Mathews DH - Search Results

1

Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design.

Lu ZJ, Mathews DH. Lu ZJ, et al. Among authors: mathews dh. Nucleic Acids Res. 2008 Jun;36(11):3738-45. doi: 10.1093/nar/gkn266. Epub 2008 May 15. Nucleic Acids Res. 2008. PMID: 18483081 Free PMC article.

2

Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure.

Mathews DH, Sabina J, Zuker M, Turner DH. Mathews DH, et al. J Mol Biol. 1999 May 21;288(5):911-40. doi: 10.1006/jmbi.1999.2700. J Mol Biol. 1999. PMID: 10329189

3

Predicting oligonucleotide affinity to nucleic acid targets.

Mathews DH, Burkard ME, Freier SM, Wyatt JR, Turner DH. Mathews DH, et al. RNA. 1999 Nov;5(11):1458-69. doi: 10.1017/s1355838299991148. RNA. 1999. PMID: 10580474 Free PMC article.

4

Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops.

Mathews DH, Turner DH. Mathews DH, et al. Biochemistry. 2002 Jan 22;41(3):869-80. doi: 10.1021/bi011441d. Biochemistry. 2002. PMID: 11790109

5

Dynalign: an algorithm for finding the secondary structure common to two RNA sequences.

Mathews DH, Turner DH. Mathews DH, et al. J Mol Biol. 2002 Mar 22;317(2):191-203. doi: 10.1006/jmbi.2001.5351. J Mol Biol. 2002. PMID: 11902836

6

Thermodynamic criteria for high hit rate antisense oligonucleotide design.

Matveeva OV, Mathews DH, Tsodikov AD, Shabalina SA, Gesteland RF, Atkins JF, Freier SM. Matveeva OV, et al. Among authors: mathews dh. Nucleic Acids Res. 2003 Sep 1;31(17):4989-94. doi: 10.1093/nar/gkg710. Nucleic Acids Res. 2003. PMID: 12930948 Free PMC article.

7

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure.

Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH. Mathews DH, et al. Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92. doi: 10.1073/pnas.0401799101. Epub 2004 May 3. Proc Natl Acad Sci U S A. 2004. PMID: 15123812 Free PMC article.

8

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization.

Mathews DH. Mathews DH. RNA. 2004 Aug;10(8):1178-90. doi: 10.1261/rna.7650904. RNA. 2004. PMID: 15272118 Free PMC article.

9

Predicting a set of minimal free energy RNA secondary structures common to two sequences.

Mathews DH. Mathews DH. Bioinformatics. 2005 May 15;21(10):2246-53. doi: 10.1093/bioinformatics/bti349. Epub 2005 Feb 24. Bioinformatics. 2005. PMID: 15731207

10

The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexes.

Kierzek E, Ciesielska A, Pasternak K, Mathews DH, Turner DH, Kierzek R. Kierzek E, et al. Among authors: mathews dh. Nucleic Acids Res. 2005 Sep 9;33(16):5082-93. doi: 10.1093/nar/gki789. Print 2005. Nucleic Acids Res. 2005. PMID: 16155181 Free PMC article.

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