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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