar/14.22.9159  0.339
1985 Jacobson AB, Kumar H, Zuker M. Effect of spermidine on the conformation of bacteriophage MS2 RNA. Electron microscopy and computer modeling Journal of Molecular Biology. 181: 517-531. PMID 2582136 DOI: 10.1016/0022-2836(85)90424-3  0.407
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  0.371
1984 Zuker M, Sankoff D. RNA secondary structures and their prediction Bulletin of Mathematical Biology. 46: 591-621. DOI: 10.1016/S0092-8240(84)80062-2  0.436
1984 ZUKER M, SANKOFF D. RNA secondary structures and their prediction Bulletin of Mathematical Biology. 46: 591-621. DOI: 10.1016/S0092-8240(84)80062-2  0.304
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  0.414
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  0.316
1982 Darlix JL, Zuker M, Spahr PF. Structure-function relationship of Rous sarcoma virus leader RNA. Nucleic Acids Research. 10: 5183-96. PMID 6292833 DOI: 10.1093/Nar/10.17.5183  0.38
1982 Yaguchi M, Visentin LP, Zuker M, Matheson AT, Roy C, Strøm AR. Amino-Terminal Sequences of Ribosomal Proteins from the 30 S Subunit of Archaebacterium Halobacterium cutirubrum Zentralblatt FüR Bakteriologie Mikrobiologie Und Hygiene: I. Abt. Originale C: Allgemeine, Angewandte Und öKologische Mikrobiologie. 3: 200-208. DOI: 10.1016/S0721-9571(82)80033-1  0.305
1981 Zuker M, Stiegler P. Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. Nucleic Acids Research. 9: 133-48. PMID 6163133 DOI: 10.1093/Nar/9.1.133  0.439
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